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;;; GNU Guix --- Functional package management for GNU
;;; Copyright © 2019 Ludovic Courtès <ludo@gnu.org>
;;;
;;; 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 <http://www.gnu.org/licenses/>.

(define-module (gnu packages jupyter)
  #:use-module ((guix licenses) #:prefix license:)
  #:use-module (guix packages)
  #:use-module (guix download)
  #:use-module (guix git-download)
  #:use-module (guix build-system cmake)
  #:use-module (guix build-system python)
  #:use-module (gnu packages check)
  #:use-module (gnu packages cpp)
  #:use-module (gnu packages linux)
  #:use-module (gnu packages networking)
  #:use-module (gnu packages pkg-config)
  #:use-module (gnu packages python)
  #:use-module (gnu packages python-xyz)
  #:use-module (gnu packages time)
  #:use-module (gnu packages tls))

(define-public python-jupyter-protocol
  (package
    (name "python-jupyter-protocol")
    (version "0.1.1")
    (source (origin
              (method url-fetch)
              (uri (pypi-uri "jupyter_protocol" version))
              (sha256
               (base32
                "1bk3as5yw9y5nmq6l15nr46aby34phmvsx9kxgqnm5pd5q2b5h57"))))
    (build-system python-build-system)
    (propagated-inputs
     `(("python-dateutil" ,python-dateutil)
       ("python-jupyter-core" ,python-jupyter-core)
       ("python-pyzmq" ,python-pyzmq)
       ("python-traitlets" ,python-traitlets)))
    (native-inputs
     `(("python-ipykernel" ,python-ipykernel)
       ("python-ipython" ,python-ipython)
       ("python-mock" ,python-mock)
       ("python-pytest" ,python-pytest)))
    (home-page "https://jupyter.org")
    (synopsis "Jupyter protocol implementation")
    (description
     "This Python library is an experimental implementation of the
@uref{https://jupyter-client.readthedocs.io/en/latest/messaging.html, Jupyter
protocol} to be used by both clients and kernels.")
    (license license:bsd-3)
    (properties '((upstream-name . "jupyter_protocol")))))

(define-public python-jupyter-kernel-mgmt
  (package
    (name "python-jupyter-kernel-mgmt")
    (version "0.4.0")
    (source (origin
              (method url-fetch)
              (uri (pypi-uri "jupyter_kernel_mgmt" version))
              (sha256
               (base32
                "0i7a78dn89ca8h0a42giyxwcmk6y4wrdr7q8h2ax9vybb84c795q"))))
    (build-system python-build-system)
    (propagated-inputs
     `(("python-dateutil" ,python-dateutil)
       ("python-entrypoints" ,python-entrypoints)
       ("python-jupyter-core" ,python-jupyter-core)
       ("python-jupyter-protocol" ,python-jupyter-protocol)
       ("python-pyzmq" ,python-pyzmq)
       ("python-traitlets" ,python-traitlets)))
    (native-inputs
     `(("python-ipykernel" ,python-ipykernel)
       ("python-ipython" ,python-ipython)
       ("python-mock" ,python-mock)
       ("python-pytest" ,python-pytest)))
    (home-page "https://jupyter.org")
    (synopsis "Discover, launch, and communicate with Jupyter kernels")
    (description
     "This package is an experimental refactoring of the machinery for
launching and using Jupyter kernels.")
    (license license:bsd-3)
    (properties '((upstream-name . "jupyter_kernel_mgmt")))))

(define-public python-jupyter-kernel-test
  (package
    (name "python-jupyter-kernel-test")
    (version "0.3")
    (home-page "https://github.com/jupyter/jupyter_kernel_test")
    (source (origin
              ;; PyPI has a ".whl" file but not a proper source release.
              ;; Thus, fetch code from Git.
              (method git-fetch)
              (uri (git-reference (url home-page) (commit version)))
              (file-name (git-file-name name version))
              (sha256
               (base32
                "00iy74i4i8is6axb9vlsm0b9wxkvyyxnbl8r0i4gaj3xd788jm83"))))
    (build-system python-build-system)
    (arguments
     ;; The repo doesn't contain a "setup.py" file so install files manually.
     '(#:phases (modify-phases %standard-phases
                  (delete 'build)
                  (delete 'check)
                  (replace 'install
                    (lambda* (#:key inputs outputs #:allow-other-keys)
                      (let* ((out (assoc-ref outputs "out"))
                             (version (python-version (assoc-ref inputs "python")))
                             (pydir (string-append out "/lib/python"
                                                   version "/site-packages/"
                                                   "jupyter_kernel_test")))
                        (for-each (lambda (file)
                                    (install-file file pydir))
                                  (find-files "jupyter_kernel_test"
                                              "\\.py$"))
                        #t))))))
    (propagated-inputs
     `(("python-jupyter-kernel-mgmt" ,python-jupyter-kernel-mgmt)
       ("python-jupyter-protocol" ,python-jupyter-protocol)
       ("python-jsonschema" ,python-jsonschema)))
    (synopsis "Test Jupyter kernels")
    (description
     "@code{jupyter_kernel_test} is a tool for testing Jupyter kernels.  It
tests kernels for successful code execution and conformance with the
@uref{https://jupyter-client.readthedocs.io/en/latest/messaging.html, Jupyter
Messaging Protocol}.")
    (license license:bsd-3)))

