From mboxrd@z Thu Jan 1 00:00:00 1970 Received: from eggs.gnu.org ([2001:4830:134:3::10]:53391) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1cvsKY-0006Cz-Ov for guix-patches@gnu.org; Wed, 05 Apr 2017 17:19:08 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1cvsKU-0001Xm-CD for guix-patches@gnu.org; Wed, 05 Apr 2017 17:19:06 -0400 Received: from debbugs.gnu.org ([208.118.235.43]:35901) by eggs.gnu.org with esmtps (TLS1.0:RSA_AES_128_CBC_SHA1:16) (Exim 4.71) (envelope-from ) id 1cvsKU-0001Xh-89 for guix-patches@gnu.org; Wed, 05 Apr 2017 17:19:02 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1cvsKT-0002di-W8 for guix-patches@gnu.org; Wed, 05 Apr 2017 17:19:02 -0400 Subject: bug#26150: [PATCH 0/15]: Add pplacer and OCaml dependencies. Resent-Message-ID: From: ludo@gnu.org (Ludovic =?UTF-8?Q?Court=C3=A8s?=) References: <9e1d5f35-c6dc-e55f-dbb2-2649ba5843df@uq.edu.au> <87wpczatcg.fsf@gnu.org> <5c839114-e4d6-41b2-5b18-fd4d459d56e6@uq.edu.au> <87mvcyzrxl.fsf@gnu.org> Date: Wed, 05 Apr 2017 23:18:12 +0200 In-Reply-To: (Ben Woodcroft's message of "Sat, 18 Mar 2017 10:36:31 +1000") Message-ID: <87zifulfjf.fsf@gnu.org> MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: guix-patches-bounces+kyle=kyleam.com@gnu.org Sender: "Guix-patches" To: Ben Woodcroft Cc: 26150@debbugs.gnu.org Hi Ben, Ben Woodcroft skribis: > On 06/03/17 19:16, Ludovic Court=C3=A8s wrote: [...] >> To make progress, how about applying the non-4.01-specific parts of the >> patch series first (I think you didn=E2=80=99t get any feedback on these= , so >> it=E2=80=99s safe to assume they=E2=80=99re OK if =E2=80=98guix lint=E2= =80=99 has nothing to say)? >> >> Second, could you submit the bits about supporting 4.01 to guix-patches? >> I=E2=80=99ll take a look if nobody beats me at it. > OK. I've pushed the non-4.01-specific parts to master, and attached > here a modified patch series which contains the rest. There's 15 steps > but most are quite trivial. [...] >>>From 1e39824159fe0a43276c810fb514f56761fb8dcd Mon Sep 17 00:00:00 2001 > From: Ben Woodcroft > Date: Mon, 2 Jan 2017 17:18:59 +1000 > Subject: [PATCH 01/15] gnu: Add ocaml-4.01. > > * gnu/packages/ocaml.scm (ocaml-4.01): New variable. OK. >>>From 6acdb4749edfeeb8a8fac3b6df75eeebad9c42cd Mon Sep 17 00:00:00 2001 > From: Ben Woodcroft > Date: Mon, 2 Jan 2017 22:29:28 +1000 > Subject: [PATCH 02/15] gnu: Add ocaml4.01-findlib. > > * gnu/packages/ocaml.scm (ocaml4.01-findlib): New variable. OK. >>>From ec75318098c99f57bb7f769c7989e929cc3fa380 Mon Sep 17 00:00:00 2001 > From: Ben Woodcroft > Date: Mon, 2 Jan 2017 22:23:34 +1000 > Subject: [PATCH 03/15] build-system: Add package-with-ocaml4.01. > > * guix/build-system/ocaml.scm (default-ocaml4.01, default-ocaml4.01-findl= ib, > package-with-explicit-ocaml, package-with-ocaml4.01, > strip-ocaml4.01-variant): New variables. [...] > +(define package-with-ocaml4.01 > + (package-with-explicit-ocaml (delay (default-ocaml4.01)) > + (delay (default-ocaml4.01-findlib)) > + "ocaml-" "ocaml4.01-" > + #:variant-property 'ocaml4.01-variant)) I choked for a few hours on this one, my main problem being that I didn=E2=80=99t want us to duplicate the logic from build-system/python.scm. This led to commits f37f2b83fa95c1fe2bf01c4b8072cfc23d4c67ec and 1618006d0bc9bfdc63f4d199fd980f29ecc78ec4. Is the =E2=80=9Cvariant=E2=80=9D property really needed? In Python it=E2= =80=99s needed because the 2.x variants sometimes need a different set of dependencies that =E2=80=98package-with-python2=E2=80=99 cannot automatically guess. Convers= ely, =E2=80=98package-with-guile-2.0=E2=80=99 has no need for that. If the variant is not needed, then I recommend using =E2=80=98package-with-input-rewriting=E2=80=99. If the variant is needed, then could you use =E2=80=98package-mapping=E2=80= =99 as in 1618006d0bc9bfdc63f4d199fd980f29ecc78ec4? >>>From 6b98a10a41179654788f49f9eb837fff0f94de65 Mon Sep 17 00:00:00 2001 > From: Ben Woodcroft > Date: Sat, 18 Mar 2017 08:59:01 +1000 > Subject: [PATCH 04/15] gnu: Add ocaml4.01-bisect. > > * gnu/packages/ocaml.scm (ocaml4.01-bisect): New variable. > (ocaml-bisect)[properties]: New field. [...] > +(define-public ocaml4.01-bisect > + (let ((base (package-with-ocaml4.01 (strip-ocaml4.01-variant ocaml-bis= ect)))) > + (package > + (inherit base) > + (arguments > + `(#:ocaml ,ocaml-4.01 > + ,@(strip-keyword-arguments '(#:make-flags) (package-arguments b= ase)))) > + (native-inputs `(,@(alist-delete "camlp4" (package-native-inputs b= ase)))) > + (propagated-inputs > + `(,@(alist-delete "camlp4" (package-propagated-inputs base))))))) Could you add comments explaining why camlp4 needs to be propagated and why #:make-flags is removed? >>>From e9deb37a918beba30fb3ce3c1f39f14dba28f6d4 Mon Sep 17 00:00:00 2001 > From: Ben Woodcroft > Date: Sat, 18 Mar 2017 07:10:55 +1000 > Subject: [PATCH 05/15] gnu: Add ocaml4.01-sqlite3. > > * gnu/packages/ocaml.scm: (ocaml4.01-sqlite3): New variable. > (ocaml-sqlite3)[properties]: New field. OK. >>>From 6861038410dee1ea663a5129d84f10a6f1cd6227 Mon Sep 17 00:00:00 2001 > From: Ben Woodcroft > Date: Sat, 18 Mar 2017 07:14:17 +1000 > Subject: [PATCH 06/15] gnu: Add ocaml4.01-csv. > > * gnu/packages/ocaml.scm (ocaml4.01-csv): New variable. > (ocaml-csv)[properties]: New field. OK. >>>From a64bee2e8d248cb227801a0b915df06530d657e0 Mon Sep 17 00:00:00 2001 > From: Ben Woodcroft > Date: Sat, 18 Mar 2017 07:15:58 +1000 > Subject: [PATCH 07/15] gnu: Add ocaml4.01-gsl. > > * gnu/packages/maths.scm (ocaml4.01-gsl): New variable. > (ocaml-gsl)[properties]: New field. OK. >>>From 7c0aaffa5e556e46a9a61319714e43f93cc808d4 Mon Sep 17 00:00:00 2001 > From: Ben Woodcroft > Date: Sat, 18 Mar 2017 07:17:07 +1000 > Subject: [PATCH 08/15] gnu: Add ocaml4.01-mcl. > > * gnu/packages/machine-learning.scm (ocaml4.01-mcl): New variable. > (ocaml-mcl)[properties]: New field. OK. >>>From 2d132b3c0d0604992dc5176cb5304978c06ed007 Mon Sep 17 00:00:00 2001 > From: Ben Woodcroft > Date: Fri, 6 Jan 2017 22:15:12 +1000 > Subject: [PATCH 09/15] gnu: Add ocaml4.01-camlzip. > > * gnu/packages/ocaml.scm (ocaml4.01-camlzip): New variable. OK. >>>From 9902aa5db83ee2b0879f4f350f7e827607b21cfd Mon Sep 17 00:00:00 2001 > From: Ben Woodcroft > Date: Fri, 6 Jan 2017 22:17:34 +1000 > Subject: [PATCH 10/15] gnu: Add ocaml4.01-qtest. > > * gnu/packages/ocaml.scm (ocaml4.01-qtest): New variable. > (ocaml-qtest)[properties]: New field. OK. >>>From 6d3b0543c22323944f13d5ca7c7233b94828a144 Mon Sep 17 00:00:00 2001 > From: Ben Woodcroft > Date: Fri, 6 Jan 2017 22:34:01 +1000 > Subject: [PATCH 11/15] gnu: Add ocaml4.01-ounit. > > * gnu/packages/ocaml.scm (ocaml4.01-ounit): New variable. > (ocaml-ounit)[properties]: New field. OK. >>>From f907957a0243c43dfe9c0c29400545b115ec92f8 Mon Sep 17 00:00:00 2001 > From: Ben Woodcroft > Date: Sat, 4 Feb 2017 12:15:39 +1000 > Subject: [PATCH 12/15] gnu: Add ocaml4.01-xmlm. > > * gnu/packages/ocaml.scm (ocaml4.01-xmlm): New variable. > (ocaml-xmlm)[properties]: New field. OK. >>>From 38c70285408cf1fd3c0d571df6b8e35abcc63236 Mon Sep 17 00:00:00 2001 > From: Ben Woodcroft > Date: Sat, 4 Feb 2017 12:16:50 +1000 > Subject: [PATCH 13/15] gnu: Add ocaml4.01-batteries. > > * gnu/packages/ocaml.scm (ocaml4.01-batteries): New variable. > (ocaml-batteries)[properties]: New field. OK. >>>From 0253fdf1f723a8029f6e2511bfcad6543394b00a Mon Sep 17 00:00:00 2001 > From: Ben Woodcroft > Date: Sat, 4 Feb 2017 15:23:45 +1000 > Subject: [PATCH 14/15] gnu: Add taxtastic. > > * gnu/packages/bioinformatics.scm (taxtastic): New variable. OK. >>>From 3d4e5e2e73067c5968e38abd1fe0e88204d6d9f8 Mon Sep 17 00:00:00 2001 > From: Ben Woodcroft > Date: Sat, 4 Feb 2017 15:25:29 +1000 > Subject: [PATCH 15/15] gnu: Add pplacer. > > * gnu/packages/bioinformatics.scm (pplacer, pplacer-scripts): New > variables. [...] > + (home-page "http://matsen.fhcrc.org/pplacer") > + (license license:gpl3)))) Version 3 only? > +;; This package is installed alongside 'pplacer'. It is a separate pack= age so > +;; that it can use the python-build-system for the scripts that are > +;; distributed alongside the main OCaml binaries. > +(define pplacer-scripts > + (package > + (inherit pplacer) > + (name "pplacer-scripts") Maybe add a different synopsis? Apologies for taking so long! Thanks, Ludo=E2=80=99.