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Merge branch 'main' into debug_dandi
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CodyCBakerPhD authored Aug 31, 2024
2 parents 68b52cf + 01908f7 commit 17ec80f
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Showing 75 changed files with 755 additions and 2,074 deletions.
9 changes: 7 additions & 2 deletions .github/workflows/daily_tests.yml
Original file line number Diff line number Diff line change
Expand Up @@ -20,6 +20,11 @@ jobs:
uses: ./.github/workflows/testing_dev_with_live_services.yml
secrets:
CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}

E2ELiveServices:
uses: ./.github/workflows/testing_dev_e2e_with_live_services.yml
secrets:
CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
DANDI_STAGING_API_KEY: ${{ secrets.DANDI_STAGING_API_KEY }}

BuildTests:
Expand All @@ -38,7 +43,7 @@ jobs:

NotifyOnAnyFailure:
runs-on: ubuntu-latest
needs: [DevTests, LiveServices, BuildTests, ExampleDataCache, ExampleDataTests]
needs: [DevTests, LiveServices, E2ELiveServices, BuildTests, ExampleDataCache, ExampleDataTests]
if: failure()
steps:
- uses: dawidd6/action-send-mail@v3
Expand All @@ -48,6 +53,6 @@ jobs:
username: ${{ secrets.MAIL_USERNAME }}
password: ${{ secrets.MAIL_PASSWORD }}
subject: NWB GUIDE Daily Test Failure
to: ${{ secrets.DAILY_FAILURE_EMAIL_LIST }}
to: [email protected],[email protected]
from: NWB Guide Daily Tests
body: "The daily tests workflow failed, please check the status at https://github.com/NeurodataWithoutBorders/nwb-guide/actions/workflows/daily_tests.yml"
5 changes: 5 additions & 0 deletions .github/workflows/deploy_tests_on_pull_request.yml
Original file line number Diff line number Diff line change
Expand Up @@ -18,6 +18,11 @@ jobs:
uses: ./.github/workflows/testing_dev_with_live_services.yml
secrets:
CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}

E2ELiveServices:
uses: ./.github/workflows/testing_dev_e2e_with_live_services.yml
secrets:
CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
DANDI_STAGING_API_KEY: ${{ secrets.DANDI_STAGING_API_KEY }}

BuildTests:
Expand Down
2 changes: 1 addition & 1 deletion .github/workflows/example_data_cache.yml
Original file line number Diff line number Diff line change
Expand Up @@ -21,7 +21,7 @@ jobs:
fail-fast: false
matrix:
python-version: ["3.12"]
os: [ubuntu-latest, macos-latest, macos-13, windows-latest]
os: [ubuntu-latest, windows-latest, macos-latest, macos-13]

steps:

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20 changes: 8 additions & 12 deletions .github/workflows/testing_dev.yml
Original file line number Diff line number Diff line change
Expand Up @@ -29,8 +29,8 @@ jobs:
- os: macos-13 # Mac x64 runner
label: environments/environment-MAC-intel.yml

# - os: windows-latest
# label: environments/environment-Windows.yml
- os: windows-latest
label: environments/environment-Windows.yml

steps:
- uses: actions/checkout@v4
Expand Down Expand Up @@ -69,6 +69,12 @@ jobs:
- name: Install GUIDE
run: npm ci --verbose

- name: Install testing dependencies
run: pip install pytest pytest-cov

- name: Manually remove matplotlib
run: pip uninstall matplotlib --yes

- if: matrix.os != 'ubuntu-latest'
name: Run tests
run: npm run test:coverage
Expand All @@ -77,16 +83,6 @@ jobs:
name: Run tests with xvfb
run: xvfb-run --auto-servernum --server-args="-screen 0 1280x960x24" -- npm run test:coverage

- name: Archive E2E Test Screenshots
if: always()
uses: actions/upload-artifact@v4
with:
name: test-screenshots-${{ matrix.os }}
path: docs/assets/tutorials
retention-days: 1
overwrite: true


