Bug Fixes
- **src/cpg_flow/,tests/,tests/assets/**: Debugging test_cohort.py
([`238ab67`](https://github.com/populationgenomics/cpg-flow/commit/238ab67fb36ce771d4efef9898180cab1a7ff026))
- **tests/,tests/assets/,tests/stages/**: Fix test mocks and files
([`aae8755`](https://github.com/populationgenomics/cpg-flow/commit/aae87550ff1b6f410a6b3d193079b3a8b40171c4))
- **tests/stages/__init__.py**: Fix file to prod-pipes 959 version
([`91b875e`](https://github.com/populationgenomics/cpg-flow/commit/91b875ebebc9251a8b435ef34996b82bc76b5896))
- Rename cpg_workflow to cpg_flow
([`b387b3c`](https://github.com/populationgenomics/cpg-flow/commit/b387b3c1ff6d9ac1726b50e52ddca00abc2522e9))
- **workflow.py**: Fix circular import error
([`8de184f`](https://github.com/populationgenomics/cpg-flow/commit/8de184fa88db81aee52ba3c5ebcc7b3f646f2907))
- **src/cpg_flow/targets/**: Fix circular import issue
([`ca793b1`](https://github.com/populationgenomics/cpg-flow/commit/ca793b1af01d568b3058abfce1b2431c9b7f3c66))
- **pyproject.toml**: Switch back to 3.10 for prod pipes, add deps fix
([`1a0e214`](https://github.com/populationgenomics/cpg-flow/commit/1a0e2144901697029f1196cc8bedc9ab7979542e))
- **test.yaml**: Fix path to tests folder
([`199b168`](https://github.com/populationgenomics/cpg-flow/commit/199b1684974159b7afa1b5c6e33decdecaad4505))
- **test.yaml**: Revert to 3.10
([`69e4f14`](https://github.com/populationgenomics/cpg-flow/commit/69e4f14d8f9dd1341021ce6ddad1a30542797ef5))
Build System
- **.github/renovate-config.json**: Removed merge commit msg debris
([`3f845a1`](https://github.com/populationgenomics/cpg-flow/commit/3f845a16fb849e3979ece711f1040ffe22f47866))
- **.github/workflows/renovate.yaml**: Attempting to fix the code checkout
([`3f326ba`](https://github.com/populationgenomics/cpg-flow/commit/3f326baf904b1226bcc36454e4afefff5ab48903))
- **.github/workflows/renovate.yaml**: Fix how the workflow dispatch call works
([`8190250`](https://github.com/populationgenomics/cpg-flow/commit/8190250a39ff05b9b1135ad8f7310722d7848f79))
- **requirements/***: Potential fix to renovatebot detecting deps
([`afaafd3`](https://github.com/populationgenomics/cpg-flow/commit/afaafd3eefd20cff9078fecb88cbbcbc0bb531a6))
- **pyproject.toml**: Allow chore tag option
([`a85e24b`](https://github.com/populationgenomics/cpg-flow/commit/a85e24b7b8fe1f5034f0b65df8f228b7650b4a23))
- **pyproject.toml,uv.lock**: Add commitizen to dev deps, rm old ones
([`17cf760`](https://github.com/populationgenomics/cpg-flow/commit/17cf760fe81f70002786af88adee129ca8503db0))
- **pyproject.toml,uv.lock**: Add pytest_mock
([`b6de677`](https://github.com/populationgenomics/cpg-flow/commit/b6de67747a16c199836457cbc54e34243a90db14))
- **pyproject.toml**: Remove unused mypy options
([`61147e5`](https://github.com/populationgenomics/cpg-flow/commit/61147e563953eb01c156d70b161a629cc6245092))
- **pyproject.toml**: Setup ruff linting and ruff isort configs, black config
([`1c769f8`](https://github.com/populationgenomics/cpg-flow/commit/1c769f8795e76bdd763b6d7a707245758bf421d2))
- **Dockerfile**: Added a skeleton Dockerfile
([`b2ee7bb`](https://github.com/populationgenomics/cpg-flow/commit/b2ee7bb89c530060b09f94538b4b0f8181c7865b))
- **pyproject.toml**: Bumped hail to 0.2.133
([`785adb5`](https://github.com/populationgenomics/cpg-flow/commit/785adb56be57d322afc7b6fc34d867c9d771cb93))
