v0.1.2

v0.1.2 (2025-02-05)

Bug Fixes

• stage.py: As_str to take in path as well as str (d50a994)

current method not useful, make it make sense

v0.1.1

v0.1.1 (2025-02-02)

Bug Fixes

• docker.yaml: Add condition to only push versioned image on bump (06f7326)

v0.1.0

v0.1.0 (2025-01-28)

Continuous Integration

• .github/workflows/updated-badges.yaml: Remove update badges workflow (b508ba4)

• update-badges.yaml: Push with cpg ci bot (c148f8e)

• web-docs.yaml: Add uv run (cf50620)

• .github/workflows/package.yaml: Reverted package workflow to working state (da95c2a)

• .github/workflows/package.yaml: Add p.a.t for package checkout (e6a2a77)

• .github/workflows: Cleanup packaging workflow (9fca024)

• .github/workflows/web-docs.yaml,docs/update_readme.py,Makefile,.pre-commit-config.yaml: Fix docs workflow, remove update-readme pre-commit hook (888afd1)

• package.yaml: Rm update alpha action (c94d52f)

Documentation

• README.md,docs/docs/index.md: Remove more broken docs links (2d6f900)

• docs/docs/index.md: Remove broken docs links (01c0651)

• README.md: Remove badges (2d2d200)

v0.1.0-alpha.18

v0.1.0-alpha.18 (2025-01-28)

Bug Fixes

• README.md: Merge alpha (0d0735f)

• ./,src/cpg_flow/: Merge alpha (953181e)

Build System

• Makefile: Refactor docs command to use mkdocs (8628f3b)

Chores

• Update badges.yaml with test results and coverage (b88bf6e)

• Update badges.yaml with test results and coverage (6b66a51)

Documentation

• README.md: Cleaup badges (e148dda)

• docs/docs,-README.md,-uv.lock,-pyproject.toml: Setup mkdocs (10b16ab)

• README.md: Run new pre-commit hook from alpha (eb98c1e)

Features

• README.md,graph.py: Major show workflow improvements (55def6b)

v0.1.0-alpha.17

v0.1.0-alpha.17 (2025-01-15)

Bug Fixes

• README.md,docs/update_readme.py: Sort list of workflows (249399d)

• docs/update_readme.py: Show diff on edit (fcc990f)

• ./,.github/workflows/,docs/: Fix when CI runs (516eedd)

• ./,.github/workflows/,docs/: Bug in update_readme (8f37ef2)

• ./,.github/workflows/: Mv update readme to pre-commit (3afe591)

Build System

• .pre-commit-config.yaml: Update-readme config (b6451a2)

Chores

• Update badges.yaml with test results and coverage (f482f9b)

• Update badges.yaml with test results and coverage (5574626)

• Update badges.yaml with test results and coverage (cb52d5e)

Code Style

• .github/workflows/lint.yaml,security.yaml: Formatting (fe55314)

Continuous Integration

• ./,.github/workflows/: Rm pull_request (a4eec4d)

• package.yaml,test.yaml: Github.ref -> github.ref_name (b1311b5)

• web-docs.yaml: Update if (9b05cb2)

• web-docs.yaml: Change var name (f7406eb)

• web-docs.yaml: Run on push (bc721a4)

• web-docs.yaml: Reorder steps (9ca2194)

• .github/workflows/test.yaml,web-docs.yaml: Update Install uv (6efe601)

• web-docs.yaml: Fix uv install (b1761ac)

• .github/workflows/package.yaml: Fix condition (31f5464)

v0.1.0-alpha.16

v0.1.0-alpha.16 (2025-01-15)

Bug Fixes

• graph.py: Fix bug with _get_node_color default (7bd8093)

Build System

• sonar-project.properties: Optimise settings (78f9f50)

Continuous Integration

• package.yaml: Only package on test success or workflow_dispatch (75ff6c7)

Documentation

• workflow_descriptions.yaml: Fix typo in web-docs.yaml key (d5ceb8e)

Refactoring

• package.yaml,web-docs.yaml-,+17: Rm generated code (53d53da)

v0.1.0-alpha.15

v0.1.0-alpha.15 (2025-01-13)

Bug Fixes

• Makefile: Add uv to to init commands (44ac58d)

• package.yaml,Makefile: Make docs out of ci-build command (4df965b)

• package.yaml,Makefile: Install uv, uv sync (5fcadd9)

• Makefile: Add debug pwd/ls (282f62c)

• src/cpg_flow/workflow.py: Fix url path (bb0e839)

• src/cpg_flow/workflow.py: Info log the url (def1d03)

• src/cpg_flow/workflow.py: Fix bucket/blob name (ebfe31a)

• src/cpg_flow/workflow.py: Fix bug on 577 to use str (89ff6fe)

• src/cpg_flow/workflow.py: Write_to_gcs_bucket convert to str (b782cfa)

• Replicate prod pipes PR#1068 (cf782c9)

• src/cpg_flow/workflow.py: Create write_to_gcs_bucket (0452eb8)

• src/cpg_flow/workflow.py: Fix plotly plot save (d3e70a6)

• src/cpg_flow/workflow.py: Don't fail on connection error (0348bd4)

• src/cpg_flow/workflow.py: Rm () from self.web_prefix (7d4f9b3)

• src/cpg_flow/workflow.py: Get_alignment_inputs_hash() (71ccd0c)

• src/cpg_flow/workflow.py: Use builtin web_prefix method (6362036)

• src/cpg_flow/,tests/: Metamist custom cohort mock fixed (1bb0ddd)

• Migrate prod pipes PR#951 (7f16948)

• src/cpg_flow/workflow.py: Fix 'skipped' attr missing in nx graph (1c64e6b)

• graph.py: Rm search in repo for stages (removed in cpg_flow) (648e7d7)

• inputs.py,tests/test_multicohort.py: Replicate prod pipes PR#989 (f1d6fcd)

• defaults.toml: Remove unnecessary options and add more comment (57f80ca)

Build System

• pyproject.toml,uv.lock: Add pre-commit as core dep (f03ecaf)

Chores

• Update badges.yaml with test results and coverage (1994f07)

• Update badges.yaml with test results and coverage (ba9fdb8)

• Update badges.yaml with test results and coverage (7f2b1ff)

• Update badges.yaml with test results and coverage (54d505d)

• Update badges.yaml with test results and coverage (0a93026)

• Update badges.yaml with test results and coverage (cd46929)

• Update badges.yaml with test results and coverage (9cfccdb)

• Update badges.yaml with test results and coverage (d3664b4)

• Update badges.yaml with test results and coverage (28a23d6)

• Update badges.yaml with test results and coverage (837d6ba)

• Update badges.yaml with test results and coverage (2deb20b)

• Update badges.yaml with test results and coverage (189c60b)

• Update badges.yaml with test results and coverage (28eac64)

• Update badges.yaml with test results and coverage (5f70383)

• Update badges.yaml with test results and coverage (1605c75)

• Update badges.yaml with test results and coverage (5ee9b6d)

• Update badges.yaml with test results and coverage (bf48667)

• Update badges.yaml with test results and coverage (e50ab94)

• Update badges.yaml with test results and coverage (478d74a)

• Update badges.yaml with test results and coverage (2174a17)

• Update badges.yaml with test results and coverage (5dad740)

Continuous Integration

• package.yaml: Continue on error build docs (4666ccb)

• Makefile: Add uv run to all docs commands (9d9bc00)

• package.yaml: Run on push to alpha, re-add if condition (8cdf8cf)

• Makefile: Fail make docs command to prevent relase (5f6f6bd)

• package.yaml: Run on PR to alpha (b7d54d1)

• package.yaml: Rm if for main/alpha (3e2a8b4)

• package.yaml: Add package run on push to alpha to debug (248ab87)

• docker.yaml: Echo out the docker tag (c991340)

• update-badges.yaml: Continue push on fail (d3fed1b)

• test.yaml: Fix removed code in test.yaml (f353a89)

• update-badges.yaml,docs/badges.yaml: Fix missing data for badges (21d4e0b)

• update-badges.yaml,docs/badges.yaml: Success if no changes to branch (8122669)

• update-badges.yaml,docs/badges.yaml: Rm trailing whitespace (2e547c0)

• update-badges.yaml: Add token to checkout (2e5de8c)

• test.yaml: Cat badge data (3221492)

• update-badges.yaml: Rm final push (a782609)

• update-badges.yaml: Add git pull...

v0.1.0-alpha.14

v0.1.0-alpha.14 (2025-01-06)

Bug Fixes

• .dummy: Force release (15b8906)

Build System

• pyproject.toml,uv.lock: Update jinja2 to 3.1.5 (4dbdf15)

• uv.lock: Upgrade jinja2 to 3.1.5 (f833517)

• pyproject.toml,uv.lock: Upgrade jinja2 as pip-audit logs (101bff5)

Continuous Integration

• test.yaml,update-badges.yaml: Add save badge data back to test (d2aab13)

• update-badges.yaml: Run after Test (22819cf)

• .github/workflows/: Change run order (84cfa2c)

• package.yaml: Run after update badges (de2fa6c)

• web-docs.yaml: Run after badge update (d986ecd)

• package.yaml: Run on completion of Test (d9af0a4)

• package.yaml,web-docs.yaml: Package on alpha/main only (4734447)

Refactoring

• .dummy: Add file (4648964)

v0.1.0-alpha.13

v0.1.0-alpha.13 (2025-01-05)

Bug Fixes

• pyproject.toml: Import coloredlogs (6a875cf)

• docs/update_readme.py,pyproject.toml-,+7: Fix linter warnings (97acdb8)

Build System

• pyproject.toml,uv.lock: Add pyyaml (9171532)

Chores

• Update badges.yaml with test results and coverage (9304439)

• Update badges.yaml with test results and coverage (db932a4)

• Update badges.yaml with test results and coverage (a750689)

• Merge alpha (b009c47)

• Update badges.yaml with test results and coverage (ea440eb)

• Update badges.yaml with test results and coverage (16f13be)

• Update badges.yaml with test results and coverage (eb8be5b)

• Update badges.yaml with test results and coverage (d3f6b6b)

Continuous Integration

• .github/workflows/: Package and web docs after test (adaa682)

• update-badges.yaml: Use env correctly (e337b5a)

• update-badges.yaml: Use env variables (47bd7fd)

• update-badges.yaml: Save env variables to GITHUB_ENV (3816a41)

• update-badges.yaml: Fix unzip (653851b)

• update-badges.yaml: List downloaded artifacts (2240494)

• update-badges.yaml: Custom download artifact (415a376)

• update-badges.yaml,docs/badges.yaml: Custom download artifact (fb177f2)

• test.yaml,update-badges.yaml: Change to using artifacts (6fea9f6)

• package.yaml: Add step to update alpha on package of main (4d9eb8a)

• update-badges.yaml: Checkout the branch so push works (2393d2a)

• update-badges.yaml: Checkout the triggering workflow ref (f1c09c9)

• test.yaml,update-badges.yaml: Merge main (01d6bd7)

• test.yaml,update-badges.yaml: Add to default branch (20ca3a4)

• test.yaml,update-badges.yaml: Back to workflow_run trigger (a1bed2d)

• test.yaml,update-badges.yaml: Download manually (1375dd6)

• update-badges.yaml: Back to workflow_run (551bd32)

• test.yaml,update-badges.yaml: Retry download-artifact (471c125)

• .github/workflows/,docs/: Test workflow upload artifact (390d162)

• update-badges.yaml: Add token (0bd20ee)

• update-badges.yaml: Try wait-for-test job (46cf28a)

• update-badges.yaml: Remove push trigger (d73a32b)

• update-badges.yaml: Trigger on push to readme (4152cdf)

• update-badges.yaml: Add manual run (ca01baf)

• web-docs.yaml: Rename to kebab case (67b1e94)

• .github/workflows/,docs/: Mv update-badges from test workflow (3b90377)

Documentation

• docs/alpha/: Create the docs page (75e772e)

Refactoring

• .dummy: Dummy commit (258223b)

• .dummy: Dummy commit (62038c0)

v0.1.0-alpha.12

v0.1.0-alpha.12 (2024-12-17)