pymrm 2.2.2__tar.gz → 2.2.3__tar.gz

{pymrm-2.2.2 → pymrm-2.2.3}/CITATION.cff

@@ -1,6 +1,6 @@
 cff-version: 1.2.0
 title: "pymrm: Python package for Multiphase Reactor Modeling"
-version: "2.2.1"
+version: "2.2.2"
 message: "If you use pymrm in your work, please cite the version you used."
 authors:
   - family-names: Peters

{pymrm-2.2.2 → pymrm-2.2.3}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: pymrm
-Version: 2.2.2
+Version: 2.2.3
 Summary: Functions for multiphase reactor modeling
 Author-email: "E.A.J.F. Peters" <e.a.j.f.peters@tue.nl>, "M. van Sint Annaland" <M.v.SintAnnaland@tue.nl>, "M. Galanti" <m.galanti@tue.nl>, "D.R. Rieder" <d.r.rieder@tue.nl>
 Maintainer-email: "E.A.J.F. Peters" <e.a.j.f.peters@tue.nl>
@@ -61,7 +61,7 @@ Dynamic: license-file
 [![Python](https://img.shields.io/pypi/pyversions/pymrm.svg)](https://pypi.org/project/pymrm/)
 [![License](https://img.shields.io/github/license/computational-chemical-engineering/pymrm)](https://github.com/computational-chemical-engineering/pymrm/blob/main/LICENSE)
 [![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black)
-[![DOI](https://zenodo.org/badge/901029258.svg)](https://zenodo.org/badge/latestdoi/901029258)
+[![DOI](https://zenodo.org/badge/latestdoi/901029258.svg)](https://zenodo.org/badge/latestdoi/901029258)
 
 
 ## Overview
@@ -99,4 +99,3 @@ coefficient matrices.
 ## Contributing
 
 Contributions are welcome! For suggestions or enhancements, please contact us or submit a pull request.
-

{pymrm-2.2.2 → pymrm-2.2.3}/README.md

@@ -5,7 +5,7 @@
 [![Python](https://img.shields.io/pypi/pyversions/pymrm.svg)](https://pypi.org/project/pymrm/)
 [![License](https://img.shields.io/github/license/computational-chemical-engineering/pymrm)](https://github.com/computational-chemical-engineering/pymrm/blob/main/LICENSE)
 [![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black)
-[![DOI](https://zenodo.org/badge/901029258.svg)](https://zenodo.org/badge/latestdoi/901029258)
+[![DOI](https://zenodo.org/badge/latestdoi/901029258.svg)](https://zenodo.org/badge/latestdoi/901029258)
 
 
 ## Overview
@@ -43,4 +43,3 @@ coefficient matrices.
 ## Contributing
 
 Contributions are welcome! For suggestions or enhancements, please contact us or submit a pull request.
-

{pymrm-2.2.2 → pymrm-2.2.3}/docs/compile_sphinx.md

@@ -55,11 +55,11 @@ language = 'en'
 html_theme = 'sphinx_rtd_theme'
 html_static_path = ['_static']
 ```
-Then run `sphinx-apidoc` in the root directory
-```bash
-sphinx-apidoc -o docs/sphinx src/pymrm/
-```
-Following that, at the generated modules.rst to the index.rst in the specified folder
+The API `*.rst` pages (`modules.rst` and `pymrm.rst`) are generated automatically by
+the Sphinx build configuration (`conf.py`) during `make html`, so they should not be
+manually generated or committed.
+
+Ensure `modules` is present in the `index.rst` toctree:
 ```bash
 .. toctree::
    :maxdepth: 2
@@ -72,4 +72,4 @@ Finally, you can invoke make to generate the documentation
 # here we are in the root folder of the package
 cd docs/sphinx
 make html
-```
+```

pymrm-2.2.3/docs/sphinx/.gitignore

@@ -0,0 +1,4 @@
+modules.rst
+pymrm.rst
+_build/
+documentation_errors.txt

{pymrm-2.2.2 → pymrm-2.2.3}/docs/sphinx/conf.py

@@ -8,6 +8,7 @@
 import os
 import sys
 from pathlib import Path
+from sphinx.ext.apidoc import main as apidoc_main
 sys.path.insert(0, os.path.abspath('../..'))    # this path should point at the root directory
 sys.path.insert(0, str(Path('../..', 'src').resolve()))  # patch so we don't need to install the repository for sphinx to work
 
@@ -43,3 +44,13 @@ language = 'en'
 
 html_theme = 'sphinx_rtd_theme'
 html_static_path = ['_static']
+
+
+def run_apidoc(_):
+    docs_dir = Path(__file__).resolve().parent
+    package_dir = docs_dir.parent.parent / 'src' / 'pymrm'
+    apidoc_main(['-f', '-o', str(docs_dir), str(package_dir)])
+
+
+def setup(app):
+    app.connect('builder-inited', run_apidoc)

