feat: yamllint to ensure yaml linting (opentargets#338)

* feat: yamllint support * feat: updates yamllint rules
thehyve · Dec 14, 2023 · 1b35c99 · 1b35c99
1 parent e275a83
commit 1b35c99
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Showing 12 changed files with 128 additions and 44 deletions.
diff --git a/.github/dependabot.yaml b/.github/dependabot.yaml
@@ -1,8 +1,5 @@
-# To get started with Dependabot version updates, you'll need to specify which
-# package ecosystems to update and where the package manifests are located.
-# Please see the documentation for all configuration options:
-# https://docs.github.com/github/administering-a-repository/configuration-options-for-dependency-updates
-
+#  To get started with Dependabot version updates, you'll need to specify which
+#  package ecosystems to update and where the package manifests are located.
 version: 2
 updates:
   - package-ecosystem: "pip" # See documentation for possible values

diff --git a/.github/workflows/pr.yaml b/.github/workflows/pr.yaml
@@ -1,6 +1,7 @@
 name: Checks
 
-on: [push]
+"on":
+  push:
 
 jobs:
   test:

diff --git a/.github/workflows/prerelease.yaml b/.github/workflows/prerelease.yaml
@@ -1,7 +1,6 @@
----
 name: Test & pre-release
 
-on:
+"on":
   push:
     branches:
       - release/*

diff --git a/.github/workflows/release.yaml b/.github/workflows/release.yaml
@@ -1,6 +1,6 @@
 name: Release and Documentation
 
-on:
+"on":
   push:
     branches:
       - main

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -1,4 +1,13 @@
 repos:
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.1.6
+    hooks:
+      - id: ruff
+        args:
+          - --fix
+      - id: ruff-format
+        files: ^((otg|utils|tests)/.+)?[^/]+\.py$
+
   - repo: https://github.com/pre-commit/pre-commit-hooks
     rev: v4.5.0
     hooks:
@@ -8,11 +17,20 @@ repos:
       - id: check-merge-conflict
       - id: check-case-conflict
       - id: check-json
+        exclude: (.vscode|.devcontainer)
+      - id: no-commit-to-branch
+        args:
+          - --branch=dev
+          - --branch=main
       - id: check-toml
       - id: check-yaml
       - id: check-ast
       - id: debug-statements
       - id: check-docstring-first
+  - repo: https://github.com/adrienverge/yamllint.git
+    rev: v1.32.0
+    hooks:
+      - id: yamllint
 
   - repo: https://github.com/pre-commit/pygrep-hooks
     rev: v1.10.0
@@ -27,14 +45,12 @@ repos:
       - id: pycln
         args: [--all]
 
-  - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.1.6
+  - repo: https://github.com/pre-commit/mirrors-prettier
+    rev: "v3.0.3"
     hooks:
-      - id: ruff
-        args:
-          - --fix
-      - id: ruff-format
-        files: ^((otg|utils|tests)/.+)?[^/]+\.py$
+      - id: prettier
+        args: ["--staged"]
+
   - repo: https://github.com/alessandrojcm/commitlint-pre-commit-hook
     rev: v9.10.0
     hooks:
@@ -46,20 +62,17 @@ repos:
     rev: "v1.7.1"
     hooks:
       - id: mypy
-        args: [
-            # --ignore-missing-imports is required to run mypy on virtual
-            # environments without installed dependencies
-            "--ignore-missing-imports",
-            "--check-untyped-defs",
-            "--disallow-any-generics",
-            "--disallow-incomplete-defs",
-            "--no-implicit-optional",
-            "--no-implicit-reexport",
-            "--strict-equality",
-            "--warn-redundant-casts",
-            "--warn-unused-ignores",
-            "--disallow-untyped-defs",
-          ]
+        args:
+          - "--ignore-missing-imports"
+          - "--check-untyped-defs"
+          - "--disallow-any-generics"
+          - "--disallow-incomplete-defs"
+          - "--no-implicit-optional"
+          - "--no-implicit-reexport"
+          - "--strict-equality"
+          - "--warn-redundant-casts"
+          - "--warn-unused-ignores"
+          - "--disallow-untyped-defs"
 
   - repo: https://github.com/econchick/interrogate
     rev: 1.5.0
@@ -82,9 +95,3 @@ repos:
     rev: 0.3.8
     hooks:
       - id: pydoclint
-
-  - repo: https://github.com/pre-commit/mirrors-prettier
-    rev: "v3.0.3"
-    hooks:
-      - id: prettier
-        args: ["--staged"]
diff --git a/.vscode/extensions.json b/.vscode/extensions.json
@@ -3,7 +3,9 @@
     "charliermarsh.ruff",
     "ms-python.mypy-type-checker",
     "ms-python.python",
-    "esbenp.prettier-vscode"
+    "esbenp.prettier-vscode",
+    "redhat.vscode-yaml",
+    "fnando.linter"
   ],
   "unwantedRecommendations": ["ms-python.flake8"]
 }
diff --git a/.vscode/settings.json b/.vscode/settings.json
@@ -4,8 +4,8 @@
     "editor.formatOnPaste": false,
     "editor.formatOnSave": true,
     "editor.codeActionsOnSave": {
-      "source.fixAll": false,
-      "source.organizeImports": true
+      "source.fixAll": "never",
+      "source.organizeImports": "explicit"
     }
   },
   "python.terminal.launchArgs": ["-m", "IPython", "--no-autoindent"],
@@ -15,7 +15,7 @@
     "editor.detectIndentation": false,
     "editor.formatOnSave": true,
     "editor.codeActionsOnSave": {
-      "source.organizeImports": true
+      "source.organizeImports": "explicit"
     }
   },
   "json.format.keepLines": true,

diff --git a/.yamllint b/.yamllint
@@ -0,0 +1,59 @@
+rules:
+  braces:
+    level: error
+    min-spaces-inside: 0
+    max-spaces-inside: 1
+    min-spaces-inside-empty: -1
+    max-spaces-inside-empty: -1
+  brackets:
+    level: error
+    min-spaces-inside: 0
+    max-spaces-inside: 0
+    min-spaces-inside-empty: -1
+    max-spaces-inside-empty: -1
+  colons:
+    level: error
+    max-spaces-before: 0
+    max-spaces-after: 1
+  commas:
+    level: error
+    max-spaces-before: 0
+    min-spaces-after: 1
+    max-spaces-after: 1
+  comments:
+    level: error
+    require-starting-space: true
+    min-spaces-from-content: 1
+  comments-indentation:
+    level: error
+  document-end:
+    level: error
+    present: false
+  document-start:
+    level: error
+    present: false
+  empty-lines:
+    level: error
+    max: 1
+    max-start: 0
+    max-end: 1
+  hyphens:
+    level: error
+    max-spaces-after: 1
+  indentation:
+    level: error
+    spaces: 2
+    indent-sequences: true
+    check-multi-line-strings: false
+  key-duplicates:
+    level: error
+  line-length: disable
+  new-line-at-end-of-file:
+    level: error
+  new-lines:
+    level: error
+    type: unix
+  trailing-spaces:
+    level: error
+  truthy:
+    level: error
diff --git a/config/datasets/gcp.yaml b/config/datasets/gcp.yaml
@@ -13,7 +13,8 @@ jung: gs://genetics-portal-raw/pchic_jung2019/jung2019_pchic_tableS3.csv
 thurman: gs://genetics-portal-input/v2g_input/thurman2012/genomewideCorrs_above0.7_promoterPlusMinus500kb_withGeneNames_32celltypeCategories.bed8.gz
 catalog_associations: ${datasets.inputs}/v2d/gwas_catalog_v1.0.2-associations_e110_r2023-11-24.tsv
 catalog_studies:
-  # To get a complete representation of all GWAS Catalog studies, we need to ingest the list of unpublished studies from a different file.
+  # To get a complete representation of all GWAS Catalog studies, we need to
+  # ingest the list of unpublished studies from a different file.
   - ${datasets.inputs}/v2d/gwas-catalog-v1.0.3-studies-r2023-11-24.tsv
   - ${datasets.inputs}/v2d/gwas-catalog-v1.0.3-unpublished-studies-r2023-11-24.tsv
 catalog_ancestries:

diff --git a/poetry.lock b/poetry.lock
diff --git a/pyproject.toml b/pyproject.toml
@@ -68,6 +68,7 @@ pydoclint = "^0.3.8"
 prettier = "^0.0.7"
 deptry = "^0.12.0"
 python-semantic-release = "^8.3.0"
+yamllint = "^1.33.0"
 
 [tool.semantic_release.branches.prerelease]
 match = "(release/*)"

diff --git a/src/airflow/docker-compose.yaml b/src/airflow/docker-compose.yaml
@@ -43,7 +43,6 @@
 #                                Default: ''
 #
 # Feel free to modify this file to suit your needs.
----
 version: "3.8"
 x-airflow-common: &airflow-common
   # In order to add custom dependencies or upgrade provider packages you can use your extended image.