Merge branch 'master' into spec-refac

Author: bclenet

.github/workflows/validation.yml

@@ -37,62 +37,33 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v4
-      - uses: actions/setup-python@v5
-        with:
-          python-version: 3
-      - name: Install dependencies
-        run: pip install yamllint
+      - uses: actions/setup-uv@v6
       - name: Lint yml files in src/schema
-        run: yamllint -f standard src/schema/ -c .yamllint.yml
+        run: uvx yamllint -f standard src/schema/ -c .yamllint.yml
 
   # Python best practices
   python-style:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v4
-      - uses: actions/setup-python@v5
-        with:
-          python-version: 3
-      - run: python -m pip install --upgrade flake8 black isort[colors]
-      - run: black --diff --color --check tools/schemacode
-      - run: isort --diff --color --check tools/schemacode
-      - run: flake8
-        working-directory: tools/schemacode
+      - uses: actions/setup-uv@v6
+      - run: uvx ruff format --diff
+      - run: uvx ruff check
 
   # Avoid Latin phrases to improve readability
   latin-phrases:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v4
-      - uses: actions/setup-python@v5
-        with:
-          python-version: 3
-      - name: Install dependencies
-        run: |
-          python -m pip install --upgrade pip
-          python -m pip install -r tools/requirements.txt
-      - name: Run Python script to check for Latin phrases - Master
-        if: github.event_name == 'push' && github.ref == 'refs/heads/master'
-        run: |
-          python no-bad-latin.py
-        working-directory: tools
-      - name: Run Python script to check for Latin phrases - Pull Request
-        if: github.event.pull_request
-        run: |
-          python no-bad-latin.py
-        working-directory: tools
+      - uses: actions/setup-uv@v6
+      - name: Check for Latin phrases
+        run: uv run tools/no-bad-latin.py
 
   # Validate CITATION.cff
   validate_cff:
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v4
-    - uses: actions/setup-python@v5
-      with:
-        python-version: 3
-    - name: Install dependencies
-      run: |
-        python -m pip install --upgrade pip setuptools
-        pip3 install cffconvert
-    - name: Validate CITATION.cff
-      run: make validate_citation_cff
+      - uses: actions/checkout@v4
+      - uses: actions/setup-uv@v6
+      - name: Validate CITATION.cff
+        run: uvx cffconvert --validate

.gitignore

@@ -1,3 +1,5 @@
+src/schema.json
+
 site/
 .DS_Store
 .idea

.pre-commit-config.yaml

@@ -26,31 +26,6 @@ repos:
         files: src/metaschema.json
       - id: check-readthedocs
         files: readthedocs.yml
-  - repo: https://github.com/psf/black
-    rev: 25.1.0
-    hooks:
-      - id: black
-        files: ^tools/(?!schemacode)
-        args: ["--verbose"]
-      - id: black
-        name: "black bidsschematools"
-        files: tools/schemacode
-        args: ["--config", "tools/schemacode/pyproject.toml", "--verbose"]
-  - repo: https://github.com/pyCQA/isort
-    rev: 6.0.1
-    hooks:
-      - id: isort
-        files: ^tools/(?!schemacode)
-        args: ["--profile", "black"]
-      - id: isort
-        name: "isort bidsschematools"
-        files: tools/schemacode
-        args: ["--settings-file", "tools/schemacode/pyproject.toml"]
-  - repo: https://github.com/pyCQA/flake8
-    rev: 7.2.0
-    hooks:
-      - id: flake8
-        args: [--config=tools/schemacode/.flake8]
   - repo: https://github.com/pre-commit/mirrors-prettier
     rev: v4.0.0-alpha.8
     hooks:
@@ -63,11 +38,11 @@ repos:
       - id: yamllint
         args: [-f=standard, -c=.yamllint.yml]
         files: src/schema/.*/.*\.yaml
-  - repo: https://github.com/macisamuele/language-formatters-pre-commit-hooks
-    rev: v2.14.0
+  - repo: https://github.com/ComPWA/taplo-pre-commit
+    rev: v0.9.3
     hooks:
-      - id: pretty-format-toml
-        args: [--autofix, --indent, '4', --no-sort]
+      - id: taplo-format
+        args: [-o, 'array_auto_collapse=false']
   - repo: https://github.com/codespell-project/codespell
     rev: v2.4.1
     hooks:
@@ -79,9 +54,9 @@ repos:
       - id: mypy
         # Sync with project.optional-dependencies.typing
         additional_dependencies:
+          - acres
           - click
           - markdown-it-py
-          - importlib_resources
           - pandas-stubs
           - pyparsing
           - pytest

pdf_build_src/check_pandoc_log.py

@@ -13,7 +13,6 @@
 # go through the logs (list of dicts)
 duplicate_link_refs = []
 for log_dict in logs:
-
     # Check for DuplicateLinkReference
     logtype = log_dict.get("type", None)
     logverbosity = log_dict.get("verbosity", None)

pdf_build_src/pandoc_script.py

@@ -66,7 +66,7 @@ def _flatten_values(lst):
     # appendices/ as a resource-path so that the relative files can
     # be found.
     build_root = HERE.parent
-    cmd += [f'--resource-path=.:{build_root / "appendices"}']
+    cmd += [f"--resource-path=.:{build_root / 'appendices'}"]
 
     # Add input files to command
     # The filenames in `markdown_list` will ensure correct order when sorted

pdf_build_src/process_markdowns.py

@@ -158,7 +158,6 @@ def remove_internal_links_reference(root_path):
                 # first find, which links need to be remove by scanning the
                 # references, and remove the reference
                 for ind, line in enumerate(data):
-
                     match = pattern_ref.search(line)
 
                     if match:
@@ -175,7 +174,6 @@ def remove_internal_links_reference(root_path):
                     # link
                     pattern = re.compile(r"\[([^\]]+)\]\[" + f"{link}" + r"\]")
                     for ind, line in enumerate(data):
-
                         match = pattern.search(line)
 
                         if match:
@@ -256,7 +254,6 @@ def assert_no_multiline_links(root_path):
                 code_context = False
                 macro_context = False
                 for ind, line in enumerate(data):
-
                     # do not check "code blocks" or "macros"
                     if line.strip().startswith("```"):
                         code_context = not code_context
@@ -277,8 +274,7 @@ def assert_no_multiline_links(root_path):
 
     if len(problems) > 0:
         msg = (
-            "Found multiline markdown links! Please reformat as single"
-            " line links.\n\n"
+            "Found multiline markdown links! Please reformat as single line links.\n\n"
         )
         msg += json.dumps(problems, indent=4)
         raise AssertionError(msg)
@@ -378,7 +374,6 @@ def correct_table(table, offset=[0.0, 0.0], debug=False):
     # correct alignment of fences and populate the new table (A List of str)
     new_table = []
     for i, row in enumerate(table):
-
         if i == 1:
             str_format = " {:-{align}{width}} "
         else:
@@ -678,7 +673,6 @@ def process_macros(duplicated_src_dir_path):
 
 
 if __name__ == "__main__":
-
     duplicated_src_dir_path = "src_copy/src"
 
     # make a copy of the src directory in the current directory

pdf_build_src/remove_admonitions.py

@@ -16,14 +16,12 @@
 def remove_admonitions(
     input_folder: str | Path, output_folder: str | Path, indent: str = None
 ):
-
     if indent is None:
         indent = INDENT
 
     md_files = Path(input_folder).glob("**/*.md")
 
     for file in md_files:
-
         with open(file, "r", encoding="utf8") as f:
             content = f.readlines()
 
@@ -32,11 +30,9 @@ def remove_admonitions(
         print(f"processing: {file}\n to: {output_file}")
 
         with open(output_file, "w", encoding="utf8") as f:
-
             is_admonition = False
             counter = 0
             for line in content:
-
                 if any(line.startswith(x) for x in ADMONITION_DELIMITERS):
                     is_admonition = True
                     counter = 0

pdf_build_src/test_remove_admonitions.py

@@ -12,7 +12,6 @@ def test_remove_admonitions(tmp_path):
     generated_files = list(tmp_path.glob("**/*.md"))
 
     for file in generated_files:
-
         expected = expected_folder / file.relative_to(tmp_path)
 
         with open(expected, "r", encoding="utf8") as f: