Make compatible with github

.github/workflows/cicd_deploy.yml

@@ -0,0 +1,74 @@
+
+name: cicd_deploy
+
+on:
+  # Also run when the pull request merges (which generates a push)
+  # So that we can tag the docker image appropriately.
+  push:
+    tags: [ 'v*.*.*' ]
+
+env:
+  IMAGE_NAME:  ${{ github.repository }}
+  REGISTRY: ghcr.io
+  TEST_TAG:  ${{ github.repository }}:test
+
+jobs:
+  deploy_docker:
+    runs-on: ubuntu-latest
+
+    permissions:
+      contents: read
+      packages: write
+
+    steps:
+    - name: Checkout branch
+      uses: actions/checkout@v4
+
+    - name: Build the Docker image
+      id: build
+      uses: docker/build-push-action@v6
+      with:
+        load: true
+        tags: ${{ env.TEST_TAG }}
+
+    # run the test on the docker image
+    - name: Run tests in docker image
+      run: >
+        docker run
+        ${{ env.TEST_TAG }}
+        python -m pytest -s
+        --log-cli-level=DEBUG
+        --log-format="%(asctime)s %(levelname)s %(message)s"
+        --log-date-format="%Y-%m-%d %H:%M:%S"
+        -m "not functional_test"
+
+    # Login against a Docker registry except on PR
+    # https://github.com/docker/login-action
+    - name: Log into registry ${{ env.REGISTRY }}
+      if: github.event_name != 'pull_request'
+      uses: docker/login-action@v3.4
+      with:
+        registry: ${{ env.REGISTRY }}
+        username: ${{ github.actor }}
+        password: ${{ secrets.GITHUB_TOKEN }}
+
+    # Extract metadata (tags, labels) for Docker
+    # https://github.com/docker/metadata-action
+    - name: Extract Docker metadata
+      if: github.event_name != 'pull_request'
+      id: meta
+      uses: docker/metadata-action@v5
+      with:
+        images: ${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}
+
+    # Build a Docker image with Buildx (don't on PR)
+    # https://github.com/docker/build-push-action
+    - name: Build and push Docker image
+      if: github.event_name != 'pull_request'
+      id: build-and-push
+      uses: docker/build-push-action@v6
+      with:
+        context: .
+        push: true
+        tags: ${{ steps.meta.outputs.tags }}
+        labels: ${{ steps.meta.outputs.labels }}

.github/workflows/cicd_full.yml

@@ -0,0 +1,69 @@
+
+name: cicd_full
+
+on:
+  # Run tests for pull-requests on master
+  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:
+      - dev
+
+env:
+  IMAGE_NAME:  ${{ github.repository }}
+  REGISTRY: ghcr.io
+  TEST_TAG:  ${{ github.repository }}:test
+
+jobs:
+  deploy_docker:
+    runs-on: ubuntu-latest
+
+    permissions:
+      contents: read
+      packages: write
+
+    steps:
+    - name: Checkout branch
+      uses: actions/checkout@v4
+
+    - name: Build the Docker image
+      id: build
+      uses: docker/build-push-action@v6
+      with:
+        load: true
+        tags: ${{ env.TEST_TAG }}
+
+    # run the test on the docker image
+    - name: Run tests in docker image
+      run: >
+        docker run
+        ${{ env.TEST_TAG }}
+        python -m pytest -s
+        --log-cli-level=DEBUG
+
+  test_local:
+    runs-on: ubuntu-latest
+    permissions:
+      contents: read
+      packages: write
+
+    steps:
+      - name: Checkout branch
+        uses: actions/checkout@v4
+
+      # See https://github.com/marketplace/actions/setup-micromamba
+      - name: setup-micromamba
+        uses: mamba-org/setup-micromamba@v2
+        with:
+          environment-file: environment.yml
+          environment-name: ctview  # 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 -s --log-cli-level=DEBUG

.github/workflows/cicd_light.yml

@@ -0,0 +1,36 @@
+name: cicd_light
+
+on:
+  # Run tests for non-draft pull request on dev
+  pull_request:
+    branches:
+      - dev
+
+
+jobs:
+  test_light:
+    runs-on: ubuntu-latest
+    permissions:
+      contents: read
+      packages: write
+
+    steps:
+      - name: Checkout branch
+        uses: actions/checkout@v4
+
+      # See https://github.com/marketplace/actions/setup-micromamba
+      - name: setup-micromamba
+        uses: mamba-org/setup-micromamba@v2
+        with:
+          environment-file: environment.yml
+          environment-name: ctview  # 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 -s --log-cli-level=DEBUG
+
+
+

