Coverage floor, README contributor section, committed uv.lock

.github/workflows/lint.yaml

@@ -10,13 +10,13 @@ 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:
     runs-on: ubuntu-latest
     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

.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

.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

.gitignore

@@ -131,4 +131,3 @@ dmypy.json
 
 *.sw[pmno]
 daisy_logs
-uv.lock

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.

pyproject.toml

@@ -33,17 +33,20 @@ 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
-# 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
 ]
 
@@ -66,3 +69,14 @@ 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