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Jupyter Notebook checks #1286

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Jupyter Notebook checks

Jupyter Notebook checks #1286

Workflow file for this run

.github/workflows/test_notebooks.yml at 0991133
name: Jupyter Notebook checks
on:
push:
paths:
- 'docs/source/tutorials/**'
- 'snippets/**'
- 'src/vfb_connect/**'
- 'requirements.txt'
- '.github/workflows/requirements.txt'
- '.github/workflows/test_notebooks.yml'
release:
types: [published]
workflow_dispatch:
schedule:
# Monthly scheduled runs on different days to spread load
- cron: '0 2 1 * *' # Overview: 1st of month at 2 AM UTC
- cron: '0 2 5 * *' # VFB Terms: 5th of month at 2 AM UTC
- cron: '0 2 10 * *' # Discovery: 10th of month at 2 AM UTC
- cron: '0 2 15 * *' # VFB Neurons: 15th of month at 2 AM UTC
- cron: '0 2 20 * *' # Connectomics: 20th of month at 2 AM UTC
- cron: '0 2 25 * *' # VFB Datasets: 25th of month at 2 AM UTC
- cron: '0 2 28 * *' # Quick Guide: 28th of month at 2 AM UTC
jobs:
# Overview Tutorial
overview-notebook:
name: "Test overview tutorial"
runs-on: ubuntu-latest
timeout-minutes: 15
if: |
github.event_name == 'release' ||
github.event_name == 'workflow_dispatch' ||
(github.event_name == 'schedule' && github.event.schedule == '0 2 1 * *') ||
contains(github.event.head_commit.modified, 'docs/source/tutorials/overview.ipynb') ||
contains(github.event.head_commit.added, 'docs/source/tutorials/overview.ipynb') ||
contains(github.event.head_commit.modified, 'src/vfb_connect/') ||
contains(github.event.head_commit.modified, 'requirements.txt') ||
contains(github.event.head_commit.modified, '.github/workflows/requirements.txt')
steps:
- uses: actions/checkout@v4
- name: Set up Python
uses: actions/setup-python@v5
with:
python-version: 3.10.14
- name: Cache VFB lookup tables
uses: actions/cache@v4
with:
path: |
src/vfb_connect/lookup_cache.pkl
~/.cache/vfb_connect/
key: vfb-lookup-cache-${{ hashFiles('**/requirements.txt') }}
restore-keys: |
vfb-lookup-cache-
- name: Install dependencies
run: |
python -m pip install -U pip
python -m pip install .
python -m pip install -r .github/workflows/requirements.txt
- name: Set performance environment variables
run: |
echo "VFB_LOAD_LIMIT=5" >> $GITHUB_ENV
echo "VFB_CACHE_ENABLED=true" >> $GITHUB_ENV
- name: Execute overview notebook
run: |
jupyter nbconvert --to notebook --execute --ExecutePreprocessor.timeout=900 docs/source/tutorials/overview.ipynb
- uses: actions/upload-artifact@v4
with:
name: overview-notebook-${{ github.sha }}
path: docs/source/tutorials/overview.nbconvert.ipynb
# VFB Terms Tutorial
vfb-terms-notebook:
name: "Test VFB terms tutorial"
runs-on: ubuntu-latest
timeout-minutes: 15
if: |
github.event_name == 'release' ||
github.event_name == 'workflow_dispatch' ||
(github.event_name == 'schedule' && github.event.schedule == '0 2 5 * *') ||
contains(github.event.head_commit.modified, 'docs/source/tutorials/vfb_terms.ipynb') ||
contains(github.event.head_commit.added, 'docs/source/tutorials/vfb_terms.ipynb') ||
contains(github.event.head_commit.modified, 'src/vfb_connect/') ||
contains(github.event.head_commit.modified, 'requirements.txt') ||
contains(github.event.head_commit.modified, '.github/workflows/requirements.txt')
steps:
- uses: actions/checkout@v4
- name: Set up Python
uses: actions/setup-python@v5
with:
python-version: 3.10.14
- name: Cache VFB lookup tables
uses: actions/cache@v4
with:
path: |
src/vfb_connect/lookup_cache.pkl
~/.cache/vfb_connect/
key: vfb-lookup-cache-${{ hashFiles('**/requirements.txt') }}
restore-keys: |
vfb-lookup-cache-
- name: Install dependencies
run: |
python -m pip install -U pip
python -m pip install .
