reverted to miniconda and added bash -l {0} to defaults

Author: tclose

.github/workflows/pythonpackage.yml

@@ -52,20 +52,20 @@ jobs:
     strategy:
       matrix:
         python-version: [3.7, 3.8, 3.9]
-
+    defaults:
+      run:
+        shell: bash -l {0}
     steps:
     - uses: actions/checkout@v2
-    - name: Install MRtrix3 dependencies
-      run: |
-        sudo apt update
-        sudo apt-get install git g++ python python-numpy libeigen3-dev zlib1g-dev libgl1-mesa-dev libfftw3-dev libtiff5-dev
-    - name: Install MRtrix3 from source
+    - name: Install Minconda
+      uses: conda-incubator/setup-miniconda@v2
+      with:
+        auto-activate-base: true
+        activate-environment: ""
+    - name: Install MRtrix via Conda
       run: |
-        git clone https://github.com/MRtrix3/mrtrix3.git
-        cd mrtrix3
-        ./configure -nogui
-        ./build bin/mrconvert
-        cd -
+        conda install -c mrtrix3 mrtrix3
+        mrconvert --version
     - name: Set up Python ${{ matrix.python-version }}
       uses: actions/setup-python@v2
       with: