Upgrade DeepCell to 0.9.2 and set up CI/CD workflows (#14)

* Update `.gitignore` and `.dockerignore` and add several other repository config files

* Update default deepcell version to 0.9.2.

* Rename `main.py` to `run_app.py`

* Refactor `MultiplexSegmentation` to `Mesmer`

* Import `get_image` from `deepcell.utils.io_utils` (Fixes #12)

* Add GitHub Actions workflows from `vanvalenlab/deepcell-tf`

* Replace `skimage` with `tifffile`

* New `deepcell_applications` for application-generalized functions

* Refactor mpp to image_mpp to match mesmer signature.

* Pin the `deepcell` version to prevent breaking changes.

* Update README with new parameters

* Refactor `get_arg_parser` for application-based subparsers.

* Add badges to README

* Add batch_size as a possible inference value.

Co-authored-by: Noah F. Greenwald <noahfgreenwald@gmail.com>

.coveragerc

@@ -0,0 +1,16 @@
+# .coveragerc to control coverage.py
+[report]
+# Regexes for lines to exclude from consideration
+exclude_lines =
+    except ImportError
+
+    # Don't complain if tests don't hit defensive assertion code:
+    raise AssertionError
+    raise NotImplementedError
+
+ignore_errors = True
+fail_under = 50
+show_missing = True
+
+omit =
+    **/*_test.py

.dockerignore

@@ -1,6 +1,7 @@
 ### Deepcell Specific ###
 lib_dormant
 app_dormant
+output/
 
 ### Development config files ###
 .pylintrc
@@ -55,6 +56,7 @@ nosetests.xml
 coverage.xml
 *,cover
 .hypothesis/
+.pytest_cache/
 
 # Translations
 *.mo
@@ -88,3 +90,6 @@ target/
 venv/
 ENV/
 env/
+
+# IDEs
+.vscode/

.editorconfig

@@ -0,0 +1,33 @@
+# EditorConfig is awesome: http://EditorConfig.org
+
+# top-most EditorConfig file
+root = true
+
+# Unix-style newlines with a newline ending every file
+[*]
+end_of_line = lf
+insert_final_newline = true
+
+# Matches multiple files with brace expansion notation
+# Set default charset
+[*.{js,py}]
+charset = utf-8
+
+# 4 space indentation
+[*.py]
+indent_style = space
+indent_size = 4
+
+# Tab indentation (no size specified)
+[Makefile]
+indent_style = tab
+
+# Indentation override for all JS under lib directory
+[lib/**.js]
+indent_style = space
+indent_size = 2
+
+# Matches the exact files either package.json or .travis.yml
+[{package.json,.travis.yml}]
+indent_style = space
+indent_size = 2

.github/release-drafter.yml

@@ -0,0 +1,55 @@
+name-template: '$RESOLVED_VERSION'
+
+tag-template: '$RESOLVED_VERSION'
+
+version-template: '$MAJOR.$MINOR.$PATCH'
+
+categories:
+  - title: '🚀 Features'
+    labels:
+      - 'feature'
+      - 'enhancement'
+  - title: '🐛 Bug Fixes'
+    labels:
+      - 'fix'
+      - 'bugfix'
+      - 'bug'
+      - 'hotfix'
+  - title: '🧰 Maintenance'
+    labels:
+      - 'chore'
+  - title: '📚️ Documentation'
+    labels:
+      - 'documentation'
+
+change-template: |
+  <details>
+    <summary>$TITLE @$AUTHOR (#$NUMBER)</summary>
+
+    $BODY
+  </details>
+
+change-title-escapes: '\<*_&' # You can add # and @ to disable mentions, and add ` to disable code blocks.
+
+version-resolver:
+  major:
+    labels:
+      - 'major'
+  minor:
+    labels:
+      - 'minor'
+      - 'enhancement'
+  patch:
+    labels:
+      - 'auto-update'
+      - 'patch'
+      - 'fix'
+      - 'bugfix'
+      - 'bug'
+      - 'hotfix'
+      - 'packages'
+      - 'documentation'
+  default: minor
+
+template: |
+  $CHANGES

