share xgboost code with scarches_xgb

.coveragerc

@@ -1,8 +1,12 @@
 [run]
 parallel = true
 branch = true
-source = openproblems
-omit = */__init__.py
+source =
+    openproblems
+    test
+omit =
+    */__init__.py
+    test/utils/*.py
 
 [report]
 exclude_lines =

.dockerignore

@@ -2,3 +2,13 @@ nf-openproblems
 workflow
 website
 .github
+.snakemake
+static
+test
+*.egg-info
+.coverage*
+.pytest_cache
+.idea
+.vscode
+*.md
+!./README.md

.github/dependabot.yml

@@ -5,63 +5,74 @@ updates:
     schedule:
       interval: "daily"
     open-pull-requests-limit: 1
+    rebase-strategy: "disabled"
 
   - package-ecosystem: "pip"
     directory: "/docker/openproblems"
     schedule:
       interval: "daily"
     open-pull-requests-limit: 1
+    rebase-strategy: "disabled"
 
   - package-ecosystem: "pip"
     directory: "/docker/openproblems-github-actions"
     schedule:
       interval: "daily"
     open-pull-requests-limit: 1
+    rebase-strategy: "disabled"
 
   - package-ecosystem: "pip"
-    directory: "/docker/openproblems-python-batch-integration"
+    directory: "/docker/openproblems-python-pytorch"
     schedule:
       interval: "daily"
     open-pull-requests-limit: 1
+    rebase-strategy: "disabled"
 
   - package-ecosystem: "pip"
     directory: "/docker/openproblems-python-extras"
     schedule:
       interval: "daily"
     open-pull-requests-limit: 1
+    rebase-strategy: "disabled"
 
   - package-ecosystem: "pip"
     directory: "/docker/openproblems-python-scvi"
     schedule:
       interval: "daily"
     open-pull-requests-limit: 1
+    rebase-strategy: "disabled"
 
   - package-ecosystem: "pip"
-    directory: "/docker/openproblems-python-tf2.4"
+    directory: "/docker/openproblems-python-tensorflow"
     schedule:
       interval: "daily"
     open-pull-requests-limit: 1
+    rebase-strategy: "disabled"
 
   - package-ecosystem: "pip"
     directory: "/docker/openproblems-r-base"
     schedule:
       interval: "daily"
     open-pull-requests-limit: 1
+    rebase-strategy: "disabled"
 
   - package-ecosystem: "pip"
     directory: "/docker/openproblems-r-extras"
     schedule:
       interval: "daily"
     open-pull-requests-limit: 1
+    rebase-strategy: "disabled"
 
   - package-ecosystem: "pip"
     directory: "/docker/openproblems-r-pytorch"
     schedule:
       interval: "daily"
     open-pull-requests-limit: 1
+    rebase-strategy: "disabled"
 
   - package-ecosystem: "github-actions"
     directory: "/"
     schedule:
       interval: "daily"
     open-pull-requests-limit: 1
+    rebase-strategy: "disabled"

.github/pull_request_template.md

@@ -12,12 +12,9 @@
 
 ### Testing
 
-* [ ] This submission was written on a forked copy of SingleCellOpenProblems
-* [ ] GitHub Actions "Run Benchmark" tests are passing on this base branch of this pull
-  request (include link to passed test: )
-* [ ] If this pull request is not ready for review (including passing the "Run
-  Benchmark" tests), I will open this PR as a draft (click on the down arrow next to the
-  "Create Pull Request" button)
+* [ ] This submission was written in a forked copy of openproblems
+* [ ] Nextflow test pipeline is passing on this base branch of this pull
+  request (include link to passed test on NF Tower found in GitHub Actions summary: )
 
 ### Submission guidelines
 
@@ -31,11 +28,6 @@
 This PR will be evaluated on the basis of the following checks:
 
 * [ ] The task addresses a valid open problem in single-cell analysis
-* [ ] The latest version of master is merged and tested
-* [ ] The methods/metrics are imported to `__init__.py` and were tested in the pipeline
-* [ ] Method and metric decorators are annotated with paper title, year, author, code
-  version, and date
-* [ ] The README gives an outline of the methods, metrics and datasets in the folder
 * [ ] The README provides a satisfactory task explanation (for new tasks)
 * [ ] The sample test data is appropriate to test implementation of all methods and
   metrics (for new tasks)

.github/workflows/check_r_dependencies.yml

@@ -12,6 +12,14 @@ on:
     branches:
       - 'main'
 
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+permissions:
+  contents: write
+  pull-requests: write
+
 jobs:
   check-r-dependencies:
     runs-on: ubuntu-latest
@@ -54,5 +62,5 @@ jobs:
         title: "Update ${{ env.PKG_CHANGED }}"
         committer: "openproblems-bio <[email protected]>"
         author: "openproblems-bio <[email protected]>"
-        commit-message: "Update ${{ env.PKG_CHANGED }}"
+        commit-message: "Update ${{ env.PKG_CHANGED }} # ci skip"
         draft: true

.github/workflows/comment_pull_request.yml

@@ -0,0 +1,20 @@
+name: Comment on Pull Request Status
+
+on:
+  pull_request_target:
+    types: [opened, synchronize, reopened, ready_for_review]
+
+permissions:
+  pull-requests: write
+
+jobs:
+  comment_pr:
+
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: thollander/actions-comment-pull-request@v2
+      with:
+        message: |
+          [![Current build status](https://img.shields.io/github/actions/workflow/status/${{ github.event.pull_request.head.repo.full_name }}/run_tests.yml?branch=${{ github.event.pull_request.head.ref }})](https://github.com/${{ github.event.pull_request.head.repo.full_name }}/actions/workflows/run_tests.yml?query=branch%3A${{ github.event.pull_request.head.ref }})
+        comment_tag: build_status

.github/workflows/pre-commit.yml

@@ -6,26 +6,25 @@ on:
   pull_request:
     types: [opened, synchronize, reopened, ready_for_review]
 
+permissions:
+  contents: write
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
 jobs:
   pre-commit:
-    runs-on: ubuntu-18.04
+    runs-on: ubuntu-latest
 
     container:
       image: singlecellopenproblems/openproblems-github-actions:latest
       options: --user root
 
     if: >-
-      !endsWith(github.event.head_commit.message, '# ci skip') &&
-      (
-        startsWith(github.ref, 'refs/heads') ||
-        github.event.pull_request.draft == false
-      )
+      !endsWith(github.event.head_commit.message, '# ci skip')
 
     steps:
-      - name: Cancel Previous Runs
-        uses: styfle/[email protected]
-        with:
-          access_token: ${{ github.token }}
 
       - uses: actions/checkout@v3
         with:

.github/workflows/process_results.yml

@@ -7,6 +7,13 @@ on:
     branches:
       - 'test_process'
 
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+permissions:
+  contents: read
+
 jobs:
   process_results:
     runs-on: ubuntu-latest
@@ -23,20 +30,21 @@ jobs:
     - name: Checkout website repo
       uses: actions/checkout@v3
       with:
-        fetch-depth: 0
+        fetch-depth: 1
         repository: openproblems-bio/website
+        ref: main
         path: website
         token: ${{ secrets.GH_ACTIONS_WEBSITE_PAT }}
 
-    - name: Set up Git branch
+    - name: Set up website Git branch
       working-directory: website
       run: |
         git checkout -b $UPDATE_BRANCH_NAME
 
     - name: Set up Python
       uses: actions/setup-python@v4
       with:
-        python-version: ${{ matrix.config.python }}
+        python-version: "3.8"
 
     - name: Install AWS CLI
       run: |
@@ -66,56 +74,48 @@ jobs:
           S3_URI="s3://openproblems-nextflow/cwd_example"
         fi
         aws s3 cp --quiet --recursive "${S3_URI}" /tmp/results/
-        rm -r website/data/results/*/
-        rm -r website/content/benchmarks/*/
-        python openproblems/workflow/parse_nextflow.py /tmp website/data/results
-        python openproblems/workflow/generate_website_markdown.py website/content/benchmarks
+        python openproblems/workflow/parse_nextflow.py /tmp website/results
 
-    - name: AWS S3 cleanup
-      if: "github.event_name == 'repository_dispatch'"
-      env:
-        AWS_ACCESS_KEY_ID: ${{ secrets.AWS_ACCESS_KEY_ID }}
-        AWS_SECRET_ACCESS_KEY: ${{ secrets.AWS_SECRET_ACCESS_KEY }}
-        AWS_DEFAULT_REGION: us-west-2
-      run: |
-        aws s3 rm --recursive "s3://openproblems-nextflow/work_main"
-        aws s3 rm --recursive "s3://openproblems-nextflow/cwd_example"
-        aws s3 cp --recursive "s3://openproblems-nextflow/cwd_main" "s3://openproblems-nextflow/cwd_example"
-        aws s3 rm --recursive "s3://openproblems-nextflow/cwd_main"
+    - name: Upload results
+      uses: actions/upload-artifact@main
+      with:
+        name: results
+        path: website/results
 
     - name: Push to openproblems-bio/website
-      if: "github.event_name == 'repository_dispatch'"
+      if: |
+        github.event_name == 'repository_dispatch' ||
+        endsWith(github.event.head_commit.message, '# publish')
       shell: bash
       working-directory: './website'
       env:
         GITHUB_TOKEN: ${{ secrets.GH_ACTIONS_WEBSITE_PAT }}
       run: |
         git push origin "${UPDATE_BRANCH_NAME}"
 
-    - name: Create Pull Request
-      if: "github.event_name == 'repository_dispatch'"
+    - name: Create website Pull Request
+      if: |
+        github.event_name == 'repository_dispatch' ||
+        endsWith(github.event.head_commit.message, '# publish')
       uses: peter-evans/create-pull-request@v4
       with:
         branch: ${{ env.UPDATE_BRANCH_NAME }}
         delete-branch: true
-        base: main
         title: '[auto] Update benchmark results'
-        reviewers: scottgigante, dburkhardt
+        reviewers: scottgigante-immunai,rcannood
         path: './website'
         token: ${{ secrets.GH_ACTIONS_WEBSITE_PAT }}
         author: "openproblems-bio <[email protected]>"
-        commit-message: "Update benchmark results # ci skip"
-
-    - name: Upload results on test
-      if: "github.event_name != 'repository_dispatch'"
-      uses: actions/upload-artifact@main
-      with:
-        name: results
-        path: website/data/results
+        commit-message: "Update benchmark results"
 
-    - name: Upload markdown on test
-      if: "github.event_name != 'repository_dispatch'"
-      uses: actions/upload-artifact@main
-      with:
-        name: markdown
-        path: website/content/benchmarks
+    - name: AWS S3 cleanup
+      if: "github.event_name == 'repository_dispatch'"
+      env:
+        AWS_ACCESS_KEY_ID: ${{ secrets.AWS_ACCESS_KEY_ID }}
+        AWS_SECRET_ACCESS_KEY: ${{ secrets.AWS_SECRET_ACCESS_KEY }}
+        AWS_DEFAULT_REGION: us-west-2
+      run: |
+        aws s3 rm --recursive "s3://openproblems-nextflow/work_main"
+        aws s3 rm --recursive "s3://openproblems-nextflow/cwd_example"
+        aws s3 cp --recursive "s3://openproblems-nextflow/cwd_main" "s3://openproblems-nextflow/cwd_example"
+        aws s3 rm --recursive "s3://openproblems-nextflow/cwd_main"