Merge pull request #1106 from agnwinds/dev

Python 88x: merge into main

.gitattributes

@@ -0,0 +1,11 @@
+# Handle line endings automatically for files detected as text
+# and leave all files detected as binary untouched.
+* text=auto
+
+# Force the following filetypes to have unix eols, so Windows does not break them
+*.* text eol=lf
+
+# Denote all files that are truly binary and should not be modified.
+*.png binary
+*.jpg binary
+*.pdf binary

.gitignore

@@ -8,6 +8,9 @@ bin/modify_wind*
 
 # Run files
 *.spec*
+*.pf.old
+*.out.pf
+mod.pf
 
 # Object files
 *.o
@@ -79,10 +82,13 @@ wiki/
 *.Plo
 *.Po
 
-# atomic data files should not be tracked by this repository
+# Some atomic data files should not be tracked by this repository
 data/
 xmod/
 
+# avoid tracking symbolic links errenously put in xdata
+xdata/xdata
+
 # we shouldn't be tracking version.h either
 source/version.h
 
@@ -105,3 +111,4 @@ logfile
 **/*.vscode/
 py_progs/.idea/
 scratch/
+

.readthedocs.yml

@@ -19,9 +19,12 @@ formats: all
 # Set the OS, Python version and other tools you might need
 build:
   os: ubuntu-22.04
+  apt_packages:
+    - libhdf4-dev
   tools:
     python: "3.12"
 
+
 # Optionally set the version of Python and requirements required to build your docs
 python:
   install:

CITATION.cff

@@ -1,6 +1,23 @@
-cff-version: 1.0.3
-message: If you use Python, please cite both the software and the outline paper.
+cff-version: 1.2.0
+title: "Python"
+repository-code: https://github.com/agnwinds/python
+abstract: "A code for Monte Carlo simulation of radiative transfer & ionisation within astrophysical compact object systems."
+message: "If you use Python, please cite both the 2002 concept paper and the software release paper."
+version: 88a
+date-released: 2024-04-11
+doi: 10.1086/342879
+identifiers:
+  - type: doi
+    value: 10.1086/342879
+    description: "2002 concept paper for the Python project."
+  - type: doi
+    value: 10.1234/567890
+    description: "[PLACEHOLDER] Software release paper for this software."
+  - type: doi
+    value: 10.1234/zenodo.5678
+    description: "[PLACEHOLDER] The Zenodo project DOI for the Python code."
 authors:
+  - name: The Python collaboration
   - family-names: Long
     given-names: Knox
     orcid: https://orcid.org/0000-0002-4134-864X
@@ -30,7 +47,7 @@ authors:
     given-names: Sam
     orcid: https://orcid.org/0000-0001-7511-5652
     affiliation: "University of Southampton"
-    email: s.w.[email protected]
+    email: [email protected]
   - family-names: Parkinson
     given-names: Edward
     orcid: https://orcid.org/0000-0003-3902-052X
@@ -39,22 +56,20 @@ authors:
   - family-names: Hewitt
     given-names: Mandy
     affiliation: "Queens University Belfast"
+    orcid: https://orcid.org/0000-0001-5263-3246
     email: [email protected]
-website: https://github.com/agnwinds/python
-title: Python
-version: 83b
-# doi: ??.?/zenodo.????
-date-released: 2019-02-24
-references:
-  - type: article
-    authors:
-      - family-names: Long
-        given-names: Knox
-      - family-names: Knigge
-        given-names: Christian
-    title: "Modeling the Spectral Signatures of Accretion Disk Winds: A New Monte Carlo Approach"
-    year: 2002
-    journal: The Astrophysical Journal
-    volume: 579
-    issue: 2
-    doi: 10.1086/342879
+  - family-names: Scepi
+    given-names: Nicholas
+    orcid: https://orcid.org/0000-0003-3909-2486
+    affiliation: "University of Southampton"
+  - family-names: Wallis
+    given-names: Austen
+    orcid: https://orcid.org/0000-0003-0770-9015
+    affiliation: "University of Southampton"
+  - family-names: Mosallanezhad
+    given-names: Amin
+    orcid: https://orcid.org/0000-0002-4601-7073
+    affiliation: "University of Southampton"
+  - family-names: Gupta
+    given-names: Rahul
+    affiliation: "Imperial College London"

docs/parameters/Central_object.bubble_size.yaml

@@ -0,0 +1,9 @@
+name: Central_object.bubble_size
+description: |
+  Multi-line description, must keep indentation.
+type: Double
+unit: co.gravitational_radius
+values: Condition e.g. greater than 0 or list e.g. [1, 2, 5]
+parent:
+  parameter: Condition e.g. greater than 0 or list e.g. [1, 2, 5]
+file: setup_star_bh.c

docs/parameters/Diag.angle.yaml

@@ -0,0 +1,10 @@
+name: Diag.angle
+description: |
+  0=pole
+type: Double
+unit: None
+values: Condition e.g. greater than 0 or list e.g. [1, 2, 5]
+parent:
+  parameter: Condition e.g. greater than 0 or list e.g. [1, 2, 5]
+file: diag.c
+advanced: true

docs/parameters/Diag.invoke_searchlight_option.yaml

@@ -0,0 +1,8 @@
+name: Diag.invoke_searchlight_option
+description: |
+  Multi-line description, must keep indentation.
+type: Boolean (yes/no)
+parent:
+  parameter: Condition e.g. greater than 0 or list e.g. [1, 2, 5]
+file: diag.c
+advanced: true

