deps: Re-resolve pixi.lock, and stop tracking generated version.py

.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

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))
 

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. Do not edit by hand.

pyproject.toml

@@ -33,9 +33,8 @@ include-package-data = true
 dependencies = { file = ["admin/requirements.txt"] }
 
 [tool.setuptools_scm]
-version_file = "singlem/version.py"
 # Otherwise the push to pypi will fail on GitHub actions, because the version is malformed.
-version_scheme = "only-version"
+version_scheme = "guess-next-dev"
 local_scheme = "no-local-version"
 
 [tool.uv.sources]

singlem/__init__.py

@@ -1,5 +1,13 @@
 
-from .version import __version__
+try:
+    from importlib.metadata import version as _pkg_version, PackageNotFoundError
+    __version__ = _pkg_version("singlem")
+except (ImportError, PackageNotFoundError):
+    # 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'