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Add ci workflow to run unit tests on pr or merge into main branches S…
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…CMSUITE-9942 SO107
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dormrod committed Aug 15, 2024
1 parent a4d9060 commit d3e5f24
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136 changes: 136 additions & 0 deletions .github/workflows/ci.yml
Original file line number Diff line number Diff line change
@@ -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:

unit-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
run: |
# black --check -t py38 -l 120 .
echo "skip for now"

- name: Run Flake8
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
48 changes: 30 additions & 18 deletions doc/build_plams_doc
Original file line number Diff line number Diff line change
Expand Up @@ -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)
4 changes: 4 additions & 0 deletions doc/requirements.txt
Original file line number Diff line number Diff line change
@@ -0,0 +1,4 @@
sphinx
sphinx_copybutton
sphinx_tabs
ipython
10 changes: 7 additions & 3 deletions doc/source/conf.py
Original file line number Diff line number Diff line change
Expand Up @@ -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)
Expand All @@ -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"]
Expand Down Expand Up @@ -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"

Expand Down
6 changes: 6 additions & 0 deletions requirements.txt
Original file line number Diff line number Diff line change
@@ -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
3 changes: 2 additions & 1 deletion setup.py
Original file line number Diff line number Diff line change
Expand Up @@ -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={
Expand Down
12 changes: 12 additions & 0 deletions unit_tests/test_helpers.py
Original file line number Diff line number Diff line change
@@ -1,4 +1,7 @@
import builtins
import pytest
import os

from scm.plams.core.settings import (
SafeRunSettings,
LogSettings,
Expand Down Expand Up @@ -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.")
8 changes: 7 additions & 1 deletion unit_tests/test_inputparser.py
Original file line number Diff line number Diff line change
Expand Up @@ -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
Expand Down Expand Up @@ -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)
Expand All @@ -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
Expand Down
3 changes: 3 additions & 0 deletions unit_tests/test_interfaces.py
Original file line number Diff line number Diff line change
Expand Up @@ -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():
Expand Down Expand Up @@ -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

Expand Down Expand Up @@ -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

Expand Down

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