pymrm 2.2.1__tar.gz → 2.2.3__tar.gz

{pymrm-2.2.1 → pymrm-2.2.3}/.github/workflows/build.yml

@@ -23,3 +23,16 @@ jobs:
 
     - name: Test Install
       run: python -m pip install .
+
+  documentation:
+    runs-on: ubuntu-latest
+    container:
+      image: python:3.10
+
+    steps:
+    - uses: actions/checkout@v4
+    - name: Configure git safe.directory for container
+      run: git config --global --add safe.directory "$GITHUB_WORKSPACE"
+
+    - name: Build documentation (with apidoc regeneration)
+      run: scripts/build_documentation.sh

{pymrm-2.2.1 → pymrm-2.2.3}/CITATION.cff

@@ -1,6 +1,6 @@
 cff-version: 1.2.0
 title: "pymrm: Python package for Multiphase Reactor Modeling"
-version: "2.2.0"
+version: "2.2.2"
 message: "If you use pymrm in your work, please cite the version you used."
 authors:
   - family-names: Peters
@@ -9,7 +9,7 @@ authors:
   - family-names: van Sint Annaland
     given-names: M.
     orcid: "https://orcid.org/0000-0002-2903-7443"
-date-released: "2026-03-24"
+date-released: "2026-04-17"
 identifiers:
   - type: doi
     value: 10.5281/zenodo.17065798

{pymrm-2.2.1 → pymrm-2.2.3}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: pymrm
-Version: 2.2.1
+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-2.2.1 → 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-2.2.1 → 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-2.2.1 → pymrm-2.2.3}/docs/installation.md

@@ -82,7 +82,7 @@ PyMRM is available on PyPI and includes all necessary dependencies.
 ## Verifying the Installation
 
 1. **Test the Installation**:
-   - Navigate to the `examples` folder in the PyMRM repository or download example notebooks from the [PyMRM documentation](https://multiscale-modelling-multiphase-flows.github.io/pymrm-book).
+   - Navigate to the `examples` folder in the PyMRM repository or download example notebooks from the [PyMRM documentation](https://computational-chemical-engineering.github.io/pymrm-book).
    - Open a notebook in VS Code or Jupyter Notebook and execute the cells to verify that PyMRM and its dependencies are working correctly.
 
 2. **Optional: Test in Spyder**:
@@ -94,4 +94,4 @@ PyMRM is available on PyPI and includes all necessary dependencies.
 
 ## Conclusion
 
-You have successfully set up your environment for using PyMRM. Whether you use VS Code or Spyder, you are now ready to start modeling multiphase reactors. For further guidance, refer to the [PyMRM documentation](https://multiscale-modelling-multiphase-flows.github.io/pymrm-book).
+You have successfully set up your environment for using PyMRM. Whether you use VS Code or Spyder, you are now ready to start modeling multiphase reactors. For further guidance, refer to the [PyMRM documentation](https://computational-chemical-engineering.github.io/pymrm-book).

pymrm-2.2.3/docs/sphinx/.gitignore

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

{pymrm-2.2.1 → 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-2.2.1 → 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 = '2.2.1'
-__version_tuple__ = version_tuple = (2, 2, 1)
+__version__ = version = '2.2.3'
+__version_tuple__ = version_tuple = (2, 2, 3)
 
-__commit_id__ = commit_id = 'g2edc02389'
+__commit_id__ = commit_id = 'geb01e7e3c'

{pymrm-2.2.1 → pymrm-2.2.3}/src/pymrm.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: pymrm
-Version: 2.2.1
+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-2.2.1 → 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-2.2.1 → pymrm-2.2.3}/tutorials/introduction_and_start.ipynb

@@ -73,7 +73,7 @@
    "source": [
     "## Tutorials\n",
     "\n",
-    "This collection of tutorials is designed to familiarize you with the basic building blocks of `PyMRM` and some of its advanced features. The full API documentation is available at [PyMRM Documentation](https://multiscale-modelling-multiphase-flows.github.io/pymrm-book/content/api/index.html).\n",
+    "This collection of tutorials is designed to familiarize you with the basic building blocks of `PyMRM` and some of its advanced features. The full API documentation is available at [PyMRM Documentation](https://computational-chemical-engineering.github.io/pymrm-book/content/api/index.html).\n",
     "\n",
     "Below is an outline of the available tutorials:\n",
     "\n",

pymrm-2.2.1/docs/sphinx/modules.rst

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

pymrm-2.2.1/docs/sphinx/pymrm.rst

@@ -1,66 +0,0 @@
-Submodules
-==========
-
-pymrm.convect module
---------------------
-
-.. automodule:: pymrm.convect
-   :members:
-   :undoc-members:
-   :show-inheritance:
-
-pymrm.grid module
------------------
-
-.. automodule:: pymrm.grid
-   :members:
-   :undoc-members:
-   :show-inheritance:
-
-pymrm.helpers module
---------------------
-
-.. automodule:: pymrm.helpers
-   :members:
-   :undoc-members:
-   :show-inheritance:
-
-pymrm.interpolate module
-------------------------
-
-.. automodule:: pymrm.interpolate
-   :members:
-   :undoc-members:
-   :show-inheritance:
-
-pymrm.numjac module
--------------------
-
-.. automodule:: pymrm.numjac
-   :members:
-   :undoc-members:
-   :show-inheritance:
-
-pymrm.operators module
-----------------------
-
-.. automodule:: pymrm.operators
-   :members:
-   :undoc-members:
-   :show-inheritance:
-
-pymrm.solve module
-------------------
-
-.. automodule:: pymrm.solve
-   :members:
-   :undoc-members:
-   :show-inheritance:
-
-Module contents
----------------
-
-.. automodule:: pymrm
-   :members:
-   :undoc-members:
-   :show-inheritance: