More improvements to actions (#83)

* Define version number in pyproject.toml

* Add uv lockfile to gitignore

* Restructure package into src layout

* Make version numbers variables

* Fix publishing action

* Redefine optional dependency groups

* Update CLI docs to use new src layout

* Update to codecov-action v5

.github/workflows/ci.yml

@@ -13,10 +13,12 @@ jobs:
   test:
     name: Python ${{ matrix.python-version }} - ${{ matrix.os }}
     runs-on: ${{ matrix.os }}
+    env:
+      uv_version: "0.5.2"
     strategy:
       matrix:
         os: ["ubuntu-latest", "macos-latest"]
-        python-version: ['3.9', '3.12']
+        python-version: ["3.9", "3.12"]
       fail-fast: false
     steps:
       - uses: actions/checkout@v2
@@ -27,12 +29,12 @@ jobs:
       - name: Install uv
         uses: astral-sh/setup-uv@v3
         with:
-          version: "0.5.2"
+          version: ${{ env.uv_version }}
       - name: Install the project
-        run: uv sync --all-extras --dev --python ${{ matrix.python-version }}
+        run: uv sync --extra test --python ${{ matrix.python-version }}
       - name: Run tests
         run: uv run pytest --cov=e3fp --cov-report=xml
       - name: Upload coverage to Codecov
-        uses: codecov/codecov-action@v4
+        uses: codecov/codecov-action@v5
         with:
           fail_ci_if_error: false

.github/workflows/publish.yml

@@ -1,26 +1,34 @@
-name: Publish package to PyPI
+name: Publish
 
 on:
   release:
     types:
       - published
 
 jobs:
-  deploy:
+  build-test:
     runs-on: ubuntu-latest
+    env:
+      uv_version: "0.5.2"
+      python_version: "3.12"
     steps:
       - uses: actions/checkout@v2
-      - name: Set up Python
-        uses: actions/setup-python@v2
-        with:
-          python-version: 3
       - name: Install uv
         uses: astral-sh/setup-uv@v3
         with:
-          version: "0.5.2"
+          version: ${{ env.uv_version }}
       - name: Build the project
-        run: uv build --no-sources
+        run: uv build --no-sources --python ${{ env.python_version }}
+      - name: Sync only the test dependencies
+        run: uv sync --no-install-project --extra test
+      - name: Install and test source distribution
+        run: |
+          uv pip install dist/*.tar.gz
+          uv run --no-sync pytest
+          uv pip uninstall e3fp
+      - name: Install and test wheel
+        run: |
+          uv pip install dist/*.whl
+          uv run --no-sync pytest
       - name: Publish to PyPI
-        run: uv publish --username __token__ --password ${{ secrets.PYPI_API_TOKEN }}
-      - name: Test package installation
-        run: uv run --with e3fp --no-project -- python -c "import e3fp"
+        run: uv publish --token ${{ secrets.PYPI_API_TOKEN }}

.gitignore

@@ -7,4 +7,5 @@ doc/_build/*
 *egg*
 *.pyc
 *.so
-*.o
+*.o
+uv.lock

doc/source/install.rst

@@ -102,7 +102,7 @@ Option 3: Install from source
 
   .. code:: bash
 
-      $ uv sync --all-extras --dev
+      $ uv sync --extra dev
 
 Testing
 -------

doc/source/usage/cli.rst

@@ -13,7 +13,7 @@ Conformer Generation CLI
 
 To see all available options, run
 
-.. command-output:: python $E3FP_REPO/e3fp/conformer/generate.py --help
+.. command-output:: python $E3FP_REPO/src/e3fp/conformer/generate.py --help
    :shell:
 
 We will generate conformers for the molecule whose SMILES string is defined in
@@ -26,7 +26,7 @@ The below example generates at most 3 conformers for this molecule.
 
 .. code-block:: shell-session
 
-    $ python $E3FP_REPO/e3fp/conformer/generate.py -s caffeine.smi --num_conf 3 -o ./
+    $ python $E3FP_REPO/src/e3fp/conformer/generate.py -s caffeine.smi --num_conf 3 -o ./
     2017-07-17 00:11:05,743|WARNING|Only 1 processes available. 'mpi' mode not available.
     2017-07-17 00:11:05,748|INFO|num_proc is not specified. 'processes' mode will use all 8 processes
     2017-07-17 00:11:05,748|INFO|Parallelizer initialized with mode 'processes' and 8 processors.
@@ -54,14 +54,14 @@ Fingerprinting CLI
 
 To see all available options, run
 
-.. command-output:: python $E3FP_REPO/e3fp/fingerprint/generate.py --help
+.. command-output:: python $E3FP_REPO/src/e3fp/fingerprint/generate.py --help
    :shell:
 
 To continue the above example, we will fingerprint our caffeine conformers.
 
 .. code-block:: shell-session
 
-    $ python $E3FP_REPO/e3fp/fingerprint/generate.py caffeine.sdf.bz2 --bits 1024
+    $ python $E3FP_REPO/src/e3fp/fingerprint/generate.py caffeine.sdf.bz2 --bits 1024
     2017-07-17 00:12:33,797|WARNING|Only 1 processes available. 'mpi' mode not available.
     2017-07-17 00:12:33,801|INFO|num_proc is not specified. 'processes' mode will use all 8 processes
     2017-07-17 00:12:33,801|INFO|Parallelizer initialized with mode 'processes' and 8 processors.

pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "flit_core.buildapi"
 
 [project]
 name = "e3fp"
-dynamic = ["version"]
+version = "1.2.6"
 requires-python = ">=3.9, <3.13"
 description = "Molecular 3D fingerprinting"
 readme = "README.rst"
@@ -47,28 +47,23 @@ optional = [
 test = [
     "mock",
     "pytest",
-    "e3fp[optional]",
-]
-dev = [
-    "e3fp[test]",
     "pytest-cov",
+    "e3fp[optional]",
 ]
 docs = [
     "sphinx",
     "sphinxcontrib-programoutput",
     "sphinx-rtd-theme",
 ]
+dev = [
+    "e3fp[docs]",
+    "e3fp[test]",
+]
 
 [project.urls]
 Homepage = "https://github.com/keiserlab/e3fp"
 Download = "https://github.com/keiserlab/e3fp/tarball/{version}"
 
-[tool.setuptools.packages.find]
-include = ["e3fp", "e3fp.*"]
-
-[tool.setuptools.dynamic]
-version = {attr = "e3fp.version"}
-
 [tool.pytest.ini_options]
 addopts = "-ra -q"
 testpaths = ["e3fp/test"]

src/e3fp/__init__.py

@@ -0,0 +1,4 @@
+import importlib.metadata
+from .util import E3FPWarning, E3FPDeprecationWarning
+
+__version__ = importlib.metadata.version("e3fp")