Merge pull request #735 from datavisyn/release-15.0.0

Release 15.0.0

.circleci/config.yml

@@ -4,7 +4,7 @@ executors:
   python-executor:
     working_directory: ~/phovea-python
     docker:
-      - image: circleci/python:3.7-buster-node-browsers # for node version see Dockerfile on https://hub.docker.com/r/circleci/python
+      - image: circleci/python:3.10-buster
   node-executor:
     working_directory: ~/phovea-web
     docker:
@@ -15,52 +15,45 @@ jobs:
     executor: python-executor
     steps:
       - checkout
-      - run:
-          name: Show Node.js and npm version
-          command: |
-            node -v
-            npm -v
-      - run:
-          name: Show Python and pip version
-          command: |
-            python --version
-            pip --version
-      - run:
-          name: Install Docker packages from docker_packages.txt
-          command: |
-            (!(test -f docker_packages.txt) || (cat docker_packages.txt | xargs sudo apt-get install -y))
       - restore_cache:
-          key: deps2-{{ .Branch }}-{{ checksum "requirements.txt" }}-{{ checksum "requirements_dev.txt" }}
+          key: deps-{{ .Branch }}-{{ checksum "requirements.txt" }}-{{ checksum "requirements_dev.txt" }}
       - run:
           name: Install pip requirements
           command: |
             virtualenv ~/venv
             . ~/venv/bin/activate
-            pip install -r requirements_dev.txt
-            pip install -r requirements.txt
+            make develop
       - save_cache:
-          key: deps2-{{ .Branch }}-{{ checksum "requirements.txt" }}-{{ checksum "requirements_dev.txt" }}
+          key: deps-{{ .Branch }}-{{ checksum "requirements.txt" }}-{{ checksum "requirements_dev.txt" }}
           paths:
           - ~/venv
       - run:
           name: Force an update of pip dependencies from git repositories # not sure if this is working ?
           command: |
             . ~/venv/bin/activate
-            pip install --upgrade --upgrade-strategy=only-if-needed -r requirements.txt
+            pip install --upgrade --upgrade-strategy=only-if-needed -e .[develop]
       - run:
           name: Show installed pip packages
-          command: pip list || true
+          command: |
+            . ~/venv/bin/activate
+            pip list || true
       - run:
-          name: Remove all from dist folder
+          name: Linting
           command: |
-            rm -rf dist && mkdir dist
+            . ~/venv/bin/activate
+            make lint check-format
       - run:
-          name: Build
+          name: Run tests
           command: |
             . ~/venv/bin/activate
-            npm run dist:python
+            make test
+      - run:
+          name: Build wheel
+          command: |
+            . ~/venv/bin/activate
+            make build
       - store_artifacts:
-          path: dist
+          path: dist_python
           destination: dist-python
       - persist_to_workspace:
           root: ~/.
@@ -88,7 +81,7 @@ jobs:
           name: Publish package
           command: |
             . ~/venv/bin/activate
-            twine upload dist/*
+            twine upload dist_python/*
   web-build:
     executor: node-executor
     steps:
@@ -99,7 +92,7 @@ jobs:
             node -v
             npm -v
       - restore_cache:
-          key: deps3-{{ .Branch }}-{{ checksum "package.json" }}
+          key: deps1-{{ .Branch }}-{{ checksum "package.json" }}
       - run:
           name: Install npm dependencies
           command: npm install
@@ -108,7 +101,7 @@ jobs:
           command: |
             (grep -l '._resolved.: .\(git[^:]*\|bitbucket\):' ./node_modules/*/package.json || true) | xargs -r dirname | xargs -r rm -rf
       - save_cache:
-          key: deps3-{{ .Branch }}-{{ checksum "package.json" }}
+          key: deps1-{{ .Branch }}-{{ checksum "package.json" }}
           paths: ./node_modules
       - run:
           name: Install npm dependencies from git repositories (always get latest commit)
@@ -118,7 +111,7 @@ jobs:
           command: npm list --depth=1 || true
       - run:
           name: Build
-          command: npm run dist:web
+          command: npm run dist
       - store_artifacts:
           path: dist
           destination: dist-web

