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gwaybioclaude
gwaybio
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claude
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Add contributing and development docs (#7)
* add docs details * add workflows * check dois * add mdformatter to precommit * add dependabot * fix links and link check * markdown formatting checks incorrectly flags content that hugo requires * restore emojies * group dependabot and remove all dois * ingore words that shouldnt trigger misspellings * ignore commune --------- Co-authored-by: Claude Sonnet 4.6 <noreply@anthropic.com>
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‎.codespell-ignore-words.txt‎

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# Words codespell should not flag as misspellings.
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# Format: one word per line (case-insensitive).
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# Add a comment above each entry explaining why it is excluded.
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# "patter" appears in Cell Press journal DOI URLs (doi.org/10.1016/j.patter.*)
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patter
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# "mAP" (mean Average Precision) — scientific metric abbreviation used in copairs docs
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# codespell may flag the lowercase form "map" variant; list both cases to be safe
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mAP
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# "Commun" — abbreviation for "Communications" used in Nature citation style (e.g. Nat. Commun.)
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Commun

‎.github/dependabot.yml‎

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version: 2
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updates:
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# Keep GitHub Actions versions current
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- package-ecosystem: github-actions
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directory: /
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schedule:
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interval: monthly
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groups:
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actions:
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patterns:
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- "*"
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# Keep pre-commit hook revisions current
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- package-ecosystem: pre-commit
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directory: /
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schedule:
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interval: monthly
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groups:
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pre-commit:
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patterns:
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- "*"

‎.github/workflows/link-check.yaml‎

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name: Link check
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on:
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pull_request:
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branches:
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- main
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jobs:
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link-check:
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runs-on: ubuntu-latest
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steps:
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- name: Checkout
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uses: actions/checkout@v4
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- name: Check links with lychee
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uses: lycheeverse/lychee-action@v2
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with:
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# Check all Markdown files in content/ and the root-level docs
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args: >-
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--verbose
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--no-progress
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--exclude-path node_modules
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--exclude "^https://forum\\.image\\.sc/"
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--exclude "^https://www\\.broadinstitute\\.org/"
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--exclude "^https://doi\\.org/"
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'content/**/*.md'
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'*.md'
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fail: true

‎.github/workflows/pre-commit-checks.yaml‎

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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v4
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- uses: actions/setup-python@v4
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- uses: actions/setup-python@v5
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with:
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python-version: "3.10"
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- uses: pre-commit/action@v3.0.0
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python-version: "3.12"
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- uses: pre-commit/action@v3.0.1

‎.pre-commit-config.yaml‎

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# See https://pre-commit.com for more information
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# See https://pre-commit.com/hooks.html for more hooks
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---
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# Exclude vendored theme — it is not our code to lint
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exclude: ^themes/
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repos:
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- repo: https://github.com/pre-commit/pre-commit-hooks
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rev: v4.5.0
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rev: v6.0.0
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hooks:
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- id: trailing-whitespace
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- id: end-of-file-fixer
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- id: check-added-large-files
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- id: detect-private-key
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# checking spelling
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- repo: https://github.com/codespell-project/codespell
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rev: v2.2.6
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rev: v2.4.2
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hooks:
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- id: codespell
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args:
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- --ignore-words=.codespell-ignore-words.txt
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# checking markdown formatting
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- repo: https://github.com/executablebooks/mdformat
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rev: 0.7.17
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rev: 1.0.0
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hooks:
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- id: mdformat
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exclude: ^content/
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additional_dependencies:
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- mdformat-gfm
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- mdformat-gfm==1.0.0
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- mdformat-frontmatter==2.0.10
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# HTML linting — exclude Hugo template files (contain {{ }} syntax)
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- repo: https://github.com/Lucas-C/pre-commit-hooks-nodejs
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rev: v1.1.2
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hooks:
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- id: htmllint
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exclude: ^layouts/

‎CONTRIBUTING.md‎

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# Contributing to cytomining.github.io
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Thank you for your interest in contributing!
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## Code of conduct
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Please uphold our [code of conduct](https://github.com/cytomining/.github/blob/main/CODE_OF_CONDUCT.md).
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Report unacceptable behavior to cytodata.info@gmail.com.
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## Reporting issues
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Open a [GitHub issue](https://github.com/cytomining/cytomining.github.io/issues) with a clear description of the problem (e.g., broken link, outdated content, rendering bug).
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## Contributing changes
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1. Fork the repository and create a branch from `main`.
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1. Make your changes. See [README.md](README.md) for local development setup.
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1. Open a pull request against `main` with a clear description of what changed and why.
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Please keep pull requests focused on a single change. All status checks must pass before merge.
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## Content guidelines
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- Keep tool descriptions factual and concise.
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- Follow the frontmatter and section order used in existing content files.
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- Verify any external links you add are reachable.

‎README.md‎

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# Cytomining organization GitHub Pages configuration
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# cytomining.github.io
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This repo includes content which helps create links via GitHub Pages related to the Cytomining Organization.
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Source for the [Cytomining organization website](https://cytomining.github.io/), built with [Hugo](https://gohugo.io/) and the [Congo](https://jpanther.github.io/congo/) theme.
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## Development
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## Prerequisites
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You may place HTML content within the `/docs` folder, which is then rendered on merge to `main`.
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We adapt work here from [the documentation found in this Gist](https://gist.github.com/domenic/1f286d415559b56d725bee51a62c24a7).
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- [Hugo extended](https://gohugo.io/installation/) v0.161.1 or later
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## Local development
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```bash
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git clone https://github.com/cytomining/cytomining.github.io.git
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cd cytomining.github.io
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# Serve locally with live reload
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hugo server
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# Build for production
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hugo --minify
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```
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The site is served at `http://localhost:1313/` by default.
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## Pre-commit hooks
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This repo uses [pre-commit](https://pre-commit.com/) to enforce formatting and catch common issues before every commit.
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```bash
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pip install pre-commit
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pre-commit install
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```
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After installation, hooks run automatically on `git commit`. To run them manually against all files:
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```bash
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pre-commit run --all-files
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```
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## Adding or editing a tool page
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Tool pages live in `content/tools/`. Each file is a Markdown file with frontmatter.
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Minimal frontmatter for a new tool page:
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```yaml
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---
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title: "Tool Name"
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description: "One-sentence description of what this tool does."
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showDate: false
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showAuthor: false
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---
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```
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Follow the section order used in existing pages: logo image(s), 1–2 sentence intro, **Key capabilities** bullet list, link to documentation or GitHub, and optionally a **Publication** section.
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## Deployment
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Pushes to `main` trigger the [hugo.yaml](.github/workflows/hugo.yaml) GitHub Actions workflow, which builds the site and deploys it to GitHub Pages automatically.
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## Theme
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This site uses [Congo v2.13.0](https://github.com/jpanther/congo). Theme configuration lives in `config/_default/params.toml`.

‎content/_index.md‎

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---
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title: "Cytomining"
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description: "Open-source tools for single-cell image-based profiling"
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title: Cytomining
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description: Open-source tools for single-cell image-based profiling
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---

‎content/contact/_index.md‎

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---
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title: "Contact"
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description: "Get in touch with the Cytomining community."
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title: Contact
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description: Get in touch with the Cytomining community.
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---
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- 💬 Join the conversation on our [Discourse forums](https://forum.image.sc/)

‎content/tools/_index.md‎

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---
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title: "Tools"
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description: "Production-ready tools for image-based profiling bioinformatics."
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title: Tools
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description: Production-ready tools for image-based profiling bioinformatics.
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---
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The Cytomining ecosystem provides a suite of production-ready tools for every stage of the image-based profiling workflow.

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