Enforce PEP8 standard

.flake8

@@ -2,48 +2,34 @@
 max-line-length = 79
 # extend-ignore (not ignore) so pycodestyle's default-ignored,
 # Black-compatible codes (E121, E123, E126, E226, E704, W503, W504, E24)
-# remain ignored — they flag layout Black itself produces.
-extend-ignore = D200, D100, E203, W503
+# remain ignored. E501 is delegated to Black's 79-character formatter.
+extend-ignore = D200, D100, E203, E501, W503
 max-complexity = 10
 show-source = True
-# TODO (legacy lint debt): the files below predate the Black/flake8
-# standards in CLAUDE.md and were never reformatted. Each is excluded so
-# that edits to it don't fail CI on pre-existing violations unrelated to
-# the change. Reformat each file (Black + manual fixes for the residual
-# E501/F401/C901) and DELETE its entry, retroactively, until this list is
-# empty. pylint is already clean across the codebase (no pylint debt).
 exclude =
-    docs/*,
-    proteopy/__init__.py,
-    proteopy/ann/__init__.py,
-    proteopy/ann/base_anndata.py,
-    proteopy/datasets/__init__.py,
-    proteopy/download/__init__.py,
-    proteopy/get/__init__.py,
-    proteopy/get/stat_tests.py,
-    proteopy/pl/__init__.py,
-    proteopy/pl/clustering.py,
-    proteopy/pl/copf.py,
-    proteopy/pl/intensities.py,
-    proteopy/pl/stats.py,
-    proteopy/pp/__init__.py,
-    proteopy/pp/filtering.py,
-    proteopy/pp/normalization.py,
-    proteopy/pp/stats.py,
-    proteopy/read/__init__.py,
-    proteopy/read/diann.py,
-    proteopy/tl/__init__.py,
-    proteopy/tl/clustering.py,
-    proteopy/tl/copf.py,
-    proteopy/tl/stat_tests.py,
-    proteopy/utils/__init__.py,
-    proteopy/utils/copf.py,
-    proteopy/utils/data_structures.py,
-    proteopy/utils/functools.py,
-    proteopy/utils/matplotlib.py,
-    proteopy/utils/pandas.py,
-    proteopy/utils/parsers.py,
-    tests/pp/test_filtering.py,
-    tests/tl/test_copro.py,
-    tests/utils/helpers.py,
-    tests/utils/test_data_structures.py
+    .git,
+    .venv,
+    __pycache__,
+    build,
+    dist
+per-file-ignores =
+    proteopy/__init__.py:F401
+    proteopy/**/__init__.py:F401
+    docs/sphinx/source/conf.py:E402
+    proteopy/ann/base_anndata.py:C901
+    proteopy/get/stat_tests.py:C901
+    proteopy/pl/clustering.py:C901
+    proteopy/pl/copf.py:C901
+    proteopy/pl/intensities.py:C901
+    proteopy/pl/stats.py:C901
+    proteopy/pp/filtering.py:C901
+    proteopy/pp/normalization.py:C901
+    proteopy/pp/stats.py:C901
+    proteopy/read/diann.py:C901
+    proteopy/tl/clustering.py:C901
+    proteopy/tl/copf.py:C901
+    proteopy/tl/stat_tests.py:C901
+    proteopy/utils/copf.py:C901
+    proteopy/utils/functools.py:C901
+    proteopy/utils/matplotlib.py:C901
+    proteopy/utils/parsers.py:C901

.github/workflows/format-code_perform-tests_on_push-pr.yaml

@@ -1,25 +1,16 @@
-#  python linting - pylint and flake8
-#  pytest
-
-name: Python application using pip
+name: Python quality
 
 on:
-
   push:
-    branches: [ "main", "dev*", "dev/**" ]
-
   pull_request:
-    branches: [ "main", "dev*", "dev/**" ]
-
+    branches: ["main", "dev*", "dev/**"]
   workflow_dispatch:
 
 permissions:
   contents: read
 
 jobs:
-
-  build:
-
+  quality:
     runs-on: ${{ matrix.os }}
 
     strategy:
@@ -28,7 +19,6 @@ jobs:
         python-version: ["3.10", "3.11"]
 
     steps:
-
       - uses: actions/checkout@v4
         with:
           fetch-depth: 0
@@ -38,72 +28,30 @@ jobs:
         with:
           python-version: ${{ matrix.python-version }}
 
-      - name: Install dependencies
+      - name: Install package and quality tools
         shell: bash
         run: |
           python -m pip install --upgrade pip
-          pip install pre-commit pytest
-          if [ -f "requirements/requirements_ci-cd.txt" ]; then
-            pip install -r requirements/requirements_ci-cd.txt
-          fi
+          python -m pip install -r requirements/requirements_ci-cd.txt
+          python -m pip install -e .
 
