Merge pull request #661 from padix-key/py-version

Support Python 3.13

.github/workflows/test_and_deploy.yml

@@ -16,7 +16,7 @@ concurrency:
   cancel-in-progress: true
 
 env:
-  CIBW_BUILD: cp310-* cp311-* cp312-*
+  CIBW_BUILD: cp310-* cp311-* cp312-* cp313-*
   CIBW_TEST_EXTRAS: test
   CIBW_TEST_COMMAND: >
     pytest {project}
@@ -42,7 +42,8 @@ jobs:
       with:
         python-version: "3.12"
     - name: Install ruff
-      run: pip install ruff==0.5.2
+      # Keep in sync with the ruff version in pyproject.toml
+      run: pip install ruff==0.6.9
     - name: Check code formatting
       run: ruff format --diff
     - name: Lint code base
@@ -58,7 +59,7 @@ jobs:
       - uses: actions/checkout@v4
       - name: Install cibuildwheel
         # MAKE SURE THIS STAYS IN SYNC WITH THE LOWER GHA cibuildwheel
-        run: pipx install cibuildwheel==2.19.1
+        run: pipx install cibuildwheel==2.20.0
       - id: set-matrix
         run: |
           MATRIX=$(
@@ -102,7 +103,7 @@ jobs:
 
       - name: Build & (optionally) test wheels
         # MAKE SURE THIS STAYS IN SYNC WITH THE UPPER pipx call to cibuildwheel
-        uses: pypa/cibuildwheel@v2.19.1
+        uses: pypa/cibuildwheel@v2.20.0
         with:
           only: ${{ matrix.dist }}
 
@@ -112,6 +113,19 @@ jobs:
           path: ./wheelhouse/*.whl
 
 
+  make-sdist:
+    name: Build source distribution
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v4
+    - name: Build source distribution
+      run: pipx run build --sdist
+    - uses: actions/upload-artifact@v4
+      with:
+        name: release-sdist
+        path: dist//*.tar.gz
+
+
   test-interfaces:
     name: Test interfaces to databases and applications
 
@@ -124,12 +138,16 @@ jobs:
       - uses: actions/checkout@v4
       - uses: conda-incubator/setup-miniconda@v3
         with:
-          mamba-version: "*"
           environment-file: environment.yml
+          miniforge-version: latest
       - name: Build distribution
         run: pip wheel --no-deps -w dist .
       - name: Install distribution
         run: pip install .//dist//*.whl
+      - name: "TEMP: Skip DSSP tests"
+        # TEMP: Omit DSSP tests for now until conda-forge DSSP is functional
+        # (https://github.com/conda-forge/dssp-feedstock/pull/4)
+        run: mamba uninstall dssp
       - name: Run tests
         # Running NCBI BLAST and SRA takes too long
         # The tests on the NCBI Entrez database are not reliable enough
@@ -143,53 +161,48 @@ jobs:
           tests//test_modname.py
           tests//database
           tests//application
+      # Use the built distribution for other downstream jobs to reduce build time
+      - uses: actions/upload-artifact@v4
+        with:
+          name: internal-build
+          path: ./dist/*.whl
 
 
   test-muscle5:
     name: Test interface to Muscle 5
 
     runs-on: ubuntu-latest
+    needs:
+      - test-interfaces
     defaults:
       run:
         shell: bash -l {0}
 
     steps:
       - uses: actions/checkout@v4
+      - uses: actions/download-artifact@v4
+        with:
+          name: internal-build
+          path: dist
       - uses: conda-incubator/setup-miniconda@v3
         with:
           activate-environment: biotite-dev
-          miniforge-variant: Mambaforge
-          python-version: "3.10"
-          channels: conda-forge,defaults
+          miniforge-version: latest
+          python-version: "3.12"
       - name: Install Muscle 5
         run: conda install -c bioconda "muscle=5"
-      - name: Build distribution
-        run: pip wheel -w dist .
-      - name: Install distribution
+      - name: Install distribution and pytest
         run: pip install .//dist//*.whl pytest
       - name: Test Muscle 5 interface
         run: pytest --durations=50 tests//application//test_msa.py
 
 
-  make-sdist:
-    name: Build source distribution
-    runs-on: ubuntu-latest
-    steps:
-    - uses: actions/checkout@v4
-    - name: Build source distribution
-      run: pipx run build --sdist
-    - uses: actions/upload-artifact@v4
-      with:
-        name: release-sdist
-        path: dist//*.tar.gz
-
-
   make-ccd:
     name: Compile the CCD subset for structure.info from the wwPDB CCD
 
     runs-on: ubuntu-latest
     needs:
-      - test-and-build
+      - test-interfaces
     defaults:
       run:
         shell: bash -l {0}
@@ -198,7 +211,7 @@ jobs:
     - uses: actions/checkout@v4
     - uses: actions/download-artifact@v4
       with:
-        name: release-cp312-manylinux_x86_64
+        name: internal-build
         path: dist
     - uses: actions/setup-python@v3
       with:
@@ -223,7 +236,7 @@ jobs:
 
     runs-on: ubuntu-20.04
     needs:
-      - test-and-build
+      - test-interfaces
     defaults:
       run:
         shell: bash -l {0}
@@ -238,12 +251,12 @@ jobs:
         fetch-tags: true
     - uses: actions/download-artifact@v4
       with:
-        name: release-cp311-manylinux_x86_64
+        name: internal-build
         path: dist
-    - uses: conda-incubator/setup-miniconda@v2
+    - uses: conda-incubator/setup-miniconda@v3
       with:
         environment-file: environment.yml
-        miniforge-variant: Mambaforge
+        miniforge-version: latest
     - name: Install distribution
       run: pip install dist//*.whl
     - name: Build base documentation
@@ -272,12 +285,12 @@ jobs:
     runs-on: ubuntu-latest
     if: github.event_name != 'release'
     needs:
-      - test-and-build
+      - test-interfaces
     steps:
       - uses: actions/checkout@v4
       - uses: actions/download-artifact@v4
         with:
-          name: release-cp312-manylinux_x86_64
+          name: internal-build
           path: dist
       - uses: actions/setup-python@v3
         with:

environment.yml

@@ -6,11 +6,10 @@ name: biotite-dev
 channels:
   - anaconda
   - conda-forge
-  - salilab
   - bioconda
 
 dependencies:
-  - python =3.11
+  - python =3.12
   # Package building
   - cython >=3.0
   - pip >=10.0
@@ -27,11 +26,11 @@ dependencies:
   - pytest >=7.0
   - pytest-codspeed >=2.0
   # Code style
-  - ruff =0.5.2
+  - ruff =0.6.9  # Keep in sync with the ruff version in pyproject.toml
   # Interfaced software in biotite.application (can also be installed separately)
   - autodock-vina
   - clustalo
-  - dssp
+  - dssp =4
   - mafft
   - muscle =3
   - sra-tools

pyproject.toml

@@ -36,6 +36,9 @@ test = [
   "pytest",
   "pytest-codspeed",
 ]
+lint = [
+  "ruff == 0.6.9"
+]
 
 [project.urls]
 homepage = "https://www.biotite-python.org"

src/biotite/application/dssp/app.py

@@ -6,10 +6,11 @@
 __author__ = "Patrick Kunzmann"
 __all__ = ["DsspApp"]
 
+from subprocess import SubprocessError
 from tempfile import NamedTemporaryFile
 import numpy as np
 from biotite.application.application import AppState, requires_state
-from biotite.application.localapp import LocalApp, cleanup_tempfile
+from biotite.application.localapp import LocalApp, cleanup_tempfile, get_version
 from biotite.structure.io.pdbx.cif import CIFFile
 from biotite.structure.io.pdbx.convert import set_structure
 
@@ -72,7 +73,13 @@ def __init__(self, atom_array, bin_path="mkdssp"):
             self._array.set_annotation(
                 "occupancy", np.ones(self._array.array_length(), dtype=float)
             )
-
+        try:
+            # The parameters have changed in version 4
+            self._new_cli = get_version(bin_path)[0] >= 4
+        except SubprocessError:
+            # In older versions, the no version is returned with `--version`
+            # -> a SubprocessError is raised
+            self._new_cli = False
         self._in_file = NamedTemporaryFile("w", suffix=".cif", delete=False)
         self._out_file = NamedTemporaryFile("r", suffix=".dssp", delete=False)
 
@@ -81,7 +88,10 @@ def run(self):
         set_structure(in_file, self._array)
         in_file.write(self._in_file)
         self._in_file.flush()
-        self.set_arguments(["-i", self._in_file.name, "-o", self._out_file.name])
+        if self._new_cli:
+            self.set_arguments([self._in_file.name, self._out_file.name])
+        else:
+            self.set_arguments(["-i", self._in_file.name, "-o", self._out_file.name])
         super().run()
 
     def evaluate(self):

