Add ci workflow to run unit tests on pr or merge into main branches S…

…CMSUITE-9942 SO107

.github/workflows/ci.yml

@@ -0,0 +1,76 @@
+name: CI
+
+on:
+# Run on creating or updating a PR
+  pull_request:
+    types: [opened, synchronize, reopened]
+
+# And pushing to the trunk or fix branches
+  push:
+    branches:
+      - trunk
+      - 'fix*'
+
+jobs:
+  build:
+
+#   Run on ubuntu, mac and windows for python 3.8 (in AMS python stack) and 3.11
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        os: [ubuntu-latest, macos-latest, windows-latest]
+        python-version: ["3.8", "3.11"]
+
+    steps:
+#     Checkout and copy into SCM namespace
+      - name: Checkout
+        uses: actions/checkout@v4
+
+      - name: Move Repo To SCM Namespace and Set PYTHONPATH
+        if: runner.os != 'Windows'
+        run: |
+          mkdir -p scm/plams
+          find . -mindepth 1 -maxdepth 1 -not -name 'scm' -not -name '.*' -exec mv {} scm/plams/ \;
+          echo "PYTHONPATH=$(pwd):$PYTHONPATH" >> $GITHUB_ENV
+
+      - name: Move Repo To SCM Namespace and Set PYTHONPATH (Windows)
+        if: runner.os == 'Windows'
+        shell: pwsh
+        run: |
+          New-Item -Path scm\plams -ItemType Directory -Force
+          
+          Get-ChildItem -Directory | Where-Object { $_.Name -ne 'scm' } | ForEach-Object {
+            Move-Item -Path $_.FullName -Destination scm\plams
+          }
+
+          Get-ChildItem -File | ForEach-Object {
+            Move-Item -Path $_.FullName -Destination scm\plams
+          }
+
+          echo "PYTHONPATH=$(pwd);$env:PYTHONPATH" >> $env:GITHUB_ENV
+
+#     Set up python env
+      - name: Set Up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Display Python Version
+        run: python -c "import sys; print(sys.version)"
+      - name: Install Dependencies
+        working-directory: scm/plams
+        run: |
+          python -m pip install --upgrade pip
+          pip install -r requirements.txt
+          pip install pytest
+          pip install coverage
+
+#     Run tests and calculate code coverage
+      - name: Run Unit Tests
+        working-directory: scm/plams
+        run: |
+          echo "PYTHONPATH is $PYTHONPATH"
+          pwd
+          coverage run -m pytest unit_tests
+      - name: Evaluate Coverage
+        working-directory: scm/plams
+        run: coverage report --omit="unit_tests/*" -i --fail-under=30

requirements.txt

@@ -0,0 +1,6 @@
+dill==0.3.6
+numpy==1.23.4
+scipy==1.9.3
+natsort==8.1.0
+ase==3.22.1
+rdkit==2024.03.1

setup.py

@@ -32,7 +32,8 @@
     ],
     keywords=["molecular modeling", "computational chemistry", "workflow", "python interface"],
     python_requires=">=3.6",
-    install_requires=["dill>=0.2.4", "numpy", "scipy", "natsort"],
+    install_requires=["dill>=0.2.4", "numpy<2", "scipy", "natsort"],
+    extras_require={"chem_tools": ["ase", "rdkit"]},
     packages=packages,
     package_dir={"scm.plams": "."},
     package_data={

unit_tests/test_helpers.py

@@ -1,4 +1,7 @@
 import builtins
+import pytest
+import os
+
 from scm.plams.core.settings import (
     SafeRunSettings,
     LogSettings,
@@ -62,3 +65,12 @@ def assert_config_as_expected(
         assert isinstance(config.job.runscript, RunScriptSettings)
         assert isinstance(config.jobmanager, JobManagerSettings)
         assert isinstance(config, ConfigSettings)
+
+
+def skip_if_no_ams_installation():
+    """
+    Check whether the AMSBIN environment variable is set, and therefore if there is an AMS installation present.
+    If there is no installation, skip the test with a warning.
+    """
+    if os.getenv("AMSBIN") is None:
+        pytest.skip("Skipping test as cannot find AMS installation. '$AMSBIN' environment variable is not set.")

unit_tests/test_inputparser.py

@@ -3,7 +3,7 @@
 from importlib import reload
 
 from scm.plams.core.settings import Settings
-from scm.plams.unit_tests.test_helpers import get_mock_import_function
+from scm.plams.unit_tests.test_helpers import get_mock_import_function, skip_if_no_ams_installation
 
 
 @pytest.fixture
@@ -96,6 +96,9 @@ def test_to_dict_with_scmlibbase_succeeds(system_text_inputs):
 
 
 def get_monkeypatched_input_parser(monkeypatch):
+    # If there is no AMS installation the input parser will not run so skip test with a warning
+    skip_if_no_ams_installation()
+
     # Mock scm.libbase import failing (even when present in the env)
     mock_import_function = get_mock_import_function("scm.libbase")
     monkeypatch.setattr(builtins, "__import__", mock_import_function)
@@ -114,6 +117,9 @@ def get_monkeypatched_input_parser(monkeypatch):
 
 
 def get_input_parser_or_skip():
+    # If there is no AMS installation the input parser will not run so skip test with a warning
+    skip_if_no_ams_installation()
+
     from scm.plams.interfaces.adfsuite.inputparser import InputParserFacade, InputParser
 
     # Get an instance of the input parser facade using the scm.libbase parser

unit_tests/test_interfaces.py

@@ -4,6 +4,7 @@
     pass
 
 from scm.plams import AMSJob, Settings
+from scm.plams.unit_tests.test_helpers import skip_if_no_ams_installation
 
 
 def test_hybrid_engine_input():
@@ -53,6 +54,7 @@ def test_hybrid_engine_input():
 EndEngine
 
 """
+    skip_if_no_ams_installation()
     job = AMSJob.from_input(AMSinput)
     assert job.get_input() == AMSinput
 
@@ -105,6 +107,7 @@ def test_list_block_input():
 EndEngine
 
 """
+    skip_if_no_ams_installation()
     job = AMSJob.from_input(AMSinput)
     assert job.get_input() == AMSinput