.github/workflows/docker-image.yaml

@@ -0,0 +1,61 @@
+name: Build & Push Docker Image
+
+on:
+  release:
+    types: [published]
+
+jobs:
+
+  docker:
+
+    runs-on: ubuntu-latest
+
+    env:
+      DEEPCELL_VERSION: 0.9.1
+
+    steps:
+    - uses: actions/checkout@v2
+
+    - name: Set up QEMU
+      uses: docker/setup-qemu-action@v1
+
+    - name: Set up Docker Buildx
+      uses: docker/setup-buildx-action@v1
+
+    - name: Login to DockerHub
+      uses: docker/login-action@v1 
+      with:
+        username: ${{ secrets.DOCKER_USERNAME }}
+        password: ${{ secrets.DOCKER_PASSWORD }}
+
+    - name: Build and push CPU Image
+      id: docker_build_cpu
+      uses: docker/build-push-action@v2
+      with:
+        context: .
+        file: ./Dockerfile
+        push: true
+        tags: |
+          ${{ github.repository }}:latest
+          ${{ github.repository }}:${{ github.event.release.tag_name }}
+        build-args: |
+          DEEPCELL_VERSION=${{ env.DEEPCELL_VERSION }}
+
+    - name: Image digest
+      run: echo ${{ steps.docker_build_cpu.outputs.digest }}
+
+    - name: Build and push GPU Image
+      id: docker_build_gpu
+      uses: docker/build-push-action@v2
+      with:
+        context: .
+        file: ./Dockerfile
+        push: true
+        tags: |
+          ${{ github.repository }}:latest-gpu
+          ${{ github.repository }}:${{ github.event.release.tag_name }}-gpu
+        build-args: |
+          DEEPCELL_VERSION=${{ env.DEEPCELL_VERSION }}-gpu
+
+    - name: Image digest
+      run: echo ${{ steps.docker_build_gpu.outputs.digest }}

.github/workflows/release-drafter.yaml

@@ -0,0 +1,25 @@
+name: Release Drafter
+
+on:
+  push:
+    # branches to consider in the event; optional, defaults to all
+    branches:
+      - master
+  # pull_request event is required only for autolabeler
+  pull_request:
+    # Only following types are handled by the action, but one can default to all as well
+    types: [opened, reopened, synchronize]
+
+jobs:
+  update_release_draft:
+    runs-on: ubuntu-latest
+    steps:
+
+      # Drafts your next Release notes as Pull Requests are merged into "master"
+      - uses: release-drafter/release-drafter@v5
+        # (Optional) specify config name to use, relative to .github/. Default: release-drafter.yml
+        # with:
+        #   config-name: my-config.yml
+        #   disable-autolabeler: true
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

.github/workflows/tests.yaml

@@ -0,0 +1,68 @@
+# This workflow will install Python dependencies, run tests and lint with a single version of Python
+# For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions
+
+name: build
+
+on: [push, pull_request]
+
+jobs:
+
+  tests:
+
+    runs-on: ubuntu-latest
+
+    strategy:
+      matrix:
+        python-version: [3.6, 3.7, 3.8]
+
+    steps:
+    - uses: actions/checkout@v2
+
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v2
+      with:
+        python-version: ${{ matrix.python-version }}
+
+    - name: Cache pip
+      uses: actions/cache@v2
+      with:
+        # 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
+      run: |
+        python -m pip install --upgrade pip
+        pip install -r requirements.txt
+        pip install -r requirements-test.txt
+
+    - name: PyTest
+      run: |
+        pytest deepcell_applications --cov deepcell_applications --pep8
+
+    - name: Coveralls
+      if: env.COVERALLS_REPO_TOKEN != null
+      env:
+        COVERALLS_REPO_TOKEN: ${{ secrets.COVERALLS_REPO_TOKEN }}
+        COVERALLS_FLAG_NAME: ${{ matrix.python-version }}
+        COVERALLS_PARALLEL: true
+      run: |
+        coveralls
+
+  coveralls:
+    name: Finish Coveralls
+    needs: tests
+    runs-on: ubuntu-latest
+    steps:
+    - name: Coveralls Finished
+      uses: coverallsapp/github-action@master
+      if: env.COVERALLS_REPO_TOKEN != null
+      env:
+        COVERALLS_REPO_TOKEN: ${{ secrets.COVERALLS_REPO_TOKEN }}
+      with:
+        github-token: ${{ secrets.GITHUB_TOKEN }}
+        parallel-finished: true

.gitignore

@@ -127,3 +127,6 @@ dmypy.json
 
 # Pyre type checker
 .pyre/
+
+# VSCode settings
+.vscode/