[FIX] Merge with main branch

Inria-Empenn · Sep 21, 2023 · ab00ac3 · ab00ac3
2 parents 208f42a + 2589123
commit ab00ac3
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diff --git a/.codespellrc b/.codespellrc
@@ -0,0 +1,4 @@
+[codespell]
+skip = .git,*.pdf,*.svg,analysis_pipelines_full_descriptions.tsv
+# softwares - key in data structures etc
+ignore-words-list = te,fpr,fwe,softwares
diff --git a/.github/ISSUE_TEMPLATE/pipeline_reproduction.yml b/.github/ISSUE_TEMPLATE/pipeline_reproduction.yml
@@ -50,12 +50,12 @@ body:
         Please tick the boxes below once the corresponding task is finished. :+1:
         - [ ] :ok_hand: A maintainer of the project approved the issue, by assigning a :checkered_flag:`status: ready for dev` label to it.
         - [ ] :deciduous_tree: Create a branch on your fork to start the reproduction.
-        - [ ] :sunrise: Create a file `team_{team_id}.py` inside the [`narps_open/pipelines/`](https://github.com/Inria-Empenn/narps_open_pipelines/blob/main/narps_open/pipelines) directory. You can use a file inside [`narps_open/pipelines/templates`](https://github.com/Inria-Empenn/narps_open_pipelines/blob/main/narps_open/pipelines/templates) file as a template if needed.
+        - [ ] :sunrise: Create a file `team_{team_id}.py` inside the [`narps_open/pipelines/`](https://github.com/Inria-Empenn/narps_open_pipelines/blob/main/narps_open/pipelines) directory. You can use a file inside [`narps_open/pipelines/templates`](https://github.com/Inria-Empenn/narps_open_pipelines/blob/main/narps_open/pipelines/templates) as a template if needed.
+        - [ ] :inbox_tray: Create a [pull request](https://github.com/Inria-Empenn/narps_open_pipelines/blob/main/CONTRIBUTING.md#pull_requests) as soon as you completed the previous task.
         - [ ] :brain: Write the code for the pipeline, using Nipype and the file architecture described in [docs/pipelines.md](https://github.com/Inria-Empenn/narps_open_pipelines/blob/main/docs/pipelines.md).
         - [ ] :blue_book: Make sure your code is documented enough.
         - [ ] :snake: Make sure your code is explicit and conforms with PEP8.
         - [ ] :microscope: Create tests for your pipeline. You can use files in [`tests/pipelines/test_team_*`](https://github.com/Inria-Empenn/narps_open_pipelines/blob/main/tests/pipelines/) as examples.
         - [ ] :microscope: Make sure your code passes all the tests you created (see [docs/testing.md](https://github.com/Inria-Empenn/narps_open_pipelines/blob/main/docs/testing.md)).
-        - [ ] :inbox_tray: create a [pull request](https://github.com/Inria-Empenn/narps_open_pipelines/blob/main/CONTRIBUTING.md#pull_requests) from your code.
     validations:
       required: true
diff --git a/.github/workflows/code_quality.yml b/.github/workflows/code_quality.yml
@@ -45,7 +45,7 @@ jobs:
     - name: Analyse the code with pylint
       run: |
         pylint --exit-zero narps_open > pylint_report_narps_open.txt
-        pylint --exit-zero tests > pylint_report_narps_open.txt
+        pylint --exit-zero tests > pylint_report_tests.txt
 
     - name: Archive pylint results
       uses: actions/upload-artifact@v3

diff --git a/.github/workflows/codespell.yml b/.github/workflows/codespell.yml
@@ -0,0 +1,22 @@
+## Disclaimer - This GitHub Actions workflow performs a check for spelling errors inside code comments and documentation
+name: codespell
+
+on:
+  push:
+    branches: [main]
+  pull_request:
+    branches: [main]
+
+permissions:
+  contents: read
+
+jobs:
+  codespell:
+    name: Check for spelling errors
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v3
+      - name: Codespell
+        uses: codespell-project/actions-codespell@v2
diff --git a/.github/workflows/pipeline_tests.yml b/.github/workflows/pipeline_tests.yml
@@ -5,9 +5,6 @@ name: pipeline_tests
 
