Merge pull request #352 from vanvalenlab/0.4-dev

Merge 0.4-dev before releasing 0.4

Author: tddough98

.env.example

@@ -3,9 +3,67 @@
 
 name: tests
 
-on: [push, pull_request]
+on: [pull_request]
 
 jobs:
+  e2e-tests:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v2
+
+      - name: Set up Python
+        uses: actions/setup-python@v2
+        with:
+          working-directory: backend
+          python-version: 3.8
+
+      - name: Cache pip
+        uses: actions/cache@v2
+        with:
+          working-directory: backend
+          # This path is specific to Ubuntu
+          path: ~/.cache/pip
+          # Look to see if there is a cache hit for the corresponding requirements file
+          key: ${{ runner.os }}-pip-${{ hashFiles('requirements.txt') }}
+          restore-keys: |
+            ${{ runner.os }}-pip-
+            ${{ runner.os }}-
+
+      - name: Install Dependencies
+        working-directory: backend
+        run: |
+          python -m pip install --upgrade pip
+          pip install -r requirements.txt
+          pip install -r requirements-test.txt
+
+      - name: Cypress run
+        uses: cypress-io/github-action@v4
+        env:
+          AWS_ACCESS_KEY_ID: ${{ secrets.AWS_ACCESS_KEY_ID }}
+          AWS_SECRET_ACCESS_KEY: ${{ secrets.AWS_SECRET_ACCESS_KEY }}
+        with:
+          working-directory: frontend
+          start: |
+            npm run cypress:frontend
+            npm run cypress:backend
+          wait-on: "http://localhost:3000, http://localhost:5000/health"
+          spec: |
+            cypress/e2e/label.cy.js
+            cypress/e2e/caliban.cy.js
+            cypress/e2e/spots.cy.js
+
+      - name: Cypress Coveralls
+        uses: coverallsapp/github-action@master
+        env:
+          COVERALLS_REPO_TOKEN: ${{ secrets.COVERALLS_REPO_TOKEN }}
+        with:
+          base-path: frontend
+          path-to-lcov: frontend/coverage/lcov.info
+          github-token: ${{ secrets.github_token }}
+          flag-name: cypress
+          parallel: true
+
   frontend-tests:
     runs-on: ubuntu-latest
 
@@ -24,22 +82,22 @@ jobs:
       - name: Cache node_modules
         uses: actions/cache@v2
         with:
-          path: "visualizer/**/node_modules"
-          key: ${{ runner.os }}-modules-${{ hashFiles('visualizer/**/yarn.lock') }}
+          path: "frontend/**/node_modules"
+          key: ${{ runner.os }}-modules-${{ hashFiles('frontend/**/yarn.lock') }}
           restore-keys: |
             ${{ runner.os }}-yarn-
             ${{ runner.os }}-
 
       - name: Yarn Install
-        working-directory: visualizer
+        working-directory: frontend
         run: yarn
 
       - name: Lint
-        working-directory: visualizer
+        working-directory: frontend
         run: yarn lint
 
       - name: Unit Tests
-        working-directory: visualizer
+        working-directory: frontend
         run: yarn test --coverage
         env:
           CI: true
@@ -49,8 +107,8 @@ jobs:
         env:
           COVERALLS_REPO_TOKEN: ${{ secrets.COVERALLS_REPO_TOKEN }}
         with:
-          base-path: visualizer
-          path-to-lcov: visualizer/coverage/lcov.info
+          base-path: frontend
+          path-to-lcov: frontend/coverage/lcov.info
           github-token: ${{ secrets.github_token }}
           flag-name: node-${{ matrix.node-version }}
           parallel: true
@@ -60,19 +118,21 @@ jobs:
 
     strategy:
       matrix:
-        python-version: ["3.8", "3.9", "3.10"]
+        python-version: ["3.8"]
 
     steps:
       - uses: actions/checkout@v2
 
       - name: Set up Python ${{ matrix.python-version }}
         uses: actions/setup-python@v2
         with:
+          working-directory: backend
           python-version: ${{ matrix.python-version }}
 
