Refactor CI workflow to use micromamba

Updated GitHub Actions workflow to use micromamba for environment setup and dependency installation.

Author: xiaochendu

.github/workflows/tests.yml

@@ -12,32 +12,46 @@ jobs:
       max-parallel: 5
 
     steps:
-    - uses: actions/checkout@v4
-    - name: Set up Python 3.11
-      uses: actions/setup-python@v3
+    # Checkout repository
+    - name: Checkout source
+      uses: actions/checkout@v4
+
+    # Setup micromamba and Python environment
+    - name: Setup micromamba with test environment
+      uses: mamba-org/setup-micromamba@v1
       with:
-        python-version: '3.11'
-    - name: Add conda to system path
-      run: |
-        # $CONDA is an environment variable pointing to the root of the miniconda directory
-        echo $CONDA/bin >> $GITHUB_PATH
-    - name: Install conda dependencies
-      run: |
-        conda env update --file environment.yml --name base
-    - name: Install pip dependencies
+        environment-file: environment.yml    # Make sure uv is included in this file OR:
+        environment-name: test-env
+        create-args: >-
+          uv
+          torch>=2.1.0,<2.6.0
+        init-shell: bash
+        generate-run-shell: true
+
+    # Install Python dependencies using uv
+    - name: Install Python dependencies with uv
+      shell: micromamba-shell bash
       run: |
-        pip install "torch<2.6.0,>=2.1.0"
-        pip install -e '.[dev]'
-    - name: Append LAMMPS paths
+        uv pip install -e '.[dev]'
+
+    # Set up environment variables for LAMMPS
+    - name: Configure LAMMPS paths
+      shell: micromamba-shell bash
       run: |
         echo "LAMMPS_POTENTIALS=$GITHUB_WORKSPACE/mcmc/potentials" >> $GITHUB_ENV
-        echo "LAMMPS_COMMAND=$CONDA/bin/lmp" >> $GITHUB_ENV
-        echo "ASE_LAMMPSRUN_COMMAND=$CONDA/bin/lmp" >> $GITHUB_ENV
-    - name: Check LAMMPS paths
+        echo "LAMMPS_COMMAND=$(which lmp)" >> $GITHUB_ENV
+        echo "ASE_LAMMPSRUN_COMMAND=$(which lmp)" >> $GITHUB_ENV
+
+    # Display configured LAMMPS paths (for debugging)
+    - name: Print LAMMPS paths
+      shell: micromamba-shell bash
       run: |
         echo "LAMMPS_POTENTIALS = $LAMMPS_POTENTIALS"
         echo "LAMMPS_COMMAND = $LAMMPS_COMMAND"
         echo "ASE_LAMMPSRUN_COMMAND = $ASE_LAMMPSRUN_COMMAND"
-    - name: Test with pytest
+
+    # Run tests
+    - name: Run tests with pytest
+      shell: micromamba-shell bash
       run: |
         pytest --capture=no --cov --cov-report=xml