Merge pull request #26 from IGNF/dev

Merge dev to main for version 0.0.1

Author: leavauchier

.env_example

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+DB_UNI_USER='TO_BE_DEFINED'
+DB_UNI_PASSWORD='TO_BE_DEFINED'

.flake8

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+[flake8]
+max-line-length = 119

.github/workflows/ci.yaml

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+name: ci
+
+on:
+  pull_request:
+    branches:
+      - main
+      - dev
+
+jobs:
+  build_and_test:
+    runs-on: ubuntu-latest
+    permissions:
+        contents: read
+        packages: write
+
+    steps:
+      # cf https://samuelsson.dev/access-private-submodules-in-github-actions/ for submodule fetching
+      - name: Checkout branch
+        uses: actions/checkout@v4
+        with:
+          ssh-key: ${{ secrets.SUBMODULE_PULL_KEY }}
+          submodules: 'recursive'
+
+      # See https://github.com/marketplace/actions/setup-micromamba
+      - name: Install conda env
+        uses: mamba-org/[email protected]
+        with:
+          environment-file: environment.yml
+          environment-name: lidro  # activate the environment
+          cache-environment: true
+          cache-downloads: true
+          generate-run-shell: true
+      - name: Unit test
+        shell: micromamba-shell {0}
+        run: |
+          cp .env_example .env
+          python -m pytest -m "not returnfile and not bduni" -s --log-cli-level INFO

.github/workflows/cicd_deploy.yml

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+name: cicd_deploy
+
+on:
+  push:
+      # Run deployment tests on every new version tag and every push to main and dev:
+      # Run actual deploymment only on push to main and tags
+      branches: [ "main", "dev" ]
+      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:
+      # cf https://samuelsson.dev/access-private-submodules-in-github-actions/ for submodule fetching
+      - name: Checkout branch
+        uses: actions/checkout@v4
+        with:
+          ssh-key: ${{ secrets.SUBMODULE_PULL_KEY }}
+          submodules: 'recursive'
+
+      # build the image
+      - name: Build Docker image for tests
+        id: build
+        uses: docker/build-push-action@v5
+        with:
+          context: .  # cf https://github.com/docker/build-push-action/issues/638
+          load: true
+          tags: ${{ env.TEST_TAG }}
+
+      - name: Run tests in docker
+        run: >
+          docker run -v $(pwd)/data:/lidro/data --ipc=host ${{ env.TEST_TAG }}
+          python -m pytest test -m "not returnfile and not bduni" -s --log-cli-level INFO
+
+      - name: Set version number
+        run: |
+          echo "VERSION=v$(python -m lidro._version)" >> $GITHUB_ENV
+
+      - name: Check tag and version number consistency
+        if: github.event_name == 'push' && contains(github.ref, 'refs/tags/')
+        run: |
+          if [[ ${{ github.ref_name }} == ${{ env.VERSION }} ]]
+          then
+          echo "OK: Tag name and _version.py (${{ env.VERSION }}) version number (${{ github.ref_name }}) match"
+          else
+          echo "NOK: Tag name and _version.py (${{ env.VERSION }}) version number (${{ github.ref_name }}) don't match"
+          exit 1
+          fi
+
+      # Login against a Docker registry except on dev branch
+      # https://github.com/docker/login-action
+      - name: Log into registry ${{ env.REGISTRY }}
+        uses: docker/login-action@v2
+        if: ${{ github.ref_name != 'dev' }}
+        with:
+          registry: ${{ env.REGISTRY }}
+          username: ${{ github.actor }}
+          password: ${{ secrets.GITHUB_TOKEN }}
+
+      # Extract metadata (tags, labels) for Docker except on dev branch
+      # https://github.com/docker/metadata-action
+      - name: Extract Docker metadata
+        id: metadata
+        if: ${{ github.ref_name != 'dev' }}
+        uses: docker/metadata-action@v5
+        with:
+          images: ${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}
+
+      # Build and push Docker image with Buildx  except on dev branch
+      # https://github.com/docker/build-push-action
+      - name: Build and push Docker image
+        id: build-and-push
+        if: ${{ github.ref_name != 'dev' }}
+        uses: docker/build-push-action@v5
+        with:
+          context: .
+          push: true
+          tags: ${{ steps.metadata.outputs.tags }}
+          labels: ${{ steps.metadata.outputs.labels }}

.gitignore

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+**/__pycache__
+tmp
+**.log
+
+.env
+
+outputs/

.gitmodules

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+[submodule "data"]
+	path = data
+	url = [email protected]:IGNF/lidro-data.git

.pre-commit-config.yaml

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+# See https://dev.to/m1yag1/how-to-setup-your-project-with-pre-commit-black-and-flake8-183k
+# for pre-commits setup
+# See https://pre-commit.com for more information
+# See https://pre-commit.com/hooks.html for more hooks
+repos:
+  - repo: https://github.com/pycqa/isort
+    rev: 5.13.2
+    hooks:
+      - id: isort
+        name: isort (python)
+  - repo: https://github.com/ambv/black
+    rev: 24.2.0
+    hooks:
+      - id: black
+        language_version: python3.11
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v2.0.0
+    hooks:
+      - id: flake8

CHANGELOG.md

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+# v0.1.0
+- Correction du bug au moment de la jonction entre les parties du squelette qui créait des
+interpolations imprévues entre des extrémités de branches qui ne devraient pas être reliées.
+cf. https://github.com/IGNF/lidro/pull/21
+
+# v0.0.1
+- Création du Dockerfile pour faire fonctionner le projet Lidro
+
+# v0.0.0
+- Première version de Lidro sans recette

Dockerfile

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+FROM mambaorg/micromamba:latest
+
+USER root
+
+WORKDIR /lidro
+
+# # Set up the Conda environment: cf https://github.com/mamba-org/micromamba-docker
+COPY environment.yml /tmp/env.yaml
+COPY requirements.txt /tmp/requirements.txt
+RUN chown $MAMBA_USER:$MAMBA_USER /tmp/env.yaml
+RUN micromamba install -y -n base -f /tmp/env.yaml && \
+    micromamba clean --all --yes
+
+ENV ENV=base
+ARG MAMBA_DOCKERFILE_ACTIVATE=1
+
+COPY lidro lidro
+COPY configs configs
+COPY test test

Makefile

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+# 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:
+SHELL = /bin/bash
+install:
+	pip install -e .
+
+install-precommit:
+	pre-commit install
+
+mamba-env-create:
+	mamba env create -n lidro -f environment.yml
+
+mamba-env-update:
+	mamba env update -n lidro -f environment.yml
+
+##############################
+# Docker
+##############################
+
+REGISTRY=ghcr.io
+IMAGE_NAME=lidro
+NAMESPACE=ignf
+VERSION=`python -m lidro._version`
+FULL_IMAGE_NAME=${REGISTRY}/${NAMESPACE}/${IMAGE_NAME}:${VERSION}
+DATA_DIR= `realpath ./data`
+
+
+docker-build:
+	docker build --no-cache -t ${IMAGE_NAME}:${VERSION} -f Dockerfile .
+
+docker-test:
+	docker run -v ${DATA_DIR}:/lidro/data --rm -it ${IMAGE_NAME}:${VERSION} python -m pytest -s test
+
+docker-remove:
+	docker rmi -f `docker images | grep ${IMAGE_NAME} | tr -s ' ' | cut -d ' ' -f 3`
+	docker rmi -f `docker images -f "dangling=true" -q`
+
+docker-deploy:
+	docker tag ${IMAGE_NAME}:${VERSION} ${FULL_IMAGE_NAME}
+	docker push ${FULL_IMAGE_NAME}
+