This repository contains Dockerfiles for creating libCellML build environments.
To make use of the Docker images for libCellML you will need to download and install Docker. Follow the Docker documentation for installing Docker on your operating system.
With Docker installed there are two Docker images that you can use:
- libCellML developer image
- libCellML documentation image
To fetch the developer image use the following command:
docker pull libcellml/build:1.0.0
To fetch the documentation image use the following command:
docker pull libcellml/docs:1.0.0
You may also pull the latest version of the images with the following commands:
docker pull libcellml/build docker pull libcellml/docs
docker run libcellml/build https://github.com/cellml/libcellml develop
This will clone, build, and run the unit tests, code coverage, clang-format, and memory checking targets.
You can also build and run the tests from a local directory on the Docker daemon host computer. This can be achieved with the following command:
docker run --mount type=bind,src=<your-local-directory>,dst=/external/drive,readonly libcellml/build /external/drive
Hopefully it goes without saying that you need to replace <your-local-directory> with the actual directory where the libCellML code you wish to build and test exists.
The build can be controlled with the following arguments
- '-s', '--serial' to build serially
- '-b', '--build-only' to only build the libraries and tests
- '-d', '--debug' to enter debug mode at the end of the build
Note: The debug mode option must be used in conjunction with '-it' flags for the 'docker run' command.
Some examples of using the command line options:
# Build serially docker run libcellml/build https://github.com/cellml/libcellml develop -s # Just build libraries and tests docker run libcellml/build https://github.com/cellml/libcellml develop -b # Enter a bash shell at the end of the build docker run -it libcellml/build https://github.com/cellml/libcellml develop -d
From the command at the top of this section you should get output similar to what is shown in Appendix A
docker run -p 8118:8000 libcellml/docs https://github.com/cellml/libcellml develop
This will clone, and build the documentation for libCellML and make the documentation available at localhost:8118.
You can also build and serve documentation from a local directory. The documentation will be automatically built and reflected in a webbrowser when any documentation related changes are saved. This gives you a live rendering of the current state of the libCellML documentation. This can be achieved with the following command:
docker run --mount type=bind,src=<your-local-directory>,dst=/external/drive,readonly -p 8118:8000 libcellml/docs /external/drive
Hopefully it goes without saying that you need to replace <your-local-directory> with the actual directory where the libCellML code you wish to render the documentation for exists.
Output from run of developer image (not verbatim as the codebase may have changed since this output was recorded):
-- The CXX compiler identification is GNU 7.4.0
-- Check for working CXX compiler: /usr/bin/c++
-- Check for working CXX compiler: /usr/bin/c++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Found Python: /usr/bin/python3.6 (found version "3.6.7") found components: Interpreter Development
-- Could NOT find Doxygen (missing: DOXYGEN_EXECUTABLE)
-- Could NOT find Sphinx (missing: SPHINX_EXECUTABLE)
-- Found SWIG: /usr/bin/swig3.0 (found suitable version "3.0.12", minimum required is "3")
-- Found LibXml2: /usr/lib/x86_64-linux-gnu/libxml2.so (found version "2.9.4")
-- Performing Test COMPILER_HAS_HIDDEN_VISIBILITY
-- Performing Test COMPILER_HAS_HIDDEN_VISIBILITY - Success
-- Performing Test COMPILER_HAS_HIDDEN_INLINE_VISIBILITY
-- Performing Test COMPILER_HAS_HIDDEN_INLINE_VISIBILITY - Success
-- Performing Test COMPILER_HAS_DEPRECATED_ATTR
