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Resent-From: Greg Hogan Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Tue, 12 Oct 2021 13:30:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 50813 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: Felix Gruber Cc: Ludovic =?UTF-8?Q?Court=C3=A8s?= , 50813@debbugs.gnu.org Received: via spool by 50813-submit@debbugs.gnu.org id=B50813.163404538024108 (code B ref 50813); Tue, 12 Oct 2021 13:30:02 +0000 Received: (at 50813) by debbugs.gnu.org; 12 Oct 2021 13:29:40 +0000 Received: from localhost ([127.0.0.1]:38834 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1maHqd-0006Gh-83 for submit@debbugs.gnu.org; Tue, 12 Oct 2021 09:29:39 -0400 Received: from mail-io1-f41.google.com ([209.85.166.41]:46004) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1maHpa-00069q-C1 for 50813@debbugs.gnu.org; Tue, 12 Oct 2021 09:28:43 -0400 Received: by mail-io1-f41.google.com with SMTP id b10so8756478iof.12 for <50813@debbugs.gnu.org>; 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Tue, 12 Oct 2021 06:28:28 -0700 (PDT) MIME-Version: 1.0 References: <87zgrldwzk.fsf@gnu.org> <20211010150434.1966-1-felgru@posteo.net> In-Reply-To: <20211010150434.1966-1-felgru@posteo.net> From: Greg Hogan Date: Tue, 12 Oct 2021 09:28:18 -0400 Message-ID: Content-Type: multipart/alternative; boundary="0000000000002c9f2305ce27d24f" X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list X-BeenThere: guix-patches@gnu.org List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: guix-patches-bounces+larch=yhetil.org@gnu.org Sender: "Guix-patches" X-Migadu-Flow: FLOW_IN ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=yhetil.org; s=key1; t=1634045466; h=from:from:sender:sender:reply-to:subject:subject:date:date: message-id:message-id:to:to:cc:cc:mime-version:mime-version: content-type:content-type:resent-cc:resent-from:resent-sender: resent-message-id:in-reply-to:in-reply-to:references:references: list-id:list-help:list-unsubscribe:list-subscribe:list-post: dkim-signature; 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dmarc=none; spf=pass (aspmx1.migadu.com: domain of guix-patches-bounces@gnu.org designates 209.51.188.17 as permitted sender) smtp.mailfrom=guix-patches-bounces@gnu.org X-Migadu-Spam-Score: -1.42 Authentication-Results: aspmx1.migadu.com; dkim=fail ("headers rsa verify failed") header.d=greghogan-com.20210112.gappssmtp.com header.s=20210112 header.b=IyLWNAKq; dmarc=none; spf=pass (aspmx1.migadu.com: domain of guix-patches-bounces@gnu.org designates 209.51.188.17 as permitted sender) smtp.mailfrom=guix-patches-bounces@gnu.org X-Migadu-Queue-Id: 15E522F899 X-Spam-Score: -1.42 X-Migadu-Scanner: scn0.migadu.com X-TUID: 32WWUBfgxTTN --0000000000002c9f2305ce27d24f Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: quoted-printable #48703 was an attempt in May to update numpy, scipy, and pandas. If and when this patchset is accepted first I can then update #48703 for the more recent numpy and scipy releases. On Sun, Oct 10, 2021 at 11:06 AM Felix Gruber wrote: > Hi Ludo=E2=80=99, > > On 10/7/21 11:07 AM, Ludovic Court=C3=A8s wrote: > > > > Felix Gruber skribis: > > > >> * gnu/packages/python-science.scm (python-pandas): Update to 1.3.3. > > > > The upgrade appears to cause build failures for python-dask and > > pigx-rnaseq (via snakemake) among other things. > > > > Could you take a look? > > I could not reproduce the build failure in pigx-rnaseq. For python-dask > the build failure could be fixed by upgrading it to 2021.9.1, whose > changelog mentioned that they've deactivated a failing test when > building against Pandas >=3D 1.3.3. After updating dask, its dependent > packages python-distributed and python-eliot failed to build. I've > fixed both by updating them to their latest releases and disabling > failing tests. > I've also took the oppurtunity to update the synapse package which was > the only package depending on python-eliot. > > > For the record, I tried to build everything reported by =E2=80=98guix r= efresh -l > > python-pandas=E2=80=99 though some of them (ocaml4.07-re, etc.) would a= lready > > fail to build before the upgrade. > > Of the remaining packages reported by `guix refresh -l python-pandas`, > I've identified the following packages with build failures: > > * clipper@2.0 > sometimes fails due to nondeterministic test > `test_get_FDR_cutoff_mean`. The docstring of this test already says > "Difficult to test because of random sampling" followed by a TODO. > I've thus deactivated this test, to make it build deterministically. > * pplacer@1.1.alpha19 > already failed on master due to unbuildable ocaml4.07-re@1.10.3. > * python-scikit-rebate@0.6 > Already failed on master in test `skrebate`: > ModuleNotFoundError: No module named 'sklearn.externals.joblib' > (A guix refresh -u python-scikit-rebate would update it to 0.62 which > was buildable, but this version seemed to come without any tests, so > I'm not sure if this is the right solution.) > * orange@3.28.0 > Already failed to build on mater, because its dependency > python-orange-canvas-core. > I've looked into updating both to their latest version, but that > would require updating python-pygments to >=3D 2.8.0 which would entail > rebuilding 561 dependent packages. > * imp@2.13.0 > I was running out of memory while building imp, which in the end > killed the build process. It seems that my 8GB of RAM are not > sufficient to build imp, so I cannot tell if the update of > python-pandas might break imp. > * tadbit@1.0.1 > depends on imp, so I couldn't build it either. > > I've prepared patches for those packages that I was able to fix. > > Best, > Felix > > Felix Gruber (6): > gnu: python-pandas: Update to 1.3.3. > gnu: python-dask: Update to 2021.9.1. > gnu: python-distributed: Update to 2021.09.1. > gnu: python-eliot: Update to 1.13.0. > gnu: synapse: Update to 1.44.0. > gnu: clipper: Disable non-deterministic test. > > gnu/packages/bioinformatics.scm | 9 ++++++++- > gnu/packages/matrix.scm | 5 +++-- > gnu/packages/python-science.scm | 15 +++++++++------ > gnu/packages/python-xyz.scm | 19 +++++++++++++++---- > 4 files changed, 35 insertions(+), 13 deletions(-) > > -- > 2.30.2 > > > > > --0000000000002c9f2305ce27d24f Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
#48703 was an attempt in May to update numpy, scipy, and p= andas. If and when this patchset is accepted first I can then update #48703= for the more recent numpy and scipy releases.