       - name: Cache pip
         uses: actions/cache@v2
         with:
+          working-directory: backend
           # This path is specific to Ubuntu
           path: ~/.cache/pip
           # Look to see if there is a cache hit for the corresponding requirements file
@@ -82,27 +142,30 @@ jobs:
             ${{ runner.os }}-
 
       - name: Install Dependencies
+        working-directory: backend
         run: |
           python -m pip install --upgrade pip
           pip install -r requirements.txt
           pip install -r requirements-test.txt
 
       - name: Run PyTest
+        working-directory: backend
         run: |
-          pytest deepcell_label --cov deepcell_label
+          PYTHONPATH=deepcell_label pytest deepcell_label --cov deepcell_label
 
       - name: Coveralls
         if: env.COVERALLS_REPO_TOKEN != null
         env:
           COVERALLS_REPO_TOKEN: ${{ secrets.COVERALLS_REPO_TOKEN }}
           COVERALLS_FLAG_NAME: python-${{ matrix.python-version }}
           COVERALLS_PARALLEL: true
+        working-directory: backend
         run: |
           coveralls
 
   coveralls:
     name: Finish Coveralls
-    needs: [frontend-tests, backend-tests]
+    needs: [e2e-tests, frontend-tests, backend-tests]
     runs-on: ubuntu-latest
     steps:
       - name: Coveralls Finished

.github/workflows/tests.yaml

@@ -124,9 +124,9 @@ venv.bak/
 node_modules
 
 # Elastic Beanstalk Files
-.elasticbeanstalk/*
-!.elasticbeanstalk/*.cfg.yml
-!.elasticbeanstalk/*.global.yml
+backend/.elasticbeanstalk/*
+!backend/.elasticbeanstalk/*.cfg.yml
+!backend/.elasticbeanstalk/*.global.yml
 
 # VS Code
 settings.json
@@ -162,5 +162,4 @@ yarn-debug.log*
 yarn-error.log*
 package-lock.json
 
-# Webpack builds javascript files into deepcell_label/static
-deepcell_label/static/js/*
+.nyc_output

.gitignore

@@ -4,81 +4,10 @@
 [![Coverage Status](https://coveralls.io/repos/github/vanvalenlab/deepcell-label/badge.svg?branch=main)](https://coveralls.io/github/vanvalenlab/deepcell-label?branch=main)
 [![Apache 2.0](https://img.shields.io/badge/License-Apache%202.0-blue.svg)](https://github.com/vanvalenlab/deepcell-label/blob/main/LICENSE)
 
-DeepCell Label is a web-based tool to visualize and label cells in biological images, and is tailored for cell segmentation. Label works with multiplexed images, 3D image stacks, and time-lapse movies. The tool can label images from scratch, or correct labels from model predictions or existing datasets.
+DeepCell Label is a web-based tool to visualize and label biological images. It can segment an image, assign cells across a timelapse, and track divisions in multiplexed images, 3D image stacks, and time-lapse movies.
 
-DeepCell Label distributes images and labeling tools through a browser, providing easy access to crowdsource data labeling and to review, correct, and curate labels as a domain expert.
+As it's available through a browser, DeepCell Label can crowdsource data labeling or review, correct, and curate labels as a domain expert.
 
-DeepCell Label is built with [React](https://reactjs.org/), [XState](https://xstate.js.org/docs/), and [Flask](https://flask.palletsprojects.com/en/2.0.x/) and [runs locally](#local-use) or [on the cloud](#cloud-deployment) (e.g. with [AWS Elastic Beanstalk](https://aws.amazon.com/elasticbeanstalk/)).
+The site is built with [React](https://reactjs.org/), [XState](https://xstate.js.org/docs/), and [Flask](https://flask.palletsprojects.com/en/2.0.x/) and [runs locally](/documentation/LOCAL_USE.md) or [on the cloud](/documentation/DEPLOYMENT.md).
 
