Format and lint with ruff

.github/workflows/ci.yaml

@@ -17,7 +17,11 @@ jobs:
     steps:
       - uses: actions/checkout@v4
       - uses: psf/black@stable
+        with:
+          src: pimmslearn
       - uses: isort/isort-action@v1
+        with:
+          sortPaths: pimmslearn
   lint:
     name: Lint with ruff
     runs-on: ubuntu-latest
@@ -101,8 +105,12 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        os: ["ubuntu-latest", "macos-latest", "windows-latest"]
-        python-version: ["3.10", "3.11", "3.12"]
+        os: [
+            "ubuntu-latest",
+            "macos-latest",
+            #"windows-latest" # tk/tcl issue in current runner images
+          ]
+        python-version: ["3.11", "3.12", "3.13"]
     steps:
       - uses: actions/checkout@v4
         with:

.gitignore

@@ -45,4 +45,7 @@ workflows/maxquant/out/
 # builds
 docs/_*
 docs/reference
-build
+build
+
+#Mac
+*.DS_Store

docs/conf.py

@@ -15,9 +15,9 @@
 
 # -- Project information -----------------------------------------------------
 
-project = 'pimms'
-copyright = '2023, Henry Webel'
-author = 'Henry Webel'
+project = "pimms"
+copyright = "2023, Henry Webel"
+author = "Henry Webel"
 
 PACKAGE_VERSION = metadata.version("pimms-learn")
 version = PACKAGE_VERSION
@@ -30,25 +30,23 @@
 # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
 # ones.
 extensions = [
-    'sphinx.ext.napoleon',
-    'sphinx.ext.autodoc',
-    'sphinx.ext.autodoc.typehints',
-    'sphinx.ext.intersphinx',
-    'sphinx.ext.viewcode',
-    'myst_nb',
-    'sphinx_new_tab_link',
+    "sphinx.ext.napoleon",
+    "sphinx.ext.autodoc",
+    "sphinx.ext.autodoc.typehints",
+    "sphinx.ext.intersphinx",
+    "sphinx.ext.viewcode",
+    "myst_nb",
+    "sphinx_new_tab_link",
 ]
 
-myst_enable_extensions = [
-    "strikethrough",
-    "dollarmath",
-    "amsmath"
-]
+myst_enable_extensions = ["strikethrough", "dollarmath", "amsmath"]
 
 
 # Plolty support through require javascript library
 # https://myst-nb.readthedocs.io/en/latest/render/interactive.html#plotly
-html_js_files = ["https://cdnjs.cloudflare.com/ajax/libs/require.js/2.3.4/require.min.js"]
+html_js_files = [
+    "https://cdnjs.cloudflare.com/ajax/libs/require.js/2.3.4/require.min.js"
+]
 
 #  https://myst-nb.readthedocs.io/en/latest/computation/execute.html
 nb_execution_mode = "auto"
@@ -62,16 +60,17 @@
 nb_merge_streams = True
 
 # Add any paths that contain templates here, relative to this directory.
-templates_path = ['_templates']
+templates_path = ["_templates"]
 
 # List of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.
 # This pattern also affects html_static_path and html_extra_path.
-exclude_patterns = ['_build',
-                    'Thumbs.db',
-                    '.DS_Store',
-                    'jupyter_execute',  # avoid local re-execution of written nbs during development
-                    ]
+exclude_patterns = [
+    "_build",
+    "Thumbs.db",
+    ".DS_Store",
+    "jupyter_execute",  # avoid local re-execution of written nbs during development
+]
 
 # Intersphinx options
 intersphinx_mapping = {
@@ -88,8 +87,8 @@
 # The theme to use for HTML and HTML Help pages.  See the documentation for
 # a list of builtin themes.
 
-html_theme = 'sphinx_book_theme'  # pip install sphinx-book-theme
-html_logo = 'logos/logo.png'
+html_theme = "sphinx_book_theme"  # pip install sphinx-book-theme
+html_logo = "logos/logo.png"
 html_favicon = "logos/logo_thumbnail.png"
 
 # See:
@@ -135,17 +134,20 @@
 
     def run_apidoc(_):
         from sphinx.ext import apidoc
-        apidoc.main([
-            "--force",
-            "--implicit-namespaces",
-            "--module-first",
-            # "--separate",
-            "-o",
-            str(PROJECT_ROOT / "docs" / "reference"),
-            str(PACKAGE_ROOT),
-            str(PACKAGE_ROOT / "*.c"),
-            str(PACKAGE_ROOT / "*.so"),
-        ])
+
+        apidoc.main(
+            [
+                "--force",
+                "--implicit-namespaces",
+                "--module-first",
+                # "--separate",
+                "-o",
+                str(PROJECT_ROOT / "docs" / "reference"),
+                str(PACKAGE_ROOT),
+                str(PACKAGE_ROOT / "*.c"),
+                str(PACKAGE_ROOT / "*.so"),
+            ]
+        )
 
     def setup(app):
-        app.connect('builder-inited', run_apidoc)
+        app.connect("builder-inited", run_apidoc)

pimmslearn/__init__.py

@@ -9,6 +9,7 @@
 
 PyPI package is called pimms-learn (with a hyphen).
 """
+
 from __future__ import annotations
 
 # Set default logging handler to avoid "No handler found" warnings.
@@ -31,14 +32,14 @@
 
 savefig = pimmslearn.plotting.savefig
 
-__license__ = 'GPLv3'
+__license__ = "GPLv3"
 __version__ = metadata.version("pimms-learn")
 
-__all__ = ['logging', 'nb', 'pandas', 'plotting', 'savefig']
+__all__ = ["logging", "nb", "pandas", "plotting", "savefig"]
 
 # set some defaults
 
 
-njab.pandas.set_pandas_number_formatting(float_format='{:,.3f}')
+njab.pandas.set_pandas_number_formatting(float_format="{:,.3f}")
 
-pimmslearn.plotting.make_large_descriptors('x-large')
+pimmslearn.plotting.make_large_descriptors("x-large")

pimmslearn/analyzers/__init__.py

@@ -1,10 +1,10 @@
-"""General classes formalizing an experiment.
-"""
+"""General classes formalizing an experiment."""
+
 from types import SimpleNamespace
 
 from pimmslearn.analyzers import compare_predictions, diff_analysis
 
-__all__ = ['diff_analysis', 'compare_predictions', 'Analysis']
+__all__ = ["diff_analysis", "compare_predictions", "Analysis"]
 
 
 class Analysis(SimpleNamespace):