Convert Azure Pipeline to Github Actions (#543)

* add test python requirements

* migrate azure pipeline to github actions

* Fix test workflow syntax

- properly embed bash calls
- fix artifact reference name
- try to fix MATLAB test discovery

* attempt to fix python setup

* switch run-test to run-command

* try to upload to codecov

* Fix CI testing

Use version of MATLAB that supports hdf5 dynamically loaded filters.

* check ci env setting

* fix debug pipeline

* more env fixing

* fix expected error test id

* remove debug prints from ci

* add source files to download repo

* try different test suite

* try different test suite (again)

* Try using MATLAB R2024a for tests in workflow

* Give test workflow a shorter name

* Add codecov settings file

* Update versions of dependent actions to latest versions

* Update test badge in README.md

* Rename utilities folder to tools

* Add codespell workflow

---------

Co-authored-by: ehennestad <ehennestad@gmail.com>
Co-authored-by: Ben Dichter <ben.dichter@gmail.com>

+tests/requirements.txt

@@ -0,0 +1,2 @@
+pynwb
+hdf5plugin

.codespellrc

@@ -1,3 +1,3 @@
 [codespell]
-skip = *.html,*logo_matnwb.svg,*fastsearch.m,*.yaml,*UpdateThirdPartyFromUpstream.sh,*testResults.xml
+skip = *.html,*logo_matnwb.svg,*fastsearch.m,*.yaml,*testResults.xml
 ignore-words-list = DNE,nd,whos

.github/.codecov.yaml

@@ -0,0 +1,12 @@
+coverage:
+  range: "90...100"
+  status:
+    project:
+      default:
+        target: 90 # Set the desired coverage target as 90%
+        threshold: 1 # Allowable drop in coverage
+    patch:
+      default:
+        # 75% of the changed code must be covered by tests
+        threshold: 25
+        only_pulls: true

.github/workflows/run_codespell.yml

@@ -0,0 +1,46 @@
+# Note: This workflow allows specifying a custom location for the Codespell 
+# configuration file by defining CONFIG_FILE as an environment variable. 
+# A defined subset of options is extracted from this file and passed to the 
+# Codespell action. This also ensures that the output of the codespell action 
+# prints out the values of these options.
+# Todo: Generalize the extraction of codespell input arguments/options.
+
+name: Codespell
+
+on:
+  pull_request:
+    branches:
+      - master
+  push:
+    branches-ignore:
+      - master
+
+jobs:
+  codespell:
+    name: Check for spelling errors
+    runs-on: ubuntu-latest
+    env:
+      CONFIG_FILE: .codespellrc
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+
+      - name: Extract codespell configurations from configuration file
+        id: config
+        run: |
+          # Extract 'skip' value from the config file, excluding 'skip = ' part
+          skip=$(grep -E '^skip' "$CONFIG_FILE" | sed 's/^skip *= *//')
+          
+          # Extract 'ignore-words-list' value from the config file, excluding 'ignore-words-list = ' part
+          ignore_words=$(grep -E '^ignore-words-list' "$CONFIG_FILE" | sed 's/^ignore-words-list *= *//')
+          
+          # Export values as environment variables
+          echo "SKIP=$skip" >> $GITHUB_ENV
+          echo "IGNORE_WORDS_LIST=$ignore_words" >> $GITHUB_ENV
+
+      - name: Codespell
+        uses: codespell-project/actions-codespell@v2
+        with:
+          skip: "${{ env.SKIP }}"
+          ignore_words_list: "${{ env.IGNORE_WORDS_LIST }}"

