From f7228e317703808a8a193f6db8a3cb6ba5380f2f Mon Sep 17 00:00:00 2001 From: Danny Milosavljevic Date: Sat, 2 May 2020 14:48:29 +0200 Subject: gnu: Add musl-cross. * gnu/packages/patches/musl-cross-locate.patch: New file. * gnu/packages/heads.scm: New file. * gnu/local.mk (dist_patch_DATA): Add one. (GNU_SYSTEM_MODULES): Add the other. --- gnu/packages/patches/musl-cross-locale.patch | 20 ++++++++++++++++++++ 1 file changed, 20 insertions(+) create mode 100644 gnu/packages/patches/musl-cross-locale.patch (limited to 'gnu/packages/patches') diff --git a/gnu/packages/patches/musl-cross-locale.patch b/gnu/packages/patches/musl-cross-locale.patch new file mode 100644 index 0000000000..7634eda381 --- /dev/null +++ b/gnu/packages/patches/musl-cross-locale.patch @@ -0,0 +1,20 @@ +Disable locales other than C and POSIX because of a compilation error. +By Danny Milosavljevic +This patch is distributed under BSD-3 license. +See https://github.com/osresearch/heads/pull/610 +diff -ruN b/source/patches/gcc-5.3.0-locale.diff guix-build-musl-cross-0.1-3.a8a6649.drv-12/source/patches/gcc-5.3.0-locale.diff +--- a/patches/gcc-5.3.0-locale.diff 1970-01-01 01:00:00.000000000 +0100 ++++ b/patches/gcc-5.3.0-locale.diff 2020-05-02 14:20:47.213564509 +0200 +@@ -0,0 +1,12 @@ ++--- gcc-5.3.0/libstdc++-v3/config/locale/gnu/ctype_members.cc.orig 2020-05-02 14:16:31.376147000 +0200 +++++ gcc-5.3.0/libstdc++-v3/config/locale/gnu/ctype_members.cc 2020-05-02 14:16:56.716279576 +0200 ++@@ -47,7 +47,8 @@ ++ this->_S_create_c_locale(this->_M_c_locale_ctype, __s); ++ this->_M_toupper = this->_M_c_locale_ctype->__ctype_toupper; ++ this->_M_tolower = this->_M_c_locale_ctype->__ctype_tolower; ++- this->_M_table = this->_M_c_locale_ctype->__ctype_b; +++ //this->_M_table = this->_M_c_locale_ctype->__ctype_b; +++ throw 3; ++ } ++ } ++ -- cgit v1.2.3 From 06ed1dba359aeb70f6da908ca5672c541c714ab1 Mon Sep 17 00:00:00 2001 From: Vincent Legoll Date: Mon, 4 May 2020 00:39:36 +0200 Subject: gnu: Add gromacs. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/chemistry.scm (gromacs): New variable. * gnu/packages/patches/gromacs-tinyxml2.patch: New file... * gnu/local.mk (dist_patch_DATA): ...add it here. Signed-off-by: Ludovic Courtès --- gnu/local.mk | 1 + gnu/packages/chemistry.scm | 90 +++++++++++++++++++++++++++++ gnu/packages/patches/gromacs-tinyxml2.patch | 67 +++++++++++++++++++++ 3 files changed, 158 insertions(+) create mode 100644 gnu/packages/patches/gromacs-tinyxml2.patch (limited to 'gnu/packages/patches') diff --git a/gnu/local.mk b/gnu/local.mk index 3c9a10b6bc..827e186501 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -1006,6 +1006,7 @@ dist_patch_DATA = \ %D%/packages/patches/gpsbabel-qstring.patch \ %D%/packages/patches/grantlee-merge-theme-dirs.patch \ %D%/packages/patches/grep-timing-sensitive-test.patch \ + %D%/packages/patches/gromacs-tinyxml2.patch \ %D%/packages/patches/groovy-add-exceptionutilsgenerator.patch \ %D%/packages/patches/grub-efi-fat-serial-number.patch \ %D%/packages/patches/gsl-test-i686.patch \ diff --git a/gnu/packages/chemistry.scm b/gnu/packages/chemistry.scm index 5b21e3309c..0540dfceb6 100644 --- a/gnu/packages/chemistry.scm +++ b/gnu/packages/chemistry.scm @@ -30,15 +30,20 @@ #:use-module (gnu packages) #:use-module (gnu packages algebra) #:use-module (gnu packages boost) + #:use-module (gnu packages check) #:use-module (gnu packages compression) #:use-module (gnu packages documentation) #:use-module (gnu packages gl) + #:use-module (gnu packages graphviz) #:use-module (gnu packages gv) #:use-module (gnu packages maths) + #:use-module (gnu packages mpi) + #:use-module (gnu packages perl) #:use-module (gnu packages pkg-config) #:use-module (gnu packages python) #:use-module (gnu packages python-xyz) #:use-module (gnu packages qt) + #:use-module (gnu packages sphinx) #:use-module (gnu packages xml) #:use-module (guix build-system cmake) #:use-module (guix build-system gnu) @@ -336,6 +341,91 @@ optionally velocities and the H-matrix. Coordinates and velocities are stored with user-specified precision.") (license license:bsd-3))) +(define-public gromacs + (package + (name "gromacs") + (version "2020.2") + (source (origin + (method url-fetch) + (uri (string-append "http://ftp.gromacs.org/pub/gromacs/gromacs-" + version ".tar.gz")) + (sha256 + (base32 + "1wyjgcdl30wy4hy6jvi9lkq53bqs9fgfq6fri52dhnb3c76y8rbl")) + ;; Our version of tinyxml2 is far newer than the bundled one and + ;; require fixing `testutils' code. See patch header for more info + (patches (search-patches "gromacs-tinyxml2.patch")))) + (build-system cmake-build-system) + (arguments + `(#:configure-flags + (list "-DGMX_DEVELOPER_BUILD=on" ; Needed to run tests + ;; Unbundling + "-DGMX_USE_LMFIT=EXTERNAL" + "-DGMX_BUILD_OWN_FFTW=off" + "-DGMX_EXTERNAL_BLAS=on" + "-DGMX_EXTERNAL_LAPACK=on" + "-DGMX_EXTERNAL_TNG=on" + "-DGMX_EXTERNAL_ZLIB=on" + "-DGMX_EXTERNAL_TINYXML2=on" + (string-append "-DTinyXML2_DIR=" + (assoc-ref %build-inputs "tinyxml2")) + ;; Workaround for cmake/FindSphinx.cmake version parsing that does + ;; not understand the guix-wrapped `sphinx-build --version' answer + (string-append "-DSPHINX_EXECUTABLE_VERSION=" + ,(package-version python-sphinx))) + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'fixes + (lambda* (#:key inputs #:allow-other-keys) + ;; Still bundled: part of gromacs, source behind registration + ;; but free software anyways + ;;(delete-file-recursively "src/external/vmd_molfile") + ;; Still bundled: threads-based OpenMPI-compatible fallback + ;; designed to be bundled like that + ;;(delete-file-recursively "src/external/thread_mpi") + ;; Unbundling + (delete-file-recursively "src/external/lmfit") + (delete-file-recursively "src/external/clFFT") + (delete-file-recursively "src/external/fftpack") + (delete-file-recursively "src/external/build-fftw") + (delete-file-recursively "src/external/tng_io") + (delete-file-recursively "src/external/tinyxml2") + (delete-file-recursively "src/external/googletest") + (copy-recursively (assoc-ref inputs "googletest-source") + "src/external/googletest") + ;; This test warns about the build host hardware, disable + (substitute* "src/gromacs/hardware/tests/hardwaretopology.cpp" + (("TEST\\(HardwareTopologyTest, HwlocExecute\\)") + "void __guix_disabled()")) + #t))))) + (native-inputs + `(("doxygen" ,doxygen) + ("googletest-source" ,(package-source googletest)) + ("graphviz" ,graphviz) + ("pkg-config" ,pkg-config) + ("python" ,python) + ("python-pygments" ,python-pygments) + ("python-sphinx" ,python-sphinx))) + (inputs + `(("fftwf" ,fftwf) + ("hwloc" ,hwloc-2 "lib") + ("lmfit" ,lmfit) + ("openblas" ,openblas) + ("perl" ,perl) + ("tinyxml2" ,tinyxml2) + ("tng" ,tng))) + (home-page "http://www.gromacs.org/") + (synopsis "Molecular dynamics software package") + (description "GROMACS is a versatile package to perform molecular dynamics, +i.e. simulate the Newtonian equations of motion for systems with hundreds to +millions of particles. It is primarily designed for biochemical molecules like +proteins, lipids and nucleic acids that have a lot of complicated bonded +interactions, but since GROMACS is extremely fast at calculating the nonbonded +interactions (that usually dominate simulations) many groups are also using it +for research on non-biological systems, e.g. polymers. GROMACS supports all the +usual algorithms you expect from a modern molecular dynamics implementation.") + (license license:lgpl2.1+))) + (define-public openbabel (package (name "openbabel") diff --git a/gnu/packages/patches/gromacs-tinyxml2.patch b/gnu/packages/patches/gromacs-tinyxml2.patch new file mode 100644 index 0000000000..cc7d7459a8 --- /dev/null +++ b/gnu/packages/patches/gromacs-tinyxml2.patch @@ -0,0 +1,67 @@ +Unbundling tinyxml2 from gromacs and using our own, which is newer, broke gromacs +build. + +This patch fixes three issues: + +- cmake now errors out if using multiple target_link_libraries with mixed styles + of signatures. + +- Error handling API changed, fix the testutils/refdata_xml.cpp code by using the + new API: document.ErrorStr() & tinyxml2::XML_SUCCESS. + +Those fixes will be submitted for inclusion to upstream, but may not be suitable +there as long as they still keep the old version bundled. + +First hunk has already been requested for merging. Third is in discussion. Second +will only be sent if third is OK'ed. + +diff -ruN gromacs-2020.2/src/testutils/CMakeLists.txt gromacs-2020.2-fixed/src/testutils/CMakeLists.txt +--- gromacs-2020.2/src/testutils/CMakeLists.txt 2020-04-30 18:33:44.000000000 +0200 ++++ gromacs-2020.2-fixed/src/testutils/CMakeLists.txt 2020-05-01 22:52:16.356000000 +0200 +@@ -73,7 +73,7 @@ + + if(HAVE_TINYXML2) + include_directories(SYSTEM ${TinyXML2_INCLUDE_DIR}) +- target_link_libraries(testutils ${TinyXML2_LIBRARIES}) ++ target_link_libraries(testutils PRIVATE ${TinyXML2_LIBRARIES}) + else() + include_directories(BEFORE SYSTEM "../external/tinyxml2") + endif() +diff -ruN gromacs-2020.2/src/testutils/refdata_xml.cpp gromacs-2020.2-fixed/src/testutils/refdata_xml.cpp +--- gromacs-2020.2/src/testutils/refdata_xml.cpp 2020-04-30 18:33:44.000000000 +0200 ++++ gromacs-2020.2-fixed/src/testutils/refdata_xml.cpp 2020-05-01 23:17:09.556000000 +0200 +@@ -206,21 +206,12 @@ + document.LoadFile(path.c_str()); + if (document.Error()) + { +- const char* errorStr1 = document.GetErrorStr1(); +- const char* errorStr2 = document.GetErrorStr2(); ++ const char* errorStr = document.ErrorStr(); + std::string errorString("Error was "); +- if (errorStr1) +- { +- errorString += errorStr1; +- } +- if (errorStr2) +- { +- errorString += errorStr2; +- } +- if (!errorStr1 && !errorStr2) +- { ++ if (errorStr) ++ errorString += errorStr; ++ else + errorString += "not specified."; +- } + GMX_THROW(TestException("Reference data not parsed successfully: " + path + "\n." + + errorString + "\n")); + } +@@ -371,7 +362,7 @@ + XMLElementPtr rootElement = createRootElement(&document); + createChildElements(rootElement, rootEntry); + +- if (document.SaveFile(path.c_str()) != tinyxml2::XML_NO_ERROR) ++ if (document.SaveFile(path.c_str()) != tinyxml2::XML_SUCCESS) + { + GMX_THROW(TestException("Reference data saving failed in " + path)); + } -- cgit v1.2.3 From bc2529cb97d35e3646be6e36f2c6a038cdd4fb8c Mon Sep 17 00:00:00 2001 From: Lars-Dominik Braun Date: Tue, 28 Apr 2020 10:50:10 +0200 Subject: gnu: Add collectd MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/monitoring.scm (collectd): New variable * gnu/local.mk (dist_patch_DATA): Add new patch * gnu/packages/patches/collectd-5.11.0-noinstallvar.patch: New file Signed-off-by: Ludovic Courtès --- gnu/local.mk | 1 + gnu/packages/monitoring.scm | 51 +++++++++++++++++++++- .../patches/collectd-5.11.0-noinstallvar.patch | 21 +++++++++ 3 files changed, 72 insertions(+), 1 deletion(-) create mode 100644 gnu/packages/patches/collectd-5.11.0-noinstallvar.patch (limited to 'gnu/packages/patches') diff --git a/gnu/local.mk b/gnu/local.mk index 827e186501..daacb1992a 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -819,6 +819,7 @@ dist_patch_DATA = \ %D%/packages/patches/clucene-pkgconfig.patch \ %D%/packages/patches/cmake-curl-certificates.patch \ %D%/packages/patches/coda-use-system-libs.patch \ + %D%/packages/patches/collectd-5.11.0-noinstallvar.patch \ %D%/packages/patches/combinatorial-blas-awpm.patch \ %D%/packages/patches/combinatorial-blas-io-fix.patch \ %D%/packages/patches/containerd-test-with-go1.13.patch \ diff --git a/gnu/packages/monitoring.scm b/gnu/packages/monitoring.scm index 8da31d6a84..d88bbc3aa3 100644 --- a/gnu/packages/monitoring.scm +++ b/gnu/packages/monitoring.scm @@ -6,6 +6,7 @@ ;;; Copyright © 2018 Gábor Boskovits ;;; Copyright © 2018, 2019 Oleg Pykhalov ;;; Copyright © 2020 Alex ter Weele +;;; Copyright © 2020 Lars-Dominik Braun ;;; ;;; This file is part of GNU Guix. ;;; @@ -32,6 +33,7 @@ #:use-module (guix build-system gnu) #:use-module (guix build-system go) #:use-module (guix utils) + #:use-module (gnu packages) #:use-module (gnu packages admin) #:use-module (gnu packages autotools) #:use-module (gnu packages base) @@ -48,11 +50,14 @@ #:use-module (gnu packages libevent) #:use-module (gnu packages pcre) #:use-module (gnu packages perl) + #:use-module (gnu packages pkg-config) #:use-module (gnu packages python) #:use-module (gnu packages python-web) #:use-module (gnu packages python-xyz) + #:use-module (gnu packages rrdtool) #:use-module (gnu packages time) - #:use-module (gnu packages tls)) + #:use-module (gnu packages tls) + #:use-module (gnu packages web)) (define-public nagios (package @@ -445,3 +450,47 @@ written in Go with pluggable metric collectors.") (description "This package provides a file system monitor.") (home-page "https://github.com/emcrisostomo/fswatch") (license license:gpl3+))) + +(define-public collectd + (package + (name "collectd") + (version "5.11.0") + (source (origin + (method url-fetch) + (uri (string-append + "https://storage.googleapis.com/collectd-tarballs/collectd-" + version + ".tar.bz2")) + (sha256 + (base32 + "1cjxksxdqcqdccz1nbnc2fp6yy84qq361ynaq5q8bailds00mc9p")) + (patches (search-patches "collectd-5.11.0-noinstallvar.patch")))) + (build-system gnu-build-system) + (arguments + `(#:configure-flags (list "--localstatedir=/var" "--sysconfdir=/etc") + #:phases (modify-phases %standard-phases + (add-before 'configure 'autoreconf + (lambda _ + ;; Required because of patched sources. + (invoke "autoreconf" "-vfi")))))) + (inputs + `(("rrdtool" ,rrdtool) + ("curl" ,curl) + ("libyajl" ,libyajl))) + (native-inputs + `(("autoconf" ,autoconf) + ("automake" ,automake) + ("libtool" ,libtool) + ("pkg-config" ,pkg-config))) + (home-page "https://collectd.org/") + (synopsis "Collect system and application performance metrics periodically") + (description + "collectd gathers metrics from various sources such as the operating system, +applications, log files and external devices, and stores this information or +makes it available over the network. Those statistics can be used to monitor +systems, find performance bottlenecks (i.e., performance analysis) and predict +future system load (i.e., capacity planning).") + ;; license:expat for the daemon in src/daemon/ and some plugins, + ;; license:gpl2 for other plugins + (license (list license:expat license:gpl2)))) + diff --git a/gnu/packages/patches/collectd-5.11.0-noinstallvar.patch b/gnu/packages/patches/collectd-5.11.0-noinstallvar.patch new file mode 100644 index 0000000000..39cd9c763e --- /dev/null +++ b/gnu/packages/patches/collectd-5.11.0-noinstallvar.patch @@ -0,0 +1,21 @@ +Disable creation of /var and /etc + +--- a/Makefile.am 2020-03-08 16:57:09.511535600 +0100 ++++ b/Makefile.am 2020-04-21 11:36:49.827182272 +0200 +@@ -2376,16 +2376,6 @@ + endif + + install-exec-hook: +- $(mkinstalldirs) $(DESTDIR)$(localstatedir)/run +- $(mkinstalldirs) $(DESTDIR)$(localstatedir)/lib/$(PACKAGE_NAME) +- $(mkinstalldirs) $(DESTDIR)$(localstatedir)/log +- $(mkinstalldirs) $(DESTDIR)$(sysconfdir) +- if test -e $(DESTDIR)$(sysconfdir)/collectd.conf; \ +- then \ +- $(INSTALL) -m 0640 $(builddir)/src/collectd.conf $(DESTDIR)$(sysconfdir)/collectd.conf.pkg-orig; \ +- else \ +- $(INSTALL) -m 0640 $(builddir)/src/collectd.conf $(DESTDIR)$(sysconfdir)/collectd.conf; \ +- fi; \ + $(mkinstalldirs) $(DESTDIR)$(cpkgdatadir) + $(INSTALL) -m 0644 $(srcdir)/src/types.db $(DESTDIR)$(cpkgdatadir)/types.db; + $(INSTALL) -m 0644 $(srcdir)/src/postgresql_default.conf \ -- cgit v1.2.3 From 31def9a9df583dd27f8604302700ff48368c43f3 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Tue, 21 Apr 2020 13:56:33 +0300 Subject: gnu: Add grocsvs. * gnu/packages/bioinformatics.scm (grocsvs): New variable. * gnu/packages/patches/grocsvs-dont-use-admiral.patch: New file. * gnu/local.mk (dist_patch_DATA): Register it. --- gnu/local.mk | 1 + gnu/packages/bioinformatics.scm | 42 +++++++++++++ .../patches/grocsvs-dont-use-admiral.patch | 69 ++++++++++++++++++++++ 3 files changed, 112 insertions(+) create mode 100644 gnu/packages/patches/grocsvs-dont-use-admiral.patch (limited to 'gnu/packages/patches') diff --git a/gnu/local.mk b/gnu/local.mk index daacb1992a..0797efb93e 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -1007,6 +1007,7 @@ dist_patch_DATA = \ %D%/packages/patches/gpsbabel-qstring.patch \ %D%/packages/patches/grantlee-merge-theme-dirs.patch \ %D%/packages/patches/grep-timing-sensitive-test.patch \ + %D%/packages/patches/grocsvs-dont-use-admiral.patch \ %D%/packages/patches/gromacs-tinyxml2.patch \ %D%/packages/patches/groovy-add-exceptionutilsgenerator.patch \ %D%/packages/patches/grub-efi-fat-serial-number.patch \ diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 65b44568e0..40f75e9e0c 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -79,6 +79,7 @@ #:use-module (gnu packages golang) #:use-module (gnu packages glib) #:use-module (gnu packages graph) + #:use-module (gnu packages graphviz) #:use-module (gnu packages groff) #:use-module (gnu packages gtk) #:use-module (gnu packages guile) @@ -15853,3 +15854,44 @@ biological processes. SBML is useful for models of metabolism, cell signaling, and more. It continues to be evolved and expanded by an international community.") (license license:lgpl2.1+))) + +(define-public grocsvs + ;; The last release is out of date and new features have been added. + (let ((commit "ecd956a65093a0b2c41849050e4512d46fecea5d") + (revision "1")) + (package + (name "grocsvs") + (version (git-version "0.2.6.1" revision commit)) + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/grocsvs/grocsvs") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 "14505725gr7qxc17cxxf0k6lzcwmgi64pija4mwf29aw70qn35cc")) + (patches (search-patches "grocsvs-dont-use-admiral.patch")))) + (build-system python-build-system) + (arguments + `(#:tests? #f ; No test suite. + #:python ,python-2)) ; Only python-2 supported. + (inputs + `(("python2-h5py" ,python2-h5py) + ("python2-ipython-cluster-helper" ,python2-ipython-cluster-helper) + ("python2-networkx" ,python2-networkx) + ("python2-psutil" ,python2-psutil) + ("python2-pandas" ,python2-pandas) + ("python2-pybedtools" ,python2-pybedtools) + ("python2-pyfaidx" ,python2-pyfaidx) + ("python2-pygraphviz" ,python2-pygraphviz) + ("python2-pysam" ,python2-pysam) + ("python2-scipy" ,python2-scipy))) + (home-page "https://github.com/grocsvs/grocsvs") + (synopsis "Genome-wide reconstruction of complex structural variants") + (description + "@dfn{Genome-wide Reconstruction of Complex Structural Variants} +(GROC-SVs) is a software pipeline for identifying large-scale structural +variants, performing sequence assembly at the breakpoints, and reconstructing +the complex structural variants using the long-fragment information from the +10x Genomics platform.") + (license license:expat)))) diff --git a/gnu/packages/patches/grocsvs-dont-use-admiral.patch b/gnu/packages/patches/grocsvs-dont-use-admiral.patch new file mode 100644 index 0000000000..cb976e19b0 --- /dev/null +++ b/gnu/packages/patches/grocsvs-dont-use-admiral.patch @@ -0,0 +1,69 @@ +python-admiral doesn't have a license +https://github.com/nspies/admiral/issues/3 + +diff --git a/setup.py b/setup.py +index 692b6a0..568f381 100755 +--- a/setup.py ++++ b/setup.py +@@ -20,7 +20,7 @@ setup( + 'console_scripts' : ["grocsvs = grocsvs.main:main"] + }, + +- install_requires = ["admiral", "h5py", "networkx>=2.0", "pandas", "pybedtools", ++ install_requires = ["h5py", "networkx>=2.0", "pandas", "pybedtools", + "pyfaidx", "pysam>=0.10.0", "scipy", "ipython-cluster-helper", + "pygraphviz", "psutil"], + +diff --git a/src/grocsvs/jobmanagers.py b/src/grocsvs/jobmanagers.py +index 6da0b58..112d7ff 100755 +--- a/src/grocsvs/jobmanagers.py ++++ b/src/grocsvs/jobmanagers.py +@@ -41,34 +41,3 @@ class MultiprocessingCluster(Cluster): + pool = multiprocessing.Pool(processes=self.processes) + return pool.map_async(fn, args).get(999999) + +- +-class AdmiralCluster(Cluster): +- def map(self, fn, args): +- from admiral import jobmanagers, remote +- +- cluster_options = self.cluster_settings.cluster_options.copy() +- +- scheduler = cluster_options.pop("scheduler") +- +- jobmanager_class = jobmanagers.get_jobmanager(scheduler) +- jobmanager = jobmanager_class( +- batch_dir=self.batch_dir, log_dir=self.batch_dir) +- +- +- if not "mem" in cluster_options: +- cluster_options["mem"] = "16g" +- if not "time" in cluster_options: +- cluster_options["time"] = "12h" +- +- jobs = [] +- #for i, arg in enumerate(args): +- +- job_name = args[0].__class__.__name__ +- args = [[arg] for arg in args] +- job = remote.run_remote(fn, jobmanager, job_name, args=args, +- array=True, overwrite=True, **cluster_options) +- +- result = jobmanagers.wait_for_jobs([job], wait=5, progress=True) +- +- if not result: +- raise Exception("Some chunks failed to complete") +diff --git a/src/grocsvs/pipeline.py b/src/grocsvs/pipeline.py +index ab1bb2d..350976f 100755 +--- a/src/grocsvs/pipeline.py ++++ b/src/grocsvs/pipeline.py +@@ -8,8 +8,7 @@ from grocsvs import utilities + def make_jobmanager(jobmanager_settings, processes, batch_dir): + jobmanager_classes = {"IPCluster":jobmanagers.IPCluster, + "local": jobmanagers.LocalCluster, +- "multiprocessing": jobmanagers.MultiprocessingCluster, +- "admiral": jobmanagers.AdmiralCluster} ++ "multiprocessing": jobmanagers.MultiprocessingCluster} + + cls = jobmanager_classes[jobmanager_settings.cluster_type] + return cls(processes, jobmanager_settings, batch_dir) -- cgit v1.2.3 From 5effc5bfe1f9bbe94be9ac8bd40e2f2875b08720 Mon Sep 17 00:00:00 2001 From: Hartmut Goebel Date: Thu, 23 Apr 2020 23:10:51 +0200 Subject: gnu: Add rust-nettle-sys-2. * gnu/packages/crates-io.scm (rust-nettle-sys-2): New variable. * gnu/packages/patches/rust-nettle-sys-disable-vendor.patch: New file. * gnu/local.mk: Add it. --- gnu/local.mk | 1 + gnu/packages/crates-io.scm | 31 ++++++++++++++ .../patches/rust-nettle-sys-disable-vendor.patch | 48 ++++++++++++++++++++++ 3 files changed, 80 insertions(+) create mode 100644 gnu/packages/patches/rust-nettle-sys-disable-vendor.patch (limited to 'gnu/packages/patches') diff --git a/gnu/local.mk b/gnu/local.mk index 0797efb93e..3d9f418133 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -1433,6 +1433,7 @@ dist_patch_DATA = \ %D%/packages/patches/rust-1.25-accept-more-detailed-gdb-lines.patch \ %D%/packages/patches/rust-bootstrap-stage0-test.patch \ %D%/packages/patches/rust-coresimd-doctest.patch \ + %D%/packages/patches/rust-nettle-sys-disable-vendor.patch \ %D%/packages/patches/rust-reproducible-builds.patch \ %D%/packages/patches/rust-openssl-sys-no-vendor.patch \ %D%/packages/patches/rxvt-unicode-escape-sequences.patch \ diff --git a/gnu/packages/crates-io.scm b/gnu/packages/crates-io.scm index a0be3575b8..5980282399 100644 --- a/gnu/packages/crates-io.scm +++ b/gnu/packages/crates-io.scm @@ -38,6 +38,7 @@ #:use-module (gnu packages gtk) #:use-module (gnu packages jemalloc) #:use-module (gnu packages llvm) + #:use-module (gnu packages nettle) #:use-module (gnu packages pcre) #:use-module (gnu packages pkg-config) #:use-module (gnu packages python) @@ -13184,6 +13185,36 @@ types as proposed in RFC 1158.") (license (list license:asl2.0 license:expat)))) +(define-public rust-nettle-sys-2 + (package + (name "rust-nettle-sys") + (version "2.0.4") + (source + (origin + (method url-fetch) + (uri (crate-uri "nettle-sys" version)) + (file-name (string-append name "-" version ".tar.gz")) + (sha256 + (base32 "1yq1w6dlcmg89x529i7s20j29afdhgim7qnsa7978fszzwrr6qmq")) + (patches (search-patches "rust-nettle-sys-disable-vendor.patch")))) + (build-system cargo-build-system) + (native-inputs + `(("clang" ,clang) + ("pkg-config" ,pkg-config))) + (inputs + `(("nettle", nettle))) + (arguments + `(#:skip-build? #t + #:cargo-development-inputs + (("rust-bindgen" ,rust-bindgen-0.51) + ("rust-pkg-config" ,rust-pkg-config-0.3)))) + (home-page "https://gitlab.com/sequoia-pgp/nettle-sys") + (synopsis "Low-level Rust bindings for the Nettle cryptographic library") + (description "This package provides low-level Rust bindings for the Nettle +cryptographic library.") + (license ;; licensed under either of these, at your option + (list license:lgpl3 license:gpl2 license:gpl3)))) + (define-public rust-new-debug-unreachable-1.0 (package (name "rust-new-debug-unreachable") diff --git a/gnu/packages/patches/rust-nettle-sys-disable-vendor.patch b/gnu/packages/patches/rust-nettle-sys-disable-vendor.patch new file mode 100644 index 0000000000..ae5ef5ebe0 --- /dev/null +++ b/gnu/packages/patches/rust-nettle-sys-disable-vendor.patch @@ -0,0 +1,48 @@ +Subject: nettle-sys: clear out "vendored" feature cruft from build.rs +From: Daniel Kahn Gillmor's avatarDaniel Kahn Gillmor + +https://salsa.debian.org/rust-team/debcargo-conf/-/commit/0c71150ad26bb66a8396dcdab055181af232ddc5 +https://sources.debian.org/src/rust-nettle-sys/2.0.4-3/debian/patches/disable-vendor.diff/ +--- a/Cargo.toml 2019-10-23 13:08:07.000000000 -0400 ++++ b/Cargo.toml 2019-10-23 14:08:46.644064014 -0400 +@@ -29,12 +29,9 @@ + version = "0.51.1" + default-features = false + +-[build-dependencies.nettle-src] +-version = "3.5.1-0" +-optional = true +- + [build-dependencies.pkg-config] + version = "0.3" + + [features] + vendored = ["nettle-src"] ++nettle-src = [] +diff --git a/build.rs b/build.rs +index 44f7af3..ede4b2f 100644 +--- a/build.rs ++++ b/build.rs +@@ -1,7 +1,5 @@ + extern crate bindgen; + extern crate pkg_config; +-#[cfg(feature = "vendored")] +-extern crate nettle_src; + + use std::env; + use std::fs; +@@ -36,14 +34,6 @@ fn main() { + println!("cargo:rerun-if-env-changed=NETTLE_STATIC"); + println!("cargo:rerun-if-env-changed={}", NETTLE_PREGENERATED_BINDINGS); + +- #[cfg(feature = "vendored")] +- { +- let artifacts = nettle_src::Build::new().build(); +- println!("cargo:vendored=1"); +- env::set_var("PKG_CONFIG_PATH", +- artifacts.lib_dir().join("pkgconfig")); +- } +- + let nettle = pkg_config::probe_library("nettle hogweed").unwrap(); + + let mode = match env::var_os("NETTLE_STATIC") { -- cgit v1.2.3 From 098f1d722ba553fddd41a2b9e183fe983b708ff9 Mon Sep 17 00:00:00 2001 From: Hartmut Goebel Date: Thu, 23 Apr 2020 23:12:36 +0200 Subject: gnu: Add rust-nettle-7. * gnu/packages/crates-io.scm (rust-nettle-7): New variable. * gnu/packages/patches/rust-nettle-disable-vendor.patch: New file. * gnu/local.mk: Add it. --- gnu/local.mk | 1 + gnu/packages/crates-io.scm | 44 ++++++++++++++++++++++ .../patches/rust-nettle-disable-vendor.patch | 13 +++++++ 3 files changed, 58 insertions(+) create mode 100644 gnu/packages/patches/rust-nettle-disable-vendor.patch (limited to 'gnu/packages/patches') diff --git a/gnu/local.mk b/gnu/local.mk index 3d9f418133..2c05360bae 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -1433,6 +1433,7 @@ dist_patch_DATA = \ %D%/packages/patches/rust-1.25-accept-more-detailed-gdb-lines.patch \ %D%/packages/patches/rust-bootstrap-stage0-test.patch \ %D%/packages/patches/rust-coresimd-doctest.patch \ + %D%/packages/patches/rust-nettle-disable-vendor.patch \ %D%/packages/patches/rust-nettle-sys-disable-vendor.patch \ %D%/packages/patches/rust-reproducible-builds.patch \ %D%/packages/patches/rust-openssl-sys-no-vendor.patch \ diff --git a/gnu/packages/crates-io.scm b/gnu/packages/crates-io.scm index 5980282399..9237a282b7 100644 --- a/gnu/packages/crates-io.scm +++ b/gnu/packages/crates-io.scm @@ -38,6 +38,7 @@ #:use-module (gnu packages gtk) #:use-module (gnu packages jemalloc) #:use-module (gnu packages llvm) + #:use-module (gnu packages multiprecision) #:use-module (gnu packages nettle) #:use-module (gnu packages pcre) #:use-module (gnu packages pkg-config) @@ -13185,6 +13186,49 @@ types as proposed in RFC 1158.") (license (list license:asl2.0 license:expat)))) +(define-public rust-nettle-7 + (package + (name "rust-nettle") + (version "7.0.0") + (source + (origin + (method url-fetch) + (uri (crate-uri "nettle" version)) + (file-name (string-append name "-" version ".tar.gz")) + (sha256 + (base32 "1n6dwy9zba8853bmxzhwaashd3np0wxpx0pj43brm0hb8n2sxbxi")) + (patches (search-patches "rust-nettle-disable-vendor.patch")))) + (build-system cargo-build-system) + (native-inputs + `(("pkg-config" ,pkg-config))) + (inputs + `(("clang" ,clang) + ("gmp" ,gmp) + ("nettle" ,nettle))) + (arguments + `(#:skip-build? #t ;; provides nothing, has no tests + #:cargo-inputs + (("rust-getrandom" ,rust-getrandom-0.1) + ("rust-libc" ,rust-libc-0.2) + ("rust-nettle-sys" ,rust-nettle-sys-2) + ("rust-thiserror" ,rust-thiserror-1.0)) + #:cargo-development-inputs + (("rust-bindgen" ,rust-bindgen-0.51) + ("rust-pkg-config" ,rust-pkg-config-0.3)) + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'set-missing-env-vars + (lambda* (#:key inputs #:allow-other-keys) + ;; FIXME: why do we need to set this? + (setenv "LIBCLANG_PATH" + (string-append (assoc-ref inputs "clang") "/lib")) + #t))))) + (home-page "https://gitlab.com/sequoia-pgp/nettle-rs") + (synopsis "Rust bindings for the Nettle cryptographic library") + (description "This package provides Rust bindings for the Nettle +cryptographic library.") + (license (list license:lgpl3 license:gpl2 license:gpl3)))) + (define-public rust-nettle-sys-2 (package (name "rust-nettle-sys") diff --git a/gnu/packages/patches/rust-nettle-disable-vendor.patch b/gnu/packages/patches/rust-nettle-disable-vendor.patch new file mode 100644 index 0000000000..5b52821cdb --- /dev/null +++ b/gnu/packages/patches/rust-nettle-disable-vendor.patch @@ -0,0 +1,13 @@ +Subject: nettle: clear out "vendored" feature cruft from build.rs +From: Daniel Kahn Gillmor's avatarDaniel Kahn Gillmor + +https://salsa.debian.org/rust-team/debcargo-conf/-/commit/b608e6beaa1d38c14fc16ad53780d94954a91900 +https://sources.debian.org/src/rust-nettle/7.0.0-1/debian/patches/disable-vendor.diff/ +--- a/Cargo.toml 1969-12-31 19:00:00.000000000 -0500 ++++ b/Cargo.toml 2019-10-23 19:12:01.076181971 -0400 +@@ -35,4 +35,4 @@ + version = "1" + + [features] +-vendored = ["nettle-sys/vendored"] ++vendored = [] -- cgit v1.2.3