-- Performing Test COMPILER_HAS_DEPRECATED_ATTR - Success
-- The C compiler identification is GNU 7.4.0
-- Check for working C compiler: /usr/bin/cc
-- Check for working C compiler: /usr/bin/cc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Detecting C compile features
-- Detecting C compile features - done
-- Looking for pthread.h
-- Looking for pthread.h - found
-- Looking for pthread_create
-- Looking for pthread_create - not found
-- Looking for pthread_create in pthreads
-- Looking for pthread_create in pthreads - not found
-- Looking for pthread_create in pthread
-- Looking for pthread_create in pthread - found
-- Found Threads: TRUE
-- Configuring done
-- Generating done
-- Build files have been written to: /usr/code/build-libcellml-release
Scanning dependencies of target gtest
[ 1%] Building CXX object tests/gtest/CMakeFiles/gtest.dir/src/gtest-all.cc.o
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[ 18%] Building CXX object src/bindings/python/CMakeFiles/___init__.dir/libcellml/__init__PYTHON_wrap.cxx.o
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[ 22%] Building CXX object src/bindings/python/CMakeFiles/_validator.dir/libcellml/validatorPYTHON_wrap.cxx.o
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[ 26%] Building CXX object src/bindings/python/CMakeFiles/_when.dir/libcellml/whenPYTHON_wrap.cxx.o
[ 27%] Building CXX object src/bindings/python/CMakeFiles/_parser.dir/libcellml/parserPYTHON_wrap.cxx.o
Scanning dependencies of target _importedentity
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[ 28%] Building CXX object src/bindings/python/CMakeFiles/_importsource.dir/libcellml/importsourcePYTHON_wrap.cxx.o
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[ 29%] Building CXX object src/bindings/python/CMakeFiles/_component.dir/libcellml/componentPYTHON_wrap.cxx.o
[ 30%] Building CXX object src/bindings/python/CMakeFiles/_entity.dir/libcellml/entityPYTHON_wrap.cxx.o
[ 31%] Building CXX object src/bindings/python/CMakeFiles/_importedentity.dir/libcellml/importedentityPYTHON_wrap.cxx.o
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[ 32%] Building CXX object src/bindings/python/CMakeFiles/_reset.dir/libcellml/resetPYTHON_wrap.cxx.o
[ 34%] Building CXX object src/bindings/python/CMakeFiles/_namedentity.dir/libcellml/namedentityPYTHON_wrap.cxx.o
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[ 35%] Building CXX object src/bindings/python/CMakeFiles/_componententity.dir/libcellml/componententityPYTHON_wrap.cxx.o
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[ 37%] Building CXX object src/bindings/python/CMakeFiles/_error.dir/libcellml/errorPYTHON_wrap.cxx.o
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[ 38%] Building CXX object src/bindings/python/CMakeFiles/_model.dir/libcellml/modelPYTHON_wrap.cxx.o
[ 39%] Building CXX object src/bindings/python/CMakeFiles/_units.dir/libcellml/unitsPYTHON_wrap.cxx.o
[ 40%] Linking CXX shared module _specificationrule.so
[ 41%] Linking CXX shared module ___init__.so
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[ 55%] Built target _importedentity
[ 55%] Built target _namedentity
[ 56%] Linking CXX shared library libgtest.so
[ 56%] Built target _entity
[ 57%] Linking CXX shared module _reset.so
[ 57%] Built target _when
[ 58%] Linking CXX shared module _componententity.so
[ 58%] Built target _printer
[ 58%] Built target _variable
[ 59%] Linking CXX shared module _component.so
[ 60%] Linking CXX shared module _error.so
[ 61%] Linking CXX shared module _model.so
[ 61%] Built target _reset
[ 61%] Built target gtest
[ 61%] Built target _componententity
[ 61%] Built target _component
Scanning dependencies of target gtest_main
[ 61%] Built target _error
[ 61%] Building CXX object tests/gtest/CMakeFiles/gtest_main.dir/src/gtest_main.cc.o
[ 61%] Built target _model
[ 62%] Linking CXX shared module _units.so
[ 62%] Built target _units
[ 63%] Linking CXX shared library libgtest_main.so
