tardis-sn · officialasishkumar · Jul 18, 2024
diff --git a/.github/workflows/benchmarks.yml b/.github/workflows/benchmarks.yml
@@ -68,11 +68,11 @@ 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 5  --pretty=format:"%H" >> tag_commits.txt
-          asv run HASHFILE:tag_commits.txt | tee asv-output.log  
+          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  
           if grep -q failed asv-output.log; then 
             echo "Some benchmarks have failed!"
             exit 1
@@ -126,7 +126,7 @@ jobs:
           echo $(git rev-parse HEAD) > commit_hashes.txt
           echo $(git merge-base HEAD upstream/master) >> commit_hashes.txt
 
-          asv run HASHFILE:commit_hashes.txt | tee asv-output-PR.log  
+          asv run -a repeat=1 -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

diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
@@ -8,7 +8,6 @@ on:
   push:
     branches:
     - '*'
-
   pull_request:
     branches:
     - '*'
@@ -22,24 +21,52 @@ on:
 env:
   CACHE_NUMBER: 0  # increase to reset cache manually
   PYTEST_FLAGS: --tardis-refdata=${{ github.workspace }}/tardis-refdata --tardis-regression-data=${{ github.workspace }}/tardis-regression-data
-                --cov=tardis --cov-report=xml --cov-report=html
   CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
 
-concurrency:
-  group: ${{ github.workflow }}-${{ github.head_ref || github.ref }}
-  cancel-in-progress: true
-
 defaults:
   run:
     shell: bash -l {0}
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.head_ref || github.ref }}
+  cancel-in-progress: true
+
 
 jobs:
-  build:
+  codecov:
     if: github.repository_owner == 'tardis-sn'
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - name: Setup LFS
+        uses: ./.github/actions/setup_lfs
+      - name: Setup environment
+        uses: ./.github/actions/setup_env
+        with:
+          os-label: linux-64
+      - name: Generate coverage report
+        run: |
+          pytest --cov=tardis --cov-report=xml --cov-report=html
+      - uses: codecov/codecov-action@v4
+        if: always()
+        with:
+          fail_ci_if_error: true
+          token: ${{ env.CODECOV_TOKEN }}
+          verbose: true
+
+  tests:
+    name: ${{ matrix.continuum }} continuum ${{ matrix.rpacket_tracking }} rpacket_tracking ${{ matrix.os }}
+    if: github.repository_owner == 'tardis-sn'
+    runs-on: ${{ matrix.os }}
     strategy:
+      fail-fast: false
       matrix:
-        pip: [true, false]
         label: [osx-arm64, linux-64]
+        continuum: ['not', '']
+        rpacket_tracking: ['not', '']
+        exclude:
+          - continuum: ''
+            rpacket_tracking: ''
         include:
           - label: osx-arm64
             os: macos-latest
@@ -48,9 +75,6 @@ jobs:
           - label: linux-64
             os: ubuntu-latest
             prefix: /usr/share/miniconda3/envs/tardis
-
-    name: ${{ matrix.label }}-pip-${{ matrix.pip }}
-    runs-on: ${{ matrix.os }}
     steps:
       - uses: actions/checkout@v4
 
@@ -59,46 +83,16 @@ jobs:
 
       - name: Setup environment
         uses: ./.github/actions/setup_env
-        with: 
+        with:
           os-label: ${{ matrix.label }}
-
-      - name: Install package editable
-        run: |
-          pip install -e .
-          echo "TARDIS_PIP_PATH=tardis" >> $GITHUB_ENV
-        if: matrix.pip == false
-
-      - name: Install package git
-        run: pip install git+https://github.com/tardis-sn/tardis.git@${{ github.ref }}
-        if: matrix.pip == true
-
-      - name: Set pip path
-        if: matrix.pip == true
-        run: |
-          location_line=$(pip show tardis | grep -i -x "Location:.*")
-          directory_path=$(echo $location_line | awk -F " " '{print $2}')
-          echo "TARDIS_PIP_PATH=$directory_path" >> $GITHUB_ENV
 
-      - name: Set install path
-        if: matrix.pip == false
+      - name: Install package editable
         run: |
-          directory_path="."
-          echo "TARDIS_PIP_PATH=$directory_path" >> $GITHUB_ENV
+          pip install -e . --user
 
       - name: Run tests
-        run: pytest tardis ${{ env.PYTEST_FLAGS }} -m "not continuum"
-        working-directory: ${{ env.TARDIS_PIP_PATH }}
-        if: always()
-
-      - name: Run continuum tests
-        run: pytest tardis ${{ env.PYTEST_FLAGS }} -m continuum
-        working-directory: ${{ env.TARDIS_PIP_PATH }}
-        if: always()
-
-      - name: Upload to Codecov
-        run: bash <(curl -s https://codecov.io/bash)
+        run: pytest tardis ${{ env.PYTEST_FLAGS }} -m "${{ matrix.continuum }} continuum and ${{ matrix.rpacket_tracking }} rpacket_tracking" 
 
       - name: Refdata Generation tests
-        run: pytest tardis ${{ env.PYTEST_FLAGS }} --generate-reference
-        working-directory: ${{ env.TARDIS_PIP_PATH }}
-        if: contains(github.event.pull_request.labels.*.name, 'run-generation-tests') || github.ref == 'refs/heads/master'
+        run: pytest tardis ${{ env.PYTEST_FLAGS }} --generate-reference -m "${{ matrix.continuum }} continuum and ${{ matrix.rpacket_tracking }} rpacket_tracking" 
+        if: contains(github.event.pull_request.labels.*.name, 'run-generation-tests') || github.ref == 'refs/heads/master'
diff --git a/benchmarks/benchmark_base.py b/benchmarks/benchmark_base.py
@@ -18,7 +18,11 @@
 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, montecarlo_configuration
+from tardis.transport.montecarlo import RPacket
+from tardis.transport.montecarlo.configuration import montecarlo_globals
+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 (
@@ -66,7 +70,8 @@ def tardis_ref_path(self):
         #       /app/tardis-refdata
         ref_data_path = Path(
             Path(__file__).parent.parent,
-            "tardis-refdata",
+            "benchmarks",
+            "data"
         ).resolve()
         return ref_data_path
 
@@ -83,7 +88,7 @@ def atomic_dataset(self) -> AtomData:
     @property
     def atomic_data_fname(self):
         atomic_data_fname = (
-            f"{self.tardis_ref_path}/atom_data/kurucz_cd23_chianti_H_He.h5"
+            f"{self.tardis_ref_path}/kurucz_cd23_chianti_H_He.h5"
         )
 
         if not Path(atomic_data_fname).exists():
@@ -235,9 +240,7 @@ def packet(self):
 
     @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
     def nb_simulation_verysimple(self):
@@ -259,7 +262,6 @@ def verysimple_opacity_state(self):
             self.nb_simulation_verysimple.plasma,
             line_interaction_type="macroatom",
             disable_line_scattering=self.nb_simulation_verysimple.transport.montecarlo_configuration.DISABLE_LINE_SCATTERING,
-            continuum_processes_enabled=self.nb_simulation_verysimple.transport.montecarlo_configuration.CONTINUUM_PROCESSES_ENABLED,
         )
 
     @property
@@ -268,27 +270,19 @@ def verysimple_enable_full_relativity(self):
 
     @property
     def verysimple_disable_line_scattering(self):
-        return (
-            self.nb_simulation_verysimple.transport.montecarlo_configuration.DISABLE_LINE_SCATTERING
-        )
+        return self.nb_simulation_verysimple.transport.montecarlo_configuration.DISABLE_LINE_SCATTERING
 
     @property
     def verysimple_continuum_processes_enabled(self):
-        return (
-            self.nb_simulation_verysimple.transport.montecarlo_configuration.CONTINUUM_PROCESSES_ENABLED
-        )
+        return montecarlo_globals.CONTINUUM_PROCESSES_ENABLED
 
     @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
     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
     def static_packet(self):
@@ -359,10 +353,10 @@ def verysimple_radfield_mc_estimators(self):
 
     @property
     def montecarlo_configuration(self):
-        return montecarlo_configuration.MonteCarloConfiguration()
+        return MonteCarloConfiguration()
 
