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/local.mk | 2 ++ 1 file changed, 2 insertions(+) (limited to 'gnu/local.mk') diff --git a/gnu/local.mk b/gnu/local.mk index 9eb64b47b3..3c9a10b6bc 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -260,6 +260,7 @@ GNU_SYSTEM_MODULES = \ %D%/packages/haskell-crypto.scm \ %D%/packages/haskell-web.scm \ %D%/packages/haskell-xyz.scm \ + %D%/packages/heads.scm \ %D%/packages/hexedit.scm \ %D%/packages/hugs.scm \ %D%/packages/hurd.scm \ @@ -1240,6 +1241,7 @@ dist_patch_DATA = \ %D%/packages/patches/mumps-shared-pord.patch \ %D%/packages/patches/mupen64plus-ui-console-notice.patch \ %D%/packages/patches/mupen64plus-video-z64-glew-correct-path.patch \ + %D%/packages/patches/musl-cross-locale.patch \ %D%/packages/patches/mutt-store-references.patch \ %D%/packages/patches/m4-gnulib-libio.patch \ %D%/packages/patches/ncompress-fix-softlinks.patch \ -- 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/local.mk') 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 @@ (define-module (gnu packages chemistry) #: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 @@ (define-public tng 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/local.mk') 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 @@ (define-module (gnu packages monitoring) #: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 @@ (define-module (gnu packages monitoring) #: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 @@ (define-public fswatch (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/local.mk') 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 @@ (define-module (gnu packages bioinformatics) #: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 @@ (define-public libsbml 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/local.mk') 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 @@ (define-module (gnu packages crates-io) #: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 @@ (define-public rust-netlib-src-0.7 (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/local.mk') 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 @@ (define-module (gnu packages crates-io) #: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 @@ (define-public rust-netlib-src-0.7 (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 From 4c4ae8b595e85e62496b4fa8ff2587eb74a1262b Mon Sep 17 00:00:00 2001 From: Hartmut Goebel Date: Thu, 5 Mar 2020 23:59:43 +0100 Subject: gnu: Add sequoia. * gnu/packages/sequoia.scm: New file. * gnu/local.mk: Add it. --- gnu/local.mk | 1 + gnu/packages/sequoia.scm | 162 +++++++++++++++++++++++++++++++++++++++++++++++ 2 files changed, 163 insertions(+) create mode 100644 gnu/packages/sequoia.scm (limited to 'gnu/local.mk') diff --git a/gnu/local.mk b/gnu/local.mk index 2c05360bae..daf6bd0306 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -472,6 +472,7 @@ GNU_SYSTEM_MODULES = \ %D%/packages/search.scm \ %D%/packages/security-token.scm \ %D%/packages/selinux.scm \ + %D%/packages/sequoia.scm \ %D%/packages/serialization.scm \ %D%/packages/serveez.scm \ %D%/packages/shells.scm \ diff --git a/gnu/packages/sequoia.scm b/gnu/packages/sequoia.scm new file mode 100644 index 0000000000..1c21c9c893 --- /dev/null +++ b/gnu/packages/sequoia.scm @@ -0,0 +1,162 @@ +;;; GNU Guix --- Functional package management for GNU +;;; Copyright © 2019, 2020 Hartmut Goebel +;;; +;;; This file is part of GNU Guix. +;;; +;;; GNU Guix is free software; you can redistribute it and/or modify it +;;; under the terms of the GNU General Public License as published by +;;; the Free Software Foundation; either version 3 of the License, or (at +;;; your option) any later version. +;;; +;;; GNU Guix is distributed in the hope that it will be useful, but +;;; WITHOUT ANY WARRANTY; without even the implied warranty of +;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +;;; GNU General Public License for more details. +;;; +;;; You should have received a copy of the GNU General Public License +;;; along with GNU Guix. If not, see . + +(define-module (gnu packages sequoia) + #:use-module (guix build-system cargo) + #:use-module (guix download) + #:use-module (guix git-download) + #:use-module ((guix licenses) #:prefix license:) + #:use-module (guix packages) + #:use-module (gnu packages) + #:use-module (gnu packages check) ;; python-pytest + #:use-module (gnu packages crates-io) + #:use-module (gnu packages libffi) ;; python-cffi + #:use-module (gnu packages llvm) + #:use-module (gnu packages multiprecision) + #:use-module (gnu packages nettle) + #:use-module (gnu packages pkg-config) + #:use-module (gnu packages python) + #:use-module (gnu packages python-xyz) ;; python-setuptools + #:use-module (gnu packages serialization) + #:use-module (gnu packages sqlite) + #:use-module (gnu packages tls)) + +(define-public sequoia + (package + (name "sequoia") + (version "0.16.0") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://gitlab.com/sequoia-pgp/sequoia.git") + (commit (string-append "v" version)))) + (sha256 + (base32 "0iwzi2ylrwz56s77cd4vcf89ig6ipy4w6kp2pfwqvd2d00x54dhk")) + (file-name (git-file-name name version)))) + (build-system cargo-build-system) + (outputs '("out" "python")) + (native-inputs + `(("clang" ,clang) + ("pkg-config" ,pkg-config) + ("python-pytest" ,python-pytest) + ("python-pytest-runner" ,python-pytest-runner))) + (inputs + `(("capnproto" ,capnproto) + ("gmp" ,gmp) + ("nettle" ,nettle) + ("openssl" ,openssl) + ("python" ,python) + ("python-cffi" ,python-cffi) + ("sqlite" ,sqlite))) + (arguments + `(#:tests? #f ;; building the tests requires 9.7GB total + #:cargo-inputs + (("rust-assert-cli" ,rust-assert-cli-0.6) + ("rust-anyhow" ,rust-anyhow-1.0) + ("rust-base64", rust-base64-0.11) + ;;("rust-buffered-reader" included + ("rust-bzip2", rust-bzip2-0.3) + ("rust-capnp" ,rust-capnp-0.10) + ("rust-capnp-rpc" ,rust-capnp-rpc-0.10) + ("rust-capnpc" ,rust-capnpc-0.10) + ("rust-chrono" ,rust-chrono-0.4) + ("rust-clap" ,rust-clap-2) + ("rust-clap" ,rust-clap-2) + ("rust-colored" ,rust-colored-1.9.1) + ("rust-crossterm" ,rust-crossterm-0.13) + ("rust-ctor", rust-ctor-0.1) + ("rust-dirs" ,rust-dirs-2.0) + ;;("rust-failure" included + ("rust-filetime" ,rust-filetime-0.2) + ("rust-flate2", rust-flate2-1.0) + ("rust-fs2" ,rust-fs2-0.4) + ("rust-futures" ,rust-futures-0.1) + ("rust-http" ,rust-http-0.1) + ("rust-hyper" ,rust-hyper-0.12) + ("rust-hyper-tls" ,rust-hyper-tls-0.3) + ("rust-idna", rust-idna-0.2) + ("rust-itertools" ,rust-itertools-0.8) + ("rust-lalrpop-util", rust-lalrpop-util-0.17) + ("rust-lazy-static", rust-lazy-static-1.3) + ("rust-libc" ,rust-libc-0.2) + ("rust-memsec", rust-memsec-0.5) + ("rust-native-tls" ,rust-native-tls-0.2) + ("rust-nettle", rust-nettle-7) + ("rust-parity-tokio-ipc" ,rust-parity-tokio-ipc-0.4) + ("rust-percent-encoding" ,rust-percent-encoding-2.1) + ("rust-prettytable-rs" ,rust-prettytable-rs-0.8) + ("rust-proc-macro2" ,rust-proc-macro2-1.0) + ("rust-quickcheck", rust-quickcheck-0.9) + ("rust-rand", rust-rand-0.7) + ("rust-regex", rust-regex-1.3) + ("rust-rusqlite" ,rust-rusqlite-0.19) + ("rust-tempfile" ,rust-tempfile-3.1) + ("rust-thiserror" ,rust-thiserror-1.0) + ("rust-tokio" ,rust-tokio-0.1) + ("rust-tokio-core" ,rust-tokio-core-0.1) + ("rust-unicode-normalization", rust-unicode-normalization-0.1) + ("rust-url" ,rust-url-2.1) + ("rust-zbase32" ,rust-zbase32-0.1)) + #:cargo-development-inputs + (("rust-bindgen" ,rust-bindgen-0.51) ;; FIXME for nettle-sys and rusqlite + ("rust-lalrpop" ,rust-lalrpop-0.17) + ("rust-rpassword" ,rust-rpassword-4)) + #:phases + (modify-phases %standard-phases + ;; Run make instead of using the rust build system, as + ;; suggested by the installation instructions + (replace 'build (lambda _ (invoke "make" "build-release") #t)) + (replace 'check + (lambda* (#:key tests? #:allow-other-keys) + (if tests? + (invoke "make" "check") + #t))) + (replace 'install (lambda _ (invoke "make" "install") #t)) + (add-after 'unpack 'adjust-prefix + (lambda* (#:key outputs #:allow-other-keys) + (setenv "PREFIX" (assoc-ref outputs "out")) + #t)) + (add-after 'unpack 'fix-fo-python-output + (lambda* (#:key outputs #:allow-other-keys) + (let ((out (assoc-ref outputs "out")) + (pyout (assoc-ref outputs "python"))) + (substitute* "ffi/lang/python/Makefile" + ;; adjust prefix for python package + (("PREFIX\\s*\\??=.*") + (string-append "PREFIX = " pyout "\n")) + ;; fix rpath to include the main package + (("\\WLDFLAGS=" text) + (string-append text "'-Wl,-rpath=" out "/lib '")) + ;; make setuptools install into the prefix, see + ;; guix/build/python-build-system.scm for explanation + (("\\ssetup.py\\s+install\\s") + " setup.py install --root=/ --single-version-externally-managed ")) + #t))) + (add-after 'unpack 'set-missing-env-vars + (lambda* (#:key inputs #:allow-other-keys) + ;; FIXME: why do we need to set this here? + (setenv "LIBCLANG_PATH" + (string-append (assoc-ref inputs "clang") "/lib")) + #t))))) + (home-page "https://sequoia-pgp.org") + (synopsis "New OpenPGP implementation") + (description "Sequoia is a new OpenPGP implementation. It consists of +several crates, providing both a low-level and a high-level API for dealing +with OpenPGP data.") + (license license:gpl2+))) -- cgit v1.2.3 From f19cf27c2b9ff92e2c0fd931ef7fde39c376adaa Mon Sep 17 00:00:00 2001 From: Mathieu Othacehe Date: Tue, 28 Apr 2020 14:15:28 +0200 Subject: image: Add a new API. Raw disk-images and ISO9660 images are created in a Qemu virtual machine. This is quite fragile, very slow, and almost unusable without KVM. For all these reasons, add support for host image generation. This implies the use new image generation mechanisms. - Raw disk images: images of partitions are created using tools such as mke2fs and mkdosfs depending on the partition file-system type. The partition images are then assembled into a final image using genimage. - ISO9660 images: the ISO root directory is populated within the store. GNU xorriso is then called on that directory, in the exact same way as this is done in (gnu build vm) module. Those mechanisms are built upon the new (gnu image) module. * gnu/image.scm: New file. * gnu/system/image.scm: New file. * gnu/build/image: New file. * gnu/local.mk: Add them. * gnu/system/vm.scm (system-disk-image): Rename to system-disk-image-in-vm. * gnu/ci.scm (qemu-jobs): Adapt to new API. * gnu/tests/install.scm (run-install): Ditto. * guix/scripts/system.scm (system-derivation-for-action): Ditto. --- gnu/build/image.scm | 273 +++++++++++++++++++++++++ gnu/build/install.scm | 1 - gnu/ci.scm | 45 ++-- gnu/image.scm | 76 +++++++ gnu/local.mk | 3 + gnu/system/image.scm | 532 ++++++++++++++++++++++++++++++++++++++++++++++++ gnu/system/vm.scm | 17 +- gnu/tests/install.scm | 22 +- guix/scripts/system.scm | 13 +- 9 files changed, 932 insertions(+), 50 deletions(-) create mode 100644 gnu/build/image.scm create mode 100644 gnu/image.scm create mode 100644 gnu/system/image.scm (limited to 'gnu/local.mk') diff --git a/gnu/build/image.scm b/gnu/build/image.scm new file mode 100644 index 0000000000..fe8e11aa1b --- /dev/null +++ b/gnu/build/image.scm @@ -0,0 +1,273 @@ +;;; GNU Guix --- Functional package management for GNU +;;; Copyright © 2013, 2014, 2015, 2016, 2017, 2018, 2019, 2020 Ludovic Courtès +;;; Copyright © 2016 Christopher Allan Webber +;;; Copyright © 2016, 2017 Leo Famulari +;;; Copyright © 2017 Marius Bakke +;;; Copyright © 2020 Tobias Geerinckx-Rice +;;; Copyright © 2020 Mathieu Othacehe +;;; +;;; This file is part of GNU Guix. +;;; +;;; GNU Guix is free software; you can redistribute it and/or modify it +;;; under the terms of the GNU General Public License as published by +;;; the Free Software Foundation; either version 3 of the License, or (at +;;; your option) any later version. +;;; +;;; GNU Guix is distributed in the hope that it will be useful, but +;;; WITHOUT ANY WARRANTY; without even the implied warranty of +;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +;;; GNU General Public License for more details. +;;; +;;; You should have received a copy of the GNU General Public License +;;; along with GNU Guix. If not, see . + +(define-module (gnu build image) + #:use-module (guix build store-copy) + #:use-module (guix build syscalls) + #:use-module (guix build utils) + #:use-module (guix store database) + #:use-module (gnu build bootloader) + #:use-module (gnu build install) + #:use-module (gnu build linux-boot) + #:use-module (gnu image) + #:use-module (gnu system uuid) + #:use-module (ice-9 ftw) + #:use-module (ice-9 match) + #:use-module (srfi srfi-19) + #:use-module (srfi srfi-34) + #:use-module (srfi srfi-35) + #:export (make-partition-image + genimage + initialize-efi-partition + initialize-root-partition + + make-iso9660-image)) + +(define (sexp->partition sexp) + "Take SEXP, a tuple as returned by 'partition->gexp', and turn it into a + record." + (match sexp + ((size file-system label uuid) + (partition (size size) + (file-system file-system) + (label label) + (uuid uuid))))) + +(define (size-in-kib size) + "Convert SIZE expressed in bytes, to kilobytes and return it as a string." + (number->string + (inexact->exact (ceiling (/ size 1024))))) + +(define (estimate-partition-size root) + "Given the ROOT directory, evalute and return its size. As this doesn't +take the partition metadata size into account, take a 25% margin." + (* 1.25 (file-size root))) + +(define* (make-ext4-image partition target root + #:key + (owner-uid 0) + (owner-gid 0)) + "Handle the creation of EXT4 partition images. See 'make-partition-image'." + (let ((size (partition-size partition)) + (label (partition-label partition)) + (uuid (partition-uuid partition)) + (options "lazy_itable_init=1,lazy_journal_init=1")) + (invoke "mke2fs" "-t" "ext4" "-d" root + "-L" label "-U" (uuid->string uuid) + "-E" (format #f "root_owner=~a:~a,~a" + owner-uid owner-gid options) + target + (format #f "~ak" + (size-in-kib + (if (eq? size 'guess) + (estimate-partition-size root) + size)))))) + +(define* (make-vfat-image partition target root) + "Handle the creation of VFAT partition images. See 'make-partition-image'." + (let ((size (partition-size partition)) + (label (partition-label partition))) + (invoke "mkdosfs" "-n" label "-C" target "-F" "16" "-S" "1024" + (size-in-kib + (if (eq? size 'guess) + (estimate-partition-size root) + size))) + (for-each (lambda (file) + (unless (member file '("." "..")) + (invoke "mcopy" "-bsp" "-i" target + (string-append root "/" file) + (string-append "::" file)))) + (scandir root)))) + +(define* (make-partition-image partition-sexp target root) + "Create and return the image of PARTITION-SEXP as TARGET. Use the given +ROOT directory to populate the image." + (let* ((partition (sexp->partition partition-sexp)) + (type (partition-file-system partition))) + (cond + ((string=? type "ext4") + (make-ext4-image partition target root)) + ((string=? type "vfat") + (make-vfat-image partition target root)) + (else + (format (current-error-port) + "Unsupported partition type~%."))))) + +(define* (genimage config target) + "Use genimage to generate in TARGET directory, the image described in the +given CONFIG file." + ;; genimage needs a 'root' directory. + (mkdir "root") + (invoke "genimage" "--config" config + "--outputpath" target)) + +(define* (register-closure prefix closure + #:key + (deduplicate? #t) (reset-timestamps? #t) + (schema (sql-schema))) + "Register CLOSURE in PREFIX, where PREFIX is the directory name of the +target store and CLOSURE is the name of a file containing a reference graph as +produced by #:references-graphs.. As a side effect, if RESET-TIMESTAMPS? is +true, reset timestamps on store files and, if DEDUPLICATE? is true, +deduplicates files common to CLOSURE and the rest of PREFIX." + (let ((items (call-with-input-file closure read-reference-graph))) + (register-items items + #:prefix prefix + #:deduplicate? deduplicate? + #:reset-timestamps? reset-timestamps? + #:registration-time %epoch + #:schema schema))) + +(define* (initialize-efi-partition root + #:key + bootloader-package + #:allow-other-keys) + "Install in ROOT directory, an EFI loader using BOOTLOADER-PACKAGE." + (install-efi-loader bootloader-package root)) + +(define* (initialize-root-partition root + #:key + bootcfg + bootcfg-location + (deduplicate? #t) + references-graphs + (register-closures? #t) + system-directory + #:allow-other-keys) + "Initialize the given ROOT directory. Use BOOTCFG and BOOTCFG-LOCATION to +install the bootloader configuration. + +If REGISTER-CLOSURES? is true, register REFERENCES-GRAPHS in the store. If +DEDUPLICATE? is true, then also deduplicate files common to CLOSURES and the +rest of the store when registering the closures. SYSTEM-DIRECTORY is the name +of the directory of the 'system' derivation." + (populate-root-file-system system-directory root) + (populate-store references-graphs root) + + (when register-closures? + (for-each (lambda (closure) + (register-closure root + closure + #:reset-timestamps? #t + #:deduplicate? deduplicate?)) + references-graphs)) + + (when bootcfg + (install-boot-config bootcfg