Merge pull request #681 from populationgenomics/dev

Release 6.7.0

.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 6.6.2
+current_version = 6.7.0
 commit = True
 tag = False
 parse = (?P<major>\d+)\.(?P<minor>\d+)\.(?P<patch>[A-z0-9-]+)

.github/workflows/test.yaml

@@ -16,13 +16,13 @@ jobs:
       run:
         shell: bash -eo pipefail -l {0}
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
-      - uses: actions/setup-python@v4
+      - uses: actions/setup-python@v5
         with:
           python-version: "3.10"
 
-      - uses: actions/setup-java@v3
+      - uses: actions/setup-java@v4
         with:
           distribution: "temurin" # See 'Supported distributions' for available options
           java-version: "17"

.pre-commit-config.yaml

@@ -19,6 +19,24 @@ repos:
       - id: markdownlint
         args: ["--config", ".markdownlint.json"]
 
+  - repo: https://github.com/populationgenomics/pre-commits
+    rev: "v0.1.3"
+    hooks:
+      - id: cpg-id-checker
+        args: ["--extra-pattern", 'TOB\d+']
+        exclude: >-
+          (?x)^(
+              test/test_generic_auditor\.py|
+              models/utils/sequencing_group_id_format\.py|
+              metamist/audit/README\.md
+          )$
+
+  - repo: https://github.com/pycqa/isort
+    rev: 5.13.2
+    hooks:
+      - id: isort
+        name: isort (python)
+
   - repo: https://github.com/ambv/black
     rev: 23.12.1
     hooks:

.pylintrc

@@ -23,7 +23,7 @@
 disable=f-string-without-interpolation,inherit-non-class,too-few-public-methods,
         fixme,logging-fstring-interpolation,import-error,missing-module-docstring,line-too-long,
         too-many-return-statements,no-name-in-module,R0801,consider-using-set-comprehension,
-        arguments-differ,unspecified-encoding,invalid-name,logging-not-lazy,I1101
+        arguments-differ,unspecified-encoding,invalid-name,logging-not-lazy,I1101,wrong-import-order
 
 # Overriding variable name patterns to allow short 1- or 2-letter variables
 attr-rgx=[a-z_][a-z0-9_]{0,30}$