Merge pull request #195 from MannLabs/development

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MannLabs · May 29, 2024 · 6b33e19 · 6b33e19
2 parents 5c612cb + 616a0d8
commit 6b33e19
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diff --git a/.github/workflows/release.yml → .github/workflows/create_release.yml b/.github/workflows/release.yml → .github/workflows/create_release.yml
@@ -1,32 +1,52 @@
 on:
-  pull_request:
-    branches: [ main ]
+  workflow_dispatch:
+    inputs:
+      commit_to_release:
+        description: 'Enter commit hash to release (example: 1a2b3c4)'
+        required: true
+      tag_to_release:
+        description: 'Enter tag to release (example: v1.5.5)'
+        required: true
 
-name: Release bundled installer
+
+name: Create Draft Release
 
 jobs:
-  Version_Bumped:
+  Get_New_Version:
     runs-on: ubuntu-latest
     outputs:
-      version: ${{ steps.master_version_bumped.outputs.version }}
+      new_version: ${{ steps.get_new_release_tag.outputs.new_version }}
     steps:
       - name: Checkout code
         uses: actions/checkout@v4
-      - uses: conda-incubator/setup-miniconda@v3
         with:
-          auto-update-conda: true
-          python-version: ${{ matrix.python-version }}
-      - name: Master version bumped
-        id: master_version_bumped
+          ref: ${{ inputs.commit_to_release }}
+
+      - name: Check release tag
         shell: bash -l {0}
         run: |
-          cd misc
-          . ./check_version.sh
-          echo "version=$current_version" >> $GITHUB_OUTPUT
+          CURRENT_VERSION=$(misc/get_current_version.sh)
+          if [ "v$CURRENT_VERSION" != "${{ inputs.tag_to_release }}" ]; then
+            echo Code version (v$CURRENT_VERSION) does not match the tag to release (${{ inputs.tag_to_release }})
+            exit 1
+          fi
+          echo "new_version=$CURRENT_VERSION" >> $GITHUB_OUTPUT
+
+      - uses: mukunku/[email protected]
+        id: check-tag
+        with:
+          tag: ${{ inputs.tag_to_release }}
+
+      - name: Check if tag already exists
+        run: |
+          echo "Tag already exists!"
+          exit 1
+        if: steps.check-tag.outputs.exists == 'true'
+
 
-  Create_Draft_On_GitHub:
+  Create_Draft_Release:
     runs-on: ubuntu-latest
-    needs: Version_Bumped
+    needs: Get_New_Version
     outputs:
       upload_url: ${{ steps.draft_release.outputs.upload_url }}
     steps:
@@ -38,13 +58,13 @@ jobs:
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
         with:
-          tag_name: v${{ needs.Version_Bumped.outputs.version }}
-          release_name: v${{ needs.Version_Bumped.outputs.version }}
+          tag_name: ${{ inputs.tag_to_release }}
+          release_name: ${{ inputs.tag_to_release }}
           draft: true
           prerelease: false
 
   Create_MacOS_Installer:
-    needs: [Create_Draft_On_GitHub, Version_Bumped]
+    needs: [Create_Draft_Release, Get_New_Version]
     env:
         ARCH: x64
         EAGER_IMPORT: true
@@ -101,13 +121,13 @@ jobs:
       env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
       with:
-          upload_url: ${{ needs.Create_Draft_On_GitHub.outputs.upload_url }}
-          asset_path: dist/alphadia-${{ needs.Version_Bumped.outputs.version }}-darwin-${{ env.ARCH }}.pkg
-          asset_name: alphadia-${{ needs.Version_Bumped.outputs.version }}-darwin-${{ env.ARCH }}.pkg
+          upload_url: ${{ needs.Create_Draft_Release.outputs.upload_url }}
+          asset_path: dist/alphadia-${{ needs.Get_New_Version.outputs.new_version }}-darwin-${{ env.ARCH }}.pkg
+          asset_name: alphadia-${{ needs.Get_New_Version.outputs.new_version }}-darwin-${{ env.ARCH }}.pkg
           asset_content_type: application/zip
 
   Create_Windows_Installer:
-    needs: [Create_Draft_On_GitHub, Version_Bumped]
+    needs: [Create_Draft_Release, Get_New_Version]
     env:
         ARCH: x64
     runs-on: windows-latest
@@ -169,7 +189,7 @@ jobs:
       env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
       with:
-          upload_url: ${{ needs.Create_Draft_On_GitHub.outputs.upload_url }}
-          asset_path: dist/alphadia-${{ needs.Version_Bumped.outputs.version }}-win-${{ env.ARCH }}.exe
-          asset_name: alphadia-${{ needs.Version_Bumped.outputs.version }}-win-${{ env.ARCH }}.exe
+          upload_url: ${{ needs.Create_Draft_Release.outputs.upload_url }}
+          asset_path: dist/alphadia-${{ needs.Get_New_Version.outputs.new_version }}-win-${{ env.ARCH }}.exe
+          asset_name: alphadia-${{ needs.Get_New_Version.outputs.new_version }}-win-${{ env.ARCH }}.exe
           asset_content_type: application/zip
diff --git a/.github/workflows/e2e_testing.yml b/.github/workflows/e2e_testing.yml
@@ -11,7 +11,7 @@ jobs:
   end2end_testing:
     name: End to end test
     runs-on: self-hosted
-    if: contains(github.event.pull_request.labels.*.name, 'test:e2e')
+    if: contains(github.event.pull_request.labels.*.name, 'test:e2e') || github.event_name == 'push' || github.event_name == 'workflow_dispatch'
     strategy:
       matrix:
         # test case name as defined in e2e_test_cases.yaml

diff --git a/.github/workflows/fdr_performance.yml b/.github/workflows/fdr_performance.yml
@@ -1,5 +1,7 @@
 on:
   pull_request:
+    types: [ labeled ]
+  push:
     branches: [ main, development ]
   workflow_dispatch:
 
@@ -11,6 +13,7 @@ concurrency:
 
 jobs:
   fdr_performance_testing:
+    if: contains(github.event.pull_request.labels.*.name, 'test:fdr') || github.event_name == 'push' || github.event_name == 'workflow_dispatch'
     name: FDR performance testing
     runs-on: AlphaDIA
     env: # Or as an environment variable

diff --git a/.github/workflows/performance_testing.yml b/.github/workflows/performance_testing.yml
@@ -4,7 +4,7 @@ on:
       - 'alpha'
   workflow_dispatch:
 
-name: performance testing
+name: Performance test
 
 concurrency:
   group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}

diff --git a/.github/workflows/pip_installation.yml b/.github/workflows/pip_installation.yml
@@ -1,9 +1,8 @@
 on:
   pull_request:
-    branches:
   workflow_dispatch:
 
-name: Default installation and tests
+name: Perform installation and run tests
 
 concurrency:
   group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}

diff --git a/.github/workflows/publish_docker.yml b/.github/workflows/publish_docker.yml
@@ -0,0 +1,66 @@
+#https://docs.github.com/en/actions/publishing-packages/publishing-docker-images
+name: Publish Docker image
+
+on:
+  workflow_dispatch:
+    inputs:
+      tag_to_release:
+        description: 'Enter tag to release (example: v1.5.5)'
+        required: true
+
+jobs:
+  push_to_registry:
+    name: Push Docker image to Docker Hub
+    runs-on: ubuntu-latest
+    permissions:
+      packages: write
+      contents: read
+      attestations: write
+    steps:
+      - name: Check out the repo
+        uses: actions/checkout@v4
+        with:
+          ref: ${{ inputs.tag_to_release }}
+      - name: Get current version
+        id: get_current_version
+        shell: bash -l {0}
+        run: |
+          CURRENT_VERSION=$(./misc/get_current_version.sh)
+          echo "current_version=$CURRENT_VERSION" >> $GITHUB_OUTPUT
+      - name: Log in to Docker Hub
+        uses: docker/login-action@f4ef78c080cd8ba55a85445d5b36e214a81df20a
+        with:
+          username: ${{ secrets.DOCKER_USERNAME }}
+          password: ${{ secrets.DOCKER_ACCESS_TOKEN }}
+
+      - name: Extract metadata (tags, labels) for Docker
+        id: meta
+        uses: docker/metadata-action@9ec57ed1fcdbf14dcef7dfbe97b2010124a938b7
+        with:
+          images: mannlabs/alphadia
+
+      - name: show metadata
+        run: |
+          echo "${{ steps.meta.outputs.tags }}"
+          echo "${{ steps.meta.outputs.labels }}"
+          echo "${{ steps.meta.outputs }}"
+
+      - name: Build and push Docker image
+        id: push
+        uses: docker/build-push-action@3b5e8027fcad23fda98b2e3ac259d8d67585f671
+        with:
+          context: .
+          file: ./Dockerfile
+          push: true
+          tags: |
+            ${{ secrets.DOCKER_USERNAME }}/alphadia:latest,
+            ${{ secrets.DOCKER_USERNAME }}/alphadia:${{ steps.get_current_version.outputs.current_version }}
+          labels: ${{ steps.meta.outputs.labels }}
+
+
+#      - name: Generate artifact attestation
+#        uses: actions/attest-build-provenance@v1
+#        with:
+#          subject-name: ${{ env.REGISTRY }}/${{ env.IMAGE_NAME}}
+#          subject-digest: ${{ steps.push.outputs.digest }}
+#          push-to-registry: true
diff --git a/.github/workflows/publish_docker_image.yml b/.github/workflows/publish_docker_image.yml
@@ -0,0 +1,66 @@
+#https://docs.github.com/en/actions/publishing-packages/publishing-docker-images
+name: Publish Docker image
+
+on:
+  workflow_dispatch:
+    inputs:
+      tag_to_release:
+        description: 'Enter tag to release (example: v1.5.5)'
+        required: true
+
+jobs:
+  push_to_registry:
+    name: Push Docker image to Docker Hub
+    runs-on: ubuntu-latest
+    permissions:
+      packages: write
+      contents: read
+      attestations: write
+    steps:
+      - name: Check out the repo
+        uses: actions/checkout@v4
+        with:
+          ref: ${{ inputs.tag_to_release }}
+      - name: Get current version
+        id: get_current_version
+        shell: bash -l {0}
+        run: |
+          CURRENT_VERSION=$(./misc/get_current_version.sh)
+          echo "current_version=$CURRENT_VERSION" >> $GITHUB_OUTPUT
+      - name: Log in to Docker Hub
+        uses: docker/login-action@f4ef78c080cd8ba55a85445d5b36e214a81df20a
+        with:
+          username: ${{ secrets.DOCKER_USERNAME }}
+          password: ${{ secrets.DOCKER_ACCESS_TOKEN }}
+
+      - name: Extract metadata (tags, labels) for Docker
+        id: meta
+        uses: docker/metadata-action@9ec57ed1fcdbf14dcef7dfbe97b2010124a938b7
+        with:
+          images: mannlabs/alphadia
+
+      - name: show metadata
+        run: |
+          echo "${{ steps.meta.outputs.tags }}"
+          echo "${{ steps.meta.outputs.labels }}"
+          echo "${{ steps.meta.outputs }}"
+
+      - name: Build and push Docker image
+        id: push
+        uses: docker/build-push-action@3b5e8027fcad23fda98b2e3ac259d8d67585f671
+        with:
+          context: .
+          file: ./Dockerfile
+          push: true
+          tags: |
+            ${{ secrets.DOCKER_USERNAME }}/alphadia:latest,
+            ${{ secrets.DOCKER_USERNAME }}/alphadia:${{ steps.get_current_version.outputs.current_version }}
+          labels: ${{ steps.meta.outputs.labels }}
+
+
+#      - name: Generate artifact attestation
+#        uses: actions/attest-build-provenance@v1
+#        with:
+#          subject-name: ${{ env.REGISTRY }}/${{ env.IMAGE_NAME}}
+#          subject-digest: ${{ steps.push.outputs.digest }}
+#          push-to-registry: true
diff --git a/.github/workflows/publish_on_pypi.yml b/.github/workflows/publish_on_pypi.yml
@@ -13,6 +13,8 @@ env:
 jobs:
   Create_PyPi_Release:
     runs-on: ubuntu-latest
+    outputs:
+      new_version: ${{ steps.get_current_version.outputs.new_version }}
     steps:
       - uses: actions/checkout@v4
         with:
@@ -25,6 +27,12 @@ jobs:
       - name: Conda info
         shell: bash -le {0}
         run: conda info
+      - name: Get current version
+        id: get_current_version
+        shell: bash -l {0}
+        run: |
+         CURRENT_VERSION=$(misc/get_current_version.sh)
+         echo "new_version=$CURRENT_VERSION" >> $GITHUB_OUTPUT
       - uses: actions/cache@v4
         with:
           path: ~/.cache/pip
@@ -53,7 +61,7 @@ jobs:
         run: |
           conda create -n pip_loose_test python=${{ env.PYTHON_VERSION }} -y
           conda activate pip_loose_test
-          pip install --index-url https://test.pypi.org/simple/ --extra-index-url https://pypi.org/simple "alphadia"
+          pip install --index-url https://test.pypi.org/simple/ --extra-index-url https://pypi.org/simple "alphadia==${{ steps.get_current_version.outputs.new_version }}"
           alphadia -v
           conda deactivate
           conda env remove --name pip_stable_test -y
@@ -62,7 +70,7 @@ jobs:
         run: |
           conda create -n pip_stable_test python=${{ env.PYTHON_VERSION }} -y
           conda activate pip_stable_test
-          pip install --index-url https://test.pypi.org/simple/ --extra-index-url https://pypi.org/simple "alphadia[stable]"
+          pip install --index-url https://test.pypi.org/simple/ --extra-index-url https://pypi.org/simple "alphadia[stable]==${{ steps.get_current_version.outputs.new_version }}"
           alphadia -v
           conda deactivate
           conda env remove --name pip_stable_test -y
@@ -97,7 +105,7 @@ jobs:
         run: |
           conda create -n pip_stable python=${{ env.PYTHON_VERSION }} -y
           conda activate pip_stable
-          pip install "alphadia[stable]"
+          pip install "alphadia[stable]==${{ needs.Create_PyPi_Release.outputs.new_version }}"
           alphadia -v
           conda deactivate
           conda env remove --name pip_stable -y
@@ -106,7 +114,7 @@ jobs:
         run: |
           conda create -n pip_loose python=${{ env.PYTHON_VERSION }} -y
           conda activate pip_loose
-          pip install alphadia
+          pip install alphadia==${{ needs.Create_PyPi_Release.outputs.new_version }}"
           alphadia -v
           conda deactivate
           conda env remove --name pip_loose -y
diff --git a/.gitignore b/.gitignore
@@ -160,3 +160,9 @@ gui/out/
 # mono crash logs #
 ###################
 mono_crash*
+
+###################
+# IDEs            #
+###################
+.idea
+.vscode
diff --git a/.readthedocs.yaml b/.readthedocs.yaml
@@ -0,0 +1,15 @@
+version: 2
+
+build:
+  os: "ubuntu-22.04"
+  tools:
+    python: "3.9"
+
+# Build from the docs/ directory with Sphinx
+sphinx:
+  configuration: docs/conf.py
+
+# Explicitly set the version of Python and its requirements
+python:
+  install:
+    - requirements: requirements/requirements_docs.txt
diff --git a/.vscode/settings.json b/.vscode/settings.json