bootcfg-location root))) + +(define* (make-iso9660-image xorriso grub-mkrescue-environment + grub bootcfg system-directory root target + #:key (volume-id "Guix_image") (volume-uuid #f) + register-closures? (references-graphs '()) + (compression? #t)) + "Given a GRUB package, creates an iso image as TARGET, using BOOTCFG as +GRUB configuration and OS-DRV as the stuff in it." + (define grub-mkrescue + (string-append grub "/bin/grub-mkrescue")) + + (define grub-mkrescue-sed.sh + (string-append (getcwd) "/" "grub-mkrescue-sed.sh")) + + ;; Use a modified version of grub-mkrescue-sed.sh, see below. + (copy-file (string-append xorriso + "/bin/grub-mkrescue-sed.sh") + grub-mkrescue-sed.sh) + + ;; Force grub-mkrescue-sed.sh to use the build directory instead of /tmp + ;; that is read-only inside the build container. + (substitute* grub-mkrescue-sed.sh + (("/tmp/") (string-append (getcwd) "/")) + (("MKRESCUE_SED_XORRISO_ARGS \\$x") + (format #f "MKRESCUE_SED_XORRISO_ARGS $(echo $x | sed \"s|/tmp|~a|\")" + (getcwd)))) + + ;; 'grub-mkrescue' calls out to mtools programs to create 'efi.img', a FAT + ;; file system image, and mtools honors SOURCE_DATE_EPOCH for the mtime of + ;; those files. The epoch for FAT is Jan. 1st 1980, not 1970, so choose + ;; that. + (setenv "SOURCE_DATE_EPOCH" + (number->string + (time-second + (date->time-utc (make-date 0 0 0 0 1 1 1980 0))))) + + ;; Our patched 'grub-mkrescue' honors this environment variable and passes + ;; it to 'mformat', which makes it the serial number of 'efi.img'. This + ;; allows for deterministic builds. + (setenv "GRUB_FAT_SERIAL_NUMBER" + (number->string (if volume-uuid + + ;; On 32-bit systems the 2nd argument must be + ;; lower than 2^32. + (string-hash (iso9660-uuid->string volume-uuid) + (- (expt 2 32) 1)) + + #x77777777) + 16)) + + (setenv "MKRESCUE_SED_MODE" "original") + (setenv "MKRESCUE_SED_XORRISO" (string-append xorriso "/bin/xorriso")) + (setenv "MKRESCUE_SED_IN_EFI_NO_PT" "yes") + + (for-each (match-lambda + ((name . value) (setenv name value))) + grub-mkrescue-environment) + + (apply invoke grub-mkrescue + (string-append "--xorriso=" grub-mkrescue-sed.sh) + "-o" target + (string-append "boot/grub/grub.cfg=" bootcfg) + root + "--" + ;; Set all timestamps to 1. + "-volume_date" "all_file_dates" "=1" + + `(,@(if compression? + '(;; ‘zisofs’ compression reduces the total image size by + ;; ~60%. + "-zisofs" "level=9:block_size=128k" ; highest compression + ;; It's transparent to our Linux-Libre kernel but not to + ;; GRUB. Don't compress the kernel, initrd, and other + ;; files read by grub.cfg, as well as common + ;; already-compressed file names. + "-find" "/" "-type" "f" + ;; XXX Even after "--" above, and despite documentation + ;; claiming otherwise, "-or" is stolen by grub-mkrescue + ;; which then chokes on it (as ‘-o …’) and dies. Don't use + ;; "-or". + "-not" "-wholename" "/boot/*" + "-not" "-wholename" "/System/*" + "-not" "-name" "unicode.pf2" + "-not" "-name" "bzImage" + "-not" "-name" "*.gz" ; initrd & all man pages + "-not" "-name" "*.png" ; includes grub-image.png + "-exec" "set_filter" "--zisofs" + "--") + '()) + "-volid" ,(string-upcase volume-id) + ,@(if volume-uuid + `("-volume_date" "uuid" + ,(string-filter (lambda (value) + (not (char=? #\- value))) + (iso9660-uuid->string + volume-uuid))) + '())))) diff --git a/gnu/build/install.scm b/gnu/build/install.scm index 59a118e905..b18654f1cc 100644 --- a/gnu/build/install.scm +++ b/gnu/build/install.scm @@ -25,7 +25,6 @@ (define-module (gnu build install) #:export (install-boot-config evaluate-populate-directive populate-root-file-system - register-closure install-database-and-gc-roots populate-single-profile-directory)) diff --git a/gnu/ci.scm b/gnu/ci.scm index fb2596c809..0430cf594b 100644 --- a/gnu/ci.scm +++ b/gnu/ci.scm @@ -38,6 +38,7 @@ (define-module (gnu ci) #:select (lookup-compressor self-contained-tarball)) #:use-module (gnu bootloader) #:use-module (gnu bootloader u-boot) + #:use-module (gnu image) #:use-module (gnu packages) #:use-module (gnu packages gcc) #:use-module (gnu packages base) @@ -49,6 +50,7 @@ (define-module (gnu ci) #:use-module (gnu packages make-bootstrap) #:use-module (gnu packages package-management) #:use-module (gnu system) + #:use-module (gnu system image) #:use-module (gnu system vm) #:use-module (gnu system install) #:use-module (gnu tests) @@ -209,32 +211,23 @@ (define MiB (expt 2 20)) (if (member system %guixsd-supported-systems) - (if (member system %u-boot-systems) - (list (->job 'flash-image - (run-with-store store - (mbegin %store-monad - (set-guile-for-build (default-guile)) - (system-disk-image - (operating-system (inherit installation-os) - (bootloader (bootloader-configuration - (bootloader u-boot-bootloader) - (target #f)))) - #:disk-image-size - (* 1500 MiB)))))) - (list (->job 'usb-image - (run-with-store store - (mbegin %store-monad - (set-guile-for-build (default-guile)) - (system-disk-image installation-os - #:disk-image-size - (* 1500 MiB))))) - (->job 'iso9660-image - (run-with-store store - (mbegin %store-monad - (set-guile-for-build (default-guile)) - (system-disk-image installation-os - #:file-system-type - "iso9660")))))) + (list (->job 'usb-image + (run-with-store store + (mbegin %store-monad + (set-guile-for-build (default-guile)) + (system-image + (image + (inherit efi-disk-image) + (size (* 1500 MiB)) + (operating-system installation-os)))))) + (->job 'iso9660-image + (run-with-store store + (mbegin %store-monad + (set-guile-for-build (default-guile)) + (system-image + (image + (inherit iso9660-image) + (operating-system installation-os))))))) '())) (define channel-build-system diff --git a/gnu/image.scm b/gnu/image.scm new file mode 100644 index 0000000000..b05fc69dc5 --- /dev/null +++ b/gnu/image.scm @@ -0,0 +1,76 @@ +;;; GNU Guix --- Functional package management for GNU +;;; Copyright © 2020 Mathieu Othacehe +;;; +;;; This file is part of GNU Guix. +;;; +;;; GNU Guix is free software; you can redistribute it and/or modify it +;;; under the terms of the GNU General Public License as published by +;;; the Free Software Foundation; either version 3 of the License, or (at +;;; your option) any later version. +;;; +;;; GNU Guix is distributed in the hope that it will be useful, but +;;; WITHOUT ANY WARRANTY; without even the implied warranty of +;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +;;; GNU General Public License for more details. +;;; +;;; You should have received a copy of the GNU General Public License +;;; along with GNU Guix. If not, see . + +(define-module (gnu image) + #:use-module (guix records) + #:export (partition + partition? + partition-device + partition-size + partition-file-system + partition-label + partition-uuid + partition-flags + partition-initializer + + image + image-name + image-format + image-size + image-operating-system + image-partitions + image-compression? + image-volatile-root? + image-substitutable?)) + + +;;; +;;; Partition record. +;;; + +(define-record-type* partition make-partition + partition? + (device partition-device (default #f)) + (size partition-size) + (file-system partition-file-system (default "ext4")) + (label partition-label (default #f)) + (uuid partition-uuid (default #f)) + (flags partition-flags (default '())) + (initializer partition-initializer (default #f))) + + +;;; +;;; Image record. +;;; + +(define-record-type* + image make-image + image? + (format image-format) ;symbol + (size image-size ;size in bytes as integer + (default 'guess)) + (operating-system image-operating-system ; + (default #f)) + (partitions image-partitions ;list of + (default '())) + (compression? image-compression? ;boolean + (default #t)) + (volatile-root? image-volatile-root? ;boolean + (default #t)) + (substitutable? image-substitutable? ;boolean + (default #t))) diff --git a/gnu/local.mk b/gnu/local.mk index daf6bd0306..4e0521baa5 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -62,6 +62,7 @@ GNU_SYSTEM_MODULES = \ %D%/bootloader/u-boot.scm \ %D%/bootloader/depthcharge.scm \ %D%/ci.scm \ + %D%/image.scm \ %D%/packages.scm \ %D%/packages/abduco.scm \ %D%/packages/abiword.scm \ @@ -606,6 +607,7 @@ GNU_SYSTEM_MODULES = \ %D%/system.scm \ %D%/system/accounts.scm \ %D%/system/file-systems.scm \ + %D%/system/image.scm \ %D%/system/install.scm \ %D%/system/keyboard.scm \ %D%/system/linux-container.scm \ @@ -626,6 +628,7 @@ GNU_SYSTEM_MODULES = \ %D%/build/activation.scm \ %D%/build/bootloader.scm \ %D%/build/cross-toolchain.scm \ + %D%/build/image.scm \ %D%/build/file-systems.scm \ %D%/build/install.scm \ %D%/build/linux-boot.scm \ diff --git a/gnu/system/image.scm b/gnu/system/image.scm new file mode 100644 index 0000000000..571b7af5f3 --- /dev/null +++ b/gnu/system/image.scm @@ -0,0 +1,532 @@ +;;; GNU Guix --- Functional package management for GNU +;;; Copyright © 2020 Mathieu Othacehe +;;; +;;; This file is part of GNU Guix. +;;; +;;; GNU Guix is free software; you can redistribute it and/or modify it +;;; under the terms of the GNU General Public License as published by +;;; the Free Software Foundation; either version 3 of the License, or (at +;;; your option) any later version. +;;; +;;; GNU Guix is distributed in the hope that it will be useful, but +;;; WITHOUT ANY WARRANTY; without even the implied warranty of +;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +;;; GNU General Public License for more details. +;;; +;;; You should have received a copy of the GNU General Public License +;;; along with GNU Guix. If not, see . + +(define-module (gnu system image) + #:use-module (guix gexp) + #:use-module (guix modules) + #:use-module (guix monads) + #:use-module (guix records) + #:use-module (guix store) + #:use-module (guix ui) + #:use-module (guix utils) + #:use-module ((guix self) #:select (make-config.scm)) + #:use-module (gnu bootloader) + #:use-module (gnu bootloader grub) + #:use-module (gnu image) + #:use-module (gnu services) + #:use-module (gnu services base) + #:use-module (gnu system) + #:use-module (gnu system file-systems) + #:use-module (gnu system uuid) + #:use-module (gnu system vm) + #:use-module (guix packages) + #:use-module (gnu packages base) + #:use-module (gnu packages bootloaders) + #:use-module (gnu packages cdrom) + #:use-module (gnu packages disk) + #:use-module (gnu packages gawk) + #:use-module (gnu packages genimage) + #:use-module (gnu packages guile) + #:autoload (gnu packages gnupg) (guile-gcrypt) + #:use-module (gnu packages linux) + #:use-module (gnu packages mtools) + #:use-module ((srfi srfi-1) #:prefix srfi-1:) + #:use-module (srfi srfi-11) + #:use-module (srfi srfi-26) + #:use-module (srfi srfi-35) + #:use-module (rnrs bytevectors) + #:use-module (ice-9 match) + #:export (esp-partition + root-partition + + efi-disk-image + iso9660-image + + find-image + system-image)) + + +;;; +;;; Images definitions. +;;; + +(define esp-partition + (partition + (size (* 40 (expt 2 20))) + (label "GNU-ESP") ;cosmetic only + ;; Use "vfat" here since this property is used when mounting. The actual + ;; FAT-ness is based on file system size (16 in this case). + (file-system "vfat") + (flags '(esp)) + (initializer (gexp initialize-efi-partition)))) + +(define root-partition + (partition + (size 'guess) + (label "Guix_image") + (file-system "ext4") + (flags '(boot)) + (initializer (gexp initialize-root-partition)))) + +(define efi-disk-image + (image + (format 'disk-image) + (partitions (list esp-partition root-partition)))) + +(define iso9660-image + (image + (format 'iso9660) + (partitions + (list (partition + (size 'guess) + (label "GUIX_IMAGE") + (flags '(boot))))) + ;; XXX: Temporarily disable compression to speed-up the tests. + (compression? #f))) + + +;; +;; Helpers. +;; + +(define not-config? + ;; Select (guix …) and (gnu …) modules, except (guix config). + (match-lambda + (('guix 'config) #f) + (('guix rest ...) #t) + (('gnu rest ...) #t) + (rest #f))) + +(define (partition->gexp partition) + "Turn PARTITION, a object, into a list-valued gexp suitable for +'make-partition-image'." + #~'(#$@(list (partition-size partition)) + #$(partition-file-system partition) + #$(partition-label partition) + #$(and=> (partition-uuid partition) + uuid-bytevector))) + +(define gcrypt-sqlite3&co + ;; Guile-Gcrypt, Guile-SQLite3, and their propagated inputs. + (srfi-1:append-map + (lambda (package) + (cons package + (match (package-transitive-propagated-inputs package) + (((labels packages) ...) + packages)))) + (list guile-gcrypt guile-sqlite3))) + +(define-syntax-rule (with-imported-modules* gexp* ...) + (with-extensions gcrypt-sqlite3&co + (with-imported-modules `(,@(source-module-closure + '((gnu build vm) + (gnu build image) + (guix store database)) + #:select? not-config?) + ((guix config) => ,(make-config.scm))) + #~(begin + (use-modules (gnu build vm) + (gnu build image) + (guix store database) + (guix build utils)) + gexp* ...)))) + + +;; +;; Disk image. +;; + +(define* (system-disk-image image + #:key + (name "disk-image") + bootcfg + bootloader + register-closures? + (inputs '())) + "Return as a file-like object, the disk-image described by IMAGE. Said +image can be copied on a USB stick as is. BOOTLOADER is the bootloader that +will be installed and configured according to BOOTCFG parameter. + +Raw images of the IMAGE partitions are first created. Then, genimage is used +to assemble the partition images into a disk-image without resorting to a +virtual machine. + +INPUTS is a list of inputs (as for packages). When REGISTER-CLOSURES? is +true, register INPUTS in the store database of the image so that Guix can be +used in the image." + + (define genimage-name "image") + + (define (image->genimage-cfg image) + ;; Return as a file-like object, the genimage configuration file + ;; describing the given IMAGE. + (define (format->image-type format) + ;; Return the genimage format corresponding to FORMAT. For now, only + ;; the hdimage format (raw disk-image) is supported. + (case format + ((disk-image) "hdimage") + (else + (raise (condition + (&message + (message + (format #f (G_ "Unsupported image type ~a~%.") format)))))))) + + (define (partition->dos-type partition) + ;; Return the MBR partition type corresponding to the given PARTITION. + ;; See: https://en.wikipedia.org/wiki/Partition_type. + (let ((flags (partition-flags partition))) + (cond + ((member 'esp flags) "0xEF") + (else "0x83")))) + + (define (partition-image partition) + ;; Return as a file-like object, an image of the given PARTITION. A + ;; directory, filled by calling the PARTITION initializer procedure, is + ;; first created within the store. Then, an image of this directory is + ;; created using tools such as 'mke2fs' or 'mkdosfs', depending on the + ;; partition file-system type. + (let* ((os (image-operating-system image)) + (schema (local-file (search-path %load-path + "guix/store/schema.sql"))) + (graph (match inputs + (((names . _) ...) + names))) + (root-builder + (with-imported-modules* + (let* ((initializer #$(partition-initializer partition))) + (sql-schema #$schema) + + ;; Allow non-ASCII file names--e.g., 'nss-certs'--to be + ;; decoded. + (setenv "GUIX_LOCPATH" + #+(file-append glibc-utf8-locales "/lib/locale")) + (setlocale LC_ALL "en_US.utf8") + + (initializer #$output + #:references-graphs '#$graph + #:deduplicate? #f + #:system-directory #$os + #:bootloader-package + #$(bootloader-package bootloader) + #:bootcfg #$bootcfg + #:bootcfg-location + #$(bootloader-configuration-file bootloader))))) + (image-root + (computed-file "partition-image-root" root-builder + #:options `(#:references-graphs ,inputs))) + (type (partition-file-system partition)) + (image-builder + (with-imported-modules* + (let ((inputs '#$(list e2fsprogs dosfstools mtools))) + (set-path-environment-variable "PATH" '("bin" "sbin") inputs) + (make-partition-image #$(partition->gexp partition) + #$output + #$image-root))))) + (computed-file "partition.img" image-builder))) + + (define (partition->config partition) + ;; Return the genimage partition configuration for PARTITION. + (let ((label (partition-label partition)) + (dos-type (partition->dos-type partition)) + (image (partition-image partition))) + #~(format #f "~/partition ~a { + ~/~/partition-type = ~a + ~/~/image = \"~a\" + ~/}" #$label #$dos-type #$image))) + + (let* ((format (image-format image)) + (image-type (format->image-type format)) + (partitions (image-partitions image)) + (partitions-config (map partition->config partitions)) + (builder + #~(begin + (let ((format (@ (ice-9 format) format))) + (call-with-output-file #$output + (lambda (port) + (format port + "\ +image ~a { +~/~a {} +~{~a~^~%~} +}~%" #$genimage-name #$image-type (list #$@partitions-config)))))))) + (computed-file "genimage.cfg" builder))) + + (let* ((substitutable? (image-substitutable? image)) + (builder + (with-imported-modules* + (let ((inputs '#$(list genimage coreutils findutils))) + (set-path-environment-variable "PATH" '("bin" "sbin") inputs) + (genimage #$(image->genimage-cfg image) #$output)))) + (image-dir (computed-file "image-dir" builder))) + (computed-file name + #~(symlink + (string-append #$image-dir "/" #$genimage-name) + #$output) + #:options `(#:substitutable? ,substitutable?)))) + + +;; +;; ISO9660 image. +;; + +(define (has-guix-service-type? os) + "Return true if OS contains a service of the type GUIX-SERVICE-TYPE." + (not (not (srfi-1:find (lambda (service) + (eq? (service-kind service) guix-service-type)) + (operating-system-services os))))) + +(define* (system-iso9660-image image + #:key + (name "iso9660-image") + bootcfg + bootloader + register-closures? + (inputs '()) + (grub-mkrescue-environment '())) + "Return as a file-like object a bootable, stand-alone iso9660 image. + +INPUTS is a list of inputs (as for packages). When REGISTER-CLOSURES? is +true, register INPUTS in the store database of the image so that Guix can be +used in the image. " + (define root-label + (match (image-partitions image) + ((partition) + (partition-label partition)))) + + (define root-uuid + (match (image-partitions image) + ((partition) + (uuid-bytevector (partition-uuid partition))))) + + (let* ((os (image-operating-system image)) + (bootloader (bootloader-package bootloader)) + (compression? (image-compression? image)) + (substitutable? (image-substitutable? image)) + (schema (local-file (search-path %load-path + "guix/store/schema.sql"))) + (graph (match inputs + (((names . _) ...) + names))) + (root-builder + (with-imported-modules* + (sql-schema #$schema) + + ;; Allow non-ASCII file names--e.g., 'nss-certs'--to be decoded. + (setenv "GUIX_LOCPATH" + #+(file-append glibc-utf8-locales "/lib/locale")) + (setlocale LC_ALL "en_US.utf8") + + (initialize-root-partition #$output + #:references-graphs '#$graph + #:deduplicate? #f + #:system-directory #$os))) + (image-root + (computed-file "image-root" root-builder + #:options `(#:references-graphs ,inputs))) + (builder + (with-imported-modules* + (let* ((inputs '#$(list parted e2fsprogs dosfstools xorriso + sed grep coreutils findutils gawk))) + (set-path-environment-variable "PATH" '("bin" "sbin") inputs) + (make-iso9660-image #$xorriso + '#$grub-mkrescue-environment + #$bootloader + #$bootcfg + #$os + #$image-root + #$output + #:references-graphs '#$graph + #:register-closures? #$register-closures? + #:compression? #$compression? + #:volume-id #$root-label + #:volume-uuid #$root-uuid))))) + (computed-file name builder + #:options `(#:references-graphs ,inputs + #:substitutable? ,substitutable?)))) + + +;; +;; Image creation. +;; + +(define (root-partition? partition) + "Return true if PARTITION is the root partition, false otherwise." + (member 'boot (partition-flags partition))) + +(define (find-root-partition image) + "Return the root partition of the given IMAGE." + (srfi-1:find root-partition? (image-partitions image))) + +(define (image->root-file-system image) + "Return the IMAGE root partition file-system type." + (let ((format (image-format image))) + (if (eq? format 'iso9660) + "iso9660" + (partition-file-system (find-root-partition image))))) + +(define (root-size image) + "Return the root partition size of IMAGE." + (let* ((image-size (image-size image)) + (root-partition (find-root-partition image)) + (root-size (partition-size root-partition))) + (cond + ((and (eq? root-size 'guess) image-size) + image-size) + (else root-size)))) + +(define* (image-with-os base-image os) + "Return an image based on BASE-IMAGE but with the operating-system field set +to OS. Also set the UUID and the size of the root partition." + (define root-file-system + (srfi-1:find + (lambda (fs) + (string=? (file-system-mount-point fs) "/")) + (operating-system-file-systems os))) + + (let*-values (((partitions) (image-partitions base-image)) + ((root-partition other-partitions) + (srfi-1:partition root-partition? partitions))) + (image + (inherit base-image) + (operating-system os) + (partitions + (cons (partition + (inherit (car root-partition)) + (uuid (file-system-device root-file-system)) + (size (root-size base-image))) + other-partitions))))) + +(define (operating-system-for-image image) + "Return an operating-system based on the one specified in IMAGE, but +suitable for image creation. Assign an UUID to the root file-system, so that +it can be used for bootloading." + (define volatile-root? (image-volatile-root? image)) + + (define (root-uuid os) + ;; UUID of the root file system, computed in a deterministic fashion. + ;; This is what we use to locate the root file system so it has to be + ;; different from the user's own file system UUIDs. + (let ((type (if (eq? (image-format image) 'iso9660) + 'iso9660 + 'dce))) + (operating-system-uuid os type))) + + (let* ((root-file-system-type (image->root-file-system image)) + (base-os (image-operating-system image)) + (file-systems-to-keep + (srfi-1:remove + (lambda (fs) + (string=? (file-system-mount-point fs) "/")) + (operating-system-file-systems base-os))) + (format (image-format image)) + (os + (operating-system + (inherit base-os) + (initrd (lambda (file-systems . rest) + (apply (operating-system-initrd base-os) + file-systems + #:volatile-root? volatile-root? + rest))) + (bootloader (if (eq? format 'iso9660) + (bootloader-configuration + (inherit + (operating-system-bootloader base-os)) + (bootloader grub-mkrescue-bootloader)) + (operating-system-bootloader base-os))) + (file-systems (cons (file-system + (mount-point "/") + (device "/dev/placeholder") + (type root-file-system-type)) + file-systems-to-keep)))) + (uuid (root-uuid os))) + (operating-system + (inherit os) + (file-systems (cons (file-system + (mount-point "/") + (device uuid) + (type root-file-system-type)) + file-systems-to-keep))))) + +(define* (make-system-image image) + "Return the derivation of IMAGE. It can be a raw disk-image or an ISO9660 +image, depending on IMAGE format." + (define substitutable? (image-substitutable? image)) + + (let* ((os (operating-system-for-image image)) + (image* (image-with-os image os)) + (register-closures? (has-guix-service-type? os)) + (bootcfg (operating-system-bootcfg os)) + (bootloader (bootloader-configuration-bootloader + (operating-system-bootloader os)))) + (case (image-format image) + ((disk-image) + (system-disk-image image* + #:bootcfg bootcfg + #:bootloader bootloader + #:register-closures? register-closures? + #:inputs `(("system" ,os) + ("bootcfg" ,bootcfg)))) + ((iso9660) + (system-iso9660-image image* + #:bootcfg bootcfg + #:bootloader bootloader + #:register-closures? register-closures? + #:inputs `(("system" ,os) + ("bootcfg" ,bootcfg)) + #:grub-mkrescue-environment + '(("MKRESCUE_SED_MODE" . "mbr_hfs"))))))) + +(define (find-image file-system-type) + "Find and return an image that could match the given FILE-SYSTEM-TYPE. This +is useful to adapt to interfaces written before the addition of the +record." + ;; XXX: Add support for system and target here, or in the caller. + (match file-system-type + ("iso9660" iso9660-image) + (_ efi-disk-image))) + +(define (system-image image) + "Wrap 'make-system-image' call, so that it is used only if the given IMAGE +is supported. Otherwise, fallback to image creation in a VM. This is +temporary and should be removed once 'make-system-image' is able to deal with +all types of images." + (define substitutable? (image-substitutable? image)) + (define volatile-root? (image-volatile-root? image)) + + (let* ((image-os (image-operating-system image)) + (image-root-filesystem-type (image->root-file-system image)) + (bootloader (bootloader-configuration-bootloader + (operating-system-bootloader image-os))) + (bootloader-name (bootloader-name bootloader)) + (size (image-size image)) + (format (image-format image))) + (mbegin %store-monad + (if (and (or (eq? bootloader-name 'grub) + (eq? bootloader-name 'extlinux)) + (eq? format 'disk-image)) + ;; Fallback to image creation in a VM when it is not yet supported + ;; by this module. + (system-disk-image-in-vm image-os + #:disk-image-size size + #:file-system-type image-root-filesystem-type + #:volatile? volatile-root? + #:substitutable? substitutable?) + (lower-object + (make-system-image image)))))) + +;;; image.scm ends here diff --git a/gnu/system/vm.scm b/gnu/system/vm.scm index 2fdf954883..37840ce355 100644 --- a/gnu/system/vm.scm +++ b/gnu/system/vm.scm @@ -77,7 +77,7 @@ (define-module (gnu system vm) system-qemu-image/shared-store system-qemu-image/shared-store-script - system-disk-image + system-disk-image-in-vm system-docker-image virtual-machine @@ -604,14 +604,13 @@ (define build ;;; VM and disk images. ;;; - -(define* (system-disk-image os - #:key - (name "disk-image") - (file-system-type "ext4") - (disk-image-size (* 900 (expt 2 20))) - (volatile? #t) - (substitutable? #t)) +(define* (system-disk-image-in-vm os + #:key + (name "disk-image") + (file-system-type "ext4") + (disk-image-size (* 900 (expt 2 20))) + (volatile? #t) + (substitutable? #t)) "Return the derivation of a disk image of DISK-IMAGE-SIZE bytes of the system described by OS. Said image can be copied on a USB stick as is. When VOLATILE? is true, the root file system is made volatile; this is useful diff --git a/gnu/tests/install.scm b/gnu/tests/install.scm index 23f60c68bf..2e5913953e 100644 --- a/gnu/tests/install.scm +++ b/gnu/tests/install.scm @@ -22,9 +22,11 @@ (define-module (gnu tests install) #:use-module (gnu) #:use-module (gnu bootloader extlinux) + #:use-module (gnu image) #:use-module (gnu tests) #:use-module (gnu tests base) #:use-module (gnu system) + #:use-module (gnu system image) #:use-module (gnu system install) #:use-module (gnu system vm) #:use-module ((gnu build vm) #:select (qemu-command)) @@ -229,14 +231,18 @@ (define* (run-install target-os target-os-source ;; we cheat a little bit by adding TARGET to its GC ;; roots. This way, we know 'guix system init' will ;; succeed. - (image (system-disk-image - (operating-system-with-gc-roots - os (list target)) - #:disk-image-size install-size - #:file-system-type - installation-disk-image-file-system-type - ;; Don't provide substitutes; too big. - #:substitutable? #f))) + (image + (system-image + (image + (inherit + (find-image + installation-disk-image-file-system-type)) + (size install-size) + (operating-system + (operating-system-with-gc-roots + os (list target))) + ;; Don't provide substitutes; too big. + (substitutable? #f))))) (define install (with-imported-modules '((guix build utils) (gnu build marionette)) diff --git a/guix/scripts/system.scm b/guix/scripts/system.scm index 2664c66a30..3c8691a08c 100644 --- a/guix/scripts/system.scm +++ b/guix/scripts/system.scm @@ -54,9 +54,11 @@ (define-module (guix scripts system) #:autoload (gnu build linux-modules) (device-module-aliases matching-modules) #:use-module (gnu system linux-initrd) + #:use-module (gnu image) #:use-module (gnu system) #:use-module (gnu bootloader) #:use-module (gnu system file-systems) + #:use-module (gnu system image) #:use-module (gnu system mapped-devices) #:use-module (gnu system linux-container) #:use-module (gnu system uuid) @@ -692,12 +694,11 @@ (define* (system-derivation-for-action os action (* 70 (expt 2 20))) #:mappings mappings)) ((disk-image) - (system-disk-image os - #:name (match file-system-type - ("iso9660" "image.iso") - (_ "disk-image")) - #:disk-image-size image-size - #:file-system-type file-system-type)) + (system-image + (image + (inherit (find-image file-system-type)) + (size image-size) + (operating-system os)))) ((docker-image) (system-docker-image os)))) -- cgit v1.2.3