Cpg-flow

Bug Fixes

- **stage.py**: As_str to take in path as well as str
([`d50a994`](https://github.com/populationgenomics/cpg-flow/commit/d50a994896124f6c645bdbf861f29c9372012f98))

current method not useful, make it make sense

Bug Fixes

- **docker.yaml**: Add condition to only push versioned image on bump
([`06f7326`](https://github.com/populationgenomics/cpg-flow/commit/06f73261323b40eeec5c830a45f094bb665d4975))

Continuous Integration

- **.github/workflows/updated-badges.yaml**: Remove update badges workflow
([`b508ba4`](https://github.com/populationgenomics/cpg-flow/commit/b508ba4a5e01874c7257cd5c91bcb7a6d47d35a2))

- **update-badges.yaml**: Push with cpg ci bot
([`c148f8e`](https://github.com/populationgenomics/cpg-flow/commit/c148f8e68700c26022d8fe3089a7fc4f47b0c0d5))

- **web-docs.yaml**: Add uv run
([`cf50620`](https://github.com/populationgenomics/cpg-flow/commit/cf506203dd7080bfb16d36d4aba48939785b270e))

- **.github/workflows/package.yaml**: Reverted package workflow to working state
([`da95c2a`](https://github.com/populationgenomics/cpg-flow/commit/da95c2a90cfd6f9947d8d30225f43b3d41c240ab))

- **.github/workflows/package.yaml**: Add p.a.t for package checkout
([`e6a2a77`](https://github.com/populationgenomics/cpg-flow/commit/e6a2a7708412c96690e9bf5a43afa9cf28a439fc))

- **.github/workflows**: Cleanup packaging workflow
([`9fca024`](https://github.com/populationgenomics/cpg-flow/commit/9fca024a88bd8dc1aaa2029594a5bdbf1e24bc68))

- **.github/workflows/web-docs.yaml,docs/update_readme.py,Makefile,.pre-commit-config.yaml**: Fix
docs workflow, remove update-readme pre-commit hook
([`888afd1`](https://github.com/populationgenomics/cpg-flow/commit/888afd1e72519c59ee295850f6fc2e22467684c3))

- **package.yaml**: Rm update alpha action
([`c94d52f`](https://github.com/populationgenomics/cpg-flow/commit/c94d52f87109bb4b58b7a9f2eae548e16cdcc68b))

Documentation

- **README.md,docs/docs/index.md**: Remove more broken docs links
([`2d6f900`](https://github.com/populationgenomics/cpg-flow/commit/2d6f900e1154af58df93132dd88cbb0813a993de))

- **docs/docs/index.md**: Remove broken docs links
([`01c0651`](https://github.com/populationgenomics/cpg-flow/commit/01c06518ed8de867c2e7ca01b543c2dff18aa537))

- **README.md**: Remove badges
([`2d2d200`](https://github.com/populationgenomics/cpg-flow/commit/2d2d2006e35392976edc81c201bd334af34d4862))

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))

Bug Fixes

- **README.md,docs/update_readme.py**: Sort list of workflows
([`249399d`](https://github.com/populationgenomics/cpg-flow/commit/249399d7cd7bef2f34a1b335595ef5064e729831))

- **docs/update_readme.py**: Show diff on edit
([`fcc990f`](https://github.com/populationgenomics/cpg-flow/commit/fcc990ff0dff954b74c4ab67faae13a701fde7ce))

- **./,.github/workflows/,docs/**: Fix when CI runs
([`516eedd`](https://github.com/populationgenomics/cpg-flow/commit/516eedd4e11ad6b0245bb5a5faa561f7ce1b57e2))

- **./,.github/workflows/,docs/**: Bug in update_readme
([`8f37ef2`](https://github.com/populationgenomics/cpg-flow/commit/8f37ef25dec0f0ab13e2bcdbc3ae7dcfb0292cea))

- **./,.github/workflows/**: Mv update readme to pre-commit
([`3afe591`](https://github.com/populationgenomics/cpg-flow/commit/3afe5918e71991ac58244dea2583c7060d4a9fff))

Build System

- **.pre-commit-config.yaml**: Update-readme config
([`b6451a2`](https://github.com/populationgenomics/cpg-flow/commit/b6451a28241705e71696c16dd58af31ecfa6d333))

Chores

- Update badges.yaml with test results and coverage
([`f482f9b`](https://github.com/populationgenomics/cpg-flow/commit/f482f9bd8d5475d56f0467312ca664cca049eba2))

- Update badges.yaml with test results and coverage
([`5574626`](https://github.com/populationgenomics/cpg-flow/commit/5574626f58d312a30a065ede403d07b6317a719a))

- Update badges.yaml with test results and coverage
([`cb52d5e`](https://github.com/populationgenomics/cpg-flow/commit/cb52d5e2d739785bc8900ebca4e2e3376f537ea8))

Code Style

- **.github/workflows/lint.yaml,security.yaml**: Formatting
([`fe55314`](https://github.com/populationgenomics/cpg-flow/commit/fe55314ab85b450eb998ff049315cac8f7c44eaa))

Continuous Integration

- **./,.github/workflows/**: Rm pull_request
([`a4eec4d`](https://github.com/populationgenomics/cpg-flow/commit/a4eec4dc549c00c66764444911fcdc4d4847ef1b))

- **package.yaml,test.yaml**: Github.ref -> github.ref_name
([`b1311b5`](https://github.com/populationgenomics/cpg-flow/commit/b1311b54503f21e371af83a9723921622ff44fdd))

- **web-docs.yaml**: Update if
([`9b05cb2`](https://github.com/populationgenomics/cpg-flow/commit/9b05cb22629cc5c0c8a03ba7f01b690a5dde633f))

- **web-docs.yaml**: Change var name
([`f7406eb`](https://github.com/populationgenomics/cpg-flow/commit/f7406eb6bf1607adc4f57e24bbf624655f682f19))

- **web-docs.yaml**: Run on push
([`bc721a4`](https://github.com/populationgenomics/cpg-flow/commit/bc721a4f48e17d2a2508685f0999088e3afd8fa9))

- **web-docs.yaml**: Reorder steps
([`9ca2194`](https://github.com/populationgenomics/cpg-flow/commit/9ca2194ddb369306a319051ed485c685a177da48))

- **.github/workflows/test.yaml,web-docs.yaml**: Update Install uv
([`6efe601`](https://github.com/populationgenomics/cpg-flow/commit/6efe601a9e2a94faf51a0529fddb3c5f0d98f05b))

- **web-docs.yaml**: Fix uv install
([`b1761ac`](https://github.com/populationgenomics/cpg-flow/commit/b1761ac21627232e0f72c84589dbfb0ec8d28c67))

- **.github/workflows/package.yaml**: Fix condition
([`31f5464`](https://github.com/populationgenomics/cpg-flow/commit/31f54642f9d20652709d81192232effd9b231e16))

Bug Fixes

- **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
([`78f9f50`](https://github.com/populationgenomics/cpg-flow/commit/78f9f50fe4688605dad88bd55480bd3e1c812db4))

Chores

- Make docs update
([`4aa5dca`](https://github.com/populationgenomics/cpg-flow/commit/4aa5dcae37b7609b29dbaee3f5651580079bc613))

- Make docs update
([`4842144`](https://github.com/populationgenomics/cpg-flow/commit/484214478fd017375b05101515565afc100b4dc3))

- Make docs update
([`1259329`](https://github.com/populationgenomics/cpg-flow/commit/12593294bad530f60cdea55ad1230ce3f09ab975))

- Make docs update
([`210da09`](https://github.com/populationgenomics/cpg-flow/commit/210da09e7101e75d4e4e97c627a954103deeea21))

- Make docs update
([`1f4cbe8`](https://github.com/populationgenomics/cpg-flow/commit/1f4cbe870889d1c4e099bd46afcfd959d1ed7d65))

- Make docs update
([`1100f7f`](https://github.com/populationgenomics/cpg-flow/commit/1100f7f6a2b26775c36a5caf26bc28f960ad56ed))

- Make docs update
([`b3a77eb`](https://github.com/populationgenomics/cpg-flow/commit/b3a77ebb7e525b484267e67f2fc3b2a5b9f19d74))

- 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
([`5ca47de`](https://github.com/populationgenomics/cpg-flow/commit/5ca47de1563e9710c8c2903bd3d21cb144711ddd))

- **web-docs.yaml**: Debug git push
([`ec7d385`](https://github.com/populationgenomics/cpg-flow/commit/ec7d385785b6c7864b8ad1b91156b932af6cd1e5))

- **web-docs.yaml**: Only push if there's a change
([`8b7ab0e`](https://github.com/populationgenomics/cpg-flow/commit/8b7ab0e8665d0cd356f29dcd3c9e0fbf6e314bcb))

