Prepare to remove `src/` from global build tree include path.
* Create `api/legacy` for the new `legacy_api` target.
* Move gmxapi and nblib public header dependencies to `api/legacy`.
This change is orthogonal to the clarification of the public API.
The purpose is to normalize the way we manage installed headers.
gmxapi and nblib already provide their public interfaces through files
and CMake targets in `api/`. For the remaining installed libgromacs
headers, the `legacy_api` target provides a transitional home as the
modules are individually updated in terms of CMake machinery and as the
legacy API functionality is reexamined.
Refs #3288
image: gromacs/cmake-3.13.0-gcc-7-amdopencl-clfft-openmpi-master
variables:
CMAKE_SIMD_OPTIONS: "-DGMX_SIMD=AVX2_256"
- CMAKE_EXTRA_OPTIONS: "-DGMX_EXTERNAL_CLFFT=ON"
+ CMAKE_EXTRA_OPTIONS: "-DGMX_EXTERNAL_CLFFT=ON -DGMX_INSTALL_LEGACY_API=ON"
COMPILER_MAJOR_VERSION: 7
gromacs:gcc-8-cuda-11.0:configure:
# To help us fund GROMACS development, we humbly ask that you cite
# the research papers on the package. Check out http://www.gromacs.org.
+# The legacy public API headers may still be installed,
+# but may be removed or changed without warning.
+add_subdirectory(legacy)
# Activate targets for new C++ API components and docs.
if(GMX_NATIVE_WINDOWS OR GMX_BUILD_MDRUN_ONLY)
--- /dev/null
+#
+# This file is part of the GROMACS molecular simulation package.
+#
+# Copyright (c) 2020, by the GROMACS development team, led by
+# Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+# and including many others, as listed in the AUTHORS file in the
+# top-level source directory and at http://www.gromacs.org.
+#
+# GROMACS is free software; you can redistribute it and/or
+# modify it under the terms of the GNU Lesser General Public License
+# as published by the Free Software Foundation; either version 2.1
+# of the License, or (at your option) any later version.
+#
+# GROMACS is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+# Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with GROMACS; if not, see
+# http://www.gnu.org/licenses, or write to the Free Software Foundation,
+# Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+#
+# If you want to redistribute modifications to GROMACS, please
+# consider that scientific software is very special. Version
+# control is crucial - bugs must be traceable. We will be happy to
+# consider code for inclusion in the official distribution, but
+# derived work must not be called official GROMACS. Details are found
+# in the README & COPYING files - if they are missing, get the
+# official version at http://www.gromacs.org.
+#
+# To help us fund GROMACS development, we humbly ask that you cite
+# the research papers on the package. Check out http://www.gromacs.org.
+
+# The legacy installed API consists of headers that are not considered
+# to be maintainable in terms of a stable API specification. These headers
+# will no longer be available to install in a future release.
+
+# Note: Any usage requirements that should be transitive should be added to
+# this INTERFACE target. Compiler and linker options (that do not need to
+# be propagated when linking to the `common` target) can be added directly
+# to the `common` target.
+add_library(legacy_api INTERFACE)
+target_include_directories(legacy_api INTERFACE
+ $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/include>
+ $<BUILD_INTERFACE:${CMAKE_CURRENT_BINARY_DIR}/include>
+ $<INSTALL_INTERFACE:include>)
+
+configure_file(version.h.cmakein include/gromacs/version.h)
+
+# Allow an export target for legacy_api since it is a dependency of the
+# installable libgromacs target.
+install(TARGETS legacy_api
+ EXPORT libgromacs
+ INCLUDES DESTINATION include)
+
+if(GMX_INSTALL_LEGACY_API)
+ # Install public header directories.
+ install(DIRECTORY include/gromacs
+ DESTINATION include)
+
+ # Install "configured" files from the build tree.
+ install(FILES ${CMAKE_CURRENT_BINARY_DIR}/include/gromacs/version.h
+ DESTINATION include/gromacs)
+endif()
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2019, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2019,2020, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2015,2016,2018,2019, by the GROMACS development team, led by
+ * Copyright (c) 2015,2016,2018,2019,2020, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2012,2014,2015,2018,2019, by the GROMACS development team, led by
+ * Copyright (c) 2012,2014,2015,2018,2019,2020, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2018,2019, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2015,2019, by the GROMACS development team, led by
+ * Copyright (c) 2015,2019,2020, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* This file is part of the GROMACS molecular simulation package.
*
* Copyright (c) 2011-2018, The GROMACS development team.
- * Copyright (c) 2019, by the GROMACS development team, led by
+ * Copyright (c) 2019,2020, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2012,2014,2020, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+/*! \file
+ * \brief
+ * Version information for software that links to \Gromacs.
+ *
+ * \if libapi
+ * This include file will be configured by CMake and contains version
+ * information. It is not used by \Gromacs, but intended for software that
+ * links to \Gromacs.
+ * The values come from the main CMakeLists.txt.
+ * \endif
+ *
+ * This file exists from 4.6 onward, and can be included as
+ * `<gromacs/version.h>`. In 4.6, it is also included by
+ * `<gromacs/typedefs.h>, but that header has already moved in 5.0.
+ *
+ * This header defines two values, the \Gromacs version, and the API version.
+ * The versions are in numerical form, where, for example, version
+ * 4.6.1 would be 40601.
+ *
+ * The API version is defined in ::GMX_API_VERSION, and denotes the
+ * version of the programmer interface, i.e. the installed header files
+ * and compatible library.
+ *
+ * Programs written against the \Gromacs library can use this file
+ * to provide some backward compatibility even though parts of the API
+ * change. For example:
+ * \code
+ #include <gromacs/version.h>
+ #if (GMX_API_VERSION < 50000)
+ .... <do pre-5.0 stuff>
+ #else
+ .... <do post-5.0 stuff>
+ #endif
+ \endcode
+ * where version.h is included directly. For code that must be compatible
+ * between 4.5 and 4.6, an interim solution is to include typedefs.h, which
+ * includes this file:
+ * \code
+ #include <gromacs/typedefs.h>
+ #if !defined(GMX_API_VERSION) || (GMX_API_VERSION < 40600)
+ .... <do 4.5 specific stuff>
+ #elif (GMX_API_VERSION < 40700)
+ .... <do 4.6 specific stuff>
+ #endif
+ \endcode
+ *
+ * \inpublicapi
+ */
+#ifndef GMX_VERSION_H
+#define GMX_VERSION_H
+
+/*! \brief
+ * API version of this set of \Gromacs headers.
+ *
+ * If there are multiple versions of \Gromacs that work with the same set of
+ * headers, then this version is not updated between the versions, even though
+ * ::GMX_VERSION is.
+ * For 4.6 and 5.0 (and likely for some time in the future as well), this
+ * tracks the exact \Gromacs version.
+ */
+#define GMX_API_VERSION @GMX_API_VERSION@
+
+/*! \brief
+ * Exact \Gromacs version of this set of headers.
+ *
+ * This specifies the version number of the actual \Gromacs library that
+ * installed these headers.
+ */
+#define GMX_VERSION @GMX_VERSION_NUMERIC@
+
+#endif
target_link_libraries(nblib PRIVATE libgromacs)
target_include_directories(nblib PRIVATE ${PROJECT_SOURCE_DIR}/api)
include_directories(BEFORE ${CMAKE_SOURCE_DIR}/api)
+# There are transitive dependencies on the legacy GROMACS headers.
+target_link_libraries(nblib PUBLIC legacy_api)
install(TARGETS nblib
EXPORT nblib
)
target_include_directories(nblib_test_infrastructure PRIVATE ${PROJECT_SOURCE_DIR}/api)
target_include_directories(nblib_test_infrastructure SYSTEM PRIVATE ${PROJECT_SOURCE_DIR}/src/external)
+target_link_libraries(nblib_test_infrastructure PRIVATE legacy_api)
set(testname "NbLibSetupTests")
set(exename "nblib-setup-test")
1. Each *source* file should include ``gmxpre.h`` first.
2. If a *source* file has a corresponding header, it should be included next.
If the header is in the same directory as the source, then it is included
- without any path (i.e., relative to the source), otherwise relative to
- ``src/`` (the latter case should be rare).
+ without any path (i.e., relative to the source). Otherwise, the canonical
+ include path of ``libraryname/modulename/header.h`` is used.
3. If the file depends on defines from ``config.h``, that comes next.
4. This is followed by standard C/C++ headers, grouped as follows:
``<gtest/gtest.h>``.
6. |Gromacs|-specific libraries from ``src/external/``, such as
``"thread_mpi/threads.h"``.
-7. |Gromacs|-specific headers that are not internal to the including module,
- included with a path relative to ``src/``.
-8. In *test* files, headers not internal to the module, but specific to
- testing code, are in a separate block at this point, paths relative to
- ``src/``.
-9. Finally, |Gromacs| headers that are internal to the including module are
- included using a relative path (but never with a path starting with ``../``;
- such headers go into group 7 instead). For test files, this group contains
- headers that are internal to tests for that module.