docs/parameters/Diag.keep_ioncycle_spectra.yaml

@@ -0,0 +1,8 @@
+name: Diag.keep_ioncycle_spectra
+description: |
+  Multi-line description, must keep indentation.
+type: Boolean (yes/no)
+parent:
+  parameter: Condition e.g. greater than 0 or list e.g. [1, 2, 5]
+file: diag.c
+advanced: true

docs/parameters/Diag.location.yaml

@@ -0,0 +1,13 @@
+name: Diag.location
+description: |
+  Multi-line description, must keep indentation.
+type: Enumerator
+values:
+  central_object: |
+    Multi-line description, must keep indentation.
+  disk: |
+    Multi-line description, must keep indentation.
+parent:
+  parameter: Condition e.g. greater than 0 or list e.g. [1, 2, 5]
+file: diag.c
+advanced: true

docs/parameters/Diag.partial_cells.yaml

@@ -0,0 +1,15 @@
+name: Diag.partial_cells
+description: |
+  Multi-line description, must keep indentation.
+type: Enumerator
+values:
+  extend_full_cells: |
+    Multi-line description, must keep indentation.
+  include: |
+    Multi-line description, must keep indentation.
+  zero_densities: |
+    Multi-line description, must keep indentation.
+parent:
+  parameter: Condition e.g. greater than 0 or list e.g. [1, 2, 5]
+file: diag.c
+advanced: true

docs/parameters/Diag.r.yaml

@@ -0,0 +1,10 @@
+name: Diag.r
+description: |
+  Multi-line description, must keep indentation.
+type: Double
+unit: co.radius
+values: Condition e.g. greater than 0 or list e.g. [1, 2, 5]
+parent:
+  parameter: Condition e.g. greater than 0 or list e.g. [1, 2, 5]
+file: diag.c
+advanced: true

docs/parameters/Diag.use_jumps_for_emissivities_in_detailed_spectra.yaml

@@ -0,0 +1,8 @@
+name: Diag.use_jumps_for_emissivities_in_detailed_spectra
+description: |
+  Multi-line description, must keep indentation.
+type: Boolean (yes/no)
+parent:
+  parameter: Condition e.g. greater than 0 or list e.g. [1, 2, 5]
+file: diag.c
+advanced: true

docs/parameters/Diag.use_upweighting_of_simple_macro_atoms.yaml

@@ -0,0 +1,8 @@
+name: Diag.use_upweighting_of_simple_macro_atoms
+description: |
+  Multi-line description, must keep indentation.
+type: Boolean (yes/no)
+parent:
+  parameter: Condition e.g. greater than 0 or list e.g. [1, 2, 5]
+file: diag.c
+advanced: true

docs/parameters/Disk.colour_correction.yaml

@@ -0,0 +1,8 @@
+name: Disk.colour_correction
+description: |
+  Done12
+type: Enumerator
+values: Condition e.g. greater than 0 or list e.g. [1, 2, 5]
+parent:
+  parameter: Condition e.g. greater than 0 or list e.g. [1, 2, 5]
+file: setup_disk.c

docs/parameters/Disk.radmin.yaml

@@ -0,0 +1,9 @@
+name: Disk.radmin
+description: |
+  Multi-line description, must keep indentation.
+type: Double
+unit: cm
+values: Condition e.g. greater than 0 or list e.g. [1, 2, 5]
+parent:
+  parameter: Condition e.g. greater than 0 or list e.g. [1, 2, 5]
+file: setup_disk.c

docs/parameters/Matom_transition_mode.yaml

@@ -0,0 +1,12 @@
+name: Matom_transition_mode
+description: |
+  Multi-line description, must keep indentation.
+type: Enumerator
+values:
+  matrix: |
+    Multi-line description, must keep indentation.
+  mc_jumps: |
+    Multi-line description, must keep indentation.
+parent:
+  parameter: Condition e.g. greater than 0 or list e.g. [1, 2, 5]
+file: setup_line_transfer.c

docs/parameters/SV.gamma.yaml

@@ -0,0 +1,9 @@
+name: SV.gamma
+description: |
+  Multi-line description, must keep indentation.
+type: Double
+unit: Kelvin
+values: Condition e.g. greater than 0 or list e.g. [1, 2, 5]
+parent:
+  parameter: Condition e.g. greater than 0 or list e.g. [1, 2, 5]
+file: sv.c

docs/parameters/Spectrum.nwave.yaml

@@ -0,0 +1,9 @@
+name: Spectrum.nwave
+description: |
+  Multi-line description, must keep indentation.
+type: Integer
+unit: None
+values: Condition e.g. greater than 0 or list e.g. [1, 2, 5]
+parent:
+  parameter: Condition e.g. greater than 0 or list e.g. [1, 2, 5]
+file: setup.c

docs/parameters/monochromatic.wavelength.yaml

@@ -0,0 +1,9 @@
+name: monochromatic.wavelength
+description: |
+  Multi-line description, must keep indentation.
+type: Double
+unit: None
+values: Condition e.g. greater than 0 or list e.g. [1, 2, 5]
+parent:
+  parameter: Condition e.g. greater than 0 or list e.g. [1, 2, 5]
+file: setup.c

docs/parameters/old/Diag.turn_off_upweighting_of_simple_macro_atoms.yaml

@@ -0,0 +1,8 @@
+name: Diag.turn_off_upweighting_of_simple_macro_atoms
+description: |
+  Multi-line description, must keep indentation.
+type: Boolean (yes/no)
+parent:
+  parameter: Condition e.g. greater than 0 or list e.g. [1, 2, 5]
+file: diag.c
+advanced: true