.gitignore

@@ -5,6 +5,7 @@
 /build/
 /storybook-static/
 /dist/tsBuildInfoFile
+/dist_python/
 /lib/
 *.egg-info/
 *.egg

MANIFEST.in

@@ -0,0 +1 @@
+recursive-include tdp_core *

Makefile

@@ -0,0 +1,58 @@
+.DEFAULT_GOAL := help
+pkg_src = tdp_core
+
+flake8 = flake8 $(pkg_src) setup.py
+isort = isort $(pkg_src) setup.py
+black = black --line-length 140 $(pkg_src) setup.py
+
+.PHONY: all  ## Perform the most common development-time rules
+all: format lint test
+
+.PHONY: ci  ## Run all CI validation steps without making any changes to code
+ci: check-format lint test
+
+.PHONY: format  ## Auto-format the source code
+format:
+	$(isort)
+	$(black)
+
+.PHONY: check-format  ## Check the source code format without changes
+check-format:
+	$(isort) --check-only
+	$(black) --check
+
+.PHONY: lint  ## Run flake8
+lint:
+	$(flake8)
+
+.PHONY: test  ## Run tests
+test:
+	pytest $(pkg_src)
+
+.PHONEY: documentation ## Generate docs
+documentation: 
+	mkdocs build
+
+.PHONY: install  ## Install the requirements
+install:
+	pip install -e .
+
+.PHONY: develop  ## Set up the development environment
+develop:
+	pip install -e .[develop]
+
+.PHONY: build  ## Build a wheel
+build:
+	python setup.py sdist bdist_wheel --dist-dir dist_python
+
+.PHONY: publish  ## Publish the ./dist/* using twine
+publish:
+	pip install twine==3.8.0
+	twine upload --repository-url https://upload.pypi.org/legacy/ dist_python/*
+
+.PHONY: help  ## Display this message
+help:
+	@grep -E \
+		'^.PHONY: .*?## .*$$' $(MAKEFILE_LIST) | \
+		sort | \
+		awk 'BEGIN {FS = ".PHONY: |## "}; {printf "\033[36m%-20s\033[0m %s\n", $$2, $$3}'

deploy/Dockerfile_dev

@@ -0,0 +1,19 @@
+FROM python:3.10-buster
+
+LABEL maintainer="[email protected]"
+WORKDIR /phovea
+
+COPY requirements*.txt ./
+RUN (apt-get update) && \
+    (pip install --no-cache-dir -r requirements.txt) && \
+    (pip install --no-cache-dir -r requirements_dev.txt)
+
+# Create entrypoint installing the volume-mounted workspace repos
+RUN echo '#!/bin/sh\npip install --no-cache-dir --no-deps -r /phovea/requirements_workspace.txt\n$@' > /tmp/entrypoint.sh
+RUN chmod +x /tmp/entrypoint.sh
+ENTRYPOINT [ "/tmp/entrypoint.sh" ]
+
+# Default command is to start the server
+CMD [ "python -m uvicorn tdp_core.server.main:app --reload --host 0.0.0.0 --port 9000" ]
+
+EXPOSE 9000

deploy/docker-compose-debug.partial.yml

@@ -2,4 +2,7 @@ version: '2.0'
 services:
   db_mongo:
     ports:
-      - '27017:27017'
+      - '27017:27017'
+  api:
+    # Override the default server command to add a debugging process. This causes the app to run slower, therefore it is optional.
+    command: 'python -m debugpy --listen 0.0.0.0:5678 -m uvicorn tdp_core.server.main:app --reload --host 0.0.0.0 --port 9000'

deploy/docker-compose.partial.yml

@@ -5,6 +5,26 @@ services:
     - db_mongo
     links:
     - db_mongo:mongo
+  api:
+    build:
+      context: .
+      dockerfile: deploy/Dockerfile_dev
+      args:
+        - http_proxy
+        - HTTP_PROXY
+        - https_proxy
+        - HTTPS_PROXY
+        - no_proxy
+        - NO_PROXY
+    ports:
+      - '9000:9000'
+      # Required port for the python debugger
+      - '5678:5678'
+    volumes:
+    - .:/phovea
+    environment:
+      - ENV=development
+      - PYTHONUNBUFFERED=1
   db_mongo:
     image: mongo:3.2
     volumes: