v3.0.0 release - #46
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- Added r/utils/status.R to track R section completion statuses per-organism and record these to a JSON file for parsing in Python.
- Modified r/sections/pca.R to implement status reporting per-organism, and to add a sample count guard to prevent attempts to analyse with too few samples for clustering.
- Modified r/sections/da.R to implement status reporting for skipping section and to ensure one fraction error does not fail the entire pipeline.
- Modified r/sections/qc.R to implement status reporting and add a sample count guard for generating upset plots and presence/absence heatmaps.
- Modified r/sections/concordance.R to implement status reporting for skipping section and to ensure one fraction error does not fail the entire pipeline.
- Modified r/sections/aux/ev-markers.R to implement status reporting.
- Modified commands/report.py to rebuild logging logic to use new status reports, allowing more granular reporting of results.
- Modified tests/unit/test_report.py to update index writing test to use new function signature.
Merge pull request #39 from holsam/report-improvements
- Added r/dependencies.R to list all required R package dependencies for running comms report sections.
- Modified r/dependencies.R to add jsonlite dependency.
- Moved r/dependencies.R and r/install_deps.R to r/deps/... to contain dependency-related scripts in single subdirectory.
- Added r/deps/check_deps.R to check if required dependencies are installed.
- Modified r/deps/install_deps.R to only install missing dependencies.
- Added utils/installrdeps.py to wrap R dependency utilities in Python for CLI access.
- Added cli/rutils.py to create new r-utils command for checking and installing R dependencies. - Modified cli/cli.py to register new r-utils command.
- Modified utils/installrdeps.py to print installed/missing dependencies to terminal, and to prompt for confirmation before installing if called directly.
- Modified cli/rutils.py to update function called by install subcommand to use terminal version that prompts for confirmation before installing.
- Modified cli/rutils.py to remove initial debug-level log message.
- Modified utils/installrdeps.py to update style of output text to use logging messages and to use single line.
- Modified utils/installrdeps.py to ensure consistent log message formatting.
- Modified utils/log.py to add a new level for inputs, which allows inputs via rich.prompt and records to both streams with the same style as other log messages.
- Modified utils/installrdeps.py to update levels used in logging, and to use new log input method.
- Modified utils/sheet.py to add a utility function for parsing TSV files (ie sample sheets) to SampleRow classes.
- Modified commands/experiment.py to add a helper function to check if an experiment already exists at a given path.
- Modified commands/experiment.py to update logic to allow editing an existing experiment using headless mode.
- Modified cli/cli.py to update experiment command to accept an experiment directory if provided.
- Modified utils/log.py to allow case_sensitive kwarg for rich.prompt to be passed through to logMsg.input.
- Modified cli/cli.py to add import statements for required libraries.
- Modified commands/experiment.py to update inputs in headless mode to use new logMsg.input class method.
- Modified docs/configuration.md to reflect v3.0.0 updates to config file creation and modification.
Merge pull request #44 from holsam/v3.0.0-docs
- Added .github/workflows/pr_ci_report.py to create a markdown file from results of Pull Request CI Report workflow to be used as auto-generated comment in repo.
- Added .github/workflows/pr-ci-report.yml to define a workflow for running Python and R tests automatically for a pull request, commenting the results as a table.
- Added .github/workflows/pr-version-check.yml to check that any pull requests raised on merged are increasing the version number.
- Added .github/workflows/publish-release.yml to build source distributions and publish release to GitHub on pushes to main.
- Modified .github/workflows/pr-ci-report.yml to fix incorrect R dependency installation path, and to use opencv-python-headless during Python tests to ensure they run on Linux.
- Modified .github/workflows/pr-ci-report.yml to fix missing testthat installation and to install the dependencies required by Qt on Linux.
- Modified tests/r/test_utils_import.R to correct R import tests which were not using the correct filenames for spectral count results files, causing issues with column names being imported.
- Modified .github/workflows/pr-ci-report.yml to include checkout step for posting summary comment so the pr_ci_report.py script is accessible.
- Modified .github/workflows/pr-ci-report.yml to download required Linux dependencies for R packages.
- Modified .github/workflows/pr-ci-report.yml to include additional Linux dependencies for running R scripts, and to add debug for report comment.
- Modified .github/workflows/pr-ci-report.yml to add debug step and remove R version 4.3.0 from matrix.
- Modified .github/workflows/pr-ci-report.yml to add additional Linux dependencies. - Modified .github/workflows/pr_ci_report.py to fix glob pattern. - Modified README.md to update minimum R version required.
- Modified .github/workflows/pr-ci-report.yml to update post comment job so checkout runs first, to stop deletion of downloaded artifacts as before.
Merge pull request #45 from holsam/gh-improvements
- Modified pyproject.toml and uv.lock to reflect version for release. Version number: 3.0.0
holsam
added
bug
- Modified .github/workflows/pr-version-check.yml to remove unterminated string literals.
Pull Request CI ReportCaution GitHub Actions runners do not have ThermoRawFileParser or Crux installed. Tests dependent on these binaries are skipped and should instead be run manually before merging. Summary
Python TestsPython versions tested: 3.14, 3.15
R TestsR versions tested: 4.4.3, 4.5.3, 4.6.1
Auto-generated by the comMS Pull Request CI Report workflow. See full logs in the Actions run for this PR. |
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Aug 13, 2026
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Pull request (PR) description:
This PR implements several changes to comMS:
reportcommand, so logs reflect the success/failure states of each section.experimentcommand to allow editing of existing experiments, both via the CLI and GUI.INPUTlevel so user inputs (e.g. from CLI) are reflected in log files.configcommand to update how configurations are stored and edited for simplicity. Also adds command-line overrides for configuration options to allow per-run modifications which are reported in aparams.tomlfile.Issues resolved:
n/a