From 87d632b1864fa1513ba7178fa66a857e6e65c7bc Mon Sep 17 00:00:00 2001
From: Remi-Andre Olsen <remi-andre.olsen@scilifelab.se>
Date: Thu, 2 Nov 2023 16:51:38 +0100
Subject: [PATCH] Switch to micromamba

---
 .github/workflows/anglerfish.yml | 15 ++++++---------
 1 file changed, 6 insertions(+), 9 deletions(-)

diff --git a/.github/workflows/anglerfish.yml b/.github/workflows/anglerfish.yml
index d7a1aaa..2077e95 100644
--- a/.github/workflows/anglerfish.yml
+++ b/.github/workflows/anglerfish.yml
@@ -7,36 +7,33 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: [3.9.18, 3.10.2]
+        python-version: [3.10.2]
 
     steps:
       # Checkout code and install miniconda + environment
       - uses: actions/checkout@v4
-      - uses: conda-incubator/setup-miniconda@v2
+      - uses: mamba-org/setup-micromamba@v1
         with:
-           activate-environment: anglerfish
+           init-shell: bash
+           create-args: >-
+            python=${{ matrix.python-version }}
+            pip
            environment-file: environment.yml
-           python-version: ${{ matrix.python-version }}
-           auto-update-conda: true
-           auto-activate-base: false
 
       # Install Anglerfish
       - shell: bash -l {0}
         name: Install Anglerfish
         run: |
-          conda activate anglerfish
           python -m pip install .
 
       # Run anglerfish --help
       - shell: bash -l {0}
         name: Test anglerfish
         run: | 
-          conda activate anglerfish
           anglerfish --help
 
       # Run anglerfish using test data
       - shell: bash -l {0}
         name: Run anglerfish with test data
         run: |
-          conda activate anglerfish
           anglerfish -s test/samples.csv