- **.github/workflows/renovate.yaml**: Fix how the workflow dispatch call works
([11](https://github.com/populationgenomics/cpg-flow/pull/11),
[`951c3b0`](https://github.com/populationgenomics/cpg-flow/commit/951c3b0a711c2d1f1d4582f7871f7b743f17bb86))
- **Makefile,README.md**: Update dev instructions and init in Makefile
([`ff111d8`](https://github.com/populationgenomics/cpg-flow/commit/ff111d831c4aa3527fe47bc9d38b14988dcabd24))
- **test.yaml**: Disable test workflow for now
([`3574ea2`](https://github.com/populationgenomics/cpg-flow/commit/3574ea2621cd5b23f1214ca0740d9e3cabbea8cc))
- **pre-commit**: Add commitlint
([`09c6915`](https://github.com/populationgenomics/cpg-flow/commit/09c691512273b6ebd519c83da756f4dd0fffe096))
- **Makefile**: Create makefile for building and installing dependencies
([`b8ab07b`](https://github.com/populationgenomics/cpg-flow/commit/b8ab07bc6133a054bb9ed531fc055fc0f31f3a90))
Chores
- Merge migration-integration into migration-03
([`a2054ef`](https://github.com/populationgenomics/cpg-flow/commit/a2054ef04201ce36647f61bd9a5fa47a2c383bb5))
- Merge remote
([`10149d5`](https://github.com/populationgenomics/cpg-flow/commit/10149d58a66244a30390065c250c1c083fbb34f8))
- Merge main
([`0fb19d8`](https://github.com/populationgenomics/cpg-flow/commit/0fb19d8a3b512367c2f0f131244510e271a66006))
Code Style
- **pyproject.toml**: Removed black and isort config, added additional ignore to ruff
([`5b550ee`](https://github.com/populationgenomics/cpg-flow/commit/5b550eea3510df7394f8c05d2724953cf94dd100))
- **.pre-commit-config.yaml,-src/***: Better linting, removed black and isort from pre-commit
([`4f05eb1`](https://github.com/populationgenomics/cpg-flow/commit/4f05eb1ddafb6c61aa2eac0752eb909ecac2670a))
- **README**: Fix title links
([`54e8031`](https://github.com/populationgenomics/cpg-flow/commit/54e8031cbb82b252a016d5a3a19cf6ab24e85388))
Continuous Integration
- **.github/workflows/renovate.yaml,-uv.lock**: Removed push calls to the workflow
([`cbb5004`](https://github.com/populationgenomics/cpg-flow/commit/cbb50049d508b4997333feb909f8c92cd876032f))
- **.github/renovate-config.json**: Selected alpha as the target branch, and switched to uv
([`f434110`](https://github.com/populationgenomics/cpg-flow/commit/f4341108fd87ed287a857b9c487d494e38afe1f5))
- **.github/renovate-config.json**: Use uv to manage deps
([`9724557`](https://github.com/populationgenomics/cpg-flow/commit/9724557eca258bb669bb0efdc1551d2700c9a851))
- **package.yaml,pyproject.toml**: Modify semantic release build command
([`b990638`](https://github.com/populationgenomics/cpg-flow/commit/b9906386085aed7c985332eee4360f468ce99ccf))
- **package.yaml**: Add fetch-depth 0
([`b1500fe`](https://github.com/populationgenomics/cpg-flow/commit/b1500fef2d13444ba73b924bdb260e4886df648d))
- **package.yaml**: Fix publish action version
([`c17bc5e`](https://github.com/populationgenomics/cpg-flow/commit/c17bc5e160177ed132a1dbd69dabfb306c967de1))
- **package.yaml**: Trigger package on push just for testing
([`1de648f`](https://github.com/populationgenomics/cpg-flow/commit/1de648f8244eed2b209d42f8d55f9ade14168347))
- **package.yaml**: Remove dependent steps
([`aa42e8f`](https://github.com/populationgenomics/cpg-flow/commit/aa42e8ff7cc30ff60eafa6df1e0253cb0f575a16))
- **lint.yaml,test.yaml**: Rm on pull_request for test and lint
([`0e6a5e6`](https://github.com/populationgenomics/cpg-flow/commit/0e6a5e6484a8a7bf505f5f4e123ef7f1df85c8db))
- **security.yaml**: Fix security.yaml
([`70fffb1`](https://github.com/populationgenomics/cpg-flow/commit/70fffb1fd9178b7c1d0b64adb01abe858b4f46af))
- **package.yaml,pyproject.toml**: Setup package.yaml workflow
([`89694c2`](https://github.com/populationgenomics/cpg-flow/commit/89694c21df57222d6fd19130c9733e2f02be7ee0))
- **package.yaml,test.yaml-,+6**: Debugging package.yaml
([`0cf28cc`](https://github.com/populationgenomics/cpg-flow/commit/0cf28cccf7ae64c75f32f0e8a57c28e2b65ff9c6))
- **./,.github/workflows/**: Fix workflows, pin python version
([`a9c91fb`](https://github.com/populationgenomics/cpg-flow/commit/a9c91fb03065686afd9f16f87360f3521e8cf257))
- **lint.yaml**: Fix lint.yaml
([`55b6df4`](https://github.com/populationgenomics/cpg-flow/commit/55b6df42d0620301dc1c34b065ebc5956f1a3f37))
- **test.yaml**: Fix test.yaml workflow
([`e382488`](https://github.com/populationgenomics/cpg-flow/commit/e38248833c3341182f5293fc31d4f3355a802698))
- **test.yaml,.gitignore-,+7**: Fixing test.yaml
([`b5f3bac`](https://github.com/populationgenomics/cpg-flow/commit/b5f3bac958de1c9f200a9ca023bb7a042698de46))
- **.github/workflows/security.yaml**: Fixed requirements path
([`4a1ae56`](https://github.com/populationgenomics/cpg-flow/commit/4a1ae562dbc4600b717379befc269817d604acec))
- **security.yaml**: Add pip-audit workflow
([`8d6ad9e`](https://github.com/populationgenomics/cpg-flow/commit/8d6ad9ecfe2ac4a130fdc1129b358da71f774569))
PR: 909 from production-pipelines
- **.github/workflows/docker.yaml**: Added a docker workflow that builds and pushes a docker image
([`4b02ff1`](https://github.com/populationgenomics/cpg-flow/commit/4b02ff11ee2baad93d717ea28bfff940d2482932))
- **.github/workflows/package.yaml**: Changed the package name to cpg_flow
([`2e54fb9`](https://github.com/populationgenomics/cpg-flow/commit/2e54fb9f41d69e39016e97afc2e1d605874317af))
- **.github/workflows/lint.yaml**: Added additional triggers
([`e0eb58e`](https://github.com/populationgenomics/cpg-flow/commit/e0eb58e31ce9ef226ee9877b75204ef7f65fa564))
Documentation
- **src/cpg_flow/targets/dataset.py**: Added better docs about the file
([`bee79ba`](https://github.com/populationgenomics/cpg-flow/commit/bee79bafc1978df0d364e32fe221d9bf87736dd5))
- **DEVELOPERS.md**: Updated dev setup instructions and Python versions
([`a4148ea`](https://github.com/populationgenomics/cpg-flow/commit/a4148ead36654538d093c60013de76164fe4cd01))
- **tests/README.md**: Remove keep tags
([`2835445`](https://github.com/populationgenomics/cpg-flow/commit/283544543ee110d778ccbec6b2da9467d7a9491f))
- **tests/README.md**: Move readme from prod pipes
([`ecbce2d`](https://github.com/populationgenomics/cpg-flow/commit/ecbce2d8a175b55d9ede8d8d9d427467b910f6a3))
Features
- **Makefile,pyproject.toml,workflows**: Upgrad to using uv
([`02a946d`](https://github.com/populationgenomics/cpg-flow/commit/02a946dfc6cda94f185423ee00b18268a1720133))
Refactoring
- **misc/attach_disk_test.py**: Remove file
([`807d886`](https://github.com/populationgenomics/cpg-flow/commit/807d886f99659c163e80e60574072e60df3b25eb))
PR6: See Matt's comment
- **src/cpg_flow**: Removed some unused code and added better docs
([`cb64bf6`](https://github.com/populationgenomics/cpg-flow/commit/cb64bf649861a31eadeb306246b57ff0c3f4aad8))
