Refactor CI workflow to use micromamba for environment setup and streamline installation steps

Author: karlnyr

.github/workflows/run_tests.yml

@@ -2,7 +2,6 @@ name: Tests
 
 on: [push]
 
-
 env:
   CONDA_PREFIX: /home/runner/work/microSALT/microSALT/tests
   COVERALLS_REPO_TOKEN: ${{ secrets.COVERALLS_REPO_TOKEN }}
@@ -14,31 +13,37 @@ jobs:
       max-parallel: 5
 
     steps:
-    - uses: actions/checkout@v4
-    - name: Set up Python 3.8
-      uses: actions/setup-python@v3
-      with:
-        python-version: '3.8.15'
-    - name: Create conda/mamba environment using micromamba
+    - name: Checkout repository
+      uses: actions/checkout@v4
+
+    - name: Set up Conda environment using micromamba
       uses: mamba-org/setup-micromamba@v1
       with:
         environment-file: environment.yml
         cache-downloads: true
-    - name: Install microSALT
+
+    - name: Activate Conda environment and install microSALT
       run: |
-        mkdir ~/.microSALT && cp configExample.json ~/.microSALT/config.json
-        GITHUB_BRANCH=${GITHUB_REF##*/}
-        pip install -r requirements.txt -r requirements-dev.txt
-        pip install -U .
+        source ~/.bashrc
+        micromamba activate microsalt-env
+        python -m pip install -r requirements.txt -r requirements-dev.txt
+        python -m pip install -U .
+
     - name: Lint with flake8
       run: |
-        # stop the build if there are Python syntax errors or undefined names
+        source ~/.bashrc
+        micromamba activate microsalt-env
         flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
-        # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
         flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
+
     - name: Test with pytest
       run: |
+        source ~/.bashrc
+        micromamba activate microsalt-env
         pytest --cov=microSALT tests
+
     - name: Run Coveralls
       run: |
-        coveralls
+        source ~/.bashrc
+        micromamba activate microsalt-env
+        coveralls