Raise Python floor to 3.11, test through 3.14, drop dead testing extra (2.2.0)

.github/workflows/lint.yml

@@ -32,17 +32,23 @@ jobs:
             echo "BRANCH_NAME=$(echo ${GITHUB_REF#refs/heads/})" >> $GITHUB_ENV
           fi
 
-      # Step 3: Install dependencies
+      # Step 3: Set up Python
+      - name: Set up Python 3.14
+        uses: actions/setup-python@v7
+        with:
+          python-version: '3.14'
+
+      # Step 4: Install dependencies
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip
           pip install tox
 
-      # Step 4: Run Tox for Linting
+      # Step 5: Run Tox for Linting
       - name: Run Tox Lint
         run: tox -e flake8
 
-      # Step 5: Commit and push changes if Black reformats files
+      # Step 6: Commit and push changes if Black reformats files
       - name: Commit and push changes
         run: |
           git config --global user.name "GitHub Actions"

.github/workflows/tests.yml

@@ -10,7 +10,7 @@ jobs:
     strategy:
       matrix:
         os: [ubuntu-latest, macos-latest]
-        python-version: ['3.10', '3.11', '3.12']
+        python-version: ['3.11', '3.12', '3.13', '3.14']
 
     steps:
     - uses: actions/checkout@v7

CHANGELOG.md

@@ -6,6 +6,12 @@
 * planned new feature: during import of long reads, (optionally) correct for short exon alignment issues.
 * separate new read import and classification of isoforms.
 
+## [2.2.0]
+
+* **breaking**: dropped support for Python 3.10; `requires-python` is now `>=3.11`. CI now tests 3.11-3.14 (added 3.13 and 3.14); verified the full dependency stack (numba, llvmlite, pyhmmer, CPAT, intervaltree) has published wheels for 3.14
+* removed the unused `pyproject.toml` `[project.optional-dependencies] testing` extra -- nothing installed from it (`tox.ini` uses `requirements_dev.txt` directly), and it referenced `mypy`, which isn't run anywhere in CI
+* regenerated the `requirements.txt` lock file under Python 3.14
+
 ## [2.1.6]
 
 * new: `export_end_sequences` now includes strand in the fasta header (`chrom:start-end:strand`)

VERSION.txt

@@ -1 +1 @@
-2.1.6
+2.2.0

pyproject.toml

@@ -10,7 +10,7 @@ authors = [
 ]
 description = "Framework for the analysis of long read transcriptome sequencing data"
 readme = "README.md"
-requires-python = ">=3.10"
+requires-python = ">=3.11"
 classifiers = [
     "Programming Language :: Python :: 3",
     "Operating System :: MacOS",
@@ -41,15 +41,6 @@ dependencies = [
 [project.scripts]
 run_isotools = "isotools.run_isotools:main"
 
-[project.optional-dependencies]
-testing = [
-    "pytest>=6.0",
-    "pytest-cov>=2.0",
-    "mypy>=0.910",
-    "flake8>=3.9",
-    "tox>=3.24",
-]
-
 [project.urls]
 Homepage = "https://github.com/HerwigLab/IsoTools2"
 Documentation = "https://isotools.readthedocs.io/"

requirements.txt

@@ -4,29 +4,29 @@
 # Regenerate with:
 #   python -m venv /tmp/isotools-lock && source /tmp/isotools-lock/bin/activate
 #   pip install .
-#   pip freeze | grep -v '^isotools==' > requirements.txt
-CPAT==3.0.5
+#   pip freeze | grep -v '^isotools' > requirements.txt
 biopython==1.88
 certifi==2026.7.22
-charset-normalizer==3.4.9
+charset-normalizer==3.5.1
 contourpy==1.3.3
+CPAT==3.0.5
 cycler==0.12.1
 fonttools==4.63.0
-idna==3.18
+idna==3.19
 intervaltree==3.2.1
 joblib==1.5.3
 kiwisolver==1.5.0
-llvmlite==0.48.0
+llvmlite==0.49.0
 matplotlib==3.11.1
 narwhals==2.24.0
-numba==0.66.0
-numpy==2.4.6
+numba==0.67.0
+numpy==2.5.2
 packaging==26.3
 pandas==3.0.5
 patsy==1.0.2
 pillow==12.3.0
 psutil==7.2.2
-pyhmmer==0.12.1
+pyhmmer==0.12.3
 pynndescent==0.6.0
 pyparsing==3.3.2
 pysam==0.24.0

tox.ini

@@ -1,13 +1,14 @@
 [tox]
 minversion = 4.0.0
-envlist = py310, py311, py312, flake8
+envlist = py311, py312, py313, py314, flake8
 isolated_build = true
 
 [gh-actions]
 python =
-    3.10: py310
     3.11: py311
-    3.12: py312, flake8
+    3.12: py312
+    3.13: py313
+    3.14: py314, flake8
 
 [testenv]
 setenv =
@@ -18,7 +19,7 @@ commands =
     pytest --basetemp={envtmpdir}
 
 [testenv:flake8]
-basepython = python3.12
+basepython = python3.14
 deps =
     -r{toxinidir}/requirements_dev.txt
 commands =