Cpg-flow

Bug Fixes

- **.dummy**: Force release of alpha
([`41dfb46`](https://github.com/populationgenomics/cpg-flow/commit/41dfb460d30c386ea82e6cb06cfebd2a982c1d5f))

Build System

- **pyproject.toml,uv.lock**: Add networkx to core deps
([`e6a0826`](https://github.com/populationgenomics/cpg-flow/commit/e6a08265a18da34df9eb93a4db0b0ffd3ce24e8e))

- **uv.lock**: Bumped tornado dep
([`58a713f`](https://github.com/populationgenomics/cpg-flow/commit/58a713f25b3c4f6f7cd7be7ad59df2a1681e3029))

- **uv.lock,pyproject.toml**: Bumped grpcio dep
([`256552f`](https://github.com/populationgenomics/cpg-flow/commit/256552f31d32788a4bbcf1bab5b9392d3a9e37a6))

- **uv.lock,pyproject.toml,.github/workflows/security.yaml**: Bumped deps, improved security
workflow
([`52449a8`](https://github.com/populationgenomics/cpg-flow/commit/52449a8cb05a5601fc859e19894e609e49902d6a))

- **Dockerfile**: Add explicit copying of deps files
([`693b3da`](https://github.com/populationgenomics/cpg-flow/commit/693b3daa4a11b68bc72a8ded3a7c550287442dda))

- **Dockerfile**: Fix typo in path
([`d181a83`](https://github.com/populationgenomics/cpg-flow/commit/d181a83b2ffdfb001f233b2852f601231b1a46e0))

- **Dockerfile,-tests/hail/workflow.py**: Force install of dev deps
([`10beaea`](https://github.com/populationgenomics/cpg-flow/commit/10beaeae82dbc461bce7c10f314c545716bc5622))

- **.dockerignore,-Dockerfile,-tests/hail/config.toml**: Improve uv setup in docker
([`652cbee`](https://github.com/populationgenomics/cpg-flow/commit/652cbeeb1cc0510b7110614b8cbfb04a719f8e36))

- **Dockerfile**: Activate venv in dockerfile
([`b086e9b`](https://github.com/populationgenomics/cpg-flow/commit/b086e9b54674ee378602249a0b7a0e86a4c56e01))

- **Dockerfile**: Uv sync after copying dir contents
([`2bb9dc8`](https://github.com/populationgenomics/cpg-flow/commit/2bb9dc8430602a92e258c4b64f14ec3c2d024c4e))

- **Dockerfile**: Use uv sync to install reqs
([`2ff5933`](https://github.com/populationgenomics/cpg-flow/commit/2ff59333f1b97132f17510e8a0f5d426189aa75a))

- **Dockerfile**: Test running uv from local bin
([`11b3477`](https://github.com/populationgenomics/cpg-flow/commit/11b3477af856bec94d2a50b5f06c85dff8f02dcf))

- **Dockerfile**: Adding source shell to Docker stage
([`4aa8e1f`](https://github.com/populationgenomics/cpg-flow/commit/4aa8e1f5cf0fba99dd0998c10a8bb01b04794297))

- **Dockerfile**: Test using uv docker img
([`6f2ec8f`](https://github.com/populationgenomics/cpg-flow/commit/6f2ec8fd4c34864fc35220e7a1660e7afa04473e))

- **Dockerfile**: Switch to uv and fix dir copy
([`b2db11d`](https://github.com/populationgenomics/cpg-flow/commit/b2db11d087e0a370bb4445fb8c8aa1de4d78048d))

Code Style

- **.dummy**: Rm file
([`087f7d9`](https://github.com/populationgenomics/cpg-flow/commit/087f7d9f84b0c2c268a2af722ceee57fc6999cb3))

Continuous Integration

- **hail.yaml**: Rm uneeded workflow
([`54ac1a9`](https://github.com/populationgenomics/cpg-flow/commit/54ac1a99731b3f2f7312086d66645eca1105329b))

- **.github/workflows/,tests/hail/**: Fix tests script again
([`03dd3a6`](https://github.com/populationgenomics/cpg-flow/commit/03dd3a651a849351dfc64927079aaa5ffffebdc1))

- **docker.yaml**: Fix build github sha
([`5cf3a7a`](https://github.com/populationgenomics/cpg-flow/commit/5cf3a7a7943e91aeed244396a384bcfff329cfad))

- **docker.yaml**: Echo sha
([`01f64d1`](https://github.com/populationgenomics/cpg-flow/commit/01f64d1e2052abeda3219d8d2de6c87cad6da4e2))

- **docker.yaml**: Fix push to images-tmp sha
([`df24a1e`](https://github.com/populationgenomics/cpg-flow/commit/df24a1e2141229becbe4f3a6a34ed2c8cc2c0e0f))

- **docker.yaml**: Change to $GITHUB_SHA
([`7d582c0`](https://github.com/populationgenomics/cpg-flow/commit/7d582c0c59f077565d70e577432afa93e08951ad))

- **manual-test.yaml**: Change to echo
([`0157daf`](https://github.com/populationgenomics/cpg-flow/commit/0157daf1b6b856931aa9d2abcf06207d042f9364))

- **manual-test.yaml**: Add a manual check for running workflow test
([`9a809cc`](https://github.com/populationgenomics/cpg-flow/commit/9a809ccc79188d412313239e5dc38ac737d27689))

- **.dummy**: Trigger commit docker build
([`d1e84bc`](https://github.com/populationgenomics/cpg-flow/commit/d1e84bcc2caaf4ec7eb54088f06793bc24826d66))

- **docker.yaml,pyproject.toml**: Get sem ver to update docker version
([`b0279b0`](https://github.com/populationgenomics/cpg-flow/commit/b0279b0cee7517ecbe5d66879f975d60b10457bb))

- **docker.yaml**: Push commit images to images-tmp
([`743a533`](https://github.com/populationgenomics/cpg-flow/commit/743a533fb28f7b8b657748b8184c01489e0b94d2))

- **docker.yaml**: Add push commit sha step
([`3d13938`](https://github.com/populationgenomics/cpg-flow/commit/3d1393817db9df8f01bd46219405975576fcaf7f))

- **.github/workflows/docker.yaml**: Added test environment
([`eff9cdc`](https://github.com/populationgenomics/cpg-flow/commit/eff9cdc1ecd3a0966c7e7ff4a6e3eee457e36b1f))

- **.github/workflows/renovate.yaml**: Removed input on workflow dispatch
([`aad0f9b`](https://github.com/populationgenomics/cpg-flow/commit/aad0f9bd4f3e3c14ca062012d76fc85c2ffe1196))

Refactoring

- **.dummy**: Add dummy file
([`6317611`](https://github.com/populationgenomics/cpg-flow/commit/63176114962beefc3277701437e97eec57330dae))

- **tests/hail/**: Move to test_workflows_shared repo
([`c146832`](https://github.com/populationgenomics/cpg-flow/commit/c1468327bb71507d4ac89862266d307c4374515f))

Testing

- **Dockerfile**: Add PYTHONPATH to Dockerfile
([`fddd50e`](https://github.com/populationgenomics/cpg-flow/commit/fddd50ef32f934e89f2ea4f43be85fe527c11004))

- **tests/hail/workflow.py**: Add import to run_cpg_flow
([`a48b8dc`](https://github.com/populationgenomics/cpg-flow/commit/a48b8dcedd7dda713fce5977e0f9f73de54c4a58))

- **tests/hail/workflow.py**: Revert stages import
([`d998be7`](https://github.com/populationgenomics/cpg-flow/commit/d998be748d36f5ffd6eb6aa83a09877ba483020b))

- **./,tests/hail/**: Make tests importable
([`7af791d`](https://github.com/populationgenomics/cpg-flow/commit/7af791dd249f29cce38b85abe7b2adac154265c0))

- **tests/hail/stages.py**: Fix?
([`765f65e`](https://github.com/populationgenomics/cpg-flow/commit/765f65ee83791b8e40c68165128ab156c1d96b04))

- **tests/hail/config.toml,tests/hail/stages.py**: Fix?
([`e113af2`](https://github.com/populationgenomics/cpg-flow/commit/e113af2f2bfef49260da7e44765b3a81bc95d47f))

- **tests/hail/stages.py**: Trying print dump in a python job
([`26a69d9`](https://github.com/populationgenomics/cpg-flow/commit/26a69d9fe6f46b33db81a5082398235f61bbb613))

- **tests/hail/stages.py**: Remove use of read_input for cumulative_calc
([`ada778e`](https://github.com/populationgenomics/cpg-flow/commit/ada778e85b629ab6ec679a34cbd4ec05941555e9))

- **tests/hail/stages.py**: Testing python jobs in stages
([`374c383`](https://github.com/populationgenomics/cpg-flow/commit/374c38397698204f84a6c53c474b2feb42206d99))

- **tests/hail/stages.py**: Testing python jobs within stages
([`5eeaa84`](https://github.com/populationgenomics/cpg-flow/commit/5eeaa84b38652c8a70ba24bb9b989fe257546883))

- **tests/hail/stages.py**: Removed single quote bug
([`30947c1`](https://github.com/populationgenomics/cpg-flow/commit/30947c178e67eb13e33dfe957d3c599e4e231dd0))

- **tests/hail/config.toml**: Remove local backend setting
([`9fdc5af`](https://github.com/populationgenomics/cpg-flow/commit/9fdc5af7adf1ed0759ecba051e718afba1c0cb2b))

- **tests/hail/workflow.py**: Temp removal of last 2 stages
([`c3d607d`](https://github.com/populationgenomics/cpg-flow/commit/c3d607d14793977345c97b63dbcbac54b6876fd5))

- **tests/hail/stage.py**: More testing
([`c044488`](https://github.com/populationgenomics/cpg-flow/commit/c044488333ed18f711e2c130273661585f1ada11))

- **tests/hail/stages.py**: Testing cumulative calc
([`af682c9`](https://github.com/populationgenomics/cpg-flow/commit/af682c9fcf2dd5fa0da95bb2be8d99e3e73da708))

- **tests/hail/*.py**: Added logging
([`03daed8`](https://github.com/populationgenomics/cpg-flow/commit/03daed807827c59aa30d9fba8e1f82bf30c31adf))

- **tests/hail/*.py**: Fix path reference for expected_outputs
([`31a14eb`](https://github.com/populationgenomics/cpg-flow/commit/31a14eba8b4c573847c0f7a8e2de19c5b35fd742))

- **tests/hail/workflow.py**: Better logging for config
([`b67dab4`](https://github.com/populationgenomics/cpg-flow/commit/b67dab4e0bec1df6b63606bd2294b6a91c7b492a))

- **tests/hail/workflow.py**: Fixed config compilation
([`20d56ce`](https://github.com/populationgenomics/cpg-flow/commit/20d56ceb528e2dc6652db27a13ed794943f443d7))

- **tests/hail/config.toml**: Added access_level and sequencing_type vars
([`5ec3812`](https://github.com/populationgenomics/cpg-flow/commit/5ec38124307e16a451989f141ac0a3c3e9e9bef0))

- **tests/hail/***: Fix linting, missing image arg to analysis-runner
([`7350986`](https://github.com/populationgenomics/cpg-flow/commit/735098694f1a2a1bc2be07aab38ff1ee9263637b))

- **tests/hail/workflow.py**: Standardise shebang
([`b405406`](https://github.com/populationgenomics/cpg-flow/commit/b4054060698dbb523165be9213227db7471079c8))

- **tests/hail/*.py,-Dockerfile**: Add explicit imports from src
([`ed0ddf3`](https://github.com/populationgenomics/cpg-flow/commit/ed0ddf3d8eb790d78575570d560b2b23e0662df0))

- **tests/hail/stages.py,tests/hail/workflow.py,Dockerfile**: Fixed some bugs, and refactored
dockerfile for more accurate paths
([`41d86e6`](https://github.com/populationgenomics/cpg-flow/commit/41d86e62639b1752397e8f4eff220023a8ce55c3))

