From 642e19159a622fbdd301adc5efccdd4fe233d732 Mon Sep 17 00:00:00 2001
From: KasukabeDefenceForce <abhinavohri13@gmail.com>
Date: Thu, 1 Aug 2024 12:56:59 +0530
Subject: [PATCH 01/10] Donot run docs, benchmarks and stardis tests on draft
 PRs. (#2761)

* Add ready to review to run tests

* Add if condition to check PR status

* Running stardis tests only on push to master

* Removing osx-64 from workflows
---
 .github/workflows/benchmarks.yml    |  2 ++
 .github/workflows/build-docs.yml    |  2 ++
 .github/workflows/stardis-tests.yml | 14 ++++++++------
 3 files changed, 12 insertions(+), 6 deletions(-)

diff --git a/.github/workflows/benchmarks.yml b/.github/workflows/benchmarks.yml
index 9ed9b5581e4..2ed44515e7b 100644
--- a/.github/workflows/benchmarks.yml
+++ b/.github/workflows/benchmarks.yml
@@ -14,6 +14,7 @@ on:
       - reopened
       - synchronize
       - labeled # benchmarks label required
+      - ready_for_review
   workflow_dispatch:
 
 env: 
@@ -31,6 +32,7 @@ jobs:
   build:
     if: github.repository_owner == 'tardis-sn' &&
       (github.event_name == 'push' ||
+      (!github.event.pull_request.draft) ||
       github.event_name == 'workflow_dispatch' ||
       (github.event_name == 'pull_request_target' &&
       contains(github.event.pull_request.labels.*.name, 'benchmarks')))
diff --git a/.github/workflows/build-docs.yml b/.github/workflows/build-docs.yml
index bb17c9581f0..254c19ffbdd 100644
--- a/.github/workflows/build-docs.yml
+++ b/.github/workflows/build-docs.yml
@@ -18,6 +18,7 @@ on:
       - reopened
       - synchronize
       - labeled # requires the `build-docs` label
+      - ready_for_review
 
   workflow_dispatch: # manual trigger
 
@@ -37,6 +38,7 @@ defaults:
 jobs:
   check-for-changes:
     runs-on: ubuntu-latest
+    if: ${{ !github.event.pull_request.draft }}
     outputs:
       trigger-check-outcome: ${{ steps.trigger_check.outcome }}
       docs-check-outcome: ${{ steps.docs_check.outcome }}
diff --git a/.github/workflows/stardis-tests.yml b/.github/workflows/stardis-tests.yml
index fad5fbaa7d9..a8e09d8a1db 100644
--- a/.github/workflows/stardis-tests.yml
+++ b/.github/workflows/stardis-tests.yml
@@ -3,12 +3,17 @@ name: stardis-tests
 on:
   push:
     branches:
-    - '*'
+    - master
 
   pull_request:
     branches:
     - '*'
 
+    types:
+      - opened
+      - reopened
+      - synchronize
+      - ready_for_review
   workflow_dispatch:
 
 defaults:
@@ -22,18 +27,15 @@ jobs:
   build:
     strategy:
       matrix:
-        label: [osx-64, linux-64]
+        label: [linux-64]
         include:
           - os: ubuntu-latest
             label: linux-64
             prefix: /usr/share/miniconda3/envs/stardis
 
-          - os: macos-latest
-            label: osx-64
-            prefix: /Users/runner/miniconda3/envs/stardis
-
     name: ${{ matrix.label }}
     runs-on: ${{ matrix.os }}
+    if: ${{ !github.event.pull_request.draft }}
     steps:     
       - uses: actions/checkout@v4
         with:

From 88835ff94edc06d9650d6f7e9ce1756e4a5be26a Mon Sep 17 00:00:00 2001
From: Sumit Gupta <53135486+Sumit112192@users.noreply.github.com>
Date: Thu, 1 Aug 2024 21:57:39 +0530
Subject: [PATCH 02/10] Add Extend Array Function (#2771)

* Add Extend Array Function

* Fix Typo and restructure

* Restructure

* Doc string update

* Was expecting numpy arrays to be passed by reference but it is not so updating it

* Add test for the extend array function
---
 .../transport/montecarlo/packet_trackers.py   | 46 +++++++++----------
 .../montecarlo/tests/test_rpacket_tracker.py  | 12 +++++
 2 files changed, 33 insertions(+), 25 deletions(-)

diff --git a/tardis/transport/montecarlo/packet_trackers.py b/tardis/transport/montecarlo/packet_trackers.py
index 7a10a992f05..466fad27843 100644
--- a/tardis/transport/montecarlo/packet_trackers.py
+++ b/tardis/transport/montecarlo/packet_trackers.py
@@ -16,6 +16,7 @@
     ("shell_id", int64[:]),
     ("interaction_type", int64[:]),
     ("num_interactions", int64),
+    ("extend_factor", int64),
 ]
 
 
@@ -47,6 +48,8 @@ class RPacketTracker(object):
             Type of interaction the rpacket undergoes
         num_interactions : int
             Internal counter for the interactions that a particular RPacket undergoes
+        extend_factor : int
+            The factor by which to extend the properties array when the size limit is reached
     """
 
     def __init__(self, length):
@@ -61,34 +64,27 @@ def __init__(self, length):
         self.shell_id = np.empty(self.length, dtype=np.int64)
         self.interaction_type = np.empty(self.length, dtype=np.int64)
         self.num_interactions = 0
+        self.extend_factor = 2
+
+    def extend_array(self, array, array_length):
+        temp_array = np.empty(
+            array_length * self.extend_factor, dtype=array.dtype
+        )
+        temp_array[:array_length] = array
+        return temp_array
 
     def track(self, r_packet):
         if self.num_interactions >= self.length:
-            temp_length = self.length * 2
-            temp_status = np.empty(temp_length, dtype=np.int64)
-            temp_r = np.empty(temp_length, dtype=np.float64)
-            temp_nu = np.empty(temp_length, dtype=np.float64)
-            temp_mu = np.empty(temp_length, dtype=np.float64)
-            temp_energy = np.empty(temp_length, dtype=np.float64)
-            temp_shell_id = np.empty(temp_length, dtype=np.int64)
-            temp_interaction_type = np.empty(temp_length, dtype=np.int64)
-
-            temp_status[: self.length] = self.status
-            temp_r[: self.length] = self.r
-            temp_nu[: self.length] = self.nu
-            temp_mu[: self.length] = self.mu
-            temp_energy[: self.length] = self.energy
-            temp_shell_id[: self.length] = self.shell_id
-            temp_interaction_type[: self.length] = self.interaction_type
-
-            self.status = temp_status
-            self.r = temp_r
-            self.nu = temp_nu
-            self.mu = temp_mu
-            self.energy = temp_energy
-            self.shell_id = temp_shell_id
-            self.interaction_type = temp_interaction_type
-            self.length = temp_length
+            self.status = self.extend_array(self.status, self.length)
+            self.r = self.extend_array(self.r, self.length)
+            self.nu = self.extend_array(self.nu, self.length)
+            self.mu = self.extend_array(self.mu, self.length)
+            self.energy = self.extend_array(self.energy, self.length)
+            self.shell_id = self.extend_array(self.shell_id, self.length)
+            self.interaction_type = self.extend_array(
+                self.interaction_type, self.length
+            )
+            self.length = self.length * self.extend_factor
 
         self.index = r_packet.index
         self.seed = r_packet.seed
diff --git a/tardis/transport/montecarlo/tests/test_rpacket_tracker.py b/tardis/transport/montecarlo/tests/test_rpacket_tracker.py
index 9a42da459e5..7dbfc03784c 100644
--- a/tardis/transport/montecarlo/tests/test_rpacket_tracker.py
+++ b/tardis/transport/montecarlo/tests/test_rpacket_tracker.py
@@ -4,6 +4,7 @@
 
 from tardis.transport.montecarlo.r_packet import InteractionType
 from tardis.transport.montecarlo.packet_trackers import (
+    RPacketTracker,
     rpacket_trackers_to_dataframe,
 )
 
@@ -102,6 +103,17 @@ def nu_rpacket_tracker(rpacket_tracker):
     return nu
 
 
+def test_extend_array():
+    rpacket_tracker = RPacketTracker(10)
+    array = np.array([1, 2, 3, 4, 5], dtype=np.int64)
+
+    new_array = rpacket_tracker.extend_array(array, array.size)
+
+    assert new_array.size == array.size * rpacket_tracker.extend_factor
+    assert new_array.dtype == array.dtype
+    npt.assert_allclose(array, new_array[: array.size])
+
+
 @pytest.mark.parametrize(
     "expected,obtained",
     [

From c82dde5fb55a81dafc67e8b182efb9084a0d58a3 Mon Sep 17 00:00:00 2001
From: Jack O'Brien <jobrien585@gmail.com>
Date: Thu, 1 Aug 2024 17:34:19 -0400
Subject: [PATCH 03/10] Opacity state slice (#2758)

* Added basic sliing operation to opacitystate and set the transport solver to use the bounds of the gemoetry indices

* Reformatted the slicing index

* Added slicing operation with __getitem__

* Added docstring

* removed old slice method

* Ran black

* Added back the 'slice' method because __getitem__ is wacky

* added missing argument

* fixed missing argument

* ran black

* fixed the tests

* ran black

* Updated the slice to use __getitem__ again and modified the opacitystate object defined in the opacities module

* Removed old slice method and print statements

* removed print statement from the test

* added type annotation to OpacityState getitem

* updated numba interface
---
 tardis/opacities/opacity_state.py             | 35 +++++++++++++++++++
 tardis/transport/montecarlo/base.py           | 11 +++---
 .../transport/montecarlo/numba_interface.py   | 35 +++++++++++++++++++
 .../montecarlo/tests/test_numba_interface.py  | 29 ++++++++++++---
 4 files changed, 101 insertions(+), 9 deletions(-)

diff --git a/tardis/opacities/opacity_state.py b/tardis/opacities/opacity_state.py
index 1f8905cd12f..7fbab4be781 100644
--- a/tardis/opacities/opacity_state.py
+++ b/tardis/opacities/opacity_state.py
@@ -106,6 +106,41 @@ def __init__(
         self.photo_ion_activation_idx = photo_ion_activation_idx
         self.k_packet_idx = k_packet_idx
 
+    def __getitem__(self, i: slice):
+        """Get a shell or slice of shells of the attributes of the opacity state
+
+        Args:
+            i (slice): shell slice.  Will fail if slice is int since class only supports array types
+
+        Returns:
+            OpacityState : a shallow copy of the current instance
+        """
+        # NOTE: This currently will not work with continuum processes since it does not slice those arrays
+        return OpacityState(
+            self.electron_density[i],
+            self.t_electrons[i],
+            self.line_list_nu,
+            self.tau_sobolev[:, i],
+            self.transition_probabilities[:, i],
+            self.line2macro_level_upper,
+            self.macro_block_references,
+            self.transition_type,
+            self.destination_level_id,
+            self.transition_line_id,
+            self.bf_threshold_list_nu,
+            self.p_fb_deactivation,
+            self.photo_ion_nu_threshold_mins,
+            self.photo_ion_nu_threshold_maxs,
+            self.photo_ion_block_references,
+            self.chi_bf,
+            self.x_sect,
+            self.phot_nus,
+            self.ff_opacity_factor,
+            self.emissivities,
+            self.photo_ion_activation_idx,
+            self.k_packet_idx,
+        )
+
 
 def opacity_state_initialize(
     plasma,
diff --git a/tardis/transport/montecarlo/base.py b/tardis/transport/montecarlo/base.py
index 8812bfab229..5137acee0a4 100644
--- a/tardis/transport/montecarlo/base.py
+++ b/tardis/transport/montecarlo/base.py
@@ -23,7 +23,7 @@
 from tardis.transport.montecarlo.montecarlo_transport_state import (
     MonteCarloTransportState,
 )
-from tardis.transport.montecarlo.numba_interface import (
+from tardis.opacities.opacity_state import ( 
     opacity_state_initialize,
 )
 from tardis.transport.montecarlo.packet_trackers import (
@@ -110,9 +110,6 @@ def initialize_transport_state(
         packet_collection = self.packet_source.create_packets(
             no_of_packets, seed_offset=iteration
         )
-        estimators = initialize_estimator_statistics(
-            plasma.tau_sobolevs.shape, gamma_shape
-        )
 
         geometry_state = simulation_state.geometry.to_numba()
         opacity_state = opacity_state_initialize(
@@ -120,6 +117,12 @@ def initialize_transport_state(
             self.line_interaction_type,
             self.montecarlo_configuration.DISABLE_LINE_SCATTERING,
         )
+        opacity_state = opacity_state[simulation_state.geometry.v_inner_boundary_index: simulation_state.geometry.v_outer_boundary_index]
+        
+        estimators = initialize_estimator_statistics(
+            opacity_state.tau_sobolev.shape, gamma_shape
+        )
+
         transport_state = MonteCarloTransportState(
             packet_collection,
             estimators,
diff --git a/tardis/transport/montecarlo/numba_interface.py b/tardis/transport/montecarlo/numba_interface.py
index f2253c7ff5d..d6db1e12e3e 100644
--- a/tardis/transport/montecarlo/numba_interface.py
+++ b/tardis/transport/montecarlo/numba_interface.py
@@ -112,6 +112,41 @@ def __init__(
         self.photo_ion_activation_idx = photo_ion_activation_idx
         self.k_packet_idx = k_packet_idx
 
+    def __getitem__(self, i: slice):
+        """Get a shell or slice of shells of the attributes of the opacity state
+
+        Args:
+            i (slice): shell slice.  Will fail if slice is int since class only supports array types
+
+        Returns:
+            OpacityState : a shallow copy of the current instance
+        """
+        # NOTE: This currently will not work with continuum processes since it does not slice those arrays
+        return OpacityState(
+            self.electron_density[i],
+            self.t_electrons[i],
+            self.line_list_nu,
+            self.tau_sobolev[:, i],
+            self.transition_probabilities[:, i],
+            self.line2macro_level_upper,
+            self.macro_block_references,
+            self.transition_type,
+            self.destination_level_id,
+            self.transition_line_id,
+            self.bf_threshold_list_nu,
+            self.p_fb_deactivation,
+            self.photo_ion_nu_threshold_mins,
+            self.photo_ion_nu_threshold_maxs,
+            self.photo_ion_block_references,
+            self.chi_bf,
+            self.x_sect,
+            self.phot_nus,
+            self.ff_opacity_factor,
+            self.emissivities,
+            self.photo_ion_activation_idx,
+            self.k_packet_idx,
+        )
+
 
 def opacity_state_initialize(
     plasma,
diff --git a/tardis/transport/montecarlo/tests/test_numba_interface.py b/tardis/transport/montecarlo/tests/test_numba_interface.py
index 25d907049f6..5e73894549f 100644
--- a/tardis/transport/montecarlo/tests/test_numba_interface.py
+++ b/tardis/transport/montecarlo/tests/test_numba_interface.py
@@ -4,8 +4,19 @@
 import numpy as np
 
 
-@pytest.mark.parametrize("input_params", ["scatter", "macroatom", "downbranch"])
-def test_opacity_state_initialize(nb_simulation_verysimple, input_params):
+@pytest.mark.parametrize(
+    "input_params,sliced",
+    [
+        ("scatter", False),
+        ("macroatom", False),
+        ("macroatom", True),
+        ("downbranch", False),
+        ("downbranch", True),
+    ],
+)
+def test_opacity_state_initialize(
+    nb_simulation_verysimple, input_params, sliced
+):
     line_interaction_type = input_params
     plasma = nb_simulation_verysimple.plasma
     actual = numba_interface.opacity_state_initialize(
@@ -14,11 +25,19 @@ def test_opacity_state_initialize(nb_simulation_verysimple, input_params):
         disable_line_scattering=False,
     )
 
+    if sliced:
+        index = slice(2, 5)
+        actual = actual[index]
+    else:
+        index = ...
+
     npt.assert_allclose(
-        actual.electron_density, plasma.electron_densities.values
+        actual.electron_density, plasma.electron_densities.values[index]
     )
     npt.assert_allclose(actual.line_list_nu, plasma.atomic_data.lines.nu.values)
-    npt.assert_allclose(actual.tau_sobolev, plasma.tau_sobolevs.values)
+    npt.assert_allclose(
+        actual.tau_sobolev, plasma.tau_sobolevs.values[:, index]
+    )
     if line_interaction_type == "scatter":
         empty = np.zeros(1, dtype=np.int64)
         npt.assert_allclose(
@@ -32,7 +51,7 @@ def test_opacity_state_initialize(nb_simulation_verysimple, input_params):
     else:
         npt.assert_allclose(
             actual.transition_probabilities,
-            plasma.transition_probabilities.values,
+            plasma.transition_probabilities.values[:, index],
         )
         npt.assert_allclose(
             actual.line2macro_level_upper,

From bd1558bdd96df1d3a21bb8464f46fe9b54a36d6f Mon Sep 17 00:00:00 2001
From: Andrew Fullard <andrewgfullard@gmail.com>
Date: Fri, 2 Aug 2024 09:44:09 -0400
Subject: [PATCH 04/10] Fixes black formatting

---
 tardis/transport/montecarlo/base.py | 8 +++++---
 1 file changed, 5 insertions(+), 3 deletions(-)

diff --git a/tardis/transport/montecarlo/base.py b/tardis/transport/montecarlo/base.py
index 5137acee0a4..af865836598 100644
--- a/tardis/transport/montecarlo/base.py
+++ b/tardis/transport/montecarlo/base.py
@@ -23,7 +23,7 @@
 from tardis.transport.montecarlo.montecarlo_transport_state import (
     MonteCarloTransportState,
 )
-from tardis.opacities.opacity_state import ( 
+from tardis.opacities.opacity_state import (
     opacity_state_initialize,
 )
 from tardis.transport.montecarlo.packet_trackers import (
@@ -117,8 +117,10 @@ def initialize_transport_state(
             self.line_interaction_type,
             self.montecarlo_configuration.DISABLE_LINE_SCATTERING,
         )
-        opacity_state = opacity_state[simulation_state.geometry.v_inner_boundary_index: simulation_state.geometry.v_outer_boundary_index]
-        
+        opacity_state = opacity_state[
+            simulation_state.geometry.v_inner_boundary_index : simulation_state.geometry.v_outer_boundary_index
+        ]
+
         estimators = initialize_estimator_statistics(
             opacity_state.tau_sobolev.shape, gamma_shape
         )

From 1807f36063614eb2c064a4bbbda4b6ca61a2864f Mon Sep 17 00:00:00 2001
From: Atharva Arya <55894364+atharva-2001@users.noreply.github.com>
Date: Fri, 2 Aug 2024 20:00:12 +0530
Subject: [PATCH 05/10] Release Pipeline Fixes (#2767)

* Fix zenodo badge

* Pick from the website

* update badge in credits.rst

* Use the all versions DOI

* Inherit secrets

* Change triggers for testing

* Reset Triggers
---
 .github/workflows/pre-release.yml | 1 +
 README.rst                        | 5 +++--
 docs/resources/credits.rst        | 4 ++--
 3 files changed, 6 insertions(+), 4 deletions(-)

diff --git a/.github/workflows/pre-release.yml b/.github/workflows/pre-release.yml
index 5b24dbfb45b..78b159e8b95 100644
--- a/.github/workflows/pre-release.yml
+++ b/.github/workflows/pre-release.yml
@@ -143,5 +143,6 @@ jobs:
   
   pip_tests:
     uses: ./.github/workflows/tests.yml
+    secrets: inherit
     with:
       pip_git: true
diff --git a/README.rst b/README.rst
index fe1b070fbbc..8603332dea9 100644
--- a/README.rst
+++ b/README.rst
@@ -112,8 +112,9 @@ The following BibTeX entries are needed for the references:
 
 .. |CITATION| replace:: kerzendorf_2023_10207663
 
-.. |DOI_BADGE| image:: https://img.shields.io/badge/DOI-10.5281/zenodo.3_10207663-blue
-                 :target: https://doi.org/10.5281/zenodo.3_10207663
+.. |DOI_BADGE| image:: https://zenodo.org/badge/DOI/10.5281/zenodo.592480.svg
+                :target: https://doi.org/10.5281/zenodo.592480
+
 
 .. code-block:: bibtex
 
diff --git a/docs/resources/credits.rst b/docs/resources/credits.rst
index db36f05d484..cacb3e9bd38 100644
--- a/docs/resources/credits.rst
+++ b/docs/resources/credits.rst
@@ -76,8 +76,8 @@ The following BibTeX entries are needed for the references:
 
 .. |CITATION| replace:: kerzendorf_2023_10207663
 
-.. |DOI_BADGE| image:: https://img.shields.io/badge/DOI-10.5281/zenodo.3_10207663-blue
-                 :target: https://doi.org/10.5281/zenodo.3_10207663
+.. |DOI_BADGE| image:: https://zenodo.org/badge/DOI/10.5281/zenodo.592480.svg
+                :target: https://doi.org/10.5281/zenodo.592480
 
 .. code-block:: bibtex
 

From d8da61e895cfdeef4dfc9b8eaa9eba904c475fc7 Mon Sep 17 00:00:00 2001
From: Atharva Arya <55894364+atharva-2001@users.noreply.github.com>
Date: Fri, 2 Aug 2024 20:06:22 +0530
Subject: [PATCH 06/10] Fix ruff comments issue (#2762)

* Fix ruff comments issue

* Only check files changed

* Testing triggers

* Fix bash commands

* No pager

* fetch depth

* Reset all changes
---
 .github/workflows/codestyle.yml | 23 +++++++++++++++++------
 1 file changed, 17 insertions(+), 6 deletions(-)

diff --git a/.github/workflows/codestyle.yml b/.github/workflows/codestyle.yml
index bf5ada7cd94..89ed4c58ec2 100644
--- a/.github/workflows/codestyle.yml
+++ b/.github/workflows/codestyle.yml
@@ -7,8 +7,7 @@ name: codestyle
 on:
   push:
     branches:
-      - "*"
-
+      - master
   pull_request_target:
     branches:
       - master
@@ -37,6 +36,8 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
 
       - name: Download Lock File
         run:  wget -q https://raw.githubusercontent.com/tardis-sn/tardis/master/conda-linux-64.lock
@@ -57,12 +58,22 @@ jobs:
           cache-downloads: true
       
       - name: Show statistics
-        run: ruff check  --statistics  --show-fixes . | tee ruff_stats.txt
-        id: ruff_stats
+        run: ruff check  --statistics  --show-fixes $(git --no-pager diff --name-only ${{ github.event.pull_request.base.sha }}  ${{ github.event.pull_request.head.sha }} --) | tee ruff_stats.txt
       
       - name: Show entire output
-        run: ruff check . --output-format=full | tee ruff_full.txt
-        id: ruff_complete
+        run: ruff check --output-format=concise $(git --no-pager diff --name-only ${{ github.event.pull_request.base.sha }}  ${{ github.event.pull_request.head.sha }} --) | tee ruff_full.txt
+
+      - name: Statistics output read
+        id: ruff_stats
+        uses: juliangruber/read-file-action@v1.0.0
+        with:
+          path: ruff_stats.txt
+
+      - name: Entire output read
+        id: ruff_complete 
+        uses: juliangruber/read-file-action@v1.0.0
+        with:
+          path: ruff_full.txt
       
       - name: Find Comment
         if: always() && github.event_name == 'pull_request_target'

From 0349e7a90c90bfb9d9dbc5a106adfcbfda9a6f39 Mon Sep 17 00:00:00 2001
From: Asish Kumar <87874775+officialasishkumar@users.noreply.github.com>
Date: Sat, 3 Aug 2024 01:18:15 +0530
Subject: [PATCH 07/10] Cache benchmark functions (#2749)

* added setup function

Signed-off-by: Asish Kumar <officialasishkumar@gmail.com>

* refactor geometry calculate distances

Signed-off-by: Asish Kumar <officialasishkumar@gmail.com>

* Refactor montecarlo estimators in benchmark code

Signed-off-by: Asish Kumar <officialasishkumar@gmail.com>

* add cache and setup functions

Signed-off-by: Asish Kumar <officialasishkumar@gmail.com>

* add cache and setup functions

Signed-off-by: Asish Kumar <officialasishkumar@gmail.com>

* ran ruff linter

Signed-off-by: Asish Kumar <officialasishkumar@gmail.com>

* Thou hath vanquished the redundant variables and functions

Signed-off-by: Asish Kumar <officialasishkumar@gmail.com>

* fix bugs

Signed-off-by: Asish Kumar <officialasishkumar@gmail.com>

* change benchmark yml

Signed-off-by: Asish Kumar <officialasishkumar@gmail.com>

* repeat in class

Signed-off-by: Asish Kumar <officialasishkumar@gmail.com>

* rounds in benchmarks

Signed-off-by: Asish Kumar <officialasishkumar@gmail.com>

* fix

Signed-off-by: Asish Kumar <officialasishkumar@gmail.com>

* fix error in formal integral

Signed-off-by: Asish Kumar <officialasishkumar@gmail.com>

* more cache

Signed-off-by: Asish Kumar <officialasishkumar@gmail.com>

* sort by ratio

Signed-off-by: Asish Kumar <officialasishkumar@gmail.com>

* cache in setup function

Signed-off-by: Asish Kumar <officialasishkumar@gmail.com>

---------

Signed-off-by: Asish Kumar <officialasishkumar@gmail.com>
---
 .github/workflows/benchmarks.yml              |  10 +-
 benchmarks/benchmark_base.py                  | 256 +++---------------
 benchmarks/opacities_opacity.py               | 104 ++-----
 benchmarks/opacities_opacity_state.py         |  20 +-
 benchmarks/run_tardis.py                      |  14 +-
 benchmarks/spectrum_formal_integral.py        |  48 ++--
 .../transport_geometry_calculate_distances.py |  61 ++---
 ...rlo_estimators_radfield_estimator_calcs.py |  51 +---
 .../transport_montecarlo_interaction.py       |  86 ++----
 benchmarks/transport_montecarlo_main_loop.py  |  24 +-
 .../transport_montecarlo_packet_trackers.py   |  42 +--
 ...transport_montecarlo_single_packet_loop.py |  11 +-
 benchmarks/transport_montecarlo_vpacket.py    | 127 ++++-----
 benchmarks/util/__init__.py                   |   0
 benchmarks/util/base.py                       |  20 --
 benchmarks/util/nlte.py                       |  78 ------
 16 files changed, 265 insertions(+), 687 deletions(-)
 delete mode 100644 benchmarks/util/__init__.py
 delete mode 100644 benchmarks/util/base.py
 delete mode 100644 benchmarks/util/nlte.py

diff --git a/.github/workflows/benchmarks.yml b/.github/workflows/benchmarks.yml
index 2ed44515e7b..95021ce994f 100644
--- a/.github/workflows/benchmarks.yml
+++ b/.github/workflows/benchmarks.yml
@@ -74,11 +74,11 @@ jobs:
       - name: Accept all asv questions
         run: asv machine --yes
 
-      - name: Run benchmarks for last 5 commits if not PR
+      - name: Run benchmarks for last 4 commits if not PR
         if: github.event_name != 'pull_request_target'
         run: |
           git log -n 4  --pretty=format:"%H" >> tag_commits.txt
-          asv run -a repeat=1 -a rounds=1 HASHFILE:tag_commits.txt | tee asv-output.log  
+          asv run -a rounds=1 HASHFILE:tag_commits.txt | tee asv-output.log
           if grep -q failed asv-output.log; then 
             echo "Some benchmarks have failed!"
             exit 1
@@ -109,17 +109,17 @@ jobs:
         run: |
           echo $(git rev-parse HEAD) > commit_hashes.txt
           echo $(git rev-parse master) >> commit_hashes.txt
-          asv run -a repeat=2 -a rounds=1 HASHFILE:commit_hashes.txt | tee asv-output-PR.log  
+          asv run -a rounds=1 HASHFILE:commit_hashes.txt | tee asv-output-PR.log  
             if grep -q failed asv-output-PR.log; then 
               echo "Some benchmarks have failed!"
               exit 1
             fi
 
       - name: Compare Master and PR head
-        run: asv compare origin/master HEAD --config asv.conf.json | tee asv-compare-output.log
+        run: asv compare origin/master HEAD --factor 1.1 --split --sort ratio | tee asv-compare-output.log
 
       - name: Compare Master and PR head but only show changed results
-        run: asv compare origin/master HEAD --only-changed --config asv.conf.json | tee asv-compare-changed-output.log
+        run: asv compare origin/master HEAD --only-changed --factor 1.1 --split --sort ratio | tee asv-compare-changed-output.log
 
       - name: Benchmarks compare output
         id: asv_pr_vs_master
diff --git a/benchmarks/benchmark_base.py b/benchmarks/benchmark_base.py
index c4ef1f2a98a..16f8cbac31a 100644
--- a/benchmarks/benchmark_base.py
+++ b/benchmarks/benchmark_base.py
@@ -1,47 +1,31 @@
+import functools
 from copy import deepcopy
 from os.path import dirname, join, realpath
 from pathlib import Path
-from tempfile import mkstemp
 
-import astropy.units as u
 import numpy as np
-from numba import njit
 
-from benchmarks.util.nlte import NLTE
 from tardis import run_tardis
 from tardis.io.atom_data import AtomData
-from tardis.io.configuration import config_reader
 from tardis.io.configuration.config_reader import Configuration
 from tardis.io.util import YAMLLoader, yaml_load_file
-from tardis.model import SimulationState
 from tardis.model.geometry.radial1d import NumbaRadial1DGeometry
 from tardis.simulation import Simulation
 from tardis.tests.fixtures.atom_data import DEFAULT_ATOM_DATA_UUID
-from tardis.tests.fixtures.regression_data import RegressionData
-from tardis.transport.montecarlo import RPacket
-from tardis.transport.montecarlo.configuration import montecarlo_globals
+from tardis.transport.montecarlo import RPacket, packet_trackers
 from tardis.transport.montecarlo.configuration.base import (
     MonteCarloConfiguration,
 )
 from tardis.transport.montecarlo.estimators import radfield_mc_estimators
 from tardis.transport.montecarlo.numba_interface import opacity_state_initialize
-from tardis.transport.montecarlo.packet_collections import (
-    VPacketCollection,
-)
-from tardis.transport.montecarlo.packet_trackers import (
-    RPacketTracker,
-    generate_rpacket_last_interaction_tracker_list,
-)
+from tardis.transport.montecarlo.packet_collections import VPacketCollection
+from tardis.transport.montecarlo.packet_trackers import RPacketTracker
 
 
 class BenchmarkBase:
-    # It allows 10 minutes of runtime for each benchmark and includes
     # the total time for all the repetitions for each benchmark.
     timeout = 600
 
-    def __init__(self):
-        self.nlte = NLTE()
-
     @staticmethod
     def get_relative_path(partial_path: str):
         path = dirname(realpath(__file__))
@@ -57,7 +41,7 @@ def get_absolute_path(self, partial_path):
 
         return self.get_relative_path(partial_path)
 
-    @property
+    @functools.cached_property
     def tardis_config_verysimple(self):
         filename = self.get_absolute_path(
             "tardis/io/configuration/tests/data/tardis_configv1_verysimple.yml"
@@ -67,7 +51,7 @@ def tardis_config_verysimple(self):
             YAMLLoader,
         )
 
-    @property
+    @functools.cached_property
     def config_rpacket_tracking(self):
         config = Configuration.from_yaml(
             f"{self.example_configuration_dir}/tardis_configv1_verysimple.yml"
@@ -75,17 +59,15 @@ def config_rpacket_tracking(self):
         config.montecarlo.tracking.track_rpacket = True
         return config
 
-    @property
+    @functools.cached_property
     def tardis_ref_path(self):
-        # TODO: This route is fixed but needs to get from the arguments given in the command line.
-        #       /app/tardis-refdata
         ref_data_path = Path(
             Path(__file__).parent.parent,
-            "tardis-refdata",
+            "tardis-refdata"
         ).resolve()
         return ref_data_path
 
-    @property
+    @functools.cached_property
     def atomic_dataset(self) -> AtomData:
         atomic_data = AtomData.from_hdf(self.atomic_data_fname)
 
@@ -95,7 +77,7 @@ def atomic_dataset(self) -> AtomData:
         else:
             return atomic_data
 
-    @property
+    @functools.cached_property
     def atomic_data_fname(self):
         atomic_data_fname = (
             f"{self.tardis_ref_path}/atom_data/kurucz_cd23_chianti_H_He.h5"
@@ -110,59 +92,11 @@ def atomic_data_fname(self):
 
         return atomic_data_fname
 
-    @property
+    @functools.cached_property
     def example_configuration_dir(self):
         return self.get_absolute_path("tardis/io/configuration/tests/data")
 
-    @property
-    def hdf_file_path(self):
-        # TODO: Delete this files after ASV runs the benchmarks.
-        #       ASV create a temporal directory in runtime per test: `tmpiuxngvlv`.
-        #       The ASV and ASV_Runner, not has some way to get this temporal directory.
-        #       The idea is use this temporal folders to storage this created temporal file.
-        _, path = mkstemp("-tardis-benchmark-hdf_buffer-test.hdf")
-        return path
-
-    def create_temporal_file(self, suffix=None):
-        # TODO: Delete this files after ASV runs the benchmarks.
-        #       ASV create a temporal directory in runtime per test: `tmpiuxngvlv`.
-        #       The ASV and ASV_Runner, not has some way to get this temporal directory.
-        #       The idea is use this temporal folders to storage this created temporal file.
-        suffix_str = "" if suffix is None else f"-{suffix}"
-        _, path = mkstemp(suffix_str)
-        return path
-
-    @property
-    def gamma_ray_simulation_state(self):
-        self.gamma_ray_config.model.structure.velocity.start = 1.0 * u.km / u.s
-        self.gamma_ray_config.model.structure.density.rho_0 = (
-            5.0e2 * u.g / u.cm**3
-        )
-        self.gamma_ray_config.supernova.time_explosion = 150 * u.d
-
-        return SimulationState.from_config(
-            self.gamma_ray_config, atom_data=self.atomic_dataset
-        )
-
-    @property
-    def gamma_ray_config(self):
-        yml_path = f"{self.example_configuration_dir}/tardis_configv1_density_exponential_nebular_multi_isotope.yml"
-
-        return config_reader.Configuration.from_yaml(yml_path)
-
-    @property
-    def example_model_file_dir(self):
-        return self.get_absolute_path("tardis/io/model/readers/tests/data")
-
-    @property
-    def kurucz_atomic_data(self) -> AtomData:
-        return deepcopy(self.atomic_dataset)
-
-    @property
-    def example_csvy_file_dir(self):
-        return self.get_absolute_path("tardis/model/tests/data/")
-
-    @property
+    @functools.cached_property
     def simulation_verysimple(self):
         atomic_data = deepcopy(self.atomic_dataset)
         sim = Simulation.from_config(
@@ -171,73 +105,13 @@ def simulation_verysimple(self):
         sim.iterate(4000)
         return sim
 
-    @property
+    @functools.cached_property
     def config_verysimple(self):
         return Configuration.from_yaml(
             f"{self.example_configuration_dir}/tardis_configv1_verysimple.yml"
         )
 
-    class CustomPyTestRequest:
-        def __init__(
-            self,
-            tardis_regression_data_path: str,
-            node_name: str,
-            node_module_name: str,
-            regression_data_dir: str,
-        ):
-            self.tardis_regression_data_path = tardis_regression_data_path
-            self.node_name = node_name
-            self.node_module_name = node_module_name
-            self.regression_data_dir = regression_data_dir
-
-        @property
-        def config(self):
-            class SubClass:
-                @staticmethod
-                def getoption(option):
-                    if option == "--tardis-regression-data":
-                        return self.tardis_regression_data_path
-                    return None
-
-            return SubClass()
-
-        @property
-        def node(self):
-            class SubClass:
-                def __init__(self, parent):
-                    self.parent = parent
-
-                @property
-                def name(self):
-                    return self.parent.node_name
-
-                @property
-                def module(self):
-                    class SubSubClass:
-                        def __init__(self, parent):
-                            self.parent = parent
-
-                        @property
-                        def __name__(self):
-                            return self.parent.node_module_name
-
-                    return SubSubClass(self.parent)
-
-            return SubClass(self)
-
-        @property
-        def cls(self):
-            return None
-
-        @property
-        def relative_regression_data_dir(self):
-            return self.regression_data_dir
-
-    @staticmethod
-    def regression_data(request: CustomPyTestRequest):
-        return RegressionData(request)
-
-    @property
+    @functools.cached_property
     def packet(self):
         return RPacket(
             r=7.5e14,
@@ -248,27 +122,25 @@ def packet(self):
             index=0,
         )
 
-    @property
+    @functools.cached_property
     def verysimple_packet_collection(self):
-        return (
-            self.nb_simulation_verysimple.transport.transport_state.packet_collection
-        )
+        return self.nb_simulation_verysimple.transport.transport_state.packet_collection
 
-    @property
+    @functools.cached_property
     def nb_simulation_verysimple(self):
         atomic_data = deepcopy(self.atomic_dataset)
         sim = Simulation.from_config(
             self.config_verysimple, atom_data=atomic_data
         )
-        sim.iterate(10)
+        sim.iterate(5)
         return sim
 
-    @property
+    @functools.cached_property
     def verysimple_time_explosion(self):
         model = self.nb_simulation_verysimple.simulation_state
         return model.time_explosion.cgs.value
 
-    @property
+    @functools.cached_property
     def verysimple_opacity_state(self):
         return opacity_state_initialize(
             self.nb_simulation_verysimple.plasma,
@@ -276,33 +148,19 @@ def verysimple_opacity_state(self):
             disable_line_scattering=self.nb_simulation_verysimple.transport.montecarlo_configuration.DISABLE_LINE_SCATTERING,
         )
 
-    @property
+    @functools.cached_property
     def verysimple_enable_full_relativity(self):
         return self.nb_simulation_verysimple.transport.enable_full_relativity
 
-    @property
-    def verysimple_disable_line_scattering(self):
-        return (
-            self.nb_simulation_verysimple.transport.montecarlo_configuration.DISABLE_LINE_SCATTERING
-        )
-
-    @property
-    def verysimple_continuum_processes_enabled(self):
-        return montecarlo_globals.CONTINUUM_PROCESSES_ENABLED
-
-    @property
+    @functools.cached_property
     def verysimple_tau_russian(self):
-        return (
-            self.nb_simulation_verysimple.transport.montecarlo_configuration.VPACKET_TAU_RUSSIAN
-        )
+        return self.nb_simulation_verysimple.transport.montecarlo_configuration.VPACKET_TAU_RUSSIAN
 
-    @property
+    @functools.cached_property
     def verysimple_survival_probability(self):
-        return (
-            self.nb_simulation_verysimple.transport.montecarlo_configuration.SURVIVAL_PROBABILITY
-        )
+        return self.nb_simulation_verysimple.transport.montecarlo_configuration.SURVIVAL_PROBABILITY
 
-    @property
+    @functools.cached_property
     def static_packet(self):
         return RPacket(
             r=7.5e14,
@@ -313,18 +171,9 @@ def static_packet(self):
             index=0,
         )
 
-    @property
-    def set_seed_fixture(self):
-        def set_seed(value):
-            np.random.seed(value)
-
-        return njit(set_seed)
-
-    @property
+    @functools.cached_property
     def verysimple_3vpacket_collection(self):
-        spectrum_frequency_grid = (
-            self.nb_simulation_verysimple.transport.spectrum_frequency_grid.value
-        )
+        spectrum_frequency_grid = self.nb_simulation_verysimple.transport.spectrum_frequency_grid.value
         return VPacketCollection(
             source_rpacket_index=0,
             spectrum_frequency_grid=spectrum_frequency_grid,
@@ -334,54 +183,25 @@ def verysimple_3vpacket_collection(self):
             temporary_v_packet_bins=0,
         )
 
-    @property
+    @functools.cached_property
     def verysimple_numba_radial_1d_geometry(self):
         return (
             self.nb_simulation_verysimple.simulation_state.geometry.to_numba()
         )
 
-    @property
-    def simulation_verysimple_vpacket_tracking(self):
-        atomic_data = deepcopy(self.atomic_dataset)
-        sim = Simulation.from_config(
-            self.config_verysimple,
-            atom_data=atomic_data,
-            virtual_packet_logging=True,
-        )
-        sim.last_no_of_packets = 4000
-        sim.run_final()
-        return sim
-
-    @property
-    def generate_reference(self):
-        # TODO: Investigate how to get the `--generate-reference` parameter passed in the command line.
-        #       `request.config.getoption("--generate-reference")`
-        option = None
-        if option is None:
-            return False
-        else:
-            return option
-
-    @property
-    def verysimple_radfield_mc_estimators(self):
-        plasma = self.nb_simulation_verysimple.plasma
-        return radfield_mc_estimators.initialize_estimator_statistics(
-            plasma.tau_sobolevs.shape, plasma.gamma.shape
-        )
-
-    @property
+    @functools.cached_property
     def montecarlo_configuration(self):
         return MonteCarloConfiguration()
 
-    @property
+    @functools.cached_property
     def rpacket_tracker(self):
         return RPacketTracker(0)
 
-    @property
+    @functools.cached_property
     def transport_state(self):
         return self.nb_simulation_verysimple.transport.transport_state
 
-    @property
+    @functools.cached_property
     def simulation_rpacket_tracking_enabled(self):
         config_verysimple = self.config_verysimple
         config_verysimple.montecarlo.iterations = 3
@@ -399,7 +219,7 @@ def simulation_rpacket_tracking_enabled(self):
         )
         return sim
 
-    @property
+    @functools.cached_property
     def geometry(self):
         return NumbaRadial1DGeometry(
             r_inner=np.array([6.912e14, 8.64e14], dtype=np.float64),
@@ -408,7 +228,7 @@ def geometry(self):
             v_outer=np.array([-1, -1], dtype=np.float64),
         )
 
-    @property
+    @functools.cached_property
     def estimators(self):
         return radfield_mc_estimators.RadiationFieldMCEstimators(
             j_estimator=np.array([0.0, 0.0], dtype=np.float64),
@@ -426,7 +246,9 @@ def estimators(self):
             photo_ion_estimator_statistics=np.empty((0, 0), dtype=np.int64),
         )
 
-    @property
+    @functools.cached_property
     def rpacket_tracker_list(self):
         no_of_packets = len(self.transport_state.packet_collection.initial_nus)
-        return generate_rpacket_last_interaction_tracker_list(no_of_packets)
+        return packet_trackers.generate_rpacket_last_interaction_tracker_list(
+            no_of_packets
+        )
diff --git a/benchmarks/opacities_opacity.py b/benchmarks/opacities_opacity.py
index de571cc2184..5352ceccc89 100644
--- a/benchmarks/opacities_opacity.py
+++ b/benchmarks/opacities_opacity.py
@@ -2,8 +2,6 @@
 Basic TARDIS Benchmark.
 """
 
-from asv_runner.benchmarks.mark import parameterize
-
 import tardis.opacities.opacities as calculate_opacity
 from benchmarks.benchmark_base import BenchmarkBase
 from tardis.opacities.opacities import compton_opacity_calculation
@@ -14,95 +12,25 @@ class BenchmarkMontecarloMontecarloNumbaOpacities(BenchmarkBase):
     Class to benchmark the numba opacities function.
     """
 
-    @parameterize(
-        {
-            "Electron number density": [
-                1.0e11,
-                1e15,
-                1e5,
-            ],
-            "Energy": [
-                511.0,
-                255.5,
-                511.0e7,
-            ],
-        }
-    )
-    def time_compton_opacity_calculation(self, electron_number_density, energy):
-        compton_opacity_calculation(energy, electron_number_density)
+    def time_compton_opacity_calculation(self):
+        energy = 511.0
+        electron_number_density = 1e15
+        calculate_opacity.compton_opacity_calculation(
+            energy, electron_number_density
+        )
 
-    @parameterize(
-        {
-            "Parameters": [
-                {
-                    "Ejecta_density": 0.01,
-                    "Energy": 511.0,
-                    "Iron_group_fraction": 0.5,
-                },
-                {
-                    "Ejecta_density": 0.01,
-                    "Energy": 5110000000.0,
-                    "Iron_group_fraction": 0.0,
-                },
-                {
-                    "Ejecta_density": 0.01,
-                    "Energy": 255.5,
-                    "Iron_group_fraction": 0.0,
-                },
-                {
-                    "Ejecta_density": 0.01,
-                    "Energy": 255.5,
-                    "Iron_group_fraction": 0.5,
-                },
-                {
-                    "Ejecta_density": 100000.0,
-                    "Energy": 255.5,
-                    "Iron_group_fraction": 1.0,
-                }
-            ]
-        }
-    )
-    def time_photoabsorption_opacity_calculation(self, parameters):
+    def time_photoabsorption_opacity_calculation(self):
+        energy = 255.5
+        ejecta_density = 100000.0
+        iron_group_fraction = 0.5
         calculate_opacity.photoabsorption_opacity_calculation(
-            parameters["Energy"],
-            parameters["Ejecta_density"],
-            parameters["Iron_group_fraction"],
+            energy, ejecta_density, iron_group_fraction
         )
 
-    @parameterize(
-        {
-            "Parameters": [
-                {
-                    "Ejecta_density": 0.01,
-                    "Energy": 511.0,
-                    "Iron_group_fraction": 0.5,
-                },
-                {
-                    "Ejecta_density": 0.01,
-                    "Energy": 5110000000.0,
-                    "Iron_group_fraction": 0.0,
-                },
-                {
-                    "Ejecta_density": 0.01,
-                    "Energy": 255.5,
-                    "Iron_group_fraction": 0.0,
-                },
-                {
-                    "Ejecta_density": 0.01,
-                    "Energy": 255.5,
-                    "Iron_group_fraction": 0.5,
-                },
-                {
-                    "Ejecta_density": 100000.0,
-                    "Energy": 255.5,
-                    "Iron_group_fraction": 1.0,
-                }
-            ]
-        }
-    )
-    def time_pair_creation_opacity_calculation(self, parameters):
+    def time_pair_creation_opacity_calculation(self):
+        energy = 255.9
+        ejecta_density = 100000.009
+        iron_group_fraction = 0.5
         calculate_opacity.pair_creation_opacity_calculation(
-            parameters["Energy"],
-            parameters["Ejecta_density"],
-            parameters["Iron_group_fraction"],
+            energy, ejecta_density, iron_group_fraction
         )
diff --git a/benchmarks/opacities_opacity_state.py b/benchmarks/opacities_opacity_state.py
index ea05e794691..18ae4769a95 100644
--- a/benchmarks/opacities_opacity_state.py
+++ b/benchmarks/opacities_opacity_state.py
@@ -2,24 +2,26 @@
 Basic TARDIS Benchmark.
 """
 
-import numpy as np
+import functools
+
 from asv_runner.benchmarks.mark import parameterize
 
-from tardis.opacities.opacity_state import opacity_state_initialize
 from benchmarks.benchmark_base import BenchmarkBase
+from tardis.opacities.opacity_state import opacity_state_initialize
 
 
+@parameterize({"Input params": ["scatter", "macroatom"]})
 class BenchmarkOpacitiesOpacityState(BenchmarkBase):
     """
     Class to benchmark the numba interface function.
     """
+    repeat = 2
+
+    @functools.cache
+    def setup(self, input_params):
+        self.sim = self.nb_simulation_verysimple
 
-    @parameterize({"Input params": ["scatter", "macroatom"]})
     def time_opacity_state_initialize(self, input_params):
         line_interaction_type = input_params
-        plasma = self.nb_simulation_verysimple.plasma
-        opacity_state_initialize(
-            plasma,
-            line_interaction_type,
-            self.verysimple_disable_line_scattering,
-        )
+        plasma = self.sim.plasma
+        opacity_state_initialize(plasma, line_interaction_type, True)
diff --git a/benchmarks/run_tardis.py b/benchmarks/run_tardis.py
index 9e00a6a3f9b..ab423ded7b4 100644
--- a/benchmarks/run_tardis.py
+++ b/benchmarks/run_tardis.py
@@ -4,6 +4,8 @@
 
 from benchmarks.benchmark_base import BenchmarkBase
 from tardis import run_tardis
+from tardis.io.atom_data import AtomData
+
 
 
 class BenchmarkRunTardis(BenchmarkBase):
@@ -11,16 +13,20 @@ class BenchmarkRunTardis(BenchmarkBase):
     Class to benchmark the `run tardis` function.
     """
 
