OncoKB MAF bug and contributing guidelines

.bumpversion.toml

@@ -1,5 +1,5 @@
 [tool.bumpversion]
-current_version = "2.3.1"
+current_version = "2.3.1.9001"
 search = "{current_version}"
 replace = "{new_version}"
 message = "Bump version: {current_version} → {new_version}"

.github/workflows/build_conda_recipes.yaml

@@ -12,7 +12,7 @@ env:
   conda_env_yaml: conda/env/yaml
   conda_env_lock: conda/env/lock
   conda_org: pcgr
-  VERSION: '2.3.1' # bump
+  VERSION: '2.3.1.9001' # bump
 jobs:
   conda_build:
     # When merging to one of the branches above and the commit message matches

CODE_OF_CONDUCT.md

@@ -60,7 +60,7 @@ representative at an online or offline event.
 
 Instances of abusive, harassing, or otherwise unacceptable behavior may be
 reported to the community leaders responsible for enforcement at
-sigven@ifi.uio.no.
+sigven@ifi.uio.no or peterdiakumis@gmail.com.
 All complaints will be reviewed and investigated promptly and fairly.
 
 All community leaders are obligated to respect the privacy and security of the

CONTRIBUTING.md

@@ -0,0 +1,133 @@
+# Contributing to PCGR
+
+Thanks for your interest in contributing to the Personal Cancer Genome Reporter
+(PCGR). Contributions of all kinds are welcome — bug reports, documentation
+improvements, feature suggestions, and code.
+
+This document explains how to report problems and how to propose changes.
+
+## Code of conduct
+
+This project follows a [Code of Conduct](CODE_OF_CONDUCT.md). By participating,
+you are expected to uphold it. Please report unacceptable behaviour to the
+maintainers.
+
+## Ways to contribute
+
+- **Report a bug** — open an issue (see below for what to include)
+- **Request a feature** — open an issue describing the use case
+- **Ask a question** — use GitHub Discussions or open an issue
+- **Improve documentation** — corrections and clarifications are very welcome
+- **Contribute code** — see *Development workflow* below
+
+## Reporting bugs
+
+Most issues we receive can only be diagnosed with the full run context, so
+please include **all** of the following. Issues without this information will
+usually need a follow-up before we can help.
+
+1. **PCGR version** (`pcgr --version`)
+2. **Reference data bundle version** and the genome assembly used
+   (`grch37` or `grch38`)
+3. **Installation method** — Conda, Docker, Singularity/Apptainer —
+   including the image tag or environment specification
+4. **Operating system** and, if relevant, the compute environment
+   (laptop, HPC/cluster, cloud)
+5. **The exact command you ran**, in full, with all arguments
+6. **The complete error message and log output** (please paste as text in a
+   fenced code block rather than as a screenshot)
+7. **Input characteristics** — variant caller used, approximate number of
+   variants, tumour type, whether CNA/expression/fusion input was supplied
+8. **A minimal example input** that reproduces the problem, if you are able to
+   share one
+
+Please do not attach patient-identifiable data to a public issue. If a problem
+can only be reproduced with sensitive data, say so in the issue and we will
+find another way to investigate.
+
+## Requesting features
+
+When proposing a feature, describe the scientific or clinical use case rather
+than only the implementation. PCGR aims to produce clinically interpretable
+output aligned with established guidelines (AMP/ASCO/CAP, ClinGen/CGC/VICC), so
