Fix inclusion of tests in source dist (#188)

* fix: tests inclusion in source dist
* docs: increase build timeout limit
* feat: PROLIF_N_JOBS env var
* chore: formatting and linting
* bump version

.github/workflows/ci.yml

@@ -23,106 +23,126 @@ jobs:
     # only run once if internal PR
     if: github.event_name == 'push' || github.event.pull_request.head.repo.full_name != github.repository
     strategy:
-        matrix:
-          include:
+      matrix:
+        include:
           - label: earliest
             os: ubuntu-latest
             python-version: 3.8
             rdkit-version: "rdkit=2021.03.1"
             coverage: false
           - label: baseline
             os: ubuntu-latest
-            python-version: 3.9
+            python-version: "3.10"
             rdkit-version: "rdkit~=2022.09"
             coverage: true
           - label: latest
             os: ubuntu-latest
-            python-version: "3.10"
+            python-version: "3.12"
             rdkit-version: "rdkit"
             coverage: false
 
     steps:
-    - uses: actions/checkout@v4
-
-    - name: Setup Conda
-      uses: conda-incubator/setup-miniconda@v2
-      with:
-        python-version: ${{ matrix.python-version }}
-        auto-update-conda: true
-        channel-priority: flexible
-        channels: conda-forge, defaults
-        add-pip-as-python-dependency: true
-        architecture: x64
-        use-mamba: true
-        miniforge-variant: Mambaforge
-
-    - name: Check conda and pip
-      run: |
-        which python
-        python --version
-        pip --version
-        conda --version
-        mamba --version
-
-    - name: Install conda dependencies
-      run: |
-        mamba install ${{ matrix.rdkit-version }}
-        mamba list
-
-    - name: Install package through pip
-      run: |
-        pip install .[dev]
-        pip list
-
-    - name: Run tests
-      run: |
-        pytest --color=yes --disable-pytest-warnings --cov=prolif --cov-report=xml tests/
-
-    - name: Measure tests coverage
-      if: matrix.coverage
-      uses: codecov/codecov-action@v3
-      with:
-        files: ./coverage.xml
-        fail_ci_if_error: true
-        verbose: true
-        token: ${{ secrets.CODECOV_TOKEN }}
-
-    - name: Build
-      run: |
-        python -m build
-
-    - name: Remove previous ProLIF install
-      run: |
-        pip uninstall -y prolif
-
-    - name: Install from tar.gz
-      run: |
-        pip install dist/prolif-*.tar.gz
-
-    - name: Test tar.gz install
-      run: |
-        python <<EOF
-        import prolif
-        import os
-        print(prolif.__version__)
-        from prolif.plotting.network import LigNetwork
-        assert os.path.isfile(prolif.datafiles.TOP)
-        EOF
-
-    - name: Remove previous ProLIF install
-      run: |
-        pip uninstall -y prolif
-
-    - name: Install from wheel
-      run: |
-        pip install dist/prolif-*.whl
-
-    - name: Test wheel install
-      run: |
-        python <<EOF
-        import prolif
-        import os
-        print(prolif.__version__)
-        from prolif.plotting.network import LigNetwork
-        assert os.path.isfile(prolif.datafiles.TOP)
-        EOF
+      - uses: actions/checkout@v4
+
+      - name: Setup Conda
+        uses: conda-incubator/setup-miniconda@v2
+        with:
+          python-version: ${{ matrix.python-version }}
+          auto-update-conda: true
+          channel-priority: flexible
+          channels: conda-forge, defaults
+          add-pip-as-python-dependency: true
+          architecture: x64
+          use-mamba: true
+          miniforge-variant: Mambaforge
+
+      - name: Check conda and pip
+        run: |
+          which python
+          python --version
+          pip --version
+          conda --version
+          mamba --version
+
+      - name: Install conda dependencies
+        run: |
+          mamba install ${{ matrix.rdkit-version }}
+          mamba list
+
+      - name: Install package through pip
+        run: |
+          pip install .[dev]
+          pip list
+
+      - name: Build
+        run: |
+          python -m build
+
+      - name: Ensure tests and data included in source dist
+        run: |
+          tar -ztvf dist/prolif-*.tar.gz | grep -E 'prolif-.+/tests/.+' || exit 1
+          tar -ztvf dist/prolif-*.tar.gz | grep -E 'prolif-.+/data/.+' || exit 1
+          tar -ztvf dist/prolif-*.tar.gz | grep -E 'prolif-.+/data/vina/.+' || exit 1
+
+      - name: Run tests
+        run: |
+          pytest --color=yes --disable-pytest-warnings --cov=prolif --cov-report=xml tests/
+
+      - name: Measure tests coverage
+        if: matrix.coverage
+        uses: codecov/codecov-action@v3
+        with:
+          files: ./coverage.xml
+          fail_ci_if_error: true
+          verbose: true
+          token: ${{ secrets.CODECOV_TOKEN }}
+
+      - name: Build
+        run: |
+          python -m build
+
+      - name: Remove previous ProLIF install
+        run: |
+          pip uninstall -y prolif
+
+      - name: Install from tar.gz
+        run: |
+          pip install dist/prolif-*.tar.gz
+
+      - name: Test tar.gz install
+        working-directory: /
+        run: |
+          python <<EOF
+          from pathlib import Path
+          from contextlib import suppress
+          import prolif
+          print(prolif.__version__)
+          from prolif.plotting.network import LigNetwork
+          assert Path(prolif.datafiles.TOP).is_file()
+          with suppress(ImportError, ModuleNotFoundError):
+              import tests
+              assert next(Path(tests.__file__).parent.glob("test_fingerprint.py"), None) is None
+          EOF
+
+      - name: Remove previous ProLIF install
+        run: |
+          pip uninstall -y prolif
+
+      - name: Install from wheel
+        run: |
+          pip install dist/prolif-*.whl
+
+      - name: Test wheel install
+        working-directory: /
+        run: |
+          python <<EOF
+          from pathlib import Path
+          from contextlib import suppress
+          import prolif
+          print(prolif.__version__)
+          from prolif.plotting.network import LigNetwork
+          assert Path(prolif.datafiles.TOP).is_file()
+          with suppress(ImportError, ModuleNotFoundError):
+              import tests
+              assert next(Path(tests.__file__).parent.glob("test_fingerprint.py"), None) is None
+          EOF