+    repeat = 2
+
+    def setup(self):
+        self.config = self.config_verysimple
+        self.atom_data = AtomData.from_hdf(self.atomic_data_fname)
+
     def time_run_tardis(self):
         run_tardis(
-            self.config_verysimple,
-            atom_data=self.atomic_dataset,
-            show_convergence_plots=False,
+            self.config, atom_data=self.atom_data, show_convergence_plots=False
         )
 
     def time_run_tardis_rpacket_tracking(self):
         run_tardis(
             self.config_rpacket_tracking,
-            atom_data=self.atomic_dataset,
+            atom_data=self.atom_data,
             show_convergence_plots=False,
         )
diff --git a/benchmarks/spectrum_formal_integral.py b/benchmarks/spectrum_formal_integral.py
index c7eb25e6f5a..8c69ea71bce 100644
--- a/benchmarks/spectrum_formal_integral.py
+++ b/benchmarks/spectrum_formal_integral.py
@@ -2,43 +2,43 @@
 Basic TARDIS Benchmark.
 """
 
-from asv_runner.benchmarks.mark import parameterize
+import functools
+
 from numba import config
 
-import tardis.spectrum.formal_integral as formal_integral
 from benchmarks.benchmark_base import BenchmarkBase
+from tardis.spectrum import formal_integral
+
+config.THREADING_LAYER = "workqueue"
 
-config.THREADING_LAYER='workqueue'
 
 class BenchmarkTransportMontecarloFormalIntegral(BenchmarkBase):
     """
     Class to benchmark the numba formal integral function.
     """
 
-    @parameterize(
-        {
-            "Parameters": [
-                {
-                    "nu": 1e14,
-                    "temperature": 1e4,
-                }
-            ]
-        }
-    )
-    def time_intensity_black_body(self, parameters):
-        nu = parameters["nu"]
-        temperature = parameters["temperature"]
+    repeat = 2
+
+    @functools.cache
+    def setup(self):
+        self.sim = self.simulation_verysimple
+        self.FormalIntegrator = formal_integral.FormalIntegrator(
+            self.sim.simulation_state, self.sim.plasma, self.sim.transport
+        )
+
+    # Bencmark for intensity black body function
+    def time_intensity_black_body(self):
+        nu = 1e14
+        temperature = 1e4
         formal_integral.intensity_black_body(nu, temperature)
 
     # Benchmark for functions in FormalIntegrator class
     def time_FormalIntegrator_functions(self):
-        FormalIntegrator = formal_integral.FormalIntegrator(
-            self.simulation_verysimple.simulation_state, self.simulation_verysimple.plasma, self.simulation_verysimple.transport
+        self.FormalIntegrator.calculate_spectrum(
+            self.sim.spectrum_solver.spectrum_real_packets.frequency
         )
-        FormalIntegrator.calculate_spectrum(self.simulation_verysimple.spectrum_solver.spectrum_real_packets.frequency)
-        FormalIntegrator.make_source_function()
-        FormalIntegrator.generate_numba_objects()
-        FormalIntegrator.formal_integral(
-            self.simulation_verysimple.spectrum_solver.spectrum_real_packets.frequency,
-            1000
+        self.FormalIntegrator.make_source_function()
+        self.FormalIntegrator.generate_numba_objects()
+        self.FormalIntegrator.formal_integral(
+            self.sim.spectrum_solver.spectrum_real_packets.frequency, 1000
         )
diff --git a/benchmarks/transport_geometry_calculate_distances.py b/benchmarks/transport_geometry_calculate_distances.py
index 4f5829f40b8..5500f60f4bb 100644
--- a/benchmarks/transport_geometry_calculate_distances.py
+++ b/benchmarks/transport_geometry_calculate_distances.py
@@ -1,4 +1,4 @@
-from asv_runner.benchmarks.mark import parameterize
+import functools
 
 import tardis.transport.frame_transformations as frame_transformations
 import tardis.transport.geometry.calculate_distances as calculate_distances
@@ -10,6 +10,15 @@ class BenchmarkTransportGeometryCalculateDistances(BenchmarkBase):
     Class to benchmark the calculate distances function.
     """
 
+    @functools.cache
+    def setup(self):
+        self.StaticPacket = self.static_packet
+        self.Geometry = self.geometry
+        doppler_factor = frame_transformations.get_doppler_factor(
+            self.StaticPacket.r, self.StaticPacket.mu, self.model, True
+        )
+        self.comov_nu = self.StaticPacket.nu * doppler_factor
+
     @property
     def model(self):
         return 5.2e7
@@ -19,50 +28,16 @@ def time_calculate_distance_boundary(self):
         r = 7.5e14
 
         calculate_distances.calculate_distance_boundary(
-            r, mu, self.geometry.r_inner[0], self.geometry.r_outer[0]
-        )
-
-    @parameterize(
-        {
-            "Parameters": [
-                {
-                    "packet": {
-                        "nu_line": 0.1,
-                        "is_last_line": True
-                    },
-                    "enable_full_relativity": True,
-                },
-                {
-                    "packet": {
-                        "nu_line": 0.2,
-                        "is_last_line": False
-                    },
-                    "enable_full_relativity": True,
-                }
-            ]
-        }
-    )
-    def time_calculate_distance_line(self, parameters):
-        packet_params = parameters["packet"]
-        nu_line = packet_params["nu_line"]
-        is_last_line = packet_params["is_last_line"]
-        enable_full_relativity = parameters["enable_full_relativity"]
-
-        time_explosion = self.model
-
-        doppler_factor = frame_transformations.get_doppler_factor(
-            self.static_packet.r,
-            self.static_packet.mu,
-            time_explosion,
-            enable_full_relativity
+            r, mu, self.Geometry.r_inner[0], self.Geometry.r_outer[0]
         )
-        comov_nu = self.static_packet.nu * doppler_factor
 
+    def time_calculate_distance_line(self):
+        nu_line = 0.2
         calculate_distances.calculate_distance_line(
-            self.static_packet,
-            comov_nu,
-            is_last_line,
+            self.StaticPacket,
+            self.comov_nu,
+            True,
             nu_line,
-            time_explosion,
-            enable_full_relativity
+            True,
+            True,
         )
diff --git a/benchmarks/transport_montecarlo_estimators_radfield_estimator_calcs.py b/benchmarks/transport_montecarlo_estimators_radfield_estimator_calcs.py
index 45a3b3b8409..8d71a27f492 100644
--- a/benchmarks/transport_montecarlo_estimators_radfield_estimator_calcs.py
+++ b/benchmarks/transport_montecarlo_estimators_radfield_estimator_calcs.py
@@ -2,15 +2,12 @@
 Basic TARDIS Benchmark.
 """
 
-import tardis.opacities.opacities as opacities
-import tardis.transport.geometry.calculate_distances as calculate_distances
-import tardis.transport.montecarlo.r_packet_transport as r_packet_transport
-import tardis.transport.montecarlo.utils as utils
+import functools
+
 from benchmarks.benchmark_base import BenchmarkBase
 from tardis.transport.montecarlo.estimators.radfield_estimator_calcs import (
     update_line_estimators,
 )
-from asv_runner.benchmarks.mark import parameterize
 
 
 class BenchmarkMontecarloMontecarloNumbaPacket(BenchmarkBase):
@@ -18,40 +15,14 @@ class BenchmarkMontecarloMontecarloNumbaPacket(BenchmarkBase):
     Class to benchmark the numba packet function.
     """
 
-    @parameterize(
-        {
-            "Parameters": [
-                {
-                    "cur_line_id": 0,
-                    "distance_trace": 1e12,
-                    "time_explosion": 5.2e7,
-                    "enable_full_relativity": True,
-                },
-                {
-                    "cur_line_id": 0,
-                    "distance_trace": 0,
-                    "time_explosion": 5.2e7,
-                    "enable_full_relativity": True,
-                },
-                {
-                    "cur_line_id": 1,
-                    "distance_trace": 1e5,
-                    "time_explosion": 1e10,
-                    "enable_full_relativity": False,
-                },
-            ]
-        }
-    )
-    def time_update_line_estimators(self, parameters):
-        cur_line_id = parameters["cur_line_id"]
-        distance_trace = parameters["distance_trace"]
-        time_explosion = parameters["time_explosion"]
-        enable_full_relativity = parameters["enable_full_relativity"]
+    repeat = 4
+
+    @functools.cache
+    def setup(self):
+        self.Estimators = self.estimators
+        self.StaticPacket = self.static_packet
+
+    def time_update_line_estimators(self):
         update_line_estimators(
-            self.estimators,
-            self.static_packet,
-            cur_line_id,
-            distance_trace,
-            time_explosion,
-            enable_full_relativity,
+            self.Estimators, self.StaticPacket, 1, 1e12, 1e10, True
         )
diff --git a/benchmarks/transport_montecarlo_interaction.py b/benchmarks/transport_montecarlo_interaction.py
index e89c486aac2..dcadc56a2da 100644
--- a/benchmarks/transport_montecarlo_interaction.py
+++ b/benchmarks/transport_montecarlo_interaction.py
@@ -2,12 +2,10 @@
 Basic TARDIS Benchmark.
 """
 
+import functools
+
 import tardis.transport.montecarlo.interaction as interaction
 from benchmarks.benchmark_base import BenchmarkBase
-from tardis.transport.montecarlo.numba_interface import (
-    LineInteractionType,
-)
-from asv_runner.benchmarks.mark import parameterize
 
 
 class BenchmarkTransportMontecarloInteraction(BenchmarkBase):
@@ -15,68 +13,44 @@ class BenchmarkTransportMontecarloInteraction(BenchmarkBase):
     Class to benchmark the numba interaction function.
     """
 
-    def time_thomson_scatter(self):
-        packet = self.packet
-        time_explosion = self.verysimple_time_explosion
-        enable_full_relativity = self.verysimple_enable_full_relativity
+    repeat = 3 
+
+    @functools.cache
+    def setup(self):
+        self.Packet = self.packet
+        self.time_explosion = self.verysimple_time_explosion
+        self.enable_full_relativity = self.verysimple_enable_full_relativity
+        self.opacity_state = self.verysimple_opacity_state
 
+    def time_thomson_scatter(self):
         interaction.thomson_scatter(
-            packet, time_explosion, enable_full_relativity
+            self.Packet, self.time_explosion, self.enable_full_relativity
         )
 
-    @parameterize(
-        {
-            "Line interaction type": [
-                LineInteractionType.SCATTER,
-                LineInteractionType.MACROATOM,
-            ],
-        }
-    )
-    def time_line_scatter(self, line_interaction_type):
-        packet = self.packet
-        packet.initialize_line_id(
-            self.verysimple_opacity_state,
-            self.verysimple_time_explosion,
-            self.verysimple_enable_full_relativity,
+    def time_line_scatter(self):
+        self.Packet.initialize_line_id(
+            self.opacity_state, self.time_explosion, self.enable_full_relativity
         )
-        time_explosion = self.verysimple_time_explosion
-
         interaction.line_scatter(
-            packet,
-            time_explosion,
-            line_interaction_type,
-            self.verysimple_opacity_state,
-            self.verysimple_enable_full_relativity,
+            self.Packet,
+            self.time_explosion,
+            "SCATTER",
+            self.opacity_state,
+            self.enable_full_relativity,
         )
 
-    @parameterize(
-        {
-            "Test packet": [
-                {
-                    "mu": 0.8599443103322428,
-                    "emission_line_id": 1000,
-                    "energy": 0.9114437898710559,
-                }
-            ]
-        }
-    )
-    def time_line_emission(self, test_packet):
-        emission_line_id = test_packet["emission_line_id"]
-        packet = self.packet
-        packet.mu = test_packet["mu"]
-        packet.energy = test_packet["energy"]
-        packet.initialize_line_id(
-            self.verysimple_opacity_state,
-            self.verysimple_time_explosion,
-            self.verysimple_enable_full_relativity,
+    def time_line_emission(self):
+        emission_line_id = 1000
+        self.Packet.mu = 0.8599443103322428
+        self.Packet.energy = 0.9114437898710559
+        self.Packet.initialize_line_id(
+            self.opacity_state, self.time_explosion, self.enable_full_relativity
         )
 
-        time_explosion = self.verysimple_time_explosion
-
         interaction.line_emission(
-            packet,
+            self.Packet,
             emission_line_id,
-            time_explosion,
-            self.verysimple_opacity_state,
-            self.verysimple_enable_full_relativity,
+            self.time_explosion,
+            self.opacity_state,
+            self.enable_full_relativity,
         )
diff --git a/benchmarks/transport_montecarlo_main_loop.py b/benchmarks/transport_montecarlo_main_loop.py
index 7d6d07ddb08..cc91fd430d3 100644
--- a/benchmarks/transport_montecarlo_main_loop.py
+++ b/benchmarks/transport_montecarlo_main_loop.py
@@ -2,6 +2,8 @@
 Basic TARDIS Benchmark.
 """
 
+import functools
+
 from benchmarks.benchmark_base import BenchmarkBase
 from tardis.transport.montecarlo.montecarlo_main_loop import (
     montecarlo_main_loop,
@@ -13,14 +15,26 @@ class BenchmarkTransportMontecarloMontecarloMainLoop(BenchmarkBase):
     class to benchmark montecarlo_main_loop function.
     """
 
+    repeat = 3
+
+    @functools.cache
+    def setup(self):
+        self.packet_collection = self.transport_state.packet_collection
+        self.geometry_state = self.transport_state.geometry_state
+        self.time_explosion = self.verysimple_time_explosion
+        self.opacity_state = self.transport_state.opacity_state
+        self.radfield_mc_estimators = (
+            self.transport_state.radfield_mc_estimators
+        )
+
     def time_montecarlo_main_loop(self):
         montecarlo_main_loop(
-            self.transport_state.packet_collection,
-            self.transport_state.geometry_state,
-            self.verysimple_time_explosion,
-            self.transport_state.opacity_state,
+            self.packet_collection,
+            self.geometry_state,
+            self.time_explosion,
+            self.opacity_state,
             self.montecarlo_configuration,
-            self.transport_state.radfield_mc_estimators,
+            self.radfield_mc_estimators,
             self.nb_simulation_verysimple.transport.spectrum_frequency_grid.value,
             self.rpacket_tracker_list,
             self.montecarlo_configuration.NUMBER_OF_VPACKETS,
diff --git a/benchmarks/transport_montecarlo_packet_trackers.py b/benchmarks/transport_montecarlo_packet_trackers.py
index a3f65f66f6d..e4207d23892 100644
--- a/benchmarks/transport_montecarlo_packet_trackers.py
+++ b/benchmarks/transport_montecarlo_packet_trackers.py
@@ -1,36 +1,38 @@
 """
 Basic TARDIS Benchmark.
 """
+import functools
+
+from asv_runner.benchmarks.mark import parameterize
+
 from benchmarks.benchmark_base import BenchmarkBase
-from tardis.transport.montecarlo.packet_trackers import (
-    rpacket_trackers_to_dataframe,
-    generate_rpacket_tracker_list,
-    generate_rpacket_last_interaction_tracker_list,
-)
+from tardis.transport.montecarlo import packet_trackers
 
 
+@parameterize({"num_packets": [10, 100], "length": [10, 50]})
 class BenchmarkTransportMontecarloPacketTrackers(BenchmarkBase):
     """
     Class to benchmark the numba R packet function.
     """
 
-    def time_rpacket_trackers_to_dataframe(self):
+    repeat = 2
+
+    @functools.cache
+    def setup(self, num_packets, length):
         sim = self.simulation_rpacket_tracking_enabled
-        transport_state = sim.transport.transport_state
-        rpacket_trackers_to_dataframe(transport_state.rpacket_tracker)
+        self.TransportState = sim.transport.transport_state
 
-    def time_generate_rpacket_tracker_list(self, no_of_packets, length):
-        generate_rpacket_tracker_list(no_of_packets, length)
+    def time_rpacket_trackers_to_dataframe(self, num_packets, length):
+        packet_trackers.rpacket_trackers_to_dataframe(
+            self.TransportState.rpacket_tracker
+        )
+
+    def time_generate_rpacket_tracker_list(self, num_packets, length):
+        packet_trackers.generate_rpacket_tracker_list(num_packets, length)
 
     def time_generate_rpacket_last_interaction_tracker_list(
-        self, no_of_packets
+        self, num_packets, length
     ):
-        generate_rpacket_last_interaction_tracker_list(no_of_packets)
-
-    time_generate_rpacket_tracker_list.params = ([1, 10, 50], [1, 10, 50])
-    time_generate_rpacket_tracker_list.param_names = ["no_of_packets", "length"]
-
-    time_generate_rpacket_last_interaction_tracker_list.params = [10, 100, 1000]
-    time_generate_rpacket_last_interaction_tracker_list.param_names = [
-        "no_of_packets"
-    ]
+        packet_trackers.generate_rpacket_last_interaction_tracker_list(
+            num_packets
+        )
diff --git a/benchmarks/transport_montecarlo_single_packet_loop.py b/benchmarks/transport_montecarlo_single_packet_loop.py
index 85bc6bbf64f..4a7138d5fb5 100644
--- a/benchmarks/transport_montecarlo_single_packet_loop.py
+++ b/benchmarks/transport_montecarlo_single_packet_loop.py
@@ -2,9 +2,10 @@
 Basic TARDIS Benchmark.
 """
 
+from numba.np.ufunc.parallel import get_num_threads, get_thread_id
+
 from benchmarks.benchmark_base import BenchmarkBase
 from tardis.transport.montecarlo import single_packet_loop
-from numba.np.ufunc.parallel import get_num_threads, get_thread_id
 
 
 class BenchmarkTransportMontecarloSinglePacketLoop(BenchmarkBase):
@@ -12,14 +13,18 @@ class BenchmarkTransportMontecarloSinglePacketLoop(BenchmarkBase):
     Class to benchmark the single packet loop function.
     """
 
+    repeat = 2
+
     def time_single_packet_loop(self):
         single_packet_loop.single_packet_loop(
             self.packet,
             self.verysimple_numba_radial_1d_geometry,
             self.verysimple_time_explosion,
             self.verysimple_opacity_state,
-            self.transport_state.radfield_mc_estimators.create_estimator_list(get_num_threads())[get_thread_id()],
+            self.transport_state.radfield_mc_estimators.create_estimator_list(
+                get_num_threads()
+            )[get_thread_id()],
             self.verysimple_3vpacket_collection,
             self.rpacket_tracker,
-            self.montecarlo_configuration
+            self.montecarlo_configuration,
         )
diff --git a/benchmarks/transport_montecarlo_vpacket.py b/benchmarks/transport_montecarlo_vpacket.py
index 4de7d198c68..b237577074d 100644
--- a/benchmarks/transport_montecarlo_vpacket.py
+++ b/benchmarks/transport_montecarlo_vpacket.py
@@ -2,15 +2,14 @@
 Basic TARDIS Benchmark.
 """
 
+import functools
+
 import numpy as np
-from asv_runner.benchmarks.mark import parameterize
 
 import tardis.transport.montecarlo.vpacket as vpacket
-from tardis.transport.montecarlo.r_packet import RPacket
 from benchmarks.benchmark_base import BenchmarkBase
-from tardis.transport.frame_transformations import (
-    get_doppler_factor,
-)
+from tardis.transport.frame_transformations import get_doppler_factor
+from tardis.transport.montecarlo.r_packet import RPacket
 
 
 class BenchmarkMontecarloMontecarloNumbaVpacket(BenchmarkBase):
@@ -18,7 +17,18 @@ class BenchmarkMontecarloMontecarloNumbaVpacket(BenchmarkBase):
     Class to benchmark the single packet loop function.
     """
 
-    @property
+    repeat = 5
+
+    def setup(self):
+        self.vpacket = self.v_packet
+        self.numba_radial_1d_geometry = self.verysimple_numba_radial_1d_geometry
+        self.time_explosion = self.verysimple_time_explosion
+        self.opacity_state = self.verysimple_opacity_state
+        self.tau_russian = self.verysimple_tau_russian
+        self.survival_probability = self.verysimple_survival_probability
+        self.enable_full_relativity = self.verysimple_enable_full_relativity
+
+    @functools.cached_property
     def v_packet(self):
         return vpacket.VPacket(
             r=7.5e14,
@@ -30,7 +40,7 @@ def v_packet(self):
             index=0,
         )
 
-    @property
+    @functools.cached_property
     def r_packet(self):
         return RPacket(
             r=7.5e14,
@@ -41,6 +51,7 @@ def r_packet(self):
             index=0,
         )
 
+    @functools.cache
     def v_packet_initialize_line_id(
         self, v_packet, opacity_state, time_explosion, enable_full_relativity
     ):
@@ -55,63 +66,45 @@ def v_packet_initialize_line_id(
         v_packet.next_line_id = next_line_id
 
     def time_trace_vpacket_within_shell(self):
-        v_packet = self.v_packet
-        verysimple_numba_radial_1d_geometry = (
-            self.verysimple_numba_radial_1d_geometry
-        )
-        verysimple_time_explosion = self.verysimple_time_explosion
-        verysimple_opacity_state = self.verysimple_opacity_state
-        enable_full_relativity = self.verysimple_enable_full_relativity
-
         # Give the vpacket a reasonable line ID
         self.v_packet_initialize_line_id(
-            v_packet,
-            verysimple_opacity_state,
-            verysimple_time_explosion,
-            enable_full_relativity,
+            self.vpacket,
+            self.opacity_state,
+            self.time_explosion,
+            self.enable_full_relativity,
         )
 
         vpacket.trace_vpacket_within_shell(
-            v_packet,
-            verysimple_numba_radial_1d_geometry,
-            verysimple_time_explosion,
-            verysimple_opacity_state,
-            enable_full_relativity,
+            self.vpacket,
+            self.numba_radial_1d_geometry,
+            self.time_explosion,
+            self.opacity_state,
+            self.enable_full_relativity,
         )
 
     def time_trace_vpacket(self):
-        v_packet = self.v_packet
-        verysimple_numba_radial_1d_geometry = (
-            self.verysimple_numba_radial_1d_geometry
-        )
-        verysimple_time_explosion = self.verysimple_time_explosion
-        verysimple_opacity_state = self.verysimple_opacity_state
-        enable_full_relativity = self.verysimple_enable_full_relativity
-        tau_russian = self.verysimple_tau_russian
-        survival_probability = self.verysimple_survival_probability
-
         # Set seed because of RNG in trace_vpacket
         np.random.seed(1)
 
         # Give the vpacket a reasonable line ID
         self.v_packet_initialize_line_id(
-            v_packet,
-            verysimple_opacity_state,
-            verysimple_time_explosion,
-            enable_full_relativity,
+            self.vpacket,
+            self.opacity_state,
+            self.time_explosion,
+            self.enable_full_relativity,
         )
 
         vpacket.trace_vpacket(
-            v_packet,
-            verysimple_numba_radial_1d_geometry,
-            verysimple_time_explosion,
-            verysimple_opacity_state,
-            tau_russian,
-            survival_probability,
-            enable_full_relativity,
+            self.vpacket,
+            self.numba_radial_1d_geometry,
+            self.time_explosion,
+            self.opacity_state,
+            self.tau_russian,
+            self.survival_probability,
+            self.enable_full_relativity,
         )
 
-    @property
+    @functools.cached_property
     def broken_packet(self):
         return vpacket.VPacket(
             r=1286064000000000.0,
@@ -125,41 +118,25 @@ def broken_packet(self):
 
     def time_trace_bad_vpacket(self):
         broken_packet = self.broken_packet
-        verysimple_numba_radial_1d_geometry = (
-            self.verysimple_numba_radial_1d_geometry
-        )
-        enable_full_relativity = self.verysimple_enable_full_relativity
-        verysimple_time_explosion = self.verysimple_time_explosion
-        verysimple_opacity_state = self.verysimple_opacity_state
-        tau_russian = self.verysimple_tau_russian
-        survival_probability = self.verysimple_survival_probability
 
         vpacket.trace_vpacket(
             broken_packet,
-            verysimple_numba_radial_1d_geometry,
-            verysimple_time_explosion,
-            verysimple_opacity_state,
-            tau_russian,
-            survival_probability,
-            enable_full_relativity,
+            self.numba_radial_1d_geometry,
+            self.time_explosion,
+            self.opacity_state,
+            self.tau_russian,
+            self.survival_probability,
+            self.enable_full_relativity,
         )
 
