From unknown Tue Sep 09 22:27:51 2025 Content-Disposition: inline Content-Transfer-Encoding: quoted-printable MIME-Version: 1.0 X-Mailer: MIME-tools 5.509 (Entity 5.509) Content-Type: text/plain; charset=utf-8 From: bug#32483 <32483@debbugs.gnu.org> To: bug#32483 <32483@debbugs.gnu.org> Subject: Status: [PATCH] import: stackage: Support recursive importing. Reply-To: bug#32483 <32483@debbugs.gnu.org> Date: Wed, 10 Sep 2025 05:27:51 +0000 retitle 32483 [PATCH] import: stackage: Support recursive importing. reassign 32483 guix-patches submitter 32483 Ricardo Wurmus severity 32483 normal tag 32483 patch thanks From debbugs-submit-bounces@debbugs.gnu.org Mon Aug 20 11:58:33 2018 Received: (at submit) by debbugs.gnu.org; 20 Aug 2018 15:58:33 +0000 Received: from localhost ([127.0.0.1]:55770 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1frmZY-0004J9-6K for submit@debbugs.gnu.org; Mon, 20 Aug 2018 11:58:33 -0400 Received: from eggs.gnu.org ([208.118.235.92]:33140) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1frmZU-0004It-Tn for submit@debbugs.gnu.org; Mon, 20 Aug 2018 11:58:26 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1frmZO-00078Q-70 for submit@debbugs.gnu.org; Mon, 20 Aug 2018 11:58:19 -0400 X-Spam-Checker-Version: SpamAssassin 3.3.2 (2011-06-06) on eggs.gnu.org X-Spam-Level: X-Spam-Status: No, score=0.8 required=5.0 tests=BAYES_50,T_DKIM_INVALID autolearn=disabled version=3.3.2 Received: from lists.gnu.org ([2001:4830:134:3::11]:38781) by eggs.gnu.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32) (Exim 4.71) (envelope-from ) id 1frmZO-00078B-1w for submit@debbugs.gnu.org; Mon, 20 Aug 2018 11:58:18 -0400 Received: from eggs.gnu.org ([2001:4830:134:3::10]:54114) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1frmZM-0003tw-Pm for guix-patches@gnu.org; Mon, 20 Aug 2018 11:58:17 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1frmZJ-00070h-9Z for guix-patches@gnu.org; Mon, 20 Aug 2018 11:58:16 -0400 Received: from sinope02.bbbm.mdc-berlin.de ([141.80.25.24]:43438) by eggs.gnu.org with esmtps (TLS1.0:DHE_RSA_AES_256_CBC_SHA1:32) (Exim 4.71) (envelope-from ) id 1frmZI-0006qe-Qc for guix-patches@gnu.org; Mon, 20 Aug 2018 11:58:13 -0400 Received: from localhost (localhost [127.0.0.1]) by sinope02.bbbm.mdc-berlin.de (Postfix) with ESMTP id B952E125885A for ; Mon, 20 Aug 2018 17:58:03 +0200 (CEST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=mdc-berlin.de; h= content-transfer-encoding:content-type:content-type:mime-version :x-mailer:message-id:date:date:subject:subject:from:from :received:received:received; s=mdc; t=1534780678; x=1536595079; bh=dIwToHigQMuNVhdOh7mg7CaHY++oPM2hf0rtGR9R/AQ=; b=bhdq5hFPZqZ6 Imn6iVS62/a61uT7pBEotvu5XBmkdnhyRM547pk46dpY+1+zH3zAYMLkdWoE0oq8 8OH9WdQhAXVgu0vOBLiJl/s2CsKbMLRQU61i2U+gI85flL0vb0JR62CcvCyL7AeW RQINLJTSDkrMGvNQbDi4EWKPIRtRaC0= X-Virus-Scanned: amavisd-new at mdc-berlin.de Received: from sinope02.bbbm.mdc-berlin.de ([127.0.0.1]) by localhost (sinope02.bbbm.mdc-berlin.de [127.0.0.1]) (amavisd-new, port 10024) with ESMTP id OuHZ0hD2SHMV for ; Mon, 20 Aug 2018 17:57:58 +0200 (CEST) Received: from SW-IT-P-CAS4.mdc-berlin.net (puck.citx.mdc-berlin.de [141.80.36.101]) (using TLSv1.2 with cipher ECDHE-RSA-AES256-SHA384 (256/256 bits)) (No client certificate requested) by sinope02.bbbm.mdc-berlin.de (Postfix) with ESMTPS for ; Mon, 20 Aug 2018 17:57:58 +0200 (CEST) Received: from localhost (141.80.113.103) by SW-IT-P-CAS4.mdc-berlin.net (141.80.113.59) with Microsoft SMTP Server (TLS) id 14.3.408.0; Mon, 20 Aug 2018 17:57:57 +0200 From: Ricardo Wurmus To: Subject: [PATCH] import: stackage: Support recursive importing. Date: Mon, 20 Aug 2018 17:57:56 +0200 Message-ID: <20180820155756.10851-1-ricardo.wurmus@mdc-berlin.de> X-Mailer: git-send-email 2.18.0 MIME-Version: 1.0 Content-Type: text/plain; charset="UTF-8" X-Originating-IP: [141.80.113.103] X-TM-AS-Product-Ver: SMEX-12.5.0.1300-8.5.1010-24044.000 X-TM-AS-Result: No-6.652700-8.000000-10 X-TMASE-MatchedRID: wB6JIZ7tFrW4c6uEFrThdpdc7I2df+mswx0jRRxcQfMUlWIKEoGBmeTU uEDszCu7Qol7vh6lSnbijpjet3oGSCmJBt+6x0vF6/xAZojbl7fhwsEcDDUFFp3oy+p5Iv9stTD LZLR3mBHviw+VO4MJgmdn/Q0D39bZrSgOnDLfi6j1RUeLAvHT8hokPBiBBj9/+Cckfm+bb6AFR7 uo2zDLCCUKZKFVFJEhfIQXFmy4Q7E13IIF3ou0V8pQKjU7fBXVsnhLev9M88mNTnqOMBIJ4f1o+ v3F3AlZV+9jx69Tv84CuuL+p5lfcRf8OfYtQgtwsyw+ZJnFumQfOdo4H355iKcQ/DCoU3fUAX8K avk10iLr/oiQcoq29h9l1zPMOb+6v1l2Uvx6idpt1O49r1VEa8RB0bsfrpPIXzYxeQR1DvsUCDM do+ED3uBhd5nV6ITUE5zOeFG6drwQWKFJ76v1bmnHCRD6//6D X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--6.652700-8.000000 X-TMASE-Version: SMEX-12.5.0.1300-8.5.1010-24044.000 Content-Transfer-Encoding: quoted-printable X-detected-operating-system: by eggs.gnu.org: GNU/Linux 2.2.x-3.x [generic] X-detected-operating-system: by eggs.gnu.org: GNU/Linux 2.6.x X-Received-From: 2001:4830:134:3::11 X-Spam-Score: -5.0 (-----) X-Debbugs-Envelope-To: submit Cc: Ricardo Wurmus X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -1.0 (-) * guix/import/hackage.scm (hackage-name->package-name): Export procedure. * guix/import/stackage.scm (lts-info-packages-lts-info): Fix match expres= sion. (stackage-recursive-import): New procedure. (stackage->guix-package): Memoize results. * guix/scripts/import/stackage.scm (show-help, %options, guix-import-stackage): Support recursive importing. * doc/guix.texi (Invoking guix import): Document option. --- doc/guix.texi | 7 ++++- guix/import/hackage.scm | 1 + guix/import/stackage.scm | 45 +++++++++++++++++++------------ guix/scripts/import/stackage.scm | 46 ++++++++++++++++++++++++-------- 4 files changed, 70 insertions(+), 29 deletions(-) diff --git a/doc/guix.texi b/doc/guix.texi index 0b72e5d8c..54f8cf5ea 100644 --- a/doc/guix.texi +++ b/doc/guix.texi @@ -6699,9 +6699,14 @@ Specific command-line options are: @itemx -t Do not include dependencies required only by the test suites. @item --lts-version=3D@var{version} -@itemx -r @var{version} +@itemx -l @var{version} @var{version} is the desired LTS release version. If omitted the latest release is used. +@item --recursive +@itemx -r +Traverse the dependency graph of the given upstream package recursively +and generate package expressions for all those packages that are not yet +in Guix. @end table =20 The command below imports metadata for the @code{HTTP} Haskell package diff --git a/guix/import/hackage.scm b/guix/import/hackage.scm index 3c00f680b..54301de2e 100644 --- a/guix/import/hackage.scm +++ b/guix/import/hackage.scm @@ -44,6 +44,7 @@ %hackage-updater =20 guix-package->hackage-name + hackage-name->package-name hackage-fetch hackage-source-url hackage-cabal-url diff --git a/guix/import/stackage.scm b/guix/import/stackage.scm index ec93fbced..afd5d997a 100644 --- a/guix/import/stackage.scm +++ b/guix/import/stackage.scm @@ -1,5 +1,6 @@ ;;; GNU Guix --- Functional package management for GNU ;;; Copyright =C2=A9 2017 Federico Beffa +;;; Copyright =C2=A9 2018 Ricardo Wurmus ;;; ;;; This file is part of GNU Guix. ;;; @@ -25,10 +26,12 @@ #:use-module (srfi srfi-35) #:use-module (guix import json) #:use-module (guix import hackage) + #:use-module (guix import utils) #:use-module (guix memoization) #:use-module (guix packages) #:use-module (guix upstream) #:export (stackage->guix-package + stackage-recursive-import %stackage-updater)) =20 =0C @@ -45,9 +48,9 @@ (_ #f))) =20 (define (lts-info-packages lts-info) - "Retruns the alist of packages contained in LTS-INFO." + "Returns the alist of packages contained in LTS-INFO." (match lts-info - ((_ ("packages" pkg ...)) pkg) + ((("packages" pkg ...) . _) pkg) (_ '()))) =20 (define (leave-with-message fmt . args) @@ -85,25 +88,33 @@ (define (hackage-name-version name version) (and version (string-append name "@" version))) =20 -(define* (stackage->guix-package package-name ; upstream name - #:key - (include-test-dependencies? #t) - (lts-version "") - (packages-info - (lts-info-packages - (stackage-lts-info-fetch lts-version)= ))) - "Fetch Cabal file for PACKAGE-NAME from hackage.haskell.org. The retr= ieved +(define stackage->guix-package + (memoize + (lambda* (package-name ; upstream name + #:key + (include-test-dependencies? #t) + (lts-version "") + (packages-info + (lts-info-packages + (stackage-lts-info-fetch lts-version)))) + "Fetch Cabal file for PACKAGE-NAME from hackage.haskell.org. The r= etrieved vesion corresponds to the version of PACKAGE-NAME specified in the LTS-V= ERSION release at stackage.org. Return the `package' S-expression correspondin= g to that package, or #f on failure. PACKAGES-INFO is the alist with the pac= kages included in the Stackage LTS release." - (let* ((version (lts-package-version packages-info package-name)) - (name-version (hackage-name-version package-name version))) - (if name-version - (hackage->guix-package name-version - #:include-test-dependencies? - include-test-dependencies?) - (leave-with-message "~a: Stackage package not found" package-nam= e)))) + (let* ((version (lts-package-version packages-info package-name)) + (name-version (hackage-name-version package-name version))) + (if name-version + (hackage->guix-package name-version + #:include-test-dependencies? + include-test-dependencies?) + (leave-with-message "~a: Stackage package not found" package-= name)))))) + +(define (stackage-recursive-import package-name . args) + (recursive-import package-name #f + #:repo->guix-package (lambda (name repo) + (apply stackage->guix-package= (cons name args))) + #:guix-name hackage-name->package-name)) =20 =0C ;;; diff --git a/guix/scripts/import/stackage.scm b/guix/scripts/import/stack= age.scm index e6676e93e..b4b12581b 100644 --- a/guix/scripts/import/stackage.scm +++ b/guix/scripts/import/stackage.scm @@ -1,5 +1,6 @@ ;;; GNU Guix --- Functional package management for GNU ;;; Copyright =C2=A9 2017 Federico Beffa +;;; Copyright =C2=A9 2018 Ricardo Wurmus ;;; ;;; This file is part of GNU Guix. ;;; @@ -26,6 +27,7 @@ #:use-module (srfi srfi-1) #:use-module (srfi srfi-11) #:use-module (srfi srfi-37) + #:use-module (srfi srfi-41) #:use-module (ice-9 match) #:use-module (ice-9 format) #:export (guix-import-stackage)) @@ -43,11 +45,13 @@ (display (G_ "Usage: guix import stackage PACKAGE-NAME Import and convert the LTS Stackage package for PACKAGE-NAME.\n")) (display (G_ " - -r VERSION, --lts-version=3DVERSION + -l VERSION, --lts-version=3DVERSION specify the LTS version to use")) (display (G_ " -h, --help display this help and exit")) (display (G_ " + -r, --recursive import packages recursively")) + (display (G_ " -t, --no-test-dependencies don't include test-only dependencies")) (display (G_ " -V, --version display version information and exit")) @@ -68,11 +72,14 @@ Import and convert the LTS Stackage package for PACKA= GE-NAME.\n")) (alist-cons 'include-test-dependencies? #f (alist-delete 'include-test-dependencies? result)))) - (option '(#\r "lts-version") #t #f + (option '(#\l "lts-version") #t #f (lambda (opt name arg result) (alist-cons 'lts-version arg (alist-delete 'lts-version result)))) + (option '(#\r "recursive") #f #f + (lambda (opt name arg result) + (alist-cons 'recursive #t result))) %standard-import-options)) =20 =0C @@ -90,6 +97,27 @@ Import and convert the LTS Stackage package for PACKAG= E-NAME.