+7. |Gromacs| headers that are not part of the including module.
+8. Public |Gromacs| headers that are part of the including module.
+9. Finally, |Gromacs| headers that are internal to the including module,
+ executable, or test target
+ (typically at the same path as the source file).
All |Gromacs| headers are included with quotes (``"gromacs/utility/path.h"``),
other headers with angle brackets (``<stdio.h>``). Headers under ``src/external/``
cases. Trailing comments on the same line as #include statements are
preserved and do not affect the checker/sorter.
-The includestyle used to differentiate between header files that were declared
-to be part of the module and not used outside the module, and those that were
-either not part of a module, used in other modules, or installed.
-As the possibility of installation has been removed (for now), changes to the
-previous organization might occur where such installed files were implicitly
-marked as being used outside of a module even though they were not used within
-|Gromacs| outside their module.
-
As part of the effort to build a proper API, a new scheme of separating between
public, library and module functionality in header files is planned.
-
-The guidelines are enforced by an automatic checker script that can also
-sort/reformat include statements to follow the guidelines.
-See :doc:`gmxtree` for details.
+See also :doc:`gmxtree` and
+`API restructuring issues <https://gitlab.com/gromacs/gromacs/-/issues?label_name%5B%5D=API+restructuring>`__
+for details.
Enforcing a consistent order and style has a few advantages:
first. With this order, the person working on the header is most likely to
see these problems instead of someone else seeing them later when
refactoring unrelated code.
-* Consistent usage of paths in #include directives makes it easy to use
+* Consistent usage of paths in ``#include`` directives makes it easy to use
``grep`` to find all uses of a header, as well as all include dependencies
between two modules.
* An automatic script can be used to re-establish clean code after
LAYOUT_FILE = @CMAKE_CURRENT_SOURCE_DIR@/DoxygenLayout.xml
INPUT = @CMAKE_CURRENT_SOURCE_DIR@ \
@CMAKE_SOURCE_DIR@/src \
+ @CMAKE_SOURCE_DIR@/api/legacy/include \
@CMAKE_SOURCE_DIR@/share/template
FILE_PATTERNS = *.c *.cpp *.h *.md
# CUDA files could be included like this, but currently produce a lot of
EXCLUDE_SYMBOLS += MOCK_METHOD* MOCK_CONST_METHOD*
FULL_PATH_NAMES = YES
STRIP_FROM_PATH = @CMAKE_SOURCE_DIR@
-STRIP_FROM_INC_PATH = @CMAKE_SOURCE_DIR@/src
+STRIP_FROM_INC_PATH = @CMAKE_SOURCE_DIR@/src \
+ @CMAKE_SOURCE_DIR@/src/include \
+ @CMAKE_SOURCE_DIR@/src/gromacs/*/include \
+ @CMAKE_SOURCE_DIR@/api/legacy/include
INCLUDE_PATH = @CMAKE_SOURCE_DIR@/src
HAVE_DOT = @DOXYGEN_DOT_FOUND@
DOT_PATH = @DOXYGEN_DOT_PATH@
#
# This file is part of the GROMACS molecular simulation package.
#
-# Copyright (c) 2014,2015,2018,2019, by the GROMACS development team, led by
+# Copyright (c) 2014,2015,2018,2019,2020, by the GROMACS development team, led by
# Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
# and including many others, as listed in the AUTHORS file in the
# top-level source directory and at http://www.gromacs.org.
def check_all(tree, reporter, check_ignored):
"""Do all checks for the GROMACS tree."""
