Merge pull request #343 from NMRLipids/restructure

Restructering the repo

Author: comcon1

.codecov.yml

@@ -0,0 +1,12 @@
+coverage:
+  ignore:
+    - tests/.*
+  status:
+    project:
+      default:
+        target: 60%
+    patch:
+      default:
+        target: 60%
+
+comment: false

.github/dependabot.yml

@@ -0,0 +1,11 @@
+version: 2
+updates:
+  - package-ecosystem: "github-actions"
+    directory: "/"
+    schedule:
+      interval: monthly
+    open-pull-requests-limit: 1
+    groups:
+      action-dependencies:
+        patterns:
+          - "*" # A wildcard to create one PR for all dependencies in the ecosystem

.github/workflows/BuildDocumentation.yml

@@ -30,7 +30,7 @@ jobs:
       - name: Build gromacs image
         run: |
           docker build \
-            -f Scripts/Docker/gromacs \
+            -f developer/docker/gromacs \
             -t nmrlipids/gromacs \
             --build-arg GROMACS_VERSION=${{ steps.version.outputs.version }} \
             .
@@ -40,27 +40,8 @@ jobs:
 
       - name: Build core image
         run: |
-          docker build -f Scripts/Docker/core -t nmrlipids/core .
+          docker build -f developer/docker/core -t nmrlipids/core .
 
       - name: Push core image
         run: docker push nmrlipids/core
 
-  build_doc_builder:
-     runs-on: ubuntu-latest
-     if: github.repository == 'NMRLipids/Databank'
-     steps:
-      - name: Log in to Docker Hub
-        uses: docker/login-action@v3
-        with:
-          username: ${{ vars.DOCKERHUB_USERNAME }}
-          password: ${{ secrets.DOCKERHUB_PASSWORD }}
-          
-      - name: Checkout Databank repo 
-        uses: actions/checkout@v4
-
-      - name: Build doc-builder image
-        run: |
-          docker build -f Scripts/Docker/doc-builder -t nmrlipids/doc-builder .
-
-      - name: Push doc-builder image
-        run: docker push nmrlipids/doc-builder

.github/workflows/RunTests.yml

@@ -0,0 +1,22 @@
+# This workflow builds and checks the package for release
+name: Build
+
+on:
+  pull_request:
+    # Check all PR
+
+jobs:
+  build:
+    if: github.repository == 'NMRLipids/Databank'
+    runs-on: ubuntu-22.04
+
+    steps:
+    - uses: actions/checkout@v4
+    - name: Set up Python
+      uses: actions/setup-python@v5
+      with:
+        python-version: "3.13"
+    - run: pip install tox
+
+    - name: Test build integrity
+      run: tox -e build

.github/workflows/ScheduledTests.yml

@@ -0,0 +1,75 @@
+name: Documentation
+
+on:
+  workflow_dispatch:
+  push:
+    branches: [main]
+    tags: ["*"]
+  pull_request_target:
+    branches: [main]
+
+permissions:
+  contents: read
+
+jobs:
+  build:
+    if: github.repository == 'NMRlipids/Databank'
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout source
+        uses: actions/checkout@v5
+        with:
+          fetch-depth: 0
+          repository: ${{ github.event.pull_request.head.repo.full_name || github.repository }}
+          ref: ${{ github.event.pull_request.head.sha || github.ref }}
+          persist-credentials: false
+
+      - name: Setup Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.13"
+          check-latest: true
+
+      - name: Install build deps
+        run: python -m pip install tox gitpython
+
+      - name: Build documentation
+        run: tox -e docs   
+
+      - name: Upload site artifact
+        uses: actions/upload-artifact@v4
+        with:
+          name: site
+          path: docs/build/html
+          if-no-files-found: error
+
+  deploy:
+    if: github.event_name == 'push' && github.repository == 'NMRlipids/Databank'
+    needs: build
+    runs-on: ubuntu-latest
+    permissions:
+      contents: write  
+
+    steps:
+      - name: Download site artifact
+        uses: actions/download-artifact@v4
+        with:
+          name: site
+          path: ./public
+
+      - name: Determine doc kind (latest|stable)
+        run: |
+          REF_KIND=$(echo "$GITHUB_REF" | cut -d/ -f2)
+          if [ "$REF_KIND" = "tags" ]; then
+            echo "DOC_KIND=stable" >> $GITHUB_ENV
+          else
+            echo "DOC_KIND=latest" >> $GITHUB_ENV
+          fi
+
+      - name: Publish to gh-pages/$DOC_KIND
+        uses: peaceiris/actions-gh-pages@v4
+        with:
+          github_token: ${{ secrets.GITHUB_TOKEN }}
+          publish_dir: ./public
+          destination_dir: ${{ env.DOC_KIND }}

.github/workflows/BuildDockerImages.yml .github/workflows/build-docker-images.yml.github/workflows/BuildDockerImages.yml renamed to .github/workflows/build-docker-images.yml

@@ -0,0 +1,22 @@
+name: Lint
+
+on:
+  pull_request:
+    branches: [main]
+
+jobs:
+  lint:
+    if: github.repository == 'NMRLipids/Databank' 
+    runs-on: ubuntu-22.04
+
+    steps:
+    - uses: actions/checkout@v4
+
+    - name: Set up Python
+      uses: actions/setup-python@v5
+      with:
+        python-version: "3.13"
+    - run: pip install tox
+
+    - name: Lint the code
+      run: tox -e lint

.github/workflows/build.yml

@@ -0,0 +1,18 @@
+name: Read the Docs link
+
+on:
+  pull_request_target:
+    types:
+      - opened
+
+permissions:
+  pull-requests: write
+
+jobs:
+  documentation-links:
+    if: github.repository == 'NMRLipids/Databank'
+    runs-on: ubuntu-latest
+    steps:
+      - uses: readthedocs/actions/preview@v1
+        with:
+          project-slug: Databank