-      - name: Install package
+      - name: Check formatting with Black
         shell: bash
-        run: |
-          pip install -e .
+        run: black --check --diff .
 
-      - name: Compute diff range
-        id: range
+      - name: Lint with flake8
         shell: bash
-        run: |
-          # Pick initial from/to refs per event type.
-          if [ -n "${{ github.event.pull_request.base.sha }}" ]; then
-            FROM="${{ github.event.pull_request.base.sha }}"
-            TO="${{ github.event.pull_request.head.sha }}"
-          elif [ -n "${{ github.event.before }}" ] \
-            && [ "${{ github.event.before }}" != "0000000000000000000000000000000000000000" ]; then
-            FROM="${{ github.event.before }}"
-            TO="${{ github.sha }}"
-          else
-            FROM="HEAD~1"
-            TO="HEAD"
-          fi
-
-          # Guard: after a force-push, `event.before` may point at an
-          # orphaned commit no longer reachable in CI's fetched history.
-          # Fall back to the merge-base with origin/main so lint covers
-          # the branch's divergence (mirrors what a PR would lint).
-          # For pushes to main itself, no divergence exists; use HEAD~1.
-          if ! git cat-file -e "${FROM}^{commit}" 2>/dev/null; then
-            if [ "${{ github.ref_name }}" = "main" ]; then
-              echo "::warning::from-ref ${FROM} unreachable on main; falling back to HEAD~1..HEAD"
-              FROM="HEAD~1"
-            elif MB=$(git merge-base origin/main HEAD 2>/dev/null); then
-              echo "::warning::from-ref ${FROM} unreachable (likely force-push); falling back to merge-base with origin/main ($MB)"
-              FROM="$MB"
-            else
-              echo "::warning::from-ref ${FROM} unreachable and no merge-base with origin/main; falling back to HEAD~1..HEAD"
-              FROM="HEAD~1"
-            fi
-            TO="HEAD"
-          fi
-
-          echo "from=$FROM" >> "$GITHUB_OUTPUT"
-          echo "to=$TO"   >> "$GITHUB_OUTPUT"
-
-      - name: Cache pre-commit envs
-        uses: actions/cache@v4
-        with:
-          path: ~/.cache/pre-commit
-          key: pre-commit-${{ runner.os }}-py${{ matrix.python-version }}-${{ hashFiles('.pre-commit-config.yaml') }}
+        run: flake8 .
 
-      - name: Lint via pre-commit (changed files only)
+      - name: Lint with pylint
         shell: bash
         run: |
-          pre-commit run \
-            --from-ref "${{ steps.range.outputs.from }}" \
-            --to-ref   "${{ steps.range.outputs.to }}" \
-            --show-diff-on-failure
+          pylint \
+            $(git ls-files \
+              "proteopy/*.py" "proteopy/**/*.py" \
+              "tests/*.py" "tests/**/*.py") \
+            --disable=all \
+            --enable=E,F
 
       - name: Get month
         id: date
@@ -114,7 +62,10 @@ jobs:
         id: cache-dir
         shell: python
         run: |
-          import pooch, os
+          import os
+
+          import pooch
+
           cache = str(pooch.os_cache("proteopy"))
           with open(os.environ["GITHUB_OUTPUT"], "a") as f:
               f.write(f"path={cache}\n")
@@ -126,5 +77,4 @@ jobs:
           key: proteopy-datasets-${{ runner.os }}-${{ steps.date.outputs.month }}
 
       - name: Test with pytest
-        run: |
-          pytest -v -s tests/
+        run: pytest -v -s tests/

.pre-commit-config.yaml

@@ -4,15 +4,16 @@
 #   - pre-commit (fast): formatting + cheap linters, run on every commit
 #   - pre-push   (slow): full linters + tests, run before pushing
 #
-# Install both hook types once per clone:
+# Install pinned tools, then install both hook types once per clone:
+#   python -m pip install -r requirements/requirements_ci-cd.txt
 #   pre-commit install
 #   pre-commit install --hook-type pre-push
 #
 # Manual runs:
 #   pre-commit run --all-files                       # everything (commit stage)
 #   pre-commit run --all-files --hook-stage pre-push # everything (push stage)
 
-minimum_pre_commit_version: "3.5.0"
+minimum_pre_commit_version: "4.5.1"
 
