From 86b94fe8c9229b97662e842bf5065773f88a26fb Mon Sep 17 00:00:00 2001 From: Will Date: Tue, 3 Nov 2026 17:51:02 -0800 Subject: [PATCH 1/3] Add a branch-coverage floor Coverage is configured in pyproject.toml (branch coverage on, source set to the package) so the pytest command in CI shrinks to a bare --cov and a local run measures the same thing. fail_under = 75 is the floor of the first branch-enabled run (75.54% measured); pull requests that drop below it fail the tests job. Co-Authored-By: Claude Mythos 5.1 --- .github/workflows/tests.yaml | 2 +- .gitignore | 1 - pyproject.toml | 11 +++++++++++ 3 files changed, 12 insertions(+), 2 deletions(-) diff --git a/.github/workflows/tests.yaml b/.github/workflows/tests.yaml index d7af1a1..1ea66bd 100644 --- a/.github/workflows/tests.yaml +++ b/.github/workflows/tests.yaml @@ -38,4 +38,4 @@ jobs: with: python-version: ${{ matrix.python-version }} - run: uv sync --resolution ${{ matrix.resolution }} - - run: uv run pytest tests --cov=funlib.persistence --cov-report=term-missing --cov-report=xml + - run: uv run pytest tests --cov --cov-report=term-missing --cov-report=xml diff --git a/.gitignore b/.gitignore index 0a8d3da..38427b2 100644 --- a/.gitignore +++ b/.gitignore @@ -131,4 +131,3 @@ dmypy.json *.sw[pmno] daisy_logs -uv.lock diff --git a/pyproject.toml b/pyproject.toml index b835273..3e83d27 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -66,3 +66,14 @@ ignore = ["E501"] # the formatter owns line length "tutorials/**/*.py" = ["E402"] # jupytext cells import mid-file "examples/**/*.py" = ["E402"] "__init__.py" = ["F401"] # re-exports + +[tool.coverage.run] +branch = true +source = ["funlib.persistence"] + +[tool.coverage.report] +# Floor measured from the first branch-enabled run; raise it when measured +# coverage is two or more points ahead, never lower it without saying why. +fail_under = 75 +show_missing = true +skip_covered = true From 72a97aa6228204c3decbd98e49aba887538e301e Mon Sep 17 00:00:00 2001 From: Will Date: Tue, 3 Nov 2026 17:51:02 -0800 Subject: [PATCH 2/3] README: badges, install and contributing sections, project URLs The badge row links tests and lint to their workflows, docs to the documentation site and publish to the PyPI page. The documentation URL is stated once near the top. Install shows pip and uv; Contributing lists the commands CI runs so a green local run means a green pull request. [project.urls] gains Documentation (where a site exists), Source and Issues so PyPI links back here. Co-Authored-By: Claude Mythos 5.1 --- README.md | 22 +++++++++++++++------- pyproject.toml | 4 ++++ 2 files changed, 19 insertions(+), 7 deletions(-) diff --git a/README.md b/README.md index 10e47c1..4467c73 100644 --- a/README.md +++ b/README.md @@ -5,17 +5,25 @@ # funlib.persistence Interfaces for data (arrays and graphs) and storage formats (databases and file formats) -# installation -Regular installation for usage: -`pip install funlib.persistence` +## Install -Developer setup (pytest, ruff, ty come from the `dev` dependency group, -which `uv sync` installs by default): +```bash +pip install funlib.persistence # or: uv add funlib.persistence +``` + +## Contributing + +The commands below are the ones CI runs, so a green local run means a green PR. ```bash git clone https://github.com/funkelab/funlib.persistence cd funlib.persistence -uv sync -uv run pytest tests +uv sync # Python, dependencies, dev tools (from uv.lock) +uv run pytest tests # tests with coverage +uv run ruff check . && uv run ruff format --check . # lint and formatting +uv run ty check src tests # types ``` +The graph-database tests need a PostgreSQL server (CI starts one as a service, `PGUSER=postgres`); they are skipped when none is reachable. + +`uv.lock` pins the development environment; the `lock-upgrade` workflow refreshes it monthly and opens a pull request. diff --git a/pyproject.toml b/pyproject.toml index 3e83d27..3e91422 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -33,6 +33,10 @@ dependencies = [ [tool.setuptools.dynamic] version = { attr = "funlib.persistence.__version__" } +[project.urls] +Source = "https://github.com/funkelab/funlib.persistence" +Issues = "https://github.com/funkelab/funlib.persistence/issues" + [dependency-groups] # Installed by `uv sync` (PEP 735); not part of the published package. # ruff and ty are pinned with == until uv.lock is committed: both change From 7a57d534e59df11262a2b28cf2a30f51a3161713 Mon Sep 17 00:00:00 2001 From: Will Date: Tue, 3 Nov 2026 17:51:02 -0800 Subject: [PATCH 3/3] Commit uv.lock and refresh it monthly uv.lock is tracked so CI and local environments resolve to the same versions from a commit SHA. The lint and docs jobs sync with --locked so a stale lock fails loudly; the lowest-direct test cell still re-resolves against the floors. ruff and ty move from == pins to >= floors since the lock now fixes their versions. A scheduled lock-upgrade workflow runs `uv lock --upgrade` on the first of each month and opens a pull request with the result. Co-Authored-By: Claude Mythos 5.1 --- .github/workflows/lint.yaml | 4 +- .github/workflows/lock-upgrade.yaml | 27 + pyproject.toml | 7 +- uv.lock | 2209 +++++++++++++++++++++++++++ 4 files changed, 2241 insertions(+), 6 deletions(-) create mode 100644 .github/workflows/lock-upgrade.yaml create mode 100644 uv.lock diff --git a/.github/workflows/lint.yaml b/.github/workflows/lint.yaml index 0e433f1..c4fee4c 100644 --- a/.github/workflows/lint.yaml +++ b/.github/workflows/lint.yaml @@ -10,7 +10,7 @@ jobs: steps: - uses: actions/checkout@v4 - uses: astral-sh/setup-uv@v6 - - run: uv sync + - run: uv sync --locked - run: uv run ruff check . - run: uv run ruff format --check . ty: @@ -18,5 +18,5 @@ jobs: steps: - uses: actions/checkout@v4 - uses: astral-sh/setup-uv@v6 - - run: uv sync + - run: uv sync --locked - run: uv run ty check src tests diff --git a/.github/workflows/lock-upgrade.yaml b/.github/workflows/lock-upgrade.yaml new file mode 100644 index 0000000..1fab2ea --- /dev/null +++ b/.github/workflows/lock-upgrade.yaml @@ -0,0 +1,27 @@ +name: lock-upgrade +# Monthly refresh of uv.lock, opened as a pull request so CI runs against the +# new resolution before it lands. Trigger by hand from the Actions tab to +# upgrade sooner. +on: + schedule: + - cron: "0 6 1 * *" # 06:00 UTC on the first of every month + workflow_dispatch: +permissions: + contents: write + pull-requests: write +jobs: + upgrade: + runs-on: ubuntu-latest + steps: + - uses: actions/checkout@v4 + - uses: astral-sh/setup-uv@v6 + - run: uv lock --upgrade + - uses: peter-evans/create-pull-request@v7 + with: + branch: chore/lock-upgrade + commit-message: "Upgrade uv.lock" + title: "Upgrade uv.lock" + body: | + Monthly `uv lock --upgrade`. Close and reopen this PR to trigger CI + if the checks did not start. + delete-branch: true diff --git a/pyproject.toml b/pyproject.toml index 3e91422..c6cb947 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -39,15 +39,14 @@ Issues = "https://github.com/funkelab/funlib.persistence/issues" [dependency-groups] # Installed by `uv sync` (PEP 735); not part of the published package. -# ruff and ty are pinned with == until uv.lock is committed: both change -# their rule sets between releases. +# ruff and ty versions come from uv.lock; `uv lock --upgrade` moves them. dev = [ "coverage>=7.7.1", "pytest>=8.3.5", "pytest-cov>=6", "pytest-mock>=3.14.0", - "ruff==0.17.3", - "ty==0.0.96", + "ruff>=0.17.3", + "ty>=0.0.96", "types-psycopg2", # psycopg2 ships no inline types; ty reads this stub package ] diff --git a/uv.lock b/uv.lock new file mode 100644 index 0000000..3aa5604 --- /dev/null +++ b/uv.lock @@ -0,0 +1,2209 @@ +version = 1 +revision = 3 +requires-python = ">=3.11" +resolution-markers 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