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.github/ISSUE_TEMPLATE/bug_report.md

@@ -8,12 +8,13 @@ assignees: ''
 ---
 
 - [ ] I have checked that this issue has not already been reported.
-- [ ] I have confirmed this bug exists on the master branch of openproblems.
+- [ ] I have confirmed this bug exists on the `main` branch of openproblems.
 
 ---
 
-**Note**: Please read [this guide](https://matthewrocklin.com/blog/work/2018/02/28/minimal-bug-reports) detailing how to provide the necessary information for us to reproduce your bug.
-
+**Note**: Please read [this
+guide](https://matthewrocklin.com/blog/work/2018/02/28/minimal-bug-reports) detailing
+how to provide the necessary information for us to reproduce your bug.
 
 ### Minimal code sample (that we can copy&paste without having any data)
 
@@ -29,6 +30,7 @@ assignees: ''
 
 <details>
 
-[Paste the output of scanpy.logging.print_versions() leaving a blank line after the details tag]
+<!-- Paste the output of scanpy.logging.print_versions() leaving a blank line after the
+details tag -->
 
 </details>

.github/ISSUE_TEMPLATE/propose-a-new-dataset.md

@@ -4,7 +4,6 @@ about: Suggest new data for one or more tasks
 title: ''
 labels: enhancement, dataset
 assignees: ''
-
 ---
 
 **What is the dataset?**
@@ -14,4 +13,5 @@ Describe it briefly and include a citation.
 Include a link to the publicly available data.
 
 **Which tasks could it be used for?**
-If the dataset is to be used for a task that is not yet included in the code base, use the issue template *propose a new task* instead.
+If the dataset is to be used for a task that is not yet included in the code base, use
+the issue template *propose a new task* instead.

.github/ISSUE_TEMPLATE/propose-a-new-method.md

@@ -14,4 +14,5 @@ Describe it briefly and include a citation.
 Include a link to the publicly available codebase.
 
 **Which task(s) could it be used for?**
-If the method is to be used for a task that is not yet included in the code base, use the issue template *propose a new task* instead.
+If the method is to be used for a task that is not yet included in the code base, use
+the issue template *propose a new task* instead.

.github/ISSUE_TEMPLATE/propose-a-new-metric.md

@@ -14,4 +14,5 @@ Describe it briefly and include a citation if applicable.
 Include a link to the publicly available codebase if available.
 
 **Which task(s) could it be used for?**
-If the method is to be used for a task that is not yet included in the code base, use the issue template *propose a new task* instead.
+If the method is to be used for a task that is not yet included in the code base, use
+the issue template *propose a new task* instead.

.github/ISSUE_TEMPLATE/propose-a-new-task.md

@@ -17,4 +17,5 @@ Include links to at least one publicly available dataset that could be used.
 Include links to codebases of at least two methods that perform the task.
 
 **Propose metrics**
-Describe at least one metric by which to measure success on the task. It must be able to be applied to the proposed datasets.
+Describe at least one metric by which to measure success on the task. It must be able to
+be applied to the proposed datasets.

.github/dependabot.yml

@@ -6,6 +6,60 @@ updates:
       interval: "daily"
     open-pull-requests-limit: 1
 
+  - package-ecosystem: "pip"
+    directory: "/docker/openproblems"
+    schedule:
+      interval: "daily"
+    open-pull-requests-limit: 1
+
+  - package-ecosystem: "pip"
+    directory: "/docker/openproblems-github-actions"
+    schedule:
+      interval: "daily"
+    open-pull-requests-limit: 1
+
+  - package-ecosystem: "pip"
+    directory: "/docker/openproblems-python-batch-integration"
+    schedule:
+      interval: "daily"
+    open-pull-requests-limit: 1
+
+  - package-ecosystem: "pip"
+    directory: "/docker/openproblems-python-extras"
+    schedule:
+      interval: "daily"
+    open-pull-requests-limit: 1
+
+  - package-ecosystem: "pip"
+    directory: "/docker/openproblems-python-scvi"
+    schedule:
+      interval: "daily"
+    open-pull-requests-limit: 1
+
+  - package-ecosystem: "pip"
+    directory: "/docker/openproblems-python-tf2.4"
+    schedule:
+      interval: "daily"
+    open-pull-requests-limit: 1
+
+  - package-ecosystem: "pip"
+    directory: "/docker/openproblems-r-base"
+    schedule:
+      interval: "daily"
+    open-pull-requests-limit: 1
+
+  - package-ecosystem: "pip"
+    directory: "/docker/openproblems-r-extras"
+    schedule:
+      interval: "daily"
+    open-pull-requests-limit: 1
+
+  - package-ecosystem: "pip"
+    directory: "/docker/openproblems-r-pytorch"
+    schedule:
+      interval: "daily"
+    open-pull-requests-limit: 1
+
   - package-ecosystem: "github-actions"
     directory: "/"
     schedule:

.github/pull_request_template.md

@@ -13,13 +13,18 @@
 ### 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)
+* [ ] 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)
 
 ### Submission guidelines
 
-* [ ] This submission follows the guidelines in our [Contributing](../blob/master/CONTRIBUTING.md) document
-* [ ] I have checked to ensure there aren't other open [Pull Requests](../pulls) for the same update/change
+* [ ] This submission follows the guidelines in our
+  [Contributing](../blob/master/CONTRIBUTING.md) document
+* [ ] I have checked to ensure there aren't other open [Pull Requests](../pulls) for the
+  same update/change
 
