Test suite & CI/CD#

cotainr comes with an extensive test suite which is run automatically via continuous integration when code is committed to the cotainr GitHub repository: DeiC-HPC/cotainr

The test suite#

The cotainr test suite is implemented using pytest and uses the pytest-cov plugin for reporting test coverage. The entire test suite is run from the repository root directory by issuing:

$ pytest

Dependencies#

In order to run the tests, you must have the Python packages listed in test-requirements.txt installed, i.e.

pytest>=6.0
pytest-cov>=2.10

Pytest marks#

The following custom pytest marks are implemented:

pytest.mark.endtoend(): end-to-end tests of workflows using cotainr (may take a long time to run)
pytest.mark.singularity_integration(): integration tests that require and use singularity (may take a long time to run)
pytest.mark.conda_integration(): integration tests that installs and manipulates a conda environment (may take a long time to run)

You may select/deselect end-to-end and integration tests using the -m option to pytest, e.g. to only run the unittest:

$ pytest -m "not endtoend and not singularity_integration and not conda_integration"

The tests folder hierarchy and naming conventions#

All tests are placed in the cotainr/tests folder. This tests folder acts as a sub-package in cotainr. The cotainr.tests sub-package contains a sub-package for each module in cotainr (structured in the same way as the modules in cotainr). Each such test sub-package contains a module for each class/function in the corresponding cotainr module. If the test module relates to a class, it contains, for each method in that class, one test class with any number of tests cases (implemented as methods). If the test module relates to a function, it contains one test class for that function and, optionally, one test class for any private “helper” function to that function. Here are a few examples to illustrate all of this:

All tests of the cotainr.pack.CondaInstall class are placed in cotainr/tests/pack/test_conda_install.py which acts as a python module reachable via cotainr.tests.pack.test_conda_install.
The tests of the cotainr.pack.CondaInstall.add_environment() method are implemented in the class cotainr.tests.pack.test_conda_install.TestAddEnvironment.
The tests of the cotainr.util.stream_subprocess(): function are implemented in the class cotainr.tests.util.test_stream_subprocess.TestStreamSubprocess. Specifically, this class implements test cases (methods) like test_completed_process() or test_check_returncode().
The module cotainr.tests.util.test_stream_subprocess also includes a class, Test_PrintAndCaptureStream, implementing the tests of the private “helper” function cotainr.utils._print_and_capture_stream().

In addition to the modules implementing the tests of the functions and classes in cotainr, the sub-packages in cotainr.tests may also include “special” modules implementing test fixtures and stubs:

patches.py: Contains all (monkey)patch fixtures related to that sub-package, e.g. the patch fixture cotainr.tests.util.patches.patch_disable_stream_subprocess(). All patch fixtures are prefixed with patch_.
data.py: Contains all test data fixtures related to that sub-package, e.g. the data fixture cotainr.tests.container.data.data_cached_ubuntu_sif(). All data fixtures are prefixed with data_.
stubs.py: Contains all test stubs related to that sub-package, e.g. the stub cotainr.tests.cli.stubs.StubValidSubcommand.

All general purpose fixtures, which do not belong in one of the sub-package specific fixture modules listed above, are defined in the tests/conftest.py module.

Finally, the cotainr.tests.test_end_to_end module contains all workflow end-to-end test using cotainr.

Imports in test modules#

Imports in test modules are based on the following conventions:

Functions and classes, subject to testing, are imported using absolute imports, e.g. import cotainr.pack.CondaInstall in tests/pack/test_conda_install.py.
Sub-package specific fixtures are explicitly imported using relative imports, e.g. from ..container.data import data_cached_ubuntu_sif in tests/pack/test_conda_install.py.
Fixtures defined in tests/conftest.py are not explicitly imported (they are implicitly imported by pytest`). Thus, if a fixture is used, but not imported, in a test module, tests/conftest.py is the only module in which it can (or at least should) be defined.

Continuous Integration (CI)#

Continuous Integration (CI) is handled via GitHub Actions in the cotainr GitHub repository DeiC-HPC/cotainr. The tests run on the GitHub-hosted ubuntu-latest runner. When running the CI test matrix, we differentiate between the following (meta)versions of dependencies:

stable: The minimum supported version of the dependency.
latest: The latest released version of the dependency.
all: All supported versions of the dependency.

CI workflows#

The following CI workflows are implemented:

CI_pull_requests.yml: Runs the unit tests, integration tests, and end-to-end tests on pull requests to the main branch. All Python versions and stable Singularity as well as stable Apptainer versions are tested.
CI_push.yml: Runs the unit tests on pushes to all branches. Restricted to stable and latest Python versions.

Continuous Delivery (CD)#

Continuous Delivery (CD) is handled partly via GitHub Actions, partly via the a Read the Docs webhook integration to the cotainr GitHub repository: DeiC-HPC/cotainr.

Read the Docs continuous documentation#

The HTML documentation served at http://cotainr.readthedocs.io is automatically built by Read the Docs based on the configuration in the .readthedocs.yml configuration file.

# Configuration file for the documentation build hosted on cotainr.readthedocs.io
# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details

version: 2
build:
  os: ubuntu-22.04
  tools:
    python: "3"
  jobs:
    pre_build:
      - make -C doc apidoc
      - make -C doc relnotes
sphinx:
  builder: html
  configuration: doc/conf.py
  fail_on_warning: true
python:
  install:
  - requirements: docs-requirements.txt

This fully automates the process of building *latest* and *stable* versions of the HTML documentation served at http://cotainr.readthedocs.io. Additionally, the “build pull requests” feature is enabled. A pull request documentation build is linked in the list of checks for the GitHub pull request.

Scheduled tests#

We run scheduled GitHub actions (weekly, every Tuesday night) in order to continuously test cotainr against its dependencies. That way we proactively monitor for changes in dependencies that end up breaking cotainr.

Currently, the following scheduled workflows are implemented:

SCHED_docs_linkcheck: Builds the documentation and checks for any broken hyperlinks.

Additionally, we currently also schedule the CI_pull_requests.yml workflow which tests the most recent point releases of Python (as provided by GitHub Actions) as well as the most recent Conda version. Ideally, this should be separated into its own workflow that also includes the latest versions of Python and Singularity/Apptainer in the test matrix.