- **tests/hail/workflow.py**: Switch back shebang
([`71de065`](https://github.com/populationgenomics/cpg-flow/commit/71de0655a96362188184b32bdc2c251d8dcbc85b))

- **tests/hail/workflow.py**: Change shebang venv path
([`96c31b9`](https://github.com/populationgenomics/cpg-flow/commit/96c31b972c7390dd29b19ad02a54f5edfbbceb41))

- **tests/hail/run-test.sh**: Write better wait for docker loop
([`91a55ea`](https://github.com/populationgenomics/cpg-flow/commit/91a55ea459889b359f30e0e278e1f7f85f9dfe50))

- **tests/hail/run-test.sh**: Fix our script
([`3b9e782`](https://github.com/populationgenomics/cpg-flow/commit/3b9e78257cdaeed274b7469d927902b3e2af208d))

- **tests/hail/run-test.sh**: Check the image exists
([`8ea7013`](https://github.com/populationgenomics/cpg-flow/commit/8ea7013d35ef62ef10b32219bc24107fc93cec5e))

- **tests/hail/run-test.sh**: Check commit has pushed
([`191f4ca`](https://github.com/populationgenomics/cpg-flow/commit/191f4cacf8c96452442b4721c00c55239ad4e58b))

- **tests/hail/config.toml,tests/hail/run-test.sh**: Add warnings
([`12fa5bd`](https://github.com/populationgenomics/cpg-flow/commit/12fa5bd351a8f8344fc4f697c8bc71f328f48a25))

- **tests/hail/stages.py,tests/hail/workflow.py**: Complete workflow
([`2f63d3d`](https://github.com/populationgenomics/cpg-flow/commit/2f63d3d0d08ffed5eb5b3b58f5d44e0fb3135464))

- **.github/workflows/,tests/hail/**: Adding more to workflow test
([`eea12e7`](https://github.com/populationgenomics/cpg-flow/commit/eea12e7cd5e5c222f60056642b19d9868b430ac4))

- **tests/hail/**: Start writing cpg-flow workflow test
([`930790a`](https://github.com/populationgenomics/cpg-flow/commit/930790a89d9d0720c7def8eb2e4784ea17db1641))

Bug Fixes

- **package.yaml**: Fix setup step add git clone
([`21c1400`](https://github.com/populationgenomics/cpg-flow/commit/21c1400a6083df40dffa66b9a642bf3f7d8892f4))

- **package.yaml**: Remove redundant checkout step
([`0634f44`](https://github.com/populationgenomics/cpg-flow/commit/0634f445361bf050d6243d142411c8738601c9e7))

- **package.yaml**: Use github token in setup step
([`8601d62`](https://github.com/populationgenomics/cpg-flow/commit/8601d62983cdac7b6a70429ac1d1c1c0aa4cf0f2))

- **package.yaml**: Use bot token
([`99814f6`](https://github.com/populationgenomics/cpg-flow/commit/99814f61d5f91bed00c49bf954da4c13b247a574))

- **package.yaml**: Add verbose logging
([`6fca5fb`](https://github.com/populationgenomics/cpg-flow/commit/6fca5fb4688840f38322db90eafb8183b9f5b835))

- **pyproject.toml,uv.lock**: Rm unused dev
([`26c9361`](https://github.com/populationgenomics/cpg-flow/commit/26c93615ed4a53ca8c239f57d98b99666dcaf6c6))

- **package.yaml,pyproject.toml**: Add ignore token for push
([`517d522`](https://github.com/populationgenomics/cpg-flow/commit/517d522fdfad4c4042f0dd4a472655ff0697c4b9))

- **package.yaml**: Deploy key to exempt action from br protection rules
([`5683a10`](https://github.com/populationgenomics/cpg-flow/commit/5683a10b95daa9a772360d75912572cac8dc9c9e))

- **package.yaml**: Push to pypi not testpypi
([`3a59082`](https://github.com/populationgenomics/cpg-flow/commit/3a59082568d6cf2d4394714020c6eb7101ea8ba3))

Chores

- Merge pull request 16 from populationgenomics/pypi-deploy
([`13a9f7d`](https://github.com/populationgenomics/cpg-flow/commit/13a9f7d737e1a73b86cca0c62c7c6c5c8aadf91a))

Pypi deploy

- Merge pull request 15 from populationgenomics/pypi-deploy
([`20b4886`](https://github.com/populationgenomics/cpg-flow/commit/20b48861685b2927186f69fa6338cec4eeb5f1c3))

fix(package.yaml): deploy key to exempt action from br protection rules

Refactoring

- **.dummy**: Test token
([`fc48eb5`](https://github.com/populationgenomics/cpg-flow/commit/fc48eb52dcd4bc8a409cf229b7a9c2ed10288939))

- **.dummy**: Test token
([`ec00646`](https://github.com/populationgenomics/cpg-flow/commit/ec006467788e26482fd06c639c649c38feaae597))

- **.dummy**: Remove file, check token permissions
([`a5a36df`](https://github.com/populationgenomics/cpg-flow/commit/a5a36df0760595a421f606dae431ebfd770aa37f))

- **.dummy**: Test push to alpha using BOT_ACCESS_TOKEN
([`8284ac1`](https://github.com/populationgenomics/cpg-flow/commit/8284ac14890432ba0182aec0f2fb1feb2f41f278))

Bug Fixes

- **./,.github/workflows/**: Get package.yaml working
([`c1992f7`](https://github.com/populationgenomics/cpg-flow/commit/c1992f7595684e0c6ae4852358ae09526e557fe0))

Bug Fixes

- **Makefile,pyproject.toml**: Debug ci-build command
([`cdf2fcf`](https://github.com/populationgenomics/cpg-flow/commit/cdf2fcfe567ec0de7d7dc8fa3109cc6b28b744ad))

- **package.yaml,pyproject.toml**: Rm uv, base build with version fix
([`559d16b`](https://github.com/populationgenomics/cpg-flow/commit/559d16b10797927caee58cd1bf4245269271eac7))

- **package.yaml**: Add git auth
([`601669c`](https://github.com/populationgenomics/cpg-flow/commit/601669cbe7363dd56636d5ba96c345854e72e557))

- **package.yaml**: Fix package.yaml manual semantic command
([`f733c90`](https://github.com/populationgenomics/cpg-flow/commit/f733c90b050a012515284dc985d116b972744c71))

- **package.yaml,.pypirc**: Run semantic release manually
([`f872765`](https://github.com/populationgenomics/cpg-flow/commit/f8727656dd072635f87dde02f9b835cd9083c61b))

- **.dummy,package.yaml**: Trigger release, use venv in workflow
([`36a4057`](https://github.com/populationgenomics/cpg-flow/commit/36a405714c1eea6684c6308f001a7bbeddae0b31))

- **pyproject.toml**: Fix build command
([`37c43ec`](https://github.com/populationgenomics/cpg-flow/commit/37c43ec53d87948dc7db984d51d58dba92b1fafa))

- **./,.github/workflows/**: Fix package.yaml build command
([`e41138c`](https://github.com/populationgenomics/cpg-flow/commit/e41138c72fcf14bda795756f0c584f429cae37fd))

- **Makefile,pyproject.toml**: Update build system
([`759ef2d`](https://github.com/populationgenomics/cpg-flow/commit/759ef2dcacee15050d49fe006ff3f4815375f1b3))

Bug Fixes

- **.dummy**: Fix forces a release
([`6e34931`](https://github.com/populationgenomics/cpg-flow/commit/6e349310bf2b470952bcedcce28b47ae01cb8d8d))

Build System

- **pyproject.toml**: Fix project version
([`ddac37c`](https://github.com/populationgenomics/cpg-flow/commit/ddac37c3e53afd0a69b1f63abccb2cf239a36ec3))

Bug Fixes

- **pyproject.toml**: Remove dynamic version
([`4dcc2b9`](https://github.com/populationgenomics/cpg-flow/commit/4dcc2b9aa219c9a2e3ba041db71f20800c5b17a6))

- **pyproject.toml**: Remove dynamic version
([`9beca1f`](https://github.com/populationgenomics/cpg-flow/commit/9beca1fa8d22edf373b998c7e6cddcfb41c5e11a))