-    @parameterize(
-        {
-            "Paramters": [
-                {"tau_russian": 10.0, "survival_possibility": 0.0},
-                {"tau_russian": 15.0, "survival_possibility": 0.1},
-            ]
-        }
-    )
-    def time_trace_vpacket_volley(self, parameters):
+    def time_trace_vpacket_volley(self):
         vpacket.trace_vpacket_volley(
             self.r_packet,
             self.verysimple_3vpacket_collection,
-            self.verysimple_numba_radial_1d_geometry,
-            self.verysimple_time_explosion,
-            self.verysimple_opacity_state,
-            False,
-            parameters["tau_russian"],
-            parameters["survival_possibility"]
+            self.numba_radial_1d_geometry,
+            self.time_explosion,
+            self.opacity_state,
+            self.enable_full_relativity,
+            self.tau_russian,
+            self.survival_probability,
         )
diff --git a/benchmarks/util/__init__.py b/benchmarks/util/__init__.py
deleted file mode 100644
index e69de29bb2d..00000000000
diff --git a/benchmarks/util/base.py b/benchmarks/util/base.py
deleted file mode 100644
index 7dd61629e3e..00000000000
--- a/benchmarks/util/base.py
+++ /dev/null
@@ -1,20 +0,0 @@
-from os.path import dirname, realpath, join
-from pathlib import Path, PosixPath
-
-
-class Base:
-    @staticmethod
-    def get_path(partial_path: str) -> Path:
-        base_path = dirname(realpath(__file__))
-        path = Path(base_path) / Path(partial_path)
-        return path
-
-    @property
-    def tardis_ref_path(self) -> Path:
-        # TODO: This route is fixed but needs to get from the arguments given in the command line.
-        #       /app/tardis-refdata
-        return Path("/app/tardis-refdata")
-
-    @property
-    def example_configuration_dir(self) -> Path:
-        return self.get_path("../../tardis/io/configuration/tests/data")
diff --git a/benchmarks/util/nlte.py b/benchmarks/util/nlte.py
deleted file mode 100644
index 7cfed4ef4dd..00000000000
--- a/benchmarks/util/nlte.py
+++ /dev/null
@@ -1,78 +0,0 @@
-from collections import OrderedDict
-from copy import deepcopy
-from pathlib import Path
-
-from benchmarks.util.base import Base
-from tardis.io.atom_data import AtomData
-from tardis.io.configuration.config_reader import Configuration
-from tardis.io.util import yaml_load_file, YAMLLoader
-from tardis.model import SimulationState
-
-
-class NLTE:
-    def __init__(self):
-        self.__base = Base()
-
-    @property
-    def tardis_config_verysimple_nlte(self) -> OrderedDict:
-        path: str = (
-            "../../tardis/io/configuration/tests/data/tardis_configv1_nlte.yml"
-        )
-        filename: Path = self.__base.get_path(path)
-
-        return yaml_load_file(
-            filename,
-            YAMLLoader,
-        )
-
-    @property
-    def nlte_raw_model_root(self) -> SimulationState:
-        return SimulationState.from_config(
-            self.tardis_model_config_nlte_root, self.nlte_atom_data
-        )
-
-    @property
-    def nlte_raw_model_lu(self) -> SimulationState:
-        return SimulationState.from_config(
-            self.tardis_model_config_nlte_lu, self.nlte_atom_data
-        )
-
-    @property
-    def nlte_atom_data(self) -> AtomData:
-        atomic_data = deepcopy(self.nlte_atomic_dataset)
-        return atomic_data
-
-    @property
-    def nlte_atomic_dataset(self) -> AtomData:
-        nlte_atomic_data = AtomData.from_hdf(self.nlte_atomic_data_fname)
-        return nlte_atomic_data
-
-    @property
-    def nlte_atomic_data_fname(self) -> str:
-        atomic_data_fname = (
-            f"{self.__base.tardis_ref_path}/nlte_atom_data/TestNLTE_He_Ti.h5"
-        )
-
-        if not Path(atomic_data_fname).exists():
-            atom_data_missing_str = (
-                f"Atomic datafiles {atomic_data_fname} does not seem to exist"
-            )
-            raise Exception(atom_data_missing_str)
-
-        return atomic_data_fname
-
-    @property
-    def tardis_model_config_nlte_root(self) -> Configuration:
-        config = Configuration.from_yaml(
-            f"{self.__base.example_configuration_dir}/tardis_configv1_nlte.yml"
-        )
-        config.plasma.nlte_solver = "root"
-        return config
-
-    @property
-    def tardis_model_config_nlte_lu(self) -> Configuration:
-        config = Configuration.from_yaml(
-            f"{self.__base.example_configuration_dir}/tardis_configv1_nlte.yml"
-        )
-        config.plasma.nlte_solver = "lu"
-        return config

From 1c55cfc6b450cd7cd7ad479ffa43640f6790318d Mon Sep 17 00:00:00 2001
From: tardis-bot <60989672+tardis-bot@users.noreply.github.com>
Date: Sun, 4 Aug 2024 06:19:41 +0530
Subject: [PATCH 08/10] Pre-release 2024.08.04 (#2775)

Automated changes for pre-release 2024.08.04
---
 .zenodo.json | 54 ++++++++++++++++++++++++++--------------------------
 1 file changed, 27 insertions(+), 27 deletions(-)

diff --git a/.zenodo.json b/.zenodo.json
index 3090e7f3aa4..544f071000e 100644
--- a/.zenodo.json
+++ b/.zenodo.json
@@ -154,10 +154,10 @@
       "name": "Holas, Alexander"
     },
     {
-      "name": "Reinecke, Martin"
+      "name": "Eweis, Youssef"
     },
     {
-      "name": "Eweis, Youssef"
+      "name": "Reinecke, Martin"
     },
     {
       "name": "Bylund, Tomas"
@@ -165,6 +165,9 @@
     {
       "name": "Black, William"
     },
+    {
+      "name": "Gupta, Sumit"
+    },
     {
       "name": "Bentil, Laud"
     },
@@ -176,31 +179,31 @@
       "name": "Kumar, Ansh"
     },
     {
-      "name": "Gupta, Sumit"
+      "name": "Alam, Arib"
     },
     {
-      "name": "Alam, Arib"
+      "name": "Kumar, Asish"
     },
     {
       "name": "Bartnik, Matthew"
     },
     {
-      "name": "Varma Buddaraju, Rohith"
+      "name": "Magee, Mark"
     },
     {
-      "name": "Magee, Mark"
+      "name": "Dutta, Anirban"
     },
     {
-      "name": "Lu, Jing"
+      "name": "Varma Buddaraju, Rohith"
     },
     {
-      "name": "Visser, Erin"
+      "name": "Livneh, Ran"
     },
     {
-      "name": "Dutta, Anirban"
+      "name": "Lu, Jing"
     },
     {
-      "name": "Kumar, Asish"
+      "name": "Visser, Erin"
     },
     {
       "name": "Daksh, Ayushi"
@@ -208,9 +211,6 @@
     {
       "name": "Kambham, Satwik"
     },
-    {
-      "name": "Livneh, Ran"
-    },
     {
       "name": "Bhakar, Jayant"
     },
@@ -228,49 +228,49 @@
       "name": "Srivastava, Sarthak"
     },
     {
-      "name": "Actions, GitHub"
+      "name": "Reichenbach, John"
     },
     {
       "name": "Jain, Rinkle"
     },
     {
-      "name": "Reichenbach, John"
+      "name": "Floers, Andreas"
     },
     {
-      "name": "Floers, Andreas"
+      "name": "Actions, GitHub"
     },
     {
-      "name": "Gupta, Harshul"
+      "name": "Chaumal, Aarya"
     },
     {
-      "name": "Brar, Antreev"
+      "name": "Gupta, Harshul"
     },
     {
-      "name": "Chaumal, Aarya"
+      "name": "Brar, Antreev"
     },
     {
       "name": "Singh, Sourav"
     },
     {
-      "name": "Selsing, Jonatan"
+      "name": "Kumar, Aman"
     },
     {
-      "name": "Matsumura, Yuki"
+      "name": "Sofiatti, Caroline"
     },
     {
       "name": "Kowalski, Nathan"
     },
     {
-      "name": "Sofiatti, Caroline"
+      "name": "Selsing, Jonatan"
     },
     {
-      "name": "Patidar, Abhishek"
+      "name": "Talegaonkar, Chinmay"
     },
     {
-      "name": "Kumar, Aman"
+      "name": "Matsumura, Yuki"
     },
     {
-      "name": "Talegaonkar, Chinmay"
+      "name": "Patidar, Abhishek"
     },
     {
       "name": "Venkat, Shashank"
@@ -339,10 +339,10 @@
       "name": "PATIDAR, ABHISHEK"
     },
     {
-      "name": "Kharkar, Atharwa"
+      "name": "Nayak U, Ashwin"
     },
     {
-      "name": "Nayak U, Ashwin"
+      "name": "Kharkar, Atharwa"
     },
     {
       "name": "Kumar, Atul"

From e1aa88723a6836e8a25cc1afb24b578b1b78651f Mon Sep 17 00:00:00 2001
From: tardis-bot <60989672+tardis-bot@users.noreply.github.com>
Date: Sun, 4 Aug 2024 06:45:27 +0530
Subject: [PATCH 09/10] Post-release 2024.08.04 (#2776)

Automated changes for post-release 2024.08.04
---
 CHANGELOG.md               | 419 +++++++++++++++++++++++++++++++++++++
 CITATION.cff               | 164 ++++++++-------
 README.rst                 |  85 ++++----
 docs/resources/credits.rst |  84 ++++----
 4 files changed, 600 insertions(+), 152 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 4f11fddddbd..aa853d91569 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -1,5 +1,22 @@
 ## Changelog
 
+### release-2024.08.04 (2024/08/03 20:49)
+- [2775](https://github.com/tardis-sn/tardis/pull/2775) Pre-release 2024.08.04 (2775) (@tardis-bot)
+- [2749](https://github.com/tardis-sn/tardis/pull/2749) Cache benchmark functions (2749) (@officialasishkumar)
+- [2762](https://github.com/tardis-sn/tardis/pull/2762) Fix ruff comments issue (2762) (@atharva-2001)
+- [2767](https://github.com/tardis-sn/tardis/pull/2767) Release Pipeline Fixes (2767) (@atharva-2001)
+- [2758](https://github.com/tardis-sn/tardis/pull/2758) Opacity state slice (2758) (@Rodot-)
+- [2771](https://github.com/tardis-sn/tardis/pull/2771) Add Extend Array Function (2771) (@Sumit112192)
+- [2761](https://github.com/tardis-sn/tardis/pull/2761) Donot run docs, benchmarks and stardis tests on draft PRs. (2761) (@KasukabeDefenceForce)
+- [2720](https://github.com/tardis-sn/tardis/pull/2720) Benchmark run_tardis with track_rpacket enabled (2720) (@Sumit112192)
+- [2675](https://github.com/tardis-sn/tardis/pull/2675) [Restructure/plasma] estimator cleanup (2675) (@wkerzendorf)
+- [2670](https://github.com/tardis-sn/tardis/pull/2670) Changed file path (2670) (@Knights-Templars)
+- [2763](https://github.com/tardis-sn/tardis/pull/2763) Add benchmark documentation (2763) (@officialasishkumar)
+- [2719](https://github.com/tardis-sn/tardis/pull/2719) Restructure Trackers (2719) (@Sumit112192)
+- [2745](https://github.com/tardis-sn/tardis/pull/2745) Address pytest warnings (2745) (@atharva-2001)
+- [2753](https://github.com/tardis-sn/tardis/pull/2753) Run stardis tests on Tardis PRs (2753) (@KasukabeDefenceForce)
+- [2754](https://github.com/tardis-sn/tardis/pull/2754) Ruff Workflow Fix (2754) (@atharva-2001)
+- [2751](https://github.com/tardis-sn/tardis/pull/2751) Post-release 2024.07.28 (2751) (@tardis-bot)
 ### release-2024.07.28 (2024/07/27 20:43)
 - [2750](https://github.com/tardis-sn/tardis/pull/2750) Pre-release 2024.07.28 (2750) (@tardis-bot)
 - [2718](https://github.com/tardis-sn/tardis/pull/2718) Weighted Packet Sampler (2718) (@Rodot-)
@@ -734,6 +751,7 @@
 - [1492](https://github.com/tardis-sn/tardis/pull/1492) Fix docstring mistakes in #1145 (1492) (@chvogl)
 - [1505](https://github.com/tardis-sn/tardis/pull/1505) Fixing Visualization Notebook Hyperlink (1505) (@KevinCawley)
 - [1481](https://github.com/tardis-sn/tardis/pull/1481) Added Documentation for Parallel execution with Numba and OpenMP (1481) (@aribalam)
+- [1145](https://github.com/tardis-sn/tardis/pull/1145) Add photoionization-related rates (1145) (@chvogl)
 - [1470](https://github.com/tardis-sn/tardis/pull/1470) Incorporating old physics section of the documentation (1470) (@isaacgsmith)
 - [1459](https://github.com/tardis-sn/tardis/pull/1459) Removed the deprecated --with-vpacket-logging flag (1459) (@antreev-brar)
 - [1462](https://github.com/tardis-sn/tardis/pull/1462) Renamed widgets subpackage to visualization and restructured modules within it (1462) (@jaladh-singhal)
@@ -749,46 +767,447 @@
 - [1441](https://github.com/tardis-sn/tardis/pull/1441) Rename SEDec to SDEC in Spectral element DEComposition plot (1441) (@jaladh-singhal)
 - [1430](https://github.com/tardis-sn/tardis/pull/1430) compare refdata with arbitrary labels (1430) (@epassaro)
 - [1431](https://github.com/tardis-sn/tardis/pull/1431) Documentation guidelines hotfix (1431) (@KevinCawley)
+- [1424](https://github.com/tardis-sn/tardis/pull/1424) Rename Kromer Plot to Spectral Element Decomposition (SEDec) Plot (1424) (@jaladh-singhal)
+- [1409](https://github.com/tardis-sn/tardis/pull/1409) add docstr-coverage workflow (1409) (@epassaro)
+- [1405](https://github.com/tardis-sn/tardis/pull/1405) Restructured development workflow and added code quality & documentation guidelines in it (1405) (@andrewfullard)
+- [1421](https://github.com/tardis-sn/tardis/pull/1421) Old physics reorganization (1421) (@andrewfullard)
+- [1423](https://github.com/tardis-sn/tardis/pull/1423) fixes for ci docs (1423) (@andrewfullard)
+- [1420](https://github.com/tardis-sn/tardis/pull/1420) Conversion of enlisted variable to int64 datatype (1420) (@andrewfullard)
+- [1403](https://github.com/tardis-sn/tardis/pull/1403) Fixing Hyperlinks in  Documentation (1403) (@andrewfullard)
+- [1410](https://github.com/tardis-sn/tardis/pull/1410) Post reference data results (1410) (@andrewfullard)
+- [1415](https://github.com/tardis-sn/tardis/pull/1415) Add .log to gitignore, disabled montecarlo log (1415) (@andrewfullard)
 ### v3.0.dev3808 (2021/01/21 11:22)
+- [1414](https://github.com/tardis-sn/tardis/pull/1414) blackify tests (1414) (@andrewfullard)
+- [1413](https://github.com/tardis-sn/tardis/pull/1413) Corrected the Hyperlink reference (1413) (@andrewfullard)
+- [1398](https://github.com/tardis-sn/tardis/pull/1398) add black check workflow (1398) (@andrewfullard)
 ### v3.0.dev3801 (2021/01/08 16:28)
+- [1399](https://github.com/tardis-sn/tardis/pull/1399) fix tests with --generate-reference flag (1399) (@andrewfullard)
+- [1393](https://github.com/tardis-sn/tardis/pull/1393) Update environment file (1393) (@epassaro)
+- [1404](https://github.com/tardis-sn/tardis/pull/1404) added functionality for automatic date updation in docs (1404) (@andrewfullard)
 ### v3.0.dev3796 (2020/12/28 12:12)
+- [1402](https://github.com/tardis-sn/tardis/pull/1402) explicitly add parso to dependencies (1402) (@andrewfullard)
 ### v3.0.dev3794 (2020/12/21 10:22)
+- [1241](https://github.com/tardis-sn/tardis/pull/1241) Add modified Kromer plot to work with widgets (1241) (@marxwillia)
 ### v3.0.dev3769 (2020/12/18 16:07)
+- [1395](https://github.com/tardis-sn/tardis/pull/1395) Update Matterbridge docs (1395) (@epassaro)
+- [1369](https://github.com/tardis-sn/tardis/pull/1369) Fix incorrect docstrings (1369) (@KevinCawley)
+- [1383](https://github.com/tardis-sn/tardis/pull/1383) add preview docs section (1383) (@epassaro)
+- [1392](https://github.com/tardis-sn/tardis/pull/1392) Fix documentation build (1392) (@epassaro)
+- [1394](https://github.com/tardis-sn/tardis/pull/1394) Revert "Fixing docs building problem" (1394) (@andrewfullard)
+- [1387](https://github.com/tardis-sn/tardis/pull/1387) Fixing docs building problem (1387) (@isaacgsmith)
+- [1380](https://github.com/tardis-sn/tardis/pull/1380) Packet logging fixes for visualization (1380) (@andrewfullard)
+- [1384](https://github.com/tardis-sn/tardis/pull/1384) Small fixes for existing workflows (1384) (@epassaro)
 ### v3.0.dev3756 (2020/12/11 14:43)
+- [1382](https://github.com/tardis-sn/tardis/pull/1382) Fixing Quickstart Problem (1382) (@andrewfullard)
+- [1379](https://github.com/tardis-sn/tardis/pull/1379) Reorganizing files in docs (2/2) (1379) (@andrewfullard)
+- [1378](https://github.com/tardis-sn/tardis/pull/1378) Adding Plasma File in TOC (1378) (@andrewfullard)
+- [1371](https://github.com/tardis-sn/tardis/pull/1371) Reorganizing files in docs (1/2) (1371) (@andrewfullard)
+- [1372](https://github.com/tardis-sn/tardis/pull/1372) Update CI doc section (1372) (@epassaro)
+- [1375](https://github.com/tardis-sn/tardis/pull/1375) Fixed real packet logging of properties (1375) (@andrewfullard)
+- [1354](https://github.com/tardis-sn/tardis/pull/1354) Virtual packet logging fix (1354) (@andrewfullard)
+- [1368](https://github.com/tardis-sn/tardis/pull/1368) Fix of Issue #1176 (1368) (@andrewfullard)
+- [1365](https://github.com/tardis-sn/tardis/pull/1365) Parallel numba setup (1365) (@andrewfullard)
+- [1331](https://github.com/tardis-sn/tardis/pull/1331) Update changelog workflow (1331) (@andrewfullard)
 ### v3.0.dev3698 (2020/12/04 14:50)
+- [1366](https://github.com/tardis-sn/tardis/pull/1366) Fix duplicate appending of scalars in HDF writer and add an overwrite option (1366) (@andrewfullard)
+- [1364](https://github.com/tardis-sn/tardis/pull/1364) Fixing issue #1357 (1364) (@andrewfullard)
+- [1359](https://github.com/tardis-sn/tardis/pull/1359) Fix of Issue #680 (1359) (@KevinCawley)
+- [1361](https://github.com/tardis-sn/tardis/pull/1361) Fixing issue #1177 (1361) (@isaacgsmith)
 ### v3.0.dev3680 (2020/11/25 13:38)
+- [1358](https://github.com/tardis-sn/tardis/pull/1358) Fix C formal integral (1358) (@andrewfullard)
+- [1352](https://github.com/tardis-sn/tardis/pull/1352) Add Arjun's emails to .mailmap (1352) (@andrewfullard)
+- [929](https://github.com/tardis-sn/tardis/pull/929) Numba montecarlo (929) (@wkerzendorf)
 ### v3.0.dev3673 (2020/11/18 11:26)
+- [1353](https://github.com/tardis-sn/tardis/pull/1353) fix doc workflow (1353) (@wkerzendorf)
+- [1349](https://github.com/tardis-sn/tardis/pull/1349) Adding documentation for research articles that used TARDIS (1349) (@andrewfullard)
 ### v3.0.dev3541 (2020/11/10 13:45)
+- [1340](https://github.com/tardis-sn/tardis/pull/1340) Moved staticmethods of line_info module to a dedicated plot_util module (1340) (@marxwillia)
 ### v3.0.dev3539 (2020/11/04 11:50)
+- [1333](https://github.com/tardis-sn/tardis/pull/1333) Rename testing pipeline (1333) (@epassaro)
+- [1300](https://github.com/tardis-sn/tardis/pull/1300) Remove pip install option from TARDIS installation docs (1300) (@jaladh-singhal)
+- [1330](https://github.com/tardis-sn/tardis/pull/1330) Small fix for release pipeline (1330) (@epassaro)
+- [1332](https://github.com/tardis-sn/tardis/pull/1332) Remove helper scripts (1332) (@epassaro)
+- [1335](https://github.com/tardis-sn/tardis/pull/1335) Updated gitignore to ignore auto-generated files (1335) (@jaladh-singhal)
+- [1326](https://github.com/tardis-sn/tardis/pull/1326) Add workflow for autodeploying documentation to github pages via an action (1326) (@morganlee123)
+- [1283](https://github.com/tardis-sn/tardis/pull/1283) Changed latex strings to raw strings (1283) (@Ak0303)
+- [1310](https://github.com/tardis-sn/tardis/pull/1310) Apply new template to refdata pipeline (1310) (@epassaro)
+- [1308](https://github.com/tardis-sn/tardis/pull/1308) Apply new template to release pipeline (1308) (@epassaro)
 ### v3.0.dev3527 (2020/10/05 12:43)
+- [1313](https://github.com/tardis-sn/tardis/pull/1313) Add Sponsor button to TARDIS (1313) (@jaladh-singhal)
 ### v3.0.dev3526 (2020/10/01 05:50)
+- [1312](https://github.com/tardis-sn/tardis/pull/1312) Add Matterbridge documentation (1312) (@epassaro)
+- [1274](https://github.com/tardis-sn/tardis/pull/1274) Add space to plasma error message (1274) (@marxwillia)
+- [1280](https://github.com/tardis-sn/tardis/pull/1280) Add widgets documentation to tardis docs (1280) (@marxwillia)
 ### v3.0.dev3510 (2020/09/25 11:56)
+- [1299](https://github.com/tardis-sn/tardis/pull/1299) Model configuration output in HDF (1299) (@andrewfullard)
+- [1304](https://github.com/tardis-sn/tardis/pull/1304) Use tardis-refdata from Azure mirror (CI/CD) (1304) (@epassaro)
+- [1264](https://github.com/tardis-sn/tardis/pull/1264) Add line info widget to widgets subpackage (1264) (@jaladh-singhal)
 ### v3.0.dev3504 (2020/09/09 06:16)
+- [1296](https://github.com/tardis-sn/tardis/pull/1296) Pin pyne to 0.7.0 (1296) (@andrewfullard)
+- [1319](https://github.com/tardis-sn/tardis/pull/1319) Numba montecarlo tests merged (1319) (@chvogl)
+- [1318](https://github.com/tardis-sn/tardis/pull/1318) Numba montecarlo profile1 (1318) (@Rodot-)
+- [1317](https://github.com/tardis-sn/tardis/pull/1317) Fixed `calculate_distance_line` showing nu_diff < 0 (1317) (@Rodot-)
+- [1309](https://github.com/tardis-sn/tardis/pull/1309) Re-add C formal integral (1309) (@chvogl)
 ### v3.0.dev3503 (2020/09/04 05:18)
+- [1291](https://github.com/tardis-sn/tardis/pull/1291) Download atom data from opensupernova mirror (1291) (@epassaro)
+- [1254](https://github.com/tardis-sn/tardis/pull/1254) Fix how virtual_packet properties are saved in hdf (1254) (@jaladh-singhal)
+- [1278](https://github.com/tardis-sn/tardis/pull/1278) Pin numpy to v1.19 (1278) (@epassaro)
 ### v3.0.dev3500 (2020/08/12 05:52)
+- [1271](https://github.com/tardis-sn/tardis/pull/1271) Move to NumPy 1.19 (1271) (@epassaro)
+- [1266](https://github.com/tardis-sn/tardis/pull/1266) Move to Pandas 1.x (1266) (@epassaro)
+- [1235](https://github.com/tardis-sn/tardis/pull/1235) test and fix for issue #1228 (1235) (@ebjordi)
 ### v3.0.dev3497 (2020/08/07 11:26)
+- [1267](https://github.com/tardis-sn/tardis/pull/1267) Temporarily fetch refdata from GDrive (1267) (@epassaro)
+- [1265](https://github.com/tardis-sn/tardis/pull/1265) add GIT_LFS_SMUDGE (1265) (@kaushik94)
+- [1262](https://github.com/tardis-sn/tardis/pull/1262) Update package versions (1262) (@epassaro)
+- [1263](https://github.com/tardis-sn/tardis/pull/1263) Clean up status badge display (1263) (@chvogl)
+- [1261](https://github.com/tardis-sn/tardis/pull/1261) Add governance document (1261) (@wkerzendorf)
 ### v3.0.dev3487 (2020/07/30 18:18)
+- [1259](https://github.com/tardis-sn/tardis/pull/1259) Emphasised reporting instructions in code of conduct (1259) (@harpolea)
+- [1255](https://github.com/tardis-sn/tardis/pull/1255) Pin pyne to v0.5 (1255) (@epassaro)
+- [1213](https://github.com/tardis-sn/tardis/pull/1213) Re-applied Black formatting to tardis after excluding undesired directories (1213) (@jaladh-singhal)
 ### v3.0.dev3484 (2020/07/19 10:30)
+- [1210](https://github.com/tardis-sn/tardis/pull/1210) [MRG] Using Mamba in Pipelines (1210) (@kaushik94)
+- [1237](https://github.com/tardis-sn/tardis/pull/1237) Add new Contribution guidelines (1237) (@jaladh-singhal)
+- [1238](https://github.com/tardis-sn/tardis/pull/1238) code of conduct symlink (1238) (@wkerzendorf)
+- [1234](https://github.com/tardis-sn/tardis/pull/1234) TARDIS Code of Conduct (1234) (@wkerzendorf)
+- [1233](https://github.com/tardis-sn/tardis/pull/1233) Update of the Governance model (1233) (@wkerzendorf)
+- [1231](https://github.com/tardis-sn/tardis/pull/1231) Roadmap Documentation Page (1231) (@marxwillia)
+- [1227](https://github.com/tardis-sn/tardis/pull/1227) Restore caching to spectrum_integrated (1227) (@arjunsavel)
 ### v3.0.dev3477 (2020/07/08 23:06)
+- [1218](https://github.com/tardis-sn/tardis/pull/1218) Move and rename coverage file (1218) (@arjunsavel)
+- [1224](https://github.com/tardis-sn/tardis/pull/1224) Added better mission statement (1224) (@ycamacho)
+- [1190](https://github.com/tardis-sn/tardis/pull/1190) Change `pytestconfig` to `request.config` (1190) (@epassaro)
+- [1219](https://github.com/tardis-sn/tardis/pull/1219) Update index.rst to add mission statement (1219) (@ycamacho)
 ### v3.0.dev3472 (2020/06/27 16:11)
+- [1203](https://github.com/tardis-sn/tardis/pull/1203) Minor changes to the environment file and cleanup (1203) (@epassaro)
+- [1209](https://github.com/tardis-sn/tardis/pull/1209) add sashank27 ORCID ID (1209) (@sashank27)
+- [1207](https://github.com/tardis-sn/tardis/pull/1207) add git-blame-ignore for code style black Changes (1207) (@wkerzendorf)
+- [1201](https://github.com/tardis-sn/tardis/pull/1201) Code style black (1201) (@wkerzendorf)
+- [1200](https://github.com/tardis-sn/tardis/pull/1200) Add jaladh-singhal's orcid to .orcid.csv (1200) (@jaladh-singhal)
+- [1197](https://github.com/tardis-sn/tardis/pull/1197) add arjun's name to the ORCID list (1197) (@arjunsavel)
+- [1166](https://github.com/tardis-sn/tardis/pull/1166) Create a new subpackage for jupyter-widgets and add shell info widgets (1166) (@jaladh-singhal)
 ### v3.0.dev3463 (2020/06/19 18:51)
+- [1195](https://github.com/tardis-sn/tardis/pull/1195) Fix badges in README.rst (1195) (@epassaro)
+- [1193](https://github.com/tardis-sn/tardis/pull/1193) Unpin astropy version (1193) (@epassaro)
+- [1191](https://github.com/tardis-sn/tardis/pull/1191) Add note to tell users which OS are supported (issue #1125) (1191) (@ebjordi)
+- [1158](https://github.com/tardis-sn/tardis/pull/1158) Make consistency edits to documentation (1158) (@arjunsavel)
 ### v3.0.dev3459 (2020/06/12 14:01)
+- [1185](https://github.com/tardis-sn/tardis/pull/1185) Upgrade pytest version (1185) (@epassaro)
 ### v3.0.dev3458 (2020/06/02 15:11)
+- [1180](https://github.com/tardis-sn/tardis/pull/1180) Remove test pipeline (1180) (@epassaro)
+- [1153](https://github.com/tardis-sn/tardis/pull/1153) update doc page to a notebook (1153) (@sashank27)
+- [1150](https://github.com/tardis-sn/tardis/pull/1150) Fix the Plasma tests (1150) (@wkerzendorf)
+- [1178](https://github.com/tardis-sn/tardis/pull/1178) Update mailmap (1178) (@epassaro)
+- [1171](https://github.com/tardis-sn/tardis/pull/1171) Print statement debug (1171) (@arjunsavel)
+- [1165](https://github.com/tardis-sn/tardis/pull/1165) Fix callbacks in run_tardis (1165) (@Rodot-)
 ### v3.0.dev3448 (2020/05/28 13:08)
+- [1173](https://github.com/tardis-sn/tardis/pull/1173) Fix GUI and plasma tests (1173) (@marxwillia)
+- [1168](https://github.com/tardis-sn/tardis/pull/1168) Add checkpoint to PR template checklist (1168) (@harpolea)
+- [1162](https://github.com/tardis-sn/tardis/pull/1162) Fix broken pipelines (1162) (@epassaro)
 ### v3.0.dev3442 (2020/05/21 19:34)
+- [1159](https://github.com/tardis-sn/tardis/pull/1159) Montecarlo/fix omp integrator (1159) (@Rodot-)
+- [1155](https://github.com/tardis-sn/tardis/pull/1155) CodeCov reintegration (1155) (@wkerzendorf)
+- [1157](https://github.com/tardis-sn/tardis/pull/1157) Update .mailmap (1157) (@epassaro)
 ### v3.0.dev3439 (2020/05/20 09:25)
+- [1142](https://github.com/tardis-sn/tardis/pull/1142) Split release pipeline (1142) (@epassaro)
+- [1151](https://github.com/tardis-sn/tardis/pull/1151) Git ignored VSCode specific files (1151) (@jaladh-singhal)
+- [1149](https://github.com/tardis-sn/tardis/pull/1149) Made plot size larger in quickstart notebook (1149) (@jaladh-singhal)
+- [1147](https://github.com/tardis-sn/tardis/pull/1147) allow downloading of example file in quickstart (1147) (@sashank27)
+- [1105](https://github.com/tardis-sn/tardis/pull/1105) Add skip condition if QT_API is no set (issue #1101) (1105) (@marxwillia)
+- [1143](https://github.com/tardis-sn/tardis/pull/1143) Set manual trigger on file (compare refdata) (1143) (@marxwillia)
+- [1144](https://github.com/tardis-sn/tardis/pull/1144) add option to execute quickstart in build (1144) (@sashank27)
 ### v3.0.dev3424 (2020/05/07 11:29)
+- [1133](https://github.com/tardis-sn/tardis/pull/1133) Solve pending issues of the release pipeline (1133) (@epassaro)
+- [1141](https://github.com/tardis-sn/tardis/pull/1141) fix warnings in quickstart (1141) (@sashank27)
+- [1137](https://github.com/tardis-sn/tardis/pull/1137) Increasing glob-like omission of coverage files (1137) (@arjunsavel)
+- [1139](https://github.com/tardis-sn/tardis/pull/1139) Added more file types to git ignore (1139) (@jaladh-singhal)
+- [1134](https://github.com/tardis-sn/tardis/pull/1134) Update mailmap (1134) (@orbitfold)
+- [1135](https://github.com/tardis-sn/tardis/pull/1135) Running tests on MacOS-10.14 (1135) (@orbitfold)
+- [1285](https://github.com/tardis-sn/tardis/pull/1285) Final numba PR (1285) (@arjunsavel)
+- [1244](https://github.com/tardis-sn/tardis/pull/1244) Fix numba_montecarlo virtual spectrum (1244) (@arjunsavel)
+- [1136](https://github.com/tardis-sn/tardis/pull/1136) Debugging relativity on numba_montecarlo (1136) (@arjunsavel)
+- [1068](https://github.com/tardis-sn/tardis/pull/1068) Migrate gui to PyQt5 (issue #988) (1068) (@ebjordi)
+- [1085](https://github.com/tardis-sn/tardis/pull/1085) Solves issue #680 for tardis.util.base (1085) (@marxwillia)
+- [1055](https://github.com/tardis-sn/tardis/pull/1055) renamed capmanager class functions to its new ones (1055) (@not4win)
+- [1048](https://github.com/tardis-sn/tardis/pull/1048) Re-activate TARDIS tests (1048) (@epassaro)
 ### v3.0.dev3409 (2020/02/24 23:02)
+- [1046](https://github.com/tardis-sn/tardis/pull/1046) Updated zenodo.json (1046) (@epassaro)
+- [1045](https://github.com/tardis-sn/tardis/pull/1045) Fix file paths at `diff` step in release pipeline (1045) (@epassaro)
+- [1040](https://github.com/tardis-sn/tardis/pull/1040) Re-activate release job (1040) (@epassaro)
+- [1039](https://github.com/tardis-sn/tardis/pull/1039) Update .mailmap (1039) (@epassaro)
 ### v3.0.dev3403 (2020/02/19 10:55)
+- [1031](https://github.com/tardis-sn/tardis/pull/1031) Create Zenodo JSON file (1031) (@epassaro)
+- [1036](https://github.com/tardis-sn/tardis/pull/1036) Update zenodo.json (1036) (@epassaro)
+- [1035](https://github.com/tardis-sn/tardis/pull/1035) Update .mailmap (1035) (@epassaro)
+- [1034](https://github.com/tardis-sn/tardis/pull/1034) Update .mailmap (1034) (@epassaro)
+- [1032](https://github.com/tardis-sn/tardis/pull/1032) Add Mark Magee to .mailmap (1032) (@epassaro)
+- [1025](https://github.com/tardis-sn/tardis/pull/1025) Add `compilers` to environment YAML file (1025) (@epassaro)
+- [1026](https://github.com/tardis-sn/tardis/pull/1026) Minor changes to Azure release (1026) (@epassaro)
 ### 3.0.dev3396 (2020/02/07 10:00)
+- [1027](https://github.com/tardis-sn/tardis/pull/1027) Added Mark Magee (1027) (@MarkMageeAstro)
+- [1024](https://github.com/tardis-sn/tardis/pull/1024) Add epassaro orcid (1024) (@epassaro)
+- [1022](https://github.com/tardis-sn/tardis/pull/1022) Added my orcid (1022) (@harpolea)
 ### 3.0.dev3384 (2020/02/02 16:56)
+- [1021](https://github.com/tardis-sn/tardis/pull/1021) Set cron job, disable CI and PR (1021) (@epassaro)
 ### 3.0.dev3383 (2020/02/02 14:01)
+- [1015](https://github.com/tardis-sn/tardis/pull/1015) Set up release TARDIS version with Azure Pipelines (1015) (@epassaro)
+- [1020](https://github.com/tardis-sn/tardis/pull/1020) Update .mailmap (1020) (@livnehra)
+- [1018](https://github.com/tardis-sn/tardis/pull/1018) Updated .mailmap (1018) (@epassaro)
+- [1010](https://github.com/tardis-sn/tardis/pull/1010) Pipeline for comparing reference data (1010) (@epassaro)
+- [1016](https://github.com/tardis-sn/tardis/pull/1016) Removed GH Action for release versions (1016) (@epassaro)
+- [1013](https://github.com/tardis-sn/tardis/pull/1013) Fixed typo in GH Action (1013) (@epassaro)
+- [1006](https://github.com/tardis-sn/tardis/pull/1006) Trying to get the right version number for automatic release (1006) (@epassaro)
+- [1008](https://github.com/tardis-sn/tardis/pull/1008) Improvements for the update_reference section [docs] (1008) (@epassaro)
+- [1011](https://github.com/tardis-sn/tardis/pull/1011) Gui fix (1011) (@marxwillia)
+- [1009](https://github.com/tardis-sn/tardis/pull/1009) Fix for packet source unit test (1009) (@epassaro)
+- [1007](https://github.com/tardis-sn/tardis/pull/1007) Fix for vboundary tests (1007) (@epassaro)
+- [995](https://github.com/tardis-sn/tardis/pull/995) Checking failing tests on Azure (995) (@kaushik94)
+- [1005](https://github.com/tardis-sn/tardis/pull/1005) Automatic TARDIS releases (1005) (@epassaro)
+- [1004](https://github.com/tardis-sn/tardis/pull/1004) Fixed csvy abundance indexing bug (1004) (@marxwillia)
+- [1003](https://github.com/tardis-sn/tardis/pull/1003) Custom source packets (1003) (@marxwillia)
+- [994](https://github.com/tardis-sn/tardis/pull/994) Large cleanup operation (994) (@wkerzendorf)
+- [992](https://github.com/tardis-sn/tardis/pull/992) Changes made to documentation for update_refdata (992) (@kowal180)
+- [967](https://github.com/tardis-sn/tardis/pull/967) log additional properties in hdf witeout when --with-vpacket-logging is present (967) (@kaushik94)
+- [969](https://github.com/tardis-sn/tardis/pull/969) Fixes numpydoc for util (969) (@kowal180)
+- [985](https://github.com/tardis-sn/tardis/pull/985) Fix typo (985) (@jreichenbach-msu)
+- [983](https://github.com/tardis-sn/tardis/pull/983) Fix installation documentation (983) (@jreichenbach-msu)
+- [982](https://github.com/tardis-sn/tardis/pull/982) Pinned `numpy` to v1.15 (982) (@epassaro)
+- [978](https://github.com/tardis-sn/tardis/pull/978) Add further fix to quickstart link (978) (@jreichenbach-msu)
+- [975](https://github.com/tardis-sn/tardis/pull/975) Add links to Quickstart (975) (@jreichenbach-msu)
+- [971](https://github.com/tardis-sn/tardis/pull/971) Fix formal integral spikes bug (971) (@chvogl)
+- [968](https://github.com/tardis-sn/tardis/pull/968) Fixed GUI #950 tardis/gui/widgets.py (968) (@marxwillia)
+- [965](https://github.com/tardis-sn/tardis/pull/965) Isotope time0 (965) (@marxwillia)
+- [966](https://github.com/tardis-sn/tardis/pull/966) fix AtomData repr (966) (@wkerzendorf)
+- [964](https://github.com/tardis-sn/tardis/pull/964) Raise error if requested atoms are not in the atomic data (964) (@chvogl)
+- [959](https://github.com/tardis-sn/tardis/pull/959) Csvy model config dict (959) (@marxwillia)
+- [960](https://github.com/tardis-sn/tardis/pull/960) Save integrated spectrum to hdf if requested (960) (@chvogl)
+- [957](https://github.com/tardis-sn/tardis/pull/957) add blondin converter (957) (@wkerzendorf)
+- [956](https://github.com/tardis-sn/tardis/pull/956) Dilution factor fix (956) (@marxwillia)
+- [953](https://github.com/tardis-sn/tardis/pull/953) add code comparison (953) (@wkerzendorf)
+- [952](https://github.com/tardis-sn/tardis/pull/952) Base schema fix (952) (@marxwillia)
+- [951](https://github.com/tardis-sn/tardis/pull/951) Documentation restructure (951) (@wkerzendorf)
+- [936](https://github.com/tardis-sn/tardis/pull/936) csvy_model (936) (@wkerzendorf)
+- [945](https://github.com/tardis-sn/tardis/pull/945) Revert "Remove PR Trigger" (945) (@wkerzendorf)
+- [928](https://github.com/tardis-sn/tardis/pull/928) Added csvy parser (928) (@marxwillia)
+- [933](https://github.com/tardis-sn/tardis/pull/933) Radiative recombination (933) (@chvogl)
 ### v3.0-alpha.3 (2019/05/13 18:05)
+- [930](https://github.com/tardis-sn/tardis/pull/930) Fix for conda-forge package (930) (@epassaro)
+- [918](https://github.com/tardis-sn/tardis/pull/918) Density docs (918) (@marxwillia)
+- [926](https://github.com/tardis-sn/tardis/pull/926) Adding a TARDIS data repo (926) (@wkerzendorf)
+- [924](https://github.com/tardis-sn/tardis/pull/924) Migrate beta_sobolev calculation from cython to numba (924) (@chvogl)
+- [925](https://github.com/tardis-sn/tardis/pull/925) Docs/fix changelog (925) (@wkerzendorf)
+- [923](https://github.com/tardis-sn/tardis/pull/923) Fix nlte normalization (923) (@wkerzendorf)
+- [831](https://github.com/tardis-sn/tardis/pull/831) Fix NLTE Normalization - issue #784 (831) (@livnehra)
+- [922](https://github.com/tardis-sn/tardis/pull/922) Revert "Fix nlte normalization " (922) (@wkerzendorf)
+- [920](https://github.com/tardis-sn/tardis/pull/920) Fix nlte normalization (920) (@wkerzendorf)
+- [921](https://github.com/tardis-sn/tardis/pull/921) Autoupdate changelog (921) (@wkerzendorf)
+- [919](https://github.com/tardis-sn/tardis/pull/919) Add possibility to bias vpacket emission based on optical depth (919) (@chvogl)
+- [914](https://github.com/tardis-sn/tardis/pull/914) make GUI python3 compatible (914) (@wkerzendorf)
+- [902](https://github.com/tardis-sn/tardis/pull/902) general overhaul of the docs for 3.0 (902) (@wkerzendorf)
+- [916](https://github.com/tardis-sn/tardis/pull/916) fix the documenation up a bit (916) (@wkerzendorf)
+- [915](https://github.com/tardis-sn/tardis/pull/915) Parsing STELLA files for TARDIS (915) (@sarafina325)
+- [911](https://github.com/tardis-sn/tardis/pull/911) Use Russian roulette to kill v-packets with negligible weight (911) (@chvogl)
+- [697](https://github.com/tardis-sn/tardis/pull/697) Relativity (697) (@chvogl)
 ### v3.0-alpha.2 (2019/03/11 10:24)
 ### v3.0.a1 (2019/03/10 11:03)
+- [901](https://github.com/tardis-sn/tardis/pull/901) .nojekyll added to docs (901) (@debajyotidasgupta)
+- [897](https://github.com/tardis-sn/tardis/pull/897) add pytest azurepipelines (897) (@wkerzendorf)
+- [896](https://github.com/tardis-sn/tardis/pull/896) Adding general build artefacts (896) (@wkerzendorf)
+- [894](https://github.com/tardis-sn/tardis/pull/894) Azure pipeline for TARDIS (894) (@wkerzendorf)
+- [893](https://github.com/tardis-sn/tardis/pull/893) add doctr to TARDIS (893) (@wkerzendorf)
+- [892](https://github.com/tardis-sn/tardis/pull/892) adding azure-pipelines (892) (@wkerzendorf)
+- [891](https://github.com/tardis-sn/tardis/pull/891) New template setup from astropy (891) (@wkerzendorf)
+- [888](https://github.com/tardis-sn/tardis/pull/888) Update installation.rst (888) (@nileshpatra)
+- [886](https://github.com/tardis-sn/tardis/pull/886) Pandas ix fix (886) (@wkerzendorf)
+- [879](https://github.com/tardis-sn/tardis/pull/879) Python3 version of TARDIS (879) (@wkerzendorf)
+- [881](https://github.com/tardis-sn/tardis/pull/881) Adds description of gcc problem to documentation (881) (@ycamacho)
+- [859](https://github.com/tardis-sn/tardis/pull/859) Use interpolated values to do formal integral with more shells (859) (@chvogl)
+- [873](https://github.com/tardis-sn/tardis/pull/873) Some small fixes related to the documentation and the building process (Fix #842) (873) (@unoebauer)
+- [868](https://github.com/tardis-sn/tardis/pull/868) Add Travis Stages: Activate Integration tests (868) (@unoebauer)
+- [866](https://github.com/tardis-sn/tardis/pull/866) Add Travis Caching and separate scripts for CI (866) (@wkerzendorf)
+- [869](https://github.com/tardis-sn/tardis/pull/869) Travis update2 (869) (@wkerzendorf)