- name: Upload coverage reports to Codecov
uses: codecov/codecov-action@v4
env:
Expand Down
106 changes: 106 additions & 0 deletions .github/workflows/testing_dev_e2e_with_live_services.yml
Original file line number Diff line number Diff line change
@@ -0,0 +1,106 @@
name: End-to-end tests with live services
on:
workflow_call:
secrets:
CODECOV_TOKEN:
required: true
DANDI_STAGING_API_KEY:
required: true

jobs:

run:
# Will read on PR dashboard as 'Deploy / E2ELiveServices / {os}'
# Action dashboard identified by 'End-to-end tests with live services'
# Requirement settings identified as 'E2ELiveServices / {os}'
name: ${{ matrix.os }}
runs-on: ${{ matrix.os }}
defaults:
run:
shell: bash -l {0}
strategy:
fail-fast: false
matrix:
include:
- os: ubuntu-latest
label: environments/environment-Linux.yml

- os: macos-latest # Mac arm64 runner
label: environments/environment-MAC-apple-silicon.yml

- os: macos-13 # Mac x64 runner
label: environments/environment-MAC-intel.yml

- os: windows-latest
label: environments/environment-Windows.yml

steps:
- uses: actions/checkout@v4
- run: git fetch --prune --unshallow --tags

# see https://github.com/conda-incubator/setup-miniconda#caching-environments
- name: Setup Mambaforge
uses: conda-incubator/setup-miniconda@v3
with:
miniforge-variant: Mambaforge
miniforge-version: latest
activate-environment: nwb-guide
use-mamba: true

- name: Set cache date
id: get-date
run: echo "today=$(/bin/date -u '+%Y%m%d')" >> $GITHUB_OUTPUT
shell: bash

- name: Cache Conda env
uses: actions/cache@v4
with:
path: ${{ env.CONDA }}/envs
key: conda-${{ runner.os }}-${{ runner.arch }}-${{steps.get-date.outputs.today }}-${{ hashFiles(matrix.label) }}-${{ env.CACHE_NUMBER }}
id: cache

- if: steps.cache.outputs.cache-hit != 'true'
name: Create and activate environment
run: mamba env update -n nwb-guide -f ${{ matrix.label }}

- name: Use Node.js 20
uses: actions/setup-node@v4
with:
node-version: 20

- name: Install GUIDE
run: npm ci --verbose

- name: Install testing dependencies
run: pip install pytest pytest-cov

- name: Manually remove matplotlib
run: pip uninstall matplotlib --yes

- name: Create env file
run: |
touch .env
echo DANDI_STAGING_API_KEY=${{ secrets.DANDI_STAGING_API_KEY }} >> .env
- if: matrix.os != 'ubuntu-latest'
name: Run tests
run: npm run coverage:tutorial

- if: matrix.os == 'ubuntu-latest'
name: Run tests with xvfb
run: xvfb-run --auto-servernum --server-args="-screen 0 1280x960x24" -- npm run coverage:tutorial

- name: Archive E2E Test Screenshots
uses: actions/upload-artifact@v4
with:
name: test-screenshots-${{ matrix.os }}
path: docs/assets/tutorials
retention-days: 1
overwrite: true

- name: Upload coverage reports to Codecov
uses: codecov/codecov-action@v4
env:
CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
with:
fail_ci_if_error: true
15 changes: 7 additions & 8 deletions .github/workflows/testing_dev_with_live_services.yml
Original file line number Diff line number Diff line change
Expand Up @@ -4,8 +4,6 @@ on:
secrets:
CODECOV_TOKEN:
required: true
DANDI_STAGING_API_KEY:
required: true

jobs:

Expand All @@ -31,8 +29,8 @@ jobs:
- os: macos-13 # Mac x64 runner
label: environments/environment-MAC-intel.yml

# - os: windows-latest
# label: environments/environment-Windows.yml
- os: windows-latest
label: environments/environment-Windows.yml

steps:
- uses: actions/checkout@v4
Expand Down Expand Up @@ -71,10 +69,11 @@ jobs:
- name: Install GUIDE
run: npm ci --verbose

- name: Create env file
run: |
touch .env
echo DANDI_STAGING_API_KEY=${{ secrets.DANDI_STAGING_API_KEY }} >> .env
- name: Install testing dependencies
run: pip install pytest pytest-cov

- name: Manually remove matplotlib
run: pip uninstall matplotlib --yes

- if: matrix.os != 'ubuntu-latest'
name: Run tests
Expand Down
29 changes: 13 additions & 16 deletions .github/workflows/testing_flask_build_and_dist.yml
Original file line number Diff line number Diff line change
Expand Up @@ -17,26 +17,16 @@ jobs:
fail-fast: false
matrix:
include:
# linux installation instructions use dev mode instead of distributable
# - python-version: "3.9"
# os: ubuntu-latest
# label: environments/environment-Linux.yml
# prefix: /usr/share/miniconda3/envs/nwb-guide

- python-version: "3.9"
os: macos-latest # Mac arm64 runner
# No linux in this matrix since installation instructions use dev mode instead of distributable

- os: macos-latest # Mac arm64 runner
label: environments/environment-MAC-apple-silicon.yml
prefix: /Users/runner/miniconda3/envs/nwb-guide

- python-version: "3.9"
os: macos-13 # Mac x64 runner
- os: macos-13 # Mac x64 runner
label: environments/environment-MAC-intel.yml
prefix: /Users/runner/miniconda3/envs/nwb-guide

- python-version: "3.9"
os: windows-latest
- os: windows-latest
label: environments/environment-Windows.yml
prefix: C:\Miniconda3\envs\nwb-guide

steps:
- uses: actions/checkout@v4
Expand Down Expand Up @@ -78,7 +68,14 @@ jobs:
with:
node-version: "20"

- run: npm ci --verbose
- name: Install GUIDE
run: npm ci --verbose

- name: Install testing dependencies
run: pip install pytest pytest-cov

- name: Manually remove matplotlib
run: pip uninstall matplotlib --yes

# Fix for macos build - remove bad sonpy file
- if: matrix.os == 'macos-latest' || matrix.os == 'macos-13'
Expand Down
7 changes: 6 additions & 1 deletion .github/workflows/testing_pipelines.yml
Original file line number Diff line number Diff line change
Expand Up @@ -30,7 +30,6 @@ jobs:
- os: windows-latest
label: environments/environment-Windows.yml


steps:
- uses: actions/checkout@v4
- run: git fetch --prune --unshallow --tags
Expand Down Expand Up @@ -67,6 +66,12 @@ jobs:
- name: Install GUIDE
run: npm ci --verbose

- name: Install testing dependencies
run: pip install pytest pytest-cov

- name: Manually remove matplotlib
run: pip uninstall matplotlib --yes

# Load example data caches
- name: Get ephy_testing_data current head hash
id: ephys
Expand Down
2 changes: 1 addition & 1 deletion .pre-commit-config.yaml
Original file line number Diff line number Diff line change
Expand Up @@ -8,7 +8,7 @@ repos:
- id: trailing-whitespace

- repo: https://github.com/psf/black
rev: 24.4.2
rev: 24.8.0
hooks:
- id: black
exclude: ^docs/
Expand Down
2 changes: 1 addition & 1 deletion docs/_static/css/custom.css
Original file line number Diff line number Diff line change
Expand Up @@ -11,7 +11,7 @@ button.btn.version-switcher__button {
.version-switcher__container.dropdown:hover .dropdown-menu {
display: block;
left: 0;
margin-top: var(--bs-dropdown-spacer);
margin-top: 0 !important;
top: 100%;
}

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14 changes: 13 additions & 1 deletion docs/_static/switcher.json
Original file line number Diff line number Diff line change
Expand Up @@ -4,11 +4,23 @@
"url": "https://nwb-guide.readthedocs.io/en/latest/",
"preferred": false
},
{
"name": "1.0.3",
"version": "v1.0.3",
"url": "https://nwb-guide.readthedocs.io/en/v1.0.3/",
"preferred": true
},
{
"name": "1.0.2",
"version": "v1.0.2",
"url": "https://nwb-guide.readthedocs.io/en/v1.0.2/",
"preferred": false
},
{
"name": "1.0.1",
"version": "v1.0.1",
"url": "https://nwb-guide.readthedocs.io/en/v1.0.1/",
"preferred": true
"preferred": false
},
{
"name": "1.0.0",
Expand Down
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