Incorporate sample_restraint repository.
authorM. Eric Irrgang <ericirrgang@gmail.com>
Tue, 4 Jun 2019 21:12:58 +0000 (16:12 -0500)
committerMark Abraham <mark.j.abraham@gmail.com>
Tue, 9 Jul 2019 21:03:06 +0000 (23:03 +0200)
commitc6d213ae3e57309cfea49c5bf0a0d5bc33afa4c0
tree895fe66acbb136d3a2f2799f4cd8bcd79e7d05fe
parenta29abd636e87637ff82ce468926a2e87c4691a40
Incorporate sample_restraint repository.

This commit transfers development of the sample MD plug-in
code from an external repository to the GROMACS repository.
It should not be considered to add or change functionality,
but serves as a base for future integrated development.

The sample_restraint subtree serves as the root of a
template repository that a researcher could start from
to develop gmxapi MD extension code. It is meant to be
self-contained and built against an existing GROMACS
installation. Moving it to a GROMACS repo subdirectory
makes it less accessible to extension developers, but
easier to test and maintain for GROMACS developers. Near
term follow-up should include the creation of an external
skeleton repository, downstream subtree repository, or
"cookie cutter" repository drawing core content from the
GROMACS subtree.

* Import project from GitHub
  - https://github.com/kassonlab/sample_restraint/releases/tag/v0.0.7.3
  - Bundled sources for external projects are omitted.
  - Bundled test data files are omitted.
* Updates for compatibility with the gmxapi Python package are deferred
  to future changes.

Refs #3027

Change-Id: I1033a4a74dbce1bf1f9220a31cc9c15055c5dbaf
44 files changed:
python_packaging/README.md
python_packaging/docker/ci.dockerfile
python_packaging/sample_restraint/.gitattributes [new file with mode: 0644]
python_packaging/sample_restraint/.gitignore [new file with mode: 0644]
python_packaging/sample_restraint/.travis.yml [new file with mode: 0644]
python_packaging/sample_restraint/CMakeLists.txt [new file with mode: 0644]
python_packaging/sample_restraint/Dockerfile [new file with mode: 0644]
python_packaging/sample_restraint/README.md [new file with mode: 0644]
python_packaging/sample_restraint/ci_scripts/install_gromacs_2019.sh [new file with mode: 0755]
python_packaging/sample_restraint/ci_scripts/install_gromacs_devel.sh [new file with mode: 0755]
python_packaging/sample_restraint/ci_scripts/pygmx_0_0_7.sh [new file with mode: 0755]
python_packaging/sample_restraint/ci_scripts/pygmx_devel.sh [new file with mode: 0755]
python_packaging/sample_restraint/ci_scripts/sample_restraint.sh [new file with mode: 0755]
python_packaging/sample_restraint/ci_scripts/set_compilers [new file with mode: 0755]
python_packaging/sample_restraint/cmake/FindGROMACS.cmake [new file with mode: 0644]
python_packaging/sample_restraint/docs/CMakeLists.txt [new file with mode: 0644]
python_packaging/sample_restraint/docs/Doxyfile.in [new file with mode: 0644]
python_packaging/sample_restraint/examples/example.ipynb [new file with mode: 0644]
python_packaging/sample_restraint/examples/job.sh [new file with mode: 0644]
python_packaging/sample_restraint/examples/restrained-ensemble.py [new file with mode: 0644]
python_packaging/sample_restraint/examples/strip_notebook.py [new file with mode: 0755]
python_packaging/sample_restraint/src/CMakeLists.txt [new file with mode: 0644]
python_packaging/sample_restraint/src/cpp/CMakeLists.txt [new file with mode: 0644]
python_packaging/sample_restraint/src/cpp/ensemblepotential.cpp [new file with mode: 0644]
python_packaging/sample_restraint/src/cpp/ensemblepotential.h [new file with mode: 0644]
python_packaging/sample_restraint/src/cpp/harmonicpotential.cpp [new file with mode: 0644]
python_packaging/sample_restraint/src/cpp/harmonicpotential.h [new file with mode: 0644]
python_packaging/sample_restraint/src/cpp/make_unique.h [new file with mode: 0644]
python_packaging/sample_restraint/src/cpp/sessionresources.cpp [new file with mode: 0644]
python_packaging/sample_restraint/src/cpp/sessionresources.h [new file with mode: 0644]
python_packaging/sample_restraint/src/pythonmodule/CMakeLists.txt [new file with mode: 0644]
python_packaging/sample_restraint/src/pythonmodule/export_plugin.cpp [new file with mode: 0644]
python_packaging/sample_restraint/src/pythonmodule/export_plugin.h [new file with mode: 0644]
python_packaging/sample_restraint/tests/CMakeLists.gtest.in [new file with mode: 0644]
python_packaging/sample_restraint/tests/CMakeLists.txt [new file with mode: 0644]
python_packaging/sample_restraint/tests/__init__.py [new file with mode: 0644]
python_packaging/sample_restraint/tests/conftest.py [new file with mode: 0644]
python_packaging/sample_restraint/tests/pytest.ini [new file with mode: 0644]
python_packaging/sample_restraint/tests/test_binding.cpp [new file with mode: 0644]
python_packaging/sample_restraint/tests/test_binding.py [new file with mode: 0644]
python_packaging/sample_restraint/tests/test_bounding_restraint.cpp [new file with mode: 0644]
python_packaging/sample_restraint/tests/test_harmonic.cpp [new file with mode: 0644]
python_packaging/sample_restraint/tests/test_histogram.cpp [new file with mode: 0644]
python_packaging/sample_restraint/tests/testingconfiguration.in.h [new file with mode: 0644]