Modernize packaging and CI (#81)

* Move all setup metadata to pyproject.toml

* Restructure workflow to use uv

* Use pyproject.toml as cache key

* Use setup-uv's own cache handling

* Use strings for Python versions

* Specify that UV uses system python

* Specify specific patch version of 3.6

* Test against 3.7

* Use uv pip install of sync

* Revert back to specifying latest Python without x

* Specify system python in each step

* Revert "Specify system python in each step"

This reverts commit 752a640.

* Revert "Use uv pip install of sync"

This reverts commit 67eb8bf.

* Use UV to install Python

* Specify a requires-python entry

* Test against 3.7

* Test against Python 3.8

* Test against Python 3.9

* Work-around llvm installation issues for numba dependency

* Install openmpi on ubuntu

* Specify dev dependencies

* Set-up mpi to make sure mpi4py can install

* Pin numba instead of llvm

* Reorder dependencies

* Drop support for Python 3.6 and 3.7, add support for 3.11 and 3.12

* Test specifically on Python 3.12

* Add six as optional dependency

* Set up Python while synching

* Make compatible with higher patch versions of 3.12

* Bump numba bound

* Require Python 3.9

* Use importlib to get e3fp version

* Use uv also to build the docs

* Remove conda environment files

* Fix outdated doctest

* Run pytest verbosely

* Set RDMAV_FORK_SAFE

* Update installation instructions

* Build docs from the correct source dir

* Revert "Run pytest verbosely"

This reverts commit 0838e20.

* Explicitly request XML coverage report

* Remove setup.py

* Use UV for building and publishing to PyPI

* Switch from setuptools to flit

* Setup uv the same for both actions

.github/workflows/ci.yml

@@ -4,46 +4,35 @@ on:
     branches: [master]
   pull_request:
 
+env:
+  # Setting RDMAV_FORK_SAFE=1 to avoid libfabric EFA provider issues with
+  # fork() on Python 3.9 and Ubuntu.
+  RDMAV_FORK_SAFE: 1
+
 jobs:
   test:
     name: Python ${{ matrix.python-version }} - ${{ matrix.os }}
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
         os: ["ubuntu-latest", "macos-latest"]
-        python-version: [3.6, 3]
+        python-version: ['3.9', '3.12']
       fail-fast: false
     steps:
       - uses: actions/checkout@v2
         with:
           fetch-depth: 2
-      - name: Cache conda packages
-        uses: actions/cache@v1
-        env:
-          # Increase this value to reset cache if environment.yml has not changed
-          CACHE_NUMBER: 0
-        with:
-          path: ~/conda_pkgs_dir
-          key: Python${{ matrix.python-version }}-${{ matrix.os }}-${{ hashFiles('environment.yml') }}
-      - name: Set-up conda and install dependencies
-        uses: conda-incubator/setup-miniconda@v2
+      - name: Setup MPI
+        uses: mpi4py/setup-mpi@v1
+      - name: Install uv
+        uses: astral-sh/setup-uv@v3
         with:
-          python-version: ${{ matrix.python-version }}
-          auto-update-conda: true
-          environment-file: environment.yml
-          activate-environment: test_env
-          use-only-tar-bz2: true # IMPORTANT: This needs to be set for caching to work properly!
-      - name: Build package
-        shell: bash -l {0}
-        run: |
-            python setup.py build_ext --inplace
-            python setup.py install
+          version: "0.5.2"
+      - name: Install the project
+        run: uv sync --all-extras --dev --python ${{ matrix.python-version }}
       - name: Run tests
-        shell: bash -l {0}
-        run: |
-            conda install -c conda-forge pytest pytest-cov mock
-            pytest --cov=e3fp --cov-report=xml e3fp
+        run: uv run pytest --cov=e3fp --cov-report=xml
       - name: Upload coverage to Codecov
-        uses: codecov/codecov-action@v1
+        uses: codecov/codecov-action@v4
         with:
           fail_ci_if_error: false

.github/workflows/publish.yml

@@ -9,27 +9,18 @@ jobs:
   deploy:
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v2
-    - name: Set up Python
-      uses: actions/setup-python@v2
-      with:
-        python-version: 3
-    - name: Install build dependencies
-      run: |
-        python -m pip install --upgrade pip
-        python -m pip install setuptools wheel
-    - name: Build wheel
-      run: |
-        python setup.py sdist bdist_wheel
-    - name: Test wheel
-      run: |
-        mkdir install_test
-        cd install_test
-        python -m pip install ../dist/*.whl
-        python -c "import e3fp"
-        cd ..
-    - name: Upload to PyPI
-      uses: pypa/gh-action-pypi-publish@master
-      with:
-        user: __token__
-        password: ${{ secrets.PYPI_API_TOKEN }}
+      - 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"
+      - name: Build the project
+        run: uv build --no-sources
+      - 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"

.readthedocs.yml

@@ -1,4 +1,12 @@
-conda:
-  file: doc/environment.yml
-python:
-  setup_py_install: true
+version: 2
+
+build:
+  os: "ubuntu-22.04"
+  tools:
+    python: "3.12"
+  commands:
+    - asdf plugin add uv
+    - asdf install uv latest
+    - asdf global uv latest
+    - uv sync --extra docs --frozen
+    - uv run -m sphinx -T -b html -d docs/_build/doctrees -D language=en doc/source $READTHEDOCS_OUTPUT/html

doc/source/conf.py

@@ -16,6 +16,7 @@
 # add these directories to sys.path here. If the directory is relative to the
 # documentation root, use os.path.abspath to make it absolute, like shown here.
 #
+import importlib.metadata
 import os
 import sys
 
@@ -24,7 +25,7 @@
 if not ON_RTD:
     sys.path.insert(0, os.path.abspath('../../'))
 
-from e3fp import __version__ as e3fp_version
+e3fp_version = importlib.metadata.version('e3fp')
 
 USE_DEFAULT_THEME = ON_RTD
 try:

doc/source/install.rst

@@ -38,89 +38,80 @@ The following packages are required for the specified features:
 
   + h5py_
 
+- faster fingerprint metric calculations:
+
+  + numba_
+
 
 Installation
 ------------
 
 The following installation approaches are listed in order of recommendation.
-All but the first of these approaches requires a prior installation of RDKit_.
-
-Option 1: Install with Conda
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-
-E3FP is on the `Anaconda distribution`_. Conda is a cross-platform package
-manager. This approach is highly recommended as it installs *all* required
-packages.
-
-1. Install with
 
-   .. code:: bash
+Option 1: Install with Pip
+~~~~~~~~~~~~~~~~~~~~~~~~~~
 
-       $ conda create -c conda-forge --name e3fp_env e3fp
-       $ conda activate e3fp_env
+Basic installation:
 
-2. To install the optional Python dependencies, run
+.. code:: bash
 
-   .. code:: bash
+    $ pip install e3fp
 
-       $ conda install -c conda-forge mpi4py h5py standardiser
+With optional dependencies:
 
-To get the latest version of E3FP, follow :ref:`Option 3: Clone the Repository`.
+.. code:: bash
 
-Option 2: Install with Pip
-~~~~~~~~~~~~~~~~~~~~~~~~~~
+    $ pip install e3fp[optional]
 
-1. Install with
 
-   .. code:: bash
+Option 2: Install from conda-forge
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
-       $ pip install e3fp
+E3FP is available on conda-forge.
 
-2. To install the optional Python dependencies, run
+.. code:: bash
 
-   .. code:: bash
+    $ conda create -n e3fp_env -c conda-forge e3fp
+    $ conda activate e3fp_env
 
-       $ pip install mpi4py h5py standardiser
+To install optional dependencies:
 
-Option 3: Clone the Repository
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.. code:: bash
 
-1. Download this repository to your machine.
+    $ conda install -c conda-forge mpi4py h5py standardiser
 
-   -  Clone this repository to your machine with
+Option 3: Install for development
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
-      .. code:: bash
+1. Clone the repository:
 
-          $ git clone https://github.com/keiserlab/e3fp.git
-          $ cd e3fp
+   .. code:: bash
 
-   -  OR download an archive by navigating to the repository_ and clicking
-      "Download ZIP". Extract the archive.
+      $ git clone https://github.com/keiserlab/e3fp.git
+      $ cd e3fp
 
-2. Install the optional dependencies and any required ones using pip or conda.
+2. Install for development in an already-activated environment.
 
