fix(github): refactor ci/cd

.github/workflows/test.yml

@@ -33,6 +33,9 @@ jobs:
   Pytest:
     needs: [Build]
     runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: [3.8, 3.9]
     defaults:
       run:
         shell: bash -l {0}
@@ -46,10 +49,11 @@ jobs:
         with:
           miniconda-version: "latest"
           environment-file: recipes/workflow.yaml
+          python-version: ${{ matrix.python-version }}
       - name: 'Run tests'
         run: |
-          conda env list
-          tox -e py37, py38
+          pip install --no-deps .
+          python -m pytest tests/unit
 
   Coverage:
     needs: [Build]
@@ -67,9 +71,11 @@ jobs:
         with:
           miniconda-version: "latest"
           environment-file: recipes/workflow.yaml
+          python-version: '3.9'
       - name: 'Run tests'
         run: |
-          tox -e py39
+          pip install --no-deps .
+          coverage run -m pytest
           coverage lcov
       - name: 'Coveralls'
         uses: coverallsapp/github-action@master

MANIFEST.in

@@ -1 +1 @@
-include environment.yml
+graft recipes

recipes/workflow.yaml

@@ -1,9 +1,21 @@
 name: test
 channels:
   - conda-forge
+  - plotly
   - bioconda
   - defaults
 dependencies:
+  # straindesign.
+  - biopython
+  - cameo
+  - cobra<0.25.0
+  - markupsafe==2.0.1
+  - pandas
+  - plotly
+  - python-kaleido
+  - python
+  - pyyaml
+  # build.
   - build
   - conda-build
   - coverage

setup.py

@@ -12,7 +12,7 @@
 
 # App name - dependencies
 env = {}
-with open("environment.yml") as fid:
+with open("recipes/workflow.yaml") as fid:
     env = yaml.safe_load(fid)
 name = env["name"]
 install_requires = []