Merge branch 'main' into dependabot/npm_and_yarn/taxonomy-editor-fron…

…tend/decode-uri-component-0.2.2

.env

@@ -12,6 +12,11 @@ TAXONOMY_EDITOR_EXPOSE=127.0.0.1:8091
 # this one is needed only in dev, to tell nginx and fastapi, which port urls should include
 # it must either start with : or be empty
 PUBLIC_TAXONOMY_EDITOR_PORT=:8091
+# this one is used to expose the websocket in dev and shoudl match PUBLIC_TAXONOMY_EDITOR_PORT but without leading ":"
+WDS_SOCKET_PORT=8091
+# API scheme is useful because, in prod, we have to proxy and already proxied request
+# and loose the original scheme
+API_SCHEME=http
 
 # This is the PAT (Personal Access Token)
 # to create PRs on openfoodfacts-server github project (must be able to read-write PRs)
@@ -24,3 +29,13 @@ REPO_URI=openfoodfacts/openfoodfacts-server
 # eventually set this to your local user id to avoid permissions errors
 # USER_UID=1000
 # USER_GID=1000
+
+# Neo4J configurations
+NEO4J_BOLT_EXPOSE=127.0.0.1:7687
+NEO4J_ADMIN_EXPOSE=127.0.0.1:7474
+# note: in prod, heap_initial__size and max__size should match, but it's ok like that for dev
+NEO4J_server_memory_heap_initial__size=512M
+NEO4J_server_memory_heap_max__size=2G
+NEO4J_server_memory_pagecache_size=1G
+NEO4J_db_memory_transaction_total_max=512M
+

.github/workflows/auto-assign-pr.yml

@@ -12,4 +12,4 @@ jobs:
   assign-author:
     runs-on: ubuntu-latest
     steps:
-      - uses: toshimaru/auto-author-assign@v1.6.1
+      - uses: toshimaru/auto-author-assign@v2.0.1

.github/workflows/codeql.yml

@@ -38,7 +38,7 @@ jobs:
 
     steps:
     - name: Checkout repository
-      uses: actions/checkout@v3
+      uses: actions/checkout@v4
 
     # Initializes the CodeQL tools for scanning.
     - name: Initialize CodeQL

.github/workflows/container-build.yml

@@ -3,7 +3,7 @@ name: Docker Image Build CI
 on:
   push:
     branches:
-    - $default-branch
+    - main
     - deploy-*
     tags:
     - v*.*.*
@@ -17,7 +17,7 @@ jobs:
           - taxonomy_frontend
           - taxonomy_api
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v4
       with:
         fetch-depth: 1
 
@@ -61,7 +61,7 @@ jobs:
           type=sha,format=long
 
     - name: Build and push
-      uses: docker/build-push-action@v2
+      uses: docker/build-push-action@v4
       with:
         context: ${{ env.build_context }}
         push: true

.github/workflows/container-deploy.yml

@@ -69,7 +69,7 @@ jobs:
         timeoutSeconds: 600 # 10m
 
     - name: Do something if build isn't launched
-      if: steps.wait-build-frontend.outputs.conclusion == 'does not exist' || steps.wait-build-api.outputs.conclusion == 'does not exist'
+      if: steps.wait-build-frontend.outputs.conclusion == 'not found' || steps.wait-build-api.outputs.conclusion == 'not found'
       run: echo job does not exist && true
 
     - name: Do something if build fail
@@ -134,11 +134,19 @@ jobs:
           echo "COMPOSE_FILE=docker-compose.yml;docker/prod.yml" >> .env
           echo "DOCKER_TAG=sha-${{ github.sha }}" >> .env
 
+          # Neo4j configuration
+          echo "NEO4J_server_memory_heap_initial__size=3G" >> .env
+          echo "NEO4J_server_memory_heap_max__size=3G" >> .env
+          echo "NEO4J_server_memory_pagecache_size=2G" >> .env
+          # we don't want transaction to grow too big
+          echo "NEO4J_db_memory_transaction_total_max=1G" >> .env
           # App environment variables
           echo "TAXONOMY_EDITOR_EXPOSE=${{ env.TAXONOMY_EDITOR_EXPOSE }}" >> .env
           echo "TAXONOMY_EDITOR_DOMAIN=${{ env.TAXONOMY_EDITOR_DOMAIN }}" >> .env
           # should be blank in production
           echo "PUBLIC_TAXONOMY_EDITOR_PORT=" >> .env
+          # we use https
+          echo "API_SCHEME=https" >> .env
           # the PAT is environment dependant
           # and must have write access to PRs on the target repo (see REPO_URI)
           echo "GITHUB_PAT=${{ secrets.OFF_SERVER_GITHUB_PAT }}" >> .env
@@ -212,7 +220,7 @@ jobs:
           cd ${{ matrix.env }}
           docker system prune -af
 
-    - uses: frankie567/grafana-annotation-action@v1.0.2
+    - uses: frankie567/grafana-annotation-action@v1.0.3
       if: ${{ always() }}
       with:
         apiHost: https://grafana.openfoodfacts.org

.github/workflows/dependency-review.yml

@@ -15,6 +15,6 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: 'Checkout Repository'
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
       - name: 'Dependency Review'
         uses: actions/dependency-review-action@v3

.github/workflows/github-projects-for-openfoodfacts-design.yml

@@ -16,3 +16,9 @@ jobs:
           github-token: ${{ secrets.ADD_TO_PROJECT_PAT }}
           labeled: mockups available, needs mockup
           label-operator: OR
+      - uses: actions/add-to-project@main
+        with:
+          project-url: https://github.com/orgs/openfoodfacts/projects/25 # Add issue to the documentation project
+          github-token: ${{ secrets.ADD_TO_PROJECT_PAT }}
+          labeled: documentation
+          label-operator: OR