[ 63%] Built target gtest_main
Scanning dependencies of target test_validator
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[ 64%] Building CXX object tests/CMakeFiles/test_validator.dir/validator/validator.cpp.o
[ 65%] Building CXX object tests/CMakeFiles/test_validator.dir/test_utils.cpp.o
[ 67%] Building CXX object tests/CMakeFiles/test_resolve_imports.dir/resolve_imports/file_parser.cpp.o
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[ 68%] Building CXX object tests/CMakeFiles/test_math.dir/test_utils.cpp.o
[ 69%] Building CXX object tests/CMakeFiles/test_version.dir/version/version.cpp.o
[ 70%] Building CXX object tests/CMakeFiles/test_resolve_imports.dir/test_utils.cpp.o
Scanning dependencies of target test_printer
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[ 71%] Building CXX object tests/CMakeFiles/test_coverage.dir/test_utils.cpp.o
[ 71%] Building CXX object tests/CMakeFiles/test_coverage.dir/coverage/coverage.cpp.o
[ 72%] Building CXX object tests/CMakeFiles/test_version.dir/test_utils.cpp.o
Scanning dependencies of target test_component
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[ 73%] Building CXX object tests/CMakeFiles/test_units.dir/test_utils.cpp.o
[ 74%] Building CXX object tests/CMakeFiles/test_reset.dir/reset/reset.cpp.o
[ 75%] Building CXX object tests/CMakeFiles/test_reset.dir/test_utils.cpp.o
[ 76%] Building CXX object tests/CMakeFiles/test_units.dir/units/units.cpp.o
[ 77%] Building CXX object tests/CMakeFiles/test_variable.dir/test_utils.cpp.o
[ 78%] Building CXX object tests/CMakeFiles/test_when.dir/test_utils.cpp.o
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Scanning dependencies of target test_parser
[ 81%] Building CXX object tests/CMakeFiles/test_error.dir/error/error.cpp.o
[ 84%] Building CXX object tests/CMakeFiles/test_model.dir/model/component_import.cpp.o
[ 84%] Building CXX object tests/CMakeFiles/test_when.dir/when/when.cpp.o
[ 85%] Building CXX object tests/CMakeFiles/test_component.dir/test_utils.cpp.o
[ 85%] Building CXX object tests/CMakeFiles/test_connection.dir/connection/connection.cpp.o
[ 86%] Building CXX object tests/CMakeFiles/test_component.dir/component/component.cpp.o
[ 87%] Building CXX object tests/CMakeFiles/test_printer.dir/test_utils.cpp.o
[ 87%] Building CXX object tests/CMakeFiles/test_model.dir/test_utils.cpp.o
[ 87%] Building CXX object tests/CMakeFiles/test_model.dir/model/model.cpp.o
[ 87%] Building CXX object tests/CMakeFiles/test_component.dir/component/encapsulation.cpp.o
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[ 91%] Building CXX object tests/CMakeFiles/test_parser.dir/test_utils.cpp.o
[ 92%] Building CXX object tests/CMakeFiles/test_parser.dir/parser/libxml_user.cpp.o
[ 93%] Linking CXX executable test_when
[ 93%] Linking CXX executable test_version
[ 94%] Linking CXX executable test_math
[ 94%] Built target test_math
[ 94%] Built target test_when
[ 94%] Built target test_version
[ 94%] Linking CXX executable test_printer
[ 94%] Linking CXX executable test_resolve_imports
[ 94%] Built target test_printer
[ 95%] Linking CXX executable test_component
[ 95%] Built target test_resolve_imports
[ 95%] Built target test_component
[ 96%] Linking CXX executable test_coverage
[ 97%] Linking CXX executable test_connection
[ 97%] Linking CXX executable test_units
[ 97%] Linking CXX executable test_reset
[ 98%] Linking CXX executable test_model
[ 98%] Linking CXX executable test_variable
[ 98%] Built target test_connection
[ 98%] Built target test_coverage
[ 98%] Built target test_units
[ 98%] Built target test_reset
[ 98%] Linking CXX executable test_validator
[ 98%] Built target test_model
[100%] Linking CXX executable test_error
[100%] Built target test_variable
[100%] Built target test_validator
[100%] Built target test_error
[100%] Linking CXX executable test_parser
[100%] Built target test_parser
Running tests...
Test project /usr/code/build-libcellml-release
Start 1: entities_unit_test_component
1/34 Test #1: entities_unit_test_component ..... Passed 0.02 sec
Start 2: entities_unit_test_connection
2/34 Test #2: entities_unit_test_connection .... Passed 0.01 sec
Start 3: misc_unit_test_coverage
3/34 Test #3: misc_unit_test_coverage .......... Passed 0.01 sec
Start 4: object_unit_test_error
4/34 Test #4: object_unit_test_error ........... Passed 0.01 sec
Start 5: entities_unit_test_math
5/34 Test #5: entities_unit_test_math .......... Passed 0.01 sec
Start 6: entities_unit_test_model
6/34 Test #6: entities_unit_test_model ......... Passed 0.01 sec
Start 7: io_unit_test_parser
7/34 Test #7: io_unit_test_parser .............. Passed 0.05 sec
Start 8: io_unit_test_printer
8/34 Test #8: io_unit_test_printer ............. Passed 0.01 sec
Start 9: entities_unit_test_reset
9/34 Test #9: entities_unit_test_reset ......... Passed 0.01 sec
Start 10: io_unit_test_resolve_imports
10/34 Test #10: io_unit_test_resolve_imports ..... Passed 0.06 sec
Start 11: entities_unit_test_units
11/34 Test #11: entities_unit_test_units ......... Passed 0.01 sec
Start 12: io_unit_test_validator
12/34 Test #12: io_unit_test_validator ........... Passed 2.66 sec
Start 13: entities_unit_test_variable
13/34 Test #13: entities_unit_test_variable ...... Passed 0.01 sec
Start 14: api_unit_test_version
14/34 Test #14: api_unit_test_version ............ Passed 0.01 sec
Start 15: entities_unit_test_when
15/34 Test #15: entities_unit_test_when .......... Passed 0.01 sec
Start 16: python_test_component
16/34 Test #16: python_test_component ............ Passed 0.14 sec
Start 17: python_test_component_entity
17/34 Test #17: python_test_component_entity ..... Passed 0.06 sec
Start 18: python_test_entity
18/34 Test #18: python_test_entity ............... Passed 0.06 sec
Start 19: python_test_error
19/34 Test #19: python_test_error ................ Passed 0.06 sec
Start 20: python_test_import_source
20/34 Test #20: python_test_import_source ........ Passed 0.06 sec
Start 21: python_test_imported_entity
21/34 Test #21: python_test_imported_entity ...... Passed 0.06 sec
Start 22: python_test_logger
22/34 Test #22: python_test_logger ............... Passed 0.06 sec
Start 23: python_test_model
23/34 Test #23: python_test_model ................ Passed 0.07 sec
Start 24: python_test_named_entity
24/34 Test #24: python_test_named_entity ......... Passed 0.06 sec
Start 25: python_test_ordered_entity
25/34 Test #25: python_test_ordered_entity ....... Passed 0.06 sec
Start 26: python_test_parser
26/34 Test #26: python_test_parser ............... Passed 0.06 sec
Start 27: python_test_printer
27/34 Test #27: python_test_printer .............. Passed 0.06 sec
Start 28: python_test_reset
28/34 Test #28: python_test_reset ................ Passed 0.06 sec
Start 29: python_test_units
29/34 Test #29: python_test_units ................ Passed 0.06 sec
Start 30: python_test_variable
30/34 Test #30: python_test_variable ............. Passed 0.06 sec
Start 31: python_test_validator
31/34 Test #31: python_test_validator ............ Passed 0.06 sec
Start 32: python_test_version
32/34 Test #32: python_test_version .............. Passed 0.05 sec
Start 33: python_test_when
33/34 Test #33: python_test_when ................. Passed 0.06 sec
Start 34: python_test_docstrings
34/34 Test #34: python_test_docstrings ........... Passed 0.06 sec
100% tests passed, 0 tests failed out of 34
Total Test time (real) = 4.06 sec
Scanning dependencies of target clean_coverage
[ 1%] Clean old coverage data
[ 1%] Built target clean_coverage
[ 16%] Built target cellml
[ 18%] Built target _printer
[ 21%] Built target _variable
[ 23%] Built target _validator
[ 25%] Built target _units
[ 27%] Built target _entity
[ 29%] Built target _enumerations
[ 31%] Built target ___init__
[ 33%] Built target _version
[ 35%] Built target _error
[ 37%] Built target _componententity
[ 40%] Built target _logger
[ 42%] Built target _component