- **web-docs.yaml**: Debug git push
([`7d9e9ae`](https://github.com/populationgenomics/cpg-flow/commit/7d9e9aef10071b47df986d0ecf020744a9fe9589))

- **web-docs.yaml**: Debug git push
([`15d3024`](https://github.com/populationgenomics/cpg-flow/commit/15d3024d7e5b093457033f7be5ff854966b04503))

- **web-docs.yaml**: Fix git push
([`296ac5d`](https://github.com/populationgenomics/cpg-flow/commit/296ac5d8715c81fc539b0846a6f39060f87f9494))

- **web-docs.yaml**: Debug git push
([`6ffa3f7`](https://github.com/populationgenomics/cpg-flow/commit/6ffa3f755d44426adfb29c4897f2a68542057658))

- **web-docs.yaml**: Debugging git push
([`eda60d7`](https://github.com/populationgenomics/cpg-flow/commit/eda60d70eaba2f803c32e1774d5782d7a228958b))

- **.github/workflows/package.yaml,web-docs.yaml**: Add secret
([`9ba0907`](https://github.com/populationgenomics/cpg-flow/commit/9ba0907f91d0e9fce1cd50a0be3ffb31151b5f04))

- **web-docs.yaml**: Fix rm in push
([`884c042`](https://github.com/populationgenomics/cpg-flow/commit/884c0424f6b9de00cc389a09395004fb0c7d999a))

- **web-docs.yaml**: Debug push
([`af31d11`](https://github.com/populationgenomics/cpg-flow/commit/af31d11b000e5ee224bbb3ac3cfadc4f71394d73))

- **web-docs.yaml**: Push doc changes to branch
([`a612c4f`](https://github.com/populationgenomics/cpg-flow/commit/a612c4f1ba0b41a5efcb20f44e4af0a63dd6057a))

- **Makefile,README.md**: Make docs command fixed
([`1085947`](https://github.com/populationgenomics/cpg-flow/commit/10859478b9e2f539892fd11d392d6ef12673d008))

- **Makefile**: If statement fix
([`39a4586`](https://github.com/populationgenomics/cpg-flow/commit/39a4586e326a5d9ea5ee05167117cd2b6fbeb9d1))

- **Makefile**: Move if to one line
([`769dff8`](https://github.com/populationgenomics/cpg-flow/commit/769dff834bfe94ea5661af074f08a2cbb8d59198))

- **Makefile**: Fix if
([`38d6702`](https://github.com/populationgenomics/cpg-flow/commit/38d6702c3ea39a44a99932d06186fbf635a4955b))

- **web-docs.yaml,Makefile**: Pass in branch to make docs
([`e5c87e5`](https://github.com/populationgenomics/cpg-flow/commit/e5c87e55ebffde5bce951c6c452f08db1044a726))

- **Makefile**: Add extra ls in make docs
([`444ef0d`](https://github.com/populationgenomics/cpg-flow/commit/444ef0d8119d7937418a5471a4b776b63337e412))

- **web-docs.yaml,Makefile**: Add ls to make docs command
([`82393c0`](https://github.com/populationgenomics/cpg-flow/commit/82393c048407b311dd1c439b80bff8d3f4ba704c))

- **web-docs.yaml**: Show generated files
([`0b20530`](https://github.com/populationgenomics/cpg-flow/commit/0b205300c69f35704fe8b908b782774add60a50c))

- **web-docs.yaml**: Fix uv install on web docs ci
([`043cb87`](https://github.com/populationgenomics/cpg-flow/commit/043cb87a6c49ab16a15bf37153d0a006bfafaa14))

- **package.yaml**: Only package on test success or workflow_dispatch
([`75ff6c7`](https://github.com/populationgenomics/cpg-flow/commit/75ff6c7a261a92457f74ec22dfeff7f9040aebf6))

Documentation

- **workflow_descriptions.yaml**: Fix typo in web-docs.yaml key
([`d5ceb8e`](https://github.com/populationgenomics/cpg-flow/commit/d5ceb8e07fb1125a083cd816b3c90c50c03a0d62))

Refactoring

- **package.yaml,web-docs.yaml-,+17**: Rm generated code
([`53d53da`](https://github.com/populationgenomics/cpg-flow/commit/53d53da512ec2624d6d202edf0f0e5e4a0b865bb))