# 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

# 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

# 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/*: *

# 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
