Merge branch 'main' into numpydoc

.github/workflows/run-tests.yml

@@ -1,12 +1,21 @@
 name: Full Tests
 on:
-  schedule:
-    - cron: "0 0 * * *"  # daily
   pull_request:
   workflow_dispatch:
+  workflow_run:
+    workflows: [update-testing-data]
+    types: [completed]
 
 jobs:
-  run:
+  on-failure:
+    name: Notify on failure
+    runs-on: ${{ matrix.os }}
+    if: ${{ github.event.workflow_run.conclusion == 'failure' }}
+    steps:
+      - run: |
+          echo 'The triggering workflow failed.'
+          0
+  on-success:
     name: Full tests on ${{ matrix.os }} with Python ${{ matrix.python-version }}
     runs-on: ${{ matrix.os }}
     strategy:
@@ -29,18 +38,17 @@ jobs:
           pip install pytest-xdist
           git config --global user.email "[email protected]"
           git config --global user.name "CI Almighty"
-          pip install wheel  # needed for scanimage
+          pip install wheel==0.41.2  # 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::$(git ls-remote https://gin.g-node.org/CatalystNeuro/ophys_testing_data.git HEAD | cut -f1)"
@@ -50,17 +58,6 @@ jobs:
         with:
           path: ./ophys_testing_data
           key: ophys-datasets-042023-${{ 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

.github/workflows/update-testing-data.yml

@@ -1,5 +1,7 @@
-name: Update testing data
+name: update-testing-data
 on:
+  schedule:
+    - cron: "0 0 * * *"  # daily
   workflow_dispatch:
 
 jobs:
@@ -24,7 +26,7 @@ jobs:
           pip install -U pip
           git config --global user.email "[email protected]"
           git config --global user.name "CI Almighty"
-          pip install wheel  # needed for scanimage
+          pip install wheel==0.41.2  # needed for scanimage
 
       - name: Get ophys_testing_data current head hash
         id: ophys
@@ -38,7 +40,7 @@ jobs:
       - if: steps.cache-ophys-datasets.outputs.cache-hit == false
         name: Install and configure AWS CLI
         run: |
-          pip install awscli==1.25.27
+          pip install awscli==1.29.56
           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

.pre-commit-config.yaml

@@ -6,7 +6,7 @@ repos:
     -   id: end-of-file-fixer
     -   id: trailing-whitespace
 -   repo: https://github.com/psf/black
-    rev: 23.7.0
+    rev: 23.9.1
     hooks:
     -   id: black
         exclude: ^docs/

README.md

@@ -1,5 +1,5 @@
 [![PyPI version](https://badge.fury.io/py/roiextractors.svg)](https://badge.fury.io/py/roiextractors)
-![Full Tests](https://github.com/catalystneuro/roiextractors/actions/workflows/testing.yml/badge.svg)
+![Full Tests](https://github.com/catalystneuro/roiextractors/actions/workflows/run-tests.yml/badge.svg)
 ![Auto-release](https://github.com/catalystneuro/roiextractors/actions/workflows/auto-publish.yml/badge.svg)
 [![codecov](https://codecov.io/github/catalystneuro/roiextractors/coverage.svg?branch=master)](https://codecov.io/github/catalystneuro/roiextractors?branch=master)
 [![documentation](https://readthedocs.org/projects/roiextractors/badge/?version=latest)](https://roiextractors.readthedocs.io/en/latest/)