.github/workflows/run_tests.yml

@@ -0,0 +1,82 @@
+# Run and publish MATLAB tests with coverage
+name: Run tests
+
+on:
+  pull_request:
+    branches:
+      - master
+    paths-ignore:
+      - "*.md"
+      - "*.codespellrc"
+      - ".github/**"
+  push:
+    branches:
+      - master
+
+jobs:
+  run_tests:
+    name: Run MATLAB tests
+    runs-on: ubuntu-latest
+    steps:
+      - name: check out repository
+        uses: actions/checkout@v4
+      - name: install python
+        uses: actions/setup-python@v5
+        with:
+          python-version: '3.10'
+      - name: configure python env
+        run: |
+          python -m pip install -U pip
+          pip install -r +tests/requirements.txt
+          echo "HDF5_PLUGIN_PATH=$(python -c "import hdf5plugin; print(hdf5plugin.PLUGINS_PATH)")" >> "$GITHUB_ENV"
+      - name: install MATLAB
+        uses: matlab-actions/setup-matlab@v2
+        with:
+          release: R2024a # this is necessary to test dynamic filters
+      - name: run tests
+        uses: matlab-actions/run-command@v2
+        with:
+          command: results = assertSuccess(nwbtest); assert(~isempty(results), 'No tests ran');
+      - name: upload JUnit results
+        uses: actions/upload-artifact@v4
+        with:
+          name: test-results
+          path: testResults.xml
+          retention-days: 1
+      - name: upload coverage results
+        uses: actions/upload-artifact@v4
+        with:
+          name: test-coverage
+          path: ./coverage.xml
+  publish_junit:
+    name: Publish JUnit Test Results
+    runs-on: ubuntu-latest
+    if: ${{ always() }}
+    needs: [run_tests]
+    steps:
+      - name: retrieve result files
+        uses: actions/download-artifact@v4
+        with:
+          name: test-results
+      - name: publish results
+        uses: mikepenz/action-junit-report@v4
+        with:
+          report_paths: 'testResults.xml'
+  publish_coverage:
+    name: Publish Cobertura Test Coverage
+    runs-on: ubuntu-latest
+    needs: [run_tests]
+    steps:
+      - name: check out repository
+        uses: actions/checkout@v4
+      - name: retrieve code coverage files
+        uses: actions/download-artifact@v4
+        with:
+          name: test-coverage
+      - name: publish on Codecov
+        uses: codecov/codecov-action@v4
+        with:
+          token: ${{ secrets.CODECOV_TOKEN }}
+          files: coverage.xml
+          name: codecov-matnwb
+          verbose: true

README.md

@@ -1,7 +1,9 @@
 ![MatNWB Logo](logo/logo_matnwb_small.png)
 
 [![Open in MATLAB Online](https://www.mathworks.com/images/responsive/global/open-in-matlab-online.svg)](https://matlab.mathworks.com/open/github/v1?repo=NeurodataWithoutBorders/matnwb&file=tutorials/basicUsage.mlx)
-[![codecov](https://codecov.io/gh/NeurodataWithoutBorders/matnwb/branch/master/graph/badge.svg?token=apA7F24NsO)](https://codecov.io/gh/NeurodataWithoutBorders/matnwb) ![Azure DevOps tests](https://img.shields.io/azure-devops/tests/NeurodataWithoutBorders/matnwb/4)
+[![codecov](https://codecov.io/gh/NeurodataWithoutBorders/matnwb/branch/master/graph/badge.svg?token=apA7F24NsO)](https://codecov.io/gh/NeurodataWithoutBorders/matnwb)
+[![Run tests](https://github.com/NeurodataWithoutBorders/matnwb/actions/workflows/run_tests.yml/badge.svg)](https://github.com/NeurodataWithoutBorders/matnwb/actions/workflows/run_tests.yml?query=event%3Apush+branch%3Amaster)
+[![Codespell](https://github.com/NeurodataWithoutBorders/matnwb/actions/workflows/run_codespell.yml/badge.svg?branch=master)](https://github.com/NeurodataWithoutBorders/matnwb/actions/workflows/run_codespell.yml?query=event%3Apush+branch%3Amaster)
 
 MatNWB is a  Matlab interface for reading and writing Neurodata Without Borders (NWB) 2.x files.
 

tools/maintenance/validateCodecovSettings.m

@@ -0,0 +1,16 @@
+function validateCodecovSettings()
+% validateCodecovSettings Validate a codecov settings file.
+%
+%   Note: This is a utility function developer's can use to check the
+%   codecov settings file in .github/.codecov.yaml
+
+    sysCommand = sprintf("curl -X POST --data-binary @%s https://codecov.io/validate", ...
+        fullfile(misc.getMatnwbDir, '.github', '.codecov.yaml'));
+
+    [status, message] = system(sysCommand);
+
+    assert(status == 0, 'Curl command failed')
+
+    assert(contains(message, 'Valid!'), ...
+        'Codecov settings file is invalid')
+end