wip: start over

.coveragerc

@@ -0,0 +1,21 @@
+# .coveragerc to control coverage.py
+
+[run]
+omit =
+        *__init__*
+        */usr/local/lib*
+        *test*
+        *_version
+        *versioneer
+        *setup*
+        *examples/*
+
+[report]
+omit =
+        *__init__*
+        */usr/local/lib*
+        *test*
+        *_version*
+        *versioneer*
+        *setup*
+        *examples/*

.cruft.json

@@ -0,0 +1,17 @@
+{
+    "template": "https://github.com/cheminfo-py/cheminfo-webservice-cookiecutter",
+    "commit": "381c11be121f7691e3bda5bd116a32ea36794d89",
+    "context": {
+        "cookiecutter": {
+            "project_name": "xtb-service",
+            "repo_name": "xtb-service",
+            "first_module_name": "xtb-service",
+            "author_name": "Kevin Jablonka",
+            "author_email": "kevin.jablonka@epfl.ch",
+            "description": "webservice providing xtb calculations",
+            "_cheminfo_cc_version": 0.1,
+            "_template": "https://github.com/cheminfo-py/cheminfo-webservice-cookiecutter"
+        }
+    },
+    "directory": null
+}

.env

@@ -1,4 +1,4 @@
-PORT=40129
-TIMEOUT=200
 WORKERS=1
-OMP_NUM_THREADS=1
+OMP_NUM_THREADS=1,1
+PORT=8051
+TIMEOUT=30

.gitchangelog.rc

@@ -0,0 +1,21 @@
+section_regexps = [
+    (
+        'BREAKING', [r'^BREAKING']
+    ),
+    ('New', [
+        r'^feat',
+     ]),
+    ('Changes', [
+        r'^chore',
+     ]),
+    ('Fix', [
+        r'^fix',
+     ]),
+
+    ('Other', None ## Match all lines
+     ),
+
+]
+
+
+tag_filter_regexp = r'^v[0-9]+\.[0-9]+(\.[0-9]+)?'

.github/ISSUE_TEMPLATE.md

@@ -0,0 +1,15 @@
+## Expected Behavior
+
+## Actual Behavior
+
+## Steps to Reproduce the Problem
+
+1.
+2.
+3.
+
+## Specifications
+
+- Version:
+- Platform:
+- Subsystem:

.github/PULL_REQUEST_TEMPLATE.md

@@ -0,0 +1,14 @@
+## Types of changes
+
+<!--- What types of changes does your code introduce? Put an `x` in all the boxes that apply: -->
+
+- [ ] Bug fix (non-breaking change which fixes an issue)
+- [ ] New feature (non-breaking change which adds functionality)
+- [ ] Breaking change (fix or feature that would cause existing functionality to change)
+
+## Actions
+
+- [ ] My change requires a change to the documentation.
+- [ ] I have updated the documentation accordingly.
+- [ ] I have added tests to cover my changes.
+- [ ] All new and existing tests passed.

.github/workflows/docker-publish.yml

@@ -0,0 +1,78 @@
+name: Docker
+
+on:
+  push:
+    # Publish `master` as Docker `latest` image.
+    branches:
+      - master
+
+    # Publish `v1.2.3` tags as releases.
+    tags:
+      - v*
+
+  # Run tests for any PRs.
+  pull_request:
+
+env:
+  # TODO: Change variable to your image's name.
+  IMAGE_NAME: xtb-service
+
+jobs:
+  # Run tests.
+  # See also https://docs.docker.com/docker-hub/builds/automated-testing/
+  test:
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v2
+
+      - name: Run tests
+        run: |
+          if [ -f docker-compose.test.yml ]; then
+            docker-compose --file docker-compose.test.yml build
+            docker-compose --file docker-compose.test.yml run sut
+          else
+            docker build . --file Dockerfile
+          fi
+
+  # Push image to GitHub Packages.
+  # See also https://docs.docker.com/docker-hub/builds/
+  push:
+    # Ensure test job passes before pushing image.
+    needs: test
+
+    runs-on: ubuntu-latest
+    if: github.event_name == 'push'
+
+    steps:
+      - uses: actions/checkout@v2
+
+      - name: Build image
+        run: docker build . --file Dockerfile --tag $IMAGE_NAME
+
+      - name: Log into GitHub Container Registry
+      # TODO: Create a PAT with `read:packages` and `write:packages` scopes and save it as an Actions secret `CR_PAT`
+
+        run: echo "${{ secrets.CR_PAT }}" | docker login https://ghcr.io -u ${{ github.actor }} --password-stdin
+
+      - name: Push image to GitHub Container Registry
+        run: |
+          IMAGE_ID=ghcr.io/${{ github.repository_owner }}/$IMAGE_NAME
+
+          # Change all uppercase to lowercase
+          IMAGE_ID=$(echo $IMAGE_ID | tr '[A-Z]' '[a-z]')
+
+          # Strip git ref prefix from version
+          VERSION=$(echo "${{ github.ref }}" | sed -e 's,.*/\(.*\),\1,')
+
+          # Strip "v" prefix from tag name
+          [[ "${{ github.ref }}" == "refs/tags/"* ]] && VERSION=$(echo $VERSION | sed -e 's/^v//')
+
+          # Use Docker `latest` tag convention
+          [ "$VERSION" == "master" ] && VERSION=latest
+
+          echo IMAGE_ID=$IMAGE_ID
+          echo VERSION=$VERSION
+
+          docker tag $IMAGE_NAME $IMAGE_ID:$VERSION
+          docker push $IMAGE_ID:$VERSION

.github/workflows/pytest.yml

@@ -0,0 +1,42 @@
+# 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: Python package
+
+on:
+  pull_request:
+    branches: [main]
+  push:
+    branches: [main]
+
+jobs:
+  build:
+    strategy:
+      matrix:
+        os: [ubuntu-latest]
+        python-version: [3.7, 3.8]
+    runs-on: ${{ matrix.os }}
+
+    steps:
+      - uses: actions/checkout@v2
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v2
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Setup conda
+        uses: s-weigand/setup-conda@v1
+        with:
+          update-conda: true
+          python-version: ${{ matrix.python-version }}
+          conda-channels: anaconda, conda-forge
+      - name: Install dependencies
+        run: |
+          conda install rdkit -c rdkit -y
+          conda install xtb-python -c conda-forge -y
+          pip install -r requirements.txt
+          pip install pytest
+      - name: Test with pytest
+        run: |
+          pytest test/simulation_regtest.py
+          pytest test/test_api.py

.github/workflows/release-please.yml

@@ -0,0 +1,14 @@
+on:
+  push:
+    branches:
+      - master
+name: release-please
+jobs:
+  release-please:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: GoogleCloudPlatform/release-please-action@v2.6.0
+        with:
+          token: ${{ secrets.GITHUB_TOKEN }}
+          release-type: python
+          package-name: xtbservice

.github/workflows/test_docker.yml

@@ -0,0 +1,18 @@
+name: Docker Image Build CI
+
+on: [push]
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    env:
+      timeout: 200
+    steps:
+      - uses: actions/checkout@v1
+      - name: Build the Docker image
+        run: pip3 install requests[security] && ./build_docker.sh
+      - name: start the docker image
+        run: ./run_docker.sh && sleep 10s
+      - name: run the test
+        run: cd test && python3 docker_test.py
+