python -m pip install -r .github/workflows/requirements.txt
- name: Set performance environment variables
run: |
echo "VFB_LOAD_LIMIT=5" >> $GITHUB_ENV
echo "VFB_CACHE_ENABLED=true" >> $GITHUB_ENV
- name: Execute VFB terms notebook
run: |
jupyter nbconvert --to notebook --execute --ExecutePreprocessor.timeout=900 docs/source/tutorials/vfb_terms.ipynb
- uses: actions/upload-artifact@v4
with:
name: vfb-terms-notebook-${{ github.sha }}
path: docs/source/tutorials/vfb_terms.nbconvert.ipynb
# Discovery Tutorial
discovery-notebook:
name: "Test discovery tutorial"
runs-on: ubuntu-latest
timeout-minutes: 15
if: |
github.event_name == 'release' ||
github.event_name == 'workflow_dispatch' ||
(github.event_name == 'schedule' && github.event.schedule == '0 2 10 * *') ||
contains(github.event.head_commit.modified, 'docs/source/tutorials/discovery.ipynb') ||
contains(github.event.head_commit.added, 'docs/source/tutorials/discovery.ipynb') ||
contains(github.event.head_commit.modified, 'src/vfb_connect/') ||
contains(github.event.head_commit.modified, 'requirements.txt') ||
contains(github.event.head_commit.modified, '.github/workflows/requirements.txt')
steps:
- uses: actions/checkout@v4
- name: Set up Python
uses: actions/setup-python@v5
with:
python-version: 3.10.14
- name: Cache VFB lookup tables
uses: actions/cache@v4
with:
path: |
src/vfb_connect/lookup_cache.pkl
~/.cache/vfb_connect/
key: vfb-lookup-cache-${{ hashFiles('**/requirements.txt') }}
restore-keys: |
vfb-lookup-cache-
- name: Install dependencies
run: |
python -m pip install -U pip
python -m pip install .
python -m pip install -r .github/workflows/requirements.txt
- name: Set performance environment variables
run: |
echo "VFB_LOAD_LIMIT=5" >> $GITHUB_ENV
echo "VFB_CACHE_ENABLED=true" >> $GITHUB_ENV
- name: Execute discovery notebook
run: |
jupyter nbconvert --to notebook --execute --ExecutePreprocessor.timeout=900 docs/source/tutorials/discovery.ipynb
- uses: actions/upload-artifact@v4
with:
name: discovery-notebook-${{ github.sha }}
path: docs/source/tutorials/discovery.nbconvert.ipynb
# VFB Neurons Tutorial
vfb-neurons-notebook:
name: "Test VFB neurons tutorial"
runs-on: ubuntu-latest
timeout-minutes: 15
if: |
github.event_name == 'release' ||
github.event_name == 'workflow_dispatch' ||
(github.event_name == 'schedule' && github.event.schedule == '0 2 15 * *') ||
contains(github.event.head_commit.modified, 'docs/source/tutorials/vfb_neurons.ipynb') ||
contains(github.event.head_commit.added, 'docs/source/tutorials/vfb_neurons.ipynb') ||
contains(github.event.head_commit.modified, 'src/vfb_connect/') ||
contains(github.event.head_commit.modified, 'requirements.txt') ||
contains(github.event.head_commit.modified, '.github/workflows/requirements.txt')
steps:
- uses: actions/checkout@v4
- name: Set up Python
uses: actions/setup-python@v5
with:
python-version: 3.10.14
- name: Cache VFB lookup tables
uses: actions/cache@v4
with:
path: |
src/vfb_connect/lookup_cache.pkl
~/.cache/vfb_connect/
key: vfb-lookup-cache-${{ hashFiles('**/requirements.txt') }}
restore-keys: |
vfb-lookup-cache-
- name: Install dependencies
run: |
python -m pip install -U pip
python -m pip install .
python -m pip install -r .github/workflows/requirements.txt
- name: Set performance environment variables
run: |
echo "VFB_LOAD_LIMIT=5" >> $GITHUB_ENV
echo "VFB_CACHE_ENABLED=true" >> $GITHUB_ENV
- name: Execute VFB neurons notebook
run: |
jupyter nbconvert --to notebook --execute --ExecutePreprocessor.timeout=900 docs/source/tutorials/vfb_neurons.ipynb
- uses: actions/upload-artifact@v4
with:
name: vfb-neurons-notebook-${{ github.sha }}
path: docs/source/tutorials/vfb_neurons.nbconvert.ipynb
# Connectomics Tutorial (longer timeout)
connectomics-notebook:
name: "Test connectomics tutorial"
runs-on: ubuntu-latest
timeout-minutes: 30
if: |
github.event_name == 'release' ||
github.event_name == 'workflow_dispatch' ||
(github.event_name == 'schedule' && github.event.schedule == '0 2 20 * *') ||
contains(github.event.head_commit.modified, 'docs/source/tutorials/connectomics.ipynb') ||
contains(github.event.head_commit.added, 'docs/source/tutorials/connectomics.ipynb') ||
contains(github.event.head_commit.modified, 'src/vfb_connect/') ||
contains(github.event.head_commit.modified, 'requirements.txt') ||
contains(github.event.head_commit.modified, '.github/workflows/requirements.txt')
steps:
- uses: actions/checkout@v4
- name: Set up Python
uses: actions/setup-python@v5
with:
python-version: 3.10.14
- name: Cache VFB lookup tables
uses: actions/cache@v4
with:
path: |
src/vfb_connect/lookup_cache.pkl
~/.cache/vfb_connect/
key: vfb-lookup-cache-${{ hashFiles('**/requirements.txt') }}
restore-keys: |
vfb-lookup-cache-
- name: Install dependencies
run: |
python -m pip install -U pip
python -m pip install .
