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Update dependencies and webpack config (#722)
* Update dependencies and webpack config * Change cryptography version * Test with different resource class * Upgrade resource class for all jobs * Added import * Remove environment marker * Skip speck tests * Remove test file * Linting * Updated webpack config and package.json for ES checks * Fix parmed version * Running tests * Update ideogram test wait timer * Add environment marker * Removing environment marker * Re-running tests
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‎.circleci/config.yml‎

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docker:
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- image: percyio/agent
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auth:
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username: dashautomation
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password: $DASH_PAT_DOCKERHUB
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username: dashautomation
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password: $DASH_PAT_DOCKERHUB
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steps:
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- run: percy finalize --all
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node:
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resource_class: medium+
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docker:
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- image: circleci/python:3.7.5-stretch-node
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auth:
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username: dashautomation
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password: $DASH_PAT_DOCKERHUB
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username: dashautomation
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password: $DASH_PAT_DOCKERHUB
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steps:
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- checkout
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- run: echo $PYTHON_VERSION > ver.txt
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- restore_cache:
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key: dep-{{ checksum ".circleci/config.yml" }}-{{ checksum "ver.txt" }}-{{ checksum "dev-requirements.txt" }}
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key: dep-{{ checksum ".circleci/config.yml" }}-{{ checksum "ver.txt" }}-{{ checksum "dev-requirements.txt" }}
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- run:
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name: 🐍 pip dev requirements
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command: |
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sudo pip install virtualenv --upgrade
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python -m venv venv || virtualenv venv && . venv/bin/activate
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python -m pip install --upgrade pip
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pip install --progress-bar off --no-cache-dir -r dev-requirements.txt
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name: 🐍 pip dev requirements
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command: |
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sudo pip install virtualenv --upgrade
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python -m venv venv || virtualenv venv && . venv/bin/activate
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python -m pip install --upgrade pip
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pip install --progress-bar off --no-cache-dir -r dev-requirements.txt
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- save_cache:
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key: dep-{{ checksum ".circleci/config.yml" }}-{{ checksum "ver.txt" }}-{{ checksum "dev-requirements.txt" }}
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paths:
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- venv
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key: dep-{{ checksum ".circleci/config.yml" }}-{{ checksum "ver.txt" }}-{{ checksum "dev-requirements.txt" }}
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paths:
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- venv
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- run:
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name: Check current version of node
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command: node -v
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name: Check current version of node
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command: node -v
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- restore_cache:
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key: deps1-{{ .Branch }}-{{ checksum "package-lock.json" }}
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key: deps1-{{ .Branch }}-{{ checksum "package-lock.json" }}
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name: Install package.json
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command: npm ci
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name: Install package.json
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command: npm ci
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- save_cache:
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key: deps1-{{ .Branch }}-{{ checksum "package-lock.json" }}
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paths:
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- node_modules
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key: deps1-{{ .Branch }}-{{ checksum "package-lock.json" }}
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paths:
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- node_modules
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- run:
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name: Run eslint
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command: ./node_modules/.bin/eslint src
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when: always
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name: Run eslint
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command: ./node_modules/.bin/eslint src
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when: always
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name: Install Dash for package build and build package
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command: |
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python -m venv venv
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. venv/bin/activate
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pip install --upgrade pip
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git clone --depth 1 https://github.com/plotly/dash.git dash-main
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cd dash-main && pip install -e .[dev,testing] --progress-bar off && renderer build && cd ../
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npm run build
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name: Install Dash for package build and build package
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command: |
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python -m venv venv
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. venv/bin/activate
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pip install --upgrade pip
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git clone --depth 1 https://github.com/plotly/dash.git dash-main
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cd dash-main && pip install -e .[dev,testing] --progress-bar off && renderer build && cd ../
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npm run build
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name: Install Dash Bio for using dash_bio.utils
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command: |
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. venv/bin/activate
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python setup.py sdist
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cd dist
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find . -name "*.gz" | xargs pip install --progress-bar off --no-cache-dir --ignore-installed --quiet && cd ..
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no_output_timeout: 20m
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name: Install Dash Bio for using dash_bio.utils
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command: |
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. venv/bin/activate
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python setup.py sdist
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cd dist
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find . -name "*.gz" | xargs pip install --progress-bar off --no-cache-dir --ignore-installed --quiet && cd ..
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no_output_timeout: 20m
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name: Run unit tests
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command: |
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. venv/bin/activate
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cd tests/unit
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python unit_test_data_setup.py
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cd ../../
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npm run test
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name: Run unit tests
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command: |
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. venv/bin/activate
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cd tests/unit
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python unit_test_data_setup.py
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cd ../../
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npm run test
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python-3.6: &test-template
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resource_class: medium+
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docker:
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- image: circleci/python:3.6.9-stretch-node-browsers
