Prepare release v1.2.0

[hannahlanzrath]

Top of stack #149, on #148. Prepares the v1.2.0 release by bumping the version in cadetrdm/__init__.py and .zenodo.json.

Remaining steps from the release checklist once the stack is merged:

• Run pytest tests -m "slow or server_api" (needs API tokens).
• Publish the GitHub release v1.2.0 from main.
• Check the PyPI deployment, the Zenodo DOI and Read the Docs.

Draft release notes

Added

• rdm push --output-only pushes only the output repository.
• rdm check --no-commit --project-only and an rdm-check pre-commit hook keep the remote links up to date for commits made with plain git.
• rdm add exposes git add in the CLI.
• Test coverage reporting to Codecov.
• Ruff linting with pre-commit hooks and a CI workflow. The codebase now has numpy-style docstrings and type annotations throughout.
• Release checklist issue template and an extended developer guide.
• A Cases page in the user guide on options, environments and reusing results, including loading results from the CLI.

Fixed

• Case.load() and reading the output log no longer check out branches or modify the output repository.
• run_study() syncs output results before looking them up.
• Case.load() updates the project repository instead of the output repository.
• log.tsv:
  • Fields are no longer re-quoted on every write.
  • Rows are split on line feeds only.
• Remote output branches are archived without creating local heads.
• Repositories with missing remotes or without an upstream branch no longer raise errors.
• A recorded environment.yml without a dependencies key no longer raises a KeyError.
• create_remotes / rdm remote create works on GitHub. Before, it created the repositories and then failed with an AttributeError.
• GitLabRemote.delete_remote only deletes the exact project instead of every project matching the search.
• Text files are opened with explicit UTF-8 encoding.
• The v1.1.0 log migration fills project_repo_branch from each entry's output branch instead of writing branch for every entry.
• The Read the Docs build installs its environment with Miniforge.
• Help texts of rdm remote add and rdm remote set-url.

Changed

• commit() defaults to add_all=False.
• Output branch names get a random suffix, so parallel runs do not collide. Pulls use rebase.
• Removed the container adapters, the Dockerfile template, the container example files and Environment.prepare_install_instructions.

Updated

• More tests run in CI, and tests that create repositories run in temporary directories.
• The GitHub/GitLab API tests read their accounts from environment variables and use random repository names, so any developer can run them.

[codecov-commenter]

Codecov Report

✅ All modified and coverable lines are covered by tests.

Files with missing lines	Coverage Δ
cadetrdm/__init__.py	100.00% <100.00%> (ø)

... and 2 files with indirect coverage changes

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