+- [864](https://github.com/tardis-sn/tardis/pull/864) Unify unittest hdfs (864) (@unoebauer)
+- [865](https://github.com/tardis-sn/tardis/pull/865) Adding CodeCov integration (865) (@wkerzendorf)
+- [860](https://github.com/tardis-sn/tardis/pull/860) Enabling the addition of callbacks in run_tardis (860) (@wkerzendorf)
+- [863](https://github.com/tardis-sn/tardis/pull/863) Thomson cross section: Continuation of PR #688 (863) (@unoebauer)
+- [850](https://github.com/tardis-sn/tardis/pull/850) Add full test for formal integral method (850) (@unoebauer)
+- [861](https://github.com/tardis-sn/tardis/pull/861) Describe refdata update and workflow refactor (861) (@wkerzendorf)
+- [848](https://github.com/tardis-sn/tardis/pull/848) Add capability to store information about the plasma state during iterations (848) (@unoebauer)
+- [857](https://github.com/tardis-sn/tardis/pull/857) Refactor logging (857) (@wkerzendorf)
+- [856](https://github.com/tardis-sn/tardis/pull/856) Extend formal integral to line_interaction_type macroatom (856) (@chvogl)
+- [855](https://github.com/tardis-sn/tardis/pull/855) Make the conda-forge channel the only channel (855) (@wkerzendorf)
+- [853](https://github.com/tardis-sn/tardis/pull/853) Fix formal integral (853) (@chvogl)
+- [849](https://github.com/tardis-sn/tardis/pull/849) Missing refdata (849) (@wkerzendorf)
+- [851](https://github.com/tardis-sn/tardis/pull/851) add atomic data description (851) (@wkerzendorf)
+- [846](https://github.com/tardis-sn/tardis/pull/846) update the OPENMP text to be correct (846) (@wkerzendorf)
+- [847](https://github.com/tardis-sn/tardis/pull/847) Revert "change to new cython version" (847) (@wkerzendorf)
+- [839](https://github.com/tardis-sn/tardis/pull/839) change to new cython version (839) (@wkerzendorf)
+- [845](https://github.com/tardis-sn/tardis/pull/845) Update Documentation: new location of tardis_example (845) (@unoebauer)
+- [843](https://github.com/tardis-sn/tardis/pull/843) Fix issue with custom_composition reader (843) (@unoebauer)
+- [844](https://github.com/tardis-sn/tardis/pull/844) Remove bbsampling from schema file (844) (@pfreddy)
+- [837](https://github.com/tardis-sn/tardis/pull/837) Add json sphinx (837) (@wkerzendorf)
+- [841](https://github.com/tardis-sn/tardis/pull/841) Fixed indentation and position of delta_treatment in plasma/standard_plasmas.py (841) (@Heringer-Epson)
+- [838](https://github.com/tardis-sn/tardis/pull/838) fix current cython installation problem (838) (@wkerzendorf)
+- [821](https://github.com/tardis-sn/tardis/pull/821) Simplify convergence strategies (821) (@unoebauer)
+- [833](https://github.com/tardis-sn/tardis/pull/833) restructure landing page to use notebooks (833) (@wkerzendorf)
+- [832](https://github.com/tardis-sn/tardis/pull/832) Fixes #830 (832) (@unoebauer)
 ### v2.0.2 (2018/06/18 16:24)
 ### v2_test3 (2018/06/18 16:13)
+- [829](https://github.com/tardis-sn/tardis/pull/829) build bleeding edge cython (829) (@wkerzendorf)
+- [828](https://github.com/tardis-sn/tardis/pull/828) trying to get travis to build (828) (@wkerzendorf)
+- [827](https://github.com/tardis-sn/tardis/pull/827) Update travis link to miniconda (827) (@unoebauer)
+- [826](https://github.com/tardis-sn/tardis/pull/826) Remove tardis_example.tar.gz from documentation; fixes #824 (826) (@unoebauer)
+- [820](https://github.com/tardis-sn/tardis/pull/820) update of mailmap (820) (@wkerzendorf)
+- [819](https://github.com/tardis-sn/tardis/pull/819) Reintroduce and update changelog (819) (@unoebauer)
+- [815](https://github.com/tardis-sn/tardis/pull/815) Update and Fix Documentation (815) (@unoebauer)
+- [816](https://github.com/tardis-sn/tardis/pull/816) Remove old and broken badges (816) (@unoebauer)
+- [814](https://github.com/tardis-sn/tardis/pull/814) Fix numpydoc problem (814) (@unoebauer)
+- [813](https://github.com/tardis-sn/tardis/pull/813) Request specific sphinx version (813) (@unoebauer)
 ### v2.0 (2018/04/05 09:03)
+- [812](https://github.com/tardis-sn/tardis/pull/812) Update of documentation (812) (@unoebauer)
+- [809](https://github.com/tardis-sn/tardis/pull/809) fix dependencies for tardis conda env (809) (@wkerzendorf)
+- [761](https://github.com/tardis-sn/tardis/pull/761) Add caching for integrated spectrum: Fix #760 (761) (@wkerzendorf)
+- [715](https://github.com/tardis-sn/tardis/pull/715) Merge 'generate_reference_path' and 'reference_path' in integration tests (bug #672) (715) (@wkerzendorf)
+- [801](https://github.com/tardis-sn/tardis/pull/801) Decay of isotopes branch (801) (@wkerzendorf)
+- [806](https://github.com/tardis-sn/tardis/pull/806) Fix reference dictionary problem (806) (@wkerzendorf)
+- [802](https://github.com/tardis-sn/tardis/pull/802) Fix for PR #801 (802) (@wkerzendorf)
+- [772](https://github.com/tardis-sn/tardis/pull/772) [TEP007] CMFGEN density parser (772) (@wkerzendorf)
+- [771](https://github.com/tardis-sn/tardis/pull/771) [TEP007] Add cmfgen2tardis script (771) (@wkerzendorf)
+- [757](https://github.com/tardis-sn/tardis/pull/757) [TEP007] Decay and merge isotopic abundance dataframe (757) (@wkerzendorf)
+- [767](https://github.com/tardis-sn/tardis/pull/767) [TEP007] Docs for isotope config (767) (@wkerzendorf)
+- [764](https://github.com/tardis-sn/tardis/pull/764) [TEP007] Isotope stratified file support (764) (@wkerzendorf)
+- [762](https://github.com/tardis-sn/tardis/pull/762) [TEP007] Isotope uniform config option (762) (@wkerzendorf)
+- [756](https://github.com/tardis-sn/tardis/pull/756) [TEP007] [WIP] Isotope Abundances class (756) (@wkerzendorf)
+- [803](https://github.com/tardis-sn/tardis/pull/803) include yml files in MANIFEST (803) (@wkerzendorf)
+- [799](https://github.com/tardis-sn/tardis/pull/799) tardis/plasma/standard_plasmas.py: old database files warning (799) (@wkerzendorf)
+- [797](https://github.com/tardis-sn/tardis/pull/797) Minor Updates: Fixes for #521 and #699 (797) (@wkerzendorf)
+- [796](https://github.com/tardis-sn/tardis/pull/796) Prevent pandas SettingWithCopyWarning by copying DataFrames when slicing (796) (@wkerzendorf)
+- [795](https://github.com/tardis-sn/tardis/pull/795) Force deactivate LaTeX in GUI - Fix #441 (795) (@wkerzendorf)
+- [793](https://github.com/tardis-sn/tardis/pull/793) Add pyside to requirements (needed for GUI) (793) (@wkerzendorf)
+- [794](https://github.com/tardis-sn/tardis/pull/794) add new readthedocs.yml (794) (@wkerzendorf)
+- [792](https://github.com/tardis-sn/tardis/pull/792) Fix compatibility with networkx 2.0 (792) (@wkerzendorf)
+- [791](https://github.com/tardis-sn/tardis/pull/791) Propagate changes to the line index into the GUI code (791) (@wkerzendorf)
+- [786](https://github.com/tardis-sn/tardis/pull/786) The final carsus merge (786) (@wkerzendorf)
+- [782](https://github.com/tardis-sn/tardis/pull/782) Plasma write_to_tex/dot unit tests (782) (@wkerzendorf)
+- [781](https://github.com/tardis-sn/tardis/pull/781) Omit coverage of test related files (781) (@wkerzendorf)
+- [785](https://github.com/tardis-sn/tardis/pull/785) [DOC] Update Running tests doc (785) (@wkerzendorf)
+- [774](https://github.com/tardis-sn/tardis/pull/774) Replace Comparison values in Plasma Unit Tests with reference HDF file (774) (@wkerzendorf)
+- [780](https://github.com/tardis-sn/tardis/pull/780) LevelBoltzmannFactorNLTE.from_config is now a staticmethod (780) (@wkerzendorf)
+- [778](https://github.com/tardis-sn/tardis/pull/778) Fix NLTE (778) (@wkerzendorf)
+- [776](https://github.com/tardis-sn/tardis/pull/776) Fix compatibility bug in radiative_properties (776) (@wkerzendorf)
+- [779](https://github.com/tardis-sn/tardis/pull/779) Save coverage report when tests use tardis-refdata (779) (@wkerzendorf)
+- [775](https://github.com/tardis-sn/tardis/pull/775) Transition from atomic-dataset config option to tardis-refdata (775) (@wkerzendorf)
+- [769](https://github.com/tardis-sn/tardis/pull/769) [TEP014] [DOC] Updated to_hdf notebook (769) (@wkerzendorf)
+- [759](https://github.com/tardis-sn/tardis/pull/759) Formal Integral: including electron scattering (759) (@wkerzendorf)
+- [768](https://github.com/tardis-sn/tardis/pull/768) [TEP014] Simulation HDF and deprecated to_hdf cleanup. (768) (@wkerzendorf)
+- [773](https://github.com/tardis-sn/tardis/pull/773) Update Documentation (773) (@wkerzendorf)
+- [752](https://github.com/tardis-sn/tardis/pull/752) [TEP014] PlasmaWriterMixin (752) (@wkerzendorf)
+- [748](https://github.com/tardis-sn/tardis/pull/748) [TEP014] Update Runner and Spectrum classes to use HDFWriter + Unit Tests (748) (@wkerzendorf)
+- [765](https://github.com/tardis-sn/tardis/pull/765) Attempt to fix up the GUI (765) (@wkerzendorf)
+- [758](https://github.com/tardis-sn/tardis/pull/758) Add new version to tardis_env27 and add pyne (758) (@wkerzendorf)
+- [753](https://github.com/tardis-sn/tardis/pull/753) [TEP014][DOC] HDFWriter Documentation (753) (@wkerzendorf)
+- [740](https://github.com/tardis-sn/tardis/pull/740) [GSoC] Formal integral Project (740) (@wkerzendorf)
+- [750](https://github.com/tardis-sn/tardis/pull/750) [TEP005][QOL] Add MontecarloRunner.spectrum_integrated (750) (@wkerzendorf)
+- [745](https://github.com/tardis-sn/tardis/pull/745) [TEP005][DOC] Documentation (745) (@wkerzendorf)
+- [746](https://github.com/tardis-sn/tardis/pull/746) [TEP005][CONFIG] Prevent incompatible configurations (746) (@wkerzendorf)
+- [741](https://github.com/tardis-sn/tardis/pull/741) Add unit tests for the formal integral (741) (@wkerzendorf)
+- [747](https://github.com/tardis-sn/tardis/pull/747) [TEP014] Update Model and Density classes to use HDFWriter + Unit Tests (747) (@wkerzendorf)
+- [749](https://github.com/tardis-sn/tardis/pull/749) [TEP014] Change name of HDFWriter to HDFWriterMixin (749) (@wkerzendorf)
+- [751](https://github.com/tardis-sn/tardis/pull/751) [QOL] Add default axis to TARDISSpectrum.plot (751) (@wkerzendorf)
+- [743](https://github.com/tardis-sn/tardis/pull/743) Fix bug in plasma (743) (@wkerzendorf)
+- [744](https://github.com/tardis-sn/tardis/pull/744) [TEP014] Added HDFWriter class + Unit Tests (744) (@wkerzendorf)
+- [742](https://github.com/tardis-sn/tardis/pull/742) Fix clash in RTD dependencies (742) (@wkerzendorf)
+- [735](https://github.com/tardis-sn/tardis/pull/735) Move common ctest fixtures into conftest.py (735) (@wkerzendorf)
+- [729](https://github.com/tardis-sn/tardis/pull/729) Refactor spectrum (729) (@wkerzendorf)
+- [730](https://github.com/tardis-sn/tardis/pull/730) Fix test_plasma_simple not skipping properly (730) (@wkerzendorf)
+- [712](https://github.com/tardis-sn/tardis/pull/712) Colorize Logger (712) (@wkerzendorf)
+- [718](https://github.com/tardis-sn/tardis/pull/718) Unit test for untested method of montecarlo simulation code (718) (@unoebauer)
+- [724](https://github.com/tardis-sn/tardis/pull/724) Rebase PR #678 (724) (@wkerzendorf)
+- [709](https://github.com/tardis-sn/tardis/pull/709) Add note about broken GUI to docu (709) (@wkerzendorf)
+- [708](https://github.com/tardis-sn/tardis/pull/708) Add new installation instructions (708) (@wkerzendorf)
+- [704](https://github.com/tardis-sn/tardis/pull/704) Fix ignoring model tests (704) (@wkerzendorf)
+- [700](https://github.com/tardis-sn/tardis/pull/700) Add contributing guidelines (700) (@wkerzendorf)
+- [686](https://github.com/tardis-sn/tardis/pull/686) converted spectrum_frequency (686) (@wkerzendorf)
+- [696](https://github.com/tardis-sn/tardis/pull/696) Add missing diagnostics property to runner's to_hdf list (696) (@wkerzendorf)
+- [694](https://github.com/tardis-sn/tardis/pull/694) Significantly reduce peak memory usage when vpacket logging is enabled (694) (@wkerzendorf)
+- [682](https://github.com/tardis-sn/tardis/pull/682) Import montecarlo.base in the __init__ module of the package. (682) (@wkerzendorf)
+- [670](https://github.com/tardis-sn/tardis/pull/670) Integrate continuum interactions into cmontecarlo (670) (@wkerzendorf)
+- [652](https://github.com/tardis-sn/tardis/pull/652) [TEP006] Aggregate TARDIS restructure and configuration system cleanup (652) (@wkerzendorf)
+- [677](https://github.com/tardis-sn/tardis/pull/677) Update link to tardis_example.yml in documentation - Fix #676 (677) (@wkerzendorf)
+- [674](https://github.com/tardis-sn/tardis/pull/674) Change matplotlib backend - fix test_integration remote plotting issue (674) (@yeganer)
+- [664](https://github.com/tardis-sn/tardis/pull/664) Kd final test (664) (@wkerzendorf)
+- [668](https://github.com/tardis-sn/tardis/pull/668) change to tardis atom data on git lfs (668) (@wkerzendorf)
+- [666](https://github.com/tardis-sn/tardis/pull/666) Remove News from main TARDIS github page (666) (@wkerzendorf)
+- [667](https://github.com/tardis-sn/tardis/pull/667) Update SOCIS and GSOC students credits (667) (@wkerzendorf)
+- [665](https://github.com/tardis-sn/tardis/pull/665) Add to_hdf compression (665) (@wkerzendorf)
+- [663](https://github.com/tardis-sn/tardis/pull/663) Develop (663) (@wkerzendorf)
+- [507](https://github.com/tardis-sn/tardis/pull/507) Unit tests for untested methods of tardis/util.py (507) (@)
+- [657](https://github.com/tardis-sn/tardis/pull/657) Require pyyaml 3.12 (657) (@wkerzendorf)
+- [659](https://github.com/tardis-sn/tardis/pull/659) Update installation docs (659) (@wkerzendorf)
+- [653](https://github.com/tardis-sn/tardis/pull/653) Facility to provide per-setup atom data as well as save report locally. (653) (@wkerzendorf)
+- [641](https://github.com/tardis-sn/tardis/pull/641) Fix detailed radiative rates (641) (@wkerzendorf)
+- [642](https://github.com/tardis-sn/tardis/pull/642) Use pytest-html==1.10.0, modify DokuReport class accordingly. (642) (@wkerzendorf)
+- [630](https://github.com/tardis-sn/tardis/pull/630) Create an overview page on Dokuwiki. (630) (@yeganer)
+- [620](https://github.com/tardis-sn/tardis/pull/620) Runner script to automate execution of integration tests. (620) (@wkerzendorf)
+- [628](https://github.com/tardis-sn/tardis/pull/628) Remove exponent property from yaml files with exponential density (628) (@wkerzendorf)
+- [626](https://github.com/tardis-sn/tardis/pull/626) Revert "Add exponent as a property for exponential density" (626) (@wkerzendorf)
+- [542](https://github.com/tardis-sn/tardis/pull/542) Updates to He NLTE treatment. (542) (@wkerzendorf)
+- [612](https://github.com/tardis-sn/tardis/pull/612) Add facility to generate and accept HDF files as reference data for Integration Tests. (612) (@wkerzendorf)
+- [614](https://github.com/tardis-sn/tardis/pull/614) Omit the integration_tests when running coveralls (614) (@wkerzendorf)
+- [619](https://github.com/tardis-sn/tardis/pull/619) Fixed incorrect name in error message (619) (@wkerzendorf)
+- [618](https://github.com/tardis-sn/tardis/pull/618) to_hdf: If only the last run is stored, do not add a counter in the name (618) (@wkerzendorf)
+- [617](https://github.com/tardis-sn/tardis/pull/617) Add a to_hdf method on TARDISSpectrum (617) (@wkerzendorf)
+- [600](https://github.com/tardis-sn/tardis/pull/600) Parametrize the Slow Test class with two setups. (600) (@wkerzendorf)
+- [613](https://github.com/tardis-sn/tardis/pull/613) Fix bug in montecarlo.pyx (613) (@wkerzendorf)
+- [595](https://github.com/tardis-sn/tardis/pull/595) Line absorption rate estimator (595) (@wkerzendorf)
+- [606](https://github.com/tardis-sn/tardis/pull/606) Merge to_hdf (606) (@wkerzendorf)
+- [597](https://github.com/tardis-sn/tardis/pull/597) Use abundances, densities filepaths relative to w7 config file. (597) (@wkerzendorf)
+- [569](https://github.com/tardis-sn/tardis/pull/569) Added a conda environment for tardis (569) (@wkerzendorf)
+- [565](https://github.com/tardis-sn/tardis/pull/565) Change the way AtomData quantities are initialized (565) (@wkerzendorf)
+- [599](https://github.com/tardis-sn/tardis/pull/599) Update the tardis_example tar file provided in the documentation. (599) (@wkerzendorf)
+- [598](https://github.com/tardis-sn/tardis/pull/598) Fix convergence handling in run_legacy_simulation - fix issue #593 (598) (@wkerzendorf)
+- [590](https://github.com/tardis-sn/tardis/pull/590) Link images of comparison plots in DokuReport using hookwrapper. (590) (@wkerzendorf)
+- [591](https://github.com/tardis-sn/tardis/pull/591) Fix path of CSS and JS files used in html report. (591) (@wkerzendorf)
+- [594](https://github.com/tardis-sn/tardis/pull/594) Provide tardis.yaml_load shortcut (594) (@wkerzendorf)
+- [592](https://github.com/tardis-sn/tardis/pull/592) Fix virt energy (592) (@wkerzendorf)
+- [583](https://github.com/tardis-sn/tardis/pull/583) Subclass pytest-html's HTMLReport to DokuReport class for report generation and upload. (583) (@yeganer)
+- [588](https://github.com/tardis-sn/tardis/pull/588) Embed comparison plots in Dokuwiki Report. (588) (@)
+- [587](https://github.com/tardis-sn/tardis/pull/587) Move the three spectra attributes from Radial1DModel to MontecarloRunner (587) (@wkerzendorf)
+- [578](https://github.com/tardis-sn/tardis/pull/578) Shift slow test related pytest hooks in lower level conftest.py (578) (@)
+- [581](https://github.com/tardis-sn/tardis/pull/581) Update several files to match package_template (581) (@yeganer)
+- [576](https://github.com/tardis-sn/tardis/pull/576) [config-system] Validator rewrite: Use jsonschema (576) (@wkerzendorf)
+- [549](https://github.com/tardis-sn/tardis/pull/549) [TEP006] Create a JSON schema in YAML to replace the old tardis_config_definition.yml (549) (@ftsamis)
+- [575](https://github.com/tardis-sn/tardis/pull/575) Replace misused calls to yaml.load with a helper function. (575) (@wkerzendorf)
+- [570](https://github.com/tardis-sn/tardis/pull/570) Enable generation of html report of integration tests, and upload to dokuwiki. (570) (@wkerzendorf)
+- [574](https://github.com/tardis-sn/tardis/pull/574) tardis/base.py: Remove duplicate code from run_tardis (574) (@wkerzendorf)
+- [573](https://github.com/tardis-sn/tardis/pull/573) io/util.py (YAMLLoader): Use OrderedDict to store loaded YAML (573) (@wkerzendorf)
+- [572](https://github.com/tardis-sn/tardis/pull/572) Change the way YAMLLoader resolves some properties (572) (@wkerzendorf)
+- [532](https://github.com/tardis-sn/tardis/pull/532) Documentation overhaul (532) (@wkerzendorf)
+- [571](https://github.com/tardis-sn/tardis/pull/571) [config] Set the exponent property as mandatory when density is exponential (571) (@ftsamis)
+- [566](https://github.com/tardis-sn/tardis/pull/566) Initial laydown of comparison plots for TestW7. (566) (@)
+- [567](https://github.com/tardis-sn/tardis/pull/567) Accept keyword arguments for Configuration.from_yaml (567) (@wkerzendorf)
+- [561](https://github.com/tardis-sn/tardis/pull/561) TestW7: Assertions for spectrum quantities, fixture for handling baseline data. (561) (@wkerzendorf)
+- [515](https://github.com/tardis-sn/tardis/pull/515) [config-system] Add a custom YAML Loader to parse astropy quantities (515) (@wkerzendorf)
+- [555](https://github.com/tardis-sn/tardis/pull/555) Use pytest's monkeypatch.chdir to change the working directory in the config_reader tests (555) (@wkerzendorf)
+- [558](https://github.com/tardis-sn/tardis/pull/558) Integration Test class for Stratified W7 setup. (558) (@wkerzendorf)
+- [557](https://github.com/tardis-sn/tardis/pull/557) Enable skipping slow tests. (557) (@unoebauer)
+- [544](https://github.com/tardis-sn/tardis/pull/544) Continue cmontecarlo tests refactor. Extend #530. (544) (@unoebauer)
+- [543](https://github.com/tardis-sn/tardis/pull/543) Fix issue #535: Treat rel. paths inside config relative to the config file (543) (@wkerzendorf)
+- [551](https://github.com/tardis-sn/tardis/pull/551) Add SOCIS 2016 advertisement (551) (@wkerzendorf)
+- [547](https://github.com/tardis-sn/tardis/pull/547) Fix Issue #548 (547) (@wkerzendorf)
+- [545](https://github.com/tardis-sn/tardis/pull/545) added mailmap to compile the commits for each person (545) (@wkerzendorf)
+- [539](https://github.com/tardis-sn/tardis/pull/539) Adding OSX to our travis build (539) (@wkerzendorf)
+- [541](https://github.com/tardis-sn/tardis/pull/541) Move progress bar update after calculation (541) (@yeganer)
+- [540](https://github.com/tardis-sn/tardis/pull/540) Mirroring C enums in Python for CMontecarlo tests. (540) (@yeganer)
+- [538](https://github.com/tardis-sn/tardis/pull/538) Upgrading to the new Readthedocs infrastructure (538) (@wkerzendorf)
+- [530](https://github.com/tardis-sn/tardis/pull/530) Refactor cmontecarlo tests for exercising parametrization. (530) (@yeganer)
+- [537](https://github.com/tardis-sn/tardis/pull/537) Ignore invalid OpenMP nthreads values (537) (@yeganer)
+- [527](https://github.com/tardis-sn/tardis/pull/527) Unit tests for untested methods of tardis/atomic.py (527) (@)
+- [533](https://github.com/tardis-sn/tardis/pull/533) Remove rpacket.recently_crossed_boundary flag (533) (@wkerzendorf)
+- [514](https://github.com/tardis-sn/tardis/pull/514) Performance (514) (@wkerzendorf)
+- [531](https://github.com/tardis-sn/tardis/pull/531) Organize headers in C-Extension (531) (@wkerzendorf)
+- [526](https://github.com/tardis-sn/tardis/pull/526) Docs: Include conda-requirements in installation.rst (526) (@ssim)
 ### v1.0.1 (2015/03/03 08:12)
 ### v1.0 (2015/03/03 07:58)
 ### 1.0rc3 (2015/03/03 07:54)
diff --git a/CITATION.cff b/CITATION.cff
index 253ecde0686..1f1b8d94734 100644
--- a/CITATION.cff
+++ b/CITATION.cff
@@ -3,8 +3,8 @@
 cff-version: 1.0.3
 message: If you use this software, please cite it using these metadata.
 # FIXME title as repository name might not be the best name, please make human readable
-title: 'tardis-sn/tardis: TARDIS v2023.11.26'
-doi: 10.5281/zenodo.10207663
+title: 'tardis-sn/tardis: TARDIS v2024.08.04'
+doi: 10.5281/zenodo.13207705
 # FIXME splitting of full names is error prone, please check if given/family name are correct
 authors:
 - given-names: Wolfgang
@@ -94,12 +94,12 @@ authors:
   family-names: Fullard
   affiliation: Michigan State University
   orcid: https://orcid.org/0000-0001-7343-1678
-- given-names: Isaac
-  family-names: Smith
-  affiliation:
 - given-names: Atharva
   family-names: Arya
   affiliation:
+- given-names: Isaac
+  family-names: Smith
+  affiliation:
 - given-names: Kevin
   family-names: Cawley
   affiliation:
@@ -107,14 +107,17 @@ authors:
   family-names: Singhal
   affiliation:
   orcid: https://orcid.org/0000-0002-8310-0829
-- given-names: Dhruv
-  family-names: Sondhi
+- given-names: Joshua
+  family-names: Shields
+  affiliation:
+- given-names: Jack
+  family-names: O'Brien
   affiliation:
 - given-names: Talytha
   family-names: Barbosa
   affiliation:
-- given-names: Jack
-  family-names: O'Brien
+- given-names: Dhruv
+  family-names: Sondhi
   affiliation:
 - given-names: Jenny
   family-names: Yu
@@ -122,12 +125,12 @@ authors:
 - given-names: Maryam
   family-names: Patel
   affiliation:
-- given-names: Kaushik
-  family-names: Varanasi
-  affiliation:
 - given-names: Shikha
   family-names: Rathi
   affiliation:
+- given-names: Kaushik
+  family-names: Varanasi
+  affiliation:
 - given-names: Sona
   family-names: Chitchyan
   affiliation:
@@ -135,121 +138,136 @@ authors:
   family-names: Gillanders
   affiliation: University of Oxford
   orcid: https://orcid.org/0000-0002-8094-6108
-- given-names: Joshua
-  family-names: Shields
+- given-names: Shreyas
+  family-names: Singh
   affiliation:
 - given-names: Arjun
   family-names: Savel
   affiliation:
-- given-names: Shreyas
-  family-names: Singh
-  affiliation:
-- given-names: Martin
-  family-names: Reinecke
+- given-names: Alexander
+  family-names: Holas
   affiliation:
 - given-names: Youssef
   family-names: Eweis
   affiliation:
+- given-names: Martin
+  family-names: Reinecke
+  affiliation:
 - given-names: Tomas
   family-names: Bylund
   affiliation:
 - given-names: William
   family-names: Black
   affiliation:
+- given-names: Sumit
+  family-names: Gupta
+  affiliation:
 - given-names: Laud
   family-names: Bentil
   affiliation:
-- given-names: Alexander
-  family-names: Holas
-  affiliation:
 - given-names: Jordi
   family-names: Eguren
   affiliation:
   orcid: https://orcid.org/0000-0002-2328-8030
+- given-names: Ansh
+  family-names: Kumar
+  affiliation:
 - given-names: Arib
   family-names: Alam
   affiliation:
-- given-names: Ansh
+- given-names: Asish
   family-names: Kumar
   affiliation:
 - given-names: Matthew
   family-names: Bartnik
   affiliation:
-- given-names: Rohith
-  family-names: Varma Buddaraju
-  affiliation:
 - given-names: Mark
   family-names: Magee
   affiliation:
+- given-names: Anirban
+  family-names: Dutta
+  affiliation:
+- given-names: Rohith
+  family-names: Varma Buddaraju
+  affiliation:
 - given-names: Ran
   family-names: Livneh
   affiliation:
+- given-names: Jing
+  family-names: Lu
+  affiliation:
+- given-names: Erin
+  family-names: Visser
+  affiliation:
+- given-names: Ayushi
+  family-names: Daksh
+  affiliation:
 - given-names: Satwik
   family-names: Kambham
   affiliation:
-- given-names: Sashank
-  family-names: Mishra
+- given-names: Jayant
+  family-names: Bhakar
   affiliation:
-  orcid: https://orcid.org/0000-0001-8302-1584
 - given-names: Srinath
   family-names: Rajagopalan
   affiliation:
-- given-names: Ayushi
-  family-names: Daksh
+- given-names: Israel
+  family-names: Roldan
   affiliation:
-- given-names: Jayant
-  family-names: Bhakar
+- given-names: Sashank
+  family-names: Mishra
+  affiliation:
+  orcid: https://orcid.org/0000-0001-8302-1584
+- given-names: Sarthak
+  family-names: Srivastava
   affiliation:
 - given-names: John
   family-names: Reichenbach
   affiliation:
+- given-names: Rinkle
+  family-names: Jain
+  affiliation:
 - given-names: Andreas
   family-names: Floers
   affiliation:
 - given-names: GitHub
   family-names: Actions
   affiliation:
-- given-names: Rinkle
-  family-names: Jain
+- given-names: Aarya
+  family-names: Chaumal
   affiliation:
-- given-names: Sourav
-  family-names: Singh
+- given-names: Harshul
+  family-names: Gupta
   affiliation:
 - given-names: Antreev
   family-names: Brar
   affiliation:
-- given-names: Anirban
-  family-names: Dutta
-  affiliation:
-- given-names: Aarya
-  family-names: Chaumal
+- given-names: Sourav
+  family-names: Singh
   affiliation:
-- given-names: Yuki
-  family-names: Matsumura
+- given-names: Aman
+  family-names: Kumar
   affiliation:
-- given-names: Abhishek
-  family-names: Patidar
+- given-names: Caroline
+  family-names: Sofiatti
   affiliation:
 - given-names: Nathan
   family-names: Kowalski
   affiliation:
-- given-names: Aman
-  family-names: Kumar
-  affiliation:
-- given-names: Harshul
-  family-names: Gupta
-  affiliation:
 - given-names: Jonatan
   family-names: Selsing
   affiliation:
 - given-names: Chinmay
   family-names: Talegaonkar
   affiliation:
-- given-names: Caroline
-  family-names: Sofiatti
+- given-names: Yuki
+  family-names: Matsumura
   affiliation:
-- given-names: Shilpi
-  family-names: Prasad
+- given-names: Abhishek
+  family-names: Patidar
+  affiliation:
+- given-names: Shashank
+  family-names: Venkat
   affiliation:
 - given-names: Johannes
   family-names: Buchner
@@ -257,6 +275,9 @@ authors:
 - given-names: Kevin
   family-names: Yap
   affiliation:
+- given-names: Laureano
+  family-names: Martinez
+  affiliation:
 - given-names: Le
   family-names: Truong
   affiliation:
@@ -272,20 +293,23 @@ authors:
 - given-names: Nilesh
   family-names: Patra
   affiliation:
-- given-names: Dmitry
-  family-names: Volodin
+- given-names: Nutan
+  family-names: Chen
   affiliation:
 - given-names: Parikshit
   family-names: Singh Rathore
   affiliation:
+- given-names: Pratik
+  family-names: Patel
+  affiliation:
 - given-names: Sampark
   family-names: Sharma
   affiliation:
-- given-names: Shashank
-  family-names: Venkat
+- given-names: Dmitry
+  family-names: Volodin
   affiliation:
-- given-names: Jing
-  family-names: Lu
+- given-names: Shilpi
+  family-names: Prasad
   affiliation:
 - given-names: Suyash
   family-names: Gupta
@@ -299,21 +323,15 @@ authors:
 - given-names: Yash
   family-names: Aggarwal
   affiliation:
-- given-names: Pratik
-  family-names: Patel
-  affiliation:
 - given-names: Debajyoti
   family-names: Dasgupta
   affiliation:
-- given-names: ABHISHEK
-  family-names: PATIDAR
-  affiliation:
-- given-names: Laureano
-  family-names: Martinez
-  affiliation:
 - given-names: Chaitanya
   family-names: Kolliboyina
   affiliation:
+- given-names: ABHISHEK
+  family-names: PATIDAR
+  affiliation:
 - given-names: Ashwin
   family-names: Nayak U
   affiliation:
@@ -323,7 +341,7 @@ authors:
 - given-names: Atul
   family-names: Kumar
   affiliation:
-version: release-2023.11.26
-date-released: 2023-11-26
+version: release-2024.08.04
+date-released: 2024-08-04
 repository-code: https://github.com/tardis-sn/tardis
 license: cc-by-4.0
diff --git a/README.rst b/README.rst
index 8603332dea9..1a269086dc1 100644
--- a/README.rst
+++ b/README.rst
@@ -110,15 +110,14 @@ The following BibTeX entries are needed for the references:
           adsnote = {Provided by the SAO/NASA Astrophysics Data System}
     }
 
-.. |CITATION| replace:: kerzendorf_2023_10207663
-
-.. |DOI_BADGE| image:: https://zenodo.org/badge/DOI/10.5281/zenodo.592480.svg
-                :target: https://doi.org/10.5281/zenodo.592480
+.. |CITATION| replace:: kerzendorf_2024_13207705
 
+.. |DOI_BADGE| image:: https://img.shields.io/badge/DOI-10.5281/zenodo.13207705-blue
+                 :target: https://doi.org/10.5281/zenodo.13207705
 
 .. code-block:: bibtex
 
-    @software{kerzendorf_2023_10207663,
+    @software{kerzendorf_2024_13207705,
       author       = {Kerzendorf, Wolfgang and
                       Sim, Stuart and
                       Vogl, Christian and
@@ -143,88 +142,94 @@ The following BibTeX entries are needed for the references:
                       Barna, Barnabás and
                       Gautam, Gaurav and
                       Fullard, Andrew and
-                      Smith, Isaac and
                       Arya, Atharva and
+                      Smith, Isaac and
                       Cawley, Kevin and
                       Singhal, Jaladh and
-                      Sondhi, Dhruv and
-                      Barbosa, Talytha and
+                      Shields, Joshua and
                       O'Brien, Jack and
+                      Barbosa, Talytha and
+                      Sondhi, Dhruv and
                       Yu, Jenny and
                       Patel, Maryam and
-                      Varanasi, Kaushik and
                       Rathi, Shikha and
+                      Varanasi, Kaushik and
                       Chitchyan, Sona and
                       Gillanders, James and
-                      Shields, Joshua and
-                      Savel, Arjun and
                       Singh, Shreyas and
-                      Reinecke, Martin and
+                      Savel, Arjun and
+                      Holas, Alexander and
                       Eweis, Youssef and
+                      Reinecke, Martin and
                       Bylund, Tomas and
                       Black, William and
+                      Gupta, Sumit and
                       Bentil, Laud and
-                      Holas, Alexander and
                       Eguren, Jordi and
-                      Alam, Arib and
                       Kumar, Ansh and
+                      Alam, Arib and
+                      Kumar, Asish and
                       Bartnik, Matthew and
-                      Varma Buddaraju, Rohith and
                       Magee, Mark and
+                      Dutta, Anirban and
+                      Varma Buddaraju, Rohith and
                       Livneh, Ran and
-                      Kambham, Satwik and
-                      Mishra, Sashank and
-                      Rajagopalan, Srinath and
+                      Lu, Jing and
+                      Visser, Erin and
                       Daksh, Ayushi and
+                      Kambham, Satwik and
                       Bhakar, Jayant and
+                      Rajagopalan, Srinath and
+                      Roldan, Israel and
+                      Mishra, Sashank and
+                      Srivastava, Sarthak and
                       Reichenbach, John and
+                      Jain, Rinkle and
                       Floers, Andreas and
                       Actions, GitHub and
-                      Jain, Rinkle and
-                      Singh, Sourav and
-                      Brar, Antreev and
-                      Dutta, Anirban and
                       Chaumal, Aarya and
-                      Matsumura, Yuki and
-                      Patidar, Abhishek and
-                      Kowalski, Nathan and
-                      Kumar, Aman and
                       Gupta, Harshul and
+                      Brar, Antreev and
+                      Singh, Sourav and
+                      Kumar, Aman and
+                      Sofiatti, Caroline and
+                      Kowalski, Nathan and
                       Selsing, Jonatan and
                       Talegaonkar, Chinmay and
-                      Sofiatti, Caroline and
-                      Prasad, Shilpi and
+                      Matsumura, Yuki and
+                      Patidar, Abhishek and
+                      Venkat, Shashank and
                       Buchner, Johannes and
                       Yap, Kevin and
+                      Martinez, Laureano and
                       Truong, Le and
                       Sandler, Morgan and
                       Zaheer, Musabbiha and
                       Sarafina, Nance and
                       Patra, Nilesh and
-                      Volodin, Dmitry and
+                      Chen, Nutan and
                       Singh Rathore, Parikshit and
+                      Patel, Pratik and
                       Sharma, Sampark and
-                      Venkat, Shashank and
-                      Lu, Jing and
+                      Volodin, Dmitry and
+                      Prasad, Shilpi and
                       Gupta, Suyash and
                       Lemoine, Thom and
                       Wahi, Ujjwal and
                       Aggarwal, Yash and
-                      Patel, Pratik and
                       Dasgupta, Debajyoti and
-                      PATIDAR, ABHISHEK and
-                      Martinez, Laureano and
                       Kolliboyina, Chaitanya and
+                      PATIDAR, ABHISHEK and
                       Nayak U, Ashwin and
                       Kharkar, Atharwa and
                       Kumar, Atul},
-      title        = {tardis-sn/tardis: TARDIS v2023.11.26},
-      month        = nov,
-      year         = 2023,
+      title        = {tardis-sn/tardis: TARDIS v2024.08.04},
+      month        = aug,
+      year         = 2024,
       publisher    = {Zenodo},
-      version      = {release-2023.11.26},
-      doi          = {10.5281/zenodo.10207663},
-      url          = {https://doi.org/10.5281/zenodo.10207663}
+      version      = {release-2024.08.04},
+      doi          = {10.5281/zenodo.13207705},
+      url          = {https://doi.org/10.5281/zenodo.13207705}
     }
 
 *******
diff --git a/docs/resources/credits.rst b/docs/resources/credits.rst
index cacb3e9bd38..b25245bdbfd 100644
--- a/docs/resources/credits.rst
+++ b/docs/resources/credits.rst
@@ -74,14 +74,14 @@ The following BibTeX entries are needed for the references:
           adsnote = {Provided by the SAO/NASA Astrophysics Data System}
     }
 
-.. |CITATION| replace:: kerzendorf_2023_10207663
+.. |CITATION| replace:: kerzendorf_2024_13207705
 
-.. |DOI_BADGE| image:: https://zenodo.org/badge/DOI/10.5281/zenodo.592480.svg
-                :target: https://doi.org/10.5281/zenodo.592480
+.. |DOI_BADGE| image:: https://img.shields.io/badge/DOI-10.5281/zenodo.13207705-blue
+                 :target: https://doi.org/10.5281/zenodo.13207705
 
 .. code-block:: bibtex
 
-    @software{kerzendorf_2023_10207663,
+    @software{kerzendorf_2024_13207705,
       author       = {Kerzendorf, Wolfgang and
                       Sim, Stuart and
                       Vogl, Christian and
@@ -106,87 +106,93 @@ The following BibTeX entries are needed for the references:
                       Barna, Barnabás and
                       Gautam, Gaurav and
                       Fullard, Andrew and
-                      Smith, Isaac and
                       Arya, Atharva and
+                      Smith, Isaac and
                       Cawley, Kevin and
                       Singhal, Jaladh and
-                      Sondhi, Dhruv and
-                      Barbosa, Talytha and
+                      Shields, Joshua and
                       O'Brien, Jack and
+                      Barbosa, Talytha and
+                      Sondhi, Dhruv and
                       Yu, Jenny and
                       Patel, Maryam and
-                      Varanasi, Kaushik and
                       Rathi, Shikha and
+                      Varanasi, Kaushik and
                       Chitchyan, Sona and
                       Gillanders, James and
-                      Shields, Joshua and
-                      Savel, Arjun and
                       Singh, Shreyas and
-                      Reinecke, Martin and
+                      Savel, Arjun and
+                      Holas, Alexander and
                       Eweis, Youssef and
+                      Reinecke, Martin and
                       Bylund, Tomas and
                       Black, William and
+                      Gupta, Sumit and
                       Bentil, Laud and
-                      Holas, Alexander and
                       Eguren, Jordi and
-                      Alam, Arib and
                       Kumar, Ansh and
+                      Alam, Arib and
+                      Kumar, Asish and
                       Bartnik, Matthew and
-                      Varma Buddaraju, Rohith and
                       Magee, Mark and
+                      Dutta, Anirban and
+                      Varma Buddaraju, Rohith and
                       Livneh, Ran and
-                      Kambham, Satwik and
-                      Mishra, Sashank and
-                      Rajagopalan, Srinath and
+                      Lu, Jing and
+                      Visser, Erin and
                       Daksh, Ayushi and
+                      Kambham, Satwik and
                       Bhakar, Jayant and
+                      Rajagopalan, Srinath and
+                      Roldan, Israel and
+                      Mishra, Sashank and
+                      Srivastava, Sarthak and
                       Reichenbach, John and
+                      Jain, Rinkle and
                       Floers, Andreas and
                       Actions, GitHub and
-                      Jain, Rinkle and
-                      Singh, Sourav and
-                      Brar, Antreev and
-                      Dutta, Anirban and
                       Chaumal, Aarya and
-                      Matsumura, Yuki and
-                      Patidar, Abhishek and
-                      Kowalski, Nathan and
-                      Kumar, Aman and
                       Gupta, Harshul and
+                      Brar, Antreev and
+                      Singh, Sourav and
+                      Kumar, Aman and
+                      Sofiatti, Caroline and
+                      Kowalski, Nathan and
                       Selsing, Jonatan and
                       Talegaonkar, Chinmay and
-                      Sofiatti, Caroline and
-                      Prasad, Shilpi and
+                      Matsumura, Yuki and
+                      Patidar, Abhishek and
+                      Venkat, Shashank and
                       Buchner, Johannes and
                       Yap, Kevin and
+                      Martinez, Laureano and
                       Truong, Le and
                       Sandler, Morgan and
                       Zaheer, Musabbiha and
                       Sarafina, Nance and
                       Patra, Nilesh and
-                      Volodin, Dmitry and
+                      Chen, Nutan and
                       Singh Rathore, Parikshit and
+                      Patel, Pratik and
                       Sharma, Sampark and
-                      Venkat, Shashank and
-                      Lu, Jing and
+                      Volodin, Dmitry and
+                      Prasad, Shilpi and
                       Gupta, Suyash and
                       Lemoine, Thom and
                       Wahi, Ujjwal and
                       Aggarwal, Yash and
-                      Patel, Pratik and
                       Dasgupta, Debajyoti and
-                      PATIDAR, ABHISHEK and
-                      Martinez, Laureano and
                       Kolliboyina, Chaitanya and
+                      PATIDAR, ABHISHEK and
                       Nayak U, Ashwin and
                       Kharkar, Atharwa and
                       Kumar, Atul},
-      title        = {tardis-sn/tardis: TARDIS v2023.11.26},
-      month        = nov,
-      year         = 2023,
+      title        = {tardis-sn/tardis: TARDIS v2024.08.04},
+      month        = aug,
+      year         = 2024,
       publisher    = {Zenodo},
-      version      = {release-2023.11.26},
-      doi          = {10.5281/zenodo.10207663},
-      url          = {https://doi.org/10.5281/zenodo.10207663}
+      version      = {release-2024.08.04},
+      doi          = {10.5281/zenodo.13207705},
+      url          = {https://doi.org/10.5281/zenodo.13207705}
     }
 

From c905e0345127eaa48a8facb70eb86db46c320c0b Mon Sep 17 00:00:00 2001
From: Jack O'Brien <jobrien585@gmail.com>
Date: Tue, 6 Aug 2024 13:44:54 -0400
Subject: [PATCH 10/10] Opacity state restructure (#2773)

* created file for opacity solver

* Added opacity states for the continuum and macroatom

* Updated the opacity state and macroatom state to work with legacy plasma

* Added numba initialize from opacity state, added methods to solve opacity state with the solver

* moved line2macro_level_upper to the macroatom state

* renamed a macroatom variable, added solver to montecarlo solver

* ran black

* corrected an import

* corrected an import

* ran black

* Added line_interaction_type to the to_numba function, should be reqorked in the future

* fixed initialization of opacity state

* Updated handling of continuum vs noncontinuum macroblock references

* Fixed a typo

* refactored the state objects to put them in the correct folders

* another typo

* added basic docstrings to the continuum state

* Added docstrings to macroatom state

* Updated docstrings onithe opacity_state file

* Added docstrings to the solver

* Updated Docstring Style

* ran black

* changed Opacity solver to take kwargs

* ran black

* Added class attributes to Opacity Solver

* Changed names of the opacity state and numba equivalent

* Added test for the opacity solver

* added conftest to the opacities module

* fixed up tests for the opacity_solver

* ran black

* Added new test for the numba opacity state

* ran black, updated name of the test

* improved tau_sobelev disable_line_scattering initialization

* Fixed tau_sobolev initialization

* added some comments

* Changed scope of the simulation in conftest
---
 tardis/opacities/continuum/continuum_state.py | 194 ++++++++++++++++
 .../opacities/macro_atom/macroatom_state.py   |  90 ++++++++
 tardis/opacities/opacity_solver.py            |  67 ++++++
 tardis/opacities/opacity_state.py             | 208 +++++++++++++++++-
 tardis/opacities/tests/conftest.py            |  11 +
 tardis/opacities/tests/test_opacity_solver.py |  67 ++++++
 .../tests/test_opacity_state_numba.py         |  83 +++++++
 tardis/transport/montecarlo/base.py           |  23 +-
 8 files changed, 732 insertions(+), 11 deletions(-)
 create mode 100644 tardis/opacities/continuum/continuum_state.py
 create mode 100644 tardis/opacities/macro_atom/macroatom_state.py
 create mode 100644 tardis/opacities/opacity_solver.py
 create mode 100644 tardis/opacities/tests/conftest.py
 create mode 100644 tardis/opacities/tests/test_opacity_solver.py
 create mode 100644 tardis/opacities/tests/test_opacity_state_numba.py

