From 6f90627d137276a1b5dba919fd262852509e7d36 Mon Sep 17 00:00:00 2001
From: Manuel Holtgrewe <manuel.holtgrewe@bih-charite.de>
Date: Fri, 5 Jan 2024 16:33:15 +0100
Subject: [PATCH] micromamba

---
 .github/workflows/main.yml | 42 ++++++++++++++++++++++++++++----------
 1 file changed, 31 insertions(+), 11 deletions(-)

diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
index 48e5a9e..0629ded 100644
--- a/.github/workflows/main.yml
+++ b/.github/workflows/main.yml
@@ -26,7 +26,7 @@ jobs:
       - name: Install Python
         uses: actions/setup-python@v2
         with:
-          python-version: "3.8"
+          python-version: "3.10"
 
       - name: Install dependencies
         run: |
@@ -55,6 +55,33 @@ jobs:
           # - "3.11"  # no pysam binaries yet
     needs: linting
     steps:
+      - name: Construct environment.yml file for python version
+        run: |
+          cat <<EOF > /tmp/environment.yml
+          name: ngs-chew
+          channels:
+            - bioconda
+            - conda-forge
+            - defaults
+          dependencies:
+            - python=${{ matrix.python-version }}
+            - pip
+            - bcftools
+            - samtools
+            - pysam
+            - pandas
+            - scipy
+            - numpy
+          EOF
+
+      - name: Setup formatting environment
+        uses: mamba-org/setup-micromamba@v1
+        with:
+          environment-file: /tmp/environment.yml
+          init-shell: bash
+          cache-environment: true
+          post-cleanup: none  # breaks otherwise
+
       - name: Install Python via conda
         uses: s-weigand/setup-conda@v1
         with:
@@ -62,23 +89,16 @@ jobs:
           conda-channels: defaults,bioconda,conda-forge
 
       - name: Checkout repository
-        uses: actions/checkout@v2
+        uses: actions/checkout@v3
         with:
           lfs: true
 
-      - name: Install mamba
-        run: conda install -y mamba
-
-      - name: Install external dependencies with mamba
-        run: mamba install -y bcftools samtools
-
-      - name: Save time by installing packages via mamba
-        run: mamba install -y pysam pandas scipy numpy
-
       - name: Install test dependencies via pip
         run: pip install -r requirements/test.txt
+        shell: bash -el {0}
 
       - name: Run tests
         run: |
           pytest
           coverage report
+        shell: bash -el {0}