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Author SHA1 Message Date
David Elsing
5aebea0116
gnu: yaehmop: Fix build with GCC 14. 
The C code calls functions from Fortran without declaration.

* gnu/packages/chemistry.scm (yaehmop)[arguments]: Add CMAKE_C_FLAGS.

Change-Id: Ib115645a414693cd42429d957d746f8435a889a6
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2025-07-31 23:19:38 +01:00
David Elsing
d8d9e51a1f
gnu: freesasa: Fix build with newer gemmi. 
* gnu/packages/chemistry.scm (freesasa)[arguments]: Add 'fix-new-gemmi phase.

Change-Id: I78997047eba8245a2d275af5ab18d0d0fe48630f
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2025-07-31 23:19:34 +01:00
David Elsing
c3e59b2ffa
gnu: gemmi: Update to 0.7.3. 
Fixes: guix/guix#1567.

* gnu/packages/chemistry.scm (gemmi): Update to 0.7.3.
[source]: Remove gemmi-fix-sajson-types.patch patch.
[arguments]: Adjust 'patch-includes and 'check phases.
[native-inputs]: Add python-nanobind and zpp-serializer. Remove pybind11 and
tinydir.

Change-Id: Ia1a894226d7d0a9536ed0c6646271d475c397ee7
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2025-07-31 23:19:24 +01:00
David Elsing
99fb22110e
gnu: openbabel: Fix build and switch to git source. 
The git source does not contain the bundled libraries.

* gnu/packages/chemistry.scm (openbabel)[source]: Switch to git-fetch.
[arguments]<#:configure-flags>: Use search-input-file and
search-input-directory.
<#:phases>: Add phase 'fix-time-check.
[inputs]: Add rapidjson.
[home-page]: Update URL.

Signed-off-by: Andreas Enge <andreas@enge.fr>
 2025-07-31 22:41:38 +02:00
Zheng Junjie
464c3b6340
gnu: qcint: Fix build. 
* gnu/packages/chemistry.scm (qcint)[arguments]: Use G-expression.

Change-Id: I4e26a872b6e78a6ea96d16c661353063b8d3fcd6
 2025-07-13 18:37:56 +08:00
Zheng Junjie
278a80f399
gnu: python-pyscf: Make tune works. 
* gnu/packages/chemistry.scm (python-pyscf)[native-inputs]:
Add (canonical-package gcc).

Change-Id: Ibee49cb64581bd9e6743cdd16aa25739ac53112c
 2025-07-13 18:37:47 +08:00
Sharlatan Hellseher
610af820d4
gnu: packages/chemistry: Sort use-module alphabetically. 
* gnu/packages/chemistry.scm: Sort use-module alphabetically.

Change-Id: Ib6df5e22d91ef443ad57cbb811906ba3bb0644d8
 2025-07-08 12:17:15 +01:00
David Elsing
631a3308f5
gnu: Add python-pyscf-properties. 
* gnu/packages/chemistry.scm (python-pyscf-properties): New variable.

Change-Id: I10823bca5df64a563521bc8f1d28a4a75678ef5d
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2025-07-08 12:17:15 +01:00
David Elsing
c6f85649b3
gnu: Add python-pyscf-dispersion. 
* gnu/packages/chemistry.scm (python-pyscf-dispersion): New variable.

Change-Id: I1e50ae57c4b79932cab87c16a6f2ab733a5544c0
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2025-07-08 12:17:15 +01:00
David Elsing
002b62199c
gnu: Add python-geometric. 
* gnu/packages/chemistry.scm (python-geometric): New variable.

Change-Id: I5d716df3d71a671c334ff2dfd1b44e15e37afc5a
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2025-07-08 12:17:15 +01:00
David Elsing
2f1193181d
gnu: Add python-pyscf. 
* gnu/packages/chemistry.scm (python-pyscf): New variable.

Change-Id: I4e265c97644a6f8765c5d509de126de0312a3f98
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2025-07-08 12:17:15 +01:00
David Elsing
d08c2a882b
gnu: Add qcint. 
* gnu/packages/chemistry.scm (qcint): New variable.

Change-Id: Ie32f97a028f847dc401a4b9772df6f0f9a550e97
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2025-07-08 12:17:14 +01:00
David Elsing
b353e5cb85
gnu: Add libcint. 
* gnu/packages/chemistry.scm (libcint): New variable.

Change-Id: I72da249743392eb8a4be1673b9fc1a7bbbb1c942
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2025-07-08 12:17:14 +01:00
David Elsing
46cb759a52
gnu: Add xcfun. 
* gnu/packages/chemistry.scm (xcfun): New variable.

Change-Id: Iaf25180a7edafffce1e8eabdbf6a81c289401f2e
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2025-07-08 12:17:14 +01:00
Sharlatan Hellseher
f9f3fe2082
gnu: packages/chemistry: Add EOF disclaimer. 
* gnu/packages/chemistry.scm: Add a comments to place packages in
alphabetical order.

Change-Id: I2af9eeeb1de77b0420093bf2776b1df7e7bda188
 2025-07-08 12:17:13 +01:00
Jakob Kirsch
a0b0a524aa
gnu: avogadro2: Update to 1.100.0. 
* gnu/packages/chemistry.scm (avogadro2): Update to 1.100.0.
[inputs]: Add openbabel and qtsvg-5.
[native-inputs]: Add avogadro-i18n.
[arguments]<#:phases>{'symlink, 'wrap-program}: New phases.

Change-Id: I9577e27021ca449426d7506589939c050a5d0cfb
Signed-off-by: Andreas Enge <andreas@enge.fr>
 2025-06-02 14:52:22 +02:00
Jakob Kirsch
fcee60c803
gnu: avogadrolibs: Update to 1.100.0. 
* gnu/packages/chemistry.scm (avogadrolibs): Update to 1.100.0.
[inputs]: Add qtsvg-5, avogadro-molecules, avogadro-crystals,
avogadro-fragments.
[arguments]<#:configure-flags>: Drop a flag.
<#:phases>{'symlink}: New phase.

Change-Id: I67e3c15db14e97394e6ef27a756c2b9dd951ad79
Signed-off-by: Andreas Enge <andreas@enge.fr>
 2025-06-02 14:37:35 +02:00
Jakob Kirsch
c04bb04a39
gnu: spglib: Update to 2.5.0. 
* gnu/packages/chemistry.scm (spglib): Update to 2.5.0.
[arguments]<#:tests?, #:test-target, #:configure-flags>: Disable tests.
<#:phases>: Adapt.

Change-Id: Ia05bb8e2f012fcf4c576db8a6e5d2f8b153493ff
Signed-off-by: Andreas Enge <andreas@enge.fr>
 2025-06-02 14:36:49 +02:00
Nicolas Goaziou
1a8b36329f
gnu: texlive-libkpathsea: Tweak "texmf.cnf" variables. 
* gnu/packages/tex.scm (texlive-libkpathsea): Use XDG variables instead of
HOME for cache and user configuration.  Re-instate TEXMFLOCAL, which may be
necessary for external TeX installations.
(texlive-luatex): Re-instate TEXFLOCAL.
* gnu/packages/algebra.scm (gap):
* gnu/packages/assembly.scm (asl):
(yaehmop):
* gnu/packages/bioinformatics.scm (discrover):
* gnu/packages/chez.scm (chez-scheme-for-racket):
* gnu/packages/engineering.scm (fastcap):
* gnu/packages/fsf.scm (book-faif):
* gnu/packages/maths.scm (hypre):
(stex-boostrap):
(suitesparse-amd):
(suitesparse-camd):
(suitesparse-cholmod):
(suitesparse-klu):
(suitesparse-ldl):
(suitesparse-mongoose):
(suitesparse-spex):
(suitesparse-spqr):
(suitesparse-umfpack):
* gnu/packages/ocaml.scm (ocaml-bibtex2html):
(unison):
* gnu/packages/python-xyz.scm (python-nbconvert):
* gnu/packages/statistics.scm (r-with-tests)[arguments]: Set TEXMFVAR to
a writable location.

Change-Id: I3d2d069cf41a92214d9d6fb7f4d54fc81fe6db7a
 2025-05-06 11:25:07 +02:00
Nicolas Goaziou
4df6eda30f
gnu: Rename texlive-updmap.cfg' into texlive-local-tree'. 
* doc/build.scm (pdf-manual):
* doc/contributing.texi (Submitting Patches):
* gnu/packages/algebra.scm (pari-gp):
(giac):
* gnu/packages/assembly.scm (asl):
* gnu/packages/audio.scm (chow-tape-model):
* gnu/packages/bioconductor.scm (r-biocstyle):
* gnu/packages/bioinformatics.scm (discrover):
(phyml):
(velvet):
* gnu/packages/chemistry.scm (yaehmop):
* gnu/packages/chez.scm (chez-scheme-for-racket):
(stex-bootstrap):
(chez-web):
(chez-sockets):
* gnu/packages/cran.scm (r-papaja):
(r-prereg):
* gnu/packages/docbook.scm (dblatex):
* gnu/packages/emacs-xyz.scm (emacs-auctex):
* gnu/packages/engineering.scm (fastcap):
* gnu/packages/finance.scm (optionmatrix):
* gnu/packages/fsf.scm (book-faif):
* gnu/packages/gettext.scm (po4a):
(po4a-minimal):
* gnu/packages/graphics.scm (mmg):
* gnu/packages/graphviz.scm (dot2tex):
* gnu/packages/guile-xyz.scm (emacsy):
(guile-cv):
* gnu/packages/lisp.scm (sbcl):
* gnu/packages/maths.scm (cddlib):
(gnuplot):
(itpp):
(octave):
(suitesparse-amd):
(suitesparse-camd):
(suitesparse-cholmod):
(suitesparse-klu):
(suitesparse-ldl):
(suitesparse-mongoose):
(suitesparse-spex):
(suitesparse-spqr):
(suitesparse-umfpack):
(hypre):
* gnu/packages/music.scm (lilypond):
* gnu/packages/ocaml.scm (unison):
(ocaml-bibtex2html):
* gnu/packages/pdf.scm (extractpdfmark):
* gnu/packages/photo.scm (enblend-enfuse):
* gnu/packages/plotutils.scm (asymptote):
* gnu/packages/python-xyz.scm (python-numpy-documentation):
(python-ipython-documentation):
(python-pypandoc):
* gnu/packages/radio.scm (gnuradio):
(libosmo-dsp):
* gnu/packages/scheme.scm (mit-scheme):
* gnu/packages/security-token.scm (yubico-piv-tool):
* gnu/packages/sphinx.scm (python-sphinx):
(python-sphinx-5):
* gnu/packages/statistics.scm (r-with-tests):
(r-spams):
* gnu/packages/tex.scm (texlive-local-tree): Renamed from…
(texlive-updmap.cfg): … this. Deprecate the latter.
(texlive-biblatex-philosophy):
(texlive-bropd):
(texlive-fontsize):
(texlive-poetrytex):
(texlive-reverxii):
(texlive-stix):
(texlive-suftesi):
(texlive-thucoursework):
(texlive-ulqda):
(texlive-yathesis):
(texlive-makecell):
(texlive-robotarm):
(texlive-bbold):
(texlive-babel-romansh):
(texlive-polyglossia):
(texlive-innerscript):
(teximpatient):
(texlive-xkeyval):
(texlive-arabxetex):
(texlive-blox):
(texlive-ecgdraw):
(texlive-gradientframe):
(texlive-everyhook):
(texlive-actuarialangle):
(texlive-actuarialsymbol):
(texlive-autopdf):
(texlive-etaremune):
(texlive-extract):
(texlive-forarray):
(texlive-graphicx-psmin):
(texlive-ha-prosper):
(texlive-namespc):
(texlive-newspaper):
(texlive-powerdot):
(texlive-recipecard):
(texlive-show2e):
(texlive-tablists):
(texlive-ted):
(texlive-xargs):
(texlive-xpeek):
* gnu/packages/xdisorg.scm (xforms):
* gnu/packages/algebra.scm (gap):
* gnu/packages/cpp.scm (jthread):
* guix/lint.scm (check-inputs-should-be-native): Rename `texlive-updmap.cfg' into `texlive-local-tree'.

Change-Id: I129280807c418e57acbcbda399545ab27a9e0a33
 2025-05-06 11:25:06 +02:00
David Elsing
2779928b9c
gnu: rdkit: Update to 2024.09.6. 
* gnu/packages/chemistry.scm (rdkit): Update to 2024.09.6.
[arguments]: Disable more failing tests.
[inputs]: Add pubchem-align3d.
[native-inputs]: Replace boost with boost-numpy. Add python-pytest.
* gnu/packages/patches/rdkit-unbundle-external-dependencies.patch: Adjust patch.

Change-Id: I165ebfeaef1f9d4b8c659cfdac65b45b0bc90188
Signed-off-by: Andreas Enge <andreas@enge.fr>
 2025-04-08 13:24:38 +02:00
David Elsing
191b96e7ee
gnu: inchi: Update to 1.07.3. 
* gnu/packages/chemistry.scm (inchi): Update to 1.07.3.
[source]: Switch to git-fetch.
[arguments]: Use gexps.  Adjust chdir-to-build-directory, build and install
phases. Enable parallel building.
[native-inputs]: Remove input label. Drop inchi-doc.
[license]: Change to Expat license.

Change-Id: I50945dc888dd01a6a5f7905874c7d68ecdfd5d4d
Signed-off-by: Andreas Enge <andreas@enge.fr>
 2025-04-08 13:24:30 +02:00
David Elsing
b2ba3def99
gnu: Add pubchem-align3d. 
* gnu/packages/chemistry.scm (pubchem-align3d): New variable.

Signed-off-by: Andreas Enge <andreas@enge.fr>
 2025-04-07 12:39:28 +02:00
David Elsing
aa55049717
gnu: yaehmop: Update to 2024.03.1. 
* gnu/packages/chemistry.scm (yaehmop): Update to 2024.03.1.

Signed-off-by: Andreas Enge <andreas@enge.fr>
 2025-04-07 12:38:50 +02:00
David Elsing
e5bfc462dd
gnu: rdkit: Update to 2023.09.4. 
* gnu/packages/chemistry.scm (rdkit): Update to 2023.09.4.
[arguments]: Skip testConrec test in check phase.
[native-inputs]: Replace catch2 with catch2-3.
* gnu/packages/patches/rdkit-unbundle-external-dependencies.patch: Adjust
patch.
[supported-systems]: New field.

Signed-off-by: Christopher Baines <mail@cbaines.net>
 2024-02-13 11:04:48 +00:00
David Elsing
cc772e7f31
gnu: freesasa: Fix memerr tests. 
* gnu/packages/chemistry.scm (freesasa)[arguments]: Add
"CFLAGS=-fno-builtin-malloc" to #:configure-flags.

Signed-off-by: Christopher Baines <mail@cbaines.net>
 2024-02-13 11:04:48 +00:00
David Elsing
52cca41c6f
gnu: avalon-toolkit: Update to 2.0.5a. 
The bug freeing static memory and the makefile have been improved upstream, so
we don't have to work around them anymore. Now, two static libraries are built
instead.

* gnu/packages/chemistry.scm (avalon-toolkit): Update to 2.0.5a.
[source]: Switch to git reference from GitHub. Adjust snippet. Add patch from
the RDKit fork.
[arguments]: Remove 'dont-free-static-memory phase. Use provided
makefile. Adjust 'install phase.
* gnu/packages/patches/avalon-toolkit-rdkit-fixes.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.

Signed-off-by: Christopher Baines <mail@cbaines.net>
 2024-02-13 11:04:48 +00:00
David Elsing
baa711441a
gnu: yaehmop: Update to 2023.03.1. 
* gnu/packages/chemistry.scm (yaehmop): Update to 2023.03.1.

Signed-off-by: Christopher Baines <mail@cbaines.net>
 2024-02-13 11:04:48 +00:00
David Elsing
805ee72237
gnu: coordgenlibs: Update to 3.0.2. 
* gnu/packages/chemistry.scm (coordgenlibs): Update to 3.0.2.

Signed-off-by: Christopher Baines <mail@cbaines.net>
 2024-02-13 11:04:48 +00:00
David Elsing
6ab278b2e7
gnu: maeparser: Update to 1.3.1. 
* gnu/packages/chemistry.scm (maeparser): Update to 1.3.1.

Signed-off-by: Christopher Baines <mail@cbaines.net>
 2024-02-13 11:04:47 +00:00
David Elsing
01ec7c3883
gnu: gemmi: Update to 0.6.4. 
* gnu/packages/chemistry.scm (gemmi): Update to 0.6.4.
[arguments]: Adjust include/gemmi/sprintf.hpp -> src/sprintf.cpp.
(freesasa)[arguments]: Link to gemmi_cpp explicitly.

Signed-off-by: Christopher Baines <mail@cbaines.net>
 2024-02-13 11:04:47 +00:00
Maxim Cournoyer
edb03ceb60
gnu: msgpack: Deprecate with msgpack-c. 
* gnu/packages/serialization.scm (msgpack-c): New variable.
(msgpack-cxx): New variable.
(msgpack): Rename to...
(msgpack-3): ... this, and inherit from msgpack-c.
* gnu/packages/vim.scm (eovim) [arguments]: Add help-cmake-find-msgpack-c
phase.
[inputs]: Replace msgpack with msgpack-c.
* gnu/packages/terminals.scm (tmate)
[inputs]: Replace msgpack with msgpack-3.
* gnu/packages/networking.scm (opendht)
[propagated-inputs]: Replace msgpack with msgpack-cxx.
* gnu/packages/chemistry.scm (mmtf-cpp) [propagated-inputs]: Likewise.
 2024-01-09 22:10:12 -05:00
Maxim Cournoyer
8c9f430a05
gnu: python-pymol: Remove msgpack from native-inputs. 
It's now propagated by mmtf-cpp.

* gnu/packages/chemistry.scm (python-pymol)
[native-inputs]: Remove msgpack.

Reviewed-by: Andreas Enge <andreas@enge.fr>
 2023-08-21 14:11:39 -04:00
Maxim Cournoyer
92f3476077
gnu: avogadrolibs: Remove msgpack from native-inputs. 
It's now propagated by mmtf-cpp.

* gnu/packages/chemistry.scm (avogadrolibs)
[native-inputs]: Remove msgpack.

Reviewed-by: Andreas Enge <andreas@enge.fr>
 2023-08-21 14:11:39 -04:00
Maxim Cournoyer
778a424444
gnu: mmtf-cpp: Update to 1.1.0. 
* gnu/packages/chemistry.scm (mmtf-cpp): Update to 1.1.0.
[propagated-inputs]: Add msgpack.

Reviewed-by: Andreas Enge <andreas@enge.fr>
 2023-08-21 14:11:32 -04:00
David Elsing
2e3edb38a5
gnu: python-pymol: Fix launch script. 
* gnu/packages/chemistry.scm (python-pymol)[#:phases]: Add 'disable-unchroot.
[native-inputs]: Remove python-setuptools.

Signed-off-by: Andreas Enge <andreas@enge.fr>
 2023-07-26 16:11:31 +02:00
Nicolas Goaziou
7a18bd9e74
gnu: Rationalize texlive-updmap.cfg and texlive-tiny inputs. 
TEXLIVE-UPDMAP.CFG and TEXLIVE-TINY should only be used as native inputs.
Also remove texlive packages already provided by them.

* doc/build.scm (pdf-manual):
* gnu/packages/algebra.scm (pari-gp):
* gnu/packages/bioinformatics.scm (discrover):
(phyml):
(velvet):
* gnu/packages/chemistry.scm (yaehmop):
* gnu/packages/chez.scm (stex-bootstrap):
(chez-web):
(chez-sockets):
* gnu/packages/cran.scm (r-prereg):
* gnu/packages/docbook.scm (dblatex):
* gnu/packages/emacs-xyz.scm (emacs-auctex):
* gnu/packages/engineering.scm (fastcap):
* gnu/packages/fsf.scm (book-faif):
* gnu/packages/graphviz.scm (dot2tex):
* gnu/packages/maths.scm (hypre):
* gnu/packages/ocaml.scm (unison):
(ocaml-bibtex2html):
* gnu/packages/plotutils.scm (asymptote):
* gnu/packages/python-xyz.scm (python-nbconvert):
(python-pypandoc):
* gnu/packages/radio.scm (gnuradio):
(libosmo-dsp):
* gnu/packages/statistics.scm (r-with-tests):
* gnu/packages/tex.scm (texlive-makecmds):
(texlive-innerscript):
(teximpatient):
(texlive-xkeyval): Remove texlive packages already provided by
TEXLIVE-UPDMAP.CFG.  Don't add TEXLIVE-TINY or TEXLIVE-UPDMAP.CFG as inputs.
 2023-07-18 18:16:47 +02:00
Nicolas Goaziou
fdf09bcd31
gnu: yaehmop: Fix build due to missing TeX Live scripts. 
* gnu/packages/chemistry.scm (yaehmop)[native-inputs]: Add missing "latexmk"
and "repstopdf" scripts.
 2023-07-18 18:16:41 +02:00
Nicolas Goaziou
76819a9655
gnu: texlive-fonts-ec -> texlive-ec. 
* gnu/packages/tex.scm (texlive-ec): New variable.
(texlive-fonts-ec): Deprecate variable.
(lyx):
(biber):
* gnu/packages/python-xyz.scm (python-pypandoc):
* gnu/packages/statistics.scm (r-with-tests):
* doc/build.scm (pdf-manual):
* gnu/packages/bioinformatics.scm (discrover):
(phyml):
(velvet):
* gnu/packages/chemistry.scm (yaehmop):
* gnu/packages/chez.scm (stex-bootstrap):
* gnu/packages/ocaml.scm (unison):
(ocaml-bibtex2html):
* gnu/packages/plotutils.scm (asymptote): Use new name.
 2023-07-18 18:10:48 +02:00
Nicolas Goaziou
9e4adea8ad
gnu: texlive-latex-geometry -> texlive-geometry. 
* gnu/packages/tex.scm (texlive-geometry): New variable.
(texlive-latex-geometry): Deprecate variable.
(texlive-xindy):
* gnu/packages/chemistry.scm (yaehmop):
* gnu/packages/cran.scm (r-prereg):
* gnu/packages/graphviz.scm (dot2tex):
* gnu/packages/maths.scm (hypre):
* gnu/packages/plotutils.scm (asymptote):
* gnu/packages/python-xyz.scm (python-nbconvert):
* gnu/packages/sphinx.scm (python-sphinx): Use new name.
 2023-07-18 18:10:44 +02:00
Christopher Baines
7df09ee0ab
Merge remote-tracking branch 'savannah/master' into core-updates 
Conflicts:
	gnu/local.mk
	gnu/packages/autotools.scm
	gnu/packages/cmake.scm
	gnu/packages/gnuzilla.scm
	gnu/packages/haskell.scm
	gnu/packages/pdf.scm
	gnu/packages/python-xyz.scm
	gnu/packages/samba.scm
	gnu/packages/tex.scm
	gnu/packages/tls.scm
	gnu/packages/wxwidgets.scm
 2023-03-02 10:55:08 +00:00
Tobias Geerinckx-Rice
1e6ddceb83
gnu: Use HTTPS package home pages wherever possible. 
* gnu/packages/accessibility.scm (florence)[home-page]: Use HTTPS.
* gnu/packages/admin.scm (netcat, nmon)[home-page]: Likewise.
* gnu/packages/algebra.scm (mpfrcx, cm, flint, fftw, r-dtt)[home-page]:
Likewise.
* gnu/packages/apr.scm (apr, apr-util)[home-page]: Likewise.
* gnu/packages/aspell.scm (aspell-dict-it)[home-page]: Likewise.
* gnu/packages/astronomy.scm (casacore, sextractor, libnova)
(xplanet)[home-page]: Likewise.
* gnu/packages/audio.scm (libtimidity, alsa-modular-synth, azr3, tao)
(freepats, rakarrack, liblo, libshout-idjc, timidity++, libsbsms)
(libmodplug, libxmp, xmp, sox, drc, gsm, gnaural)
(streamripper)[home-page]: Likewise.
* gnu/packages/authentication.scm (pamtester)[home-page]: Likewise.
* gnu/packages/backup.scm (grsync)[home-page]: Likewise.
* gnu/packages/bioconductor.scm (r-nmf, r-edger, r-limma)
(r-plgem)[home-page]: Likewise.
* gnu/packages/bioinformatics.scm (python-biom-format, bowtie, bowtie1)
(bwa, crossmap, java-htsjdk, java-htsjdk-latest, java-picard)
(java-picard-2.10.3, kaiju, proteinortho, rsem, rseqc, seek, samtools)
(snap-aligner, subread, stringtie, r-centipede, prinseq, emboss, phylip)
(libsbml)[home-page]: Likewise.
* gnu/packages/build-tools.scm (tup)[home-page]: Likewise.
* gnu/packages/cdrom.scm (libcddb, cdrdao, cdrtools)
(cd-discid)[home-page]: Likewise.
* gnu/packages/check.scm (cunit, python-nose)
(python-pyhamcrest)[home-page]: Likewise.
* gnu/packages/chemistry.scm (gromacs)[home-page]: Likewise.
* gnu/packages/chez.scm (chez-fmt)[home-page]: Likewise.
* gnu/packages/code.scm (lcov, uncrustify, cscope)[home-page]: Likewise.
* gnu/packages/compression.scm (p7zip)[home-page]: Likewise.
* gnu/packages/cran.scm (r-emdist, r-proj4, r-zoo, r-ggalluvial)
(r-orgmassspecr, r-polychrome, r-partykit, r-rcpp, r-ff, r-emdbook)
(r-fitdistrplus, r-linprog, r-geometry, r-dtw, r-fst, r-rjags)
(r-intergraph, r-qualv, r-labelled, r-survey, r-coin, r-fmsb, r-tm)
(r-corpcor, r-rmpfr, r-spatialextremes, r-longitudinal, r-genenet)
(r-bayesm, r-seqinr, r-mpm, r-text2vec, r-rgdal, r-seewave, r-hdrcde)
(r-shapes, r-anytime, r-stm, r-d3network, r-tam, r-directlabels)
(r-spatstat-utils, r-spatstat-sparse, r-spatstat-data, r-spatstat-geom)
(r-spatstat-core, r-spatstat-linnet, r-spatstat-random, r-spatstat)
(r-rcpptoml, r-mlecens, r-seurat, r-mlearning, r-zooimage)[home-page]:
Likewise.
* gnu/packages/crates-io.scm (rust-nickel-0.11, rust-thrift-0.13)
(rust-trust-dns-https-0.20, rust-trust-dns-native-tls-0.20)
(rust-trust-dns-openssl-0.20, rust-trust-dns-proto-0.20)
(rust-trust-dns-resolver-0.20, rust-trust-dns-rustls-0.20)
(rust-uint-0.9, rust-yaml-rust-0.4)[home-page]: Likewise.
* gnu/packages/crypto.scm (libdecaf, ccrypt)[home-page]: Likewise.
* gnu/packages/curl.scm (curlpp)[home-page]: Likewise.
* gnu/packages/databases.scm (python-pylibmc, unixodbc, wiredtiger)
(libpqxx, mdbtools, virtuoso-ose, libdbi, libdbi-drivers)
(soci)[home-page]: Likewise.
* gnu/packages/debian.scm (apt-mirror)[home-page]: Likewise.
* gnu/packages/debug.scm (remake)[home-page]: Likewise.
* gnu/packages/disk.scm (sdparm, idle3-tools, duc)[home-page]: Likewise.
* gnu/packages/django.scm (python-django-haystack)[home-page]: Likewise.
* gnu/packages/djvu.scm (djvulibre, djview)[home-page]: Likewise.
* gnu/packages/dns.scm (dnsmasq)[home-page]: Likewise.
* gnu/packages/docbook.scm (dblatex, docbook2x)[home-page]: Likewise.
* gnu/packages/documentation.scm (scrollkeeper)[home-page]: Likewise.
* gnu/packages/ebook.scm (liblinebreak)[home-page]: Likewise.
* gnu/packages/electronics.scm (xoscope)[home-page]: Likewise.
* gnu/packages/emacs-xyz.scm (emacs-bbdb, emacs-caps-lock, emacs-djvu)
(emacs-pabbrev, emacs-twittering-mode, emacs-filladapt, emacs-rudel)
(emacs-stream, emacspeak, emacs-cc-mode, emacs-eldoc, emacs-jsonrpc)
(emacs-gtk-look, emacs-xclip, emacs-slime-volleyball, emacs-minimap)
(emacs-auto-dictionary-mode, emacs-persist, emacs-shell-command+)
(emacs-map, emacs-xref, emacs-dictionary)[home-page]: Likewise.
* gnu/packages/embedded.scm (sdcc)[home-page]: Likewise.
* gnu/packages/engineering.scm (asco, libngspice, libspnav)
(openctm)[home-page]: Likewise.
* gnu/packages/erlang.scm (erlang-erlware-commons)[home-page]: Likewise.
* gnu/packages/file-systems.scm (jfsutils, curlftpfs)[home-page]:
Likewise.
* gnu/packages/finance.scm (gbonds)[home-page]: Likewise.
* gnu/packages/flashing-tools.scm (dfu-util, srecord)[home-page]:
Likewise.
* gnu/packages/fltk.scm (ntk)[home-page]: Likewise.
* gnu/packages/fonts.scm (font-terminus, font-tex-gyre)
(font-comic-neue)[home-page]: Likewise.
* gnu/packages/fontutils.scm (ttf2pt1, potrace, libspiro)[home-page]:
Likewise.
* gnu/packages/fpga.scm (icestorm, gtkwave, gtkwave)
(python-myhdl)[home-page]: Likewise.
* gnu/packages/freedesktop.scm (libatasmart)[home-page]: Likewise.
* gnu/packages/ftp.scm (weex)[home-page]: Likewise.
* gnu/packages/game-development.scm (dds, python-tmx, sfxr, quesoglc)
(eureka, plib)[home-page]: Likewise.
* gnu/packages/games.scm (abe, alex4, armagetronad, barony)
(foobillard++, golly, ltris, pipewalker, prboom-plus, trigger-rally)
(cmatrix, pinball, pioneers, tennix, chromium-bsu, freeciv, kiki)
(quakespasm, frotz, frotz-dumb-terminal, frotz-sdl, btanks)
(flare-engine, chessx, barrage, cgoban, passage)[home-page]: Likewise.
* gnu/packages/geo.scm (python-geopandas, saga)[home-page]: Likewise.
* gnu/packages/gl.scm (freeglut, gl2ps)[home-page]: Likewise.
* gnu/packages/gnome.scm (cogl, clutter-gtk, clutter-gst, bluefish)
(workrave)[home-page]: Likewise.
* gnu/packages/gnustep.scm (wmnd, wmfire, wmfire)[home-page]: Likewise.
* gnu/packages/graph.scm (mscgen)[home-page]: Likewise.
* gnu/packages/graphics.scm (assimp, alembic, ctl, agg)
(opencsg)[home-page]: Likewise.
* gnu/packages/graphviz.scm (gts)[home-page]: Likewise.
* gnu/packages/gtk.scm (gtkspell3)[home-page]: Likewise.
* gnu/packages/guile-xyz.scm (guile-irregex)[home-page]: Likewise.
* gnu/packages/haskell-apps.scm (cpphs)[home-page]: Likewise.
* gnu/packages/haskell-check.scm (ghc-hunit)[home-page]: Likewise.
* gnu/packages/haskell-web.scm (ghc-http-client-restricted)
(ghc-blaze-html, ghc-happstack-server, ghc-sourcemap)[home-page]:
Likewise.
* gnu/packages/haskell-xyz.scm (ghc-assoc, ghc-cairo, ghc-cborg)
(ghc-csv, ghc-glob, ghc-gtk2hs-buildtools, ghc-hmatrix-gsl-stats)
(ghc-intervalmap, ghc-lens-family-core, ghc-managed, ghc-mountpoints)
(ghc-network-multicast, ghc-optional-args, ghc-regex, ghc-spoon)
(ghc-transformers, ghc-turtle, ghc-utf8-light, ghc-wizards)
(ghc-template-haskell, ghc-boot-th, ghc-binary-orphans)
(ghc-postgresql-simple)[home-page]: Likewise.
* gnu/packages/hexedit.scm (ht, bvi)[home-page]: Likewise.
* gnu/packages/hunspell.scm (hunspell-dict-hu)[home-page]: Likewise.
* gnu/packages/image-processing.scm (mia)[home-page]: Likewise.
* gnu/packages/image-viewers.scm (geeqie, gpicview, luminance-hdr)
(qiv)[home-page]: Likewise.
* gnu/packages/image.scm (libuemf, devil, steghide, optipng, niftilib)
(sng, mtpaint)[home-page]: Likewise.
* gnu/packages/java-xml.scm (java-simple-xml, java-jaxp)
(java-apache-xml-commons-resolver)[home-page]: Likewise.
* gnu/packages/java.scm (java-cisd-base, java-cisd-args4j)
(java-hamcrest-core, java-jsr305, java-eclipse-osgi)
(java-eclipse-equinox-common, java-eclipse-core-jobs)
(java-eclipse-equinox-registry, java-eclipse-equinox-app)
(java-eclipse-equinox-preferences, java-eclipse-core-contenttype)
(java-eclipse-text, java-treelayout, java-aopalliance, java-jeromq)
(java-cdi-api)[home-page]: Likewise.
* gnu/packages/jemalloc.scm (jemalloc-4.5.0)[home-page]: Likewise.
* gnu/packages/julia-xyz.scm (julia-recipespipeline)[home-page]:
Likewise.
* gnu/packages/kde-internet.scm (kget)[home-page]: Likewise.
* gnu/packages/kde-systemtools.scm (dolphin-plugins)
(konsole)[home-page]: Likewise.
* gnu/packages/kodi.scm (fstrcmp)[home-page]: Likewise.
* gnu/packages/language.scm (hime, libchewing)[home-page]: Likewise.
* gnu/packages/lego.scm (nqc)[home-page]: Likewise.
* gnu/packages/lesstif.scm (lesstif)[home-page]: Likewise.
* gnu/packages/libcanberra.scm (libcanberra)[home-page]: Likewise.
* gnu/packages/libdaemon.scm (libdaemon)[home-page]: Likewise.
* gnu/packages/libffi.scm (libffi)[home-page]: Likewise.
* gnu/packages/libreoffice.scm (libwpd, libwpg, libwps)[home-page]:
Likewise.
* gnu/packages/libusb.scm (libmtp, gmtp)[home-page]: Likewise.
* gnu/packages/linux.scm (e2fsprogs, extundelete, lsscsi, net-tools)
(kbd, sysfsutils, cpuid, libpfm4)[home-page]: Likewise.
* gnu/packages/lisp-check.scm (sbcl-ptester, sbcl-xlunit)[home-page]:
Likewise.
* gnu/packages/lisp-xyz.scm (sbcl-html-encode, sbcl-py-configparser)
(sbcl-cl-utilities, sbcl-series, sbcl-uffi, sbcl-clsql, sbcl-sycamore)
(sbcl-osicat, sbcl-hu.dwim.common, sbcl-caveman, sbcl-trivial-shell)
(sbcl-trivial-benchmark, sbcl-screamer, sbcl-smug)[home-page]: Likewise.
* gnu/packages/lisp.scm (lush2)[home-page]: Likewise.
* gnu/packages/logging.scm (log4cpp)[home-page]: Likewise.
* gnu/packages/lua.scm (lua-ldoc)[home-page]: Likewise.
* gnu/packages/machine-learning.scm (mcl, openfst, rxcpp)[home-page]:
Likewise.
* gnu/packages/mail.scm (muchsync, procmail, sendmail)
(opensmtpd-filter-dkimsign, crm114)[home-page]: Likewise.
* gnu/packages/man.scm (libpipeline, man-db)[home-page]: Likewise.
* gnu/packages/maths.scm (lapack, scalapack, hdf-eos5, itpp, gmsh)
(metamath, p4est, armadillo, suitesparse, atlas, lpsolve, wcalc, why3)
(frama-c)[home-page]: Likewise.
* gnu/packages/mcrypt.scm (mcrypt, libmcrypt, libmhash)[home-page]:
Likewise.
* gnu/packages/minetest.scm (minetest-advtrains)[home-page]: Likewise.
* gnu/packages/monitoring.scm (python-whisper, python-carbon)
(hostscope)[home-page]: Likewise.
* gnu/packages/mp3.scm (id3lib, libmp3splt, mp3splt, mpg321)
(lame)[home-page]: Likewise.
* gnu/packages/multiprecision.scm (mpc)[home-page]: Likewise.
* gnu/packages/music.scm (aria-maestosa, lingot, setbfree, bristol)
(portmidi, python-pyportmidi, zynaddsubfx, yoshimi, aj-snapshot)
(schismtracker, midicsv, midicsv, qmidiarp, qmidiroute, dssi, tap-lv2)
(shiru-lv2)[home-page]: Likewise.
* gnu/packages/ncurses.scm (stfl)[home-page]: Likewise.
* gnu/packages/networking.scm (lksctp-tools, mbuffer, ifstatus, bird)
(tunctl, traceroute)[home-page]: Likewise.
* gnu/packages/node-xyz.scm (node-mersenne)[home-page]: Likewise.
* gnu/packages/ntp.scm (openntpd)[home-page]: Likewise.
* gnu/packages/ocaml.scm (opam, hevea, ocaml-menhir, ocaml-piqilib)
(ocaml-graph, cubicle)[home-page]: Likewise.
* gnu/packages/opencl.scm (python-pyopencl)[home-page]: Likewise.
* gnu/packages/package-management.scm (xstow, modules)[home-page]:
Likewise.
* gnu/packages/parallel.scm (xjobs)[home-page]: Likewise.
* gnu/packages/pdf.scm (podofo, qpdf, xournal, impressive)[home-page]:
Likewise.
* gnu/packages/perl.scm (perl-math-vecstat, perltidy)[home-page]:
Likewise.
* gnu/packages/photo.scm (libpano13, enblend-enfuse, hugin)[home-page]:
Likewise.
* gnu/packages/plan9.scm (drawterm)[home-page]: Likewise.
* gnu/packages/plotutils.scm (guile-charting, ploticus)[home-page]:
Likewise.
* gnu/packages/popt.scm (argtable, popt)[home-page]: Likewise.
* gnu/packages/profiling.scm (otf2)[home-page]: Likewise.
* gnu/packages/pulseaudio.scm (pulseaudio)[home-page]: Likewise.
* gnu/packages/python-check.scm (python-mypy)[home-page]: Likewise.
* gnu/packages/python-web.scm (python-cssutils)
(python-translationstring)[home-page]: Likewise.
* gnu/packages/python-xyz.scm (python-diskcache, python-doxyqml)
(python-docutils, python-pexpect, python-importlib-resources)
(python-simplegeneric, python-urwid, python-xlrd, python-xlwt)
(python-pyasn1, python-pythondialog, python-tftpy, python-random2)
(python-arcp, python-pyopengl, python-sortedcollections)
(python-sortedcontainers, python-yapsy, python-pydispatcher)
(python-posix-ipc)[home-page]: Likewise.
* gnu/packages/qt.scm (qwt, libqglviewer, signond)[home-page]: Likewise.
* gnu/packages/radio.scm (unixcw, gnuais)[home-page]: Likewise.
* gnu/packages/raspberry-pi.scm (bcm2835)[home-page]: Likewise.
* gnu/packages/rdf.scm (clucene, rasqal, redland)[home-page]: Likewise.
* gnu/packages/regex.scm (tre)[home-page]: Likewise.
* gnu/packages/rsync.scm (librsync)[home-page]: Likewise.
* gnu/packages/ruby.scm (ruby-packnga, ruby-nokogiri, ruby-oj, ruby-ox)
(ruby-sinatra, ruby-citrus, ruby-cbor, ruby-roda)[home-page]: Likewise.
* gnu/packages/scheme.scm (scheme48, tinyscheme)[home-page]: Likewise.
* gnu/packages/screen.scm (dtach)[home-page]: Likewise.
* gnu/packages/scsi.scm (sg3-utils)[home-page]: Likewise.
* gnu/packages/sdl.scm (libmikmod, sdl-pango)[home-page]: Likewise.
* gnu/packages/shellutils.scm (hstr, rig)[home-page]: Likewise.
* gnu/packages/simulation.scm (python-dolfin-adjoint)[home-page]:
Likewise.
* gnu/packages/smalltalk.scm (smalltalk)[home-page]: Likewise.
* gnu/packages/speech.scm (espeak)[home-page]: Likewise.
* gnu/packages/stalonetray.scm (stalonetray)[home-page]: Likewise.
* gnu/packages/statistics.scm (jags, r-mass, r-class, r-lattice)
(r-matrix, r-nnet, r-spatial, r-bit, r-bit64, r-digest, r-xtable)
(python-statsmodels, r-ade4, r-latticeextra, r-rcurl, r-xml, r-mvtnorm)
(r-robustbase, r-minqa, r-fdrtool, java-jdistlib, xlispstat)[home-page]:
Likewise.
* gnu/packages/swig.scm (swig)[home-page]: Likewise.
* gnu/packages/task-management.scm (wtime)[home-page]: Likewise.
* gnu/packages/tcl.scm (itcl, tclxml, tclx)[home-page]: Likewise.
* gnu/packages/terminals.scm (libtermkey, mlterm, libvterm)
(libvterm)[home-page]: Likewise.
* gnu/packages/tex.scm (texlive-lm, texlive-lm-math, texlive-cs)
(texlive-csplain, biber, texmaker)[home-page]: Likewise.
* gnu/packages/text-editors.scm (joe)[home-page]: Likewise.
* gnu/packages/textutils.scm (drm-tools, docx2txt)[home-page]: Likewise.
* gnu/packages/tv.scm (tvtime)[home-page]: Likewise.
* gnu/packages/unicode.scm (libunibreak)[home-page]: Likewise.
* gnu/packages/upnp.scm (libupnp)[home-page]: Likewise.
* gnu/packages/version-control.scm (cvs)[home-page]: Likewise.
* gnu/packages/video.scm (transcode, libquicktime, mjpegtools, aalib)
(liba52, libmpeg2, x265, libdv, dvdauthor, aegisub, pitivi, gavl)
(dvdbackup, guvcview, video-contact-sheet)[home-page]: Likewise.
* gnu/packages/virtualization.scm (bochs)[home-page]: Likewise.
* gnu/packages/w3m.scm (w3m)[home-page]: Likewise.
* gnu/packages/web.scm (qjson, libquvi-scripts, libquvi, quvi)
(tidy-html, htmlcxx)[home-page]: Likewise.
* gnu/packages/wm.scm (evilwm, menumaker)[home-page]: Likewise.
* gnu/packages/wv.scm (wv)[home-page]: Likewise.
* gnu/packages/wxwidgets.scm (wxsvg)[home-page]: Likewise.
* gnu/packages/xdisorg.scm (mtdev, xsel)[home-page]: Likewise.
* gnu/packages/xfig.scm (xfig, transfig)[home-page]: Likewise.
* gnu/packages/xml.scm (openjade, python-pyxb, xmlstarlet, xmlrpc-c)
(opensp)[home-page]: Likewise.
* gnu/packages/xorg.scm (xf86-video-qxl)[home-page]: Likewise.
 2023-02-19 01:00:01 +01:00
Efraim Flashner
672036c6df
gnu: Remove unneeded module imports. 
* gnu/packages/abiword.scm,
* gnu/packages/ada.scm,
* gnu/packages/agda.scm,
* gnu/packages/backup.scm,
* gnu/packages/barrier.scm,
* gnu/packages/bioinformatics.scm,
* gnu/packages/bootstrap.scm,
* gnu/packages/bqn.scm,
* gnu/packages/c.scm,
* gnu/packages/chemistry.scm,
* gnu/packages/coq.scm,
* gnu/packages/cross-base.scm,
* gnu/packages/databases.scm,
* gnu/packages/emacs-xyz.scm,
* gnu/packages/enlightenment.scm,
* gnu/packages/games.scm,
* gnu/packages/geo.scm,
* gnu/packages/ghostscript.scm,
* gnu/packages/gl.scm,
* gnu/packages/golang.scm,
* gnu/packages/jami.scm,
* gnu/packages/java-maths.scm,
* gnu/packages/kde-frameworks.scm,
* gnu/packages/kde-plasma.scm,
* gnu/packages/language.scm,
* gnu/packages/libreoffice.scm,
* gnu/packages/linphone.scm,
* gnu/packages/lisp.scm,
* gnu/packages/llvm.scm,
* gnu/packages/machine-learning.scm,
* gnu/packages/minetest.scm,
* gnu/packages/monitoring.scm,
* gnu/packages/nfs.scm,
* gnu/packages/ocr.scm,
* gnu/packages/opencl.scm,
* gnu/packages/pdf.scm,
* gnu/packages/python-xyz.scm,
* gnu/packages/racket.scm,
* gnu/packages/rust.scm,
* gnu/packages/syncthing.scm,
* gnu/packages/syndication.scm,
* gnu/packages/telegram.scm,
* gnu/packages/vulkan.scm,
* gnu/packages/web-browsers.scm,
* gnu/packages/web.scm,
* gnu/packages/webkit.scm: Remove some unecessary module imports.
 2023-02-16 22:41:03 +02:00
Efraim Flashner
bd3e3d87a9
gnu: texlive-graphics: Use over deprecated texlive-latex-graphics. 
* gnu/packages/bioinformatics.scm (phyml)[native-inputs],
* gnu/packages/chemistry.scm (yaehmop)[native-inputs],
* gnu/packages/graphviz.scm (dot2tex)[propagated-inputs],
* gnu/packages/maths.scm (cddlib)[native-inputs],
* gnu/packages/statistics.scm (r-with-tests)[native-inputs],
* gnu/packages/tex.scm (texlive-apa6)[propagated-inputs]: Replace
texlive-latex-graphics with texlive-graphics.
 2023-01-30 20:07:49 +02:00
Ludovic Courtès
88572ededc
gnu: gromacs: Mark as tunable. 
* gnu/packages/chemistry.scm (gromacs)[properties]: New field.
 2023-01-12 23:14:44 +01:00
Ludovic Courtès
04bf1d9634
gnu: gromacs: Remove input labels and use gexps. 
* gnu/packages/chemistry.scm (gromacs)[arguments]: Turn into gexps.
[native-inputs]: Remove labels.  Remove (package-source googletest).
 2023-01-10 11:49:13 +01:00
Ludovic Courtès
7934e9c556
gnu: gromacs: Update to 2022.4. 
* gnu/packages/chemistry.scm (gromacs): Update to 2022.4.
* gnu/packages/patches/gromacs-tinyxml2.patch: Adjust accordingly.
 2023-01-10 11:49:13 +01:00
Lars-Dominik Braun
c485a9d8af
gnu: python-setuptools: Move to python-build. 
* gnu/packages/python-xyz.scm (python-setuptools): Move…
* gnu/packages/python-build.scm: …here.
* gnu/packages/chemistry.scm,
gnu/packages/messaging.scm,
gnu/packages/sequoia.scm,
tests/lint.scm: Adjust module imports accordingly.

Co-authored-by: Marius Bakke <marius@gnu.org>
 2022-10-27 19:43:06 +02:00
David Elsing
18f95f9335
gnu: Add rdkit. 
* gnu/packages/chemistry.scm (rdkit): New variable.

Signed-off-by: Liliana Marie Prikler <liliana.prikler@gmail.com>
 2022-10-15 12:05:15 +02:00
David Elsing
175d1a0151
gnu: Add ringdecomposerlib. 
* gnu/packages/chemistry.scm (ringdecomposerlib): New variable.

Signed-off-by: Liliana Marie Prikler <liliana.prikler@gmail.com>
 2022-10-15 12:05:15 +02:00