Merge pull request #1037 from romainx/test_packages

Test packages

Makefile

@@ -94,3 +94,5 @@ tx-en: ## rebuild en locale strings and push to master (req: GH_TOKEN)
 test/%: ## run tests against a stack (only common tests or common tests + specific tests)
 	@if [ ! -d "$(notdir $@)/test" ]; then TEST_IMAGE="$(OWNER)/$(notdir $@)" pytest -m "not info" test; \
 	else TEST_IMAGE="$(OWNER)/$(notdir $@)" pytest -m "not info" test $(notdir $@)/test; fi
+
+test-all: $(foreach I,$(ALL_IMAGES),test/$(I)) ## test all stacks
\ No newline at end of file

test/helpers.py

@@ -88,9 +88,21 @@ class CondaPackageHelper:
     def _packages_from_json(env_export):
         """Extract packages and versions from the lines returned by the list of specifications"""
         dependencies = json.loads(env_export).get("dependencies")
-        packages_list = map(lambda x: x.split("=", 1), dependencies)
-        # TODO: could be improved
-        return {package[0]: set(package[1:]) for package in packages_list}
+        packages_dict = dict()
+        for split in map(lambda x: x.split("=", 1), dependencies):
+            # default values
+            package = split[0]
+            version = set()
+            # cheking if it's a proper version by testing if the first char is a digit
+            if len(split) > 1:
+                if split[1][0].isdigit():
+                    # package + version case
+                    version = set(split[1:])
+                else:
+                    # The split was incorrect and the package shall not be splitted
+                    package = f"{split[0]}={split[1]}"
+            packages_dict[package] = version
+        return packages_dict
 
     def available_packages(self):
         """Return the available packages"""

test/test_packages.py

+# Copyright (c) Jupyter Development Team.
+# Distributed under the terms of the Modified BSD License.
+
+"""
+test_packages
+~~~~~~~~~~~~~~~
+This test module tests if R and Python packages installed can be imported.
+It's a basic test aiming to prove that the package is working properly.
+
+The goal is to detect import errors that can be caused by incompatibilities between packages for example:
+
+- #1012: issue importing `sympy`
+- #966: isssue importing `pyarrow`
+
+This module checks dynmamically, through the `CondaPackageHelper`, only the specified packages i.e. packages requested by `conda install` in the `Dockerfiles`.
+This means that it does not check dependencies. This choice is a tradeoff to cover the main requirements while achieving reasonable test duration.
+However it could be easily changed (or completed) to cover also dependencies `package_helper.installed_packages()` instead of `package_helper.specified_packages()`.
+
+Example:
+
+    $ make test/datascience-notebook
+
+    # [...]
+    # test/test_packages.py::test_python_packages 
+    # --------------------------------------------------------------------------------------------- live log setup ----------------------------------------------------------------------------------------------
+    # 2020-03-08 09:56:04 [    INFO] Starting container jupyter/datascience-notebook ... (helpers.py:51)
+    # 2020-03-08 09:56:04 [    INFO] Running jupyter/datascience-notebook with args {'detach': True, 'ports': {'8888/tcp': 8888}, 'tty': True, 'command': ['start.sh', 'bash', '-c', 'sleep infinity']} ... (conftest.py:78)
+    # 2020-03-08 09:56:04 [    INFO] Grabing the list of specifications ... (helpers.py:76)
+    # ---------------------------------------------------------------------------------------------- live log call ----------------------------------------------------------------------------------------------
+    # 2020-03-08 09:56:07 [    INFO] Testing the import of packages ... (test_packages.py:125)
+    # 2020-03-08 09:56:07 [    INFO] Trying to import conda (test_packages.py:127)
+    # 2020-03-08 09:56:07 [    INFO] Trying to import notebook (test_packages.py:127)
+    # 2020-03-08 09:56:08 [    INFO] Trying to import jupyterhub (test_packages.py:127)
+    # [...]
+
+"""
+
+import logging
+
+import pytest
+
+from helpers import CondaPackageHelper
+
+LOGGER = logging.getLogger(__name__)
+
+# Mapping between package and module name
+PACKAGE_MAPPING = {
+    # Python
+    "matplotlib-base": "matplotlib",
+    "beautifulsoup4": "bs4",
+    "scikit-learn": "sklearn",
+    "scikit-image": "skimage",
+    "spylon-kernel": "spylon_kernel",
+    # R
+    "randomforest": "randomForest",
+    "rsqlite": "DBI",
+    "rcurl": "RCurl",
+    "rodbc": "RODBC",
+}
+
+# List of packages that cannot be tested in a standard way
+EXCLUDED_PACKAGES = [
+    "tini",
+    "python",
+    "hdf5",
+    "conda-forge::blas[build=openblas]",
+    "protobuf",
+    "r-irkernel",
+    "unixodbc",
+]
+
+
+@pytest.fixture(scope="function")
+def package_helper(container):
+    """Return a package helper object that can be used to perform tests on installed packages"""
+    return CondaPackageHelper(container)
+
+
+@pytest.fixture(scope="function")
+def packages(package_helper):
+    """Return the list of specified packages (i.e. packages explicitely installed excluding dependencies)"""
+    return package_helper.specified_packages()
+
+
+def package_map(package):
+    """Perform a mapping between the python package name and the name used for the import"""
+    _package = package
+    if _package in PACKAGE_MAPPING:
+        _package = PACKAGE_MAPPING.get(_package)
+    return _package
+
+
+def excluded_package_predicate(package):
+    """Return whether a package is excluded from the list (i.e. a package that cannot be tested with standard imports)"""
+    return package in EXCLUDED_PACKAGES
+
+
+def python_package_predicate(package):
+    """Predicate matching python packages"""
+    return not excluded_package_predicate(package) and not r_package_predicate(package)
+
+
+def r_package_predicate(package):
+    """Predicate matching R packages"""
+    return not excluded_package_predicate(package) and package.startswith("r-")
+
+
+def _check_import_package(package_helper, command):
+    """Generic function executing a command"""
+    LOGGER.debug(f"Trying to import a package with [{command}] ...")
+    rc = package_helper.running_container.exec_run(command)
+    return rc.exit_code
+
+
+def check_import_python_package(package_helper, package):
+    """Try to import a Python package from the command line"""
+    return _check_import_package(package_helper, ["python", "-c", f"import {package}"])
+
+
+def check_import_r_package(package_helper, package):
+    """Try to import a R package from the command line"""
+    return _check_import_package(
+        package_helper, ["R", "--slave", "-e", f"library({package})"]
+    )
+
+
+def _import_packages(package_helper, filtered_packages, check_function, max_failures):
+    """Test if packages can be imported
+
+    Note: using a list of packages instead of a fixture for the list of packages since pytest prevents use of multiple yields
+    """
+    failures = {}
+    LOGGER.info(f"Testing the import of packages ...")
+    for package in filtered_packages:
+        LOGGER.info(f"Trying to import {package}")
+        try:
+            assert (
+                check_function(package_helper, package) == 0
+            ), f"Package [{package}] import failed"
+        except AssertionError as err:
+            failures[package] = err
+    if len(failures) > max_failures:
+        raise AssertionError(failures)
+    elif len(failures) > 0:
+        LOGGER.warning(f"Some import(s) has(have) failed: {failures}")
+
+
+@pytest.fixture(scope="function")
+def r_packages(packages):
+    """Return an iterable of R packages"""
+    # package[2:] is to remove the leading "r-" appended by conda on R packages
+    return map(
+        lambda package: package_map(package[2:]), filter(r_package_predicate, packages)
+    )
+
+
+def test_python_packages(package_helper, python_packages, max_failures=0):
+    """Test the import of specified python packages"""
+    return _import_packages(
+        package_helper, python_packages, check_import_python_package, max_failures
+    )
+
+
+@pytest.fixture(scope="function")
+def python_packages(packages):
+    """Return an iterable of Python packages"""
+    return map(package_map, filter(python_package_predicate, packages))
+
+
+def test_r_packages(package_helper, r_packages, max_failures=0):
+    """Test the import of specified R packages"""
+    return _import_packages(
+        package_helper, r_packages, check_import_r_package, max_failures
+    )