Merge pull request #171 from StochSS/develop

Release v1.0

api.dockerfile → .api.dockerfile

@@ -1,4 +1,4 @@
-FROM python:3.8.10-buster
+FROM python:3.11.1-buster
 
 LABEL authors="Ethan Green <egreen4@unca.edu>, Matthew Dippel <mdip226@gmail.com>"
 
@@ -13,15 +13,10 @@ VOLUME [ "/opt/venv" ]
 
 WORKDIR /usr/src/app
 
-COPY requirements.txt .
-RUN pip install -r requirements.txt
-
-COPY . /usr/src/app
-
-ARG FLASK_ENV="production"
-ENV FLASK_ENV="${FLASK_ENV}" \
-    PYTHONUNBUFFERED="true"
+COPY stochss_compute /usr/src/app/stochss_compute
+COPY requirements.txt *.py *.md *.dockerfile *.cfg /usr/src/app/
+RUN pip install .
 
 EXPOSE 29681
 
-CMD [ "python", "startup.py", "--host", "0.0.0.0"]
+CMD [ "stochss-compute-cluster"]

.coveragerc

@@ -0,0 +1,3 @@
+[run]
+concurrency = 
+	multiprocessing

.dockerignore

@@ -3,6 +3,16 @@
 .venv
 .vscode
 dist
+env/
 **/*__pycache__
-.ipynb_checkpoints/
-examples/
+**/.ipynb_checkpoints/
+tests/
+kubernetes/
+docker/
+.github/
+**/docker-compose.yml
+**/dask-worker-space
+docker-build.sh
+**/.sssc/
+**/cache/*
+**/.env

.examples.dockerfile

@@ -0,0 +1,27 @@
+FROM jupyter/minimal-notebook:latest
+
+LABEL authors="Ethan Green <egreen4@unca.edu>, Matthew Dippel <mdip226@gmail.com>"
+
+USER root
+
+RUN apt-get update && apt-get install -y g++ make
+
+USER jovyan
+
+RUN pip install --no-cache-dir bokeh
+
+COPY --chown=jovyan:users stochss_compute stochss_compute
+
+COPY --chown=jovyan:users examples examples
+
+COPY --chown=jovyan:users   setup.py \
+                            setup.cfg \
+                            requirements.txt \
+                            README.md \
+                            LICENSE.md \
+                            CONTRIBUTORS.md \
+                            ./
+
+RUN pip install .
+
+WORKDIR /home/jovyan/examples

.github/workflows/PR-lint.yml

@@ -0,0 +1,75 @@
+name: PyLint On Pull Request
+on: [pull_request]
+jobs:
+  build:
+    runs-on: ubuntu-20.04
+    steps:
+    - name: Set Up Python
+      uses: actions/setup-python@v2
+    - name: Install PyLint
+      run: pip install --upgrade pylint
+    - name: Checkout
+      uses: actions/checkout@v2
+      with:
+        fetch-depth: 0
+    - name: Checkout Head
+      run: git checkout $HEAD_REF
+      env:
+        HEAD_REF: ${{ github.event.pull_request.head.ref }}
+    - name: Checkout Base
+      run: git checkout $BASE_REF
+      env:
+        BASE_REF: ${{ github.event.pull_request.base.ref }}
+    - name: Get Base Lint Score
+      run: |
+        echo BASE_LINT=$(git diff --name-only --diff-filter=M $HEAD_REF | grep -E "\.py" | xargs pylint | grep -E -o "at [0-9.-]+" | grep -E -o [0-9.-]+) >> $GITHUB_ENV
+      env:
+        HEAD_REF: ${{ github.event.pull_request.head.ref }}
+      if: always()
+    - name: Set Base Lint to 0
+      run: echo BASE_LINT=0 >> $GITHUB_ENV
+      if: env.BASE_LINT == ''
+    - name: Checkout Head
+      run: git checkout $HEAD_REF
+      env:
+        HEAD_REF: ${{ github.event.pull_request.head.ref }}
+    - name: Get Head Lint Score
+      run: |
+        echo HEAD_LINT=$(git diff --name-only --diff-filter=M $BASE_REF | grep -E "\.py" | xargs pylint | grep -E -o "at [0-9.-]+" | grep -E -o [0-9.-]+) >> $GITHUB_ENV
+      env:
+        BASE_REF: ${{ github.event.pull_request.base.ref }}
+      if: always()
+    - name: Set Head Lint to 0
+      run: echo HEAD_LINT=0 >> $GITHUB_ENV
+      if: env.HEAD_LINT == ''
+    - name: Get Added Files Lint Score
+      run: |
+        echo ADDED_LINT=$(git diff --name-only --diff-filter=A $BASE_REF | grep -E "\.py" | xargs pylint | grep -E -o "at [0-9.-]+" | grep -E -o [0-9.-]+) >> $GITHUB_ENV
+      env:
+        BASE_REF: ${{ github.event.pull_request.base.ref }}
+      if: always()
+    - name: Get Delta
+      run: |
+        import os
+        base = float(os.environ['BASE_LINT'])
+        head = float(os.environ['HEAD_LINT'])
+        delta = head - base
+        os.popen(f"echo DELTA={round(delta, 2)} >> $GITHUB_ENV")
+      shell: python
+    - name: Display Results
+      run: |
+        echo "Lint of modified files in base:"
+        echo ${{ env.BASE_LINT }}
+        echo "Lint of modified files in head:"
+        echo ${{ env.HEAD_LINT }}
+        echo "Delta (+/-):"
+        echo ${{ env.DELTA }}
+        echo "Lint of files added by head:"
+        echo ${{ env.ADDED_LINT }}
+      if: always()
+    - name: Fail If Negative Delta
+      run: |
+        import os
+        if float(os.environ['HEAD_LINT']) < 9 and float(os.environ['DELTA']) < 0:
+            raise Exception("Head lint score < 9 and negative delta.")
+      shell: python

.github/workflows/docker-develop.yml

@@ -28,6 +28,6 @@ jobs:
         uses: docker/build-push-action@v2
         with:
           push: true
-          file: api.dockerfile
+          file: .api.dockerfile
           tags: stochss/stochss-compute:dev
       - run: echo "🍏 This job's status is ${{ job.status }}."

.github/workflows/docker.yml

@@ -28,6 +28,6 @@ jobs:
         uses: docker/build-push-action@v2
         with:
           push: true
-          file: api.dockerfile
-          tags: stochss/stochss-compute:latest
+          file: .api.dockerfile
+          tags: stochss/stochss-compute:latest, stochss/stochss-compute:cloud
       - run: echo "🍏 This job's status is ${{ job.status }}."

.github/workflows/test.yml

@@ -0,0 +1,48 @@
+# This workflow will install Python dependencies, run tests and lint with a variety of Python versions
+# For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions
+
+name: Tests
+
+on:
+  push:
+
+jobs:
+  build:
+
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ["3.8", "3.9", "3.10", "3.11"]
+
+    steps:
+    - uses: actions/checkout@v3
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v3
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        python -m pip install .
+        python -m pip install '.[AWS]'
+        python -m pip install '.[dev]'
+
+    - name: Run integration tests
+      run: |
+        cd test
+        python -m coverage run --source=../stochss_compute run_integration_tests.py
+
+    - name: Run unit tests
+      run: |
+        cd test
+        python -m coverage run -a --source=../stochss_compute run_unit_tests.py
+
+    - name: Run system tests
+      run: |
+        cd test
+        # python -m coverage run -a --source=../stochss_compute run_system_tests.py
+
+    # - name: Coverage score
+    #   run: |
+    #     python -m coverage report

.gitignore

@@ -69,8 +69,6 @@ instance/
 .scrapy
 
 # Sphinx documentation
-docs/_build/
-doc/_build/
 
 # PyBuilder
 target/
@@ -152,3 +150,5 @@ Thumbs.db #thumbnail cache on Windows
 !.vscode/launch.json
 !.vscode/extensions.json
 *.code-workspace
+
+**/dask-worker-space