python -m pip install -r .github/workflows/requirements.txt
- name: Set performance environment variables
run: |
echo "VFB_LOAD_LIMIT=5" >> $GITHUB_ENV
echo "VFB_CACHE_ENABLED=true" >> $GITHUB_ENV
- name: Execute connectomics notebook
run: |
jupyter nbconvert --to notebook --execute --ExecutePreprocessor.timeout=1800 docs/source/tutorials/connectomics.ipynb
- uses: actions/upload-artifact@v4
with:
name: connectomics-notebook-${{ github.sha }}
path: docs/source/tutorials/connectomics.nbconvert.ipynb
# VFB Datasets Tutorial
vfb-datasets-notebook:
name: "Test VFB datasets tutorial"
runs-on: ubuntu-latest
timeout-minutes: 15
if: |
github.event_name == 'release' ||
github.event_name == 'workflow_dispatch' ||
(github.event_name == 'schedule' && github.event.schedule == '0 2 25 * *') ||
contains(github.event.head_commit.modified, 'docs/source/tutorials/vfb_datasets.ipynb') ||
contains(github.event.head_commit.added, 'docs/source/tutorials/vfb_datasets.ipynb') ||
contains(github.event.head_commit.modified, 'src/vfb_connect/') ||
contains(github.event.head_commit.modified, 'requirements.txt') ||
contains(github.event.head_commit.modified, '.github/workflows/requirements.txt')
steps:
- uses: actions/checkout@v4
- name: Set up Python
uses: actions/setup-python@v5
with:
python-version: 3.10.14
- name: Cache VFB lookup tables
uses: actions/cache@v4
with:
path: |
src/vfb_connect/lookup_cache.pkl
~/.cache/vfb_connect/
key: vfb-lookup-cache-${{ hashFiles('**/requirements.txt') }}
restore-keys: |
vfb-lookup-cache-
- name: Install dependencies
run: |
python -m pip install -U pip
python -m pip install .
python -m pip install -r .github/workflows/requirements.txt
- name: Set performance environment variables
run: |
echo "VFB_LOAD_LIMIT=5" >> $GITHUB_ENV
echo "VFB_CACHE_ENABLED=true" >> $GITHUB_ENV
- name: Execute VFB datasets notebook
run: |
jupyter nbconvert --to notebook --execute --ExecutePreprocessor.timeout=900 docs/source/tutorials/vfb_datasets.ipynb
- uses: actions/upload-artifact@v4
with:
name: vfb-datasets-notebook-${{ github.sha }}
path: docs/source/tutorials/vfb_datasets.nbconvert.ipynb
# Quick Guide Snippet
quick-guide-notebook:
name: "Test quick guide snippet"
runs-on: ubuntu-latest
timeout-minutes: 15
if: |
github.event_name == 'release' ||
github.event_name == 'workflow_dispatch' ||
(github.event_name == 'schedule' && github.event.schedule == '0 2 28 * *') ||
contains(github.event.head_commit.modified, 'snippets/VFB_connect_Quick_Guide.ipynb') ||
contains(github.event.head_commit.added, 'snippets/VFB_connect_Quick_Guide.ipynb') ||
contains(github.event.head_commit.modified, 'src/vfb_connect/') ||
contains(github.event.head_commit.modified, 'requirements.txt') ||
contains(github.event.head_commit.modified, '.github/workflows/requirements.txt')
steps:
- uses: actions/checkout@v4
- name: Set up Python
uses: actions/setup-python@v5
with:
python-version: 3.10.14
- name: Cache VFB lookup tables
uses: actions/cache@v4
with:
path: |
src/vfb_connect/lookup_cache.pkl
~/.cache/vfb_connect/
key: vfb-lookup-cache-${{ hashFiles('**/requirements.txt') }}
restore-keys: |
vfb-lookup-cache-
- name: Install dependencies
run: |
python -m pip install -U pip
python -m pip install .
python -m pip install -r .github/workflows/requirements.txt
- name: Set performance environment variables
run: |
echo "VFB_LOAD_LIMIT=5" >> $GITHUB_ENV
echo "VFB_CACHE_ENABLED=true" >> $GITHUB_ENV
- name: Execute quick guide notebook
run: |
jupyter nbconvert --to notebook --execute --ExecutePreprocessor.timeout=900 snippets/VFB_connect_Quick_Guide.ipynb
- uses: actions/upload-artifact@v4
with:
name: quick-guide-notebook-${{ github.sha }}
path: snippets/VFB_connect_Quick_Guide.nbconvert.ipynb