{pymrm-2.2.2 → pymrm-2.2.3}/scripts/build_documentation.sh

@@ -5,16 +5,6 @@
 
 pip install myst-parser # workaround. Should be included in Docker image?
 pip install -e .
-sphinx-apidoc -f -o docs/sphinx src/pymrm
-if [[ "${CI}" == "true" ]]; then
-    api_rst_files=(docs/sphinx/pymrm.rst docs/sphinx/modules.rst)
-    if ! git diff --quiet HEAD -- "${api_rst_files[@]}"; then
-        echo "Detected outdated autogenerated Sphinx API files:"
-        git --no-pager diff HEAD -- "${api_rst_files[@]}"
-        echo "Run 'sphinx-apidoc -f -o docs/sphinx src/pymrm' and commit the updated rst files."
-        exit 1
-    fi
-fi
 cd docs/sphinx
 mkdir -p _static
 make html 2>documentation_errors.txt

{pymrm-2.2.2 → pymrm-2.2.3}/src/pymrm/_version.py

@@ -18,7 +18,7 @@ version_tuple: tuple[int | str, ...]
 commit_id: str | None
 __commit_id__: str | None
 
-__version__ = version = '2.2.2'
-__version_tuple__ = version_tuple = (2, 2, 2)
+__version__ = version = '2.2.3'
+__version_tuple__ = version_tuple = (2, 2, 3)
 
-__commit_id__ = commit_id = 'g471977efe'
+__commit_id__ = commit_id = 'geb01e7e3c'

{pymrm-2.2.2 → pymrm-2.2.3}/src/pymrm.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: pymrm
-Version: 2.2.2
+Version: 2.2.3
 Summary: Functions for multiphase reactor modeling
 Author-email: "E.A.J.F. Peters" <e.a.j.f.peters@tue.nl>, "M. van Sint Annaland" <M.v.SintAnnaland@tue.nl>, "M. Galanti" <m.galanti@tue.nl>, "D.R. Rieder" <d.r.rieder@tue.nl>
 Maintainer-email: "E.A.J.F. Peters" <e.a.j.f.peters@tue.nl>
@@ -61,7 +61,7 @@ Dynamic: license-file
 [![Python](https://img.shields.io/pypi/pyversions/pymrm.svg)](https://pypi.org/project/pymrm/)
 [![License](https://img.shields.io/github/license/computational-chemical-engineering/pymrm)](https://github.com/computational-chemical-engineering/pymrm/blob/main/LICENSE)
 [![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black)
-[![DOI](https://zenodo.org/badge/901029258.svg)](https://zenodo.org/badge/latestdoi/901029258)
+[![DOI](https://zenodo.org/badge/latestdoi/901029258.svg)](https://zenodo.org/badge/latestdoi/901029258)
 
 
 ## Overview
@@ -99,4 +99,3 @@ coefficient matrices.
 ## Contributing
 
 Contributions are welcome! For suggestions or enhancements, please contact us or submit a pull request.
-

{pymrm-2.2.2 → pymrm-2.2.3}/src/pymrm.egg-info/SOURCES.txt

@@ -24,12 +24,11 @@ docs/compile_sphinx.md
 docs/dependencies_format.md
 docs/helpers.md
 docs/installation.md
+docs/sphinx/.gitignore
 docs/sphinx/Makefile
 docs/sphinx/conf.py
 docs/sphinx/index.rst
 docs/sphinx/make.bat
-docs/sphinx/modules.rst
-docs/sphinx/pymrm.rst
 examples/counter_current_reaction.ipynb
 examples/counter_diffusion_reaction.ipynb
 examples/darcy_flow.ipynb

pymrm-2.2.2/docs/sphinx/modules.rst

@@ -1,7 +0,0 @@
-pymrm
-=====
-
-.. toctree::
-   :maxdepth: 4
-
-   pymrm

pymrm-2.2.2/docs/sphinx/pymrm.rst

@@ -1,77 +0,0 @@
-pymrm package
-=============
-
-Submodules
-----------
-
-pymrm.convect module
---------------------
-
-.. automodule:: pymrm.convect
-   :members:
-   :show-inheritance:
-   :undoc-members:
-
-pymrm.coupling module
----------------------
-
-.. automodule:: pymrm.coupling
-   :members:
-   :show-inheritance:
-   :undoc-members:
-
-pymrm.grid module
------------------
-
-.. automodule:: pymrm.grid
-   :members:
-   :show-inheritance:
-   :undoc-members:
-
-pymrm.helpers module
---------------------
-
-.. automodule:: pymrm.helpers
-   :members:
-   :show-inheritance:
-   :undoc-members:
-
-pymrm.interpolate module
-------------------------
-
-.. automodule:: pymrm.interpolate
-   :members:
-   :show-inheritance:
-   :undoc-members:
-
-pymrm.numjac module
--------------------
-
-.. automodule:: pymrm.numjac
-   :members:
-   :show-inheritance:
-   :undoc-members:
-
-pymrm.operators module
-----------------------
-
-.. automodule:: pymrm.operators
-   :members:
-   :show-inheritance:
-   :undoc-members:
-
-pymrm.solve module
-------------------
-
-.. automodule:: pymrm.solve
-   :members:
-   :show-inheritance:
-   :undoc-members:
-
-Module contents
----------------
-
-.. automodule:: pymrm
-   :members:
-   :show-inheritance:
-   :undoc-members: