diff --git a/.github/workflows/docker.yaml b/.github/workflows/docker.yaml index 6dfded0f..2c4b71c4 100644 --- a/.github/workflows/docker.yaml +++ b/.github/workflows/docker.yaml @@ -21,7 +21,7 @@ permissions: contents: read env: - VERSION: 0.1.0-alpha.17 + VERSION: 0.1.0-alpha.18 jobs: docker: diff --git a/CHANGELOG.md b/CHANGELOG.md index cab0b7a6..cb742b42 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,6 +1,46 @@ # CHANGELOG +## v0.1.0-alpha.18 (2025-01-28) + +### Bug Fixes + +- **README.md**: Merge alpha + ([`0d0735f`](https://github.com/populationgenomics/cpg-flow/commit/0d0735fe1e4eaf02b57eb34f8cb3d037bece1187)) + +- **./,src/cpg_flow/**: Merge alpha + ([`953181e`](https://github.com/populationgenomics/cpg-flow/commit/953181e597fd7b9b064d471679f9a442a9266a9c)) + +### Build System + +- **Makefile**: Refactor docs command to use mkdocs + ([`8628f3b`](https://github.com/populationgenomics/cpg-flow/commit/8628f3b43e50a84e6745016e6a6b0717826e18de)) + +### Chores + +- Update badges.yaml with test results and coverage + ([`b88bf6e`](https://github.com/populationgenomics/cpg-flow/commit/b88bf6eb295d6b8def6e18678e7b923e616b23a9)) + +- Update badges.yaml with test results and coverage + ([`6b66a51`](https://github.com/populationgenomics/cpg-flow/commit/6b66a51ffeaffaa08f7c7eef21b55f663bf7de6b)) + +### Documentation + +- **README.md**: Cleaup badges + ([`e148dda`](https://github.com/populationgenomics/cpg-flow/commit/e148dda76f6744f393bec77b3bc2881a5d54aff5)) + +- **docs/docs,-README.md,-uv.lock,-pyproject.toml**: Setup mkdocs + ([`10b16ab`](https://github.com/populationgenomics/cpg-flow/commit/10b16ab60840b73c2eed10f636cb30f301ac6b02)) + +- **README.md**: Run new pre-commit hook from alpha + ([`eb98c1e`](https://github.com/populationgenomics/cpg-flow/commit/eb98c1e29ee0e01fd2925c7e4ecb08fdd27d48a7)) + +### Features + +- **README.md,graph.py**: Major show workflow improvements + ([`55def6b`](https://github.com/populationgenomics/cpg-flow/commit/55def6b5816b72f9c3c94fbd169484bc44d85995)) + + ## v0.1.0-alpha.17 (2025-01-15) ### Bug Fixes @@ -78,6 +118,17 @@ - **graph.py**: Fix bug with _get_node_color default ([`7bd8093`](https://github.com/populationgenomics/cpg-flow/commit/7bd8093d7f4828f81b2bb65400d4cfc139d13407)) +- Add original change and extra log statement + ([`aa44f2b`](https://github.com/populationgenomics/cpg-flow/commit/aa44f2b7921342cb74cd71abc43b8993459e615a)) + +to continue testing + +- Undo name change to check error and provide informative logs + ([`048db79`](https://github.com/populationgenomics/cpg-flow/commit/048db791c3205a74dcceaf6196b64f615f4e7fa5)) + +- Add logging statements to help find bug + ([`d439901`](https://github.com/populationgenomics/cpg-flow/commit/d4399019ecde919feba2b0b103797c129297672e)) + ### Build System - **sonar-project.properties**: Optimise settings @@ -109,6 +160,22 @@ - Make docs update ([`af3b29b`](https://github.com/populationgenomics/cpg-flow/commit/af3b29b8a11af0cc545b22792a30c37286f606b3)) +- Update badges.yaml with test results and coverage + ([`2b7c222`](https://github.com/populationgenomics/cpg-flow/commit/2b7c2223953f91573f0e77701f7b2ec497244c4f)) + +- Update badges.yaml with test results and coverage + ([`0588ce1`](https://github.com/populationgenomics/cpg-flow/commit/0588ce103d143e186d75283bb2f685c935f0bcfd)) + +- Update badges.yaml with test results and coverage + ([`3eef434`](https://github.com/populationgenomics/cpg-flow/commit/3eef43447682aa8b0b429fae53c423349f94450d)) + +### Code Style + +- Remove verbose logging and comments + ([`c87879f`](https://github.com/populationgenomics/cpg-flow/commit/c87879fe972d00d2eefdfe1719680f2ac6b4b507)) + +testing artifacts + ### Continuous Integration - **web-docs.yaml**: Fix token @@ -204,6 +271,9 @@ - **Makefile**: Add debug pwd/ls ([`282f62c`](https://github.com/populationgenomics/cpg-flow/commit/282f62c40223de18769f22f3fd470db57f5d01e7)) +- **pyproject.toml,src/cpg_flow/metamist.py-,+5**: Merge alpha + ([`84ef763`](https://github.com/populationgenomics/cpg-flow/commit/84ef7632eae5abab9c1ef2fa4b3ed6f423d22e85)) + - **src/cpg_flow/workflow.py**: Fix url path ([`bb0e839`](https://github.com/populationgenomics/cpg-flow/commit/bb0e83949b9c1ff55d002bf884374897ae38d1d1)) @@ -219,9 +289,6 @@ - **src/cpg_flow/workflow.py**: Write_to_gcs_bucket convert to str ([`b782cfa`](https://github.com/populationgenomics/cpg-flow/commit/b782cfaf95cf9cc705cc631f85c86ffb87de9b9b)) -- Replicate prod pipes PR#1068 - ([`cf782c9`](https://github.com/populationgenomics/cpg-flow/commit/cf782c93686ec4346e3730af165a892986cf68fc)) - - **src/cpg_flow/workflow.py**: Create write_to_gcs_bucket ([`0452eb8`](https://github.com/populationgenomics/cpg-flow/commit/0452eb8c588ff328d9dc3b2b41c31f41fa40a83b)) @@ -243,15 +310,23 @@ - **src/cpg_flow/,tests/**: Metamist custom cohort mock fixed ([`1bb0ddd`](https://github.com/populationgenomics/cpg-flow/commit/1bb0ddd6c6bfb67fbb7be8531c423b4610786c05)) -- Migrate prod pipes PR#951 - ([`7f16948`](https://github.com/populationgenomics/cpg-flow/commit/7f169485444438ae260ae10dbfea1c5d022c6b8a)) - - **src/cpg_flow/workflow.py**: Fix 'skipped' attr missing in nx graph ([`1c64e6b`](https://github.com/populationgenomics/cpg-flow/commit/1c64e6bdf7e680ed01c6fb844ff95a2caf098a40)) - **graph.py**: Rm search in repo for stages (removed in cpg_flow) ([`648e7d7`](https://github.com/populationgenomics/cpg-flow/commit/648e7d7b269c80150640abbd0fdc422e411e29cc)) +- **multicohort**: Replace multicohort name with hash + ([`7ce04bd`](https://github.com/populationgenomics/cpg-flow/commit/7ce04bda8ed4b0cd9efb3984679b3e8c15ee3770)) + +multicohort.name too long for *nix. hash will be static in length + +- Replicate prod pipes PR#1068 + ([`cf782c9`](https://github.com/populationgenomics/cpg-flow/commit/cf782c93686ec4346e3730af165a892986cf68fc)) + +- Migrate prod pipes PR#951 + ([`7f16948`](https://github.com/populationgenomics/cpg-flow/commit/7f169485444438ae260ae10dbfea1c5d022c6b8a)) + - **inputs.py,tests/test_multicohort.py**: Replicate prod pipes PR#989 ([`f1d6fcd`](https://github.com/populationgenomics/cpg-flow/commit/f1d6fcdbd6390c0d6eaa09ae72f589294f90e2ef)) @@ -265,6 +340,9 @@ ### Chores +- Update badges.yaml with test results and coverage + ([`52aa984`](https://github.com/populationgenomics/cpg-flow/commit/52aa9841781820c5c43936f351cea678440e2209)) + - Update badges.yaml with test results and coverage ([`1994f07`](https://github.com/populationgenomics/cpg-flow/commit/1994f07de95f0bdccaac68ff465130e3c0196df2)) @@ -274,9 +352,6 @@ - Update badges.yaml with test results and coverage ([`7f2b1ff`](https://github.com/populationgenomics/cpg-flow/commit/7f2b1ff4b8442936fe1c568aecc5832a59f086c3)) -- Update badges.yaml with test results and coverage - ([`54d505d`](https://github.com/populationgenomics/cpg-flow/commit/54d505d9a5bf174f934bfdee64886842842eb9ee)) - - Update badges.yaml with test results and coverage ([`0a93026`](https://github.com/populationgenomics/cpg-flow/commit/0a9302638ed75acfe2a0858516f2b8ca00d7c4f2)) @@ -295,15 +370,21 @@ - Update badges.yaml with test results and coverage ([`837d6ba`](https://github.com/populationgenomics/cpg-flow/commit/837d6ba911bc47b665a18e920d915417773039ac)) -- Update badges.yaml with test results and coverage - ([`2deb20b`](https://github.com/populationgenomics/cpg-flow/commit/2deb20b5dc1e9ba8b9c5088ee8a3ecd9240166c7)) - - Update badges.yaml with test results and coverage ([`189c60b`](https://github.com/populationgenomics/cpg-flow/commit/189c60bbdb48766dc6e491ead97bf36c300b3f55)) - Update badges.yaml with test results and coverage ([`28eac64`](https://github.com/populationgenomics/cpg-flow/commit/28eac6433c9f9d62bd99d9de7114d6f9a09be047)) +- Update badges.yaml with test results and coverage + ([`b0c3331`](https://github.com/populationgenomics/cpg-flow/commit/b0c333119e3c11a8a66e9ed66a81a64285fc48ea)) + +- Update badges.yaml with test results and coverage + ([`54d505d`](https://github.com/populationgenomics/cpg-flow/commit/54d505d9a5bf174f934bfdee64886842842eb9ee)) + +- Update badges.yaml with test results and coverage + ([`2deb20b`](https://github.com/populationgenomics/cpg-flow/commit/2deb20b5dc1e9ba8b9c5088ee8a3ecd9240166c7)) + - Update badges.yaml with test results and coverage ([`5f70383`](https://github.com/populationgenomics/cpg-flow/commit/5f70383ede7d4b4232bd3ecc57966ca9f06795c3)) diff --git a/src/__init__.py b/src/__init__.py index 7762f4f0..f141f1b3 100644 --- a/src/__init__.py +++ b/src/__init__.py @@ -1 +1 @@ -__version__ = '0.1.0-alpha.17' +__version__ = '0.1.0-alpha.18'