Automatic distribution to PyPI and TestPyPI

.github/workflows/deploy.yml

@@ -0,0 +1,102 @@
+name: Publish to PyPI and TestPyPI
+
+on: push
+
+jobs:
+  build:
+    name: Build Distribution
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - name: Get history and tags for SCM versioning to work
+        if: ${{ !startsWith(github.ref, 'refs/tags/') }}
+        run: |
+          git fetch --prune --unshallow
+          git tag -d $(git tag --points-at HEAD)
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.x"
+      - name: Install pypa/build
+        run: pip install build --user
+      - name: Build a binary wheel and a source tarball
+        run: python3 -m build
+      - name: Store the distribution packages
+        uses: actions/upload-artifact@v4
+        with:
+          name: python-package-distributions
+          path: dist/
+
+  publish-to-pypi:
+    name: Publish to PyPI
+    if: startsWith(github.ref, 'refs/tags/') # only publish to PyPI on tag pushes
+    needs: [build]
+    runs-on: ubuntu-latest
+    environment:
+      name: pypi
+      url: https://pypi.org/p/TopoEmbedX
+    permissions:
+      id-token: write
+
+    steps:
+      - name: Download all the dists
+        uses: actions/download-artifact@v4
+        with:
+          name: python-package-distributions
+          path: dist/
+      - name: Publish distribution 📦 to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1
+
+  github-release:
+    name: Sign and Upload as GitHub Release
+    needs: [publish-to-pypi]
+    runs-on: ubuntu-latest
+
+    permissions:
+      contents: write
+      id-token: write
+
+    steps:
+      - name: Download all the dists
+        uses: actions/download-artifact@v4
+        with:
+          name: python-package-distributions
+          path: dist/
+      - name: Sign the dists with Sigstore
+        uses: sigstore/[email protected]
+        with:
+          inputs: >-
+            ./dist/*.tar.gz
+            ./dist/*.whl
+      - name: Create GitHub Release
+        env:
+          GITHUB_TOKEN: ${{ github.token }}
+        run: gh release create '${{ github.ref_name }}' --repo '${{ github.repository }}' --notes ""
+      - name: Upload artifact signatures to GitHub Release
+        env:
+          GITHUB_TOKEN: ${{ github.token }}
+        run: gh release upload '${{ github.ref_name }}' dist/** --repo '${{ github.repository }}'
+
+  publish-to-testpypi:
+    name: Publish to TestPyPI
+    if: ${{ github.event_name == 'push' && github.ref == 'refs/heads/main' }}
+    needs: [build]
+    runs-on: ubuntu-latest
+
+    environment:
+      name: testpypi
+      url: https://test.pypi.org/p/TopoEmbedX
+
+    permissions:
+      id-token: write
+
+    steps:
+      - name: Download all the dists
+        uses: actions/download-artifact@v4
+        with:
+          name: python-package-distributions
+          path: dist/
+      - name: Publish distribution 📦 to TestPyPI
+        uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          repository-url: https://test.pypi.org/legacy/

.gitignore

@@ -14,5 +14,10 @@ coverage.xml
 **/*.cpython-38.pyc
 **/__pycache__/**
 __pycache__/
+dist/
 docs/build/
-toponetx/.DS_Store
+topoembedx/.DS_Store
+topoembedx/_version.py
+
+# Sphinx documentation
+docs/_build/

pyproject.toml

@@ -1,27 +1,32 @@
 [build-system]
-requires = ["setuptools"]
+requires = ["setuptools>=64.0", "setuptools_scm>=8"]
 build-backend = "setuptools.build_meta"
 
 [project]
 name = "TopoEmbedX"
 dynamic = ["version"]
 authors = [
-    {name = "PyT-Team Authors", email = "[email protected]"}
+    {name = "Mustafa Hajij", email = "[email protected]"},
+    {name = "Mathilde Papillon", email = "[email protected]"},
+    {name = "Florian Frantzen", email = "[email protected]"}
 ]
 readme = "README.md"
 description = "Representation Learning on Topological Domains"
 license = {file = "LICENSE.txt"}
 classifiers = [
-    "License :: OSI Approved :: MIT License",
-    "Development Status :: 4 - Beta",
+    "Development Status :: 3 - Alpha",
+    "Intended Audience :: Developers",
     "Intended Audience :: Science/Research",
+    "Operating System :: OS Independent",
+    "License :: OSI Approved :: MIT License",
+    "Programming Language :: Python :: 3",
+    "Programming Language :: Python :: 3 :: Only",
+    "Programming Language :: Python :: 3.10",
+    "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.12",
     "Topic :: Scientific/Engineering",
     "Topic :: Scientific/Engineering :: Mathematics",
     "Topic :: Scientific/Engineering :: Artificial Intelligence",
-    "Natural Language :: English",
-    "Programming Language :: Python :: 3",
-    "Programming Language :: Python :: 3.10",
-    "Programming Language :: Python :: 3.11"
 ]
 requires-python = ">= 3.10"
 dependencies=[
@@ -60,11 +65,8 @@ dev = ["TopoEmbedX[test, lint]"]
 all = ["TopoEmbedX[dev, doc]"]
 
 [project.urls]
-homepage="https://github.com/pyt-team/TopoEmbedX"
-repository="https://github.com/pyt-team/TopoEmbedX"
-
-[tool.ruff]
-extend-include = ["*.ipynb"]
+documentation="https://pyt-team.github.io/topoembedx/"
+source="https://github.com/pyt-team/TopoEmbedX/"
 
 [tool.ruff.format]
 docstring-code-format = true
@@ -93,19 +95,18 @@ ignore = ["E501"] # line too long
 [tool.ruff.lint.pydocstyle]
 convention = "numpy"
 
-[tool.setuptools.dynamic]
-version = {attr = "topoembedx.__version__"}
-
 [tool.setuptools.packages.find]
-include = [
-    "topoembedx",
-    "topoembedx.*"
-]
+include = ["topoembedx"]
+
+[tool.setuptools_scm]
+local_scheme = "no-local-version"
+version_file = "topoembedx/_version.py"
 
 [tool.mypy]
 warn_redundant_casts = true
+warn_unreachable = true
 warn_unused_ignores = true
-show_error_codes = true
+enable_error_code = ["ignore-without-code", "redundant-expr", "truthy-bool"]
 disable_error_code = ["import-untyped"]
 plugins = "numpy.typing.mypy_plugin"
 

topoembedx/__init__.py

@@ -1,5 +1,4 @@
 """Initialize the library with modules and other content."""
-__version__ = "0.0.1"
 
 from .classes.cell2vec import Cell2Vec
 from .classes.cell_diff2vec import CellDiff2Vec