Makefile

@@ -1,3 +1,9 @@
+# Makefile to manage main tasks
+# cf. https://blog.ianpreston.ca/conda/python/bash/2020/05/13/conda_envs.html#makefile
+
+# Oneshell means I can run multiple lines in a recipe in the same shell, so I don't have to
+# chain commands together with semicolon
+.ONESHELL:
 
 install:
 	mamba env update -n ctview -f environment.yml
@@ -6,27 +12,27 @@ install-precommit:
 	pre-commit install
 
 testing:
-	./ci/test.sh
+	python -m pytest -s ./test -v
 
 ##############################
 # Docker
 ##############################
 
-PROJECT_NAME=lidar_hd/ct_view
+REGISTRY=ghcr.io
+NAMESPACE=ignf
+IMAGE_NAME=ctview
 VERSION=`python -m ctview._version`
-REGISTRY=docker-registry.ign.fr
+FULL_IMAGE_NAME=${REGISTRY}/${NAMESPACE}/${IMAGE_NAME}:${VERSION}
 
 docker-build:
-	docker build -t ${PROJECT_NAME}:${VERSION} -f Dockerfile .
+	docker build -t ${IMAGE_NAME}:${VERSION} -f Dockerfile .
 
 docker-test:
-	docker run --rm -it ${PROJECT_NAME}:${VERSION} python -m pytest -s
+	docker run --rm ${IMAGE_NAME}:${VERSION} python -m pytest -s -m "not functional_test"
 
 docker-remove:
-	docker rmi -f `docker images | grep ${PROJECT_NAME} | tr -s ' ' | cut -d ' ' -f 3`
-	docker rmi -f `docker images -f "dangling=true" -q`
+	docker rmi -f `docker images | grep ${IMAGE_NAME}:${VERSION} | tr -s ' ' | cut -d ' ' -f 3`
 
 docker-deploy:
-	docker login docker-registry.ign.fr -u svc_lidarhd
-	docker tag ${PROJECT_NAME}:${VERSION} ${REGISTRY}/${PROJECT_NAME}:${VERSION}
-	docker push ${REGISTRY}/${PROJECT_NAME}:${VERSION}
+	docker tag ${IMAGE_NAME}:${VERSION} ${FULL_IMAGE_NAME}
+	docker push ${FULL_IMAGE_NAME}

configs/config_control.yaml

@@ -88,7 +88,7 @@ class_map:
   - {value: 202, description: "Candidats Batiment", color: [255, 128, 128]}
   dxm_filter:  # Paramètres pour le calcul du MNS (utilisé pour l'ombrage), dimension à filtrer et
                # valeur à garder, par défaut on utilise la dimension créée dans la phase de preprocessing
-               # des produits dérivés
+               # de las_digital_models
     dimension: dsm_marker
     keep_values: [1]
   post_processing:  # Traitements à appliquer à la carte de classe

configs/config_metadata.yaml

@@ -96,7 +96,7 @@ class_map:
     - {value: 162, description: "VirtPont", color: [85, 97, 137]}
   dxm_filter:  # Paramètres pour le calcul du MNS (utilisé pour l'ombrage), dimension à filtrer et
                # valeur à garder, par défaut on utilise la dimension créée dans la phase de preprocessing
-               # des produits dérivés
+               # de las_digital_models
     dimension: dsm_marker
     keep_values: [1]
   post_processing:  # Traitements à appliquer à la carte de classe

ctview/map_DXM.py

@@ -3,7 +3,7 @@
 import tempfile
 from typing import List
 
-import produits_derives_lidar.ip_one_tile
+import las_digital_models.ip_one_tile
 from omegaconf import DictConfig
 from osgeo_utils import gdal_calc
 
@@ -19,10 +19,10 @@ def create_raw_dxm(
     config_io: DictConfig,
 ):
     """Create a Digital Model (DSM or DTM) using the filter defined with
-    dxm_filter_dimension/dxm_filter_keep_values using the produits_derives_lidar
+    dxm_filter_dimension/dxm_filter_keep_values using the las_digital_models
     library
 
-    WARNING: the dtm bounds are inferred from the filename inside the produits_derives_lidar library
+    WARNING: the dtm bounds are inferred from the filename inside the las_digital_models library
     (dtm is not computed on the potential additional buffer)
 
     Args:
@@ -42,10 +42,10 @@ def create_raw_dxm(
               }
         cf. configs/config_control.yaml for an example.
         The config will be completed with pixel_size, dxm_filter_dimension and dxm_filter_keep_values
-        to match produits_derive_lidar configuration expectations
+        to match las_digital_models configuration expectations
     """
 
-    # Generate config that suits for produits_derive_lidar interpolation
+    # Generate config that suits for las_digital_models interpolation
     pdl_config = {}
     spatial_ref = (
         f"EPSG:{config_io.spatial_reference}"
@@ -60,7 +60,7 @@ def create_raw_dxm(
     log.debug("Config for dxm generation")
     log.debug(pdl_config)
 
-    produits_derives_lidar.ip_one_tile.interpolate_from_config(
+    las_digital_models.ip_one_tile.interpolate_from_config(
         input_file=input_file, output_raster=output_dxm, config=pdl_config
     )
 
@@ -104,7 +104,7 @@ def add_dxm_hillshade_to_raster(
               }
         cf. configs/config_control.yaml for an example ("io" subdivision)
         The config will be completed with pixel_size, dxm_filter_dimension and dxm_filter_keep_values
-        to match produits_derive_lidar configuration expectations
+        to match las_digital_models configuration expectations
     """
     os.makedirs(os.path.dirname(output_dxm_raw), exist_ok=True)
     os.makedirs(os.path.dirname(output_dxm_hillshade), exist_ok=True)