[ 44%] Built target _importedentity
[ 46%] Built target _model
[ 48%] Built target _parser
[ 50%] Built target _specificationrule
[ 52%] Built target _reset
[ 54%] Built target _importsource
[ 56%] Built target _namedentity
[ 58%] Built target _orderedentity
[ 61%] Built target _when
Scanning dependencies of target python_bindings
[ 61%] Built target python_bindings
[ 63%] Built target gtest
[ 64%] Built target gtest_main
[ 66%] Built target test_error
[ 68%] Built target test_units
[ 70%] Built target test_math
[ 73%] Built target test_component
[ 76%] Built target test_parser
[ 78%] Built target test_reset
[ 81%] Built target test_printer
[ 83%] Built target test_resolve_imports
[ 85%] Built target test_coverage
[ 87%] Built target test_variable
[ 89%] Built target test_connection
[ 91%] Built target test_version
[ 93%] Built target test_validator
[ 96%] Built target test_when
[100%] Built target test_model
Scanning dependencies of target prepare_coverage
[100%] Prepare for coverage tests
[100%] Built target prepare_coverage
Scanning dependencies of target coverage
[100%] Running coverage tests
------------------------------------------------------------------------------
libCellML Code Coverage Report
Directory: /usr/code/build-libcellml-release/src/CMakeFiles/cellml.dir
------------------------------------------------------------------------------
File Lines Exec Cover Missing
------------------------------------------------------------------------------
/component.cpp 135 135 100%
/componententity.cpp 137 137 100%
/entity.cpp 54 54 100%
/error.cpp 136 136 100%
/importedentity.cpp 36 36 100%
/importsource.cpp 37 37 100%
/logger.cpp 34 34 100%
/model.cpp 157 157 100%
/namedentity.cpp 28 28 100%
/orderedentity.cpp 36 36 100%
/parser.cpp 923 923 100%
/printer.cpp 333 333 100%
/reset.cpp 76 76 100%
/units.cpp 141 141 100%
/utilities.cpp 71 71 100%
/validator.cpp 600 600 100%
/variable.cpp 158 158 100%
/version.cpp 5 5 100%
/when.cpp 34 34 100%
/xmlattribute.cpp 41 41 100%
/xmldoc.cpp 50 50 100%
/xmlnode.cpp 77 77 100%
------------------------------------------------------------------------------
TOTAL 3299 3299 100%
------------------------------------------------------------------------------
[100%] Built target coverage
[ 3%] Built target gtest
[ 31%] Built target cellml
[ 33%] Built target gtest_main
[ 38%] Built target test_model
Scanning dependencies of target prepare_memcheck
[ 40%] Prepare for memcheck tests
[ 40%] Built target prepare_memcheck
[ 44%] Built target test_error
[ 48%] Built target test_units
[ 51%] Built target test_math
[ 57%] Built target test_component
[ 62%] Built target test_parser
[ 66%] Built target test_reset
[ 70%] Built target test_printer
[ 74%] Built target test_resolve_imports
[ 77%] Built target test_coverage
[ 81%] Built target test_variable
[ 85%] Built target test_connection
[ 88%] Built target test_version
[ 92%] Built target test_validator
[ 98%] Built target test_when
Scanning dependencies of target memcheck
[100%] Running memcheck tests
>> running valgrind memcheck on: 'test_component' - PASS
>> running valgrind memcheck on: 'test_connection' - PASS
>> running valgrind memcheck on: 'test_coverage' - PASS
>> running valgrind memcheck on: 'test_error' - PASS
>> running valgrind memcheck on: 'test_math' - PASS
>> running valgrind memcheck on: 'test_model' - PASS
>> running valgrind memcheck on: 'test_parser' - PASS
>> running valgrind memcheck on: 'test_printer' - PASS
>> running valgrind memcheck on: 'test_reset' - PASS
>> running valgrind memcheck on: 'test_resolve_imports' - PASS
>> running valgrind memcheck on: 'test_units' - PASS
>> running valgrind memcheck on: 'test_validator' - PASS
>> running valgrind memcheck on: 'test_variable' - PASS
>> running valgrind memcheck on: 'test_version' - PASS
>> running valgrind memcheck on: 'test_when' - PASS
>> Summary
100.0% tests passed, 0 tests failed out of 15
[100%] Built target memcheck
The libCellML repository passed all tests.