(define-public xeus
  (package
    (name "xeus")
    (version "0.23.2")
    (source (origin
              (method git-fetch)
              (uri (git-reference
                    (url "https://github.com/QuantStack/xeus")
                    (commit version)))
              (sha256
               (base32
                "1m1b6z1538r7mv2ggn7bdbd9570ja7cadplq64zl8rgl2c8vdi2a"))
              (file-name (git-file-name name version))))
    (build-system cmake-build-system)
    (arguments
     '(#:configure-flags '("-DBUILD_STATIC_LIBS=OFF"
                           "-DDISABLE_ARCH_NATIVE=ON" ;no '-march=native'
                           "-DBUILD_TESTING=ON")))
    (native-inputs
     `(("pkg-config" ,pkg-config)

       ;; The following inputs are used by the test suite.
       ("googletest" ,googletest)
       ("python-pytest" ,python-pytest)
       ("python" ,python-3)
       ("python-jupyter-kernel-test" ,python-jupyter-kernel-test)
       ("python-jupyter-client" ,python-jupyter-client)))
    (inputs
     `(("xtl" ,xtl)
       ("json-modern-cxx" ,json-modern-cxx)
       ("cppzmq" ,cppzmq)
       ("zeromq" ,zeromq)
       ("openssl" ,openssl)
       ("util-linux" ,util-linux "lib")))         ;libuuid
    (home-page "https://quantstack.net/xeus")
    (synopsis "C++ implementation of the Jupyter Kernel protocol")
    (description
     "@code{xeus} is a library meant to facilitate the implementation of
kernels for Jupyter.  It takes the burden of implementing the Jupyter Kernel
protocol so developers can focus on implementing the interpreter part of the
kernel.

Several Jupyter kernels are built upon @code{xeus}, such as @code{xeus-cling},
a kernel for the C++ programming language, and @code{xeus-python}, an
alternative Python kernel for Jupyter.")
    (license license:bsd-3)))
apm/accumulate-builds' through FILTERM. (gexp->sexp)[self-quoting?]: Remove. * tests/gexp.scm ("let-system", "let-system, target") ("let-system, ungexp-native, target") ("let-system, nested"): New tests. * doc/guix.texi (G-Expressions): Document it. Ludovic Courtès 2020-03-22store: Add 'with-build-handler'....* guix/store.scm (current-build-prompt): New variable. (call-with-build-handler, invoke-build-handler): New procedures. (with-build-handler): New macro. * tests/store.scm ("with-build-handler"): New test. Ludovic Courtès 2020-03-12gexp: Add 'with-parameters'....* guix/gexp.scm (<parameterized>): New record type. (with-parameters): New macro. (compile-parameterized): New gexp compiler. * tests/gexp.scm ("with-parameters for %current-system") ("with-parameters for %current-target-system") ("with-parameters + file-append"): New tests. * doc/guix.texi (G-Expressions): Document it. Ludovic Courtès 2019-11-29ui: Factorize 'with-profile-lock'....* guix/ui.scm (profile-lock-handler, profile-lock-file): New procedures. (with-profile-lock): New macro. * guix/scripts/package.scm (process-actions): Use 'with-profile-lock' instead of 'with-file-lock/no-wait'. * guix/scripts/pull.scm (guix-pull): Likewise. Ludovic Courtès 2019-11-19pull: Acquire a lock for the target profile....This is a followup to b1fb663404894268b5ee92c040f12c52c0bee425. * guix/scripts/pull.scm (guix-pull): Wrap 'run-with-store' call in 'with-file-lock/no-wait'. Ludovic Courtès 2019-09-23git: Add 'commit-difference'....* guix/git.scm (commit-closure, commit-difference): New procedures. * guix/tests/git.scm, tests/git.scm: New files. * Makefile.am (dist_noinst_DATA): Add guix/tests/git.scm. (SCM_TESTS): Add tests/git.scm. Ludovic Courtès 2019-06-05syscalls: Add 'with-file-lock' macro....* guix/scripts/offload.scm (lock-file, unlock-file, with-file-lock): Move to... * guix/build/syscalls.scm: ... here. Ludovic Courtès 2019-05-27publish: Add support for lzip....* guix/scripts/publish.scm (show-help, %options): Support '-C METHOD' and '-C METHOD:LEVEL'. (default-compression): New procedure. (bake-narinfo+nar): Add lzip. (nar-response-port): Likewise. (string->compression-type): New procedure. (make-request-handler): Generalize /nar/gzip handler to handle /nar/lzip as well. * tests/publish.scm ("/nar/lzip/*"): New test. ("/*.narinfo with lzip compression"): New test. * doc/guix.texi (Invoking guix publish): Document it. (Requirements): Mention lzlib. Ludovic Courtès 2019-03-07database: Make 'register-items' transactional....* guix/store/database.scm (SQLITE_BUSY, register-output-sql): New variables. (add-references): Don't try finalizing after each use, only after all the uses (otherwise a finalized statement would be used if #:cache? was #f). (call-with-transaction): New procedure. (register-items): Use call-with-transaction to prevent broken intermediate states from being visible. * .dir-locals.el (call-with-transaction): indent it. Signed-off-by: Ludovic Courtès <ludo@gnu.org> Caleb Ristvedt 2019-01-11status: Add 'with-status-verbosity'....* guix/status.scm (logger-for-level, call-with-status-verbosity): New procedures. (with-status-verbosity): New macro. * guix/scripts/environment.scm (guix-environment): Use 'with-status-verbosity' instead of 'with-status-report'. * guix/scripts/pack.scm (guix-pack): Likewise. * guix/scripts/package.scm (guix-package): Likewise. * guix/scripts/pull.scm (guix-pull): Likewise. * guix/scripts/system.scm (guix-system): Likewise. * build-aux/run-system-tests.scm (run-system-tests): Likewise. Ludovic Courtès 2018-10-19tests: Run 'guix pack' tests using the external store....Fixes <https://bugs.gnu.org/32184>. * guix/tests.scm (call-with-external-store): New procedure. (with-external-store): New macro. * tests/pack.scm (%store): Remove. (test-assertm): Add 'store' parameter. ("self-contained-tarball"): Wrap in 'with-external-store'. * tests/guix-pack.sh: Connect to the external store, if possible, by setting NIX_STORE_DIR and GUIX_DAEMON_SOCKET. Remove most uses of '--bootstrap'. Ludovic Courtès 2018-09-27Add (guix status) and use it for pretty colored output....* guix/progress.scm (progress-reporter/trace): New procedure. (%progress-interval): New variable. (progress-reporter/file): Use it. * guix/scripts/build.scm (set-build-options-from-command-line): Pass #:print-extended-build-trace?. (%default-options): Add 'print-extended-build-trace?'. (guix-build): Parameterize CURRENT-TERMINAL-COLUMNS. Use 'build-status-updater'. * guix/scripts/environment.scm (%default-options): Add 'print-extended-build-trace?'. (guix-environment): Wrap body in 'with-status-report'. * guix/scripts/pack.scm (%default-options): Add 'print-build-trace?' and 'print-extended-build-trace?'. (guix-pack): Wrap body in 'with-status-report'. * guix/scripts/package.scm (%default-options, guix-package): Likewise. * guix/scripts/system.scm (%default-options, guix-system): Likewise. * guix/scripts/pull.scm (%default-options, guix-pull): Likewise. * guix/scripts/substitute.scm (progress-report-port): Don't call STOP when TOTAL is zero. (process-substitution): Add #:print-build-trace? and honor it. (guix-substitute)[print-build-trace?]: New variable. Pass #:print-build-trace? to 'process-substitution'. * guix/status.scm: New file. * guix/store.scm (set-build-options): Add #:print-extended-build-trace?; pass it into PAIRS. (%protocol-version): Bump. (protocol-version, nix-server-version): New procedures. (current-store-protocol-version): New variable. (with-store, build-things): Parameterize it. * guix/ui.scm (build-output-port): Remove. (colorize-string): Export. * po/guix/POTFILES.in: Add guix/status.scm. * tests/status.scm: New file. * Makefile.am (SCM_TESTS): Add it. * nix/libstore/worker-protocol.hh (PROTOCOL_VERSION): Bump to 0x162. * nix/libstore/build.cc (DerivationGoal::registerOutputs) (SubstitutionGoal::finished): Print a "@ hash-mismatch" trace before throwing. Ludovic Courtès 2018-06-01Add (gnu store database)....* guix/config.scm.in (%store-database-directory): New variable. * guix/store/database.scm: New file. * tests/store-database.scm: New file. * Makefile.am (STORE_MODULES): New variable. (MODULES, MODULES_NOT_COMPILED): Adjust accordingly. (SCM_TESTS) [HAVE_GUILE_SQLITE3]: Add tests/store-database.scm. Co-authored-by: Ludovic Courtès <ludo@gnu.org> Caleb Ristvedt 2018-06-01gexp: Add 'with-extensions'....* guix/gexp.scm (<gexp>)[extensions]: New field. (gexp-attribute): New procedure. (gexp-modules): Write in terms of 'gexp-attribute'. (gexp-extensions): New procedure. (gexp->derivation): Add #:effective-version. [extension-flags]: New procedure. Honor extensions of EXP. (current-imported-extensions): New syntax parameter. (with-extensions): New macro. (gexp): Honor CURRENT-IMPORTED-EXTENSIONS. (compiled-modules): Add #:extensions and honor it. (load-path-expression): Likewise. (gexp->script, gexp->file): Honor extensions. * tests/gexp.scm (%extension-package): New variable. ("gexp-extensions & ungexp") ("gexp-extensions & ungexp-splicing") ("gexp-extensions and literal Scheme object") ("gexp->derivation & with-extensions") ("program-file & with-extensions"): New tests. * doc/guix.texi (G-Expressions): Document 'with-extensions'. Ludovic Courtès