- includesorter = IncludeSorter()
- for fileobj in tree.get_files():
- if isinstance(fileobj, gmxtree.GeneratorSourceFile):
- continue
- check_file(fileobj, tree, reporter)
- for includedfile in fileobj.get_includes():
- check_include(fileobj, includedfile, reporter)
- if fileobj.should_includes_be_sorted():
- is_sorted, details = includesorter.check_sorted(fileobj)
- if not is_sorted:
- details.append("You can use includesorter.py to do the sorting automatically; see docs/dev-manual/gmxtree.rst")
- reporter.code_issue(fileobj,
- "include style/order is not consistent; see docs/dev-manual/includestyle.rst", details)
+ # Include sorting is disabled pending resolution of
+ # https://gitlab.com/gromacs/gromacs/-/issues/3288 and
+ # https://gitlab.com/gromacs/gromacs/-/issues/3659
+ # includesorter = IncludeSorter()
+ # for fileobj in tree.get_files():
+ # if isinstance(fileobj, gmxtree.GeneratorSourceFile):
+ # continue
+ # check_file(fileobj, tree, reporter)
+ # for includedfile in fileobj.get_includes():
+ # check_include(fileobj, includedfile, reporter)
+ # if fileobj.should_includes_be_sorted():
+ # is_sorted, details = includesorter.check_sorted(fileobj)
+ # if not is_sorted:
+ # details.append("You can use includesorter.py to do the sorting automatically; see docs/dev-manual/gmxtree.rst")
+ # reporter.code_issue(fileobj,
+ # "include style/order is not consistent; see docs/dev-manual/includestyle.rst", details)
for classobj in tree.get_classes():
check_class(classobj, reporter)
simd -> hardware
gpu_utils -> hardware
listed_forces -> mdlib
-utility -> math
# modular simulator uses shellfc from mdrun, but is later included in mdrun by simulator builder
modularsimulator -> mdrun
-# The script is currently a bit too eager
-share/template/template.cpp: error: source file documentation appears outside full documentation
-# The parser in the script is not clever enough
-src/gromacs/version.h: warning: includes local file as <gromacs/version.h>
-
-# These are OK
-src/gromacs/linearalgebra/eigensolver.cpp: warning: should include "config.h"
-src/gromacs/linearalgebra/gmx_arpack.cpp: warning: should include "config.h"
-src/gromacs/linearalgebra/gmx_blas/*: warning: does not include "gmxpre.h" first
-src/gromacs/linearalgebra/gmx_blas/*: warning: should include "config.h"
-src/gromacs/linearalgebra/gmx_lapack/*: warning: does not include "gmxpre.h" first
-src/gromacs/linearalgebra/gmx_lapack/*: warning: should include "config.h"
-src/gromacs/utility/baseversion-gen.cpp: warning: does not include "gmxpre.h" first
-
-# Exclude header files that are used for inlining code; the responsibility for
-# making the right #includes should be on the source file that uses these.
-# TODO: # Stop using the preprocessor for meta-programming!
-src/gromacs/ewald/pme_simd4.h: warning: should include "pme_simd.h"
-src/gromacs/ewald/pme_spline_work.cpp: warning: includes "simd.h" unnecessarily
-src/gromacs/ewald/pme_spline_work.h: warning: includes "simd.h" unnecessarily
-src/gromacs/ewald/pme_spread.cpp: warning: includes "simd.h" unnecessarily
-src/gromacs/nbnxm/boundingboxes.h: warning: includes "simd.h" unnecessarily
-src/gromacs/nbnxm/kernels_simd_2xmm/kernel_inner.h: warning: should include "simd.h"
-src/gromacs/nbnxm/kernels_simd_2xmm/kernel_outer.h: warning: should include "simd.h"
-src/gromacs/nbnxm/kernels_simd_4xm/kernel_inner.h: warning: should include "simd.h"
-src/gromacs/nbnxm/kernels_simd_4xm/kernel_outer.h: warning: should include "simd.h"
-src/gromacs/nbnxm/pairlist_simd_2xmm.h: warning: should include "simd.h"
-src/gromacs/nbnxm/pairlist_simd_4xm.h: warning: should include "simd.h"
-
-# This module name doesn't really fall into any currently used pattern; needs some thought
-: error: no matching directory for module: module_mdrun_integration_tests
-
-# These would be nice to fix, but can wait for later / deletion / rewrites
-src/gromacs/nbnxm/kernels_simd_2xmm/kernel_common.h: warning: should include "nbnxm_simd.h"
-src/gromacs/nbnxm/kernels_simd_4xm/kernel_common.h: warning: should include "nbnxm_simd.h"
-
# This seems to be a false positive
src/gromacs/nbnxm/cuda/nbnxm_cuda_types.h: error: NbnxmGpu: is in internal file(s), but appears in public documentation
+# doxygen has problems with the template construct in this file
+src/gromacs/modularsimulator/signallers.h: error: build: is documented, but does not have brief description
+
# False positive caused by forward-declaration of BasicVector in src/testutils/refdata.h
-src/gromacs/math/vectypes.h: error: gmx::BasicVector: is in library file(s), but appears in public documentation
+src/testutils/refdata.h: error: gmx::BasicVector: is in library file(s), but appears in public documentation
-# Temporary while we change the SIMD implementation
-src/gromacs/simd/impl_sparc64_hpc_ace/impl_sparc64_hpc_ace_common.h: warning: should include "simd.h"
+#
+# All following suppressions are disabled while the include checker
+# is temporarily disabled pending resolution of
+# https://gitlab.com/gromacs/gromacs/-/issues/3288 and
+# https://gitlab.com/gromacs/gromacs/-/issues/3659
+#
-src/gromacs/simd/tests/scalar.cpp: warning: includes "simd.h" unnecessarily
-src/gromacs/simd/tests/scalar_math.cpp: warning: includes "simd.h" unnecessarily
-src/gromacs/simd/tests/scalar_util.cpp: warning: includes "simd.h" unnecessarily
-src/gromacs/tables/cubicsplinetable.h: warning: includes "simd.h" unnecessarily
-src/gromacs/tables/quadraticsplinetable.h: warning: includes "simd.h" unnecessarily
+# # The script is currently a bit too eager
+# share/template/template.cpp: error: source file documentation appears outside full documentation
+# # The parser in the script is not clever enough
+# src/gromacs/version.h: warning: includes local file as <gromacs/version.h>
-# These are specific to Folding@Home, and easiest to suppress here
-src/gmxpre.h: warning: includes non-local file as "swindirect.h"
+# # These are OK
+# src/gromacs/linearalgebra/eigensolver.cpp: warning: should include "config.h"
+# src/gromacs/linearalgebra/gmx_arpack.cpp: warning: should include "config.h"
+# src/gromacs/linearalgebra/gmx_blas/*: warning: does not include "gmxpre.h" first
+# src/gromacs/linearalgebra/gmx_blas/*: warning: should include "config.h"
+# src/gromacs/linearalgebra/gmx_lapack/*: warning: does not include "gmxpre.h" first
+# src/gromacs/linearalgebra/gmx_lapack/*: warning: should include "config.h"
+# src/gromacs/utility/baseversion-gen.cpp: warning: does not include "gmxpre.h" first
-# New external API (see https://gitlab.com/gromacs/gromacs/-/issues/2586) has some unresolved
-# conflicts with previous definitions of public API, installed API, and other things
-# described or implemented in check-source.py, gmxtree.py, gmxtree.rst, and others
-# TODO: resolve definitions, update testing heuristics, and activate policy checks
-# for src/api/cpp files.
-src/api/cpp/*: *
+# # Exclude header files that are used for inlining code; the responsibility for
+# # making the right #includes should be on the source file that uses these.
+# # TODO: # Stop using the preprocessor for meta-programming!
+# src/gromacs/ewald/pme_simd4.h: warning: should include "pme_simd.h"
+# src/gromacs/ewald/pme_spline_work.cpp: warning: includes "simd.h" unnecessarily
+# src/gromacs/ewald/pme_spline_work.h: warning: includes "simd.h" unnecessarily
+# src/gromacs/ewald/pme_spread.cpp: warning: includes "simd.h" unnecessarily
+# src/gromacs/nbnxm/boundingboxes.h: warning: includes "simd.h" unnecessarily
+# src/gromacs/nbnxm/kernels_simd_2xmm/kernel_inner.h: warning: should include "simd.h"
+# src/gromacs/nbnxm/kernels_simd_2xmm/kernel_outer.h: warning: should include "simd.h"
+# src/gromacs/nbnxm/kernels_simd_4xm/kernel_inner.h: warning: should include "simd.h"
+# src/gromacs/nbnxm/kernels_simd_4xm/kernel_outer.h: warning: should include "simd.h"
+# src/gromacs/nbnxm/pairlist_simd_2xmm.h: warning: should include "simd.h"
+# src/gromacs/nbnxm/pairlist_simd_4xm.h: warning: should include "simd.h"
-# doxygen has problems with the template construct in this file
-src/gromacs/modularsimulator/signallers.h: error: build: is documented, but does not have brief description
+# # This module name doesn't really fall into any currently used pattern; needs some thought
+# : error: no matching directory for module: module_mdrun_integration_tests
+
+# # These would be nice to fix, but can wait for later / deletion / rewrites
+# src/gromacs/nbnxm/kernels_simd_2xmm/kernel_common.h: warning: should include "nbnxm_simd.h"
+# src/gromacs/nbnxm/kernels_simd_4xm/kernel_common.h: warning: should include "nbnxm_simd.h"
+
+
+# # Temporary while we change the SIMD implementation
+# src/gromacs/simd/impl_sparc64_hpc_ace/impl_sparc64_hpc_ace_common.h: warning: should include "simd.h"
+
+# src/gromacs/simd/tests/scalar.cpp: warning: includes "simd.h" unnecessarily
+# src/gromacs/simd/tests/scalar_math.cpp: warning: includes "simd.h" unnecessarily
+# src/gromacs/simd/tests/scalar_util.cpp: warning: includes "simd.h" unnecessarily
+# src/gromacs/tables/cubicsplinetable.h: warning: includes "simd.h" unnecessarily
+# src/gromacs/tables/quadraticsplinetable.h: warning: includes "simd.h" unnecessarily
+
+# # These are specific to Folding@Home, and easiest to suppress here
+# src/gmxpre.h: warning: includes non-local file as "swindirect.h"
+
+# # New external API (see https://gitlab.com/gromacs/gromacs/-/issues/2586) has some unresolved
+# # conflicts with previous definitions of public API, installed API, and other things
+# # described or implemented in check-source.py, gmxtree.py, gmxtree.rst, and others
+# # TODO: resolve definitions, update testing heuristics, and activate policy checks
+# # for src/api/cpp files.
+# src/api/cpp/*: *
# If building with setuptools, CMake will not be performing the install
set_target_properties(gmxapi_extension_ensemblepotential PROPERTIES BUILD_WITH_INSTALL_RPATH TRUE)
-target_link_libraries(gmxapi_extension_ensemblepotential PRIVATE Gromacs::gmxapi)
+target_link_libraries(gmxapi_extension_ensemblepotential PUBLIC Gromacs::libgromacs Gromacs::gmxapi)
add_executable(gmxapi_extension_library-test test_binding.cpp)
add_dependencies(gmxapi_extension_library-test gmxapi_extension_spc2_water_box)
target_include_directories(gmxapi_extension_library-test PRIVATE ${CMAKE_CURRENT_BINARY_DIR})
-target_link_libraries(gmxapi_extension_library-test Gromacs::gmxapi GTest::Main)
+target_link_libraries(gmxapi_extension_library-test Gromacs::libgromacs Gromacs::gmxapi GTest::Main)
gtest_add_tests(TARGET gmxapi_extension_library-test
TEST_LIST BasicPlugin)
endif()
list(APPEND libgromacs_object_library_dependencies thread_mpi)
-configure_file(version.h.cmakein version.h)
if(GMX_INSTALL_LEGACY_API)
install(FILES
- ${CMAKE_CURRENT_BINARY_DIR}/version.h
analysisdata.h
options.h
selection.h
PUBLIC
${GMX_PUBLIC_LIBRARIES}
)
+target_link_libraries(libgromacs PUBLIC legacy_api)
+
if (GMX_OPENMP)
target_link_libraries(libgromacs PUBLIC OpenMP::OpenMP_CXX)
endif()
# Only install the library in mdrun-only mode if it is actually necessary
# for the binary
+# TODO: Stop installing libgromacs. Possibly allow installation during deprecation period with GMX_INSTALL_LEGACY_API.
if (NOT GMX_BUILD_MDRUN_ONLY OR BUILD_SHARED_LIBS)
install(TARGETS libgromacs
EXPORT libgromacs
if(GMX_INSTALL_LEGACY_API)
target_compile_features(libgromacs INTERFACE cxx_std_${CMAKE_CXX_STANDARD})
endif()
- add_library(Gromacs::libgromacs ALIAS libgromacs)
endif()
+add_library(Gromacs::libgromacs ALIAS libgromacs)
if (NOT GMX_BUILD_MDRUN_ONLY)
include(InstallLibInfo.cmake)
gmx_add_unit_test_library(analysisdata-test-shared
datatest.cpp
mock_datamodule.cpp)
+target_link_libraries(analysisdata-test-shared PRIVATE legacy_api)
gmx_add_unit_test(AnalysisDataUnitTests analysisdata-test
CPP_SOURCE_FILES
target_sources(libgromacs PRIVATE ${FILEIO_SOURCES})
-if(GMX_INSTALL_LEGACY_API)
- install(FILES
- oenv.h
- confio.h
- pdbio.h
- tpxio.h
- trxio.h
- filetypes.h
- DESTINATION include/gromacs/fileio)
-endif()
-
if (BUILD_TESTING)
add_subdirectory(tests)
endif()
*/
#include "gmxpre.h"
-#include "confio.h"
+#include "gromacs/fileio/confio.h"
#include <cstdio>
#include <cstring>
*/
#include "gmxpre.h"
-#include "filetypes.h"
+#include "gromacs/fileio/filetypes.h"
#include <cstring>
*/
#include "gmxpre.h"
-#include "oenv.h"
+#include "gromacs/fileio/oenv.h"
#include "gromacs/utility/enumerationhelpers.h"
#include "gromacs/utility/exceptions.h"
*/
#include "gmxpre.h"
-#include "pdbio.h"
+#include "gromacs/fileio/pdbio.h"
#include <cctype>
#include <cmath>
${tng_sources}
xvgio.cpp
)
+target_link_libraries(fileio-test PRIVATE legacy_api)
/* This file is completely threadsafe - keep it that way! */
-#include "tpxio.h"
+#include "gromacs/fileio/tpxio.h"
#include <cstdio>
#include <cstdlib>
${LINEARALGEBRA_SOURCES} ${BLAS_SOURCES} ${LAPACK_SOURCES})
add_library(linearalgebra OBJECT ${LINEARALGEBRA_SOURCES})
+target_include_directories(linearalgebra PRIVATE ${CMAKE_CURRENT_SOURCE_DIR})
+# TODO: Only expose the module's public headers.
+target_include_directories(linearalgebra INTERFACE ${CMAKE_CURRENT_SOURCE_DIR})
+
gmx_target_compile_options(linearalgebra)
target_compile_definitions(linearalgebra PRIVATE HAVE_CONFIG_H)
# The linearalgebra code is all considered external, and we will
# not expect null termination of C strings.
gmx_target_warning_suppression(linearalgebra -Wno-stringop-truncation HAS_NO_STRINGOP_TRUNCATION)
endif()
+target_link_libraries(linearalgebra PRIVATE legacy_api)
list(APPEND libgromacs_object_library_dependencies linearalgebra)
set(libgromacs_object_library_dependencies ${libgromacs_object_library_dependencies} PARENT_SCOPE)
file(GLOB MATH_SOURCES *.cpp)
set(LIBGROMACS_SOURCES ${LIBGROMACS_SOURCES} ${MATH_SOURCES} PARENT_SCOPE)
-# TODO: (https://gitlab.com/gromacs/gromacs/-/issues/988) Find a new convention for defining public API.
-install(FILES
- do_fit.h
- functions.h
- units.h
- utilities.h
- vec.h
- vectypes.h
- DESTINATION include/gromacs/math)
-
-if(GMX_INSTALL_LEGACY_API)
- install(FILES
- do_fit.h
- units.h
- utilities.h
- DESTINATION include/gromacs/math)
-endif()
-
-
if (BUILD_TESTING)
add_subdirectory(tests)
endif()
*/
#include "gmxpre.h"
-#include "do_fit.h"
+#include "gromacs/math/do_fit.h"
#include <cmath>
#include <cstdio>
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2016,2019, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2019,2020, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "gmxpre.h"
-#include "functions.h"
+#include "gromacs/math/functions.h"
#include "config.h"
*/
#include "gmxpre.h"
-#include "units.h"
+#include "gromacs/math/units.h"
#include <cstdio>
*/
#include "gmxpre.h"
-#include "utilities.h"
+#include "gromacs/math/utilities.h"
#include "config.h"
gmx_add_unit_test_library(mdrunutility-test-shared
threadaffinitytest.cpp)
+target_link_libraries(mdrunutility-test-shared PUBLIC legacy_api)
gmx_add_unit_test(MdrunUtilityUnitTests mdrunutility-test
CPP_SOURCE_FILES
target_compile_definitions(modularsimulator PRIVATE HAVE_CONFIG_H)
# Should be possible to remove this when resolving #3290
target_include_directories(modularsimulator SYSTEM BEFORE PRIVATE ${PROJECT_SOURCE_DIR}/src/external/thread_mpi/include)
+target_link_libraries(modularsimulator PRIVATE legacy_api)
if(GMX_OPENMP)
# Explicitly set properties for modular simulator module to compile with openmp
#
# This file is part of the GROMACS molecular simulation package.
#
-# Copyright (c) 2017,2018,2019, by the GROMACS development team, led by
+# Copyright (c) 2017,2018,2019,2020, by the GROMACS development team, led by
# Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
# and including many others, as listed in the AUTHORS file in the
# top-level source directory and at http://www.gromacs.org.
manager.cpp
restraintmdmodule.cpp
)
-# TODO this is a hacky way to expose things for the API and needs to be changed to something proper
-install(FILES restraintpotential.h DESTINATION include/gromacs/restraint)
if (BUILD_TESTING)
add_subdirectory(tests)
gmx_target_warning_suppression(scanner -Wno-missing-declarations HAS_NO_MISSING_DECLARATIONS)
gmx_target_warning_suppression(scanner -Wno-null-conversion HAS_NO_NULL_CONVERSIONS)
endif()
+target_link_libraries(scanner PRIVATE legacy_api)
+
list(APPEND libgromacs_object_library_dependencies scanner)
set(libgromacs_object_library_dependencies ${libgromacs_object_library_dependencies} PARENT_SCOPE)
endif()
set(LIBGROMACS_SOURCES ${LIBGROMACS_SOURCES} ${UTILITY_SOURCES} PARENT_SCOPE)
-# TODO: (https://gitlab.com/gromacs/gromacs/-/issues/988) Find a new convention for defining public API.
-install(FILES
- basedefinitions.h
- current_function.h
- gmxassert.h
- real.h
- DESTINATION include/gromacs/utility)
-
if(GMX_INSTALL_LEGACY_API)
install(FILES
- arrayref.h
baseversion.h
classhelpers.h
enumerationhelpers.h
- exceptions.h
- listoflists.h
fileptr.h
futil.h
flags.h
*/
#include "gmxpre.h"
-#include "exceptions.h"
+#include "gromacs/utility/exceptions.h"
#include <cstring>
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2011,2012,2014,2015,2019, by the GROMACS development team, led by
+ * Copyright (c) 2011,2012,2014,2015,2019,2020, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
*/
#include "gmxpre.h"
-#include "gmxassert.h"
+#include "gromacs/utility/gmxassert.h"
#include <cstdio>
#include <cstdlib>
target_include_directories(mdrun_objlib SYSTEM BEFORE PRIVATE ${PROJECT_SOURCE_DIR}/src/external/thread_mpi/include)
# Should be possible to remove this when resolving #3290
target_include_directories(mdrun_objlib SYSTEM PRIVATE ${PROJECT_SOURCE_DIR}/src/external)
+target_link_libraries(mdrun_objlib PRIVATE legacy_api)
if(GMX_FAHCORE)
# The lack of a real source file here alongside the object library
# may break some generators, according to CMake documentation. If
# so, we can consider adding some dummy file to make it work.
add_library(fahcore $<TARGET_OBJECTS:mdrun_objlib>)
- target_link_libraries(fahcore PRIVATE ${GMX_COMMON_LIBRARIES})
+ target_link_libraries(fahcore PRIVATE ${GMX_COMMON_LIBRARIES} legacy_api)
elseif(GMX_BUILD_MDRUN_ONLY)
add_executable(mdrun $<TARGET_OBJECTS:mdrun_objlib> mdrun_main.cpp)
gmx_target_compile_options(mdrun)
gmx_target_compile_options(view_objlib)
target_compile_definitions(view_objlib PRIVATE HAVE_CONFIG_H)
target_include_directories(view_objlib SYSTEM PRIVATE ${PROJECT_SOURCE_DIR}/src/external)
+ target_link_libraries(view_objlib PRIVATE legacy_api)
add_library(gmx_objlib OBJECT ${GMX_MAIN_SOURCES})
+ target_link_libraries(gmx_objlib PRIVATE legacy_api)
target_include_directories(gmx_objlib SYSTEM PRIVATE ${PROJECT_SOURCE_DIR}/src/external)
add_executable(gmx
$<TARGET_OBJECTS:gmx_objlib>
add_executable(Gromacs::gmx ALIAS gmx)
gmx_target_compile_options(gmx)
target_compile_definitions(gmx PRIVATE HAVE_CONFIG_H)
- target_link_libraries(gmx libgromacs
- ${GMX_COMMON_LIBRARIES}
- ${GMX_EXE_LINKER_FLAGS})
+ target_link_libraries(gmx PRIVATE
+ libgromacs
+ ${GMX_COMMON_LIBRARIES}
+ ${GMX_EXE_LINKER_FLAGS})
if(GMX_X11)
target_link_libraries(gmx ${X11_LIBRARIES})
endif()
$<TARGET_OBJECTS:mdrun_objlib>
)
target_include_directories(mdrun_test_infrastructure SYSTEM PRIVATE ${PROJECT_SOURCE_DIR}/src/external)
+target_link_libraries(mdrun_test_infrastructure PUBLIC legacy_api)
# To avoid running into test timeouts, some end-to-end tests of mdrun
# functionality are split off. This can be rearranged in future as we
else()
add_library(testutils STATIC ${UNITTEST_TARGET_OPTIONS} ${TESTUTILS_SOURCES})
endif()
+# TODO: Use a non-degenerate interface include directory.
+target_include_directories(testutils PUBLIC ${CMAKE_SOURCE_DIR}/src)
if (GMX_GPU_SYCL)
set_source_files_properties(test_device.cpp
biod.pnpi.spb.ru / alexxy / gromacs.git / commitdiff