From 7f16ca0a199b82ec0fd71546e8ba30153e90fb34 Mon Sep 17 00:00:00 2001 From: Ben Woodcroft Date: Tue, 8 Sep 2026 17:28:33 +1000 Subject: [PATCH 1/2] deps: Re-resolve pixi.lock, and stop tracking generated version.py. `pixi update` was unsolvable: admin/requirements.txt was committed with pins from the v0.21.3 release (tqdm==4.67.3), which conflict with whatever the fresh conda solve picks (tqdm 4.70.0). The tracked file is now the stub again, as .gitignore already documents - the pinned version is generated by admin/build_dep_defs_from_pixi.py locally and in CI before the wheel build. Notable updates: diamond 2.2.0 -> 2.2.6, smafa 0.8.0 -> 0.9.0, polars 1.40.1 -> 1.44.1, pyarrow 24 -> 25, sqlalchemy 2.0.49 -> 2.0.52, sqlparse 0.5.5 -> 0.6.0, tqdm 4.67.3 -> 4.70.0, biopython 1.87 -> 1.88, bird_tool_utils 0.6.0 -> 0.7.2, numpy 2.4.4 -> 2.5.3. The version.py changes are ported from dev (707c1f8, and the non-lock part of 6e3c5cf) so the two branches agree: __init__.py reads the installed package metadata, and setuptools_scm no longer writes a tracked singlem/version.py. That untracking needs two fixes dev does not yet have. In admin/release.py the --force-write-version-files step now writes nothing, so `git commit -a` would fail with nothing to commit; the tag is applied to the already-clean HEAD instead. And publish-to-pypi.yml needs fetch-depth: 0, because the wheel version now comes from `git describe` rather than the committed version.py. Full test suite passes: 224 passed, 25 skipped. Co-Authored-By: Claude Opus 5 (1M context) --- .github/workflows/publish-to-pypi.yml | 5 + admin/release.py | 13 +- admin/requirements.txt | 21 +- pixi.lock | 8172 ++++++++++++++----------- pyproject.toml | 3 +- singlem/__init__.py | 6 +- singlem/version.py | 34 - 7 files changed, 4593 insertions(+), 3661 deletions(-) delete mode 100644 singlem/version.py diff --git a/.github/workflows/publish-to-pypi.yml b/.github/workflows/publish-to-pypi.yml index 5684e319..2425ba58 100644 --- a/.github/workflows/publish-to-pypi.yml +++ b/.github/workflows/publish-to-pypi.yml @@ -9,6 +9,11 @@ jobs: runs-on: ubuntu-latest steps: - uses: actions/checkout@v2 + with: + # setuptools_scm derives the version from the git tag, so the tags + # (and history) must be present - singlem/version.py is no longer + # committed. + fetch-depth: 0 - uses: actions/setup-python@v2 # admin/requirements.txt is tracked only as a stub; the real pinned # contents are generated here from pixi.toml/pixi.lock so setuptools diff --git a/admin/release.py b/admin/release.py index 2aacb1b1..0317e8fc 100755 --- a/admin/release.py +++ b/admin/release.py @@ -31,6 +31,11 @@ print("Building dependency definition files based on pixi.toml and pixi.lock") # TODO: Do we need to update pixi.lock first? extern.run('pixi run admin/build_dep_defs_from_pixi.py') + # admin/requirements.txt is only tracked as a stub - committing the pinned + # versions makes future `pixi update` runs unsolvable, because the pins + # conflict with the fresh conda solve. CI regenerates the pinned file from + # pixi.lock before building the wheel. + extern.run('git checkout -- admin/requirements.txt') print("building docs") extern.run("pixi run python3 admin/build_docs.py --version {}".format(version)) @@ -40,12 +45,8 @@ ) extern.run('if [[ $(git diff --shortstat 2> /dev/null | tail -n1) != "" ]]; then exit 1; fi') - # Generate the version file based on the git tag - extern.run("pixi run -e dev bash -c 'SETUPTOOLS_SCM_PRETEND_VERSION={} python -m setuptools_scm --force-write-version-files'".format(version)) - - print("Committing the version file") - extern.run('git commit -a -m "v{}"'.format(version)) - + # No version file is committed - singlem/__init__.py reads the installed + # package metadata, which setuptools_scm derives from the tag below. print("Tagging the release as v{}".format(version)) extern.run('git tag v{}'.format(version)) diff --git a/admin/requirements.txt b/admin/requirements.txt index 5ed6b823..3f9fbc17 100644 --- a/admin/requirements.txt +++ b/admin/requirements.txt @@ -1,17 +1,4 @@ -# This file was autogenerated by build_dep_defs_from_pixi.py - do not change manually. -biopython==1.87 -bird_tool_utils==0.6.0 -extern==0.4.1 -fastalite -graftm==0.15.1 -Jinja2==3.1.6 -pip==26.1.1 -polars==1.40.1 -pyarrow==24.0.0 -pyranges==0.1.4 -seqmagick==0.8.6 -SQLAlchemy==2.0.49 -sqlparse==0.5.5 -squarify==0.4.3 -tqdm==4.67.3 -zenodo_backpack==0.4.0 +# Stub file — pyproject.toml requires this to exist for setuptools to read +# `[project].dependencies`. The real contents are generated from pixi.toml +# and pixi.lock by admin/build_dep_defs_from_pixi.py, which runs locally +# during release and in CI before the PyPI build. 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-__all__ = [ - "__version__", - "__version_tuple__", - "version", - "version_tuple", - "__commit_id__", - "commit_id", -] - -TYPE_CHECKING = False -if TYPE_CHECKING: - from typing import Tuple - from typing import Union - - VERSION_TUPLE = Tuple[Union[int, str], ...] - COMMIT_ID = Union[str, None] -else: - VERSION_TUPLE = object - COMMIT_ID = object - -version: str -__version__: str -__version_tuple__: VERSION_TUPLE -version_tuple: VERSION_TUPLE -commit_id: COMMIT_ID -__commit_id__: COMMIT_ID - -__version__ = version = '0.21.4' -__version_tuple__ = version_tuple = (0, 21, 4) - -__commit_id__ = commit_id = None From 0e58bf3908cfe152bec802f4cd3afdadee520024 Mon Sep 17 00:00:00 2001 From: Ben Woodcroft Date: Tue, 8 Sep 2026 17:35:59 +1000 Subject: [PATCH 2/2] fix: Do not import the deleted version module as a fallback. Codex review on #322: with singlem/version.py untracked and no longer generated, `from .version import __version__` raises ModuleNotFoundError whenever importlib.metadata finds no installed distribution. Reproduced on a pristine clone: ModuleNotFoundError: No module named 'singlem.version' The same path is taken on python <3.8, which has no importlib.metadata at all, and pyproject.toml still declares requires-python = ">=3.7". Fall back to 'unknown' instead. Installed and editable installs are unaffected, they read the version from the distribution metadata as before. Co-Authored-By: Claude Opus 5 (1M context) --- singlem/__init__.py | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/singlem/__init__.py b/singlem/__init__.py index eb4d0155..9b81adca 100644 --- a/singlem/__init__.py +++ b/singlem/__init__.py @@ -3,7 +3,11 @@ from importlib.metadata import version as _pkg_version, PackageNotFoundError __version__ = _pkg_version("singlem") except (ImportError, PackageNotFoundError): - from .version import __version__ + # Either python <3.8, which has no importlib.metadata, or singlem was + # imported from a source tree that has never been built or installed, so + # there is no distribution metadata to read. setuptools_scm no longer + # writes singlem/version.py, so there is nothing to fall back to. + __version__ = 'unknown' OTU_TABLE_OUTPUT_FORMAT = 'standard' ARCHIVE_TABLE_OUTPUT_FORMAT = 'archive'