Skip tests with missing requirements (#1032)

Skip tests with missing requirements

---------

Co-authored-by: Francesca L. Bleken <[email protected]>

.github/workflows/ci_tests.yml

@@ -63,21 +63,15 @@ jobs:
       run: |
         python3 -c 'import numpy as np; print(np.get_include())'
 
-    - name: Workaround - install CMake 3.25.2 since 3.26.0 doesn't work
-      # Normally we would install cmake with the package manager, but
-      # ubuntu 20.04 doesn't seems to keep older versions of cmake around...
-      # Fortunately, there exists a pip package
-      run: |
-        python3 -m pip install cmake==3.25.2
-        cmake --version
-
     - name: List installed Python packages
       run: |
         uname -a
         python --version
         pip freeze
 
     - name: Configure
+      env:
+        DLITE_IMPORTSKIP_EXITCODE: 1
       run: |
         Python3_ROOT=$(python3 -c 'import sys; print(sys.exec_prefix)') \
         CFLAGS='-Wno-missing-field-initializers' \

CMakeLists.txt

@@ -336,6 +336,13 @@ if(WITH_PYTHON)
   # endif()
   # message(STATUS "ENV{Python3_LIBRARY}: $ENV{Python3_LIBRARY}")
 
+  add_custom_target(wheel
+    COMMAND ${Python3_EXECUTABLE} -m pip wheel -w dist
+        ${dlite_SOURCE_DIR}/python
+    DEPENDS ${dlite}
+    COMMENT "Build Python wheels"
+  )
+
 
   message(STATUS "CMAKE_INSTALL_PREFIX = ${CMAKE_INSTALL_PREFIX}")
   message(STATUS "Python3_prefix = ${Python3_prefix}")
@@ -942,6 +949,7 @@ configure_package_config_file(
   PATH_VARS ${DLITE_CONFIG_VARS}
   )
 
+
 #################################################################
 
 # Install

bindings/python/tests/CMakeLists.txt

@@ -54,6 +54,8 @@ foreach(test ${tests})
     ENVIRONMENT "DLITE_USE_BUILD_ROOT=YES")
 
   # Skip tests that exit with return code 44
+  set_property(TEST ${name} APPEND PROPERTY
+    ENVIRONMENT "DLITE_IMPORTSKIP_EXITCODE=$ENV{DLITE_IMPORTSKIP_EXITCODE}")
   set_property(TEST ${name} PROPERTY SKIP_RETURN_CODE 44)
 
 endforeach()

bindings/python/testutils.py

@@ -1,5 +1,6 @@
 """Some utilities for testing."""
 import importlib
+import os
 import socket
 import sys
 
@@ -71,15 +72,44 @@ def importcheck(module_name, package=None):
         return None
 
 
-def importskip(module_name, package=None, exitcode=44):
+def importskip(module_name, package=None, exitcode=44,
+               env_exitcode="DLITE_IMPORTSKIP_EXITCODE"):
     """Import and return the requested module.
 
     Calls `sys.exit()` with given exitcode if the module cannot be imported.
+
+    Arguments:
+        module_name: Name of module to try to import.
+        package: Optional package name that the module might reside in.
+        exitcode: The default exit code of `sys.exit()` if the module cannot
+            be imported.
+        env_exitcode: Name of environment variable containing an exitcode
+            to call `sys.exit()` with if the module cannot be imported.
+            This overrides `exitcode`.
+
+    Notes:
+        If you want to run the tests and get an error if a module
+        cannot be imported, set environment variable
+        `DLITE_IMPORTSKIP_EXITCODE=1` before running the tests (if you
+        run with ctest, set `DLITE_IMPORTSKIP_EXITCODE` at configure
+        time).
+
+        For packages that depend on external services like postgresql,
+        call `importskip()` with `env_exitcode=None` to skip the test
+        regardless of whether `DLITE_IMPORTSKIP_EXITCODE` is set or not.
+
     """
     try:
         return importlib.import_module(module_name, package=package)
     except ModuleNotFoundError as exc:
-        print(f"{exc}: skipping test", file=sys.stderr)
+        if env_exitcode and env_exitcode in os.environ:
+            try:
+                exitcode = int(os.environ[env_exitcode])
+            except:
+                pass
+        else:
+            print(f"{exc}: skipping test", file=sys.stderr)
+
         sys.exit(exitcode)
 
 

doc/user_guide/environment_variables.md

@@ -96,6 +96,11 @@ DLITE_USE_BUILD_ROOT is set).
       - a glob pattern (/path/to/*.json)
     In the two last cases, the file extension must match the driver name.
 