-Visit [label.deepcell.org](https://label.deepcell.org) and create a project from an example file or upload a .tiff, .png, or .npz. Detailed instructions on how to use the app are in the dropdown instructions tab when working in DeepCell Label.
-
-## Local use
-
-To run DeepCell Label locally, you will set up the client and the server from your computer. If you haven't worked with Python or Javascript projects before, follow the [first time setup instructions](FIRST_TIME_SETUP.md) to install Python and Node.js.
-
-To start, clone the repository with:
-
-```bash
-git clone https://github.com/vanvalenlab/deepcell-label.git
-```
-
-and open the repository with:
-
-```bash
-cd deepcell-label
-```
-
-### Set up Flask server
-
-The backend is a Flask HTTP API that stores and updates project data.
-
-#### Run Python backend
-
-We recommend using Python virtual environment, either with [conda](https://conda.io/projects/conda/en/latest/user-guide/tasks/manage-environments.html) or [venv](https://docs.python.org/3/library/venv.html).
-After setting up a virtual environment, install the Python dependencies with:
-
-```bash
-pip install -r requirements.txt
-pip install -r requirements-test.txt
-```
-
-Flask requires some environment variables to be set, like [FLASK_APP](https://flask.palletsprojects.com/en/2.0.x/cli/). We need to set `export FLASK_APP=application` in the terminal or in an `.env` file. There is an example `.env.example` with FLASK_APP already set. Make a copy and rename the file `.env`. Then, start the server with:
-
-```bash
-flask run
-```
-
-By default, DeepCell Label creates a temporary database in `/tmp`. Change `SQLALCHEMY_DATABASE_URI` in your `.env`, for example `SQLALCHEMY_DATABASE_URI=sqlite:///~/Documents/deepcell_label.db`, to make a persistent database in another location.
-
-#### Run with Docker
-
-The backend can also be containerized with [Docker](https://www.docker.com). To build a production-ready Docker image, run:
-
-```bash
-docker build -t vanvalenlab/deepcell-label:$USER
-```
-
-The built image can run the backend on port 5000 with:
-
-```bash
-docker run -p 5000:5000 -it vanvalenlab/deepcell-label:$USER
-```
-
-Envrionment variables like `SQLALCHEMY_DATABASE_URI` can be passed to the run command using the [environment variable flags](https://docs.docker.com/engine/reference/commandline/run/#set-environment-variables--e---env---env-file): `-e` and `--env`.
-
-### Set up React client
-
-Once the server is running, we need to set up the frontend. Install the dependencies for the frontend with:
-
-```bash
-cd visualizer
-yarn
-```
-
-Then, start the frontend with:
-
-```bash
-yarn start
-```
-
-Visit [localhost:3000](http://localhost:3000) to see the DeepCell Label homepage.
+Visit [label.deepcell.org](https://label.deepcell.org) to create a project from an example file or your own .tiff, .png, or .npz. Dropdown instructions are available while working on a project in DeepCell Label.

README.md

@@ -16,14 +16,6 @@ omit =
     **/*_test.py
     env/**/*.py
     venv/**/*.py
+    .venv/**/*.py
     ENV/**/*.py
     VENV/**/*.py
-    desktop/env/**/*.py
-    desktop/venv/**/*.py
-    desktop/ENV/**/*.py
-    desktop/VENV/**/*.py
-    browser/env/**/*.py
-    browser/venv/**/*.py
-    browser/ENV/**/*.py
-    browser/VENV/**/*.py
-    browser/conftest.py

.coveragerc backend/.coveragerc.coveragerc renamed to backend/.coveragerc

@@ -5,7 +5,7 @@ Dockerfile
 .vscode
 .gitignore
 .dockerignore
-visualizer
+frontend
 
 /credentials
 /cache