Infrastructure updates (#7)

PicoCentauri · web-flow · commit 62f234b66ea7 · 2025-11-04T11:18:41.000+01:00
diff --git a/.codecov.yml b/.codecov.yml
@@ -0,0 +1,12 @@
+coverage:
+  ignore:
+    - "examples/.*"
+    - "src/scatterkit/_version.py"
+    - "tests/.*"
+  status:
+    project:
+      default:
+        target: 90%
+    patch: false
+
+comment: false
diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml
@@ -49,7 +49,7 @@ jobs:
       - name: setup Python
         uses: actions/setup-python@v5
         with:
-          python-version: "3.13"
+          python-version: "3.14"
           check-latest: true
 
       - name: Install dependencies
diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml
@@ -20,7 +20,7 @@ jobs:
       - name: setup Python
         uses: actions/setup-python@v5
         with:
-          python-version: "3.13"
+          python-version: "3.14"
           check-latest: true
 
       - name: install dependencies
diff --git a/.github/workflows/lint.yml b/.github/workflows/lint.yml
@@ -16,7 +16,7 @@ jobs:
     - name: Set up Python
       uses: actions/setup-python@v5
       with:
-        python-version: "3.13"
+        python-version: "3.14"
         check-latest: true
 
     - name: Install dependencies
diff --git a/.github/workflows/tests-dev.yml b/.github/workflows/tests-dev.yml
@@ -10,7 +10,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ["3.10", "3.13"]
+        python-version: ["3.11", "3.14"]
 
     steps:
       - uses: actions/checkout@v4
diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
@@ -17,13 +17,13 @@ jobs:
       matrix:
         include:
           - os: ubuntu-24.04
-            python-version: "3.10"
+            python-version: "3.11"
           - os: ubuntu-24.04
-            python-version: "3.13"
+            python-version: "3.14"
           - os: macos-15
-            python-version: "3.13"
+            python-version: "3.14"
           - os: windows-2025
-            python-version: "3.13"
+            python-version: "3.14"
 
     steps:
     - uses: actions/checkout@v4
diff --git a/CHANGELOG.rst b/CHANGELOG.rst
@@ -1,20 +1,17 @@
 CHANGELOG file
 --------------
 
-The rules for scatterkit's CHANGELOG file:
-
-- entries are sorted newest-first.
-- summarize sets of changes (don't reproduce every git log comment here).
-- don't ever delete anything.
-- keep the format consistent (79 char width, Y/M/D date format) and do not
-  use tabs but use spaces for formatting
-
-.. inclusion-marker-changelog-start
+..
+  The rules for scatterkit's CHANGELOG file:
+  - entries are sorted newest-first.
+  - summarize sets of changes (don't reproduce every git log comment here).
+  - don't ever delete anything.
+  - keep the format consistent (79 char width, Y/M/D date format) and do not
+    use tabs but use spaces for formatting
 
 v0.0.1 (2025/08/05)
 -------------------
 Kira Fischer, Philip Loche
 
+- Update to Python 3.14 support
 - Migrated code from maicos to scatterkit
-
-.. inclusion-marker-changelog-end
diff --git a/MANIFEST.in b/MANIFEST.in
@@ -1,19 +1,18 @@
 graft src
 
-include AUTHORS.rst
-include CHANGELOG.rst
-include README.md
-include MANIFEST.in
-
-exclude example.ipynb
+include *.rst
+include LICENSE
 
+prune docs
+prune examples
 prune tests
 prune developer
 prune .tox
 
+exclude .codecov.yml
 exclude .gitattributes
 exclude .gitignore
+exclude .readthedocs.yml
 exclude tox.ini
 
 global-exclude *.py[cod] __pycache__/* *.so *.dylib
-
diff --git a/README.rst b/README.rst
@@ -15,8 +15,8 @@ Documentation
 For details, tutorials, and examples, visit our official `documentation`_. We also
 provide the `latest documentation`_ for the current development version of Scatterkit.
 
-.. _`documentation`: https://scatterkit.readthedocs.io
-.. _`latest documentation`: https://scatterkit.readthedocs.io/en/latest
+.. _`documentation`: https://maicos-devel.github.io/scatterkit
+.. _`latest documentation`: https://maicos-devel.github.io/scatterkit/latest
 
 .. inclusion-readme-installation-start
 
diff --git a/developer/check_changelog.py b/developer/check_changelog.py
@@ -22,7 +22,21 @@ class ChangelogError(Exception):
     workfile = f.read()
 
 if file.strip() == workfile.strip():
-    raise ChangelogError("You have not updated the CHANGELOG file. Please "
-                         f"add a summary of your additions to {changelog}.")
+    # Check for changed files and ignore .github/ changes
+    head_commit = repo.head.commit
+    diff = head_commit.diff("origin/main")
+    changed_files = []
+    for x in diff:
+        if x.a_blob.path not in changed_files:
+            changed_files.append(x.a_blob.path)
+        if x.b_blob is not None and x.b_blob.path not in changed_files:
+            changed_files.append(x.b_blob.path)
+    changed_files = [x for x in changed_files if not x.startswith(".github/")]
+
+    if len(changed_files) > 0:
+        raise ChangelogError("You have not updated the CHANGELOG file. Please "
+                             f"add a summary of your additions to {changelog}.")
+    else:
+        print("No changes detected.")
 else:
     print("CHANGELOG is up to date.")
diff --git a/examples/saxs.py b/examples/saxs.py
@@ -10,8 +10,8 @@
 Small-angle X-ray scattering
 ============================
 