- **src/cpg_flow/inputs.py**: Refactor to remove infinite loop, and cleanup
([`06591c5`](https://github.com/populationgenomics/cpg-flow/commit/06591c52e16ca2f9178aa05ec356f9609be76415))
- **src/cpg_flow**: Moved more stages out of the workflow file
([`9f67ab4`](https://github.com/populationgenomics/cpg-flow/commit/9f67ab47462932ba3e4f403e2a086ba02ac23918))
- **src/cpg_flow/targets**: Switched filenames to snake case and refactored linting
([`4345a82`](https://github.com/populationgenomics/cpg-flow/commit/4345a82c826b88cb0ff2e7be159fd6b2ac779c4a))
- **src/cpg_flow/defaults.toml**: Removed unused configs
([`fba83dc`](https://github.com/populationgenomics/cpg-flow/commit/fba83dceb9ce7be3339234db7b5da62d82bd748f))
- **src/cpg_flow/inputs.py**: Removed dead code and fixed some method calls
([`49e70a3`](https://github.com/populationgenomics/cpg-flow/commit/49e70a3e4e2857e50f07fbc09c4ceb56bb9d9e79))
Migration from production-pipelines
- **src/cpg_flow**: Fixed imports from targets
([`2d8348b`](https://github.com/populationgenomics/cpg-flow/commit/2d8348b7f43b05a78e2f1e521b1a1daa6d271037))
- **resources.py**: Migrate file, remove one unused section
([`38c3c9e`](https://github.com/populationgenomics/cpg-flow/commit/38c3c9e4e7a616395327e003f96c0b53394073dd))
- **cpg_flow/targets/**: Add init file and simplify imports
([`89fe513`](https://github.com/populationgenomics/cpg-flow/commit/89fe513a65e504ca51f9d26cc8fdbdc2c959d491))
- **utils.py**: Move cpg_workflows/batch.py into utils
([`28733a5`](https://github.com/populationgenomics/cpg-flow/commit/28733a52e35f1e033cb4b52e1f0a247704fa7f1a))
- **cpg_flow/targets/**: Add targets.py file, split by class
([`39db87c`](https://github.com/populationgenomics/cpg-flow/commit/39db87cd3d6d9c77b01fc2bb0d0cb9d5a6972831))
- **src/cpg_flow/metamist.py**: Removed dead code that we no longer needed
([`3d54754`](https://github.com/populationgenomics/cpg-flow/commit/3d54754f038ea358c5d6e2bd790114d31f1ebc4a))
Migration from production-pipelines
- **src/cpg_flow/workflow.py**: Removed the Stage class and other related classes from this file
([`941272d`](https://github.com/populationgenomics/cpg-flow/commit/941272dd58d4781c6ca85b3d7b1f85cec1125d1b))
- **src/cpg_flow/stage.py**: Split the Stage class into its own file
([`4dad84e`](https://github.com/populationgenomics/cpg-flow/commit/4dad84e738529bf46a5eb50eb4ddec4b02499100))
Migration from production-pipelines
- **cpg_flow/status.py**: Migrate the whole file
([`771b767`](https://github.com/populationgenomics/cpg-flow/commit/771b767226cd8cd5e3b0333f2e5f4fc14b187c45))
- **cpg_flow/defaults.toml**: Migrate the whole file
([`8c36fd4`](https://github.com/populationgenomics/cpg-flow/commit/8c36fd4ceae1680d20da7a4c996356c644f48e58))
- **cpg_flow/utils.py**: Migrate the whole file
([`8345483`](https://github.com/populationgenomics/cpg-flow/commit/8345483a30bcaed20a374b16d479f075f100de79))
- **cpg_flow/filetypes.py**: Migrate file, update deps
([`1f9406d`](https://github.com/populationgenomics/cpg-flow/commit/1f9406d60c059eb248585ccb3f18c5eaf48b94a8))
- **test/__init__.py**: Move to new tests folder
([`74d1f18`](https://github.com/populationgenomics/cpg-flow/commit/74d1f187e01753a6e6718c28f1cd4a81717c0cf7))
- **.files,-pyproject.toml,-__init__.py,-README.md**: Added config files and update to readme
([`1fd7ae6`](https://github.com/populationgenomics/cpg-flow/commit/1fd7ae69dfafc6a58435723d14a4a452822d5e0a))
