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Add rpy2 to the dependencies

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- add a Jupyter notebook that allows to install all project-external
  dependencies regarding R and R packages
- adjust the GitHub Action workflow to also install R and the R packages
  used within the project
- add a `init_r` module that initializes all R packages globally
  once the `urban_meal_delivery` package is imported
This commit is contained in:
Alexander Hess 2021-01-11 12:24:15 +01:00
commit b0f2fdde10
Signed by: alexander
GPG key ID: 344EA5AB10D868E0
10 changed files with 2152 additions and 52 deletions
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135
noxfile.py
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@ -25,26 +25,6 @@ as unified tasks to assure the quality of the source code:
+ accepts extra arguments, e.g., `poetry run nox -s test -- --no-cov`,
that are passed on to `pytest` and `xdoctest` with no changes
=> may be paths or options
GitHub Actions implements the following CI workflow:
- "format", "lint", and "test" as above
- "safety": check if dependencies contain known security vulnerabilites
- "docs": build the documentation with sphinx
The pre-commit framework invokes the following tasks:
- before any commit:
+ "format" and "lint" as above
+ "fix-branch-references": replace branch references with the current one
- before merges: run the entire "test-suite" independent of the file changes
"""
import contextlib
@ -92,7 +72,7 @@ nox.options.envdir = '.cache/nox'
# Avoid accidental successes if the environment is not set up properly.
nox.options.error_on_external_run = True
# Run only CI related checks by default.
# Run only local checks by default.
nox.options.sessions = (
'format',
'lint',
@ -220,24 +200,50 @@ def test(session):
'xdoctest[optional]',
)
session.run('pytest', '--version')
# When the CI server runs the slow tests, we only execute the R related
# test cases that require the slow installation of R and some packages.
if session.env.get('_slow_ci_tests'):
session.run(
'pytest', '--randomly-seed=4287', '-m', 'r', PYTEST_LOCATION,
)
# In the "ci-tests-slow" session, we do not run any test tool
# other than pytest. So, xdoctest, for example, is only run
# locally or in the "ci-tests-fast" session.
return
# When the CI server executes pytest, no database is available.
# Therefore, the CI server does not measure coverage.
elif session.env.get('_fast_ci_tests'):
pytest_args = (
'--randomly-seed=4287',
'-m',
'not (db or r)',
PYTEST_LOCATION,
)
# When pytest is executed in the local develop environment,
# both R and a database are available.
# Therefore, we require 100% coverage.
else:
pytest_args = (
'--cov',
'--no-cov-on-fail',
'--cov-branch',
'--cov-fail-under=100',
'--cov-report=term-missing:skip-covered',
'--randomly-seed=4287',
PYTEST_LOCATION,
)
# Interpret extra arguments as options for pytest.
# They are "dropped" by the hack in the pre_merge() function
# if this function is run within the "pre-merge" session.
# They are "dropped" by the hack in the test_suite() function
# if this function is run within the "test-suite" session.
posargs = () if session.env.get('_drop_posargs') else session.posargs
args = posargs or (
'--cov',
'--no-cov-on-fail',
'--cov-branch',
'--cov-fail-under=100',
'--cov-report=term-missing:skip-covered',
'--randomly-seed=4287',
'-m',
'not (db or e2e)',
PYTEST_LOCATION,
)
session.run('pytest', '--version')
session.run('pytest', *args)
session.run('pytest', *(posargs or pytest_args))
# For xdoctest, the default arguments are different from pytest.
args = posargs or [PACKAGE_IMPORT_NAME]
@ -301,6 +307,60 @@ def docs(session):
print(f'Docs are available at {os.getcwd()}/{DOCS_BUILD}index.html') # noqa:WPS421
@nox.session(name='ci-tests-fast', python=PYTHON)
def fast_ci_tests(session):
"""Fast tests run by the GitHub Actions CI server.
These regards all test cases NOT involving R via `rpy2`.
Also, coverage is not measured as full coverage can only be
achieved by running the tests in the local develop environment
that has access to a database.
"""
# Re-using an old environment is not so easy here as the "test" session
# runs `poetry install --no-dev`, which removes previously installed packages.
if session.virtualenv.reuse_existing:
raise RuntimeError(
'The "ci-tests-fast" session must be run without the "-r" option',
)
# Little hack to pass arguments to the "test" session.
session.env['_fast_ci_tests'] = 'true'
# Cannot use session.notify() to trigger the "test" session
# as that would create a new Session object without the flag
# in the env(ironment).
test(session)
@nox.session(name='ci-tests-slow', python=PYTHON)
def slow_ci_tests(session):
"""Slow tests run by the GitHub Actions CI server.
These regards all test cases involving R via `rpy2`.
They are slow as the CI server needs to install R and some packages
first, which takes a couple of minutes.
Also, coverage is not measured as full coverage can only be
achieved by running the tests in the local develop environment
that has access to a database.
"""
# Re-using an old environment is not so easy here as the "test" session
# runs `poetry install --no-dev`, which removes previously installed packages.
if session.virtualenv.reuse_existing:
raise RuntimeError(
'The "ci-tests-slow" session must be run without the "-r" option',
)
# Little hack to pass arguments to the "test" session.
session.env['_slow_ci_tests'] = 'true'
# Cannot use session.notify() to trigger the "test" session
# as that would create a new Session object without the flag
# in the env(ironment).
test(session)
@nox.session(name='test-suite', python=PYTHON)
def test_suite(session):
"""Run the entire test suite.
@ -324,8 +384,7 @@ def test_suite(session):
# Cannot use session.notify() to trigger the "test" session
# as that would create a new Session object without the flag
# in the env(ironment). Instead, run the test() function within
# the "pre-merge" session.
# in the env(ironment).
test(session)