Add more support for typing, fix some typing-related edge case bugs

.github/workflows/publish.yml

@@ -19,7 +19,7 @@ jobs:
       - name: Set up Python
         uses: actions/setup-python@v5
         with:
-          python-version: "3.9"
+          python-version: "3.10"
 
       - name: Install dependencies
         run: |

.github/workflows/test.yml

@@ -13,25 +13,30 @@ jobs:
     steps:
       - uses: actions/checkout@v4
 
-      - name: Set up Python 3.9
+      - name: Set up Python
         uses: actions/setup-python@v5
         with:
-          python-version: "3.9"
+          python-version: "3.10"
 
-      - name: Install dependencies
-        run: |
-          python -m pip install --upgrade pip
-          pip install ruff
+      - name: Lint with Ruff
+        uses: astral-sh/ruff-action@v3
+        with:
+          args: check --exclude docs,tests
 
-      - name: Check with Ruff
-        run: ruff check --output-format=github .
+      - name: Check formatting with Ruff
+        uses: astral-sh/ruff-action@v3
+        with:
+          args: format --check --diff --exclude docs,tests
 
       - name: Install package and its dependencies
         run: pip install --editable .[dev,idxml]
 
+      - name: Static type checking with mypy
+        run: mypy --non-interactive
+
       - name: Test with pytest and codecov
         run: |
-          pytest --cov=psm_utils  --cov-report=xml tests/
+          pytest --cov=psm_utils --cov-report=xml tests/
 
       - name: Upload coverage reports to Codecov
         uses: codecov/codecov-action@v3
@@ -46,7 +51,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ["3.8", "3.9", "3.10", "3.11", "3.12", "3.13"]
+        python-version: ["3.10", "3.11", "3.12", "3.13"]
     steps:
       - uses: actions/checkout@v4
 

online/Home.py

@@ -4,6 +4,8 @@
 
 
 class StreamlitPageHome(StreamlitPage):
+    """Streamlit page for the home section."""
+
     def _main_page(self):
         pass
 

online/_utils.py

@@ -11,6 +11,7 @@ class ECDF:
     ----------
     x : array_like
         Observations
+
     """
 
     def __init__(self, x):
@@ -101,15 +102,15 @@ def pp_plot(psm_df):
 
 def fdr_plot(psm_df, fdr_threshold):
     """Plot number of identifications in function of FDR threshold."""
-    df = (
+    target_psm_df = (
         psm_df[~psm_df["is_decoy"]]
         .reset_index(drop=True)
         .sort_values("qvalue", ascending=True)
         .copy()
     )
-    df["count"] = (~df["is_decoy"]).cumsum()
+    target_psm_df["count"] = (~target_psm_df["is_decoy"]).cumsum()
     fig = px.line(
-        df,
+        target_psm_df,
         x="qvalue",
         y="count",
         log_x=True,

psm_utils/__main__.py

@@ -32,6 +32,7 @@
 
 
 def main():
+    """Run the main entry point for the psm_utils CLI."""
     logging.basicConfig(
         level="NOTSET",
         format="%(message)s",
@@ -47,6 +48,7 @@ def main():
 
 @click.group()
 def cli():
+    """Command line interface for psm_utils."""
     pass