\n")) (alist-cons 'argument arg result)) %default-options)) =20 + (define (run-importer package-name opts error-fn) + (let* ((arguments (list + package-name + #:include-test-dependencies? + (assoc-ref opts 'include-test-dependencies?) + #:lts-version (assoc-ref opts 'lts-version))) + (sexp (if (assoc-ref opts 'recursive) + ;; Recursive import + (map (match-lambda + ((and ('package ('name name) . rest) pkg) + `(define-public ,(string->symbol name) + ,pkg)) + (_ #f)) + (reverse + (stream->list + (apply stackage-recursive-import arguments))= )) + ;; Single import + (apply stackage->guix-package arguments)))) + (unless sexp (error-fn)) + sexp)) + (let* ((opts (parse-options)) (args (filter-map (match-lambda (('argument . value) @@ -99,15 +127,11 @@ Import and convert the LTS Stackage package for PACK= AGE-NAME.\n")) (match args ((package-name) (with-error-handling - (let ((sexp (stackage->guix-package - package-name - #:include-test-dependencies? - (assoc-ref opts 'include-test-dependencies?) - #:lts-version (assoc-ref opts 'lts-version)))) - (unless sexp - (leave (G_ "failed to download cabal file for package '~a'~%= ") - package-name)) - sexp))) + (run-importer package-name opts + (lambda () + (leave (G_ "failed to download cabal file \ +for package '~a'~%") + package-name))))) (() (leave (G_ "too few arguments~%"))) ((many ...) --=20 2.18.0 From debbugs-submit-bounces@debbugs.gnu.org Mon Aug 20 12:03:10 2018 Received: (at 32483) by debbugs.gnu.org; 20 Aug 2018 16:03:10 +0000 Received: from localhost ([127.0.0.1]:55775 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1frme1-0004RV-LV for submit@debbugs.gnu.org; Mon, 20 Aug 2018 12:03:10 -0400 Received: from sinope02.bbbm.mdc-berlin.de ([141.80.25.24]:34340) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1frmdz-0004RC-Qe for 32483@debbugs.gnu.org; Mon, 20 Aug 2018 12:03:04 -0400 Received: from localhost (localhost [127.0.0.1]) by sinope02.bbbm.mdc-berlin.de (Postfix) with ESMTP id B47151258A35 for <32483@debbugs.gnu.org>; Mon, 20 Aug 2018 18:03:02 +0200 (CEST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=mdc-berlin.de; h= content-transfer-encoding:content-type:content-type:mime-version :x-mailer:message-id:date:date:subject:subject:from:from :received:received:received; s=mdc; t=1534780977; x=1536595378; bh=ojvbdSOgGk+QNMnw0Z3Ty3lbeI0GHEXB4Fg7IRPF/AY=; b=DlHULThlUOR6 q5u06ZBpZwllNU154ZzSz/y3U96alIPTqDbgX+rQ/Otu8o3f2zi2B9RBsFSStCva UbKyyn7R19Plu/gXWBCuqWuNO4L+JXoGvJK7gz5VLVPYRc6tHag1OPP0jq+1VE2V JQ/Uf/5Yg75okMewenLdTyS9zvIzfE0= X-Virus-Scanned: amavisd-new at mdc-berlin.de Received: from sinope02.bbbm.mdc-berlin.de ([127.0.0.1]) by localhost (sinope02.bbbm.mdc-berlin.de [127.0.0.1]) (amavisd-new, port 10024) with ESMTP id RQaE0xEodizB for <32483@debbugs.gnu.org>; Mon, 20 Aug 2018 18:02:57 +0200 (CEST) Received: from SW-IT-P-CAS4.mdc-berlin.net (puck.citx.mdc-berlin.de [141.80.36.101]) (using TLSv1.2 with cipher ECDHE-RSA-AES256-SHA384 (256/256 bits)) (No client certificate requested) by sinope02.bbbm.mdc-berlin.de (Postfix) with ESMTPS for <32483@debbugs.gnu.org>; Mon, 20 Aug 2018 18:02:57 +0200 (CEST) Received: from localhost (141.80.113.103) by SW-IT-P-CAS4.mdc-berlin.net (141.80.113.59) with Microsoft SMTP Server (TLS) id 14.3.408.0; Mon, 20 Aug 2018 18:02:56 +0200 From: Ricardo Wurmus To: <32483@debbugs.gnu.org> Subject: [PATCH 1/4] gnu: Add python-llvmlite. Date: Mon, 20 Aug 2018 18:02:49 +0200 Message-ID: <20180820160252.11219-1-ricardo.wurmus@mdc-berlin.de> X-Mailer: git-send-email 2.18.0 MIME-Version: 1.0 Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: 8bit X-Originating-IP: [141.80.113.103] X-TM-AS-Product-Ver: SMEX-12.5.0.1300-8.5.1010-24044.000 X-TM-AS-Result: No-2.107700-8.000000-10 X-TMASE-MatchedRID: d+BGjaEADBV7qToVEfwBPCmjEOrcO6AyTJDl9FKHbrkAhmnHHeGnvQn9 ofQNoBQF77K5BwW7h4sh79bj8XiT0SOGf4qrcS6PzUbMjomcmMqy4iyjvVWTog2Y8xyy93kWkA/ oON3vcwB7t5gXD1JuXCmsFBPte54Xs1RWeqLGIw7Da1qWPNOExjGZtPrBBPZrT4wYQUnw8tkOsb dDU8hPqMTLo5l8hmoVX7bicKxRIU0Es/H1wMyspoDH9tzzuv1v+gtHj7OwNO34ZhR52Rc1asvM5 ONlhKAp19xWPnBfhJugaudrTeMyLlJFkOCHVR0Ggpi4Vuzi0ERxvKC15cyTOs9huu5zXbrdC7Gi u70uSkcTLa1ztxPz2If4l3W0tVe7u49q1sWEC7dHBp5ZT1n34TddPuHwt7TAgPUJDvCW8W4= X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10-2.107700-8.000000 X-TMASE-Version: SMEX-12.5.0.1300-8.5.1010-24044.000 X-Spam-Score: 0.0 (/) X-Debbugs-Envelope-To: 32483 Cc: Ricardo Wurmus X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -1.0 (-) * gnu/packages/llvm.scm (python-llvmlite): New variable. --- gnu/packages/llvm.scm | 53 ++++++++++++++++++++++++++++++++++++++++++- 1 file changed, 52 insertions(+), 1 deletion(-) diff --git a/gnu/packages/llvm.scm b/gnu/packages/llvm.scm index 98592ad09..e9b7065ab 100644 --- a/gnu/packages/llvm.scm +++ b/gnu/packages/llvm.scm @@ -3,7 +3,7 @@ ;;; Copyright © 2015 Mark H Weaver ;;; Copyright © 2015, 2017, 2018 Ludovic Courtès ;;; Copyright © 2016 Dennis Mungai -;;; Copyright © 2016 Ricardo Wurmus +;;; Copyright © 2016, 2018 Ricardo Wurmus ;;; Copyright © 2017 Roel Janssen ;;; Copyright © 2018 Marius Bakke ;;; @@ -29,6 +29,7 @@ #:use-module (guix utils) #:use-module (guix build-system gnu) #:use-module (guix build-system cmake) + #:use-module (guix build-system python) #:use-module (gnu packages) #:use-module (gnu packages gcc) #:use-module (gnu packages bootstrap) ;glibc-dynamic-linker @@ -379,3 +380,53 @@ code analysis tools.") (patches (list (search-patch "llvm-for-extempore.patch"))))) ;; Extempore refuses to build on architectures other than x86_64 (supported-systems '("x86_64-linux")))) + +(define-public python-llvmlite + (package + (name "python-llvmlite") + (version "0.24.0") + (source + (origin + (method url-fetch) + (uri (pypi-uri "llvmlite" version)) + (sha256 + (base32 + "01zwjlc3c5mhrwmv4b73zgbskwqps9ly0nrh54bbj1f1l72f839j")))) + (build-system python-build-system) + (inputs + `(("llvm" + ,(package + (inherit llvm) + (source (origin + (inherit (package-source llvm)) + (patches + (list + (origin + (method url-fetch) + (uri (string-append "https://raw.githubusercontent.com/numba/" + "llvmlite/v" version "/conda-recipes/" + "D47188-svml.patch")) + (sha256 + (base32 + "0mrj24jvkv3hjcmyg98zmvmyl1znlh2j63rdr69f6g7s96d2pfv1"))) + (origin + (method url-fetch) + (uri (string-append "https://raw.githubusercontent.com/numba/" + "llvmlite/v" version "/conda-recipes/" + "twine_cfg_undefined_behavior.patch")) + (sha256 + (base32 + "07h71n2m1mn9zcfgw04zglffknplb233zqbcd6pckq0wygkrxflp"))) + (origin + (method url-fetch) + (uri (string-append "https://raw.githubusercontent.com/numba/" + "llvmlite/v" version "/conda-recipes/" + "0001-Transforms-Add-missing-header-for-InstructionCombini.patch")) + (sha256 + (base32 + "1pp0z9696l6j4dwz7ypjrm4vvkj0d3mlf1g8zmiyk08akw5lz0cb"))))))))))) + (home-page "http://llvmlite.pydata.org") + (synopsis "Wrapper around basic LLVM functionality") + (description + "This package provides a Python binding to LLVM for use in Numba.") + (license license:bsd-3))) -- 2.18.0 From debbugs-submit-bounces@debbugs.gnu.org Mon Aug 20 12:03:12 2018 Received: (at 32483) by debbugs.gnu.org; 20 Aug 2018 16:03:12 +0000 Received: from localhost ([127.0.0.1]:55779 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1frme7-0004Ru-MG for submit@debbugs.gnu.org; Mon, 20 Aug 2018 12:03:12 -0400 Received: from sinope02.bbbm.mdc-berlin.de ([141.80.25.24]:34356) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1frme5-0004Ra-FJ for 32483@debbugs.gnu.org; Mon, 20 Aug 2018 12:03:10 -0400 Received: from localhost (localhost [127.0.0.1]) by sinope02.bbbm.mdc-berlin.de (Postfix) with ESMTP id BC3DD1258A48 for <32483@debbugs.gnu.org>; Mon, 20 Aug 2018 18:03:08 +0200 (CEST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=mdc-berlin.de; h= content-type:content-type:mime-version:references:in-reply-to :x-mailer:message-id:date:date:subject:subject:from:from :received:received:received; s=mdc; t=1534780983; x=1536595384; bh=CdX4s2NOC3mkikcRpvuYIREOGLNBbQVT12c0ngm/wa4=; b=jMTq47RA9JWZ GF3p1QZV4ydWbNzKp+OvZV1Jg44g709OE4J98X4szr9sG2L8ur47XS5xIlwmO1DV PVfzVEVMBL8ayo6WRe+8LGmz9MwfiZHr95Y9+9HBZnFzLcY0Kxay3RxmphshF3RH Pu9gvxAqML1pLYUJ6oq+z3QTN64azco= X-Virus-Scanned: amavisd-new at mdc-berlin.de Received: from sinope02.bbbm.mdc-berlin.de ([127.0.0.1]) by localhost (sinope02.bbbm.mdc-berlin.de [127.0.0.1]) (amavisd-new, port 10024) with ESMTP id 7-TWD3gO6sad for <32483@debbugs.gnu.org>; Mon, 20 Aug 2018 18:03:03 +0200 (CEST) Received: from SW-IT-P-CAS4.mdc-berlin.net (puck.citx.mdc-berlin.de [141.80.36.101]) (using TLSv1.2 with cipher ECDHE-RSA-AES256-SHA384 (256/256 bits)) (No client certificate requested) by sinope02.bbbm.mdc-berlin.de (Postfix) with ESMTPS for <32483@debbugs.gnu.org>; Mon, 20 Aug 2018 18:03:03 +0200 (CEST) Received: from localhost (141.80.113.103) by SW-IT-P-CAS4.mdc-berlin.net (141.80.113.59) with Microsoft SMTP Server (TLS) id 14.3.408.0; Mon, 20 Aug 2018 18:03:02 +0200 From: Ricardo Wurmus To: <32483@debbugs.gnu.org> Subject: [PATCH 2/4] gnu: Add python-numba. Date: Mon, 20 Aug 2018 18:02:50 +0200 Message-ID: <20180820160252.11219-2-ricardo.wurmus@mdc-berlin.de> X-Mailer: git-send-email 2.18.0 In-Reply-To: <20180820160252.11219-1-ricardo.wurmus@mdc-berlin.de> References: <20180820160252.11219-1-ricardo.wurmus@mdc-berlin.de> MIME-Version: 1.0 Content-Type: text/plain X-Originating-IP: [141.80.113.103] X-TM-AS-Product-Ver: SMEX-12.5.0.1300-8.5.1010-24044.000 X-TM-AS-Result: No-1.911100-8.000000-10 X-TMASE-MatchedRID: lNgRljLggNJ7qToVEfwBPAPZZctd3P4BUAjrAJWsTe+n5yDc9PwlXBFx R5JQAS6OChkKs9v88jPlVA1Tb3zHTT09o8PhVkSdYwaJXrf2IXQza2zV+sjx6k+u8oS4XkKMYHk 3pEJdwIemlHbHSFj7vsuDOWmE3d0c6c6GXyQATrpc/msUC5wFQUld5Rsl9tmXVI7KaIl9NhehAR hvJE8md13U5i4vdFnSXZZXNV16gdun0rKwexwo/r50lYduDghOBGvINcfHqhd85YbmMPCbE5mIq RMt9utb3f0e/BgwI9CriZtkLgsYzcLko0U8v7J0bBu6+EIezdzWSrKtwxqWpRuOL3jygJQja2By QZcfaScm5rHAoJdQe+fq45TJ8Up5r78SC5iivxwURSScn+QSXt0H8LFZNFG7MGpgBNI6BaO81tw K4dD7rgttNPIE9SPyOZkiXnps6o/WpMdrZ7fxAC1N4MHRV7WzEttirixzUsO3cRmdNOrXLqMYTK haJljtZ0AuV3wPqYVcKRK3DM/KmiQGdl1tQI7t0/5HQxvVB1U0+aGhUx8J2mWd1BH5zkrEftwZ3 X11IV0= X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10-1.911100-8.000000 X-TMASE-Version: SMEX-12.5.0.1300-8.5.1010-24044.000 X-Spam-Score: 0.0 (/) X-Debbugs-Envelope-To: 32483 Cc: Ricardo Wurmus X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -1.0 (-) * gnu/packages/python.scm (python-numba): New variable. --- gnu/packages/python.scm | 84 +++++++++++++++++++++++++++++++++++++++++ 1 file changed, 84 insertions(+) diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index 3db29e23f..7f343bdab 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -99,6 +99,7 @@ #:use-module (gnu packages libevent) #:use-module (gnu packages libffi) #:use-module (gnu packages linux) + #:use-module (gnu packages llvm) #:use-module (gnu packages