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

…CMSUITE-9942 SO107

.github/workflows/ci.yml

@@ -0,0 +1,136 @@
+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_and_test:
+#   Run on ubuntu, mac and windows for python 3.8 (in AMS python stack) and 3.11
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        os: [ubuntu-latest, macos-latest, windows-latest]
+        python-version: ["3.8", "3.11"]
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+
+      - name: Move Repo To SCM Namespace and Set PYTHONPATH
+        if: runner.os != 'Windows'
+        run: |
+          mkdir -p scm/plams
+          find . -mindepth 1 -maxdepth 1 -not -name 'scm' -not -name '.*' -exec mv {} scm/plams/ \;
+          echo "PYTHONPATH=$(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
+
+      - name: Set Up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Install Dependencies
+        working-directory: scm/plams
+        run: |
+          python -m pip install --upgrade pip
+          pip install -r requirements.txt
+          pip install pytest
+          pip install coverage
+          pip install black
+
+      - name: Run Unit Tests
+        working-directory: scm/plams
+        run: |
+          pwd
+          coverage run -m pytest unit_tests
+#     ToDo: Bump the fail-under threshold over time until acceptable level is reached
+      - name: Evaluate Coverage
+        working-directory: scm/plams
+        run: coverage report --omit="unit_tests/*" -i --fail-under=30
+
+
+  lint:
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout Code
+        uses: actions/checkout@v4
+
+      - name: Set Up Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: "3.11"
+
+      - name: Install Dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install black
+          pip install "black[jupyter]"
+          pip install flake8
+
+      - name: Run Black Formatting Check
+        run: |
+#          black --check -t py38 -l 120 .
+          echo "skip for now"
+
+      - name: Run Flake8 Check
+        run: |
+          flake8 --color never --count --config .flake8 .
+          
+
+  build-docs:
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout Code
+        uses: actions/checkout@v4
+
+      - name: Move Repo To SCM Namespace and Set PYTHONPATH
+        if: runner.os != 'Windows'
+        run: |
+          mkdir -p scm/plams
+          find . -mindepth 1 -maxdepth 1 -not -name 'scm' -not -name '.*' -exec mv {} scm/plams/ \;
+          echo "PYTHONPATH=$(pwd):$PYTHONPATH" >> $GITHUB_ENV
+
+      - name: Set Up Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: "3.11"
+
+      - name: Install Dependencies
+        working-directory: scm/plams
+        run: |
+          python -m pip install --upgrade pip
+          pip install -r requirements.txt
+          cd doc
+          pip install -r requirements.txt
+
+#     Turn on the -W flag when building once warnings to external links have been resolved
+#     ToDo: add a warning allowlist to check the warnings logged via -w
+      - name: Build Sphinx Docs
+        working-directory: scm/plams/doc
+        run: |
+          python build_plams_doc

doc/build_plams_doc

@@ -6,45 +6,57 @@ import sys
 from os.path import join as opj
 
 command = ""
-#Try to locate sphinx-build executable
-if 'AMSBIN' in os.environ:
-    command = opj(os.path.expandvars('$AMSBIN'), 'python3.5', 'bin', 'sphinx-build')
+# Try to locate sphinx-build executable
+if "AMSBIN" in os.environ:
+    command = opj(os.path.expandvars("$AMSBIN"), "python3.5", "bin", "sphinx-build")
     if not os.path.exists(command):
         # This might be a windows machine
-        command = opj(os.path.expandvars('$AMSBIN'), 'python3.5', 'Scripts', 'sphinx-build.exe')
+        command = opj(
+            os.path.expandvars("$AMSBIN"), "python3.5", "Scripts", "sphinx-build.exe"
+        )
         if os.path.exists(command):
             # starting sphinx-build on windows is tricky...
-            command = ['sh', opj(os.path.expandvars('$AMSBIN'), 'amspython'), '-m', 'sphinx']
+            command = [
+                "sh",
+                opj(os.path.expandvars("$AMSBIN"), "amspython"),
+                "-m",
+                "sphinx",
+            ]
         else:
-            print('Warning: AMSBIN found in environment, but failed to locate sphinx-build')
+            print(
+                "Warning: AMSBIN found in environment, but failed to locate sphinx-build"
+            )
             command = ""
 if command == "":
-    null = open(os.devnull, 'wb')
+    null = open(os.devnull, "wb")
     try:
-        subprocess.call(['sphinx-build','--version'], stdout=null, stderr=null)
-        command = 'sphinx-build'
+        subprocess.call(["sphinx-build", "--version"], stdout=null, stderr=null)
+        command = "sphinx-build"
     except OSError:
         try:
-            subprocess.call(['sphinx-build2','--version'], stdout=null, stderr=null)
-            command = 'sphinx-build2'
+            subprocess.call(["sphinx-build2", "--version"], stdout=null, stderr=null)
+            command = "sphinx-build2"
         except OSError:
-            print('Error: Sphinx executable not found!')
+            print("Error: Sphinx executable not found!")
             null.close()
             sys.exit(0)
     null.close()
 
 location = os.path.dirname(os.path.realpath(__file__))
-#Source of documentation should be located in "source" subfolder next to this script
-source = opj(location, 'source')
+# Source of documentation should be located in "source" subfolder next to this script
+source = opj(location, "source")
 
-#Target can be given as command line argument, if not the "build" subfolder is used
+# Target can be given as command line argument, if not the "build" subfolder is used
 if len(sys.argv) > 1:
     target = sys.argv[1]
 else:
-    target = opj(location, 'build')
+    target = opj(location, "build")
 
+warning_file = "build_plams_doc_warn_errors.txt"
 if isinstance(command, list):
     # on windows command is a list of multiple items
-    subprocess.call(command + [source, target])
+    return_code = subprocess.call(command + [source, target, "-w", warning_file])
 else:
-    subprocess.call([command, source, target])
+    return_code = subprocess.call([command, source, target, "-w", warning_file])
+
+sys.exit(return_code)

doc/requirements.txt

@@ -0,0 +1,4 @@
+sphinx
+sphinx_copybutton
+sphinx_tabs
+ipython

doc/source/conf.py

@@ -21,7 +21,7 @@ def modify_signature(app, what, name, obj, options, signature, return_annotation
 
 def setup(app):
     if not tags.has("scm_theme"):
-        app.add_stylesheet("boxes.css")
+        app.add_css_file("boxes.css")
     app.add_directive("warning", Danger)
     app.add_directive("technical", Important)
     app.connect("autodoc-process-signature", modify_signature)
@@ -41,7 +41,7 @@ def setup(app):
 
 else:
 
-    extensions = []
+    extensions = ["sphinx_tabs.tabs"]
 
     # Add any paths that contain templates here, relative to this directory.
     templates_path = ["_templates"]
@@ -200,7 +200,11 @@ def setup(app):
 # configuration for intersphinx: refer to the Python standard library.
 intersphinx_mapping = {"python3": ("http://docs.python.org/3.8", None)}
 
-autodoc_default_options = {"members": True, "private-members": True, "special-members": True}
+autodoc_default_options = {
+    "members": True,
+    "private-members": True,
+    "special-members": True,
+}
 autodoc_member_order = "bysource"
 autodoc_typehints = "none"
 

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