+proposals that affect variant classification or tier assignment should reference
+the relevant guideline or evidence source.
+
+## Development workflow
+
+We use a simple two-branch model:
+
+- **`main`** — reflects the current released version. Do not open pull requests
+  against `main`.
+- **`dev`** — the active development branch. **All pull requests should target
+  `dev`.**
+
+To contribute code:
+
+1. Fork the repository and create a branch from `dev`
+   (e.g. `feature/short-description` or `fix/short-description`)
+2. Make your changes, keeping the pull request focused on a single concern
+3. Update documentation and the changelog where relevant
+4. Open a pull request against `dev`, describing **what** the change does and
+   **why** it is needed
+
+For anything substantial — new annotation sources, changes to classification or
+tiering logic, or architectural changes — please open an issue to discuss the
+approach before writing code. This saves time on both sides.
+
+## Code organisation
+
+PCGR spans two languages, and it helps to know where a change belongs:
+
+- **Python** — the pipeline, variant annotation, and much of the interpretation
+  logic (including oncogenicity classification and biomarker matching)
+- **R** (the [`pcgrr`](https://github.com/sigven/pcgrr) package) — report
+  generation and visualisation via Quarto, together with parts of the clinical
+  interpretation logic, notably AMP/ASCO/CAP tier assignment
+
+Note that this split is not absolute: some classification logic currently lives
+in `pcgrr` alongside the reporting code. If you are unsure where a change
+belongs, open an issue and ask before starting work.
+
+## Coding conventions
+
+- Follow the style of the surrounding code
+- Python: follow PEP 8 where practical; add docstrings to new functions
+- R: follow the existing style in `pcgrr`
+- Keep commits reasonably self-contained with descriptive messages
+- Do **not** commit reference data bundles, large binary files, or test data
+  containing patient information
+
+## Testing and validation
+
+Automated test coverage is currently limited and is actively being expanded. In
+the meantime, we ask contributors to describe how a change was validated:
+
+- State the command(s) you ran to exercise the change
+- For changes affecting annotation, classification or tiering, show the effect
+  on output — for example, the relevant rows or fields before and after
+- Confirm that an end-to-end run completes on example data
+- Where tests exist, please run them and add new ones covering your change
+
+Continuous integration runs automatically on pull requests. Please make sure it
+passes before requesting review.
+
+## Releases and versioning
+
+PCGR follows semantic versioning. Releases are cut from `dev` into `main` by the
+maintainers, accompanied by an updated changelog. Reference data bundles are
+versioned separately and tied to specific releases — see the documentation for
+the compatible bundle for each version.
+
+## Licence
+
+PCGR is released under the MIT licence. By contributing, you agree that your
+contributions will be licensed under the same terms.
+
+## Getting in touch
+
+- **Bugs and feature requests** — GitHub Issues
+- **Questions and general discussion** — GitHub Discussions (to come)
+- **Documentation** — https://sigven.github.io/pcgr/
+
+Thanks for your effort to improve PCGR!

README.md

@@ -153,6 +153,15 @@ Sigve Nakken, Ghislain Fournous, Daniel Vodák, Lars Birger Aaasheim, Ola Mykleb
 
 Sigve Nakken, Vladislav Saveliev, Oliver Hofmann, Pål Møller, Ola Myklebost, and Eivind Hovig. **Cancer Predisposition Sequencing Reporter (CPSR): a flexible variant report engine for high-throughput germline screening in cancer** (2021). *Int J Cancer*. [doi:[10.1002/ijc.33749](doi:%5B10.1002/ijc.33749)](https://doi.org/10.1002/ijc.33749)
 
+## Contributing
+
+Contributions are welcome — bug reports, documentation improvements, feature
+suggestions, and code. See [CONTRIBUTING.md](CONTRIBUTING.md) for how to report
+issues and submit pull requests (note that all PRs should target the `dev`
+branch).
+
+This project follows a [Code of Conduct](CODE_OF_CONDUCT.md).
+
 ## Contact
 
 sigven AT ifi.uio.no

conda/env/lock/pcgr-linux-64.lock

@@ -1,6 +1,6 @@
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conda/env/lock/pcgr-osx-64.lock

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conda/env/lock/pcgrr-linux-64.lock

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-https://conda.anaconda.org/conda-forge/osx-64/libjpeg-turbo-3.1.4.1-ha1e9b39_0.conda#57cc1464d457d01ac78f5860b9ca1714
+https://conda.anaconda.org/conda-forge/osx-64/libjpeg-turbo-3.2.0-ha1e9b39_0.conda#d86c1b9259377fb4dcd76fe7472bd2d2
 https://conda.anaconda.org/conda-forge/osx-64/liblzma-5.8.3-hbb4bfdb_0.conda#becdfbfe7049fa248e52aa37a9df09e2
 https://conda.anaconda.org/conda-forge/osx-64/libmpdec-4.0.0-hf3981d6_1.conda#ec88ba8a245855935b871a7324373105
 https://conda.anaconda.org/conda-forge/osx-64/libuv-1.52.1-ha3d0635_0.conda#703303067839cd1da659528a84b3c0cc
@@ -338,5 +338,5 @@ https://conda.anaconda.org/bioconda/noarch/bioconductor-bsgenome.hsapiens.ucsc.h
 https://conda.anaconda.org/bioconda/noarch/bioconductor-bsgenome.hsapiens.ucsc.hg38-1.4.5-r45hdfd78af_4.conda#4baa0dd494a2955755bb00fcd0242f00
 https://conda.anaconda.org/bioconda/osx-64/bioconductor-variantannotation-1.56.0-r45h010771c_0.conda#2bc0fa9167469b8ee04400d3b7d3e7f3
 https://conda.anaconda.org/bioconda/noarch/bioconductor-mutationalpatterns-3.19.1-r45hdfd78af_0.conda#8a1832a474ae43bb4b015b5a106dbe04
-https://conda.anaconda.org/pcgr/noarch/r-pcgrr-2.3.1-h4616a5c_0.conda#15cb05daf8edd1b6b488651bd553dd1a
-https://conda.anaconda.org/pcgr/noarch/r-cpsr-2.3.0-h4616a5c_0.conda#00834de27a1f7e2a41953f72b48dfcdb
+https://conda.anaconda.org/pcgr/label/dev/noarch/r-pcgrr-2.3.1.9001-h4616a5c_0.conda#b44c3c14e2af1087ad753de83a2a2601
+https://conda.anaconda.org/pcgr/label/dev/noarch/r-cpsr-2.2.5.9012-h4616a5c_0.conda#28080c1c508222229783123de6b5e4e7

conda/env/yaml/pcgr.yaml

@@ -6,7 +6,7 @@ channels:
   - bioconda
 
 dependencies:
-  - pcgr ==2.3.1 # bump
+  - pcgr ==2.3.1.9001 # bump
   - bioconda::bedtools
   - bioconda::bcftools
   - bioconda::ensembl-vep ==115.1

conda/env/yaml/pcgrr.yaml

@@ -7,7 +7,7 @@ channels:
 
 dependencies:
   - python
-  - r-pcgrr ==2.3.1 # bump
+  - r-pcgrr ==2.3.1.9001 # bump
   - r-cpsr
   - r-argparse
   - bioconductor-bsgenome.hsapiens.ucsc.hg38

conda/env/yaml/pkgdown.yaml

@@ -4,7 +4,7 @@ channels:
   - bioconda
   - conda-forge
 dependencies:
-  - r-pcgrr ==2.3.1 # bump
+  - r-pcgrr ==2.3.1.9001 # bump
   - r-pkgdown
   - r-readr
   - r-glue

conda/recipe/pcgr/recipe.yaml

@@ -1,6 +1,6 @@
 context:
   name: pcgr
-  version: 2.3.1 # bump
+  version: 2.3.1.9001 # bump
 
 package:
   name: ${{ name|lower }}

conda/recipe/pcgrr/recipe.yaml

@@ -1,6 +1,6 @@
 context:
   name: r-pcgrr
-  version: 2.3.1 # bump
+  version: 2.3.1.9001 # bump
 
 package:
   name: ${{ name|lower }}

pcgr/_version.py

@@ -1 +1 @@
-__version__ = '2.3.1' # bump
+__version__ = '2.3.1.9001' # bump