From 1b2eb7d6d154f7f59da2112fa4c007e543aa31e7 Mon Sep 17 00:00:00 2001
From: Cody Baker <51133164+CodyCBakerPhD@users.noreply.github.com>
Date: Wed, 21 Jun 2023 10:42:33 -0400
Subject: [PATCH] re-add testing workflow

---
 .github/workflows/run-tests.yml | 75 +++++++++++++++++++++++++++++++++
 1 file changed, 75 insertions(+)
 create mode 100644 .github/workflows/run-tests.yml

diff --git a/.github/workflows/run-tests.yml b/.github/workflows/run-tests.yml
new file mode 100644
index 00000000..b68e169f
--- /dev/null
+++ b/.github/workflows/run-tests.yml
@@ -0,0 +1,75 @@
+name: Full Tests
+on:
+  schedule:
+    - cron: "0 0 * * *"  # daily
+  pull_request:
+  workflow_dispatch:
+
+jobs:
+  run:
+    name: Full tests on ${{ matrix.os }} with Python ${{ matrix.python-version }}
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: [3.8, 3.9, "3.10", 3.11]
+        os: [ubuntu-latest, windows-latest, macos-latest]
+    steps:
+      - uses: s-weigand/setup-conda@v1
+      - uses: actions/checkout@v2
+      - run: git fetch --prune --unshallow --tags
+      - name: Setup Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v2
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Global Setup
+        run: |
+          pip install -U pip
+          pip install pytest-xdist
+          git config --global user.email "CI@example.com"
+          git config --global user.name "CI Almighty"
+          pip install wheel  # needed for scanimage
+
+      - name: Install roiextractors with minimal requirements
+        run: pip install .[test]
+      - name: Run minimal tests
+        run: pytest tests/test_internals -n auto --dist loadscope
+
+      - name: Test full installation (-e needed for codecov report)
+        run: pip install -e .[full]
+
+
+
+      - name: Get ophys_testing_data current head hash
+        id: ophys
+        run: echo "::set-output name=HASH_OPHYS_DATASET::$(git ls-remote https://gin.g-node.org/CatalystNeuro/ophys_testing_data.git HEAD | cut -f1)"
+      - name: Cache ophys dataset - ${{ steps.ophys.outputs.HASH_OPHYS_DATASET }}
+        uses: actions/cache@v2
+        id: cache-ophys-datasets
+        with:
+          path: ./ophys_testing_data
+          key: ophys-datasets-042023-${{ matrix.os }}-${{ steps.ophys.outputs.HASH_OPHYS_DATASET }}
+      - if: steps.cache-ophys-datasets.outputs.cache-hit == false
+        name: Install and configure AWS CLI
+        run: |
+          pip install awscli==1.25.27
+          aws configure set aws_access_key_id ${{ secrets.AWS_ACCESS_KEY_ID }}
+          aws configure set aws_secret_access_key ${{ secrets.AWS_SECRET_ACCESS_KEY }}
+      - if: steps.cache-ophys-datasets.outputs.cache-hit == false
+        name: Download data from S3
+        run: aws s3 cp --recursive s3://${{ secrets.S3_GIN_BUCKET }}//ophys_testing_data ./ophys_testing_data
+
+
+
+      - name: Run full pytest with coverage
+        run: pytest -n auto --dist loadscope --cov=./ --cov-report xml:./codecov.xml
+      - if: ${{ matrix.python-version == '3.9' && matrix.os == 'ubuntu-latest'}}
+        name: Upload full coverage to Codecov
+        uses: codecov/codecov-action@v1
+        with:
+          token: ${{ secrets.CODECOV_TOKEN }}
+          file: ./codecov.xml
+          flags: unittests
+          name: codecov-umbrella
+          yml: ./codecov.yml