From 5bffdbea93753aba269c14d0d5cd62074768c6e2 Mon Sep 17 00:00:00 2001
From: Anna Moeller <je30bery@idea-ramses.aibe.uni-erlangen.de>
Date: Fri, 19 Jun 2026 09:57:38 +0200
Subject: [PATCH] Modernise CI workflow
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- Switch from setup-miniconda to mamba-org/setup-micromamba (faster,
  built-in environment caching)
- Update actions/checkout v2 → v4
- Add pull_request trigger and pyproject.toml to watched paths
- Add fail-fast: false so one Python version failure doesn't cancel others
- Install package with pip install -e ".[test]" to get pytest and pytest-cov
- Replace python tests/test_mwe.py with pytest -m "not slow"

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
---
 .github/workflows/python-package-conda.yml | 49 ++++++++++++----------
 1 file changed, 26 insertions(+), 23 deletions(-)

diff --git a/.github/workflows/python-package-conda.yml b/.github/workflows/python-package-conda.yml
index 480629d..debddd0 100644
--- a/.github/workflows/python-package-conda.yml
+++ b/.github/workflows/python-package-conda.yml
@@ -1,42 +1,45 @@
-name: Test MWE with Python 3.9-3.13
+name: CI
 
 on:
   push:
     paths:
       - 'scxmatch/**'
       - 'tests/**'
+      - 'pyproject.toml'
+      - '.github/workflows/**'
+  pull_request:
+    paths:
+      - 'scxmatch/**'
+      - 'tests/**'
+      - 'pyproject.toml'
       - '.github/workflows/**'
-
 
 jobs:
-  test-bioconda-install:
+  test:
     runs-on: ubuntu-latest
 
     strategy:
+      fail-fast: false
       matrix:
         python-version: ["3.9", "3.10", "3.11", "3.12", "3.13"]
 
     steps:
-      - name: Checkout repo
-        uses: actions/checkout@v2
+      - uses: actions/checkout@v4
 
-      - name: Set up Miniconda
-        uses: conda-incubator/setup-miniconda@v2
+      - name: Set up Micromamba
+        uses: mamba-org/setup-micromamba@v2
         with:
-          miniconda-version: 'latest'
-          channels: conda-forge, bioconda
-          auto-activate-base: true
+          environment-name: test-env
+          create-args: >-
+            python=${{ matrix.python-version }}
+            graph-tool
+          channels: conda-forge
+          cache-environment: true
+
+      - name: Install package with test dependencies
+        shell: bash -el {0}
+        run: pip install -e ".[test]"
 
-      - name: Install dependencies and run test
-        shell: bash -l {0}
-        run: |
-          conda create -n test-environment -y \
-            python=${{ matrix.python-version }} \
-            pip
-      
-          conda install -n test-environment -y -c conda-forge graph-tool
-      
-          conda run -n test-environment python -m pip install --upgrade pip
-          conda run -n test-environment python -m pip install .
-      
-          conda run -n test-environment python tests/test_mwe.py
+      - name: Run tests
+        shell: bash -el {0}
+        run: pytest -m "not slow"