     @property
-    def rpacket_tracker(self): 
+    def rpacket_tracker(self):
         return RPacketTracker(0)
 
     @property
@@ -396,7 +390,6 @@ def geometry(self):
             v_outer=np.array([-1, -1], dtype=np.float64),
         )
 
-
     @property
     def estimators(self):
         return radfield_mc_estimators.RadiationFieldMCEstimators(

diff --git a/benchmarks/transport_geometry_calculate_distances.py b/benchmarks/transport_geometry_calculate_distances.py
@@ -1,10 +1,11 @@
-from asv_runner.benchmarks.mark import parameterize
+from asv_runner.benchmarks.mark import parameterize, skip_benchmark
 
 import tardis.transport.frame_transformations as frame_transformations
 import tardis.transport.geometry.calculate_distances as calculate_distances
 from benchmarks.benchmark_base import BenchmarkBase
 
 
+@skip_benchmark
 class BenchmarkTransportGeometryCalculateDistances(BenchmarkBase):
     """
     Class to benchmark the calculate distances function.

diff --git a/benchmarks/transport_montecarlo_interaction.py b/benchmarks/transport_montecarlo_interaction.py
@@ -10,7 +10,6 @@
 from asv_runner.benchmarks.mark import parameterize
 
 
-
 class BenchmarkMontecarloMontecarloNumbaInteraction(BenchmarkBase):
     """
     Class to benchmark the numba interaction function.
@@ -52,7 +51,6 @@ def time_line_scatter(self, line_interaction_type):
             line_interaction_type,
             self.verysimple_opacity_state,
             self.verysimple_enable_full_relativity,
-            self.verysimple_continuum_processes_enabled,
         )
 
     @parameterize(
@@ -63,17 +61,7 @@ def time_line_scatter(self, line_interaction_type):
                     "emission_line_id": 1000,
                     "energy": 0.9114437898710559,
                 },
-                {
-                    "mu": -0.6975116557422458,
-                    "emission_line_id": 2000,
-                    "energy": 0.8803098648913266,
-                },
-                {
-                    "mu": -0.7115661419975774,
-                    "emission_line_id": 0,
-                    "energy": 0.8800385929341252,
-                },
-            ]
+             ]
         }
     )
     def time_line_emission(self, test_packet):

diff --git a/benchmarks/transport_montecarlo_numba_formal_integral_p.py b/benchmarks/transport_montecarlo_numba_formal_integral_p.py
@@ -24,14 +24,6 @@ class BenchmarkMontecarloMontecarloNumbaNumbaFormalIntegral(BenchmarkBase):
                 {
                     "nu": 1e14,
                     "temperature": 1e4,
-                },
-                {
-                    "nu": 0,
-                    "temperature": 1,
-                },
-                {
-                    "nu": 1,
-                    "temperature": 1,
                 }
             ]
         }
@@ -41,7 +33,7 @@ def time_intensity_black_body(self, parameters):
         temperature = parameters["temperature"]
         formal_integral.intensity_black_body(nu, temperature)
 
-    @parameterize({"N": (1e2, 1e3, 1e4, 1e5)})
+    @parameterize({"N": (1e2, 1e3)})
     def time_trapezoid_integration(self, n):
         h = 1.0
         data = np.random.random(int(n))
@@ -98,7 +90,7 @@ def time_calculate_z(self, p, test_data):
         for r in r_outer:
             formal_integral.calculate_z(r, p, inv_t)
 
-    @parameterize({"N": [100, 1000, 10000]})
+    @parameterize({"N": [100, 1000]})
     def time_calculate_p_values(self, N):
         r = 1.0
         formal_integral.calculate_p_values(r, N)

diff --git a/benchmarks/transport_montecarlo_numba_interface.py b/benchmarks/transport_montecarlo_numba_interface.py
@@ -14,13 +14,12 @@ class BenchmarkMontecarloMontecarloNumbaNumbaInterface(BenchmarkBase):
     Class to benchmark the numba interface function.
     """
 
-    @parameterize({"Input params": ["scatter", "macroatom", "downbranch"]})
+    @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,
-            self.verysimple_continuum_processes_enabled,
-        )
+        )