 # Define when it runs
 on:
-  push:
-    paths:
-      - 'narps_open/pipelines/team**'
   pull_request:
     paths:
       - 'narps_open/pipelines/team**'
@@ -19,14 +16,9 @@ jobs:
   identify-tests:
     runs-on: ubuntu-latest
     outputs:
+      teams: ${{ steps.identify.outputs.teams }}
       tests: ${{ steps.identify.outputs.tests }}
     steps:
-    - name: Checkout main branch for comparison
-      uses: actions/checkout@v3
-      with:
-        ref: main
-        fetch-depth: 0
-
     - name: Checkout current branch
       uses: actions/checkout@v3
       with:
@@ -35,48 +27,75 @@ jobs:
     - name: Create a list of tests for changed pipelines
       id: identify
       run: |
-        # Loop through modified files
-        for file in $(git diff --name-only remotes/origin/main...$GITHUB_SHA)
+        # Loop through modified files between PR base and last head
+        for file in $(git diff --name-only --diff-filter=d remotes/origin/main...$GITHUB_SHA)
         do
           # echo each file
           echo $file
           # List team id corresponding to team_* files
-          if [[ "$file" =~ .*"narps_open/pipelines/team_".* ]]; then
+          if [[ "$file" =~ narps_open/pipelines/team_[A-Z0-9]{4}.py ]]; then
             echo "Modified pipeline = $file"
             tmp=${file#*"team_"} # remove prefix ending in "team_"
             team_id=${tmp%".py"*}   # remove suffix starting with ".py"
-            # Populate the list of test files
+            # Populate the lists of test files and teams
             test_files="$test_files tests/pipelines/test_team_$team_id.py"
+            teams="$teams $team_id"
           fi
         done
         # Send the test list as job output
         echo $test_files
         echo "tests=$test_files" >> $GITHUB_OUTPUT
+        echo "teams=$teams" >> $GITHUB_OUTPUT
 
-  # A job to run the identified tests
+  # A job to identify and run the tests
   pytest:
     needs: identify-tests
-    runs-on: ubuntu-latest
+    runs-on: self-hosted
+    timeout-minutes: 2880 # 48h
     steps:
-    - name: Checkout repository
+    - name: Checkout PR branch
       uses: actions/checkout@v3
 
-    - name: Set up Python 3.9
-      uses: actions/setup-python@v3
-      with:
-        python-version: 3.9
-
-    - uses: actions/cache@v3
-      with:
-        path: ~/.cache/pip
-        key: ${{ runner.os }}-pip-${{ hashFiles('setup.py') }}
-        restore-keys: |
-          ${{ runner.os }}-pip-
+    - name: Load configuration for self-hosted runner
+      run: cp /home/neuro/local_testing_config.toml narps_open/utils/configuration/testing_config.toml
 
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
         pip install .[tests]
 
-    - name: Collect tests with pytest
-      run: pytest --collect-only -q -m "pipeline_test" ${{ needs.identify-tests.outputs.tests }}
+    - name: Remove test reports if any existing
+      run: rm -f test_pipeline-*.txt
+
+    - name: Execute tests with pytest
+      run: |
+        if [[ "${{ needs.identify-tests.outputs.tests }}" != "" ]]; then
+          pytest -s -q -m "pipeline_test" ${{ needs.identify-tests.outputs.tests }}
+        fi
+
+    - name: Archive pipeline execution failures
+      if: ${{ failure() }} # Run only if previous job fails
+      uses: actions/upload-artifact@v3
+      with:
+        name: pipeline_tests-reports
+        path: |
+          crash-*.pklz
+        retention-days: 15
+
+    - name: Report results on GitHub
+      if: ${{ always() }}
+      run: |
+        # Start report
+        echo "# Correlation values" >> $GITHUB_STEP_SUMMARY
+        echo "Unthresholded maps, reproduced vs. results" >> $GITHUB_STEP_SUMMARY
+        echo "Correlation values are sorted from hypotheses 1 to 9" >> $GITHUB_STEP_SUMMARY
+
+        # Start report table
+        echo "| Team    | Number of subjects | Test status | Correlation values |" >> $GITHUB_STEP_SUMMARY
+        echo "| -------- | ------- | ------- | ------- |" >> $GITHUB_STEP_SUMMARY
+
+        # Loop through test report files
+        for team in ${{ needs.identify-tests.outputs.teams }}
+        do
+          cat test_pipeline-$team.txt >> $GITHUB_STEP_SUMMARY
+        done
diff --git a/.github/workflows/test_changes.yml b/.github/workflows/test_changes.yml
@@ -5,9 +5,6 @@ name: test_changes
 
 # Define when it runs
 on:
-  push:
-    paths:
-      - 'tests/**/test_*.py'
   pull_request:
     paths:
       - 'tests/**/test_*.py'
@@ -16,37 +13,21 @@ on:
 jobs:
 
   # A job to list the tests to be run
-  pytest:
+  identify-tests:
     runs-on: ubuntu-latest
+    outputs:
+      tests: ${{ steps.identify.outputs.tests }}
     steps:
     - name: Checkout main branch for comparison
       uses: actions/checkout@v3
       with:
-        ref: main
         fetch-depth: 0
 
-    - name: Checkout current branch
-      uses: actions/checkout@v3
-      with:
-        fetch-depth: 0
-
-    - name: Set up Python 3.9
-      uses: actions/setup-python@v3
-      with:
-        python-version: 3.9
-
-    - uses: actions/cache@v3
-      with:
-        path: ~/.cache/pip
-        key: ${{ runner.os }}-pip-${{ hashFiles('setup.py') }}
-        restore-keys: |
-          ${{ runner.os }}-pip-
-
     - name: Create a list of tests for changed tests
       id: identify
       run: |
-        # Loop through modified files
-        for file in $(git diff --name-only remotes/origin/main...$GITHUB_SHA)
+        # Loop through modified files between PR base and last head
+        for file in $(git diff --name-only --diff-filter=d remotes/origin/main...$GITHUB_SHA)
         do
           # List files corresponding to tests/**/test_**.py
           if [[ "$file" =~ .*"tests".*"test_".*".py" ]]; then
@@ -57,10 +38,25 @@ jobs:
         echo $test_files
         echo "tests=$test_files" >> $GITHUB_OUTPUT
 
+  # A job to list the tests to be run
+  pytest:
+    needs: identify-tests
+    runs-on: self-hosted
+    timeout-minutes: 2880 # 48h
+    steps:
+    - name: Checkout PR branch
+      uses: actions/checkout@v3
+
+    - name: Load configuration for self-hosted runner
+      run: cp /home/neuro/local_testing_config.toml narps_open/utils/configuration/testing_config.toml
+
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
         pip install .[tests]
 
-    - name: Collect tests with pytest
-      run: pytest --collect-only -q ${{ steps.identify.outputs.tests }}
+    - name: Execute tests with pytest
+      run: |
+        if [[ "${{ needs.identify-tests.outputs.tests }}" != "" ]]; then
+          pytest -s -q ${{ needs.identify-tests.outputs.tests }}
+        fi
diff --git a/.github/workflows/unit_tests.yml b/.github/workflows/unit_tests.yml
@@ -27,24 +27,15 @@ jobs:
   pytest:
 
     # Define the runner for this job
-    runs-on: ubuntu-latest
+    runs-on: self-hosted
 
     # Steps that define the job
     steps:
     - name: Checkout repository
       uses: actions/checkout@v3
 
-    - name: Set up Python 3.9
-      uses: actions/setup-python@v3
-      with:
-        python-version: 3.9
-
-    - uses: actions/cache@v3
-      with:
-        path: ~/.cache/pip
-        key: ${{ runner.os }}-pip-${{ hashFiles('setup.py') }}
-        restore-keys: |
-          ${{ runner.os }}-pip-
+    - name: Load configuration for self-hosted runner
+      run: cp /home/neuro/local_testing_config.toml narps_open/utils/configuration/testing_config.toml
 
     - name: Install dependencies
       run: |
@@ -58,6 +49,7 @@ jobs:
         coverage xml
 
     - name: Archive pytest results
+      if: ${{ failure() }} # Run only if previous job fails
       uses: actions/upload-artifact@v3
       with:
         name: unit_tests-reports

diff --git a/.gitignore b/.gitignore
@@ -1,7 +1,6 @@
 
 # to avoid commiting data
-data/
-tests/data/
+./data/
 
 # neuro user in docker image
 neuro