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>
Lars-Dominik Braun
Guillaume Le Vaillant
Michael Rohleder
Ivan Gankevich
Paul A. Patience
Efraim Flashner
Tanguy Le Carrour
raingloom
Matthew James Kraai
Raghav Gururajan
Alexandre Hannud Abdo
Charles
Jonathan Brielmaier
Vinicius Monego
Franck Pérignon
Ryan Prior
itd
Morgan Smith
Kyle Meyer