Skip name-sort (perf) + rename to filtersam-tools + PyPI publishing#8
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The identity and matched filters evaluate each segment independently, so the parallel chunks do not need reads grouped by query name. Pass sort_by_name=False to parallelizeBAMoperation so it skips the full serial samtools name-sort that dominated runtime on large files and made parallel mode slower than single-processor mode. Requires the sort_by_name option added in parallelbam 0.0.20, so: - bump the dependency to parallelbam>=0.0.20 (setup.py, requirements.txt); - CI installs parallelbam from the repo until 0.0.20 is on PyPI. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
Re-publishing under a new PyPI account requires a new distribution name (the old `filtersam` name belongs to the previous account). The import name is unchanged (`import filtersam`); only `pip install` changes to `filter-sam`. The parallelbam dependency is likewise renamed to `parallel-bam>=0.0.20`. - setup.py: NAME -> 'filter-sam'; dependency -> 'parallel-bam>=0.0.20'. - requirements.txt: parallel-bam>=0.0.20. - pyproject.toml: declare the setuptools build backend (PEP 517). - publish.yml: build + publish to PyPI via Trusted Publishing (OIDC) on GitHub Release. - tests.yml: install parallel-bam from the parallelBAM repo without asserting the distribution name, so CI is robust to the rename until parallel-bam 0.0.20 is on PyPI. Verified locally: builds as filter_sam-0.0.11 (Requires-Dist parallel-bam>=0.0.20), twine check passes, 32 tests pass. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
Robaina
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…m/parallel-bam too similar to existing PyPI projects) Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
Robaina
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This PR does two related things needed to ship the parallel-mode speedup under the new PyPI account.
1. Performance: skip parallelbam's name-sort (closes #3)
Both filters evaluate each segment independently, so parallel chunks don't need reads grouped by query name. We pass
sort_by_name=FalsetoparallelizeBAMoperation, skipping the full serialsamtools sort -nthat made-pslower than single-processor mode. (Relies on thesort_by_nameoption in parallelBAM, Robaina/parallelBAM#3.)2. Rename distribution to
filtersam-tools+ PyPI publishingRe-publishing under a new PyPI account needs a new distribution name.
filtersam/filter-samare rejected (PyPI flagsfilter-samas "too similar" tofiltersam), so the new distribution isfiltersam-tools. Import name unchanged (import filtersam); onlypip installbecomesfiltersam-tools. Dependency renamed toparallelbam-tools>=0.0.20to match Robaina/parallelBAM#4.setup.py:NAME→filtersam-tools; dependency →parallelbam-tools>=0.0.20.requirements.txt:parallelbam-tools>=0.0.20.pyproject.toml(new): setuptools PEP 517 build backend..github/workflows/publish.yml(new): build + publish to PyPI via Trusted Publishing (OIDC) on a published GitHub Release..github/workflows/tests.yml: install parallelbam-tools from the parallelBAM repo without asserting the dist name (robust to the rename) until it is on PyPI.Required PyPI setup (one-time)
On https://pypi.org/manage/account/publishing/, add a pending publisher:
filtersam-tools· Owner:Robaina· Repo:filterSAM· Workflow:publish.yml· Environment:pypiMerge order
Merge Robaina/parallelBAM#4 (the
parallelbam-toolsrename) first, then this PR.Verification
Builds as
filtersam_tools-0.0.11(Requires-Dist: parallelbam-tools>=0.0.20),twine checkpasses, full suite 32 passed (incl. the end-to-end parallel run usingsort_by_name=False).