other edits

.github/workflows/dev_ci_cd_conda.yml

@@ -13,9 +13,18 @@ jobs:
       max-parallel: 4
       matrix:
         python-version: ["3.10"]
-
+    defaults:
+          run:
+            shell: bash -l {0}
     steps:
     - uses: actions/checkout@v4
+    - uses: conda-incubator/setup-miniconda@v2
+      with:
+        miniconda-version: "latest"
+        channels: bioconda, conda-forge, defaults
+        use-only-tar-bz2: true  # IMPORTANT: This needs to be set for caching to work properly!
+        auto-update-conda: true
+        auto-activate-base: true
     - name: Set up Python ${{ matrix.python-version }}
       uses: actions/setup-python@v5
       with:
@@ -31,9 +40,8 @@ jobs:
         conda install gdal --yes
         conda upgrade numpy --yes
     - name: Initialize Environment
-      shell: bash -el {0}
       run: |
-        conda init --all --quiet
+        source ~/.bashrc
         conda activate env
     - name: Run Tests
       env: