pythonradex 2.0.0__tar.gz → 2.0.2__tar.gz

{pythonradex-2.0.0 → pythonradex-2.0.2}/.readthedocs.yaml

@@ -14,9 +14,12 @@ build:
 # Build documentation in the docs/ directory with Sphinx
 sphinx:
   configuration: docs/conf.py
+  fail_on_warning: true
 
 # We recommend specifying your dependencies to enable reproducible builds:
 # https://docs.readthedocs.io/en/stable/guides/reproducible-builds.html
 python:
-   install:
-   - requirements: docs/requirements.txt
+  install:
+    - method: pip
+      path: .
+    - requirements: docs/requirements.txt

{pythonradex-2.0.0 → pythonradex-2.0.2}/CITATION.cff

@@ -1,15 +1,17 @@
 cff-version: 1.2.0
 title: "pythonradex"
-version: 2.0.0
 license: "MIT"
 type: software
 repository-code: "https://github.com/gica3618/pythonradex"
 abstract: "pythonradex solves the 1D non-LTE radiative transfer for a homogeneous medium. It is a tool to quickly estimate the radiation from an astrophysical gas. It also provides a convenient function to read data files in the LAMDA format. pythonradex is a python re-implementation of the RADEX code, with additional functionality not included in RADEX (treatment of overlapping lines, treatment of dust continuum, output of spectra, and more)."
-message: "Please cite this software using the metadata from 'preferred-citation'."
+message: "If you use this software, please cite our article in the Journal of Open Source Software."
 authors:
   - given-names: Gianni
     family-names: Cataldi
-    affiliation: National Astronomical Observatory of Japan
+    orcid: "https://orcid.org/0000-0002-2700-9676"
+contact:
+  - family-names: Cataldi
+    given-names: Gianni
     orcid: "https://orcid.org/0000-0002-2700-9676"
 keywords:
   - python
@@ -19,3 +21,21 @@ keywords:
   - non-LTE
   - escape probability
   - line emission
+preferred-citation:
+  authors:
+  - family-names: Cataldi
+    given-names: Gianni
+    orcid: "https://orcid.org/0000-0002-2700-9676"
+  date-published: 2026-02-24
+  doi: 10.21105/joss.09233
+  issn: 2475-9066
+  issue: 118
+  journal: Journal of Open Source Software
+  publisher:
+    name: Open Journals
+  start: 9233
+  title: "pythonradex: a fast Python re-implementation of RADEX with
+    extended functionality"
+  type: article
+  url: "https://joss.theoj.org/papers/10.21105/joss.09233"
+  volume: 11

{pythonradex-2.0.0 → pythonradex-2.0.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: pythonradex
-Version: 2.0.0
+Version: 2.0.2
 Summary: 1D non-LTE radiative transfer
 Project-URL: Documentation, https://pythonradex.readthedocs.io/en/latest/
 Project-URL: Issues, https://github.com/gica3618/pythonradex/issues
@@ -27,16 +27,34 @@ Requires-Dist: nbsphinx; extra == 'dev'
 Requires-Dist: pandas; extra == 'dev'
 Requires-Dist: pytest; extra == 'dev'
 Requires-Dist: sphinx; extra == 'dev'
+Requires-Dist: sphinx-rtd-theme; extra == 'dev'
 Provides-Extra: notebooks
 Requires-Dist: jupyter; extra == 'notebooks'
 Requires-Dist: matplotlib; extra == 'notebooks'
 Requires-Dist: pandas; extra == 'notebooks'
-Description-Content-Type: text/plain
+Description-Content-Type: text/markdown
 
 pythonradex solves the 1D non-LTE radiative transfer for a homogeneous medium. It is a tool to quickly estimate the radiation from an astrophysical gas. It also provides a convenient function to read data files in the LAMDA format. pythonradex is a python re-implementation of the RADEX code, with additional functionality not included in RADEX (treatment of overlapping lines, treatment of dust continuum, output of spectra, and more).
 
 For more details, please refer to the documentation: http://pythonradex.readthedocs.io/
 
+If you use pythonradex in your research, please cite the following [JOSS article](https://doi.org/10.21105/joss.09233):
+
+```tex
+@article{pythonradex,
+    doi = {10.21105/joss.09233},
+    url = {https://doi.org/10.21105/joss.09233},
+    year = {2026},
+    publisher = {The Open Journal},
+    volume = {11},
+    number = {118},
+    pages = {9233},
+    author = {Cataldi, Gianni},
+    title = {pythonradex: a fast Python re-implementation of RADEX with extended functionality},
+    journal = {Journal of Open Source Software}
+}
+```
+
 For questions, bug reports, or feature suggestions, please open an issue on github.
 
 pythonradex is written and maintained by Gianni Cataldi.

pythonradex-2.0.0/README.txt → pythonradex-2.0.2/README.md

@@ -2,6 +2,23 @@ pythonradex solves the 1D non-LTE radiative transfer for a homogeneous medium. I
 
 For more details, please refer to the documentation: http://pythonradex.readthedocs.io/
 
+If you use pythonradex in your research, please cite the following [JOSS article](https://doi.org/10.21105/joss.09233):
+
+```tex
+@article{pythonradex,
+    doi = {10.21105/joss.09233},
+    url = {https://doi.org/10.21105/joss.09233},
+    year = {2026},
+    publisher = {The Open Journal},
+    volume = {11},
+    number = {118},
+    pages = {9233},
+    author = {Cataldi, Gianni},
+    title = {pythonradex: a fast Python re-implementation of RADEX with extended functionality},
+    journal = {Journal of Open Source Software}
+}
+```
+
 For questions, bug reports, or feature suggestions, please open an issue on github.
 
 pythonradex is written and maintained by Gianni Cataldi.

{pythonradex-2.0.0 → pythonradex-2.0.2}/docs/API.rst

@@ -8,7 +8,7 @@ The ``Source`` class
 The core of ``pyhonradex`` is the ``Source`` class which is used to solve the radiative transfer.
 
 .. autoclass:: pythonradex.radiative_transfer.Source
-    :members: __init__, update_parameters, solve_radiative_transfer, frequency_integrated_emission, tau, spectrum, emission_at_line_center, print_results 
+    :members: __init__, update_parameters, solve_radiative_transfer, frequency_integrated_emission, tau, spectrum, emission_at_line_center, print_results
 
 .. _read_LAMDA_API:
 

{pythonradex-2.0.0 → pythonradex-2.0.2}/docs/Makefile

@@ -3,7 +3,8 @@
 
 # You can set these variables from the command line, and also
 # from the environment for the first two.
-SPHINXOPTS    ?=
+# Gianni addition: added option "-W --keep-going -T" to turn warnings into errors
+SPHINXOPTS    ?= -W --keep-going -T
 SPHINXBUILD   ?= sphinx-build
 SOURCEDIR     = .
 BUILDDIR      = _build

pythonradex-2.0.2/docs/citation.rst

@@ -0,0 +1,18 @@
+Citation
+===================
+If you use ``pythonradex`` in your research, please cite the following `JOSS article <https://doi.org/10.21105/joss.09233>`__:
+
+.. code-block:: tex
+
+    @article{pythonradex,
+        doi = {10.21105/joss.09233},
+        url = {https://doi.org/10.21105/joss.09233},
+        year = {2026},
+        publisher = {The Open Journal},
+        volume = {11},
+        number = {118},
+        pages = {9233},
+        author = {Cataldi, Gianni},
+        title = {pythonradex: a fast Python re-implementation of RADEX with extended functionality},
+        journal = {Journal of Open Source Software}
+    } 

{pythonradex-2.0.0 → pythonradex-2.0.2}/docs/conf.py

@@ -4,21 +4,6 @@
 # list see the documentation:
 # https://www.sphinx-doc.org/en/master/usage/configuration.html
 
-# -- Path setup --------------------------------------------------------------
-
-# If extensions (or modules to document with autodoc) are in another directory,
-# add these directories to sys.path here. If the directory is relative to the
-# documentation root, use os.path.abspath to make it absolute, like shown here.
-#
-import os
-import sys
-
-sys.path.insert(0, os.path.abspath(".."))
-
-# Gianni:
-sys.path.append(os.path.abspath("../src"))
-
-
 # -- Project information -----------------------------------------------------
 
 project = "pythonradex"
@@ -61,7 +46,7 @@ html_theme = "sphinx_rtd_theme"
 # Add any paths that contain custom static files (such as style sheets) here,
 # relative to this directory. They are copied after the builtin static files,
 # so a file named "default.css" will overwrite the builtin "default.css".
-html_static_path = ["_static"]
+html_static_path = []
 
 # Gianni additions
 autodoc_member_order = "bysource"