Repo management

.coveragerc

@@ -12,6 +12,6 @@ ignore_errors = True
 fail_under = 50
 show_missing = True
 
- omit =
+omit =
     **/*_test.py
-    deepcell-spots/data/*
+    data/*

.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/pypi.yaml

@@ -0,0 +1,31 @@
+# This workflows will upload a Python Package using Twine when a release is created
+# For more information see: https://help.github.com/en/actions/language-and-framework-guides/using-python-with-github-actions#publishing-to-package-registries
+
+name: Upload Python Package
+
+on:
+  release:
+    types: [published]
+
+jobs:
+  deploy:
+
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v2
+
+    - name: Set up Python
+      uses: actions/setup-python@v2
+      with:
+        python-version: '3.x'
+
+    - name: Build a source distribution
+      run: python setup.py sdist
+
+    - name: Publish distribution 📦 to PyPI
+      if: startsWith(github.ref, 'refs/tags')
+      uses: pypa/gh-action-pypi-publish@master
+      with:
+        user: __token__
+        password: ${{ secrets.PYPI_PASSWORD }}

.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 +1,64 @@
+# 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:
+        path: ${{ env.pythonLocation }}
+        key: ${{ env.pythonLocation }}-${{ hashFiles('setup.py') }}
+        restore-keys: |
+          ${{ env.pythonLocation }}-
+
+    - name: Install Dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install -r requirements.txt
+        pip install -r requirements-test.txt
+
+    - name: PyTest
+      run: |
+        python -m pytest deepcell_spots --pep8 --cov deepcell_spots
+
+    - 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

Dockerfile

@@ -1,9 +1,9 @@
 # Use tensorflow/tensorflow as the base image
 # Change the build arg to edit the tensorflow version.
 # Only supporting python3.
-ARG TF_VERSION=2.4.1-gpu
+ARG DEEPCELL_VERSION=0.9.0
 
-FROM tensorflow/tensorflow:${TF_VERSION}
+FROM deepcell:${DEEPCELL_VERSION}
 
 # System maintenance
 RUN /usr/bin/python3 -m pip install --upgrade pip

README.md

@@ -54,7 +54,7 @@ coords = app.predict(image,threshold=0.9)
 
 ## Copyright
 
-Copyright © 2019-2020 [The Van Valen Lab](http://www.vanvalen.caltech.edu/) at the California Institute of Technology (Caltech), with support from the Shurl and Kay Curci Foundation, Google Research Cloud, the Paul Allen Family Foundation, & National Institutes of Health (NIH) under Grant U24CA224309-01.
+Copyright © 2019-2021 [The Van Valen Lab](http://www.vanvalen.caltech.edu/) at the California Institute of Technology (Caltech), with support from the Shurl and Kay Curci Foundation, Google Research Cloud, the Paul Allen Family Foundation, & National Institutes of Health (NIH) under Grant U24CA224309-01.
 All rights reserved.
 
 ## License

deepcell_spots/__init__.py

@@ -0,0 +1,44 @@
+# Copyright 2019-2021 The Van Valen Lab at the California Institute of
+# Technology (Caltech), with support from the Paul Allen Family Foundation,
+# Google, & National Institutes of Health (NIH) under Grant U24CA224309-01.
+# All rights reserved.
+#
+# Licensed under a modified Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.github.com/vanvalenlab/deepcell-spots/LICENSE
+#
+# The Work provided may be used for non-commercial academic purposes only.
+# For any other use of the Work, including commercial use, please contact:
+# [email protected]
+#
+# Neither the name of Caltech nor the names of its contributors may be used
+# to endorse or promote products derived from this software without specific
+# prior written permission.
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+# ==============================================================================
+
+from deepcell_spots._version import __version__
+
+from deepcell_spots import applications
+from deepcell_spots import cluster_vis
+from deepcell_spots import data_utils
+from deepcell_spots import dotnet_losses
+from deepcell_spots import dotnet
+from deepcell_spots import image_alignment
+from deepcell_spots import image_generators
+from deepcell_spots import multiplex
+from deepcell_spots import point_metrics
+from deepcell_spots import postprocessing_utils
+from deepcell_spots import preprocessing_utils
+from deepcell_spots import simulate_data
+from deepcell_spots import singleplex
+from deepcell_spots import spot_em
+from deepcell_spots import training
+from deepcell_spots import utils

deepcell_spots/_version.py

@@ -0,0 +1,36 @@
+# Copyright 2016-2021 The Van Valen Lab at the California Institute of
+# Technology (Caltech), with support from the Paul Allen Family Foundation,
+# Google, & National Institutes of Health (NIH) under Grant U24CA224309-01.
+# All rights reserved.
+#
+# Licensed under a modified Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.github.com/vanvalenlab/deepcell-tf/LICENSE
+#
+# The Work provided may be used for non-commercial academic purposes only.
+# For any other use of the Work, including commercial use, please contact:
+# [email protected]
+#
+# Neither the name of Caltech nor the names of its contributors may be used
+# to endorse or promote products derived from this software without specific
+# prior written permission.
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+# ==============================================================================
+
+__title__ = 'DeepCell Spots'
+__description__ = 'Deep learning for fluorescent spot detection'
+__url__ = 'https://github.com/vanvalenlab/deepcell-spots'
+__version__ = '0.1.0'
+__download_url__ = '{}/tarball/{}'.format(__url__, __version__)
+__author__ = 'The Van Valen Lab'
+__author_email__ = '[email protected]'
+__license__ = 'LICENSE'
+__copyright__ = 'Copyright 2019-2021 The Van Valen Lab at the ' \
+    'California Institute of Technology (Caltech)'

deepcell_spots/applications/__init__.py

@@ -0,0 +1,30 @@
+# Copyright 2019-2021 The Van Valen Lab at the California Institute of
+# Technology (Caltech), with support from the Paul Allen Family Foundation,
+# Google, & National Institutes of Health (NIH) under Grant U24CA224309-01.
+# All rights reserved.
+#
+# Licensed under a modified Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.github.com/vanvalenlab/deepcell-spots/LICENSE
+#
+# The Work provided may be used for non-commercial academic purposes only.
+# For any other use of the Work, including commercial use, please contact:
+# [email protected]
+#
+# Neither the name of Caltech nor the names of its contributors may be used
+# to endorse or promote products derived from this software without specific
+# prior written permission.
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+# ==============================================================================
+
+from deepcell_spots._version import __version__
+
+from deepcell_spots.applications.spots_application import Application
+from deepcell_spots.applications.spot_detection import SpotDetection