-  .. note:: The easiest way to install the dependencies is with
+   You can do this using pip:
 
-    .. code:: bash
+   .. code:: bash
 
-        $ conda env create --name e3fp_env --file environment.yml
-        $ conda activate e3fp_env
+      $ pip install -e .[dev]
 
-3. Install with
+  Or use uv_ to set up a development environment:
 
-   .. code:: bash
+  .. code:: bash
 
-       $ python setup.py build_ext --inplace
-       $ python setup.py install
+      $ uv sync --all-extras --dev
 
 Testing
 -------
 
-After installation, it is recommended to run all tests with ``pytest``.
-After running :code:`pip install pytest` or :code:`conda install -c conda-forge pytest`, run
+Run tests using pytest:
 
 .. code:: bash
 
+    $ pip install pytest  # if not already installed
     $ pytest e3fp
 
 

doc/source/substitutions.rst

@@ -11,8 +11,9 @@
 .. _standardiser: https://wwwdev.ebi.ac.uk/chembl/extra/francis/standardiser
 .. _cxcalc: https://docs.chemaxon.com/display/CALCPLUGS/cxcalc+command+line+tool
 .. _h5py: http://www.h5py.org/
-.. _Anaconda distribution: https://docs.continuum.io/anaconda
+.. _numba: https://numba.pydata.org/
 .. _Anaconda: https://anaconda.org/conda-forge/e3fp
+.. _uv: https://docs.astral.sh/uv/
 .. _repository: https://github.com/keiserlab/e3fp
 .. _paper repository: https://github.com/keiserlab/e3fp-paper
 .. _issue tracker: https://github.com/keiserlab/e3fp/issues

e3fp/fingerprint/db.py

@@ -106,8 +106,8 @@ class FingerprintDatabase(object):
     Alternatively, the underlying `scipy.sparse.csr_matrix` may be accessed.
 
     >>> db.array
-    <Compressed Sparse Row sparse matrix of dtype 'bool'
-    ...with 327 stored elements and shape (3, 1024)>
+    <3x1024 sparse matrix of type '<class 'numpy.bool'>'
+    ...with 327 stored elements in Compressed Sparse Row format>
     >>> db.array.toarray()
     array([[False, False, False, ..., False, False, False],
            [False, False, False, ..., False, False, False],

pyproject.toml

@@ -1,2 +1,77 @@
 [build-system]
-requires = ["setuptools", "wheel"]
+requires = ["flit_core >=3.2,<4"]
+build-backend = "flit_core.buildapi"
+
+[project]
+name = "e3fp"
+dynamic = ["version"]
+requires-python = ">=3.9, <3.13"
+description = "Molecular 3D fingerprinting"
+readme = "README.rst"
+authors = [
+    {name = "Seth Axen", email = "seth.axen@gmail.com"},
+]
+license = {text = "LGPLv3"}
+keywords = ["e3fp", "3d", "molecule", "fingerprint", "conformer"]
+classifiers = [
+    "Programming Language :: Python",
+    "Programming Language :: Python :: 3.9",
+    "Programming Language :: Python :: 3.10",
+    "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.12",
+    "License :: OSI Approved :: GNU Lesser General Public License v3 (LGPLv3)",
+    "Operating System :: OS Independent",
+    "Development Status :: 4 - Beta",
+    "Intended Audience :: Science/Research",
+    "Intended Audience :: Developers",
+    "Topic :: Scientific/Engineering :: Chemistry",
+    "Topic :: Software Development :: Libraries :: Python Modules",
+]
+dependencies = [
+    "mmh3>=2.3.1",
+    "numpy>=1.11.3",
+    "rdkit>=2016.03.4",
+    "scipy>=0.18.0",
+    "sdaxen_python_utilities>=0.1.5",
+    "smart_open>=1.8.3",
+]
+
+[project.optional-dependencies]
+optional = [
+    "h5py",
+    "mpi4py",
+    "numba",
+    "six", # needed by standardiser, but not listed as a dependency
+    "standardiser",
+]
+test = [
+    "mock",
+    "pytest",
+    "e3fp[optional]",
+]
+dev = [
+    "e3fp[test]",
+    "pytest-cov",
+]
+docs = [
+    "sphinx",
+    "sphinxcontrib-programoutput"
+]
+
+[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"]
+
+# https://github.com/astral-sh/uv/issues/6281
+[tool.uv]
+constraint-dependencies = ["numba>=0.60.0"]