split system and unit tests for matlab linux and mac os

cpp-lln-lab · Aug 18, 2024 · 361c416 · 361c416
1 parent e3261be
commit 361c416
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diff --git a/.github/workflows/system_tests.yml b/.github/workflows/system_tests.yml
@@ -0,0 +1,114 @@
+---
+name: system tests matlab
+
+# Uses the cron schedule for github actions
+#
+# https://docs.github.com/en/free-pro-team@latest/actions/reference/events-that-trigger-workflows#scheduled-events
+#
+# ┌───────────── minute (0 - 59)
+# │ ┌───────────── hour (0 - 23)
+# │ │ ┌───────────── day of the month (1 - 31)
+# │ │ │ ┌───────────── month (1 - 12 or JAN-DEC)
+# │ │ │ │ ┌───────────── day of the week (0 - 6 or SUN-SAT)
+# │ │ │ │ │
+# │ │ │ │ │
+# │ │ │ │ │
+# * * * * *
+
+concurrency:
+    group: ${{ github.workflow }}-${{ github.ref }}
+    cancel-in-progress: true
+
+on:
+    push:
+        branches: [main]
+    pull_request:
+        branches: [main]
+    schedule:
+    -   cron: 0 0 1,15 * *
+
+  # Allows you to run this workflow manually from the Actions tab
+    workflow_dispatch:
+
+jobs:
+
+    tests:
+
+        if: github.repository_owner == 'cpp-lln-lab'
+
+        strategy:
+            matrix:
+                script: [moae, facerep, fmriprep]
+                os: [ubuntu-latest, macos-13]
+                matlab: [R2023b]
+                include:
+        # only run bms on ubuntu because of datalad setup
+                -   os: ubuntu-latest
+                    matlab: R2023b
+                    script: bms
+            fail-fast: false
+
+        runs-on: ${{ matrix.os }}
+
+        steps:
+
+        -   name: test ${{ matrix.script }}
+            run: test ${{ matrix.script }}
+
+        -   name: Install Node
+            uses: actions/setup-node@v4
+            with:
+                node-version: 18
+
+        -   name: Install python
+            uses: actions/setup-python@v5
+            with:
+                python-version: '3.11'
+
+        -   name: Install dependencies
+            if: matrix.os == 'ubuntu-latest'
+            run: |
+                sudo apt-get -y -qq update
+                sudo apt-get -y install unzip wget git-annex
+                python -m pip install --upgrade pip setuptools
+                pip install datalad
+
+        -   name: Clone bidspm
+            uses: actions/checkout@v4
+            with:
+                submodules: recursive
+                fetch-depth: 0
+
+        -   name: Install validators
+            run: make install
+
+        -   name: Install SPM
+            run: |
+                git clone https://github.com/spm/spm12.git --depth 1
+
+        -   name: Get moae fmriprep data from OSF
+            run: |
+                mkdir -p demos/MoAE/inputs/
+                cd demos/MoAE/inputs/
+                wget https://osf.io/vufjs/download
+                unzip download
+                mv moae_fmriprep fmriprep
+
+        -   name: Prepare test data unix
+            run: |
+                cd tests
+                make data
+
+        -   name: Get data for BMS
+            if: matrix.script == 'bms'
+            run: make -C demos/bayes data_ds000114
+
+        -   name: Install MATLAB
+            uses: matlab-actions/setup-matlab@v2.2.0
+            with:
+                release: ${{ matrix.matlab }}
+
+        -   name: Run system tests MATLAB ${{ matrix.script }}
+            uses: matlab-actions/run-command@v2.1.1
+            with:
+                command: cd(fullfile(getenv('GITHUB_WORKSPACE'), '.github', 'workflows')); run system_tests_${{ matrix.script }};
diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
@@ -1,5 +1,5 @@
 ---
-name: tests matlab
+name: unit tests matlab
 
 # Uses the cron schedule for github actions
 #
@@ -27,7 +27,7 @@ on:
     schedule:
     -   cron: 0 0 1,15 * *
 
-  # Allows you to run this workflow manually from the Actions tab
+    # Allows you to run this workflow manually from the Actions tab
     workflow_dispatch:
 
 jobs:
@@ -38,46 +38,15 @@ jobs:
 
         strategy:
             matrix:
-                test_type: [system]
-                script: [moae, facerep, fmriprep]
+                mode: [fast, slow]
                 os: [ubuntu-latest, macos-13]
                 matlab: [R2023b]
-                include:
-        # only run bms on ubuntu because of datalad setup
-                -   test_type: system
-                    os: ubuntu-latest
-                    matlab: R2023b
-                    script: bms
-                -   test_type: unit
-                    os: ubuntu-latest
-                    matlab: R2023b
-                    mode: fast
-                -   test_type: unit
-                    os: macos-13
-                    matlab: R2023b
-                    mode: fast
-                -   test_type: unit
-                    os: ubuntu-latest
-                    matlab: R2023b
-                    mode: slow
-                -   test_type: unit
-                    os: macos-13
-                    matlab: R2023b
-                    mode: slow
-                -   test_type: unit
-                    os: macos-13
-                    matlab: R2023b
-                    mode: fast
             fail-fast: false
 
         runs-on: ${{ matrix.os }}
 
         steps:
 
-        -   name: ${{ matrix.test_type }} test
-            if: matrix.test_type == 'system'
-            run: echo ${{ matrix.test_type }} test ${{ matrix.script }}
-
         -   name: Install Node
             uses: actions/setup-node@v4
             with:
@@ -129,10 +98,6 @@ jobs:
                 cd tests
                 make data
 
-        -   name: Get data for BMS
-            if: matrix.script == 'bms'
-            run: make -C demos/bayes data_ds000114
-
         -   name: Install Moxunit and MOcov
             run: |
                 git clone https://github.com/MOxUnit/MOxUnit.git --depth 1
@@ -144,29 +109,22 @@ jobs:
                 release: ${{ matrix.matlab }}
 
         -   name: Run fast unit tests MATLAB
-            if: matrix.test_type == 'unit' && matrix.mode == 'fast'
+            if: matrix.mode == 'fast'
             uses: matlab-actions/run-command@v2.1.1
             with:
                 command: cd(fullfile(getenv('GITHUB_WORKSPACE'), '.github', 'workflows')); run tests_matlab;
 
         -   name: Run slow unit tests MATLAB
-            if: matrix.test_type == 'unit' && matrix.mode == 'slow'
+            if: matrix.mode == 'slow'
             uses: matlab-actions/run-command@v2.1.1
             with:
                 command: cd(fullfile(getenv('GITHUB_WORKSPACE'), '.github', 'workflows')); global SLOW; SLOW=true; run tests_matlab;
 
         -   name: Code coverage matlab
-            if: matrix.test_type == 'unit'
             uses: codecov/codecov-action@v4
             with:
                 file: coverage.xml
                 flags: ${{ matrix.os }}_matlab-${{ matrix.matlab }}_${{ matrix.mode }}
                 name: codecov-matlab
                 fail_ci_if_error: false
                 token: ${{ secrets.CODECOV_TOKEN }}
-
-        -   name: Run system tests MATLAB ${{ matrix.script }}
-            if: matrix.test_type == 'system'
-            uses: matlab-actions/run-command@v2.1.1
-            with:
-                command: cd(fullfile(getenv('GITHUB_WORKSPACE'), '.github', 'workflows')); run system_tests_${{ matrix.script }};