-Small-angle X-ray scattering (SAXS) can be extracted using Scatterkit. To follow this how-to
-guide, you should download the :download:`topology <water.tpr>` and the
+Small-angle X-ray scattering (SAXS) can be extracted using Scatterkit. To follow this
+how-to guide, you should download the :download:`topology <water.tpr>` and the
 :download:`trajectory <water.trr>` files of the water system.
 
 For more details on the theory see :ref:`saxs-explanations`.
@@ -24,8 +24,8 @@
 import MDAnalysis as mda
 from MDAnalysis.analysis.rdf import InterRDF
 
-from scatterkit.lib.math import atomic_form_factor, rdf_structure_factor
 import scatterkit
+from scatterkit.lib.math import atomic_form_factor, rdf_structure_factor
 
 # %%
 # The `water` system consists of 510 water molecules in the liquid state. The
@@ -47,8 +47,8 @@
 # Extract small angle x-ray scattering (SAXS) intensities
 # -------------------------------------------------------
 #
-# Let us use the :class:`scatterkit.Saxs` class of Scatterkit and apply it to all atoms in the
-# system:
+# Let us use the :class:`scatterkit.Saxs` class of Scatterkit and apply it to all atoms
+# in the system:
 
 saxs = scatterkit.Saxs(u.atoms).run(stop=30)
 
@@ -115,9 +115,9 @@
 # %%
 # Let us plot the results for the structure factor, the squared atomic form factor as
 # well scattering intensities together. For computing the atomic form factor we will use
-# :func:`scatterkit.lib.math.atomic_form_factor`. Note that for the ``structure_factors``
-# and the ``scattering_intensities` we access the results directly from the ``results``
-# attribute without storing them in individual variables as before:
+# :func:`scatterkit.lib.math.atomic_form_factor`. Note that for the
+# ``structure_factors`` and the ``scattering_intensities` we access the results directly
+# from the ``results`` attribute without storing them in individual variables as before:
 
 fig2, ax2 = plt.subplots(nrows=3, sharex=True, layout="constrained")
 
diff --git a/pyproject.toml b/pyproject.toml
@@ -30,10 +30,10 @@ classifiers = [
     "Operating System :: Microsoft :: Windows",
     "Programming Language :: Python",
     "Programming Language :: Python :: 3",
-    "Programming Language :: Python :: 3.10",
     "Programming Language :: Python :: 3.11",
     "Programming Language :: Python :: 3.12",
     "Programming Language :: Python :: 3.13",
+    "Programming Language :: Python :: 3.14",
     "Topic :: Scientific/Engineering",
     "Topic :: Scientific/Engineering :: Bio-Informatics",
     "Topic :: Scientific/Engineering :: Chemistry",
@@ -57,13 +57,8 @@ maintainers = [
 ]
 name = "scatterkit"
 readme = "README.rst"
-requires-python = ">=3.10"
-dependencies = [
-    "mdacli>=0.1.28",
-    "MDAnalysis>=2.8.0",
-    "typing_extensions",
-	"maicos",
-]
+requires-python = ">=3.11"
+dependencies = ["maicos>=0.11"]
 
 [project.optional-dependencies]
 examples = ["matplotlib"]
diff --git a/setup.py b/setup.py
@@ -19,9 +19,8 @@
 from pathlib import Path
 
 import numpy as np
-from setuptools import Extension, setup
-
 import versioneer
+from setuptools import Extension, setup
 
 VERSION = versioneer.get_version()
 
diff --git a/src/scatterkit/__init__.py b/src/scatterkit/__init__.py
@@ -1,18 +1,16 @@
-"""scatterkit: SAXS analysis of MD trajectories"""
+"""scatterkit: SAXS analysis of MD trajectories."""
 
 __authors__ = "MAICoS Developer Team"
 
-import warnings
-
 from ._version import get_versions
+from .saxs import Saxs
 
 __authors__ = "MAICoS Developer Team"
 #: Version information for MAICoS, following :pep:`440`
 #: and `semantic versioning <http://semver.org/>`_.
 __version__ = get_versions()["version"]
 del get_versions
 
-from .saxs import Saxs
 
 __all__ = [
     "Saxs",
diff --git a/src/scatterkit/lib/math.py b/src/scatterkit/lib/math.py
@@ -49,9 +49,9 @@ def atomic_form_factor(q: float, element: str) -> float:
         The magnitude of the scattering vector in reciprocal angstroms (1/Å).
     element : str
         The element for which the atomic form factor is calculated. Known elements are
-        listed in the :attr:`scatterkit.lib.tables.elements` set. United-atom models such as
-        ``"CH1"``, ``"CH2"``, ``"CH3"``, ``"CH4"``, ``"NH1"``, ``"NH2"``, and ``"NH3"``
-        are also supported.
+        listed in the :attr:`scatterkit.lib.tables.elements` set. United-atom models
+        such as ``"CH1"``, ``"CH2"``, ``"CH3"``, ``"CH4"``, ``"NH1"``, ``"NH2"``, and
+        ``"NH3"`` are also supported.
 
         .. note::
 
@@ -99,6 +99,7 @@ def atomic_form_factor(q: float, element: str) -> float:
 
     return form_factor.reshape(q2.shape)
 
+
 def rdf_structure_factor(
     rdf: np.ndarray, r: np.ndarray, density: float
 ) -> tuple[np.ndarray, np.ndarray]:
diff --git a/src/scatterkit/lib/util.py b/src/scatterkit/lib/util.py
@@ -9,8 +9,6 @@
 
 import re
 from collections.abc import Callable
-from pathlib import Path
-import sys
 
 DOC_REGEX_PATTERN = re.compile(r"\$\{([^\}]+)\}")
 
@@ -134,29 +132,3 @@ def render_docs(func: Callable) -> Callable:
 
     """
     return _render_docs(func, doc_dict=DOC_DICT)
-
-
-def scatterkit_banner(version: str = "", frame_char: str = "-") -> str:
-    """Prints ASCII banner resembling the MAICoS Logo with 80 chars width.
-
-    Parameters
-    ----------
-    version : str
-        Version string to add to the banner.
-    frame_char : str
-        Character used to as framing around the banner.
-
-    Returns
-    -------
-    banner : str
-        formatted banner
-
-    """
-    banner = rf"""
-@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
-@                           SCATTERKIT {version:^8}                                @
-@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
-"""
-    return banner.replace("@", frame_char)
-
-
diff --git a/src/scatterkit/saxs.py b/src/scatterkit/saxs.py
@@ -11,8 +11,8 @@
 
 import MDAnalysis as mda
 import numpy as np
-
 from maicos.core import AnalysisBase
+
 from .lib.math import atomic_form_factor, structure_factor
 from .lib.util import render_docs
 
diff --git a/tests/data/__init__.py b/tests/data/__init__.py
@@ -28,5 +28,3 @@
 # An SPC/E water molecule pointing in z-direction
 SPCE_ITP = DIR_PATH / "spce.itp"
 SPCE_GRO = DIR_PATH / "spce.gro"
-
-
diff --git a/tests/lib/test_math.py b/tests/lib/test_math.py
@@ -13,13 +13,13 @@
 import MDAnalysis as mda
 import numpy as np
 import pytest
-from numpy.testing import assert_allclose, assert_equal
+from numpy.testing import assert_allclose
 
 import scatterkit.lib.math
 import scatterkit.lib.util
 
 sys.path.append(str(Path(__file__).parents[1]))
-from data import SPCE_GRO, SPCE_ITP, WATER_GRO_NPT, WATER_TPR_NPT  # noqa: E402
+from data import WATER_GRO_NPT, WATER_TPR_NPT  # noqa: E402
 
 
 class Test_sfactor:
diff --git a/tests/lib/test_util.py b/tests/lib/test_util.py
@@ -7,35 +7,15 @@
 # SPDX-License-Identifier: GPL-3.0-or-later
 """Tests for the utilities."""
 
-import pytest
-from numpy.testing import assert_allclose, assert_equal
 import sys
 from pathlib import Path
 
+import pytest
+
 import scatterkit.lib.util
 
 sys.path.append(str(Path(__file__).parents[1]))
 
-def test_banner():
-    """Test banner string by checking some necesarry features.
-
-    The banner is not tested for exact string equality. We just check the necessary
-    features. Everything else is up to the developers to get creative.
-    """
-    # Test the character replacement
-    assert scatterkit.lib.util.scatterkit_banner(frame_char="%")[1] == "%"
-    # Check for correct number of lines as a sanity check
-    assert scatterkit.lib.util.scatterkit_banner().count("\n") == 4
-    # Check that newlines are added top and bottom
-    assert scatterkit.lib.util.scatterkit_banner().startswith("\n")
-    assert scatterkit.lib.util.scatterkit_banner().endswith("\n")
-    # Check for correct length of lines (80 characters excluding top and bottom)
-    # Also add in a long version string to check that it doesn't overflow
-    for line in scatterkit.lib.util.scatterkit_banner(version="v1.10.11").split("\n")[1:-1]:
-        assert len(line) == 80
-    # Check that the version is correctly inserted
-    assert "v0.0.1" in scatterkit.lib.util.scatterkit_banner(version="v0.0.1")
-
 
 @pytest.mark.parametrize(
     ("doc", "new_doc"),
diff --git a/tox.ini b/tox.ini