machine-learning) #:use-module (gnu packages man) #:use-module (gnu packages maths) @@ -13889,3 +13890,86 @@ Let's Encrypt.") development that supports command line argument parsing, command string validation testing and application logic.") (license license:expat))) + +;; Make sure to upgrade python-llvmlite in (gnu packages llvm) together with +;; python-numba. They have a very unflexible relationship. +(define-public python-numba + (package + (name "python-numba") + (version "0.39.0") + (source + (origin + (method url-fetch) + (uri (pypi-uri "numba" version)) + (sha256 + (base32 + "1bibvkwga1v8293i9ivl469d8bzgabn3vgr2ig7c1i68v8frsx07")))) + (build-system python-build-system) + (arguments + `(#:modules ((guix build utils) + (guix build python-build-system) + (ice-9 ftw) + (srfi srfi-1) + (srfi srfi-26)) + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'disable-proprietary-features + (lambda _ + (setenv "NUMBA_DISABLE_HSA" "1") + (setenv "NUMBA_DISABLE_CUDA" "1") + #t)) + (add-after 'unpack 'remove-failing-tests + (lambda _ + ;; FIXME: these tests fail for unknown reasons: + ;; test_non_writable_pycache, test_non_creatable_pycache, and + ;; test_frozen (all in numba.tests.test_dispatcher.TestCache). + (substitute* "numba/tests/test_dispatcher.py" + (("def test(_non_writable_pycache)" _ m) + (string-append "def guix_skip" m)) + (("def test(_non_creatable_pycache)" _ m) + (string-append "def guix_skip" m)) + (("def test(_frozen)" _ m) + (string-append "def guix_skip" m))) + + ;; These tests fail because we don't run the tests from the build + ;; directory: test_setup_py_distutils, test_setup_py_setuptools + ;; They ar in numba.tests.test_pycc.TestDistutilsSupport. + (substitute* "numba/tests/test_pycc.py" + (("def test(_setup_py_distutils|_setup_py_setuptools)" _ m) + (string-append "def guix_skip" m))) + #t)) + (replace 'check + (lambda _ + (let ((cwd (getcwd))) + (setenv "PYTHONPATH" + (string-append cwd "/build/" + (find (cut string-prefix? "lib" <>) + (scandir (string-append cwd "/build"))) + ":" + (getenv "PYTHONPATH"))) + ;; Something is wrong with the PYTHONPATH when running the + ;; tests from the build directory, as it complains about not being + ;; able to import certain modules. + (with-directory-excursion "/tmp" + (invoke "python3" "-m" "numba.runtests" "-v" "-m"))) + #t))))) + (propagated-inputs + `(("python-llvmlite" ,python-llvmlite) + ("python-numpy" ,python-numpy) + ("python-singledispatch" ,python-singledispatch))) + ;; Needed for tests. + (inputs + `(("python-jinja2" ,python-jinja2) + ("python-pygments" ,python-pygments))) + (home-page "https://numba.pydata.org") + (synopsis "Compile Python code using LLVM") + (description "Numba gives you the power to speed up your applications with +high performance functions written directly in Python. With a few +annotations, array-oriented and math-heavy Python code can be just-in-time +compiled to native machine instructions, similar in performance to C, C++ and +Fortran, without having to switch languages or Python interpreters. + +Numba works by generating optimized machine code using the LLVM compiler +infrastructure at import time, runtime, or statically (using the included pycc +tool).") + (license license:bsd-3))) -- 2.18.0 From debbugs-submit-bounces@debbugs.gnu.org Mon Aug 20 12:03:16 2018 Received: (at 32483) by debbugs.gnu.org; 20 Aug 2018 16:03:16 +0000 Received: from localhost ([127.0.0.1]:55781 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1frmeA-0004S4-PA for submit@debbugs.gnu.org; Mon, 20 Aug 2018 12:03:16 -0400 Received: from venus.bbbm.mdc-berlin.de ([141.80.25.30]:52314) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1frme6-0004Rc-Mi for 32483@debbugs.gnu.org; Mon, 20 Aug 2018 12:03:11 -0400 Received: from localhost (localhost [127.0.0.1]) by venus.bbbm.mdc-berlin.de (Postfix) with ESMTP id D7205380572 for <32483@debbugs.gnu.org>; Mon, 20 Aug 2018 18:03:09 +0200 (CEST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=mdc-berlin.de; h= content-type:content-type:mime-version:references:in-reply-to :x-mailer:message-id:date:date:subject:subject:from:from :received:received:received; s=mdc; t=1534780989; x=1536595390; bh=OtPas0OSZeZDHjsTYVTY/XsZrZhokXnqITqYiPzhxw0=; b=X+dlcpVjjyEa 9kCEzM6Z4pA137IZWs6hSpwa/q5ZkRTOGsfdXW0glJa9YuLYTvj3WNz8rzsIOKoc bjbgQK0sQOLIeUY8HkNmcZ5Pu0EZv0TLN7Zpf3QNCVO1HeiWZ3JzVHaMVeuOetHV QawCIpN8mIVIgDLhlQ8ztVmnJ632zTQ= X-Virus-Scanned: amavisd-new at mdc-berlin.de Received: from venus.bbbm.mdc-berlin.de ([127.0.0.1]) by localhost (venus.bbbm.mdc-berlin.de [127.0.0.1]) (amavisd-new, port 10024) with ESMTP id EFl8mUTkZjMx for <32483@debbugs.gnu.org>; Mon, 20 Aug 2018 18:03:09 +0200 (CEST) Received: from SW-IT-P-CAS4.mdc-berlin.net (puck.citx.mdc-berlin.de [141.80.36.101]) (using TLSv1.2 with cipher ECDHE-RSA-AES256-SHA384 (256/256 bits)) (No client certificate requested) by venus.bbbm.mdc-berlin.de (Postfix) with ESMTPS for <32483@debbugs.gnu.org>; Mon, 20 Aug 2018 18:03:09 +0200 (CEST) Received: from localhost (141.80.113.103) by SW-IT-P-CAS4.mdc-berlin.net (141.80.113.59) with Microsoft SMTP Server (TLS) id 14.3.408.0; Mon, 20 Aug 2018 18:03:08 +0200 From: Ricardo Wurmus To: <32483@debbugs.gnu.org> Subject: [PATCH 3/4] gnu: Add python-anndata. Date: Mon, 20 Aug 2018 18:02:51 +0200 Message-ID: <20180820160252.11219-3-ricardo.wurmus@mdc-berlin.de> X-Mailer: git-send-email 2.18.0 In-Reply-To: <20180820160252.11219-1-ricardo.wurmus@mdc-berlin.de> References: <20180820160252.11219-1-ricardo.wurmus@mdc-berlin.de> MIME-Version: 1.0 Content-Type: text/plain X-Originating-IP: [141.80.113.103] X-TM-AS-Product-Ver: SMEX-12.5.0.1300-8.5.1010-24044.000 X-TM-AS-Result: No-4.473600-8.000000-10 X-TMASE-MatchedRID: GOhvqnuss097qToVEfwBPAPZZctd3P4B2NaZtAHkymrJYIv7y0tu9v1o +v3F3AlZdVR7NAThmwa7/LlTYfsWi+o3TaQdFshVnVTWWiNp+v9bAoaK+wS4jUsHGbVW/dGwFIC 2rjcQXCZkTB4k7xrYxcNx5T5AHyX1hPc4FTJN6V6eAiCmPx4NwBnUJ0Ek6yhjxEHRux+uk8jfhP 1xgyx3DOOXpMApVKKspkqw+ISlr0+o05LvKaIU4vd6FvWMPVzOaGnpeJ5AxWDup+sLMhF+DsHsR GWWLKB/Y79ijgM9afgeyWsIkjBBrIISrdkIFqeuO4Y2dUBhL/BTBYT7RGXoWxJAEJH0NuHT9aAn bWsWzHc= X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--4.473600-8.000000 X-TMASE-Version: SMEX-12.5.0.1300-8.5.1010-24044.000 X-Spam-Score: -5.0 (-----) X-Debbugs-Envelope-To: 32483 Cc: Ricardo Wurmus X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -6.0 (------) * gnu/packages/python.scm (python-anndata): New variable. --- gnu/packages/python.scm | 26 ++++++++++++++++++++++++++ 1 file changed, 26 insertions(+) diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index 7f343bdab..2838d2ae5 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -13973,3 +13973,29 @@ Numba works by generating optimized machine code using the LLVM compiler infrastructure at import time, runtime, or statically (using the included pycc tool).") (license license:bsd-3))) + +(define-public python-anndata + (package + (name "python-anndata") + (version "0.6.9") + (source + (origin + (method url-fetch) + (uri (pypi-uri "anndata" version)) + (sha256 + (base32 + "1fh461xyyc7pcrjfgd013bdc2alf53r46ss3gfw3431mbb1gappi")))) + (build-system python-build-system) + (propagated-inputs + `(("python-h5py" ,python-h5py) + ("python-natsort" ,python-natsort) + ("python-pandas" ,python-pandas) + ("python-scipy" ,python-scipy))) + (home-page "https://github.com/theislab/anndata") + (synopsis "Annotated data for data analysis pipelines") + (description "Anndata is a package for simple (functional) high-level APIs +for data analysis pipelines. In this context, it provides an efficient, +scalable way of keeping track of data together with learned annotations and +reduces the code overhead typically encountered when using a mostly +object-oriented library such as @code{scikit-learn}.") + (license license:bsd-3))) -- 2.18.0 From debbugs-submit-bounces@debbugs.gnu.org Mon Aug 20 12:03:18 2018 Received: (at 32483) by debbugs.gnu.org; 20 Aug 2018 16:03:18 +0000 Received: from localhost ([127.0.0.1]:55784 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1frmeE-0004SQ-3U for submit@debbugs.gnu.org; Mon, 20 Aug 2018 12:03:18 -0400 Received: from sinope02.bbbm.mdc-berlin.de ([141.80.25.24]:34374) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1frmeC-0004SC-4c for 32483@debbugs.gnu.org; Mon, 20 Aug 2018 12:03:16 -0400 Received: from localhost (localhost [127.0.0.1]) by sinope02.bbbm.mdc-berlin.de (Postfix) with ESMTP id 728BA1258A5C for <32483@debbugs.gnu.org>; Mon, 20 Aug 2018 18:03:15 +0200 (CEST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=mdc-berlin.de; h= content-type:content-type:mime-version:references:in-reply-to :x-mailer:message-id:date:date:subject:subject:from:from :received:received:received; s=mdc; t=1534780990; x=1536595391; bh=LC85AzRUfHRBDmf4NJGAjLpHQVTjXRI8VKWDzHpMZ38=; b=cjK7H8R6TKJa ViNzZkwQNH43/gOsKgsfuMuMdZ5jWU1ys7NPsHZ67L4Fr/ksjf/+ae7TIAFDh6um CRbTys7iuBAopLTIDD24Qov6k1xm72iaSbt/7BUPvhxxBN3+YklLncKZ4y0OLCCO h1WUST9yMN/qNQ/s4uziIA3ikmwfTlU= X-Virus-Scanned: amavisd-new at mdc-berlin.de Received: from sinope02.bbbm.mdc-berlin.de ([127.0.0.1]) by localhost (sinope02.bbbm.mdc-berlin.de [127.0.0.1]) (amavisd-new, port 10024) with ESMTP id IkEnzVFDDOc3 for <32483@debbugs.gnu.org>; Mon, 20 Aug 2018 18:03:10 +0200 (CEST) Received: from SW-IT-P-CAS4.mdc-berlin.net (puck.citx.mdc-berlin.de [141.80.36.101]) (using TLSv1.2 with cipher ECDHE-RSA-AES256-SHA384 (256/256 bits)) (No client certificate requested) by sinope02.bbbm.mdc-berlin.de (Postfix) with ESMTPS for <32483@debbugs.gnu.org>; Mon, 20 Aug 2018 18:03:10 +0200 (CEST) Received: from localhost (141.80.113.103) by SW-IT-P-CAS4.mdc-berlin.net (141.80.113.59) with Microsoft SMTP Server (TLS) id 14.3.408.0; Mon, 20 Aug 2018 18:03:09 +0200 From: Ricardo Wurmus To: <32483@debbugs.gnu.org> Subject: [PATCH 4/4] gnu: Add python-scanpy. Date: Mon, 20 Aug 2018 18:02:52 +0200 Message-ID: <20180820160252.11219-4-ricardo.wurmus@mdc-berlin.de> X-Mailer: git-send-email 2.18.0 In-Reply-To: <20180820160252.11219-1-ricardo.wurmus@mdc-berlin.de> References: <20180820160252.11219-1-ricardo.wurmus@mdc-berlin.de> MIME-Version: 1.0 Content-Type: text/plain X-Originating-IP: [141.80.113.103] X-TM-AS-Product-Ver: SMEX-12.5.0.1300-8.5.1010-24044.000 X-TM-AS-Result: No-1.533100-8.000000-10 X-TMASE-MatchedRID: UHN19ZU8rvl7qToVEfwBPAPZZctd3P4BrrEvQogcy/EoFW8VuxQzlWmC ti+JzZB1M5WjfvgSIUhQnYSj2WqcBxR+nWctg3+/ngIgpj8eDcCbifj2/J/1cS8z+bJ2nm9UKra uXd3MZDUal568aygjlykUy4HtLOA5MxdaGh8ecar0l6395rVj1pdbNu73Hrb1FGhzNIo9XkBL36 jBsMppDs8ZrP6Pxu06KXo3N5VYEry0kME8iwVzlBvWZa4Q0Lk6pyaqDjQGQtuOKd4yXKlFURjrV 2fDtBTsftwZ3X11IV0= X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--1.533100-8.000000 X-TMASE-Version: SMEX-12.5.0.1300-8.5.1010-24044.000 X-Spam-Score: 0.0 (/) X-Debbugs-Envelope-To: 32483 Cc: Ricardo Wurmus X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -1.0 (-) * gnu/packages/bioinformatics.scm (python-scanpy): New variable. --- gnu/packages/bioinformatics.scm | 36 +++++++++++++++++++++++++++++++++ 1 file changed, 36 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index dce8ab62f..ef9d81435 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -13406,3 +13406,39 @@ conversions, region filtering, FASTA sequence extraction and more.") ;; gffread is under Expat, but gclib is under Artistic 2.0 (license (list license:expat license:artistic2.0))))) + +(define-public python-scanpy + (package + (name "python-scanpy") + (version "1.2.2") + (source + (origin + (method url-fetch) + (uri (pypi-uri "scanpy" version)) + (sha256 + (base32 + "1ak7bxms5a0yvf65prppq2g38clkv7c7jnjbnfpkh3xxv7q512jz")))) + (build-system python-build-system) + (propagated-inputs + `(("python-anndata" ,python-anndata) + ("python-igraph" ,python-igraph) + ("python-numba" ,python-numba) + ("python-joblib" ,python-joblib) + ("python-natsort" ,python-natsort) + ("python-networkx" ,python-networkx) + ("python-statsmodels" ,python-statsmodels) + ("python-scikit-learn" ,python-scikit-learn) + ("python-matplotlib" ,python-matplotlib) + ("python-pandas" ,python-pandas) + ("python-scipy" ,python-scipy) + ("python-seaborn" ,python-seaborn) + ("python-h5py" ,python-h5py) + ("python-tables" ,python-tables))) + (home-page "http://github.com/theislab/scanpy") + (synopsis "Single-Cell Analysis in Python.") + (description "Scanpy is a scalable toolkit for analyzing single-cell gene +expression data. It includes preprocessing, visualization, clustering, +pseudotime and trajectory inference and differential expression testing. The +Python-based implementation efficiently deals with datasets of more than one +million cells.") + (license license:bsd-3))) -- 2.18.0 From debbugs-submit-bounces@debbugs.gnu.org Mon Aug 20 12:15:08 2018 Received: (at 32483) by debbugs.gnu.org; 20 Aug 2018 16:15:08 +0000 Received: from localhost ([127.0.0.1]:55809 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1frmpg-0004lr-4P for submit@debbugs.gnu.org; Mon, 20 Aug 2018 12:15:08 -0400 Received: from venus.bbbm.mdc-berlin.de ([141.80.25.30]:52680) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1frmpe-0004li-OU for 32483@debbugs.gnu.org; Mon, 20 Aug 2018 12:15:07 -0400 Received: from localhost (localhost [127.0.0.1]) by venus.bbbm.mdc-berlin.de (Postfix) with ESMTP id 3B6D1380834 for <32483@debbugs.gnu.org>; Mon, 20 Aug 2018 18:15:06 +0200 (CEST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=mdc-berlin.de; h= content-type:content-type:mime-version:message-id:date:date :in-reply-to:subject:subject:from:from:user-agent:references :received:received:received; s=mdc; t=1534781706; x=1536596107; bh=tvVYQ28vYupVvC6bOViNiURT9eSnsRsxSMXzYc06GNw=; b=k1ppESJQFMw/ v6znFvpQy9WwDxbzdO1TjMuRd+5Yuo41eNNLw9i1oz2OWAN27m3bZUwwdINLTpV+ NWyQL423+fVfKBjMO5BRD7aYy4om/j2aV1XW5QwiHuLKbwOnQppQrg/yBMKPH6Jq NMQj+dEQrigIORbpYUh9QzfOWedMsqE= X-Virus-Scanned: amavisd-new at mdc-berlin.de Received: from venus.bbbm.mdc-berlin.de ([127.0.0.1]) by localhost (venus.bbbm.mdc-berlin.de [127.0.0.1]) (amavisd-new, port 10024) with ESMTP id 0R2nivU3KGAv for <32483@debbugs.gnu.org>; Mon, 20 Aug 2018 18:15:06 +0200 (CEST) Received: from SW-IT-P-CAS4.mdc-berlin.net (puck.citx.mdc-berlin.de [141.80.36.101]) (using TLSv1.2 with cipher ECDHE-RSA-AES256-SHA384 (256/256 bits)) (No client certificate requested) by venus.bbbm.mdc-berlin.de (Postfix) with ESMTPS for <32483@debbugs.gnu.org>; Mon, 20 Aug 2018 18:15:05 +0200 (CEST) Received: from localhost (141.80.113.103) by SW-IT-P-CAS4.mdc-berlin.net (141.80.113.59) with Microsoft SMTP Server (TLS) id 14.3.408.0; Mon, 20 Aug 2018 18:15:05 +0200 References: <20180820155756.10851-1-ricardo.wurmus@mdc-berlin.de> User-agent: mu4e 1.0; emacs 26.1 From: Ricardo Wurmus To: <32483@debbugs.gnu.org> Subject: Re: bug#32483: [PATCH] import: stackage: Support recursive importing. In-Reply-To: X-URL: https://elephly.net X-PGP-Key: https://elephly.net/rekado.pubkey X-PGP-Fingerprint: BCA6 89B6 3655 3801 C3C6 2150 197A 5888 235F ACAC Date: Mon, 20 Aug 2018 18:15:05 +0200 Message-ID: MIME-Version: 1.0 Content-Type: text/plain X-Originating-IP: [141.80.113.103] X-TM-AS-Product-Ver: SMEX-12.5.0.1300-8.5.1010-24044.000 X-TM-AS-Result: No-1.184000-8.000000-10 X-TMASE-MatchedRID: 2yoavFRFKjHxlOJuQNHlfbGj3LN0+Ey9fS0Ip2eEHnwj/1Rbkzl1E+jt 8OidvMO5W5xd15ThVVjdB/CxWTRRu9bFCwAgdKkSmymSGbHVCql/koKH4F39wArS+f2LBwMQnxB A5Nv4gTKzvLSoW3MYNZhZZYVLLwA8KDIJNtpK8WAKEK5kkKD/bnaCdZlHyT7+ftwZ3X11IV0= X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--1.184000-8.000000 X-TMASE-Version: SMEX-12.5.0.1300-8.5.1010-24044.000 X-Spam-Score: -5.0 (-----) X-Debbugs-Envelope-To: 32483 X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -6.0 (------) My apologies for sending a bunch of unrelated patches here! They were supposed to go to a separate bug instead. -- Ricardo From debbugs-submit-bounces@debbugs.gnu.org Thu Aug 23 11:03:15 2018 Received: (at 32483) by debbugs.gnu.org; 23 Aug 2018 15:03:15 +0000 Received: from localhost ([127.0.0.1]:58994 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1fsr8l-0006em-Lq for submit@debbugs.gnu.org; Thu, 23 Aug 2018 11:03:15 -0400 Received: from eggs.gnu.org ([208.118.235.92]:59590) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1fsr8k-0006ea-A3 for 32483@debbugs.gnu.org; Thu, 23 Aug 2018 11:03:14 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1fsr8a-0007JA-Er for 32483@debbugs.gnu.org; Thu, 23 Aug 2018 11:03:09 -0400 X-Spam-Checker-Version: SpamAssassin 3.3.2 (2011-06-06) on eggs.gnu.org X-Spam-Level: X-Spam-Status: No, score=-1.9 required=5.0 tests=BAYES_00 autolearn=disabled version=3.3.2 Received: from fencepost.gnu.org ([2001:4830:134:3::e]:35858) by eggs.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1fsr8a-0007Iy-99; Thu, 23 Aug 2018 11:03:04 -0400 Received: from [193.50.110.186] (port=39738 helo=ribbon) by fencepost.gnu.org with esmtpsa (TLS1.2:RSA_AES_256_CBC_SHA1:256) (Exim 4.82) (envelope-from ) id 1fsr8Z-0007j7-SM; Thu, 23 Aug 2018 11:03:04 -0400 From: ludo@gnu.org (Ludovic =?utf-8?Q?Court=C3=A8s?=) To: Ricardo Wurmus Subject: Re: [bug#32483] [PATCH] import: stackage: Support recursive importing. References: <20180820155756.10851-1-ricardo.wurmus@mdc-berlin.de> X-URL: http://www.fdn.fr/~lcourtes/ X-Revolutionary-Date: 6 Fructidor an 226 de la =?utf-8?Q?R=C3=A9volution?= X-PGP-Key-ID: 0x090B11993D9AEBB5 X-PGP-Key: http://www.fdn.fr/~lcourtes/ludovic.asc X-PGP-Fingerprint: 3CE4 6455 8A84 FDC6 9DB4 0CFB 090B 1199 3D9A EBB5 X-OS: x86_64-pc-linux-gnu Date: Thu, 23 Aug 2018 17:03:02 +0200 In-Reply-To: <20180820155756.10851-1-ricardo.wurmus@mdc-berlin.de> (Ricardo Wurmus's message of "Mon, 20 Aug 2018 17:57:56 +0200") Message-ID: <87y3cxm8gp.fsf@gnu.org> User-Agent: Gnus/5.13 (Gnus v5.13) Emacs/26.1 (gnu/linux) MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable X-detected-operating-system: by eggs.gnu.org: GNU/Linux 2.2.x-3.x [generic] X-Received-From: 2001:4830:134:3::e X-Spam-Score: -5.0 (-----) X-Debbugs-Envelope-To: 32483 Cc: 32483@debbugs.gnu.org X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -6.0 (------) Hello! Ricardo Wurmus skribis: > * guix/import/hackage.scm (hackage-name->package-name): Export procedure. > * guix/import/stackage.scm (lts-info-packages-lts-info): Fix match expres= sion. > (stackage-recursive-import): New procedure. > (stackage->guix-package): Memoize results. > * guix/scripts/import/stackage.scm (show-help, %options, > guix-import-stackage): Support recursive importing. > * doc/guix.texi (Invoking guix import): Document option. Could you add a test for recursive imports, similar to what Oleg did in tests/gem.scm? Or perhaps that=E2=80=99d be redundant since it does little= more than call =E2=80=98recursive-import=E2=80=99 from (guix import utils)? (An= d I realize tests/elpa.scm doesn=E2=80=99t have recursive import tests.) Anyway, apart from that it LGTM. Thanks! Ludo=E2=80=99. From debbugs-submit-bounces@debbugs.gnu.org Thu Sep 13 09:18:28 2018 Received: (at 32483-done) by debbugs.gnu.org; 13 Sep 2018 13:18:28 +0000 Received: from localhost ([127.0.0.1]:38835 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1g0RVs-00034O-3D for submit@debbugs.gnu.org; Thu, 13 Sep 2018 09:18:28 -0400 Received: from sender-of-o51.zoho.com ([135.84.80.216]:21126) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1g0RVq-00034D-El for 32483-done@debbugs.gnu.org; Thu, 13 Sep 2018 09:18:26 -0400 ARC-Seal: i=1; a=rsa-sha256; t=1536844691; cv=none; d=zoho.com; s=zohoarc; b=TkSIurzbTKNUfRHFc4tAB1/XItgWMrP1rvBbdXBZ4d5fTkb/qTIjL+n98ViKSlLpxd6SLtRB9/TgejdlGlN4AAsSwtM2yTgt7CqyarycB4G0aCJ/mF4Grskor0mSsUm1Hy7qC+zuHsHjJa5v+nQVMqdhytl6caFfgBDfQSR3Tf8= ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=zoho.com; s=zohoarc; t=1536844691; h=Content-Type:Content-Transfer-Encoding:Date:From:MIME-Version:Message-ID:Subject:To:ARC-Authentication-Results; bh=8593h83KjU8Jz9depCO3f8AOzSAlcNq9NbvnjzlwcW4=; b=lnANhCzROV5zJ0WWVxr1WbX2IQ3c0eQ6H2SFSWH55iqxbAYJW3toV/LqRUixb5w3sL5SCuY7LjrKpfsHyrI2/LlpoqmewosHhG4a74LvL0FxD1GZAeiXI/hqTnO7MWIUO0GseXbI5NTyfUWg6RMzwjNWjc8tgACBEZjkYFfQuq0= ARC-Authentication-Results: i=1; mx.zoho.com; dkim=pass header.i=elephly.net; spf=pass smtp.mailfrom=rekado@elephly.net; dmarc=pass header.from= header.from= DKIM-Signature: v=1; a=rsa-sha256; q=dns/txt; c=relaxed/relaxed; t=1536844691; s=zoho; d=elephly.net; i=rekado@elephly.net; h=From:To:Subject:Date:Message-ID:MIME-Version:Content-Type:Content-Transfer-Encoding; l=270; bh=8593h83KjU8Jz9depCO3f8AOzSAlcNq9NbvnjzlwcW4=; b=LF4QIDI7McEQOE7YwibvyeFbjXLsFhQmXvNgBOJ47pRi9a4fAhom2/xDaowR/DQg wzfLDVq2kwmvhQO3uMs/wt90g/7+iQPwe4XMSmntu3nVdjP0KlT9IPclBNt8AP0/InZ yAf58llmimqRV+hBjnWLGedqHVnRrNH3YiReytkw= Received: from localhost (141.80.247.166 [141.80.247.166]) by mx.zohomail.com with SMTPS id 1536844691354253.84288614710135; Thu, 13 Sep 2018 06:18:11 -0700 (PDT) User-agent: mu4e 1.0; emacs 26.1 From: Ricardo Wurmus To: 32483-done@debbugs.gnu.org Subject: [PATCH] import: stackage: Support recursive importing. X-URL: https://elephly.net X-PGP-Key: https://elephly.net/rekado.pubkey X-PGP-Fingerprint: BCA6 89B6 3655 3801 C3C6 2150 197A 5888 235F ACAC Date: Thu, 13 Sep 2018 15:18:08 +0200 Message-ID: <87va79ilin.fsf@elephly.net> MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable X-ZohoMailClient: External X-Spam-Score: 0.0 (/) X-Debbugs-Envelope-To: 32483-done X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -1.0 (-) Thanks for the review. I chose not to add a test for the recursive option because that behaviour is implemented independent of the stackage importer. Pushed to =E2=80=9Cmaster=E2=80=9D branch with commit a3ece51a29241c7060323cbbfc602c83200ffe4a. -- Ricardo From unknown Tue Sep 09 22:27:51 2025 Received: (at fakecontrol) by fakecontrolmessage; To: internal_control@debbugs.gnu.org From: Debbugs Internal Request Subject: Internal Control Message-Id: bug archived. Date: Fri, 12 Oct 2018 11:24:06 +0000 User-Agent: Fakemail v42.6.9 # This is a fake control message. # # The action: # bug archived. thanks # This fakemail brought to you by your local debbugs # administrator