Skip to content

improve read_tiff:

improve read_tiff: #40

name: Test tutorials
on: [push]
jobs:
build:
runs-on: ubuntu-latest
steps:
# This cancels any such job that is still running
- name: Cancel Previous Runs
uses: styfle/[email protected]
with:
access_token: ${{ github.token }}
- uses: actions/checkout@v4
- name: Set up Python 3.10
uses: actions/setup-python@v5
with:
python-version: '3.10'
- name: Install graphviz
run: |
sudo apt-get update -y -qq
sudo apt-get install -y libdbus-1-3 libxkbcommon-x11-0 libxcb-icccm4 \
libxcb-image0 libxcb-keysyms1 libxcb-randr0 libxcb-render-util0 \
libxcb-xinerama0 libxcb-xinput0 graphviz graphviz-dev \
libegl1-mesa libgl1-mesa-dri libxcb-xfixes0-dev mesa-vulkan-drivers \
libxcb-cursor0
- name: Install dependencies
run: |
python -m pip install --upgrade pip
python -m pip install pathos pygraphviz neuron cloud-volume k3d scikit-image open3d
python -m pip install -e .[test-notebook,all]
- name: Download test data
run: |
chmod +x download_test_data.sh
./download_test_data.sh
- name: Download downsampled test transform
run: |
mkdir -p -- $HOME/flybrain-data
curl -o $HOME/flybrain-data/JRC2018F_JRCFIB2018F.h5 https://flyem.mrc-lmb.cam.ac.uk/flyconnectome/misc/JRC2018F_JRCFIB2018F.h5
curl -o $HOME/flybrain-data/JRC2018F_FAFB.h5 https://flyem.mrc-lmb.cam.ac.uk/flyconnectome/misc/JRC2018F_FAFB.h5
- name: Run tutorials
uses: coactions/setup-xvfb@v1
env:
NEUPRINT_APPLICATION_CREDENTIALS: ${{ secrets.neuprint }}
INSECT_BRAIN_DB_USER: ${{ secrets.insect_brain_db_user }}
INSECT_BRAIN_DB_PASSWORD: ${{ secrets.insect_brain_db_password }}
CAVE_SECRET: ${{ secrets.cave_secret }}
NAVIS_PLOT3D_BACKEND: plotly
QT_QPA_PLATFORM: offscreen
with:
run: |
python -c "import os;from caveclient import CAVEclient;client=CAVEclient();client.auth.save_token(os.getenv('CAVE_SECRET'))"
python tests/test_tutorials.py