WIP: Try to get GHA workflow to work

WIP: Try to get GHA workflow to work

.github/workflows/python-package-conda.yml

@@ -14,32 +14,32 @@ jobs:
       uses: actions/setup-python@v3
       with:
         python-version: '3.6.15'
-    - name: Add conda to system path
+    - name: Install micromamba
       run: |
-        # $CONDA is an environment variable pointing to the root of the miniconda directory
-        echo $CONDA/bin >> $GITHUB_PATH
+        bash <(curl -L micro.mamba.pm/install.sh)
+        export MAMBA_EXE='/home/runner/.local/bin/micromamba'
+        export MAMBA_ROOT_PREFIX='/home/runner/micromamba'
     - name: Install dependencies
       run: |
         export LANG=en_US.iso885915
-        conda info
         echo $LANG
-        conda env update --file environment.yml --name base
+        micromamba create --file environment.yml
     - name: Install microSALT
       run: |
-         mkdir ~/.microSALT && cp configExample.json ~/.microSALT/config.json
-         GITHUB_BRANCH=${GITHUB_REF##*/}
-         branch=$GITHUB_BRANCH; yes | bash <(cat install.sh) $branch  
-         conda activate microSALT
-    - name: Lint with flake8
-      run: |
-        conda install flake8
-        # stop the build if there are Python syntax errors or undefined names
-        flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
-        # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
-        flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
+        micromamba activate microSALT
+        mkdir ~/.microSALT && cp configExample.json ~/.microSALT/config.json
+        GITHUB_BRANCH=${GITHUB_REF##*/}
+        pip install -r requirements.txt -r requirements-dev.txt
+        pip install -U .
+    #- name: Lint with flake8
+    #  run: |
+    #    #micromamba install flake8
+    #    # stop the build if there are Python syntax errors or undefined names
+    #    #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: |
-        conda install pytest
         pytest --cov=microSALT tests/
     - name: Run Coveralls
       run: |

environment.yml

@@ -1,4 +1,4 @@
-name: P_microSALT
+name: microSALT
 channels:
   - conda-forge
   - bioconda
@@ -8,11 +8,12 @@ dependencies:
   - blast=2.12.0
   - bwa=0.7.17
   - picard=2.20.3
-  - pigz=2.4
+  - pigz>=2.4
   - quast=5.0.2
   - samtools=1.13
   - spades=3.13.1
   - trimmomatic=0.39
   - r-base=4.1.1
   - openjdk=11.0.9.1
-
+  - pytest=6.2.5
+  - pytest-cov=2.12.1

install.sh

@@ -1,6 +1,7 @@
 #!/usr/bin/env bash
 
 set -e
+set -x
 shopt -s nullglob
 
 #Suggests provided branch. Else suggests master
@@ -52,11 +53,11 @@ done
 echo "Thank you, setting up environment $cname!"
 
 #Unload environment
-conda info | tac | tac | grep -q $cname && source deactivate || :
+micromamba info | tac | tac | grep -q $cname && source deactivate || :
 #Remove environment if already present
-conda remove -y -n $cname --all || :
+micromamba remove -y -n $cname --all || :
 
-conda env create -n $cname -f https://raw.githubusercontent.com/Clinical-Genomics/microSALT/$branch/environment.yml
+micromamba env create -y -f <(curl -L https://raw.githubusercontent.com/Clinical-Genomics/microSALT/$branch/environment.yml )
 source activate $cname
 
 if [[ $type == "release" ]]; then