Releases: populationgenomics/cpg-flow
v1.3.1
v1.3.1 (2026-01-29)
Bug Fixes
-
pyproject.toml: Python version (
a4becea) -
stage.py: Add implementation (
324d6a6) -
test_utils.py: Add a depends-on-last (
2694aff) -
test_utils.py: Add error handling (
ed3ab86) -
test_utils.py: Added dependency test cases (
a670906) -
test_utils.py: Changes following review (
fd50d09) -
test_utils.py: Extra test case (
ebc3fc9) -
test_utils.py: Less deepcopy (
0c9e474) -
test_utils.py: Linting following method deletion (
fd167dd) -
test_utils.py: Pytest.parametrize (
c98ac05) -
test_utils.py: Remove commented out tests (
628acae) -
test_utils.py: Remove Iterable import (
cd87c5f) -
test_utils.py: Split logic to please sonar (
2fb89b7) -
utils.py: Add dependency handling wrapper (
ba523d4) -
utils.py: Remove duplicated operation (
51ff494) -
utils.py: Strange logging error (
e8b43b5)
Detailed Changes: v1.3.0...v1.3.1
v1.3.0
v1.3.0 (2026-01-20)
Features
- cpg-flow: Remove python 310 version lock, allowing 311 (
5f69e1f)
Testing
- test_workflow.py: Adds explicit test cases for altered stageoutput get methods (
dad5e53)
Detailed Changes: v1.2.3...v1.3.0
v1.2.3
v1.2.3 (2026-01-06)
Bug Fixes
-
pyproject.toml: Modernise the uv dev dependencies section syntax (
96f3f53) -
stage.py: Altered logical flow to correctly report error modes if incorrect arguments are passed (
0930671)
_get requires a dictionary object to be accompanied by a key value. The previous logical tests to confirm this were conditional on the existence of a key. If a dict is given, but no key, the error message wrongly reported that the object was not a dictionary as a null logical case
Detailed Changes: v1.2.2...v1.2.3
v1.2.2
v1.2.1
v1.2.1 (2025-12-15)
Bug Fixes
- output_version: Update usage readme with workflow output version (
45f6232)
Detailed Changes: v1.2.0...v1.2.1
v1.2.0
v1.2.0 (2025-12-04)
Bug Fixes
- sg_hash: Add SG-only hashing method, for WFs with no assays loaded (
f98f4a2)
Adds a new SG-based hashing method
Detailed Changes: v1.1.1...v1.2.0
v1.1.1
v1.1.1 (2025-12-02)
Bug Fixes
-
metamist-cohorts query: [set-856] ruff format (
2a10cad) -
metamist-cohorts query: [set-856] support upper and lower case enum formats (
0db034a) -
metamist-cohorts query: [set-856] use lowercase for cohortstatus (
a71f584)
Documentation
-
Add exclude-newer upgrade option (
7c73dee) -
Change to warning symbols for cutoff (
a748488) -
Clean up upgrade docs (
8ad151a) -
Update docs for package upgrades and precommit (
cadda5d)
Detailed Changes: v1.1.0...v1.1.1
v1.1.0
v1.1.0 (2025-11-27)
Features
-
metamist-graphql: [set-842] fetch cohort and verify status (
b8f3cd1) -
metamist-graphql: [set-842] fetch only active cohorts (
84d6d1c) -
metamist-graphql: [set-842] fix grapQL query (
5964d5b) -
metamist-graphql: [set-842] fix lint issues (
1090482) -
metamist-graphql: [set-842] fix unit tests and populate status field in test data (
e51da42) -
metamist-graphql: [set-842] include cohort id in the msg (
534da2f) -
metamist-graphql: [set-842] update metamist version (
42a7e16) -
metamist-graphql: [set-842] update metamist version in uv lock (
7932c22)
Detailed Changes: v1.0.1...v1.1.0
v1.0.1
v1.0.1 (2025-11-21)
Bug Fixes
- type: Make populating assays opt-in (
e1f781c)
Assays populated by default but this causes failures when the reads meta is missing the location. With population of assays not necessary for all pipelines we can choose to opt-in where needed and skip it by default
Build System
- Bumped pip to 25.3 (
4f9f7a7)
Testing
- Populate assays in test cohort config (
61af4bf)
Detailed Changes: v1.0.0...v1.0.1
v1.0.0
v1.0.0 (2025-10-09)
Bug Fixes
- Removed unneeded uv.lock changes (
574931c)
Detailed Changes: v0.4.1...v1.0.0