diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml index 313b1ee..a76d63f 100644 --- a/.github/workflows/tests.yml +++ b/.github/workflows/tests.yml @@ -26,7 +26,7 @@ jobs: gtfparse: "gtfparse>=3.0.2,<4" - python-version: "3.11" pandas: "pandas>=2.2.2,<3" - gtfparse: "gtfparse==2.9.1" + gtfparse: "gtfparse>=3.0.2,<4" - python-version: "3.11" pandas: "pandas>=3,<4" gtfparse: "gtfparse>=3.0.2,<4" diff --git a/CHANGELOG.md b/CHANGELOG.md index 67b82dc..7f84b10 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,5 +1,10 @@ # Change Log +## [v10.11.9](https://github.com/openvax/varcode/tree/v10.11.9) (2026-10-06) + +- Require gtfparse 3.0.2+ across the supported Python/pandas matrix, coordinated + with Topiary 5.94.2's gtfparse 3 migration (openvax/topiary#484). + ## [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 diff --git a/docs/getting_started.md b/docs/getting_started.md index d6efd77..1e4eed0 100644 --- a/docs/getting_started.md +++ b/docs/getting_started.md @@ -10,7 +10,7 @@ use Python 3.9 or later. pip install varcode ``` -Varcode requires PyEnsembl 2.24.1+ and gtfparse 2.9.1+, and supports pandas +Varcode requires PyEnsembl 2.24.1+ and gtfparse 3.0.2+, 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: @@ -19,8 +19,8 @@ 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. +Environments shared with Topiary require Topiary 5.94.2 or later for its +gtfparse 3 support. ## Reference data diff --git a/requirements.txt b/requirements.txt index dbc8fd8..b38b8eb 100644 --- a/requirements.txt +++ b/requirements.txt @@ -1,7 +1,7 @@ numpy>=2.0.0,<3.0.0 pandas>=2.2.2,<4.0.0 pyensembl>=2.24.1 -gtfparse>=2.9.1,<4.0.0 +gtfparse>=3.0.2,<4.0.0 memoized_property>=1.0.2 serializable>=1.1.0 sercol>=1.0.3 diff --git a/tests/README.md b/tests/README.md index e4cfe6b..f9b1003 100644 --- a/tests/README.md +++ b/tests/README.md @@ -34,8 +34,7 @@ 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 3.9/3.10/3.11/3.12. 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+. +Python 3.9/3.10 use pandas 2. All jobs require gtfparse 3.0.2+. To reproduce this locally, first install the development tools and reference releases from [CONTRIBUTING.md](../CONTRIBUTING.md), then: diff --git a/varcode/version.py b/varcode/version.py index 5a16b3f..a65cffb 100644 --- a/varcode/version.py +++ b/varcode/version.py @@ -1 +1 @@ -__version__ = "10.11.8" +__version__ = "10.11.9"