Enables parallel pytest execution and micromamba CI

.github/workflows/ci.yml

@@ -91,6 +91,9 @@ jobs:
       - name: Install all extras - CI
         shell: micromamba-shell {0}
         working-directory: ARC
+        env:
+          MAMBA_ALWAYS_YES: "true"
+          CONDA_ALWAYS_YES: "true"
         run: make install-ci
 
       - name: Set TS-GCN and AutoTST in PYTHONPATH
@@ -111,15 +114,15 @@ jobs:
         run: |
           echo "Running Unit Tests..."
           export PYTHONPATH="${{ github.workspace }}/AutoTST:${{ github.workspace }}/KinBot:$PYTHONPATH"
-          pytest arc/ --cov --cov-report=xml -ra -vv
+          pytest arc/ --cov --cov-report=xml -ra -vv -n auto
 
       - name: Run Functional Tests
         shell: micromamba-shell {0}
         working-directory: ${{ github.workspace }}/ARC
         run: |
           echo "Running Functional Tests from $(pwd)..."
           export PYTHONPATH="${{ github.workspace }}/AutoTST:${{ github.workspace }}/KinBot:$PYTHONPATH"
-          pytest functional/ -ra -vv
+          pytest functional/ -ra -vv -n auto
 
       - name: Upload coverage data
         uses: codecov/codecov-action@v3

.github/workflows/update-cache.yml

@@ -111,32 +111,4 @@ jobs:
           ref: v2.0.6
           fetch-depth: 1
 
-      # ────────── Conda package cache ──────────
-      - name: Cache Conda packages
-        id: cache-conda-pkgs
-        uses: actions/cache@v4
-        with:
-          path: ~/conda_pkgs_dir
-          key: ${{ runner.os }}-conda-0-${{ hashFiles('environment.yml') }}
-
-      # ────────── Create / restore env ──────────
-      - name: Setup ARC Env
-        uses: conda-incubator/setup-miniconda@v3.2.0
-        with:
-          auto-update-conda: true
-          environment-file: environment.yml
-          activate-environment: arc_env
-          miniconda-version: latest
-          conda-solver: libmamba
-
-      # ────────── Update env & save to cache ──────────
-      - name: Update environment
-        run: conda env update -n arc_env -f environment.yml
-
-      - name: Cache ARC env
-        if: github.event_name == 'push'
-        uses: actions/cache@v4
-        with:
-          path: ${{ env.CONDA }}/envs
-          key: conda-${{ runner.os }}-${{ runner.arch }}-0
-
+      # ────────── Env caching handled in CI workflow ──────────

Makefile

@@ -50,13 +50,13 @@ help:
 test: test-unittests
 
 test-unittests:
-	pytest arc/ --cov --cov-report=xml -ra -vv
+	pytest arc/ --cov --cov-report=xml -ra -vv -n auto
 
 test-functional:
-	pytest functional/ -ra -vv
+	pytest functional/ -ra -vv -n auto
 
 test-all:
-	pytest arc/ functional/ --cov --cov-report=xml -ra -vv
+	pytest arc/ functional/ --cov --cov-report=xml -ra -vv -n auto
 
 install-all: install
 

devtools/install_rmg.sh

@@ -104,10 +104,10 @@ fi
 
 if $COMMAND_PKG env list | awk '{print $1}' | grep -qx "$ENV_NAME"; then
     echo ">>> Updating existing environment: $ENV_NAME"
-    $COMMAND_PKG env update -n "$ENV_NAME" -f environment.yml --prune
+    $COMMAND_PKG env update -n "$ENV_NAME" -f environment.yml --prune --strict-channel-priority
 else
     echo ">>> Creating new environment: $ENV_NAME"
-    $COMMAND_PKG env create -n "$ENV_NAME" -f environment.yml -y
+    $COMMAND_PKG env create -n "$ENV_NAME" -f environment.yml -y --strict-channel-priority
 fi
 
 ###############################################################################

devtools/install_torchani.sh

@@ -1,5 +1,5 @@
 #!/usr/bin/env bash
-set -euo pipefail
+set -eo pipefail
 
 # Enable tracing of each command, but tee it to a logfile
 exec 3>&1 4>&2

devtools/tani_environment.yml

@@ -4,14 +4,14 @@ channels:
   - conda-forge
   - defaults
 dependencies:
-  - python
-  - numpy
+  - python =3.10.8
+  - numpy =1.24
   - pandas
   - ase
-  - torchani >=2.2.3
-  - pytorch
-  - torchvision
-  - torchaudio
+  - torchani =2.2
+  - pytorch =1.13.1
+  - torchvision =0.14.1
+  - torchaudio =0.13.1
   - cpuonly
   - scikit-learn
   - matplotlib

environment.yml

@@ -39,6 +39,7 @@ dependencies:
   - conda-forge::pytables
   - conda-forge::pytest
   - conda-forge::pytest-cov
+  - conda-forge::pytest-xdist
   - conda-forge::pyyaml
   - conda-forge::rdkit >=2025.03
   - conda-forge::scipy

requirements.txt

@@ -32,6 +32,7 @@ sphinxcontrib-jsmath
 # For running the unit tests
 pytest
 pytest-cov
+pytest-xdist
 coverage
 
 # For interactive use