Create ci.yml

.github/workflows/ci.yml

@@ -0,0 +1,88 @@
+name: ci
+
+on:
+  pull_request:
+    branches:
+     - dev
+  push:
+    branches:
+      - '*'
+
+jobs:
+
+  static-code-analysis:
+    runs-on: ubuntu-latest
+    defaults:
+      run:
+        shell: bash -l {0}
+
+    steps:
+      - name: check out repository
+        uses: actions/checkout@v4
+
+      - name: Setup Conda/Mamba
+        uses: conda-incubator/setup-miniconda@v2
+        with:
+          mamba-version: "*"
+          auto-update-conda: true
+          activate-environment: scrnasim
+          environment-file: environment.yml
+          auto-activate-base: false
+
+      - name: Update scrnasim env with dev packages
+        run: mamba env update -n scrnasim -f environment.dev.yml
+
+      - name: display environment info
+        run: |
+          conda info -a
+          conda list
+
+      - name: flake8
+        run: flake8
+
+      - name: pylint
+        run: pylint --rcfile pylint.cfg setup.py scRNAsim_toolz/
+
+      - name: mypy
+        run: mypy scRNAsim_toolz
+
+  unit-testing:
+    runs-on: ubuntu-latest
+    defaults:
+      run:
+        shell: bash -l {0}
+
+    steps:
+
+      - name: checkout repository
+        uses: actions/checkout@v4
+
+      - name: setup Conda/Mamba
+        uses: conda-incubator/setup-miniconda@v2
+        with:
+          mamba-version: "*"
+          auto-update-conda: true
+          activate-environment: scrnasim
+          environment-file: environment.yml
+          auto-activate-base: false
+
+      - name: update scrnasim env with dev packages
+        run: mamba env update -n scrnasim -f environment.dev.yml
+
+      - name: display environment info
+        run: |
+          conda info -a
+          conda list
+      
+      - name: run unit tests
+        run: |
+          coverage run --source scRNAsim_toolz -m pytest
+          coverage xml
+
+      - name: submit coverage report
+        uses: codecov/codecov-action@v2
+        with:
+          token: ${{ secrets.CODECOV_TOKEN }}
+          files: ./coverage.xml
+          verbose: true
+          fail_ci_if_error: false