From 46832029240e7798233d40b180df93d72e756822 Mon Sep 17 00:00:00 2001
From: Tom Close <tom.g.close@gmail.com>
Date: Wed, 20 Mar 2024 10:15:34 +1100
Subject: [PATCH 1/2] consolidate tests within ci-cd

---
 .github/workflows/ci-cd.yaml | 49 +++++++++---------------------------
 1 file changed, 12 insertions(+), 37 deletions(-)

diff --git a/.github/workflows/ci-cd.yaml b/.github/workflows/ci-cd.yaml
index a879998..fab95d4 100644
--- a/.github/workflows/ci-cd.yaml
+++ b/.github/workflows/ci-cd.yaml
@@ -99,41 +99,9 @@ jobs:
         python -c "import pydra as m; print(f'{m.__name__} {m.__version__} @ {m.__file__}')"
         python -c "import fileformats.medimage_afni as m; print(f'{m.__name__} {m.__version__} @ {m.__file__}')"
         python -c "import fileformats.extras.medimage_afni as m; print(f'{m.__name__} {m.__version__} @ {m.__file__}')"
-  
-  fileformats-test:
-    runs-on: ubuntu-latest
-    strategy:
-      matrix:
-        python-version: ['3.8', '3.11']
-    steps:
-
-    - uses: actions/checkout@v4
-
-    - name: Revert version to most recent version tag on upstream update
-      if: github.event_name == 'repository_dispatch'
-      run: git checkout $(git tag -l | grep 'v.*' | tail -n 1 | awk -F post '{print $1}')
-
-    - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v5
-      with:
-        python-version: ${{ matrix.python-version }}
-
-    - name: Install build dependencies
-      run: |
-        python -m pip install --upgrade pip
-
-    - name: Install task package
-      run: |
-        pip install "./related-packages/fileformats[test]" "./related-packages/fileformats-extras[test]"
-        python -c "import fileformats.medimage_afni as m; print(f'{m.__name__} {m.__version__} @ {m.__file__}')"
-
-    - name: Test fileformats with pytest
-      run: |
-        pytest ./related-packages -sv --cov fileformats.medimage_afni --cov fileformats.extras.medimage_afni --cov-report xml .
-
 
   test:
-    needs: [nipype-conv, fileformats-test]
+    needs: [nipype-conv]
     runs-on: ubuntu-22.04
     strategy:
       matrix:
@@ -187,19 +155,26 @@ jobs:
         python -c "import pydra as m; print(f'{m.__name__} {m.__version__} @ {m.__file__}')"
 
     - name: Test with pytest
-      run: |
-        pytest -sv ./pydra/tasks/afni --cov pydra.tasks.afni --cov-report xml
+      run: >- 
+        pytest -sv
+        ./pydra/tasks/afni
+        ./related-packages/fileformats
+        ./related-packages/fileformats-extras
+        --cov pydra.tasks.afni
+        --cov fileformats.medimage_afni
+        --cov fileformats.extras.medimage_afni
+        --cov-report xml
 
     - name: Upload to CodeCov
       uses: codecov/codecov-action@v3
       if: ${{ always() }}
       with:
-        files: coverage.xml,./fileformats/coverage.xml
+        files: coverage.xml
         name: pydra-afni
 
 
   deploy-fileformats:
-    needs: [devcheck, test, fileformats-test]
+    needs: [devcheck, test]
     runs-on: ubuntu-latest
     steps:
 

From d7fe6912a6c95639e30532db73e7a629bbdf1694 Mon Sep 17 00:00:00 2001
From: Tom Close <tom.g.close@gmail.com>
Date: Wed, 20 Mar 2024 10:19:21 +1100
Subject: [PATCH 2/2] touched up devcheck in ci-cd

---
 .github/workflows/ci-cd.yaml | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/ci-cd.yaml b/.github/workflows/ci-cd.yaml
index fab95d4..6d267cf 100644
--- a/.github/workflows/ci-cd.yaml
+++ b/.github/workflows/ci-cd.yaml
@@ -93,7 +93,8 @@ jobs:
 
     - name: Install task package
       run: |
-        pip install "./related-packages/fileformats[dev]" "related-packages/fileformats-extras[dev]"
+        pip install ${{ matrix.pip-flags }} "./related-packages/fileformats[dev]"
+        pip install ${{ matrix.pip-flags }} "related-packages/fileformats-extras[dev]"
         pip install ${{ matrix.pip-flags }} ".[dev]"
         python -c "import pydra.tasks.afni as m; print(f'{m.__name__} {m.__version__} @ {m.__file__}')"
         python -c "import pydra as m; print(f'{m.__name__} {m.__version__} @ {m.__file__}')"