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Add a callback with micro-average Accuracy, Precision, Recall, F1Score and IoU #683

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Add a callback with micro-average Accuracy, Precision, Recall, F1Score and IoU

Add a callback with micro-average Accuracy, Precision, Recall, F1Score and IoU #683

Workflow file for this run

.github/workflows/cicd.yaml at 718d4b2
name: CICD
on:
# Run CICD for non-draft pull request
pull_request:
branches:
- main
# Also run when the pull request merges (which generates a push)
# So that we can tag the docker image appropriately.
push:
branches:
- main
- staging-*
jobs:
CICD:
runs-on: self-hosted
env:
http_proxy: ${{ secrets.PROXY_URL }}
https_proxy: ${{ secrets.PROXY_URL }}
steps:
- name: Checkout branch
uses: actions/checkout@v4
- name: Build docker image
run: docker build --build-arg http_proxy=${{ secrets.PROXY_URL }} --build-arg https_proxy=${{ secrets.PROXY_URL }} -t myria3d .
- name: Run pytest
run: >
docker run
--ipc=host
myria3d
python -m
pytest -rA -v
--ignore=actions-runner
# IMPORTANT: Always run images with --ipc=host and --shm-size=2gb (at least) to enable
# sufficient shared memory when predicting on large files.
- name: Example inference run via Docker with default config and checkpoint
run: >
docker run
-v /var/data/cicd/CICD_github_assets/myria3d_V3.7.0/inputs/:/inputs/
-v /var/data/cicd/CICD_github_assets/myria3d_V3.7.0/outputs/:/outputs/
--ipc=host
--shm-size=2gb
myria3d
python run.py
predict.src_las=/inputs/792000_6272000_subset_buildings.las
datamodule.epsg=2154
predict.output_dir=/outputs/
task.task_name=predict
# predict.subtile_overlap specifies overlap between adjacent samples (in meters).
- name: Example inference run via Docker with inference-time subtiles overlap to smooth-out results.
run: >
docker run
-v /var/data/cicd/CICD_github_assets/myria3d_V3.7.0/inputs/:/inputs/
-v /var/data/cicd/CICD_github_assets/myria3d_V3.7.0/outputs/:/outputs/
--ipc=host
--shm-size=2gb
myria3d
python run.py
--config-path /inputs/
--config-name proto151_V2.0_epoch_100_Myria3DV3.1.0_predict_config_V3.7.0
predict.ckpt_path=/inputs/proto151_V2.0_epoch_100_Myria3DV3.1.0.ckpt
datamodule.epsg=2154
predict.src_las=/inputs/792000_6272000_subset_buildings.las
predict.output_dir=/outputs/
predict.subtile_overlap=25
datamodule.batch_size=10
predict.interpolator.probas_to_save=[building,ground]
task.task_name=predict
- name: Check code neatness (linter)
run: docker run myria3d python -m flake8
# Everything ran so we tag the valid docker image to keep it
# This happens for push events, which are in particular
# triggered when a pull request is merged.
- name: Tag the docker image with branch name
if: github.event_name == 'push'
run: |
docker tag myria3d:latest myria3d:${{github.ref_name}}
docker run myria3d:${{github.ref_name}} bash # Run the new, tagged image at least once so that is it not prunned by mistake when using docker system prune
# docker save myria3d:${{github.ref_name}} -o /var/data/cicd/CICD_github_assets/CICD_docker_images/myria3d_${github.ref_name}.tar # Save the docker image as myria3d_${github.ref_name}.tar
# get version number and date, to tag the image pushed to a private docker registry
- name: get version number
id: tag
run: |
echo "VERSION=$(docker run myria3d python -m myria3d._version)" >> $GITHUB_ENV
echo "DATE=$(date '+%Y.%m.%d')" >> $GITHUB_ENV
# show possible tags, for debugging purpose
- name: Print tags
run: |
echo "${{ env.VERSION }}"
echo "${{ env.DATE }}"
- name: push main docker on nexus (tagged with a date)
# we push on nexus an image from the main branch when it has been updated (push or accepted pull request)
if: ((github.ref_name == 'main') && (github.event_name == 'push'))
run: |
docker tag myria3d ${{ secrets.DOCKER_REGISTRY }}/lidar_hd/myria3d:${{ env.VERSION }}-${{ env.DATE }}
docker login ${{ secrets.DOCKER_REGISTRY }} --username svc_lidarhd --password ${{ secrets.PASSWORD_SVC_LIDARHD }}
docker push ${{ secrets.DOCKER_REGISTRY }}/lidar_hd/myria3d:${{ env.VERSION }}-${{ env.DATE }}
- name: push branch docker on nexus (tagged with the branch name)
# we push on nexus an image from a branch when it's pushed
if: ((github.event_name == 'push') && (github.ref_name != 'main'))
run: |
docker tag myria3d ${{ secrets.DOCKER_REGISTRY }}/lidar_hd/myria3d:${{ env.VERSION }}-${{github.ref_name}}
docker login ${{ secrets.DOCKER_REGISTRY }} --username svc_lidarhd --password ${{ secrets.PASSWORD_SVC_LIDARHD }}
docker push ${{ secrets.DOCKER_REGISTRY }}/lidar_hd/myria3d:${{ env.VERSION }}-${{github.ref_name}}
- name: Clean dangling docker images
if: always() # always do it, even if something failed
run: docker system prune --force # remove dangling docker images, without asking user for confirmation
publish-pypi:
runs-on: ubuntu-latest
if: ((github.ref_name == 'main') && (github.event_name == 'push'))
environment:
name: pypi
url: https://pypi.org/p/myria3d/
permissions:
contents: read
packages: write
id-token: write # IMPORTANT: this permission is mandatory for trusted publishing
steps:
- name: Checkout branch
uses: actions/checkout@v4
# See https://github.com/marketplace/actions/setup-micromamba
- name: setup-micromamba
uses: mamba-org/[email protected]
with:
environment-file: environment.yml
environment-name: myria3d # activate the environment
cache-environment: true
cache-downloads: true
generate-run-shell: true
- name: Run tests with pytest
shell: micromamba-shell {0}
run: python -m pytest ./tests -rA -v
- name: Clean up before building package
run: rm -rf tmp myria3d.egg-info dist
- name: Build pip package
shell: micromamba-shell {0}
run: python -m build
- name: pypi-publish
uses: pypa/[email protected]
with:
skip-existing: true