Move prepmd to the shared CCPBioSim workflows and add pre-commit

.github/renovate.json

@@ -0,0 +1,8 @@
+{
+  "$schema": "https://docs.renovatebot.com/renovate-schema.json",
+  "extends": [
+    "github>CCPBioSim/.github//renovate/default",
+    "github>CCPBioSim/.github//renovate/python"
+  ],
+  "reviewers": ["harryswift01", "jimboid"]
+}

.github/workflows/coveralls-main.yaml

@@ -0,0 +1,35 @@
+name: Coveralls Main
+
+on:
+  push:
+    branches: [main]
+
+  workflow_dispatch:
+
+permissions:
+  contents: read
+
+concurrency:
+  group: coveralls-main-${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  coveralls:
+    name: Build main coverage baseline
+    uses: CCPBioSim/.github/.github/workflows/ci-test-conda.yaml@2bf63339f2515ec54777e952e8db3d8674d4e5ca # 0.14.0
+    permissions:
+      contents: read
+      checks: write
+      statuses: write
+    with:
+      package: prepmd
+      python-versions: '["3.13"]'
+      coverage-python-version: "3.13"
+      os: '["ubuntu-26.04", "macos-26"]'
+      environment-file: environment.yaml
+      activate-environment: prep
+      channels: salilab,conda-forge
+      test-path: test
+      pytest-args: -v
+      coverage: true
+      timeout-minutes: 360

.github/workflows/pr.yaml

@@ -0,0 +1,63 @@
+name: Pull Request CI
+
+on:
+  pull_request:
+
+permissions:
+  contents: read
+
+concurrency:
+  group: pr-ci-${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  unit:
+    name: Unit
+    uses: CCPBioSim/.github/.github/workflows/ci-test-conda.yaml@2bf63339f2515ec54777e952e8db3d8674d4e5ca # 0.14.0
+    permissions:
+      contents: read
+      checks: write
+      statuses: write
+    with:
+      package: prepmd
+      python-versions: '["3.13"]'
+      coverage-python-version: "3.13"
+      os: '["ubuntu-26.04", "macos-26"]'
+      environment-file: environment.yaml
+      activate-environment: prep
+      channels: salilab,conda-forge
+      test-path: test
+      pytest-args: -v
+      coverage: true
+      timeout-minutes: 360
+
+  docs:
+    name: Docs
+    needs: unit
+    uses: CCPBioSim/.github/.github/workflows/ci-docs.yaml@2bf63339f2515ec54777e952e8db3d8674d4e5ca # 0.14.0
+    permissions:
+      contents: read
+    with:
+      python-versions: '["3.13"]'
+      build-dir: build
+      timeout-minutes: 20
+
+  pre-commit:
+    name: Pre-commit
+    needs: unit
+    uses: CCPBioSim/.github/.github/workflows/ci-pre-commit.yaml@2bf63339f2515ec54777e952e8db3d8674d4e5ca # 0.14.0
+    permissions:
+      contents: read
+    with:
+      python-version: "3.13"
+      timeout-minutes: 15
+
+  conda-build:
+    name: Conda build
+    needs: unit
+    uses: CCPBioSim/.github/.github/workflows/ci-conda-build.yaml@2bf63339f2515ec54777e952e8db3d8674d4e5ca # 0.14.0
+    permissions:
+      contents: read
+    with:
+      python-versions: '["3.13"]'
+      timeout-minutes: 360

.github/workflows/release.yaml

@@ -0,0 +1,63 @@
+name: Release prepmd
+
+on:
+  workflow_dispatch:
+    inputs:
+      version:
+        description: Version to release, in X.Y.Z form.
+        required: true
+        type: string
+      dry-run:
+        description: Check and build everything but do not open the version PR, tag, release or publish.
+        type: boolean
+        default: false
+
+permissions:
+  contents: read
+
+jobs:
+  prepare:
+    name: Prepare
+    uses: CCPBioSim/.github/.github/workflows/release-prepare.yaml@2bf63339f2515ec54777e952e8db3d8674d4e5ca # 0.14.0
+    permissions:
+      contents: write
+      pull-requests: write
+    with:
+      version: ${{ inputs.version }}
+      dry-run: ${{ inputs.dry-run }}
+      version-files: >-
+        [
+          {"path": "prepmd/__init__.py", "pattern": "^__version__ =.*", "replace": "__version__ = \"{version}\""},
+          {"path": "CITATION.cff", "pattern": "^version:.*", "replace": "version: {version}"},
+          {"path": "CITATION.cff", "pattern": "^date-released:.*", "replace": "date-released: '{date}'"}
+        ]
+    secrets:
+      AUTO_PR_MERGE: ${{ secrets.AUTO_PR_MERGE }}
+      ZULIP_BOT_EMAIL: ${{ secrets.ZULIP_BOT_EMAIL }}
+      ZULIP_BOT_API_KEY: ${{ secrets.ZULIP_BOT_API_KEY }}
+      ZULIP_SITE: ${{ secrets.ZULIP_SITE }}
+
+  website:
+    name: Website
+    needs: prepare
+    uses: CCPBioSim/.github/.github/workflows/release-website.yaml@2bf63339f2515ec54777e952e8db3d8674d4e5ca # 0.14.0
+    permissions:
+      contents: read
+    with:
+      version: ${{ inputs.version }}
+      tag: ${{ needs.prepare.outputs.tag }}
+      dry-run: ${{ inputs.dry-run }}
+    secrets:
+      BUILD_TOKEN: ${{ secrets.BUILD_TOKEN }}
+
+  conda:
+    name: Conda
+    needs: prepare
+    uses: CCPBioSim/.github/.github/workflows/release-conda.yaml@2bf63339f2515ec54777e952e8db3d8674d4e5ca # 0.14.0
+    permissions:
+      contents: read
+    with:
+      tag: ${{ needs.prepare.outputs.tag || inputs.version }}
+      dry-run: ${{ inputs.dry-run }}
+    secrets:
+      ANACONDA_TOKEN: ${{ secrets.ANACONDA_TOKEN }}