Merge pull request #20 from effigies/mnt/py39

chore: Drop py38, add py313, use tox-uv

Author: effigies

.github/workflows/build-test-deploy.yml

@@ -47,17 +47,17 @@ jobs:
       fail-fast: false
       matrix:
         os: [ubuntu-latest, macos-latest, windows-latest]
-        python-version: ['3.8', '3.9', '3.10', '3.11', '3.12']
+        python-version: ['3.9', '3.10', '3.11', '3.12']
         dependencies: ['full', 'pre']
         include:
           - os: ubuntu-latest
-            python-version: '3.8'
+            python-version: '3.9'
             dependencies: 'min'
         exclude:
           # Skip pre-release tests for Pythons out of SPEC0
-          - python-version: 3.8
+          - python-version: '3.9'
             dependencies: pre
-          - python-version: 3.9
+          - python-version: '3.10'
             dependencies: pre
 
     env:
@@ -70,12 +70,8 @@ jobs:
           git config --global user.email "[email protected]"
           git config --global user.name "bids-maintenance"
 
-      - name: Set up Python ${{ matrix.python-version }} via conda
-        uses: conda-incubator/setup-miniconda@v3
-        if: matrix.os == 'ubuntu-latest'
-        with:
-          auto-update-conda: true
-          python-version: ${{ matrix.python-version }}
+      - name: Install the latest version of uv
+        uses: astral-sh/setup-uv@v5
 
       - name: Set up Python ${{ matrix.python-version }}
         uses: actions/setup-python@v5
@@ -86,7 +82,7 @@ jobs:
 
       - name: Install git-annex ubuntu
         if: matrix.os == 'ubuntu-latest'
-        run: conda install -c conda-forge git-annex
+        run: sudo apt-get update && sudo apt-get install git-annex
 
       - name: Install git-annex macos
         if: matrix.os == 'macos-latest'
@@ -106,8 +102,7 @@ jobs:
 
       - name: Install tox
         run: |
-          python -m pip install --upgrade pip
-          python -m pip install tox tox-gh-actions
+          uv tool install --with=tox-uv --with=tox-gh-actions tox
       - name: Show tox config
         run: tox c
       - name: Run tox

.pre-commit-config.yaml

@@ -1,6 +1,6 @@
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.4.0
+    rev: v5.0.0
     hooks:
       - id: trailing-whitespace
       - id: end-of-file-fixer
@@ -9,10 +9,8 @@ repos:
       - id: check-toml
       - id: check-added-large-files
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.4.3
+    rev: v0.11.0
     hooks:
       - id: ruff
         args: [ --fix ]
       - id: ruff-format
-      - id: ruff
-        args: [ --select, ISC001, --fix ]

LICENSE

@@ -17,4 +17,4 @@ IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS
 FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR
 COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER
 IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
-CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

pyproject.toml

@@ -20,17 +20,17 @@ classifiers = [
     "Programming Language :: Python",
     "Topic :: Scientific/Engineering",
 ]
-requires-python = ">=3.8"
+requires-python = ">=3.9"
 dependencies = [
-    "bidsschematools >=0.11",
+    "bidsschematools >=1.0",
 ]
 
 [project.optional-dependencies]
 test = [
-  "pytest",
-  "pytest-cov",
-  "coverage[toml]",
-  "datalad",
+  "pytest >=8",
+  "pytest-cov >=5",
+  "coverage[toml] >=7.2",
+  "datalad >=1.1",
 ]
 
 [project.urls]
@@ -54,13 +54,24 @@ versionfile_build = "bids_validator/_version.py"
 tag_prefix = ""
 parentdir_prefix = ""
 
+[tool.pytest.ini_options]
+doctest_optionflags = ["NORMALIZE_WHITESPACE", "IGNORE_EXCEPTION_DETAIL"]
+
 [tool.coverage.run]
 branch = true
 parallel = true
+source = ["bids_validator"]
 omit = [
+  "setup.py",
   "*/_version.py",
 ]
 
+[tool.coverage.paths]
+source = [
+  "src/bids_validator/",
+  "*/site-packages/bids_validator/",
+]
+
 [tool.coverage.report]
 exclude_lines = [
   "no cov",

tox.ini

@@ -1,17 +1,17 @@
 [tox]
 requires =
   tox>=4
+  tox-uv
 envlist =
-  py3{8,9,10,11,12}-{full,pre}
-  py38-min
+  py3{9,10,11,12}-{full,pre}
+  py39-min
   style
   spellcheck
 skip_missing_interpreters = true
 
 # Configuration that allows us to split tests across GitHub runners effectively
 [gh-actions]
 python =
-  3.8: py38
   3.9: py39
   3.10: py310
   3.11: py311
@@ -45,17 +45,14 @@ pass_env =
   CLICOLOR
   CLICOLOR_FORCE
 extras = test
+uv_resolution =
+  min: lowest-direct
 deps =
-  min: bidsschematools ==0.11.0
   pre: git+https://github.com/bids-standard/bids-specification.git\#subdirectory=tools/schemacode
-commands =
-  pytest --doctest-modules --cov bids_validator --cov-report xml --cov-report term \
-  --junitxml=test-results.xml -v src/ {posargs}
 
-[testenv:long]
 commands =
-  pytest --doctest-modules --cov fmripost_aroma --cov-report xml \
-  --junitxml=test-results.xml -v tests/ {posargs}
+  python -m pytest --doctest-modules --cov . --cov-report xml --cov-report term \
+    --junitxml=test-results.xml -v {posargs}
 
 [testenv:docs]
 description = Build documentation site
@@ -74,7 +71,6 @@ skip_install = true
 commands =
   fix: ruff check --fix src/
   fix: ruff format src/
-  fix: ruff check --select ISC001 --fix src/
   !fix: ruff check src/
   !fix: ruff format --diff src/