Testing
- **tests/,tests/assets/test_cohort/**: Refactor test_cohort.py
([`e4dca3f`](https://github.com/populationgenomics/cpg-flow/commit/e4dca3f5a7068b1fa5ea773ec4ed8d0b51588e20))
- **src/cpg_flow/,tests/**: Fix tests in cpg flow
([`0682555`](https://github.com/populationgenomics/cpg-flow/commit/0682555ba66479d7f1ed0358da726a862a45a7d4))
- **tests/conftest.py**: Add conftest to try to get tests working
([`d8e6d64`](https://github.com/populationgenomics/cpg-flow/commit/d8e6d64c1500dcd8f6d9dcb1e902971005676450))
- **test.yaml,src/cpg_flow/inputs.py-,+4**: Fix cpg-flow tests, try ci
([`aadef8b`](https://github.com/populationgenomics/cpg-flow/commit/aadef8b2882f0d8b0b94cb04f4c4d5a1b5def2ce))
- **tests/test_workflow.py**: Add test, cpg_workflow -> cpg_flow
([`6028ef0`](https://github.com/populationgenomics/cpg-flow/commit/6028ef0861cf7b07f03aab8aaeed00f45bcc6811))
- **cpg_flow/__init__.py,test_status.py**: Add test, fix stage imports
([`ec45f3b`](https://github.com/populationgenomics/cpg-flow/commit/ec45f3b18c18c6944827723c2f137253049d5f96))
- **tests/test_multicohort.py**: Add test, cpg_workflow -> cpg_flow
([`b28140d`](https://github.com/populationgenomics/cpg-flow/commit/b28140df021ccf060938b9668da90aa1df258b45))
- **tests/test_cohort.py**: Add test, cpg_workflow -> cpg_flow
([`e78f1f4`](https://github.com/populationgenomics/cpg-flow/commit/e78f1f427bd1b2aed6769d60ef3a9808682102eb))
- **test_metamist.py**: Add test, remove unused import, fix deps
([`bf4dbe4`](https://github.com/populationgenomics/cpg-flow/commit/bf4dbe42bac5afc062b6fb67a7e9990ad1cbd206))
- **test_stage_types.py**: Add test, add helper functions
([`ff6eb2c`](https://github.com/populationgenomics/cpg-flow/commit/ff6eb2cd1225c9e6cb3e51ccb2fddb938984be37))
- **test_skip_stages.py**: Add test
([`bc665da`](https://github.com/populationgenomics/cpg-flow/commit/bc665dacc68a0d2446ed37134a6d3077bba59abd))
- **test_skip_stages_fail.py**: Add test
([`108b52e`](https://github.com/populationgenomics/cpg-flow/commit/108b52edac54f92374e5b1e537c43eb8507e57d9))
- **test_only_stages.py**: Add test
([`8fe01dc`](https://github.com/populationgenomics/cpg-flow/commit/8fe01dc3b7edf094b9adabb1c02173f6c81e2b2a))
- **test_last_stages.py**: Add test
([`63ebc43`](https://github.com/populationgenomics/cpg-flow/commit/63ebc436ad29cd36403f3c34c017f527c5de67d5))
- **test_force_stages.py**: Add test
([`9cc2a54`](https://github.com/populationgenomics/cpg-flow/commit/9cc2a5459c4f55fc8dc5f7995be64d0fb5ba1592))
- **test_first_last_stages.py**: Add test
([`9e9870d`](https://github.com/populationgenomics/cpg-flow/commit/9e9870decd8aa7d24d2b2ffce00e0204eb98fb2f))
- **src/cpg_flow/,tests/**: Fix imports, add test first last stage
([`0501661`](https://github.com/populationgenomics/cpg-flow/commit/05016612cd9c0fc6f2c63aa4cf498b35bce7195f))
- **test/stages/__init__.py**: Copy over test stages init
([`8636c6d`](https://github.com/populationgenomics/cpg-flow/commit/8636c6da5b28c52f959f2c4dd8399af8a82fa6ab))
- **test/__init__.py**: Moved from production-pipelines
([`49ee73b`](https://github.com/populationgenomics/cpg-flow/commit/49ee73b0903c383da51faadd6df10c1ab4230746))
- **misc/attach_disk_test.py**: Moved from production-pipelines
([`38ab29a`](https://github.com/populationgenomics/cpg-flow/commit/38ab29a2bdc3b494f0a4f124f729ff7cc3504ef1))