[ENH] Add filename template legend

.circleci/config.yml

@@ -13,7 +13,6 @@ jobs:
             source env/bin/activate
             python -m pip install --upgrade pip
             pip install -r requirements.txt
-            pip install ~/project/tools/schemacode/[render]
       - run:
           name: generate docs
           command: |

.codecov.yml

@@ -1,4 +1,3 @@
 ignore:
     - "*/*/tests/*"
     - "**/tests/*"
-

.pre-commit-config.yaml

@@ -1,13 +1,30 @@
 # See https://pre-commit.com for more information
 # See https://pre-commit.com/hooks.html for more hooks
+exclude: 'tools/schemacode/bidsschematools/tests/data/broken_dataset_description.json'
 repos:
-  - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.0.1
-    hooks:
-      - id: trailing-whitespace
-      - id: end-of-file-fixer
-      - id: check-yaml
-      - id: check-json
-      - id: check-ast
-      - id: check-added-large-files
-      - id: check-case-conflict
+
+-   repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.3.0
+    hooks:
+    -   id: trailing-whitespace
+    -   id: end-of-file-fixer
+    -   id: check-yaml
+    -   id: check-json
+    -   id: check-ast
+    -   id: check-added-large-files
+    -   id: check-case-conflict
+
+-   repo: https://github.com/psf/black
+    rev: 22.6.0
+    hooks:
+    -   id: black
+
+-   repo: https://github.com/pycqa/flake8
+    rev: '4.0.1'
+    hooks:
+    -   id: flake8
+
+-   repo: https://github.com/asottile/reorder_python_imports
+    rev: "v3.8.2"
+    hooks:
+    -   id: reorder-python-imports

CONTRIBUTING.md

@@ -302,7 +302,6 @@ is to use the `requirements.txt` file contained in this repository as follows:
 ```bash
 pip install -U pip
 pip install -r requirements.txt
-pip install -e tools/schemacode/
 ```
 
 The first command ensures you are using an up to date version of `pip`,

pdf_build_src/check_pandoc_log.py

@@ -1,5 +1,4 @@
 """Inspect the pandoc log for warnings that should be raised as errors."""
-
 # %%
 import json
 

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)