[MNT] update pre-commit config and apply (#1329)

* update precommit config and apply

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* fix import

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* Apply suggestions from code review

Co-authored-by: Chris Markiewicz <effigies@gmail.com>

* Update pdf_build_src/process_markdowns.py

Co-authored-by: Chris Markiewicz <effigies@gmail.com>

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: Chris Markiewicz <markiewicz@stanford.edu>
Co-authored-by: Chris Markiewicz <effigies@gmail.com>

.pre-commit-config.yaml

@@ -12,6 +12,27 @@ repos:
       - id: check-ast
       - id: check-added-large-files
       - id: check-case-conflict
+  - repo: https://github.com/psf/black
+    rev: 22.10.0
+    hooks:
+      - id: black
+        files: tools/schemacode
+        args: [--verbose]
+  - repo: https://github.com/pyCQA/isort
+    rev: 5.10.1
+    hooks:
+      - id: isort
+        files: tools/
+  - repo: https://github.com/pyCQA/flake8
+    rev: 5.0.4
+    hooks:
+      - id: flake8
+        args: [--config=tools/schemacode/setup.cfg]
+  - repo: https://github.com/pre-commit/mirrors-prettier
+    rev: v3.0.0-alpha.2
+    hooks:
+      - id: prettier
+        files: src/schema/.*/.*\.yaml
   - repo: https://github.com/codespell-project/codespell
     rev: v2.2.2
     hooks:

pdf_build_src/pandoc_script.py

@@ -22,25 +22,25 @@ def build_pdf(filename="bids-spec.pdf", logfile="bids-spec_pandoc_log.json"):
 
     # Get all input files
     markdown_list = []
-    for root, dirs, files in os.walk('.'):
+    for root, dirs, files in os.walk("."):
         for file in files:
             fpath = os.path.join(root, file)
             if fpath.endswith(".md") and fpath not in EXCLUDE:
                 markdown_list.append(fpath)
-            elif fpath.endswith('index.md'):
+            elif fpath.endswith("index.md"):
                 # Special role for index.md
                 index_page = fpath
 
     # Prepare the command options
     cmd = [
-        'pandoc',
-        '--from=markdown_github+yaml_metadata_block',
-        '--include-before-body=./cover.tex',
-        '--include-in-header=./header.tex',
-        '--include-in-header=./header_setup.tex',
-        '--pdf-engine=xelatex',
-        f'--log={logfile}',
-        f'--output={filename}',
+        "pandoc",
+        "--from=markdown_github+yaml_metadata_block",
+        "--include-before-body=./cover.tex",
+        "--include-in-header=./header.tex",
+        "--include-in-header=./header_setup.tex",
+        "--pdf-engine=xelatex",
+        f"--log={logfile}",
+        f"--output={filename}",
     ]
 
     # location of this file: This is also the working directory when
@@ -62,7 +62,7 @@ def build_pdf(filename="bids-spec.pdf", logfile="bids-spec_pandoc_log.json"):
     cmd += [str(root / i) for i in ["../../metadata.yml"] + sorted(markdown_list)]
 
     # print and run
-    print('running: \n\n' + '\n'.join(cmd))
+    print("running: \n\n" + "\n".join(cmd))
     subprocess.run(cmd)