Merge pull request #25 from gipplab/dev

📦 New Release

.flake8

@@ -2,6 +2,5 @@
 exclude = .venv, venv/
 docstring-convention = google
 max-line-length = 100
-
-ignore = D104, D205, D415, W503
+ignore = D104, D205, D415, W503, ANN401
 per-file-ignores = tests/*: D1

.github/workflows/main.yml

@@ -8,24 +8,28 @@ jobs:
   Test:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
-      - uses: actions/setup-python@v2
+      - name: 🏁 Checkout
+        uses: actions/checkout@v2
+
+      - name: ✅ Setup python
+        uses: actions/setup-python@v2
         with:
           python-version: 3.8
-      - name: Install poetry
+
+      - name: 💿 Install poetry
         uses: snok/install-poetry@v1
         with:
           virtualenvs-create: true
           virtualenvs-in-project: true
-      - name: Load cached venv
-        id: cached-poetry-dependencies
-        uses: actions/cache@v2
-        with:
-          path: .venv
-          key: venv-${{ runner.os }}-${{ hashFiles('**/poetry.lock') }}
-      - name: Install dependencies
+
+      - name: 📦 Install dependencies
         run: poetry install
-        if: steps.cached-poetry-dependencies.outputs.cache-hit != 'true'
-      - name: Run tests
+
+      - name: 🌱 Start MongoDB
+        uses: supercharge/mongodb-github-action@1.7.0
+        with:
+          mongodb-version: 5.0.9
+
+      - name: 🧪 Run tests
         run: |
           poetry run poe alltest

.github/workflows/release.yml

@@ -8,113 +8,140 @@ jobs:
   Test:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
-      - uses: actions/setup-python@v2
+      - name: 🏁 Checkout
+        uses: actions/checkout@v2
+
+      - name: ✅ Setup python
+        uses: actions/setup-python@v2
         with:
           python-version: 3.8
-      - name: Install poetry
+
+      - name: 💿 Install poetry
         uses: snok/install-poetry@v1
         with:
           virtualenvs-create: true
           virtualenvs-in-project: true
-      - name: Load cached venv
-        id: cached-poetry-dependencies
-        uses: actions/cache@v2
-        with:
-          path: .venv
-          key: venv-${{ runner.os }}-${{ hashFiles('**/poetry.lock') }}
-      - name: Install dependencies
+
+      - name: 📦 Install dependencies
         run: poetry install
         if: steps.cached-poetry-dependencies.outputs.cache-hit != 'true'
-      - name: Run test
+
+      - name: 🌱 Start MongoDB
+        uses: supercharge/mongodb-github-action@1.7.0
+        with:
+          mongodb-version: 5.0.9
+
+      - name: 🧪 Run tests
         run: |
           poetry run poe alltest
 
   Release:
     needs: [Test]
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
+      - name: 🏁 Checkout
+        uses: actions/checkout@v2
         with:
           fetch-depth: "0"#
           persist-credentials: false
-      - uses: actions/setup-python@v2
+
+      - name: ✅ Setup python
+        uses: actions/setup-python@v2
         with:
           python-version: 3.8
-      - name: Bump version and push tag
+
+      - name: 🏷 Bump version and push tag
         uses: anothrNick/github-tag-action@1.36.0
         id: tagging
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
           WITH_V: true
-      - name: Build Changelog
+
+      - name: 📝 Build Changelog
         id: build_changelog
         uses: mikepenz/release-changelog-builder-action@v1
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-      - name: Install poetry
+
+      - name: 📦 Create Release
+        uses: actions/create-release@v1
+        with:
+          release_name: ${{steps.tagging.outputs.tag}}
+          body: ${{steps.build_changelog.outputs.changelog}}
+          tag_name: ${{steps.tagging.outputs.tag}}
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+
+      - name: 💿 Install poetry
         uses: snok/install-poetry@v1
         with:
           virtualenvs-create: true
           virtualenvs-in-project: true
-      - name: Load cached venv
-        id: cached-poetry-dependencies
-        uses: actions/cache@v2
-        with:
-          path: .venv
-          key: venv-${{ runner.os }}-${{ hashFiles('**/poetry.lock') }}
-      - name: Install dependencies
+
+      - name: 📦 Install dependencies
         run: poetry install
         if: steps.cached-poetry-dependencies.outputs.cache-hit != 'true'
-      - name: Update package version to git tag
+
+      - name: ⬆️ Update package version
         run: |
           poetry version $(git describe --tags --abbrev=0)
-      - name: Commit files
+      
+      - name: ➕ Commit files
         run: |
           git config --local user.email "jan.philip.wahle@gmail.com"
           git config --local user.name "github-actions[bot]"
           git add pyproject.toml
           git commit -m "[release-bot] Update pyproject.toml version"
-      - name: Push changes
+      
+      - name: 💨 Push changes
         uses: ad-m/github-push-action@master
         with:
           github_token: ${{ secrets.ACCESS_TOKEN }}
           branch: ${{ github.ref }}
-      - name: Create Release
-        uses: actions/create-release@v1
-        with:
-          release_name: ${{steps.tagging.outputs.tag}}
-          body: ${{steps.build_changelog.outputs.changelog}}
-          tag_name: ${{steps.tagging.outputs.tag}}
-        env:
-          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+
+      - name: 🔑 Docker GitHub package login
+        run: docker login ghcr.io -u ${{ github.actor }} -p ${{ secrets.GITHUB_TOKEN }}
+
+      - name: 🐳 Build docker image
+        run: docker build -t ghcr.io/gipplab/cs-insights-backend:${{steps.tagging.outputs.tag}} -t ghcr.io/gipplab/cs-insights-prediction-endpoint:latest .
+
+      - name: 📦 Push docker image
+        run: |
+          docker push ghcr.io/gipplab/cs-insights-prediciton-endpoint:${{steps.tagging.outputs.tag}}
+          docker push ghcr.io/gipplab/cs-insights-prediction-endpoint:latest
 
   Coverage:
     needs: [Test]
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
-      - uses: actions/setup-python@v2
+      - name: 🏁 Checkout
+        uses: actions/checkout@v2
+
+      - name: ✅ Setup python
+        uses: actions/setup-python@v2
         with:
           python-version: 3.8
-      - name: Install poetry
+
+      - name: 💿 Install poetry
         uses: snok/install-poetry@v1
         with:
           virtualenvs-create: true
           virtualenvs-in-project: true
-      - name: Load cached venv
-        id: cached-poetry-dependencies
-        uses: actions/cache@v2
-        with:
-          path: .venv
-          key: venv-${{ runner.os }}-${{ hashFiles('**/poetry.lock') }}
-      - name: Install dependencies
+
+      - name: 📦 Install dependencies
         run: poetry install
         if: steps.cached-poetry-dependencies.outputs.cache-hit != 'true'
-      - name: Run tests
+
+      - name: 🌱 Start MongoDB
+        uses: supercharge/mongodb-github-action@1.7.0
+        with:
+          mongodb-version: 5.0.9
+
+      - name: 🧪 Run tests
         run: |
-          poetry run poe test
-      - name: Upload coverage report
+          poetry run poe alltest
+      
+      - name: ⬆ Upload coverage report
         uses: codecov/codecov-action@v2
         with:
           token: ${{ secrets.CODECOV_TOKEN }}
@@ -125,27 +152,26 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v2
+
       - uses: actions/setup-python@v2
         with:
           python-version: 3.8
-      - name: Install poetry
+
+      - name: 💿 Install poetry
         uses: snok/install-poetry@v1
         with:
           virtualenvs-create: true
           virtualenvs-in-project: true
-      - name: Load cached venv
-        id: cached-poetry-dependencies
-        uses: actions/cache@v2
-        with:
-          path: .venv
-          key: venv-${{ runner.os }}-${{ hashFiles('**/poetry.lock') }}
-      - name: Install dependencies
+
+      - name: 📦 Install dependencies
         run: poetry install
         if: steps.cached-poetry-dependencies.outputs.cache-hit != 'true'
-      - name: Generate docs
+
+      - name: 📘 Generate docs
         run: |
           poetry run poe doc
-      - name: Deploy docs 🚀
+      
+      - name: 🚀 Deploy docs
         uses: JamesIves/github-pages-deploy-action@4.0.0
         with:
           branch: docs

.gitignore

@@ -132,7 +132,6 @@ dmypy.json
 .vercel
 .DS_Store
 docs/oas.json
-poetry.lock
 
 # vim specific swap files
 *.swp

.vscode/settings.json

@@ -11,8 +11,12 @@
     "--experimental-string-processing"
   ],
   "editor.formatOnSave": true,
-  "editor.rulers": [100],
-  "python.testing.pytestArgs": ["tests"],
+  "editor.rulers": [
+    100
+  ],
+  "python.testing.pytestArgs": [
+    "tests"
+  ],
   "python.testing.unittestEnabled": false,
   "python.testing.pytestEnabled": true
-}
+}

Dockerfile

@@ -1,9 +1,11 @@
 FROM python:3.8
 
-WORKDIR /app
-ADD pyproject.toml /app/pyproject.toml
-
+RUN apt-get update &&\
+    apt-get install liblapack-dev libblas-dev gfortran -y
 RUN pip install poetry
-RUN poetry install
 
-COPY . /app
+WORKDIR /cs-insights-prediction-endpoint
+COPY test.env /cs-insights-prediction-endpoint/.env
+COPY . /cs-insights-prediction-endpoint
+
+RUN poetry install --no-dev

Dockerfile.development

@@ -0,0 +1,8 @@
+FROM python:3.8
+
+RUN apt-get update &&\
+    apt-get install liblapack-dev libblas-dev gfortran -y
+RUN /usr/local/bin/python -m pip install --upgrade pip 
+RUN pip install poetry
+
+WORKDIR /cs-insights-prediction-endpoint

README.md

@@ -12,35 +12,7 @@
 
 ## Installation & Setup
 
-### Production
-
-To spin up the production version of this project, switch into the root directory of this project and run:
-
-```console
-docker-compose up --build
-```
-
-### Development
-
-For development install [poetry](https://python-poetry.org/):
-
-```console
-pip install poetry
-```
-
-Then run:
-
-```console
-poetry install
-```
-
-Then you can use the api like this:
-
-```console
-poetry run python dev.py
-```
-
-If you are using VSCode, you can also run debugging using the `.vscode/launch.json`.
+This project is part of the `cs-insights`-ecosystem. Please refer to the readme [here](https://github.com/gipplab/cs-insights-main) to spin up the development and production system.
 
 ## Code quality and tests