From a268a9722a60befcd1696562e21bf27b8417704a Mon Sep 17 00:00:00 2001
From: maxulysse <max.u.garcia@gmail.com>
Date: Fri, 13 Dec 2024 16:53:40 +0100
Subject: [PATCH] fix conda pytests cf #7215

---
 .github/workflows/pytest-workflow.yml | 19 ++++++-------------
 tests/config/nextflow.config          |  4 ++--
 2 files changed, 8 insertions(+), 15 deletions(-)

diff --git a/.github/workflows/pytest-workflow.yml b/.github/workflows/pytest-workflow.yml
index 01fa7f39a98..7c0d70c77c2 100644
--- a/.github/workflows/pytest-workflow.yml
+++ b/.github/workflows/pytest-workflow.yml
@@ -29,7 +29,7 @@ env:
   NXF_SINGULARITY_LIBRARYDIR: ${{ github.workspace }}/.singularity
   GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
   # renovate: datasource=github-releases depName=nextflow-io/nextflow versioning=semver
-  NXF_VER: "24.10.1"
+  NXF_VER: "24.10.2"
 
 jobs:
   pytest-changes:
@@ -278,20 +278,13 @@ jobs:
           mkdir -p $NXF_SINGULARITY_CACHEDIR
           mkdir -p $NXF_SINGULARITY_LIBRARYDIR
 
-      - name: Set up miniconda
+      - name: Conda setup
+        if: matrix.profile == 'conda'
         uses: conda-incubator/setup-miniconda@d2e6a045a86077fb6cad6f5adf368e9076ddaa8d # v3
         with:
-          miniconda-version: "latest"
-          channels: conda-forge,bioconda
-          python-version: "3.11"
-
-      - name: Conda setup
-        run: |
-          conda clean -a
-          conda install -n base conda-libmamba-solver
-          conda config --set solver libmamba
-          echo $(realpath $CONDA)/condabin >> $GITHUB_PATH
-          echo $(realpath python) >> $GITHUB_PATH
+          auto-update-conda: true
+          conda-solver: libmamba
+          conda-remove-defaults: true
 
       # Test the module
       - name: Run pytest-workflow
diff --git a/tests/config/nextflow.config b/tests/config/nextflow.config
index 9c55a92a7df..de3b5fd8b1e 100644
--- a/tests/config/nextflow.config
+++ b/tests/config/nextflow.config
@@ -17,8 +17,8 @@ if ("$PROFILE" == "singularity") {
     singularity.enabled = true
     singularity.autoMounts = true
 } else if ("$PROFILE" == "conda") {
-    conda.enabled = true
-    conda.useMicromamba = true
+    conda.enabled  = true
+    conda.channels = ['conda-forge', 'bioconda']
 } else if ("$PROFILE" == "mamba") {
     conda.enabled  = true
     conda.useMamba = true