Add contributing and development docs

.codespell-ignore-words.txt

@@ -0,0 +1,13 @@
+# Words codespell should not flag as misspellings.
+# Format: one word per line (case-insensitive).
+# Add a comment above each entry explaining why it is excluded.
+
+# "patter" appears in Cell Press journal DOI URLs (doi.org/10.1016/j.patter.*)
+patter
+
+# "mAP" (mean Average Precision) — scientific metric abbreviation used in copairs docs
+# codespell may flag the lowercase form "map" variant; list both cases to be safe
+mAP
+
+# "Commun" — abbreviation for "Communications" used in Nature citation style (e.g. Nat. Commun.)
+Commun

.github/dependabot.yml

@@ -0,0 +1,21 @@
+version: 2
+updates:
+  # Keep GitHub Actions versions current
+  - package-ecosystem: github-actions
+    directory: /
+    schedule:
+      interval: monthly
+    groups:
+      actions:
+        patterns:
+          - "*"
+
+  # Keep pre-commit hook revisions current
+  - package-ecosystem: pre-commit
+    directory: /
+    schedule:
+      interval: monthly
+    groups:
+      pre-commit:
+        patterns:
+          - "*"

.github/workflows/link-check.yaml

@@ -0,0 +1,28 @@
+name: Link check
+
+on:
+  pull_request:
+    branches:
+      - main
+
+jobs:
+  link-check:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+
+      - name: Check links with lychee
+        uses: lycheeverse/lychee-action@v2
+        with:
+          # Check all Markdown files in content/ and the root-level docs
+          args: >-
+            --verbose
+            --no-progress
+            --exclude-path node_modules
+            --exclude "^https://forum\\.image\\.sc/"
+            --exclude "^https://www\\.broadinstitute\\.org/"
+            --exclude "^https://doi\\.org/"
+            'content/**/*.md'
+            '*.md'
+          fail: true

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

@@ -10,7 +10,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v4
-      - uses: actions/setup-python@v4
+      - uses: actions/setup-python@v5
         with:
-          python-version: "3.10"
-      - uses: pre-commit/action@v3.0.0
+          python-version: "3.12"
+      - uses: pre-commit/action@v3.0.1

.pre-commit-config.yaml

@@ -1,27 +1,36 @@
 # See https://pre-commit.com for more information
 # See https://pre-commit.com/hooks.html for more hooks
 ---
+# Exclude vendored theme — it is not our code to lint
+exclude: ^themes/
+
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.5.0
+    rev: v6.0.0
     hooks:
       - id: trailing-whitespace
       - id: end-of-file-fixer
       - id: check-added-large-files
       - id: detect-private-key
   # checking spelling
   - repo: https://github.com/codespell-project/codespell
-    rev: v2.2.6
+    rev: v2.4.2
     hooks:
       - id: codespell
+        args:
+          - --ignore-words=.codespell-ignore-words.txt
   # checking markdown formatting
   - repo: https://github.com/executablebooks/mdformat
-    rev: 0.7.17
+    rev: 1.0.0
     hooks:
       - id: mdformat
+        exclude: ^content/
         additional_dependencies:
-          - mdformat-gfm
+          - mdformat-gfm==1.0.0
+          - mdformat-frontmatter==2.0.10
+  # HTML linting — exclude Hugo template files (contain {{ }} syntax)
   - repo: https://github.com/Lucas-C/pre-commit-hooks-nodejs
     rev: v1.1.2
     hooks:
       - id: htmllint
+        exclude: ^layouts/

CONTRIBUTING.md

@@ -0,0 +1,26 @@
+# Contributing to cytomining.github.io
+
+Thank you for your interest in contributing!
+
+## Code of conduct
+
+Please uphold our [code of conduct](https://github.com/cytomining/.github/blob/main/CODE_OF_CONDUCT.md).
+Report unacceptable behavior to cytodata.info@gmail.com.
+
+## Reporting issues
+
+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).
+
+## Contributing changes
+
+1. Fork the repository and create a branch from `main`.
+1. Make your changes. See [README.md](README.md) for local development setup.
+1. Open a pull request against `main` with a clear description of what changed and why.
+
+Please keep pull requests focused on a single change. All status checks must pass before merge.
+
+## Content guidelines
+
+- Keep tool descriptions factual and concise.
+- Follow the frontmatter and section order used in existing content files.
+- Verify any external links you add are reachable.

README.md

@@ -1,8 +1,62 @@
-# Cytomining organization GitHub Pages configuration
+# cytomining.github.io
 
-This repo includes content which helps create links via GitHub Pages related to the Cytomining Organization.
+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.
 
-## Development
+## Prerequisites
 
-You may place HTML content within the `/docs` folder, which is then rendered on merge to `main`.
-We adapt work here from [the documentation found in this Gist](https://gist.github.com/domenic/1f286d415559b56d725bee51a62c24a7).
+- [Hugo extended](https://gohugo.io/installation/) v0.161.1 or later
+
+## Local development
+
+```bash
+git clone https://github.com/cytomining/cytomining.github.io.git
+cd cytomining.github.io
+
+# Serve locally with live reload
+hugo server
+
+# Build for production
+hugo --minify
+```
+
+The site is served at `http://localhost:1313/` by default.
+
+## Pre-commit hooks
+
+This repo uses [pre-commit](https://pre-commit.com/) to enforce formatting and catch common issues before every commit.
+
+```bash
+pip install pre-commit
+pre-commit install
+```
+
+After installation, hooks run automatically on `git commit`. To run them manually against all files:
+
+```bash
+pre-commit run --all-files
+```
+
+## Adding or editing a tool page
+
+Tool pages live in `content/tools/`. Each file is a Markdown file with frontmatter.
+
+Minimal frontmatter for a new tool page:
+
+```yaml
+---
+title: "Tool Name"
+description: "One-sentence description of what this tool does."
+showDate: false
+showAuthor: false
+---
+```
+
+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.
+
+## Deployment
+
+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.
+
+## Theme
+
+This site uses [Congo v2.13.0](https://github.com/jpanther/congo). Theme configuration lives in `config/_default/params.toml`.

content/_index.md

@@ -1,4 +1,4 @@
 ---
-title: "Cytomining"
-description: "Open-source tools for single-cell image-based profiling"
+title: Cytomining
+description: Open-source tools for single-cell image-based profiling
 ---

content/contact/_index.md

@@ -1,6 +1,6 @@
 ---
-title: "Contact"
-description: "Get in touch with the Cytomining community."
+title: Contact
+description: Get in touch with the Cytomining community.
 ---
 
 - 💬 Join the conversation on our [Discourse forums](https://forum.image.sc/)

content/tools/_index.md

@@ -1,6 +1,6 @@
 ---
-title: "Tools"
-description: "Production-ready tools for image-based profiling bioinformatics."
+title: Tools
+description: Production-ready tools for image-based profiling bioinformatics.
 ---
 
 The Cytomining ecosystem provides a suite of production-ready tools for every stage of the image-based profiling workflow.

content/tools/copairs.md

@@ -1,6 +1,6 @@
 ---
-title: "copairs"
-description: "Downstream evaluation — measures how reproducibly perturbation profiles retrieve their matched replicates, quantifying profile quality and similarity."
+title: copairs
+description: Downstream evaluation — measures how reproducibly perturbation profiles retrieve their matched replicates, quantifying profile quality and similarity.
 showDate: false
 showAuthor: false
 ---

content/tools/cosmicqc.md

@@ -1,9 +1,9 @@
 ---
-title: "coSMicQC"
-description: "Quality control step — flags and removes low-quality cells before profile processing to prevent artifacts from propagating downstream."
+title: coSMicQC
+description: Quality control step — flags and removes low-quality cells before profile processing to prevent artifacts from propagating downstream.
 showDate: false
 showAuthor: false
-logoUrl: "https://raw.githubusercontent.com/cytomining/coSMicQC/main/media/logo/just-icon.png"
+logoUrl: https://raw.githubusercontent.com/cytomining/coSMicQC/main/media/logo/just-icon.png
 ---
 
 <img class="logo-light" src="https://raw.githubusercontent.com/cytomining/coSMicQC/main/media/logo/with-text-for-light-bg.png" alt="coSMicQC logo" width="400">

content/tools/cytodataframe.md

@@ -3,7 +3,7 @@ title: "CytoDataFrame"
 description: "Interactive exploration — view and inspect morphology profiles alongside their source cell images directly in Jupyter notebooks."
 showDate: false
 showAuthor: false
-logoUrl: "https://raw.githubusercontent.com/cytomining/CytoDataFrame/main/logo/just-icon.png"
+logoUrl: https://raw.githubusercontent.com/cytomining/CytoDataFrame/main/logo/just-icon.png
 ---
 
 <img class="logo-light" src="https://raw.githubusercontent.com/cytomining/CytoDataFrame/main/logo/with-text-for-light-bg.png" alt="CytoDataFrame logo" width="400">

content/tools/cytotable.md

@@ -1,9 +1,9 @@
 ---
-title: "CytoTable"
-description: "Upstream ingestion — converts raw CellProfiler, DeepProfiler, and IN Carta outputs into scalable, analysis-ready Parquet tables."
+title: CytoTable
+description: Upstream ingestion — converts raw CellProfiler, DeepProfiler, and IN Carta outputs into scalable, analysis-ready Parquet tables.
 showDate: false
 showAuthor: false
-logoUrl: "https://raw.githubusercontent.com/cytomining/CytoTable/main/logo/just-icon.png"
+logoUrl: https://raw.githubusercontent.com/cytomining/CytoTable/main/logo/just-icon.png
 ---
 
 <img class="logo-light" src="https://raw.githubusercontent.com/cytomining/CytoTable/main/logo/with-text-for-light-bg.png" alt="CytoTable logo" width="400">

content/tools/deepprofiler.md

@@ -1,11 +1,11 @@
 ---
-title: "DeepProfiler"
-description: "Alternative feature extraction — deep learning embeddings from raw microscopy images, bypassing classical segmentation-and-measurement pipelines."
+title: DeepProfiler
+description: Alternative feature extraction — deep learning embeddings from raw microscopy images, bypassing classical segmentation-and-measurement pipelines.
 showDate: false
 showAuthor: false
 ---
 
-<img src="https://raw.githubusercontent.com/cytomining/DeepProfiler/main/figures/logo/banner.png" alt="DeepProfiler logo" width="400">
+<img src="https://raw.githubusercontent.com/cytomining/DeepProfiler/master/figures/logo/banner.png" alt="DeepProfiler logo" width="400">
 
 `DeepProfiler` uses deep neural networks to extract morphological features directly from raw microscopy images, bypassing traditional segmentation-and-measurement pipelines.
 It is designed for high-throughput screens where deep learning representations outperform classical feature sets.

content/tools/pycytominer.md

@@ -3,7 +3,7 @@ title: "Pycytominer"
 description: "Core processing pipeline — aggregates, normalizes, and feature-selects morphology profiles for downstream analysis."
 showDate: false
 showAuthor: false
-logoUrl: "https://raw.githubusercontent.com/cytomining/pycytominer/main/logo/just-icon.png"
+logoUrl: https://raw.githubusercontent.com/cytomining/pycytominer/main/logo/just-icon.png
 ---
 
 <img class="logo-light" src="https://raw.githubusercontent.com/cytomining/pycytominer/main/logo/with-text-for-light-bg.png" alt="Pycytominer logo" width="400">

layouts/index.html

@@ -30,9 +30,9 @@ <h1 style="font-size: 2.5rem; font-weight: 800; letter-spacing: -0.02em; margin:
           📊 Feature Extraction
         </div>
         <span class="hero-arrow" style="color: #d1d5db;">→</span>
-        <a href="/tools/cytotable/" class="pipeline-step hero-pill-purple" style="background: #ede9fe; border-radius: 8px; padding: 0.4rem 0.8rem; font-size: 0.78rem; color: #5b21b6; font-weight: 600; border: 1px solid #ddd6fe; text-decoration: none;"><img class="pill-icon" src="https://raw.githubusercontent.com/cytomining/CytoTable/main/logo/just-icon.png" alt="">CytoTable</a>
+        <a href="/tools/cytotable/" class="pipeline-step hero-pill-purple" style="background: #ede9fe; border-radius: 8px; padding: 0.4rem 0.8rem; font-size: 0.78rem; color: #5b21b6; font-weight: 600; border: 1px solid #ddd6fe; text-decoration: none;"><img class="pill-icon" src="https://raw.githubusercontent.com/cytomining/CytoTable/main/logo/just-icon.png" alt="CytoTable icon">CytoTable</a>
         <span class="hero-arrow" style="color: #d1d5db;">→</span>
-        <a href="/tools/cosmicqc/" class="pipeline-step hero-pill-blue" style="background: #dbeafe; border-radius: 8px; padding: 0.4rem 0.8rem; font-size: 0.78rem; color: #1e40af; font-weight: 600; border: 1px solid #bfdbfe; text-decoration: none;"><img class="pill-icon" src="https://raw.githubusercontent.com/cytomining/coSMicQC/main/media/logo/just-icon.png" alt="">coSMicQC</a>
+        <a href="/tools/cosmicqc/" class="pipeline-step hero-pill-blue" style="background: #dbeafe; border-radius: 8px; padding: 0.4rem 0.8rem; font-size: 0.78rem; color: #1e40af; font-weight: 600; border: 1px solid #bfdbfe; text-decoration: none;"><img class="pill-icon" src="https://raw.githubusercontent.com/cytomining/coSMicQC/main/media/logo/just-icon.png" alt="coSMicQC icon">coSMicQC</a>
         <span class="hero-arrow" style="color: #d1d5db;">→</span>
         <a href="/tools/pycytominer/" class="pipeline-step hero-pill-blue" style="background: #dbeafe; border-radius: 8px; padding: 0.4rem 0.8rem; font-size: 0.78rem; color: #1e40af; font-weight: 600; border: 1px solid #bfdbfe; text-decoration: none;"><img class="pill-icon" src="https://raw.githubusercontent.com/cytomining/pycytominer/main/logo/just-icon.png" alt="">Pycytominer</a>
         <span class="hero-arrow" style="color: #d1d5db;">→</span>