Merge development to master for 0.0.7 release finalization. #227
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Also make sure development version has `gmx.version.release = False` and note in RELEASE.txt
Miscellaneous updates to infrastructure. ## Import gmxapi target at more outer scope. Assume C++ code dependent on gmxapi target could exist in the `src` directory outside of `core`. ## Add some exception classes `src/gmx/core/exceptions.h` uses `gmxapicomat` namespace to remind us that these exceptions ought to be coming from code ported to the GROMACS `gmxapi` target and mapped to `gmxpy` Python exceptions, where appropriate (e.g. KeyError, TypeError, ValueError) ## Don't bind `gmx.core.MDArgs` to `std::vector<std::string>` Turn gmxpy::MDArgs from a type alias into a named type. Avoids binding all std::vector<std::string> to class gmx.core.MDArgs ## Update to C++14. Update CMake config and Travis-CI config for C++14 standard, gcc 6. Use std::make_unique. ## Remove unused bindings exporter. `export_session()`` was declared, but undefined and unused.
Remove legacy test. Catch deprecation warning from outdated networkx.
gmx.context.DefaultContext will have to go away very soon. I want to raise as many alarm bells as possible and not worry about breaking it. Note, already officially deprecated (use get_context).
Clean up test_pymd.py
Issue deprecation warning for DefaultContext.
* Remove unused bindings export declaration. * Add some header includes. * Remove some noisy stdio output.
Remove deprecated exceptions.
Create export_tprfile
* Add initial GmxMdParams stuff * Export basic bindings for "TprFile" -> TprFileHandle and "read_tprfile" -> &readTprFile
* Separate GmxMdParams into public and implementation classes. * Produce a GmxMdParams in a TprFile member function. * Get a list of keys from a gmx.core.TprFile.params()
Use some additional helpers to map C++ types to GROMACS types. As a design decision (at least for the moment), allow that all API input will be converted to a reduced set of types (e.g. float64 and int64), with precision reduced if needed based on the TPR file implementation. In a future change, we could check that the provided values will fit in the actual type when setting. Note that the basic Python API has a single integer type and a single floating point type.
Produce a Python dictionary with appropriate value types.
The current GmxMdParamsImpl class is specialized for TPR-based parameter sources. Remove dependency of TprFile on GmxMdParamsImpl and allow GmxMdParamsImpl to be dependent on TprFile. Reimplement getMdParams in terms of new GmxMdParamsImpl constructor.
Fixes kassonlab#192 Add gmx.fileio.read_tpr() to get an object providing simulation run input data from a TPR file. In this change, the interface to TprFile contents is not firm or well-documented, but the functionality is sufficient to allow proper inspection of the effects of the `end_time` parameter provided through the gmx.core.copy_tpr function (also not part of the public interface yet).
Allow setting of parameters in SimulationParameters objects. Allow SimulationParameters objects to be used as input for gmx.core.write_tpr()
Basic TPR reader
Fixes kassonlab#86 gmx.fileio.read_tpr() and gmx.fileio.write_tpr_file() work as standalone tools to read, manipulate, and rewrite a TPR file. We defer several enhancements to other issues, including: * use in work graphs (see kassonlab#85) * integration with checkpoint data (see kassonlab#71) * several missing parameters that should be added to tprfile.cpp (kassonlab#192) See kassonlab#187 for more discussion.
Rewrite TPR file with updated parameters (standalone operation)
Minor layout updates in reference.rst.
Add a SOURCE_URL build-arg to Dockerfile.
Exclude `venv` directory (created in the project directory by default by CLion), and `.python-version` (used by `pyenv` to set a working-directory scoped default Python installation).
Disable testing against GROMACS 2019: gmxapi 0.0.8 development does not currently prioritize GROMACS 2019 compatibility. Install newer CMake in CI builds: The version of cmake available in Travis-CI Ubuntu 14 containers is too old to satisfy newer GROMACS requirements.
Change URL in setup.py to point to the devel branch of gromacs-gmxapi.
CMake argument `-DGMXAPI=ON` was used for all cmake invocations in setup.py, but should only apply to optional private GROMACS builds (e.g. readthedocs.org)
Update host environment in .travis.yml Fixes kassonlab#222
* Require WorkElement.name to be str type. * Use str in WorkElement.depends * Consistently use native str for keys in dict of WorkElement.
If a tuple or list of dependencies is added to a work element, map the context_rank to the list item when setting up the graph builders in Context.__enter__ Fixes kassonlab#221
Fix broken link for devel branch build
Tie gmxapi 0.0.7 to GROMACS 2019
jmhays
approved these changes
Jul 1, 2019
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Accept initial 0.0.8 development as a tweak revision to the 0.0.7 branch (0.0.7.2). Development external to the GROMACS repository will be collected as a (hopefully) final tweak to the 0.0.7 release branch, which will be tied to GROMACS 2019 from now on.
develis being merged tomaster, then torelease-0_0_7with a new tag.It is worth noting that we changed the C++ stdlib requirement from 11 to 14 for std::make_unique. That's a bigger change than I would normally want without a more substantial version number increase, but I don't really think it is worth reverting at this point.
Candidate final 0.0.7 documentation is here
Refs #188