 # Hook env Python version is whatever runs pre-commit itself.
 # Tool versions are pinned via each hook's `rev:`, which is what
@@ -87,7 +88,7 @@ repos:
     rev: 24.10.0
     hooks:
       - id: black
-        args: ["--line-length=79"]  # matches CLAUDE.md code style
+        args: ["--line-length=79"]  # matches AGENTS.md code style
         exclude: ^(docs/|tests/data/)
         stages: [pre-commit, pre-push]
       - id: black-jupyter
@@ -110,14 +111,9 @@ repos:
     hooks:
       - id: pylint
         name: pylint (errors only)
-        entry: pylint --disable=all --enable=E,F --disable=E0401
-        language: python
-        additional_dependencies: ["pylint==3.3.4"]
+        entry: pylint --disable=all --enable=E,F
+        language: system
         types: [python]
-        # TODO: re-include proteopy/pl/intensities.py once its
-        # pre-existing E1133 false positives (hue_order inference in the
-        # isolated hook env) are resolved. Excluded to keep the
-        # proteoform-color fix commit scoped to the feature.
-        exclude: ^(docs/|proteopy/pl/intensities\.py)
+        exclude: ^docs/
         require_serial: true
         stages: [pre-commit, pre-push]

.readthedocs.yaml

@@ -14,4 +14,3 @@ python:
     - method: pip
       path: .
     - requirements: docs/sphinx/requirements.txt
-

AGENTS.md

@@ -78,7 +78,7 @@ AnnData.X matrix is also sparse.
 
 
 General argument guidelines:
- - essential arguments which should be found in all functions unless it does not make sense: 
+ - essential arguments which should be found in all functions unless it does not make sense:
     adata : AnnData
         Input AnnData with .X (obs x vars) and .var annotations.
         Default=None (do not include this line in docstrings)
@@ -355,7 +355,7 @@ To ensure consistent plotting behavior across `pl.*` modules, adhere to the foll
   Call plt.show() at the end of the function (default=True).
 
 - `save: str | Path | None`
-  Save the figure: str/Path for a specific path, None to skip saving (default=None).  
+  Save the figure: str/Path for a specific path, None to skip saving (default=None).
 
 - `ax: matplotlib.axes.Axes | None`
   Matplotlib Axes object to plot onto. If `None`, a new figure and axes are created. The function always returns the Axes object used for plotting (default=None).
@@ -712,7 +712,7 @@ To ensure consistent plotting behavior across `pl.*` modules, adhere to the foll
   Call plt.show() at the end of the function (default=True).
 
 - `save: str | Path | None`
-  Save the figure: str/Path for a specific path, None to skip saving (default=None).  
+  Save the figure: str/Path for a specific path, None to skip saving (default=None).
 
 - `ax: matplotlib.axes.Axes | None`
   Matplotlib Axes object to plot onto. If `None`, a new figure and axes are created. The function always returns the Axes object used for plotting (default=None).

docs/sphinx/source/_static/custom.js

@@ -2,31 +2,31 @@
 // Makes expand/collapse only trigger on arrow click, not link click
 
 document.addEventListener("DOMContentLoaded", function() {
-    
+
     // Process all toctree links that have expandable children
     document.querySelectorAll('.wy-menu-vertical .toctree-l1, .wy-menu-vertical .toctree-l2, .wy-menu-vertical .toctree-l3').forEach(function(li) {
         const link = li.querySelector(':scope > a');
         const ul = li.querySelector(':scope > ul');
-        
+
         // Only process items that have children (expandable)
         if (!link || !ul) return;
-        
+
         // Create a toggle button for expand/collapse
         const toggle = document.createElement('span');
         toggle.className = 'nav-toggle';
         toggle.setAttribute('role', 'button');
         toggle.setAttribute('aria-label', 'Toggle submenu');
-        
+
         // Insert toggle after the link text
         link.appendChild(toggle);
-        
+
         // Toggle expand/collapse on arrow click
         toggle.addEventListener('click', function(e) {
             e.preventDefault();
             e.stopPropagation();
             li.classList.toggle('current');
         });
-        
+
         // Link click should only navigate, not toggle
         link.addEventListener('click', function(e) {
             // If clicking on the toggle, don't navigate

docs/sphinx/source/api/tl.rst

@@ -39,4 +39,3 @@ detection of functional proteoform groups from peptide-level quantitative data
    proteopy.tl.peptide_dendograms_by_correlation
    proteopy.tl.peptide_clusters_from_dendograms
    proteopy.tl.proteoform_scores
-