Use current PyEnsembl and gtfparse with explicit pandas 3 coverage

.github/workflows/tests.yml

@@ -17,7 +17,22 @@ jobs:
     strategy:
       fail-fast: true
       matrix:
-        python-version: ["3.9", "3.10", "3.11"]
+        include:
+          - python-version: "3.9"
+            pandas: "pandas>=2.2.2,<3"
+            gtfparse: "gtfparse>=3.0.2,<4"
+          - python-version: "3.10"
+            pandas: "pandas>=2.2.2,<3"
+            gtfparse: "gtfparse>=3.0.2,<4"
+          - python-version: "3.11"
+            pandas: "pandas>=2.2.2,<3"
+            gtfparse: "gtfparse==2.9.1"
+          - python-version: "3.11"
+            pandas: "pandas>=3,<4"
+            gtfparse: "gtfparse>=3.0.2,<4"
+          - python-version: "3.12"
+            pandas: "pandas>=3,<4"
+            gtfparse: "gtfparse>=3.0.2,<4"
 
     steps:
       - name: Checkout repository
@@ -29,10 +44,13 @@ jobs:
           cache: pip
           cache-dependency-path: requirements.txt
       - name: Install dependencies
+        env:
+          PANDAS_REQUIREMENT: ${{ matrix.pandas }}
+          GTFPARSE_REQUIREMENT: ${{ matrix.gtfparse }}
         run: |
           python -m pip install --upgrade pip
           python -m pip install flake8 pytest pytest-cov coveralls ruff build 'setuptools>=64'
-          pip install -r requirements.txt
+          python -m pip install -r requirements.txt "$PANDAS_REQUIREMENT" "$GTFPARSE_REQUIREMENT"
       - name: Verify, build and install the source distribution
         run: |
           python -m pytest -q tests/test_source_distribution.py
@@ -42,6 +60,8 @@ jobs:
           # Osteosarc 0.14.x supports every Python version in this matrix;
           # run native adapter checks against the bundled historical snapshot.
           python -m pip install "$RUNNER_TEMP/varcode-sdist[test-data]"
+          python -m pip check
+          python -m pip show pandas pyensembl gtfparse
       - name: Lint with flake8
         run: |
           # stop the build if there are Python syntax errors or undefined names
@@ -86,7 +106,7 @@ jobs:
       # the shared point-edit domain; the full suite above separately checks
       # SV refusal, partial plugins, and explicit dual-annotator regressions.
       - name: Cross-annotator parity gate (shared point-edit domain)
-        if: matrix.python-version == '3.11'
+        if: matrix.python-version == '3.11' && matrix.pandas == 'pandas>=3,<4'
         working-directory: ${{ runner.temp }}/varcode-sdist
         env:
           COVERAGE_FILE: .coverage.parity

CHANGELOG.md

@@ -1,5 +1,13 @@
 # Change Log
 
+## [v10.11.8](https://github.com/openvax/varcode/tree/v10.11.8) (2026-10-06)
+
+- Require PyEnsembl 2.24.1+ and gtfparse 2.9.1+, with explicit coverage of
+  gtfparse 3.0.2+. Support pandas 2.2.2+ and 3.x, retaining Python 3.9/3.10
+  and existing Topiary dependency compatibility.
+- Explicitly test pandas 2 and 3 on Python 3.11, plus pandas 3 on Python 3.12,
+  including the installed source distribution and cross-annotator parity.
+
 ## [v10.11.7](https://github.com/openvax/varcode/tree/v10.11.7) (2026-10-06)
 
 - Cache RNA variant support counts under the variant key, keeping it separate

docs/getting_started.md

@@ -10,6 +10,18 @@ use Python 3.9 or later.
 pip install varcode
 ```
 
+Varcode requires PyEnsembl 2.24.1+ and gtfparse 2.9.1+, and supports pandas
+2.2.2+ and 3.x. To upgrade an existing environment to pandas 3, use Python
+3.11 or later and run:
+
+```bash
+pip install --upgrade varcode pyensembl 'gtfparse>=3.0.2,<4' 'pandas>=3,<4'
+```
+
+Python 3.9 and 3.10 remain supported with pandas 2.
+Environments shared with Topiary can keep gtfparse 2.9.1 until its
+[gtfparse 3 migration](https://github.com/openvax/topiary/issues/484) ships.
+
 ## Reference data
 
 Varcode uses [PyEnsembl](https://github.com/openvax/pyensembl) for gene annotations

requirements.txt

@@ -1,6 +1,7 @@
 numpy>=2.0.0,<3.0.0
-pandas>=2.0.0,<4.0.0
-pyensembl>=2.6.4
+pandas>=2.2.2,<4.0.0
+pyensembl>=2.24.1
+gtfparse>=2.9.1,<4.0.0
 memoized_property>=1.0.2
 serializable>=1.1.0
 sercol>=1.0.3

tests/README.md

@@ -32,7 +32,11 @@ uses the installed backend without downloading build dependencies.
 
 CI builds and unpacks the source distribution outside the checkout, installs
 that source with the `test-data` extra, and runs the full suite and parity
-checks from the unpacked directory on Python 3.9/3.10/3.11. To reproduce this
+checks from the unpacked directory on Python 3.9/3.10/3.11/3.12. Python 3.11
+tests both pandas 2 and 3; Python 3.12 and the parity gate use pandas 3.
+Python 3.9/3.10 use pandas 2. The Python 3.11/pandas 2 job also checks the
+gtfparse 2.9.1 compatibility floor; other jobs require gtfparse 3.0.2+.
+To reproduce this
 locally, first install the development tools and reference releases from
 [CONTRIBUTING.md](../CONTRIBUTING.md), then:
 

varcode/version.py

@@ -1 +1 @@
-__version__ = "10.11.7"
+__version__ = "10.11.8"