Update package to newest Python and Biotite versions

.github/workflows/test_and_deploy.yml

@@ -11,7 +11,7 @@ on:
     - published
 
 env:
-  CIBW_BUILD: cp39-* cp310-* cp311-*
+  CIBW_BUILD: cp310-* cp311-* cp312-*
   CIBW_ARCHS_LINUX: "x86_64"
   CIBW_ARCHS_MACOS: "x86_64 arm64"
   CIBW_ARCHS_WINDOWS: "x86 AMD64"
@@ -27,15 +27,30 @@ env:
 
 
 jobs:
+  lint:
+    name: Check code style
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v4
+    - uses: actions/setup-python@v5
+      with:
+        python-version: "3.12"
+    - name: Install ruff
+      run: pip install ruff==0.5.2
+    - name: Check code formatting
+      run: ruff format --diff
+    - name: Lint code base
+      run: ruff check
+
   test-and-build:
     name: "Build & Test"
     strategy:
       matrix:
-        os: [ubuntu-20.04, windows-2019, macos-11]
-    
+        os: [ubuntu-latest, windows-latest, macos-latest]
+
     runs-on: ${{ matrix.os }}
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - name: Set up QEMU
         if: runner.os == 'Linux'
@@ -44,7 +59,7 @@ jobs:
           platforms: all
 
       - name: Build & (optionally) test wheels
-        uses: pypa/cibuildwheel@v2.12.1
+        uses: pypa/cibuildwheel@v2.19.1
 
       - uses: actions/upload-artifact@v3
         with:
@@ -57,7 +72,7 @@ jobs:
     name: Build source distribution
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
       with:
         fetch-depth: 0
         submodules: true
@@ -79,7 +94,7 @@ jobs:
         shell: bash -l {0}
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - uses: conda-incubator/setup-miniconda@v2
         with:
           activate-environment: hydride
@@ -102,7 +117,11 @@ jobs:
     name: Upload to GitHub Releases & PyPI
     permissions:
       contents: write
-    needs: [test-and-build, make-sdist, make-doc]
+    needs:
+      - lint
+      - test-and-build
+      - make-sdist
+      - make-doc
     runs-on: ubuntu-latest
     steps:
     - uses: actions/download-artifact@v3

.gitignore

@@ -19,7 +19,6 @@ htmlcov
 # Ignore all compiled python files (e.g. from running the unit tests)
 *.pyc
 *.pyo
-*.py{}
 *.py-e
 
 # Ignore files created via Cython
@@ -42,5 +41,6 @@ htmlcov
 *.code-workspace
 .vscode/*
 
-# Ignore fuse_hidden files on Linux systems
+# Ignore OS specific files
 *.fuse_hidden*
+.DS_Store

doc/cli.rst

@@ -22,7 +22,7 @@ Structure input and output
 
 ``--infile``/``-i`` and ``-outfile``/``-o`` define the paths of the input or
 output structure file, respectively.
-*Hydride* supports the *PDB*, *PDBx/mmCIF*, *MMTF*, *MOL* and *SDF*
+*Hydride* supports the *PDB*, *PDBx/mmCIF*, *BinaryCIF*, *MOL* and *SDF*
 format.
 By default, the format is determined from the file extension, but it can also
 be explicitly provided via the ``--informat``/``-I`` or
@@ -38,8 +38,6 @@ used is specified with ``--model``/``-m``. By default, the first model is used.
 
 The addition of hydrogen atoms requires complete information about the
 bonds between atoms.
-Currently, this information can only be read from *PDB*, *MMTF*, *MOL* and
-*SDF* files.
 If bond information is absent, *Hydride* automatically connects
 atoms based on the molecule/residue name and the atom names.
 However, the automatic bond detection only works for molecules in the
@@ -97,7 +95,7 @@ libraries by providing a path to a corresponding structure file via
 Analogous to the input and output file parameters, the file format can be
 specified with ``--fragformat``/``-f``.
 Note that the file must contain proper bond information and correct formal
-charges, so effectively a *MMTF*, *MOL* and *SDF* must be supplied.
+charges.
 
