Cpg-flow

Bug Fixes

- **Workflow**: Catch the correct ConnectionError and rm useless log line
([`eba1c37`](https://github.com/populationgenomics/cpg-flow/commit/eba1c37714456f87e87a0169dde19de0f46a4aa2))

This change was motivated by the local dry_run of cpg-flow always failing by attempting to contact
metamist. By catching the appropriate error this is no longer the case. We also log a final line
with dry_run complete.

SET-448

Build System

- Removes cpg-flow from deps
([`7063dcb`](https://github.com/populationgenomics/cpg-flow/commit/7063dcb844eac9d75d38cd992d57e77db837f8d0))

- **Dockerfile,pyproject.toml**: Bump uv version in Dockerfile
([`feecc9c`](https://github.com/populationgenomics/cpg-flow/commit/feecc9c25d5af7405575da0a1fdb5a9b346f475b))

- **uv.lock**: Pin cryptography [security]
([`c30380c`](https://github.com/populationgenomics/cpg-flow/commit/c30380cbfb15cc3795e69feef6d12517fc31ebdd))

Continuous Integration

- **.github/workflows/package.yaml,pyproject.toml,uv.lock**: Add step to publish tagged versions on
docs
([`f32bd9f`](https://github.com/populationgenomics/cpg-flow/commit/f32bd9f84255c88524d364b51de133ec03b77fdc))

Documentation

- **mkdocs.yml,docs/index.md**: Adding versioning to docs
([`8a56baa`](https://github.com/populationgenomics/cpg-flow/commit/8a56baa4de8e5c0a632f56048c9e4e6eb7f99080))

Testing

- **test_cohort**: Fix bug in mock get_analyses_by_sgid
([`c071979`](https://github.com/populationgenomics/cpg-flow/commit/c07197948a0c8a44ae29d68b23dcce1c40622fb7))

- Move test data into assets/
([`b2f5b61`](https://github.com/populationgenomics/cpg-flow/commit/b2f5b61348851bfcc4f985ae4c5b868a8ee50aba))

SET-369

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))