.github/workflows/pull_request.yml

@@ -4,48 +4,15 @@ on:
   pull_request:
 
 jobs:
-  # Parser quality
-  parser-checks:
-    runs-on: ubuntu-latest
-    strategy:
-      matrix:
-        python-version:
-        - "3.10"
-        - "3.9"
-
-    steps:
-      #----------------------------------------------
-      #       check-out repo and set-up python
-      #----------------------------------------------
-      - name: Check out repository
-        uses: actions/checkout@v3
-      - name: build docker
-        run: |
-          export USER_UID=$(id -u)
-          export USER_GID=$(id -g)
-          DOCKER_BUILDKIT=1 docker-compose build
-      - name: Set up python
-        uses: actions/setup-python@v4
-        with:
-          python-version: ${{ matrix.python-version }}
-      - name: Install Packages
-        run: |
-          cd parser
-          pip install -r requirements-dev.txt
-      - name: Make checks
-        run: |
-          cd parser
-          make checks
-
-  # taxonomy editor quality
+  # taxonomy editor quality for frontend and backend
   taxonomy-editor-checks:
     runs-on: ubuntu-latest
     steps:
       #----------------------------------------------
       #       check-out repo
       #----------------------------------------------
       - name: Check out repository
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
       - name: Make checks
         run: |
           export USER_UID=$(id -u)

CONTRIBUTING.md

@@ -55,7 +55,7 @@ Ready to contribute code? Here's how to set up Taxonomy Editor for local develop
     ```
     git clone git@github.com:your_name_here/taxonomy-editor.git
     ```
-3. Follow [install documentation](./docs/explanations/docker-compose-setup.md)
+3. Follow [install documentation](./doc/introduction/setup-dev.md)
 
 4. code!
 
@@ -96,4 +96,4 @@ Before you submit a pull request, check that it meets these guidelines:
 2. If the pull request adds functionality, the docs should be updated. Put your new functionality into a function with a docstring.
 
 
-This contributing page was adapted from [Pyswarms documentation](https://github.com/ljvmiranda921/pyswarms/blob/master/CONTRIBUTING.rst).
+This contributing page was adapted from [Pyswarms documentation](https://github.com/ljvmiranda921/pyswarms/blob/master/CONTRIBUTING.rst).

Makefile

@@ -1,3 +1,11 @@
+# to suppress the path translation in Windows
+export MSYS_NO_PATHCONV=1
+
+ifeq ($(findstring cmd.exe,$(SHELL)),cmd.exe)
+    $(error "We do not suppport using cmd.exe on Windows, please run in a 'git bash' console")
+endif
+
+# use bash everywhere !
 SHELL := /bin/bash
 ENV_FILE ?= .env
 
@@ -13,22 +21,45 @@ export DOCKER_BUILDKIT=1
 export COMPOSE_DOCKER_CLI_BUILD=1
 
 DOCKER_COMPOSE=docker-compose --env-file=${ENV_FILE}
-DOCKER_COMPOSE_TEST=COMPOSE_PROJECT_NAME=test_taxonomy docker-compose --env-file=${ENV_FILE}
+# tweak some config to avoid port conflicts
+DOCKER_COMPOSE_TEST=COMPOSE_PROJECT_NAME=test_taxonomy NEO4J_ADMIN_EXPOSE=127.0.0.1:7475 NEO4J_BOLT_EXPOSE=127.0.0.1:7688 docker-compose --env-file=${ENV_FILE}
 
 .PHONY: tests
 
+#------------#
+# dev setup  #
+#------------#
+
+build:
+	@echo "🍜 Building docker images"
+	${DOCKER_COMPOSE} build
+	@echo "🍜 Project setup done"
+
+up:
+	@echo "🍜 Running project (ctrl+C to stop)"
+	${DOCKER_COMPOSE} up
+
+dev: build up
+
+
 #-----------#
 # dev tools #
 #-----------#
 
+
 # lint code
-lint: backend_lint
+lint: backend_lint frontend_lint
 
 backend_lint:
 	@echo "🍜 Linting python code"
 	${DOCKER_COMPOSE} run --rm taxonomy_api isort .
 	${DOCKER_COMPOSE} run --rm taxonomy_api black .
 
+frontend_lint:
+	@echo "🍜 Linting react code"
+	${DOCKER_COMPOSE} run --rm taxonomy_node npx prettier -w src/
+
+
 # check code quality
 quality: backend_quality frontend_quality
 
@@ -40,15 +71,20 @@ backend_quality:
 
 frontend_quality:
 	@echo "🍜 Quality checks JS"
+	${DOCKER_COMPOSE} run --rm taxonomy_node npx prettier -c src/
 	${DOCKER_COMPOSE} run --rm -e CI=true taxonomy_node npm run build
+# restore the .empty file (if possible)
+	git checkout taxonomy-editor-frontend/build/.empty || true
+
 
 
 tests: backend_tests
 
 backend_tests:
 	@echo "🍜 Running python tests"
 	${DOCKER_COMPOSE_TEST} up -d neo4j
-	${DOCKER_COMPOSE_TEST}  run --rm taxonomy_api pytest . /parser
+	${DOCKER_COMPOSE_TEST}  run --rm taxonomy_api pytest /parser /parser
+	${DOCKER_COMPOSE_TEST}  run --rm taxonomy_api pytest /code/tests
 	${DOCKER_COMPOSE_TEST} stop neo4j
 
 checks: quality tests
@@ -61,4 +97,3 @@ checks: quality tests
 create_external_volumes:
 	@echo "🍜 Creating external volumes (production only) …"
 	docker volume create ${COMPOSE_PROJECT_NAME}_neo4j-data
-