diff --git a/tardis/opacities/continuum/continuum_state.py b/tardis/opacities/continuum/continuum_state.py
new file mode 100644
index 00000000000..8d3618e30f3
--- /dev/null
+++ b/tardis/opacities/continuum/continuum_state.py
@@ -0,0 +1,194 @@
+import numpy as np
+
+
+class ContinuumState:
+    def __init__(
+        self,
+        nu_i,
+        level2continuum_idx,
+        p_fb_deactivation,
+        photo_ion_cross_sections,
+        chi_bf,
+        ff_cooling_factor,
+        fb_emission_cdf,
+        photo_ion_idx,
+        k_packet_idx,
+    ):
+        """
+        Current State of the Continuum Required for Opacity Computation
+
+        Parameters
+        ----------
+        nu_i : pd.DataFrame
+            frequencies for the bound-free thresholds
+        level2continuum_idx : pd.DataFrame
+            mapping from levels to the continuum
+        p_fb_deactivation : pd.DataFrame
+            probabilities of free-bound deactivation channels
+        photo_ion_cross_sections : pd.DataFrame
+            Photoionization cross sections
+        chi_bf : pd.DataFrame
+            Bound-free opacities
+        ff_cooling_factor : np.ndarray
+            free-free cooling factor
+        fb_emission_cdf : pd.DataFrame
+            free-bound emission cumulative distribution function
+        photo_ion_idx : pd.DataFrame
+            photoionization indices
+        k_packet_idx : pd.DataFrame
+            k-packet indices
+        """
+        self.nu_i = nu_i
+        self.level2continuum_idx = level2continuum_idx
+        self.p_fb_deactivation = p_fb_deactivation
+        self.photo_ion_cross_sections = photo_ion_cross_sections
+        self._chi_bf = chi_bf
+        self.ff_cooling_factor = ff_cooling_factor
+        self.fb_emission_cdf = fb_emission_cdf
+        self.photo_ion_idx = photo_ion_idx
+        self.k_packet_idx = k_packet_idx
+
+    @classmethod
+    def from_legacy_plasma(cls, plasma):
+        """
+        Generates a ContinuumState object from a tardis BasePlasma
+
+        Parameters
+        ----------
+        plasma : tarids.plasma.BasePlasma
+            legacy base plasma
+
+        Returns
+        -------
+        ContinuumState
+        """
+        nu_i = plasma.nu_i
+        level2continuum_idx = plasma.level2continuum_idx
+        p_fb_deactivation = plasma.p_fb_deactivation
+        photo_ion_cross_sections = plasma.photo_ion_cross_sections
+        chi_bf = plasma.chi_bf
+        ff_cooling_factor = plasma.ff_cooling_factor
+        fb_emission_cdf = plasma.fb_emission_cdf
+        photo_ion_idx = plasma.photo_ion_idx
+        k_packet_idx = plasma.k_packet_idx
+
+        return cls(
+            nu_i,
+            level2continuum_idx,
+            p_fb_deactivation,
+            photo_ion_cross_sections,
+            chi_bf,
+            ff_cooling_factor,
+            fb_emission_cdf,
+            photo_ion_idx,
+            k_packet_idx,
+        )
+
+    @property
+    def bf_threshold_list_nu(self):
+        """
+        List of Bound-Free Threshold Frequencies
+
+        Returns
+        -------
+        pd.DataFrame
+        """
+        return self.nu_i.loc[self.level2continuum_idx.index]
+
+    @property
+    def phot_nus(self):
+        """
+        Frequencies corresponding to Photoionization Cross Sections
+
+        Returns
+        -------
+        pd.DataFrame
+        """
+        return self.photo_ion_cross_sections.nu.loc[
+            self.level2continuum_idx.index
+        ]
+
+    @property
+    def photo_ion_block_references(self):
+        """Photoionization Block References
+
+        Returns
+        -------
+        np.ndarray
+        """
+        return np.pad(
+            self.phot_nus.groupby(level=[0, 1, 2], sort=False)
+            .count()
+            .values.cumsum(),
+            [1, 0],
+        )
+
+    @property
+    def photo_ion_nu_threshold_mins(self):
+        """
+        Minimum Edges of the photoionization threshold frequencies
+
+        Returns
+        -------
+        pd.DataFrame
+        """
+        return self.phot_nus.groupby(level=[0, 1, 2], sort=False).first()
+
+    @property
+    def photo_ion_nu_threshold_maxs(self):
+        """
+        Maximum Edges of the photoionization threshold frequencies
+
+        Returns
+        -------
+        pd.DataFrame
+        """
+        return self.phot_nus.groupby(level=[0, 1, 2], sort=False).last()
+
+    @property
+    def x_sect(self):
+        """
+        Photoionization Cross Sections mapped to the continuum indices
+
+        Returns
+        -------
+        pd.DataFrame
+        """
+        return self.photo_ion_cross_sections.x_sect.loc[
+            self.level2continuum_idx.index
+        ]
+
+    @property
+    def chi_bf(self):
+        """
+        Bound-Free Opacities indices corresponding to the continuum levels
+
+        Returns
+        -------
+        pd.DataFrame
+        """
+        return self._chi_bf.loc[self.level2continuum_idx.index]
+
+    @property
+    def emissivities(self):
+        """
+        Free-bound Emissivities corresponding to the continuum levels
+
+        Returns
+        -------
+        pd.DataFrame
+        """
+        return self.fb_emission_cdf.loc[self.level2continuum_idx.index]
+
+    @property
+    def photo_ion_activation_idx(self):
+        """
+        Index corresponding to photoionization activation
+
+        Returns
+        -------
+        pd.DataFrame
+        """
+        return self.photo_ion_idx.loc[
+            self.level2continuum_idx.index, "destination_level_idx"
+        ]
diff --git a/tardis/opacities/macro_atom/macroatom_state.py b/tardis/opacities/macro_atom/macroatom_state.py
new file mode 100644
index 00000000000..b3cb78eebb6
--- /dev/null
+++ b/tardis/opacities/macro_atom/macroatom_state.py
@@ -0,0 +1,90 @@
+from tardis.transport.montecarlo.configuration import montecarlo_globals
+from tardis.io.util import HDFWriterMixin
+
+
+class MacroAtomState(HDFWriterMixin):
+
+    hdf_name = "macro_atom_state"
+
+    hdf_properties = [
+        "transition_probabilities",
+        "transition_type",
+        "destination_level_id",
+        "transition_line_id",
+        "macro_block_references",
+        "line2macro_level_upper",
+    ]
+
+    def __init__(
+        self,
+        transition_probabilities,
+        transition_type,
+        destination_level_id,
+        transition_line_id,
+        macro_block_references,
+        line2macro_level_upper,
+    ):
+        """
+        Current State of the MacroAtom
+
+        Parameters
+        ----------
+        transition_probabilities : pd.DataFrame
+            Macro Atom Transition probabilities between levels
+        transition_type : pd.DataFrame)
+            Macro Atom transition types
+        destination_level_id : pd.DataFrame
+            ID of destination levels of the Macro Atom
+        transition_line_id : pd.DataFrame
+            ID of lines corresponding to Macro Atom transitions
+        macro_block_references : pd.DataFrame or np.ndarray
+            Index references to the Macro Atom blocks
+        line2macro_level_upper : pd.DataFrame
+            Mapping from lines to Macro Atom upper levels
+        """
+        self.transition_probabilities = transition_probabilities
+        self.transition_type = transition_type
+        self.destination_level_id = destination_level_id
+        self.transition_line_id = transition_line_id
+        self.macro_block_references = macro_block_references
+        self.line2macro_level_upper = line2macro_level_upper
+
+    @classmethod
+    def from_legacy_plasma(cls, plasma):
+        """
+        Generates a MacroAtomState object from a tardis BasePlasma
+
+        Parameters
+        ----------
+        plasma : tarids.plasma.BasePlasma
+            legacy base plasma
+
+        Returns
+        -------
+        MacroAtomState
+        """
+        transition_probabilities = plasma.transition_probabilities
+        transition_type = plasma.macro_atom_data["transition_type"]
+        destination_level_id = plasma.macro_atom_data["destination_level_idx"]
+        transition_line_id = plasma.macro_atom_data["lines_idx"]
+        line2macro_level_upper = (
+            plasma.atomic_data.lines_upper2macro_reference_idx
+        )
+
+        if (
+            montecarlo_globals.CONTINUUM_PROCESSES_ENABLED
+        ):  # TODO: Unify this in the plasma solver
+            macro_block_references = plasma.macro_block_references
+        else:
+            macro_block_references = plasma.atomic_data.macro_atom_references[
+                "block_references"
+            ]
+
+        return cls(
+            transition_probabilities,
+            transition_type,
+            destination_level_id,
+            transition_line_id,
+            macro_block_references,
+            line2macro_level_upper,
+        )
diff --git a/tardis/opacities/opacity_solver.py b/tardis/opacities/opacity_solver.py
new file mode 100644
index 00000000000..9b3b63f48ad
--- /dev/null
+++ b/tardis/opacities/opacity_solver.py
@@ -0,0 +1,67 @@
+from tardis.opacities.tau_sobolev import calculate_sobolev_line_opacity
+from tardis.opacities.opacity_state import (
+    OpacityState,
+)
+import numpy as np
+import pandas as pd
+
+
+class OpacitySolver(object):
+
+    line_interaction_type: str = "scatter"
+    disable_line_scattering: bool = False
+
+    def __init__(
+        self, line_interaction_type="scatter", disable_line_scattering=False
+    ):
+        """Solver class for opacities
+
+        Parameters
+        ----------
+        line_interaction_type: str
+            "scatter", "downbranch", or "macroatom"
+        disable_line_scattering: bool
+        """
+
+        self.line_interaction_type = line_interaction_type
+        self.disable_line_scattering = disable_line_scattering
+
+    def solve(self, legacy_plasma) -> OpacityState:
+        """
+        Solves the opacity state
+
+        Parameters
+        ----------
+        plasma : tarids.plasma.BasePlasma
+            legacy base plasma
+
+        Returns
+        -------
+        OpacityState
+        """
+        if self.disable_line_scattering:
+            tau_sobolev = pd.DataFrame(
+                np.zeros(
+                    (
+                        legacy_plasma.atomic_data.lines.shape[
+                            0
+                        ],  # number of lines
+                        legacy_plasma.abundance.shape[1],  # number of shells
+                    ),
+                    dtype=np.float64,
+                ),
+                index=legacy_plasma.atomic_data.lines.index,
+            )
+        else:
+            tau_sobolev = calculate_sobolev_line_opacity(
+                legacy_plasma.atomic_data.lines,
+                legacy_plasma.level_number_density,
+                legacy_plasma.time_explosion,
+                legacy_plasma.stimulated_emission_factor,
+            )
+
+        opacity_state = OpacityState.from_legacy_plasma(
+            legacy_plasma, tau_sobolev
+        )
+
+        return opacity_state
diff --git a/tardis/opacities/opacity_state.py b/tardis/opacities/opacity_state.py
index 7fbab4be781..ef5cc7d19ac 100644
--- a/tardis/opacities/opacity_state.py
+++ b/tardis/opacities/opacity_state.py
@@ -4,6 +4,79 @@
 
 from tardis.opacities.tau_sobolev import calculate_sobolev_line_opacity
 from tardis.transport.montecarlo.configuration import montecarlo_globals
+from tardis.opacities.continuum.continuum_state import ContinuumState
+from tardis.opacities.macro_atom.macroatom_state import MacroAtomState
+
+
+class OpacityState:
+    def __init__(
+        self,
+        electron_density,
+        t_electrons,
+        line_list_nu,
+        tau_sobolev,
+        macroatom_state,
+        continuum_state,
+    ):
+        """
+        Opacity State in Python
+
+        Parameters
+        ----------
+        electron_density : pd.DataFrame
+        t_electrons : numpy.ndarray
+        line_list_nu : pd.DataFrame
+        tau_sobolev : pd.DataFrame
+        macroatom_state: tardis.opacities.macro_atom.macroatom_state.MacroAtomState
+        continuum_state: tardis.opacities.continuum.continuum_state.ContinuumState
+        """
+        self.electron_density = electron_density
+        self.t_electrons = t_electrons
+        self.line_list_nu = line_list_nu
+
+        self.tau_sobolev = tau_sobolev
+
+        # Continuum Opacity Data
+        self.continuum_state = continuum_state
+        self.macroatom_state = macroatom_state
+
+    @classmethod
+    def from_legacy_plasma(cls, plasma, tau_sobolev):
+        """
+        Generates an OpacityStatePython object from a tardis BasePlasma
+
+        Parameters
+        ----------
+        plasma : tarids.plasma.BasePlasma
+            legacy base plasma
+        tau_sobolev : pd.DataFrame
+            Expansion Optical Depths
+
+        Returns
+        -------
+        OpacityStatePython
+        """
+        if hasattr(plasma, "macro_atom_data"):
+            macroatom_state = MacroAtomState.from_legacy_plasma(plasma)
+        else:
+            macroatom_state = None
+
+        if hasattr(plasma, "photo_ion_cross_sections"):
+            continuum_state = ContinuumState.from_legacy_plasma(plasma)
+        else:
+            continuum_state = None
+
+        atomic_data = plasma.atomic_data
+
+        return cls(
+            plasma.electron_densities,
+            plasma.t_electrons,
+            atomic_data.lines.nu,
+            tau_sobolev,
+            macroatom_state,
+            continuum_state,
+        )
+
 
 opacity_state_spec = [
     ("electron_density", float64[:]),
@@ -32,7 +105,7 @@
 
 
 @jitclass(opacity_state_spec)
-class OpacityState:
+class OpacityStateNumba:
     def __init__(
         self,
         electron_density,
@@ -116,7 +189,7 @@ def __getitem__(self, i: slice):
             OpacityState : a shallow copy of the current instance
         """
         # NOTE: This currently will not work with continuum processes since it does not slice those arrays
-        return OpacityState(
+        return OpacityStateNumba(
             self.electron_density[i],
             self.t_electrons[i],
             self.line_list_nu,
@@ -142,6 +215,135 @@ def __getitem__(self, i: slice):
         )
 
 
+def opacity_state_to_numba(
+    opacity_state: OpacityState, line_interaction_type
+) -> OpacityStateNumba:
+    """
+    Initialize the OpacityStateNumba object and copy over the data over from OpacityState class
+
+    Parameters
+    ----------
+    opacity_state : tardis.opacities.opacity_state.OpacityState
+    line_interaction_type : enum
+    """
+
+    electron_densities = opacity_state.electron_density.values
+    t_electrons = opacity_state.t_electrons
+    line_list_nu = opacity_state.line_list_nu.values
+
+    # NOTE: Disabled line scattering is handled by the opacitystate solver
+    tau_sobolev = np.ascontiguousarray(
+        opacity_state.tau_sobolev, dtype=np.float64
+    )
+
+    if line_interaction_type == "scatter":
+        # to adhere to data types, we must have an array of minimum size 1
+        array_size = 1
+        transition_probabilities = np.zeros(
+            (array_size, array_size), dtype=np.float64
+        )  # to adhere to data types
+        line2macro_level_upper = np.zeros(array_size, dtype=np.int64)
+        macro_block_references = np.zeros(array_size, dtype=np.int64)
+        transition_type = np.zeros(array_size, dtype=np.int64)
+        destination_level_id = np.zeros(array_size, dtype=np.int64)
+        transition_line_id = np.zeros(array_size, dtype=np.int64)
+    else:
+        transition_probabilities = np.ascontiguousarray(
+            opacity_state.macroatom_state.transition_probabilities.values.copy(),
+            dtype=np.float64,
+        )
+        line2macro_level_upper = (
+            opacity_state.macroatom_state.line2macro_level_upper
+        )
+        # TODO: Fix setting of block references for non-continuum mode
+
+        macro_block_references = np.asarray(
+            opacity_state.macroatom_state.macro_block_references
+        )
+
+        transition_type = opacity_state.macroatom_state.transition_type.values
+
+        # Destination level is not needed and/or generated for downbranch
+        destination_level_id = (
+            opacity_state.macroatom_state.destination_level_id.values
+        )
+        transition_line_id = (
+            opacity_state.macroatom_state.transition_line_id.values
+        )
+
+    if montecarlo_globals.CONTINUUM_PROCESSES_ENABLED:
+        bf_threshold_list_nu = (
+            opacity_state.continuum_state.bf_threshold_list_nu.values
+        )
+        p_fb_deactivation = np.ascontiguousarray(
+            opacity_state.continuum_state.p_fb_deactivation.values.copy(),
+            dtype=np.float64,
+        )
+
+        phot_nus = opacity_state.continuum_state.phot_nus
+        photo_ion_block_references = (
+            opacity_state.continuum_state.photo_ion_block_references
+        )
+        photo_ion_nu_threshold_mins = (
+            opacity_state.continuum_state.photo_ion_nu_threshold_mins.values
+        )
+        photo_ion_nu_threshold_maxs = (
+            opacity_state.continuum_state.photo_ion_nu_threshold_maxs.values
+        )
+
+        chi_bf = opacity_state.continuum_state.chi_bf.values
+        x_sect = opacity_state.continuum_state.x_sect.values
+
+        phot_nus = phot_nus.values
+        ff_opacity_factor = (
+            opacity_state.continuum_state.ff_cooling_factor
+            / np.sqrt(t_electrons)
+        ).astype(np.float64)
+        emissivities = opacity_state.continuum_state.emissivities.values
+        photo_ion_activation_idx = (
+            opacity_state.continuum_state.photo_ion_activation_idx.values
+        )
+        k_packet_idx = np.int64(opacity_state.continuum_state.k_packet_idx)
+    else:
+        bf_threshold_list_nu = np.zeros(0, dtype=np.float64)
+        p_fb_deactivation = np.zeros((0, 0), dtype=np.float64)
+        photo_ion_nu_threshold_mins = np.zeros(0, dtype=np.float64)
+        photo_ion_nu_threshold_maxs = np.zeros(0, dtype=np.float64)
+        photo_ion_block_references = np.zeros(0, dtype=np.int64)
+        chi_bf = np.zeros((0, 0), dtype=np.float64)
+        x_sect = np.zeros(0, dtype=np.float64)
+        phot_nus = np.zeros(0, dtype=np.float64)
+        ff_opacity_factor = np.zeros(0, dtype=np.float64)
+        emissivities = np.zeros((0, 0), dtype=np.float64)
+        photo_ion_activation_idx = np.zeros(0, dtype=np.int64)
+        k_packet_idx = np.int64(-1)
+
+    return OpacityStateNumba(
+        electron_densities,
+        t_electrons,
+        line_list_nu,
+        tau_sobolev,
+        transition_probabilities,
+        line2macro_level_upper,
+        macro_block_references,
+        transition_type,
+        destination_level_id,
+        transition_line_id,
+        bf_threshold_list_nu,
+        p_fb_deactivation,
+        photo_ion_nu_threshold_mins,
+        photo_ion_nu_threshold_maxs,
+        photo_ion_block_references,
+        chi_bf,
+        x_sect,
+        phot_nus,
+        ff_opacity_factor,
+        emissivities,
+        photo_ion_activation_idx,
+        k_packet_idx,
+    )
+
+
 def opacity_state_initialize(
     plasma,
     line_interaction_type,
@@ -258,7 +460,7 @@ def opacity_state_initialize(
         photo_ion_activation_idx = np.zeros(0, dtype=np.int64)
         k_packet_idx = np.int64(-1)
 
-    return OpacityState(
+    return OpacityStateNumba(
         electron_densities,
         t_electrons,
         line_list_nu,
diff --git a/tardis/opacities/tests/conftest.py b/tardis/opacities/tests/conftest.py
new file mode 100644
index 00000000000..af116184d6d
--- /dev/null
+++ b/tardis/opacities/tests/conftest.py
@@ -0,0 +1,11 @@
+import pytest
+from copy import deepcopy
+from tardis.simulation import Simulation
+
+
+@pytest.fixture(scope="module")
+def nb_simulation_verysimple(config_verysimple, atomic_dataset):
+    atomic_data = deepcopy(atomic_dataset)
+    sim = Simulation.from_config(config_verysimple, atom_data=atomic_data)
+    sim.iterate(10)
+    return sim
diff --git a/tardis/opacities/tests/test_opacity_solver.py b/tardis/opacities/tests/test_opacity_solver.py
new file mode 100644
index 00000000000..a62be7134a2
--- /dev/null
+++ b/tardis/opacities/tests/test_opacity_solver.py
@@ -0,0 +1,67 @@
+import pytest
+import numpy as np
+import numpy.testing as npt
+import pandas.testing as pdt
+from tardis.opacities.opacity_solver import OpacitySolver
+from tardis.opacities.opacity_state import OpacityState
+from tardis.opacities.tau_sobolev import calculate_sobolev_line_opacity
+
+
+@pytest.mark.parametrize(
+    "line_interaction_type,disable_line_scattering",
+    [
+        ("scatter", False),
+        ("macroatom", False),
+        ("macroatom", True),
+        ("downbranch", False),
+        ("downbranch", True),
+    ],
+)
+def test_opacity_solver(
+    nb_simulation_verysimple, line_interaction_type, disable_line_scattering
+):
+
+    legacy_plasma = nb_simulation_verysimple.plasma
+
+    opacity_solver = OpacitySolver(
+        line_interaction_type=line_interaction_type,
+        disable_line_scattering=disable_line_scattering,
+    )
+    actual = opacity_solver.solve(legacy_plasma)
+
+    pdt.assert_series_equal(
+        actual.electron_density, legacy_plasma.electron_densities
+    )
+    pdt.assert_series_equal(
+        actual.line_list_nu, legacy_plasma.atomic_data.lines.nu
+    )
+    if not disable_line_scattering:
+        pdt.assert_frame_equal(actual.tau_sobolev, legacy_plasma.tau_sobolevs)
+    if line_interaction_type == "scatter":
+        pass  # TODO: Impliment once solver has proper settings
+    else:
+        macroatom_state = actual.macroatom_state
+        pdt.assert_frame_equal(
+            macroatom_state.transition_probabilities,
+            legacy_plasma.transition_probabilities,
+        )
+        npt.assert_allclose(
+            macroatom_state.line2macro_level_upper,
+            legacy_plasma.atomic_data.lines_upper2macro_reference_idx,
+        )
+        pdt.assert_series_equal(
+            macroatom_state.macro_block_references,
+            legacy_plasma.atomic_data.macro_atom_references["block_references"],
+        )
+        pdt.assert_series_equal(
+            macroatom_state.transition_type,
+            legacy_plasma.atomic_data.macro_atom_data["transition_type"],
+        )
+        pdt.assert_series_equal(
+            macroatom_state.destination_level_id,
+            legacy_plasma.atomic_data.macro_atom_data["destination_level_idx"],
+        )
+        pdt.assert_series_equal(
+            macroatom_state.transition_line_id,
+            legacy_plasma.atomic_data.macro_atom_data["lines_idx"],
+        )
diff --git a/tardis/opacities/tests/test_opacity_state_numba.py b/tardis/opacities/tests/test_opacity_state_numba.py
new file mode 100644
index 00000000000..6ac3a206089
--- /dev/null
+++ b/tardis/opacities/tests/test_opacity_state_numba.py
@@ -0,0 +1,83 @@
+import pytest
+from tardis.opacities.opacity_state import opacity_state_to_numba
+from tardis.opacities.opacity_solver import OpacitySolver
+import numpy.testing as npt
+import numpy as np
+
+
+@pytest.mark.parametrize(
+    "line_interaction_type,sliced",
+    [
+        ("scatter", False),
+        ("macroatom", False),
+        ("macroatom", True),
+        ("downbranch", False),
+        ("downbranch", True),
+    ],
+)
+def test_opacity_state_to_numba(
+    nb_simulation_verysimple, line_interaction_type, sliced
+):
+    legacy_plasma = nb_simulation_verysimple.plasma
+
+    opacity_solver = OpacitySolver(
+        line_interaction_type=line_interaction_type,
+        disable_line_scattering=False,
+    )
+    opacity_state = opacity_solver.solve(legacy_plasma)
+    actual = opacity_state_to_numba(opacity_state, line_interaction_type)
+
+    if sliced:
+        index = slice(2, 5)
+        actual = actual[index]
+    else:
+        index = ...
+
+    npt.assert_allclose(
+        actual.electron_density, legacy_plasma.electron_densities.values[index]
+    )
+    npt.assert_allclose(
+        actual.line_list_nu, legacy_plasma.atomic_data.lines.nu.values
+    )
+    npt.assert_allclose(
+        actual.tau_sobolev, legacy_plasma.tau_sobolevs.values[:, index]
+    )
+    if line_interaction_type == "scatter":
+        empty = np.zeros(1, dtype=np.int64)
+        npt.assert_allclose(
+            actual.transition_probabilities, np.zeros((1, 1), dtype=np.float64)
+        )
+        npt.assert_allclose(actual.line2macro_level_upper, empty)
+        npt.assert_allclose(actual.macro_block_references, empty)
+        npt.assert_allclose(actual.transition_type, empty)
+        npt.assert_allclose(actual.destination_level_id, empty)
+        npt.assert_allclose(actual.transition_line_id, empty)
+    else:
+        npt.assert_allclose(
+            actual.transition_probabilities,
+            legacy_plasma.transition_probabilities.values[:, index],
+        )
+        npt.assert_allclose(
+            actual.line2macro_level_upper,
+            legacy_plasma.atomic_data.lines_upper2macro_reference_idx,
+        )
+        npt.assert_allclose(
+            actual.macro_block_references,
+            legacy_plasma.atomic_data.macro_atom_references[
+                "block_references"
+            ].values,
+        )
+        npt.assert_allclose(
+            actual.transition_type,
+            legacy_plasma.atomic_data.macro_atom_data["transition_type"].values,
+        )
+        npt.assert_allclose(
+            actual.destination_level_id,
+            legacy_plasma.atomic_data.macro_atom_data[
+                "destination_level_idx"
+            ].values,
+        )
+        npt.assert_allclose(
+            actual.transition_line_id,
+            legacy_plasma.atomic_data.macro_atom_data["lines_idx"].values,
+        )
diff --git a/tardis/transport/montecarlo/base.py b/tardis/transport/montecarlo/base.py
index af865836598..cd9e00c5b59 100644
--- a/tardis/transport/montecarlo/base.py
+++ b/tardis/transport/montecarlo/base.py
@@ -24,7 +24,7 @@
     MonteCarloTransportState,
 )
 from tardis.opacities.opacity_state import (
-    opacity_state_initialize,
+    opacity_state_to_numba,
 )
 from tardis.transport.montecarlo.packet_trackers import (
     generate_rpacket_tracker_list,
@@ -37,6 +37,8 @@
     update_iterations_pbar,
 )
 
+from tardis.opacities.opacity_solver import OpacitySolver
+
 logger = logging.getLogger(__name__)
 
 
@@ -94,6 +96,11 @@ def __init__(
         mc_tracker.DEBUG_MODE = debug_packets
         mc_tracker.BUFFER = logger_buffer
 
+        self.opacity_solver = OpacitySolver(
+            self.line_interaction_type,
+            self.montecarlo_configuration.DISABLE_LINE_SCATTERING,
+        )
+
     def initialize_transport_state(
         self,
         simulation_state,
@@ -112,24 +119,24 @@ def initialize_transport_state(
         )
 
         geometry_state = simulation_state.geometry.to_numba()
-        opacity_state = opacity_state_initialize(
-            plasma,
-            self.line_interaction_type,
-            self.montecarlo_configuration.DISABLE_LINE_SCATTERING,
+
+        opacity_state = self.opacity_solver.solve(plasma)
+        opacity_state_numba = opacity_state_to_numba(
+            opacity_state, self.opacity_solver.line_interaction_type
         )
-        opacity_state = opacity_state[
+        opacity_state_numba = opacity_state_numba[
             simulation_state.geometry.v_inner_boundary_index : simulation_state.geometry.v_outer_boundary_index
         ]
 
         estimators = initialize_estimator_statistics(
-            opacity_state.tau_sobolev.shape, gamma_shape
+            opacity_state_numba.tau_sobolev.shape, gamma_shape
         )
 
         transport_state = MonteCarloTransportState(
             packet_collection,
             estimators,
             geometry_state=geometry_state,
-            opacity_state=opacity_state,
+            opacity_state=opacity_state_numba,
             time_explosion=simulation_state.time_explosion,
         )