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auth:
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username: dashautomation
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password: $DASH_PAT_DOCKERHUB
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username: dashautomation
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password: $DASH_PAT_DOCKERHUB
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environment:
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PYTHON_VERSION: py36
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PERCY_ENABLE: 0
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- run: echo $PYVERSION > ver.txt
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- restore_cache:
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key: deps1-{{ .Branch }}-{{ checksum "dev-requirements.txt" }}-{{ checksum "tests/requirements.txt" }}-{{ checksum "ver.txt" }}-{{ checksum ".circleci/config.yml" }}
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key: deps1-{{ .Branch }}-{{ checksum "dev-requirements.txt" }}-{{ checksum "tests/requirements.txt" }}-{{ checksum "ver.txt" }}-{{ checksum ".circleci/config.yml" }}
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name: Create virtualenv
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command: |
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python3 -m venv venv
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name: Create virtualenv
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command: |
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python3 -m venv venv
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name: Install requirements
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command: |
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. venv/bin/activate
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pip install --upgrade pip
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pip install --progress-bar off -r tests/requirements.txt --quiet
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no_output_timeout: 20m
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name: Install requirements
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command: |
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. venv/bin/activate
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pip install --upgrade pip
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pip install --progress-bar off -r tests/requirements.txt --quiet
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no_output_timeout: 20m
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- save_cache:
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key: deps1-{{ .Branch }}-{{ checksum "dev-requirements.txt" }}-{{ checksum "tests/requirements.txt" }}-{{ checksum "ver.txt" }}-{{ checksum ".circleci/config.yml" }}
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paths:
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- venv
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key: deps1-{{ .Branch }}-{{ checksum "dev-requirements.txt" }}-{{ checksum "tests/requirements.txt" }}-{{ checksum "ver.txt" }}-{{ checksum ".circleci/config.yml" }}
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paths:
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- venv
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name: Install Dash
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command: |
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. venv/bin/activate
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git clone --depth 1 https://github.com/plotly/dash.git dash-main
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cd dash-main && pip install -e .[dev,testing] --progress-bar off && renderer build && cd ../
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name: Install Dash
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command: |
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. venv/bin/activate
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git clone --depth 1 https://github.com/plotly/dash.git dash-main
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cd dash-main && pip install -e .[dev,testing] --progress-bar off && renderer build && cd ../
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name: Run pylint
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command: |
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. venv/bin/activate
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pylint tests/ dash_bio/component_factory/ dash_bio/utils/
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when: always
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name: Run pylint
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command: |
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. venv/bin/activate
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pylint tests/ dash_bio/component_factory/ dash_bio/utils/
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when: always
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name: Run flake8
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command: |
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. venv/bin/activate
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flake8 --max-line-length=100 tests/ dash_bio/component_factory/ dash_bio/utils/
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when: always
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name: Run flake8
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command: |
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. venv/bin/activate
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flake8 --max-line-length=100 tests/ dash_bio/component_factory/ dash_bio/utils/
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when: always
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name: Run integration tests
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command: |
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. venv/bin/activate
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npm ci
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npm run build
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python setup.py sdist
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cd dist
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find . -name "*.gz" | xargs pip install --progress-bar off --no-cache-dir --ignore-installed --quiet && cd ..
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pytest --nopercyfinalize tests/integration
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name: Run integration tests
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command: |
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. venv/bin/activate
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npm ci
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npm run build
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python setup.py sdist
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cd dist
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find . -name "*.gz" | xargs pip install --progress-bar off --no-cache-dir --ignore-installed --quiet && cd ..
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pytest --nopercyfinalize tests/integration
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no_output_timeout: 20m
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name: Run unit tests
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command: |
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python -m venv venv
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. venv/bin/activate
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pytest tests/unit
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name: Run unit tests
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command: |
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python -m venv venv
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. venv/bin/activate
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pytest tests/unit
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python-3.7:
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<<: *test-template
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resource_class: medium+
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docker:
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- image: circleci/python:3.7.5-stretch-node-browsers
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auth:
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username: dashautomation
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password: $DASH_PAT_DOCKERHUB
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username: dashautomation
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password: $DASH_PAT_DOCKERHUB
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environment:
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PYTHON_VERSION: py37
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PERCY_ENABLE: 1
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PERCY_PARALLEL_TOTAL: -1
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workflows:
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version: 2
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build:
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jobs:
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- python-3.6
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- python-3.7
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- node
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- percy-finalize:
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requires:
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version: 2
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build:
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jobs:
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- python-3.6
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- python-3.7
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- node
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- percy-finalize:
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requires:
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- python-3.7

‎.eslintrc‎

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#"flowVersion": "0.53" // Flow version
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}
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},
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"parser": "babel-eslint",
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"parser": "@babel/eslint-parser",
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"parserOptions": {
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"ecmaVersion": 6,
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"sourceType": "module",
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"react/no-did-update-set-state": ["error"],
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"react/no-direct-mutation-state": ["error"],
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"react/no-is-mounted": ["error"],
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"react/no-unknown-property": ["error"],
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"react/no-unknown-property": ["error", { "ignore": ["eventDatum", "eventdatum", "config", "layout", "tracks"] }],
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"react/prefer-es6-class": ["error", "always"],
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"react/prop-types": "error",
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"valid-jsdoc": ["off"],

‎NAMESPACE‎

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export(dashbioPileup)
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export(dashbioSequenceViewer)
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export(dashbioSpeck)
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export(dashbioVolcano)
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export(dashbioManhattan)
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export(dashbioVolcano)
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import(manhattanly)
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import(dash)

‎R/dashbioAlignmentChart.R‎

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# AUTO GENERATED FILE - DO NOT EDIT
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#' @export
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dashbioAlignmentChart <- function(id=NULL, colorscale=NULL, conservationcolor=NULL, conservationcolorscale=NULL, conservationmethod=NULL, conservationopacity=NULL, correctgap=NULL, data=NULL, eventDatum=NULL, extension=NULL, gapcolor=NULL, gapcolorscale=NULL, gapopacity=NULL, groupbars=NULL, height=NULL, loading_state=NULL, numtiles=NULL, opacity=NULL, overview=NULL, scrollskip=NULL, sequenceIds=NULL, showconsensus=NULL, showconservation=NULL, showgap=NULL, showid=NULL, showlabel=NULL, textcolor=NULL, textsize=NULL, tickstart=NULL, ticksteps=NULL, tileheight=NULL, tilewidth=NULL, width=NULL) {
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props <- list(id=id, colorscale=colorscale, conservationcolor=conservationcolor, conservationcolorscale=conservationcolorscale, conservationmethod=conservationmethod, conservationopacity=conservationopacity, correctgap=correctgap, data=data, eventDatum=eventDatum, extension=extension, gapcolor=gapcolor, gapcolorscale=gapcolorscale, gapopacity=gapopacity, groupbars=groupbars, height=height, loading_state=loading_state, numtiles=numtiles, opacity=opacity, overview=overview, scrollskip=scrollskip, sequenceIds=sequenceIds, showconsensus=showconsensus, showconservation=showconservation, showgap=showgap, showid=showid, showlabel=showlabel, textcolor=textcolor, textsize=textsize, tickstart=tickstart, ticksteps=ticksteps, tileheight=tileheight, tilewidth=tilewidth, width=width)

‎R/dashbioCircos.R‎

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# AUTO GENERATED FILE - DO NOT EDIT
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#' @export
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dashbioCircos <- function(id=NULL, config=NULL, enableDownloadSVG=NULL, enableZoomPan=NULL, eventDatum=NULL, layout=NULL, loading_state=NULL, selectEvent=NULL, size=NULL, style=NULL, tracks=NULL) {
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props <- list(id=id, config=config, enableDownloadSVG=enableDownloadSVG, enableZoomPan=enableZoomPan, eventDatum=eventDatum, layout=layout, loading_state=loading_state, selectEvent=selectEvent, size=size, style=style, tracks=tracks)

‎R/dashbioFornaContainer.R‎

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# AUTO GENERATED FILE - DO NOT EDIT
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#' @export
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dashbioFornaContainer <- function(id=NULL, allowPanningAndZooming=NULL, colorScheme=NULL, customColors=NULL, height=NULL, hoverPattern=NULL, loading_state=NULL, nodeFillColor=NULL, sequences=NULL, width=NULL) {
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props <- list(id=id, allowPanningAndZooming=allowPanningAndZooming, colorScheme=colorScheme, customColors=customColors, height=height, hoverPattern=hoverPattern, loading_state=loading_state, nodeFillColor=nodeFillColor, sequences=sequences, width=width)

‎R/dashbioIdeogram.R‎

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# AUTO GENERATED FILE - DO NOT EDIT
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#' @export
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dashbioIdeogram <- function(id=NULL, accessToken=NULL, ancestors=NULL, annotationHeight=NULL, annotationTracks=NULL, annotations=NULL, annotationsColor=NULL, annotationsData=NULL, annotationsLayout=NULL, annotationsPath=NULL, assembly=NULL, barWidth=NULL, brush=NULL, brushData=NULL, chrHeight=NULL, chrMargin=NULL, chrWidth=NULL, chromosomeScale=NULL, chromosomes=NULL, className=NULL, container=NULL, dataDir=NULL, demarcateCollinearChromosomes=NULL, filterable=NULL, fullChromosomeLabels=NULL, geometry=NULL, heatmaps=NULL, histogramScaling=NULL, homology=NULL, legend=NULL, loading_state=NULL, organism=NULL, orientation=NULL, perspective=NULL, ploidy=NULL, ploidyDesc=NULL, rangeSet=NULL, resolution=NULL, rotatable=NULL, rotated=NULL, rows=NULL, sex=NULL, showAnnotTooltip=NULL, showBandLabels=NULL, showChromosomeLabels=NULL, showFullyBanded=NULL, showNonNuclearChromosomes=NULL, style=NULL) {
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props <- list(id=id, accessToken=accessToken, ancestors=ancestors, annotationHeight=annotationHeight, annotationTracks=annotationTracks, annotations=annotations, annotationsColor=annotationsColor, annotationsData=annotationsData, annotationsLayout=annotationsLayout, annotationsPath=annotationsPath, assembly=assembly, barWidth=barWidth, brush=brush, brushData=brushData, chrHeight=chrHeight, chrMargin=chrMargin, chrWidth=chrWidth, chromosomeScale=chromosomeScale, chromosomes=chromosomes, className=className, container=container, dataDir=dataDir, demarcateCollinearChromosomes=demarcateCollinearChromosomes, filterable=filterable, fullChromosomeLabels=fullChromosomeLabels, geometry=geometry, heatmaps=heatmaps, histogramScaling=histogramScaling, homology=homology, legend=legend, loading_state=loading_state, organism=organism, orientation=orientation, perspective=perspective, ploidy=ploidy, ploidyDesc=ploidyDesc, rangeSet=rangeSet, resolution=resolution, rotatable=rotatable, rotated=rotated, rows=rows, sex=sex, showAnnotTooltip=showAnnotTooltip, showBandLabels=showBandLabels, showChromosomeLabels=showChromosomeLabels, showFullyBanded=showFullyBanded, showNonNuclearChromosomes=showNonNuclearChromosomes, style=style)

‎R/dashbioIgv.R‎

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# AUTO GENERATED FILE - DO NOT EDIT
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#' @export
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dashbioIgv <- function(id=NULL, className=NULL, genome=NULL, loading_state=NULL, locus=NULL, minimumBases=NULL, reference=NULL, style=NULL, tracks=NULL) {
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props <- list(id=id, className=className, genome=genome, loading_state=loading_state, locus=locus, minimumBases=minimumBases, reference=reference, style=style, tracks=tracks)

‎R/dashbioJsme.R‎

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# AUTO GENERATED FILE - DO NOT EDIT
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#' @export
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dashbioJsme <- function(id=NULL, eventSmiles=NULL, height=NULL, loading_state=NULL, options=NULL, smiles=NULL, style=NULL, width=NULL) {
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props <- list(id=id, eventSmiles=eventSmiles, height=height, loading_state=loading_state, options=options, smiles=smiles, style=style, width=width)

‎R/dashbioMolecule2dViewer.R‎

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# AUTO GENERATED FILE - DO NOT EDIT
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#' @export
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dashbioMolecule2dViewer <- function(id=NULL, height=NULL, loading_state=NULL, modelData=NULL, scrollZoom=NULL, selectedAtomIds=NULL, width=NULL) {
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props <- list(id=id, height=height, loading_state=loading_state, modelData=modelData, scrollZoom=scrollZoom, selectedAtomIds=selectedAtomIds, width=width)

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