Renamed from python2-checkm-genome to checkm to better reflect its
status as standalone-application and support for Python 3.
* gnu/packages/bioinformatics.scm (python2-checkm-genome): Redirect to…
(checkm): …here and update to 1.1.3.
[propagated-inputs]: Move to inputs.
[inputs]: Use Python 3 dependencies.
[home-page]: Point to real home-page.
The cleanup notably:
* Builds and installs the documentation into a separate doc output (in
the process moving around some files erroneously installed into the root
directory); and
* Removes unnecessary inputs and moves some inputs into
propagated-inputs (the candidates of which were determined with a search
for "include.*LIBNAME" in include/deal.II).
* gnu/packages/maths.scm (dealii): Reword comments.
[version]: Update to 9.3.1.
[outputs]: New field including doc output.
[native-inputs]: New field.
[inputs]: Sort them. Remove p4est (deal.II interfaces with it only when
MPI is enabled). Move boost, suitesparse and tbb to...
[propagated-inputs]: ...here. New field including hdf5, which is
actually supported in deal.II without MPI.
[arguments]<#:tests?>: New argument. The tests were not being run before
anyway.
<#:configure-flags>[-DDEAL_II_COMPONENT_DOCUMENTATION]: New flag.
[-DDEAL_II_DOCREADME_RELDIR]: New flag. Prevents the LICENSE.md,
README.md, detailed.log and summary.log files from being installed in
the root directory (though note that the logs are removed in the new
remove-build-logs phase).
[-DDEAL_II_DOCHTML_RELDIR]: New flag.
[-DDEAL_II_COMPILE_EXAMPLES]: New flag.
[-DDEAL_II_EXAMPLES_RELDIR]: New flag. Prevents the examples directory
from being installed in the root directory.
[-DCMAKE_POSITION_INDEPENDENT_CODE]: Remove flag. The issue has been
resolved.
<#:phases>{remove-build-logs}: New phase.
[home-page]: Add trailing slash.
(dealii-openmpi): Use package/inherit.
[inputs]: Sort them. Remove mumps-metis-openmpi (deal.II no longer
interfaces with MUMPS). Move hdf5-parallel-openmpi, openmpi,
p4est-openmpi, petsc-openmpi and slepc-openmpi to...
[propagated-inputs]: ...here. New field.
[arguments]<#:configure-flags>: Rename cf variable to flags.
<#:phases>{mpi-setup}: Remove phase which is unused because the tests
are disabled.
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
* gnu/packages/lisp.scm (txr)[version]: Update to 266.
[inputs]: Add bash.
[arguments]<#:phases>{inhibit-doc-syms-generation}: Correct the path to
doc-syms.tl to its new location.
{fix-tests}: Fix another test.
{fix-paths}: New phase.
Co-authored-by: Guillaume Le Vaillant <glv@posteo.net>
The install-license-files phase was installing LICENSE-CYG when it
shouldn't have, because that license applies only to TXR builds for
Microsoft Windows; and it was also ignoring the METALICENSE file.
However, TXR's Makefile was already installing the LICENSE and
METALICENSE files into share/txr (the datadir), so redirect them into
the appropriate doc directory and delete the install-license-files
phase.
* gnu/packages/lisp.scm (txr)[arguments]<#:phases>
{fix-license-installation}: New phase.
{install-license-files}: Delete phase.
Signed-off-by: Guillaume Le Vaillant <glv@posteo.net>
* gnu/packages/lisp.scm (man-for-txr): New variable.
(txr)[native-inputs]: New field.
[inputs]: Move above the arguments field.
[arguments]<#:phases>{inhibit-doc-syms-generation, build-doc, install-doc}:
New phases.
{fix-tests}: Add after the unpack phase rather than after the configure
phase so that all file-modifying phases are performed after unpacking.
Signed-off-by: Guillaume Le Vaillant <glv@posteo.net>
* guix/import/print.scm (package->code)<license->code>: Update generated
licence object to match record constructor.
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