src/biotite/application/localapp.py

@@ -8,7 +8,10 @@
 
 import abc
 import copy
+import re
+import subprocess
 from os import chdir, getcwd, remove
+from pathlib import Path
 from subprocess import PIPE, Popen, SubprocessError, TimeoutExpired
 from biotite.application.application import (
     Application,
@@ -306,3 +309,34 @@ def cleanup_tempfile(temp_file):
     except FileNotFoundError:
         # File was already deleted, e.g. due to `TemporaryFile(delete=True)`
         pass
+
+
+def get_version(bin_path, version_option="--version"):
+    """
+    Get the version of a locally installed application.
+
+    Parameters
+    ----------
+    bin_path : str or Path
+        Path of the application.
+    version_option : str, optional
+        The command line option to get the version.
+
+    Returns
+    -------
+    major, minor : int
+        The major and minor version number.
+    """
+    output = subprocess.run(
+        [bin_path, version_option], capture_output=True, text=True
+    ).stdout
+    # Find matches for version string containing major and minor version
+    match = re.search(r"\d+\.\d+", output)
+    if match is None:
+        raise subprocess.SubprocessError(
+            f"Could not determine '{Path(bin_path).name}' version "
+            f"from the string '{output}'"
+        )
+    version_string = match.group(0)
+    splitted = version_string.split(".")
+    return int(splitted[0]), int(splitted[1])

src/biotite/application/muscle/app3.py

@@ -7,13 +7,11 @@
 __all__ = ["MuscleApp"]
 
 import numbers
-import re
-import subprocess
 import warnings
 from collections.abc import Sequence
 from tempfile import NamedTemporaryFile
 from biotite.application.application import AppState, VersionError, requires_state
-from biotite.application.localapp import cleanup_tempfile
+from biotite.application.localapp import cleanup_tempfile, get_version
 from biotite.application.msaapp import MSAApp
 from biotite.sequence.phylo.tree import Tree
 
@@ -54,7 +52,7 @@ class MuscleApp(MSAApp):
     """
 
     def __init__(self, sequences, bin_path="muscle", matrix=None):
-        major_version = get_version(bin_path)[0]
+        major_version = get_version(bin_path, "-version")[0]
         if major_version != 3:
             raise VersionError(f"Muscle 3 is required, got version {major_version}")
 
@@ -227,14 +225,3 @@ def align(cls, sequences, bin_path=None, matrix=None, gap_penalty=None):
         app.start()
         app.join()
         return app.get_alignment()
-
-
-def get_version(bin_path="muscle"):
-    output = subprocess.run([bin_path, "-version"], capture_output=True, text=True)
-    # Find matches for version string containing major and minor version
-    match = re.search(r"\d+\.\d+", output.stdout)
-    if match is None:
-        raise subprocess.SubprocessError("Could not determine Muscle version")
-    version_string = match.group(0)
-    splitted = version_string.split(".")
-    return int(splitted[0]), int(splitted[1])

src/biotite/application/muscle/app5.py

@@ -7,8 +7,8 @@
 __all__ = ["Muscle5App"]
 
 from biotite.application.application import AppState, VersionError, requires_state
+from biotite.application.localapp import get_version
 from biotite.application.msaapp import MSAApp
-from biotite.application.muscle.app3 import get_version
 
 
 class Muscle5App(MSAApp):
@@ -49,7 +49,7 @@ class Muscle5App(MSAApp):
     """
 
     def __init__(self, sequences, bin_path="muscle"):
-        major_version = get_version(bin_path)[0]
+        major_version = get_version(bin_path, "-version")[0]
         if major_version < 5:
             raise VersionError(
                 f"At least Muscle 5 is required, got version {major_version}"

src/biotite/database/rcsb/query.py

@@ -146,9 +146,9 @@ class BasicQuery(SingleQuery):
     Examples
     --------
 
-    >>> query = BasicQuery("tc5b")
+    >>> query = BasicQuery("Miniprotein Construct")
     >>> print(sorted(search(query)))
-    ['1L2Y', '8ANG', '8ANH', '8ANI', '8ANM', '8QWW']
+    ['1L2Y']
     """
 
     def __init__(self, term):
@@ -346,9 +346,9 @@ class SequenceQuery(SingleQuery):
     --------
 
     >>> sequence = "NLYIQWLKDGGPSSGRPPPS"
-    >>> query = SequenceQuery(sequence, scope="protein", min_identity=0.8)
+    >>> query = SequenceQuery(sequence, scope="protein", min_identity=0.95)
     >>> print(sorted(search(query)))
-    ['1L2Y', '1RIJ', '2JOF', '2LDJ', '2LL5', '2MJ9', '3UC7', '3UC8']
+    ['1L2Y', '2LDJ', '9G22', '9G2N', '9G2O', '9G31', '9G32', '9GDL', '9GDN', '9GDT', '9GDU', '9GE1']
     """
 
     def __init__(self, sequence, scope, min_identity=0.0, max_expect_value=10000000.0):