Fix setuptools-scm integration (#167)

* Full checkout for packaging
* Don't hardcode version for sphinx builds
* Fix README
* Add contributing.rst to docs
* Fix link

Author: dweindl

.github/workflows/python-publish.yml

@@ -21,6 +21,9 @@ jobs:
 
     steps:
       - uses: actions/checkout@v4
+        with:
+          # Fetch full history for setuptools-scm
+          fetch-depth: 0
 
       - uses: actions/setup-python@v5
         with:
@@ -56,7 +59,8 @@ jobs:
       # ALTERNATIVE: if your GitHub Release name is the PyPI project version string
       # ALTERNATIVE: exactly, uncomment the following line instead:
       # url: https://pypi.org/project/YOURPROJECT/${{ github.event.release.name }}
-
+    env:
+      SETUPTOOLS_SCM_OVERRIDES_FOR_PETAB_GUI: '{"local_scheme": "no-local-version"}'
     steps:
       - name: Retrieve release distributions
         uses: actions/download-artifact@v4

.readthedocs.yaml

@@ -22,3 +22,10 @@ build:
   os: "ubuntu-24.04"
   tools:
     python: "3.11"
+  jobs:
+    post_checkout:
+      # Avoid setuptools-scm dirty Git index issues
+      - git reset --hard HEAD
+      - git clean -fdx
+      # Enforce fail_on_shallow for setuptools-scm
+      - export SETUPTOOLS_SCM_OVERRIDES_FOR_${READTHEDOCS_PROJECT//-/_}='{scm.git.pre_parse="fail_on_shallow"}'

README.md

@@ -21,7 +21,7 @@ pip install petab_gui
 To install the latest development version from GitHub, run:
 
 ```bash
-    pip3 install git+https://github.com/PaulJonasJost/PEtab_GUI/
+pip install git+https://github.com/PaulJonasJost/PEtab_GUI/
 ```
 
 ### From a local copy
@@ -52,7 +52,7 @@ The PEtabGUI provides a Python-based graphical user interface that simplifies
 the creation, editing, and validation of PEtab parameter estimation problems.
 
 - **Unified Environment**
-  - Integrates all PEtab components (SBML/PySB models, conditions, observables,
+  - Integrates all PEtab components (SBML models, conditions, observables,
     measurements, parameters, and visualization files).
   - Supports drag-and-drop import of YAML or individual component files.
   - Automatically resolves mismatches and converts matrix-format experimental data

docs/source/conf.py

@@ -2,6 +2,7 @@
 #
 # For the full list of built-in configuration values, see the documentation:
 # https://www.sphinx-doc.org/en/master/usage/configuration.html
+from importlib.metadata import version as get_version
 
 rst_prolog = """
 .. |petab_doc_url| replace:: https://petab.readthedocs.io/en/latest/index.html
@@ -13,7 +14,7 @@
 project = "PEtab GUI"
 copyright = "2025, Paul Jonas Jost, Frank T. Bergmann"
 author = "Paul Jonas Jost, Frank T. Bergmann"
-release = "0.1.3"
+release: str = get_version("petab-gui")
 
 # -- General configuration ---------------------------------------------------
 # https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration

docs/source/contributing.rst

@@ -42,7 +42,7 @@ Filing an Issue
 ----------------
 
 If you encounter any bugs or have feature requests, please file an issue on GitHub.
-[Open a new issue](https://github.com/PaulJonasJost/PEtab_GUI/issues/new/choose).
+`Open a new issue <https://github.com/PaulJonasJost/PEtab_GUI/issues/new/choose>`__.
 
 When filing an issue, provide as much detail as possible,
 including steps to reproduce the issue, expected behavior, and any relevant logs or screenshots.

docs/source/index.rst

@@ -55,3 +55,4 @@ To get started with PEtab GUI, check out the :doc:`installation instructions <re
    :caption: Development
 
    GitHub Repository <https://github.com/PaulJonasJost/PEtab_GUI>
+   contributing