Merge pull request #229 from DigitalSlideArchive/56-consistent-yaml

Clean up yaml files we commit to source control

.git-blame-ignore-revs

@@ -1,2 +1,5 @@
 # Reformat code to standardize double quoted strings
 92c1ec85ab680851055c16f022ab9ce80c600e3c
+
+# Format yaml files
+8846ba15625de7bfb68d40c4eb224c2c2d59dda2

.github/workflows/ci.yml → .github/workflows/ci.yaml

@@ -1,3 +1,4 @@
+---
 name: ci
 on:
   pull_request:

.github/workflows/release.yml → .github/workflows/release.yaml

@@ -1,7 +1,9 @@
+---
 name: release
 on:
   release:
-    types: [published]
+    types:
+      - published
 jobs:
   publish:
     runs-on: ${{ matrix.os }}

README.md

@@ -23,7 +23,7 @@ Image redaction is determined by a set of rules. By default, the base set of rul
 ## Rule Application
 All runs of `imagedephi` use the provided base set of rules as a foundation. End users can use the ruleset framework to build custom rulesets that handle additional or custom metadata not covered by the base rules, or override the behavior of the base rule set.
 
-Override rule sets can be specified by using the `-r my_ruleset.yml` or `--override-rules my_ruleset.yml` option. This option is available for both the `imagedephi run` and `imagedephi plan` commands. Override rules sets are not provided by `imagedephi`, and must de defined by the end user.
+Override rule sets can be specified by using the `-r my_ruleset.yaml` or `--override-rules my_ruleset.yaml` option. This option is available for both the `imagedephi run` and `imagedephi plan` commands. Override rules sets are not provided by `imagedephi`, and must de defined by the end user.
 
 When `imagedephi` determines the steps to redact a file, it checks each piece of metadata in the file. For each piece of metadata found this way, it will first consult the override rule set, if present, for an applicable rule. If the override rule set does not contain a rule for that piece of metadata, the program will check the base ruleset.
 
@@ -34,7 +34,7 @@ For whole slide image formats based on the tiff standard, `imagedephi` allows a
 
 
 ## Ruleset Format Overview
-In order to read the base rules and build your own custom rule sets, it is important to understand the format in which rulesets are specified. Rulesets are defined by `.yml` files (one ruleset per file), and are a dictionary with the following top-level tags: `name`, `description`, `output_file_name`, `tiff`, and `svs`.
+In order to read the base rules and build your own custom rule sets, it is important to understand the format in which rulesets are specified. Rulesets are defined by `.yaml` files (one ruleset per file), and are a dictionary with the following top-level tags: `name`, `description`, `output_file_name`, `tiff`, and `svs`.
 
 ### Generic Properties
 The following three properties belong to the rulesets themselves, and don't influence redaction behavior.

imagedephi/base_rules.yaml

@@ -1,7 +1,6 @@
+---
 name: Base rules
-description: These are the default rules for each potential piece of redactable material
-  (metadata, image) to be used as a fallback if there are no user defined rules for
-  a piece of redactable material.
+description: These are the default rules for each potential piece of redactable material (metadata, image) to be used as a fallback if there are no user defined rules for a piece of redactable material.
 output_file_name: study_slide
 tiff:
   associated_images:

imagedephi/minimum_rules.yaml

@@ -1,6 +1,6 @@
+---
 name: Minimum Rules
-description: A set of rules that defines a minimum amount of metadata for images
-  to be read. Metadata not specified by a rule is deleted (controlled by the metadata_fallback_action).
+description: A set of rules that defines a minimum amount of metadata for images to be read. Metadata not specified by a rule is deleted (controlled by the metadata_fallback_action).
 output_file_name: study_slide
 tiff:
   metadata_fallback_action: delete

pyproject.toml

@@ -74,3 +74,8 @@ testpaths = ["tests"]
 
 [tool.pyright]
 stubPath = "stubs"
+
+[tool.yamlfix]
+line_length = 200
+preserve_quotes = true
+sequence_style = "block_style"

tests/override_rule_sets/example_user_rules.yml → tests/override_rule_sets/example_user_rules.yaml

@@ -12,7 +12,6 @@ tiff:
       action: check_type
       expected_type: number
       expected_count: 2
-
 svs:
   associated_images: {}
   metadata:

tests/test_e2e.py

@@ -23,7 +23,7 @@ def test_e2e_run(
         main.imagedephi,
         [
             "--override-rules",
-            str(rules_dir / "example_user_rules.yml"),
+            str(rules_dir / "example_user_rules.yaml"),
             "run",
             str(data_dir / "input" / "tiff"),
             "--output-dir",
@@ -66,7 +66,7 @@ def test_e2e_plan(
         main.imagedephi,
         [
             "--override-rules",
-            str(rules_dir / "example_user_rules.yml"),
+            str(rules_dir / "example_user_rules.yaml"),
             "plan",
             str(data_dir / "input" / "tiff" / "test_image.tif"),
         ],

tests/test_redact.py

@@ -22,7 +22,7 @@ def base_rule_set():
 
 @pytest.fixture
 def override_rule_set(rules_dir: Path):
-    rule_file = rules_dir / "example_user_rules.yml"
+    rule_file = rules_dir / "example_user_rules.yaml"
     with rule_file.open() as rule_stream:
         return Ruleset.parse_obj(yaml.safe_load(rule_stream))
 

tox.ini

@@ -4,7 +4,7 @@ minversion = 4
 env_list =
     lint,
     type,
-    test
+    test,
 
 [testenv]
 base_python = python3.11
@@ -20,17 +20,21 @@ deps =
     flake8-docstrings
     flake8-isort
     pep8-naming
+    yamlfix
 commands =
     flake8 {posargs:.}
+    yamlfix -c pyproject.toml --exclude ./build/**/* --exclude ./client/node_modules/**/* . --check
 
 [testenv:format]
 package = skip
 deps =
     black
     isort
+    yamlfix
 commands =
     isort {posargs:.}
     black {posargs:.}
+    yamlfix -c pyproject.toml --exclude ./build/**/* --exclude ./client/node_modules/**/* .
 
 [testenv:type]
 # Editable ensures dependencies are installed, but full packaging isn't necessary
@@ -92,3 +96,8 @@ ignore =
     D10,
     # Multiple statements on one line (https://github.com/psf/black/issues/3887)
     E704,
+
+[yamlfix]
+line_length = 200
+preserve_quotes = True
+sequence_style = YamlNodeStyle.BLOCK_STYLE