 By default, *Hydride* does not consider periodic boundary conditions,
 as they appear e.g. in MD simulations.

doc/conf.py

@@ -7,37 +7,40 @@
 try:
     import numpy as np
     import pyximport
+
     pyximport.install(
         build_in_temp=False,
-        setup_args={"include_dirs":np.get_include()},
-        language_level=3
+        setup_args={"include_dirs": np.get_include()},
+        language_level=3,
     )
 except ImportError:
     pass
 
-from os.path import realpath, dirname, join, isdir, isfile, basename
-from os import listdir, makedirs
 import sys
+from os.path import dirname, join, realpath
 
 doc_path = dirname(realpath(__file__))
 # Include hydride/src in PYTHONPATH
 # in order to import the 'hydride' package
 package_path = join(dirname(doc_path), "src")
 sys.path.insert(0, package_path)
 import hydride
+
 # Include gecos/doc in PYTHONPATH
 # in order to import modules for plot genaration etc.
 sys.path.insert(0, doc_path)
 
 
 #### General ####
 
-extensions = ["sphinx.ext.autodoc",
-              "sphinx.ext.autosummary",
-              "sphinx.ext.doctest",
-              "sphinx.ext.mathjax",
-              "sphinx.ext.viewcode",
-              "numpydoc"]
+extensions = [
+    "sphinx.ext.autodoc",
+    "sphinx.ext.autosummary",
+    "sphinx.ext.doctest",
+    "sphinx.ext.mathjax",
+    "sphinx.ext.viewcode",
+    "numpydoc",
+]
 
 templates_path = ["templates"]
 source_suffix = [".rst"]
@@ -62,25 +65,26 @@
 
 html_theme = "alabaster"
 html_static_path = ["static"]
-html_css_files = [
-    "hydride.css",
-    "fonts.css"
-]
+html_css_files = ["hydride.css", "fonts.css"]
 html_favicon = "static/assets/hydride_icon_32p.png"
 htmlhelp_basename = "HydrideDoc"
-html_sidebars = {"**": ["about.html",
-                        "navigation.html",
-                        "relations.html",
-                        "searchbox.html",
-                        "donate.html"]}
+html_sidebars = {
+    "**": [
+        "about.html",
+        "navigation.html",
+        "relations.html",
+        "searchbox.html",
+        "donate.html",
+    ]
+}
 html_theme_options = {
-    "description"   : "Adding hydrogen atoms to molecular models",
-    "logo"          : "assets/hydride_logo.png",
-    "logo_name"     : "false",
-    "github_user"   : "biotite-dev",
-    "github_repo"   : "hydride",
-    "github_type"   : "star",
-    "github_banner" : "true",
-    "page_width"    : "85%",
-    "fixed_sidebar" : "true"
+    "description": "Adding hydrogen atoms to molecular models",
+    "logo": "assets/hydride_logo.png",
+    "logo_name": "false",
+    "github_user": "biotite-dev",
+    "github_repo": "hydride",
+    "github_type": "star",
+    "github_banner": "true",
+    "page_width": "85%",
+    "fixed_sidebar": "true",
 }

doc/figure_scripts/api.py

@@ -5,13 +5,12 @@
 """
 
 import tempfile
+import ammolite
 import biotite.structure as struc
-import biotite.structure.io.mol as mol
 import biotite.structure.info as info
-import ammolite
+import biotite.structure.io.mol as mol
 from util import COLORS, init_pymol_parameters
 
-
 ZOOM = 1.5
 PNG_SIZE = (400, 400)
 
@@ -63,7 +62,7 @@ def color_atoms(pymol_object, atom_array):
 
 print("\nEND OF SNIPPET\n")
 pymol_heavy = ammolite.PyMOLObject.from_structure(molecule, "heavy")
-#pymol_heavy.orient()
+# pymol_heavy.orient()
 pymol_heavy.zoom(buffer=ZOOM)
 color_atoms(pymol_heavy, molecule)
 ammolite.cmd.png("api_01.png", *PNG_SIZE)
@@ -168,9 +167,10 @@ def color_atoms(pymol_object, atom_array):
 
 
 print("\nEND OF SNIPPET\n", end="")
-import matplotlib.pyplot as plt
 import matplotlib as mpl
-plt.rcParams['axes.prop_cycle'] = mpl.cycler(color=[COLORS["N"]])
+import matplotlib.pyplot as plt
+
+plt.rcParams["axes.prop_cycle"] = mpl.cycler(color=[COLORS["N"]])
 
 
 ########################################################################
@@ -201,6 +201,7 @@ def color_atoms(pymol_object, atom_array):
 fig.savefig("api_04.png")
 
 import biotite.structure.info as info
+
 molecule = info.residue("ASP")
 
 
@@ -229,4 +230,4 @@ def color_atoms(pymol_object, atom_array):
 
 #
 #
-########################################################################
+########################################################################

doc/figure_scripts/cover_structure.py

@@ -1,24 +1,21 @@
 import numpy as np
 import pyximport
+
 pyximport.install(
-    build_in_temp=False,
-    setup_args={"include_dirs":np.get_include()},
-    language_level=3
+    build_in_temp=False, setup_args={"include_dirs": np.get_include()}, language_level=3
 )
 
-from os.path import join
-import numpy as np
-import biotite.structure as struc
-import biotite.structure.io.mmtf as mmtf
-import biotite.database.rcsb as rcsb
-import hydride
 import ammolite
+import biotite.database.rcsb as rcsb
+import biotite.structure as struc
+import biotite.structure.io.pdbx as pdbx
+import numpy as np
 from util import COLORS, init_pymol_parameters
+import hydride
 
-
-mmtf_file = mmtf.MMTFFile.read(rcsb.fetch("1bna", "mmtf"))
-heavy_atoms = mmtf.get_structure(
-    mmtf_file, model=1, include_bonds=True, extra_fields=["charge"]
+pdbx_file = pdbx.BinaryCIFFile.read(rcsb.fetch("1bna", "bcif"))
+heavy_atoms = pdbx.get_structure(
+    pdbx_file, model=1, include_bonds=True, extra_fields=["charge"]
 )
 heavy_atoms = heavy_atoms[heavy_atoms.res_name != "HOH"]
 
@@ -43,9 +40,7 @@
 pymol_all.zoom(buffer=1.0)
 ammolite.cmd.rotate("z", 90)
 
-for pymol_object, atoms in zip(
-    (pymol_heavy, pymol_all), (heavy_atoms, all_atoms)
-):
+for pymol_object, atoms in zip((pymol_heavy, pymol_all), (heavy_atoms, all_atoms)):
     for element in ("H", "C", "N", "O", "P"):
         pymol_object.color(COLORS[element], atoms.element == element)
 
@@ -56,9 +51,8 @@
 pymol_heavy.disable()
 pymol_all.enable()
 for i, (_, atom_i, atom_j) in enumerate(bonds):
-    color = COLORS["N"] if all_atoms.element[atom_j] == "N"\
-            else COLORS["O"]
+    color = COLORS["N"] if all_atoms.element[atom_j] == "N" else COLORS["O"]
     pymol_all.distance(str(i), atom_i, atom_j, show_label=False)
     ammolite.cmd.set_color(f"bond_color_{i}", list(color))
     ammolite.cmd.color(f"bond_color_{i}", str(i))
-ammolite.cmd.png("cover_hydrogenated.png", 400, 800)
+ammolite.cmd.png("cover_hydrogenated.png", 400, 800)