+  - **DLITE_IMPORTSKIP_EXITCODE**: Exit code from tests that fail to
+    load a python module with `importskip()`.  Define this to 1 at
+    configure time if you want the tests not to be skipped if they
+    cannot import a needed module.
+
 
 Environment variables for controlling error handling
 ----------------------------------------------------

examples/CMakeLists.txt

@@ -107,6 +107,9 @@ if(FORCE_EXAMPLES OR EXISTS ${CMAKE_INSTALL_PREFIX}/share/dlite/examples)
     endif()
     set_property(TEST ${name} APPEND PROPERTY
       ENVIRONMENT "DLITE_USE_BUILD_ROOT=YES")
+    set_property(TEST ${name} APPEND PROPERTY
+      ENVIRONMENT "DLITE_IMPORTSKIP_EXITCODE=$ENV{DLITE_IMPORTSKIP_EXITCODE}")
+
     set_property(TEST ${name} PROPERTY
       SKIP_RETURN_CODE 44)
   endforeach()

examples/mappings/oteexample.py

@@ -1,16 +1,17 @@
 """Mapping example using OTELib."""
 from pathlib import Path
 
-try:
-    from tripper import EMMO, MAP, Triplestore
-    from otelib import OTEClient
-    import oteapi_dlite  # To check that it is installed
-except ModuleNotFoundError as exc:
-    print(f"Skipping OTE example because of missing module: {exc}")
-    import sys
-    sys.exit(44)  # Exit code 44 -> skip test because of missing dependencies
-
 import dlite
+from dlite.testutils import importskip
+
+importskip("tripper")
+from tripper import EMMO, MAP, Triplestore
+
+importskip("otelib", env_exitcode=None)
+from otelib import OTEClient
+
+oteapi_dlite = importskip("oteapi_dlite", env_exitcode=None)
+
 
 
 # Paths

examples/read-csv/main.py

@@ -1,8 +1 @@
-try:
-    import pandas  # noqa: F401
-    import tables  # noqa: F401
-except ImportError:
-    import sys
-    sys.exit(44)  # skip this test if pandas is not available
-
 import readcsv  # noqa: F401

examples/read-csv/readcsv.py

@@ -1,6 +1,11 @@
 from pathlib import Path
 
 import dlite
+from dlite.testutils import importskip
+
+importskip("pandas")
+importskip("tables")
+importskip("yaml")
 
 
 # Set up some paths

storages/python/tests-python/CMakeLists.txt

@@ -78,6 +78,8 @@ foreach(test ${python-tests})
   set_property(TEST ${test} APPEND PROPERTY
     ENVIRONMENT "LD_LIBRARY_PATH=${dlite_LD_LIBRARY_PATH_NATIVE}")
   endif()
+  set_property(TEST ${name} APPEND PROPERTY
+    ENVIRONMENT "DLITE_IMPORTSKIP_EXITCODE=$ENV{DLITE_IMPORTSKIP_EXITCODE}")
 
   # Skip tests that exit with return code 44
   set_property(TEST ${test} PROPERTY SKIP_RETURN_CODE 44)

storages/python/tests-python/test_image.py

@@ -2,12 +2,12 @@
 from pathlib import Path
 
 import numpy as np
+
 import dlite
+from dlite.testutils import importskip
 
-try:
-    import skimage
-except ImportError:
-    sys.exit(44)  # skip test
+importskip("scipy")
+importskip("skimage")
 
 
 thisdir = Path(__file__).absolute().parent

storages/python/tests-python/test_mongodb-atlas_python.py

@@ -1,7 +1,12 @@
 import sys
 import os
 from pathlib import Path
+
 import dlite
+from dlite.testutils import importskip
+
+importskip("pymongo", env_exitcode=None)
+
 
 # Get the current file path
 current_file = Path(__file__).resolve()

storages/python/tests-python/test_mongodb_python.py

@@ -7,8 +7,10 @@
 from dlite.options import Options
 from dlite.testutils import importskip
 
-importskip("pymongo")
-mongomock = importskip("mongomock")
+importskip("pymongo", env_exitcode=None)
+mongomock = importskip("mongomock", env_exitcode=None)
+
+from dlite.testutils import importskip
 
 
 @mongomock.patch(servers=(('localhost', 27017),))

storages/python/tests-python/test_postgresql_storage_python.py

@@ -5,14 +5,14 @@
 from pathlib import Path
 
 sys.dont_write_bytecode = True
-try:
-    import psycopg2
-except ImportError:
-    sys.exit(44)
-from psycopg2 import sql
 
 import dlite
 from dlite.utils import instance_from_dict
+from dlite.testutils import importskip
+
+psycopg2 = importskip("psycopg2", env_exitcode=None)
+from psycopg2 import sql
+
 from run_python_storage_tests import print_test_exception
 
 

storages/python/tests-python/test_redis.py

@@ -7,7 +7,7 @@
 import dlite
 from dlite.testutils import importskip, serverskip
 
-importskip("redis")  # skip this test if redis is not available
+importskip("redis", env_exitcode=None)  # skip this test if redis is not available
 serverskip("localhost", 6379)  # skip test if redis is down