Merge pull request #41 from effigies/fix/deps

chore: Drop Python 3.9, test through 3.14, lock test environments

Author: effigies

.github/dependabot.yml

@@ -10,3 +10,11 @@ updates:
       actions-infrastructure:
         patterns:
           - "actions/*"
+  - package-ecosystem: uv
+    directory: "/"
+    schedule:
+      interval: monthly
+    groups:
+      uv:
+        patterns:
+          - "*"

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

@@ -48,18 +48,18 @@ jobs:
       fail-fast: false
       matrix:
         os: [ubuntu-latest, macos-latest, windows-latest]
-        python-version: ['3.9', '3.10', '3.11', '3.12']
+        python-version: ['3.10', '3.11', '3.12', '3.13', '3.14']
         dependencies: ['full', 'pre']
         include:
           - os: ubuntu-latest
-            python-version: '3.9'
+            python-version: '3.10'
             dependencies: 'min'
         exclude:
           # Skip pre-release tests for Pythons out of SPEC0
-          - python-version: '3.9'
-            dependencies: pre
           - python-version: '3.10'
             dependencies: pre
+          - python-version: '3.11'
+            dependencies: pre
 
     env:
       DEPENDS: ${{ matrix.dependencies }}

pyproject.toml

@@ -20,7 +20,7 @@ classifiers = [
     "Programming Language :: Python",
     "Topic :: Scientific/Engineering",
 ]
-requires-python = ">=3.9"
+requires-python = ">=3.10"
 dependencies = [
     "attrs >=24.1",
     "bidsschematools >=1.1",

src/bids_validator/__main__.py

@@ -9,7 +9,7 @@
 
 import sys
 from collections.abc import Iterator
-from typing import Annotated, Optional
+from typing import Annotated
 
 from bidsschematools.schema import load_schema
 from bidsschematools.types import Namespace
@@ -100,7 +100,7 @@ def version_callback(value: bool):
 @app.command()
 def main(
     bids_path: str,
-    schema_path: Optional[str] = None,
+    schema_path: str | None = None,
     verbose: Annotated[bool, typer.Option('--verbose', '-v', help='Show verbose output')] = False,
     version: Annotated[
         bool,

src/bids_validator/bidsignore.py

@@ -3,15 +3,15 @@
 import os
 import re
 from functools import lru_cache
-from typing import Protocol, Union
+from typing import Protocol
 
 import attrs
 
 from .types.files import FileTree
 
 
 @lru_cache
-def compile_pat(pattern: str) -> Union[re.Pattern, None]:
+def compile_pat(pattern: str) -> re.Pattern | None:
     """Compile .gitignore-style ignore lines to regular expressions."""
     orig = pattern
     # A line starting with # serves as a comment.

src/bids_validator/context.py

@@ -67,7 +67,7 @@ def load_tsv(file: FileTree, *, max_rows=0) -> Namespace:
             fobj = itertools.islice(fobj, max_rows)
         contents = (line.rstrip('\r\n').split('\t') for line in fobj)
         # Extract headers then transpose rows to columns
-        return Namespace(zip(next(contents), zip(*contents)))
+        return Namespace(zip(next(contents), zip(*contents, strict=False), strict=False))
 
 
 @cache
@@ -78,7 +78,7 @@ def load_tsv_gz(file: FileTree, headers: tuple[str], *, max_rows=0) -> Namespace
         if max_rows > 0:
             gzobj = itertools.islice(gzobj, max_rows)
         contents = (line.decode().rstrip('\r\n').split('\t') for line in gzobj)
-        return Namespace(zip(headers, zip(*contents)))
+        return Namespace(zip(headers, zip(*contents, strict=False), strict=False))
 
 
 @cache

tests/test_context.py

@@ -163,24 +163,28 @@ def test_sessions(synthetic_dataset):
 
 
 def test_load_tsv(synthetic_dataset):
-
     tsv_file_tree = synthetic_dataset / 'participants.tsv'
     tsv_file = context.load_tsv(tsv_file_tree)
 
     data_set = {
-        "participant_id": ("sub-01", "sub-02", "sub-03", "sub-04", "sub-05"),
-        "age": (34, 38, 22, 21, 42),
-        "sex": ("F", "M", "M", "F", "M")
+        'participant_id': ('sub-01', 'sub-02', 'sub-03', 'sub-04', 'sub-05'),
+        'age': (34, 38, 22, 21, 42),
+        'sex': ('F', 'M', 'M', 'F', 'M'),
     }
 
     assert tsv_file.keys() == data_set.keys()
-    assert [tsv_file[key] == data_set[key] for key in tsv_file.keys()]  
+    assert [tsv_file[key] == data_set[key] for key in tsv_file.keys()]
 
 
 def test_load_tsv_gz(synthetic_dataset):
-
-    headers = ("respiratory", "cardiac")
-    tsvgz_file_tree = synthetic_dataset / "sub-01" / "ses-01" / "func" /"sub-01_ses-01_task-nback_run-01_stim.tsv.gz"
+    headers = ('respiratory', 'cardiac')
+    tsvgz_file_tree = (
+        synthetic_dataset
+        / 'sub-01'
+        / 'ses-01'
+        / 'func'
+        / 'sub-01_ses-01_task-nback_run-01_stim.tsv.gz'
+    )
 
     tsvgz_file = context.load_tsv_gz(tsvgz_file_tree, headers)
 

tox.ini

@@ -3,19 +3,20 @@ requires =
   tox>=4
   tox-uv
 envlist =
-  py3{9,10,11,12}-{full,pre}
-  py39-min
+  py31{0,1,2,3,4}-{full,pre}
+  py310-min
   style
   spellcheck
 skip_missing_interpreters = true
 
 # Configuration that allows us to split tests across GitHub runners effectively
 [gh-actions]
 python =
-  3.9: py39
   3.10: py310
   3.11: py311
   3.12: py312
+  3.13: py313
+  3.14: py314
 
 [gh-actions:env]
 DEPENDS =
@@ -46,6 +47,9 @@ pass_env =
   CLICOLOR_FORCE
 extras =
   cli
+runner =
+  full: uv-venv-lock-runner
+  !full: uv-venv-runner
 dependency_groups =
   test
 uv_resolution =
@@ -60,20 +64,13 @@ commands =
     --junitxml=test-results.xml {posargs}
   coverage xml
 
-[testenv:docs]
-description = Build documentation site
-labels = docs
-allowlist_externals = make
-extras = doc
-commands =
-  make -C doc html
-
 [testenv:style{,-fix}]
 description = Check and attempt to fix style
 labels = check
 deps =
   ruff
 skip_install = true
+runner = uv-venv-runner
 commands =
   fix: ruff check --fix src/
   fix: ruff format src/
@@ -86,29 +83,7 @@ labels = check
 deps =
   codespell[toml]
 skip_install = true
+runner = uv-venv-runner
 commands =
   fix: codespell -w {posargs}
   !fix: codespell {posargs}
-
-[testenv:build{,-strict}]
-labels =
-  check
-  pre-release
-deps =
-  build
-  twine
-skip_install = true
-set_env =
-  build-strict: PYTHONWARNINGS=error,once:Unimplemented abstract methods {'locate_file'}:DeprecationWarning:pip._internal.metadata.importlib._dists,once:pkg_resources is deprecated as an API.:DeprecationWarning:pip._internal.metadata.importlib._envs
-commands =
-  python -m build
-  python -m twine check dist/*
-
-[testenv:publish]
-depends = build
-labels = release
-deps =
-  twine
-skip_install = true
-commands =
-  python -m twine upload dist/*