chore: adding .github/ files for templates and dependabot (#47)

.github/ISSUE_TEMPLATE/bug_report.md

@@ -0,0 +1,46 @@
+---
+name: Bug report
+about: Create a report to help us improve
+title: ''
+labels: bug
+assignees: ''
+
+---
+
+<!--
+For general questions please use the Discussions section of the project:
+
+https://github.com/bihealth/varfish-server/discussions
+
+For bug reports and feature requests please open a ticket using the templates!
+-->
+
+**Describe the bug**
+A clear and concise description of what the bug is.
+
+**To Reproduce**
+Steps to reproduce the behavior:
+1. Go to '...'
+2. Click on '....'
+3. Scroll down to '....'
+4. See error
+
+**Expected behavior**
+A clear and concise description of what you expected to happen.
+
+**Screenshots**
+If applicable, add screenshots to help explain your problem.
+
+**Desktop (please complete the following information):**
+ - OS: [e.g. iOS]
+ - Browser [e.g. chrome, safari]
+ - Version [e.g. 22]
+
+**Smartphone (please complete the following information):**
+ - Device: [e.g. iPhone6]
+ - OS: [e.g. iOS8.1]
+ - Browser [e.g. stock browser, safari]
+ - Version [e.g. 22]
+
+**Additional context**
+Add any other context about the problem here.

.github/ISSUE_TEMPLATE/feature_request.md

@@ -0,0 +1,28 @@
+---
+name: Feature request
+about: Suggest an idea for this project
+title: ''
+labels: enhancement
+assignees: ''
+
+---
+
+<!--
+For general questions please use the Discussions section of the project:
+
+https://github.com/bihealth/varfish-server/discussions
+
+For bug reports and feature requests please open a ticket using the templates!
+-->
+
+**Is your feature request related to a problem? Please describe.**
+A clear and concise description of what the problem is. Ex. I'm always frustrated when [...]
+
+**Describe the solution you'd like**
+A clear and concise description of what you want to happen.
+
+**Describe alternatives you've considered**
+A clear and concise description of any alternative solutions or features you've considered.
+
+**Additional context**
+Add any other context or screenshots about the feature request here.

.github/PULL_REQUEST_TEMPLATE.md

@@ -0,0 +1,14 @@
+<!--
+
+NOTE
+NOTE In most cases, you should create an issue first, and only then
+NOTE a pull request.  Please see the contribution guidelines for
+NOTE further information.  In particular related to conventional
+NOTE commit messages.
+NOTE
+
+The title should have the following format:
+
+  <type>: description (#<issue>)
+
+-->

.github/dependabot.yml

@@ -0,0 +1,9 @@
+# Please see the documentation for all configuration options:
+# https://docs.github.com/github/administering-a-repository/configuration-options-for-dependency-updates
+
+version: 2
+updates:
+  - package-ecosystem: "pip"
+    directory: "/"
+    schedule:
+      interval: "weekly"

.github/workflows/main.yml

@@ -26,7 +26,7 @@ jobs:
       - name: Install Python
         uses: actions/setup-python@v2
         with:
-          python-version: "3.8"
+          python-version: "3.10"
 
       - name: Install dependencies
         run: |
@@ -55,32 +55,46 @@ jobs:
           # - "3.11"  # no pysam binaries yet
     needs: linting
     steps:
-      - name: Install Python via conda
-        uses: s-weigand/setup-conda@v1
+      - name: Construct environment.yml file for python version
+        run: |
+          cat <<EOF > /tmp/environment.yml
+          name: ngs-chew
+          channels:
+            - bioconda
+            - conda-forge
+            - defaults
+          dependencies:
+            - python=${{ matrix.python-version }}
+            - pip
+            - bcftools
+            - samtools
+            - pysam
+            - pandas
+            - scipy
+            - numpy
+          EOF
+
+      - name: Setup micromamba environment
+        uses: mamba-org/setup-micromamba@v1
         with:
-          python-version: ${{ matrix.python-version }}
-          conda-channels: defaults,bioconda,conda-forge
+          environment-file: /tmp/environment.yml
+          init-shell: bash
+          cache-environment: true
+          post-cleanup: none  # breaks otherwise
 
       - name: Checkout repository
-        uses: actions/checkout@v2
+        uses: actions/checkout@v3
         with:
           lfs: true
 
-      - name: Install mamba
-        run: conda install -y mamba
-
-      - name: Install external dependencies with mamba
-        run: mamba install -y bcftools samtools
-
-      - name: Save time by installing packages via mamba
-        run: mamba install -y pysam pandas scipy numpy
-
       - name: Install test dependencies via pip
         run: pip install -r requirements/test.txt
+        shell: bash -el {0}
 
       - name: Run tests
         run: |
           pytest
           coverage report
+        shell: bash -el {0}
 
       - uses: codecov/codecov-action@v3