CHANGELOG.md

@@ -7,6 +7,26 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 ## [Unreleased]
 
 
+## [2.0.2] - 2024-03-01
+
+Maintenance update:
+
+### Added
+
+- `PROLIF_N_JOBS` environment variable to control multiprocessing during the
+  documentation build.
+
+### Changed
+
+- Updated CI pipelines to test on Python 3.8, 3.10 and 3.12.
+
+### Fixed
+
+- Packaging maintenance to fix the `tests/` directory being included as a module rather
+  than as plain data files. This could interfere with `pytest` during test collection
+  in other packages.
+
+
 ## [2.0.1] - 2023-10-11
 
 ### Added

docs/conf.py

@@ -54,7 +54,7 @@
 ]
 nb_execution_allow_errors = False
 nb_execution_raise_on_error = True
-nb_execution_timeout = 180
+nb_execution_timeout = 300
 
 mathjax_path = "https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.0/MathJax.js?config=TeX-AMS-MML_HTMLorMML"
 autosectionlabel_prefix_document = True

prolif/_version.py

@@ -1 +1 @@
-__version__ = "2.0.1"
+__version__ = "2.0.2-rc1"

prolif/fingerprint.py

@@ -24,6 +24,8 @@
     fp = prolif.Fingerprint.from_pickle("fingerprint.pkl")
 
 """
+
+import os
 import warnings
 from collections.abc import Sized
 from functools import wraps
@@ -462,6 +464,8 @@ def run(
             raise ValueError("converter_kwargs must be a list of 2 dicts")
 
         converter_kwargs = converter_kwargs or ({}, {})
+        if n_jobs is None:
+            n_jobs = int(os.environ.get("PROLIF_N_JOBS", 0)) or None
         if residues == "all":
             residues = list(Molecule.from_mda(prot, **converter_kwargs[1]).residues)
         if n_jobs != 1:

prolif/ifp.py

@@ -2,6 +2,7 @@
 Storing interactions --- :mod:`prolif.ifp`
 ==========================================
 """
+
 from collections import UserDict
 
 from prolif.residue import ResidueId

prolif/interactions/base.py

@@ -4,6 +4,7 @@
 
 This module contains the base classes used to build most of the interactions.
 """
+
 import warnings
 from itertools import product
 from math import degrees, radians

prolif/interactions/interactions.py

@@ -64,9 +64,7 @@ class Hydrophobic(Distance):
 
     def __init__(
         self,
-        hydrophobic=(
-            "[c,s,Br,I,S&H0&v2," "$([D3,D4;#6])&!$([#6]~[#7,#8,#9])&!$([#6X4H0]);+0]"
-        ),
+        hydrophobic="[c,s,Br,I,S&H0&v2,$([D3,D4;#6])&!$([#6]~[#7,#8,#9])&!$([#6X4H0]);+0]",
         distance=4.5,
     ):
         super().__init__(
@@ -99,11 +97,7 @@ class HBAcceptor(SingleAngle):
 
     def __init__(
         self,
-        acceptor=(
-            "[#7&!$([nX3])&!$([NX3]-*=[O,N,P,S])&!$([NX3]-[a])&!$([Nv4&+1]),"
-            "O&!$([OX2](C)C=O)&!$(O(~a)~a)&!$(O=N-*)&!$([O-]-N=O),o+0,"
-            "F&$(F-[#6])&!$(F-[#6][F,Cl,Br,I])]"
-        ),
+        acceptor="[#7&!$([nX3])&!$([NX3]-*=[O,N,P,S])&!$([NX3]-[a])&!$([Nv4&+1]),O&!$([OX2](C)C=O)&!$(O(~a)~a)&!$(O=N-*)&!$([O-]-N=O),o+0,F&$(F-[#6])&!$(F-[#6][F,Cl,Br,I])]",
         donor="[$([O,S;+0]),$([N;v3,v4&+1]),n+0]-[H]",
         distance=3.5,
         DHA_angle=(130, 180),

prolif/molecule.py

@@ -2,6 +2,7 @@
 Reading proteins and ligands --- :mod:`prolif.molecule`
 =======================================================
 """
+
 import copy
 from collections import defaultdict
 from collections.abc import Sequence
@@ -116,7 +117,7 @@ def from_mda(cls, obj, selection=None, **kwargs):
         """
         ag = obj.select_atoms(selection) if selection else obj.atoms
         if ag.n_atoms == 0:
-            raise mda.SelectionError(f"AtomGroup is empty, please check your selection")
+            raise mda.SelectionError("AtomGroup is empty, please check your selection")
         mol = ag.convert_to.rdkit(**kwargs)
         return cls(mol)
 

prolif/parallel.py

@@ -7,6 +7,7 @@
 in :meth:`~prolif.fingerprint.Fingerprint.run` and
 :meth:`~prolif.fingerprint.Fingerprint.run_from_iterable` respectively.
 """
+
 from ctypes import c_uint32
 from threading import Event, Thread
 from time import sleep

prolif/pickling.py

@@ -9,6 +9,7 @@
 behavior upon importing the `prolif` package to ensure that the parallelization code
 works as on other platforms.
 """
+
 import sys
 from typing import Optional
 

prolif/plotting/barcode.py

@@ -8,6 +8,7 @@
    :members:
 
 """
+
 from __future__ import annotations
 
 from typing import TYPE_CHECKING, ClassVar, Dict, List, Literal, Optional, Tuple
@@ -73,9 +74,9 @@ def _bit_to_color_value(s: pd.Series) -> pd.Series:
             """Replaces a bit value with it's corresponding color value"""
             interaction = s.name[-1]
             return s.apply(
-                lambda v: self.color_mapper[interaction]
-                if v
-                else self.color_mapper[None]
+                lambda v: (
+                    self.color_mapper[interaction] if v else self.color_mapper[None]
+                )
             )
 
         self.df = df.astype(np.uint8).T.apply(_bit_to_color_value, axis=1)
@@ -85,7 +86,8 @@ def from_fingerprint(cls, fp: Fingerprint) -> Barcode:
         """Creates a barcode object from a fingerprint."""
         if not hasattr(fp, "ifp"):
             raise RunRequiredError(
-                "Please run the fingerprint analysis before attempting to display results."
+                "Please run the fingerprint analysis before attempting to display"
+                " results."
             )
         return cls(fp.to_dataframe())