From a144c3e023d23204b03c65c085caa27abc22bc32 Mon Sep 17 00:00:00 2001
From: Christian Diener <ch.diener@gmail.com>
Date: Thu, 21 Nov 2024 13:17:37 +0100
Subject: [PATCH] switch to conda with libmamba

---
 .github/workflows/qiime_dev.yml    | 10 +++-------
 .github/workflows/test_package.yml | 12 ++++--------
 2 files changed, 7 insertions(+), 15 deletions(-)

diff --git a/.github/workflows/qiime_dev.yml b/.github/workflows/qiime_dev.yml
index ba21b58..39388a0 100644
--- a/.github/workflows/qiime_dev.yml
+++ b/.github/workflows/qiime_dev.yml
@@ -23,10 +23,6 @@ jobs:
     - uses: actions/checkout@v4
     - name: Setup conda
       uses: conda-incubator/setup-miniconda@v3
-      with:
-        miniforge-variant: Mambaforge
-        miniforge-version: latest
-        use-mamba: true
     - shell: bash -l {0}
       run: |
         conda info
@@ -35,19 +31,19 @@ jobs:
       shell: bash -l {0}
       run: |
         wget https://raw.githubusercontent.com/qiime2/environment-files/master/latest/staging/qiime2-latest-py38-${{matrix.os.short}}-conda.yml
-        mamba env create -n qiime2-dev --file qiime2-latest-py38-${{matrix.os.short}}-conda.yml
+        conda env create -n qiime2-dev --file qiime2-latest-py38-${{matrix.os.short}}-conda.yml
         rm qiime2-latest-py38-${{matrix.os.short}}-conda.yml
     - name: Install q2-micom
       shell: bash -l {0}
       run: |
         conda activate qiime2-dev
-        mamba env update -n qiime2-dev -f q2-micom.yml
+        conda env update -n qiime2-dev -f q2-micom.yml
         pip install -e .
     - name: Install CPLEX
       shell: bash -l {0}
       run: |
         conda activate qiime2-dev
-        mamba install -y -c ibmdecisionoptimization cplex
+        conda install -y -c ibmdecisionoptimization cplex
     - name: Lint with flake8
       shell: bash -l {0}
       run: |
diff --git a/.github/workflows/test_package.yml b/.github/workflows/test_package.yml
index eaf669a..84cec4e 100644
--- a/.github/workflows/test_package.yml
+++ b/.github/workflows/test_package.yml
@@ -33,12 +33,8 @@ jobs:
 
     steps:
     - uses: actions/checkout@v4
-    - name: Setup Mambaforge
+    - name: Setup conda
       uses: conda-incubator/setup-miniconda@v3
-      with:
-        miniforge-variant: Mambaforge
-        miniforge-version: latest
-        use-mamba: true
     - shell: bash -l {0}
       run: |
         conda info
@@ -51,17 +47,17 @@ jobs:
     - name: Install Qiime 2
       shell: bash -l {0}
       run: |
-        mamba env create -n qiime2-dev --file env.yml
+        conda env create -n qiime2-dev --file env.yml
     - name: Install CPLEX
       shell: bash -l {0}
       run: |
         conda activate qiime2-dev
-        mamba install -v -c ibmdecisionoptimization cplex
+        conda install -v -c ibmdecisionoptimization cplex
     - name: Install q2-micom
       shell: bash -l {0}
       run: |
         conda activate qiime2-dev
-        mamba env update -n qiime2-dev -f q2-micom.yml
+        conda env update -n qiime2-dev -f q2-micom.yml
         pip install -e .
     - name: Lint with flake8
       shell: bash -l {0}