 ### PR review checklist
 
@@ -28,7 +33,9 @@ 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
+* [ ] 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)
+* [ ] The sample test data is appropriate to test implementation of all methods and
+  metrics (for new tasks)

.github/workflows/check_r_dependencies.yml

@@ -26,7 +26,33 @@ jobs:
         for REQUIREMENTS in $(ls -1 docker/*/r_requirements.txt); do
           IMAGE=$(echo ${REQUIREMENTS} | sed 's:^docker/::' | sed 's:/.*::')
           docker pull -q singlecellopenproblems/${IMAGE}
-          docker run -t --rm --user=root singlecellopenproblems/${IMAGE} \
-            Rscript /usr/src/singlecellopenproblems/scripts/upgrade_renv.R \
-            /usr/src/singlecellopenproblems/${REQUIREMENTS}
+          PKG_CHANGED=$(
+            docker run -t --rm --user=root \
+              -v $(pwd):/usr/src/singlecellopenproblems \
+              singlecellopenproblems/${IMAGE} \
+              Rscript /usr/src/singlecellopenproblems/scripts/upgrade_renv.R \
+              /usr/src/singlecellopenproblems/${REQUIREMENTS} | \
+              tee /dev/stderr | \
+              tail -n 1 | \
+              sed 's-::-/-g'
+          )
+          git diff --exit-code || break
+          PKG_CHANGED=""
         done
+        echo "PKG_CHANGED=$(echo ${PKG_CHANGED} | sed 's/@/ to /')" >> $GITHUB_ENV
+        echo "UPDATE_BRANCH_NAME=dependencies/r/${PKG_CHANGED}" >> $GITHUB_ENV
+
+    - name: Create Pull Request
+      if: >-
+        env.PKG_CHANGED != ''
+      uses: peter-evans/create-pull-request@v4
+      with:
+        branch: ${{ env.UPDATE_BRANCH_NAME }}
+        delete-branch: true
+        base: main
+        labels: dependencies,r
+        title: "Update ${{ env.PKG_CHANGED }}"
+        committer: "openproblems-bio <[email protected]>"
+        author: "openproblems-bio <[email protected]>"
+        commit-message: "Update ${{ env.PKG_CHANGED }}"
+        draft: true

.github/workflows/pre-commit.yml

@@ -23,11 +23,11 @@ jobs:
 
     steps:
       - name: Cancel Previous Runs
-        uses: styfle/[email protected].0
+        uses: styfle/[email protected].1
         with:
           access_token: ${{ github.token }}
 
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
         with:
           fetch-depth: 0
 
@@ -47,15 +47,15 @@ jobs:
         if: startsWith(runner.os, 'Linux')
         with:
           path: /usr/local/lib/R/site-library
-          key: precommit-${{env.LINUX_VERSION}}-${{env.R_VERSION}}-renv-${{ hashFiles('.pre-commit.r_requirements.txt') }}-
+          key: precommit-${{env.LINUX_VERSION}}-${{env.R_VERSION}}-renv-${{ hashFiles('./docker/openproblems-github-actions/r_requirements.txt') }}-
           restore-keys: |
             precommit-${{env.LINUX_VERSION}}-${{env.R_VERSION}}-renv-
 
       - name: Install R packages
         run: |
           renv::restore()
           source("./scripts/install_renv.R")
-          install_renv(".pre-commit.r_requirements.txt")
+          install_renv("./docker/openproblems-github-actions/r_requirements.txt")
         shell: Rscript {0}
 
       - name: Cache pre-commit

.github/workflows/process_results.yml

@@ -66,8 +66,10 @@ 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/tasks
+        python openproblems/workflow/generate_website_markdown.py website/content/benchmarks
 
     - name: AWS S3 cleanup
       if: "github.event_name == 'repository_dispatch'"
@@ -81,21 +83,18 @@ jobs:
         aws s3 cp --recursive "s3://openproblems-nextflow/cwd_main" "s3://openproblems-nextflow/cwd_example"
         aws s3 rm --recursive "s3://openproblems-nextflow/cwd_main"
 
-    - name: Commit result
-      uses: EndBug/add-and-commit@v9
+    - name: Push to openproblems-bio/website
       if: "github.event_name == 'repository_dispatch'"
-      with:
-        author_name: openproblems-bio
-        author_email: [email protected]
-        message: 'Update benchmark results # ci skip'
-        add: "['data/results', 'content/tasks']"
-        new_branch: ${{ env.UPDATE_BRANCH_NAME }}
-        push: true
-        cwd: './website'
+      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'"
-      uses: peter-evans/create-pull-request@v3
+      uses: peter-evans/create-pull-request@v4
       with:
         branch: ${{ env.UPDATE_BRANCH_NAME }}
         delete-branch: true
@@ -104,3 +103,19 @@ jobs:
         reviewers: scottgigante, dburkhardt
         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
+
+    - name: Upload markdown on test
+      if: "github.event_name != 'repository_dispatch'"
+      uses: actions/upload-artifact@main
+      with:
+        name: markdown
+        path: website/content/benchmarks