On Sun, Oct 10, 2021 at 11:06= AM Felix Gruber <felgru@posteo.net= > wrote:
= Hi Ludo=E2=80=99,

On 10/7/21 11:07 AM, Ludovic Court=C3=A8s wrote:
>
> Felix Gruber <felgru@posteo.net> skribis:
>
>> * gnu/packages/python-science.scm (python-pandas): Update to 1.3.3= .
>
> The upgrade appears to cause build failures for python-dask and
> pigx-rnaseq (via snakemake) among other things.
>
> Could you take a look?

I could not reproduce the build failure in pigx-rnaseq. For python-dask
the build failure could be fixed by upgrading it to 2021.9.1, whose
changelog mentioned that they've deactivated a failing test when
building against Pandas >=3D 1.3.3. After updating dask, its dependent packages python-distributed and python-eliot failed to build.=C2=A0 I'v= e
fixed both by updating them to their latest releases and disabling
failing tests.
I've also took the oppurtunity to update the synapse package which was<= br> the only package depending on python-eliot.

> For the record, I tried to build everything reported by =E2=80=98guix = refresh -l
> python-pandas=E2=80=99 though some of them (ocaml4.07-re, etc.) would = already
> fail to build before the upgrade.

Of the remaining packages reported by `guix refresh -l python-pandas`,
I've identified the following packages with build failures:

* clipper@2.0
=C2=A0 sometimes fails due to nondeterministic test
=C2=A0 `test_get_FDR_cutoff_mean`.=C2=A0 The docstring of this test already= says
=C2=A0 "Difficult to test because of random sampling" followed by= a TODO.
=C2=A0 I've thus deactivated this test, to make it build deterministica= lly.
* pplacer@1.1.alpha19
=C2=A0 already failed on master due to unbuildable ocaml4.07-re@1.10.3.
* python-scikit-rebate@0.6
=C2=A0 Already failed on master in test `skrebate`:
=C2=A0 ModuleNotFoundError: No module named 'sklearn.externals.joblib&#= 39;
=C2=A0 (A guix refresh -u python-scikit-rebate would update it to 0.62 whic= h
=C2=A0 =C2=A0was buildable, but this version seemed to come without any tes= ts, so
=C2=A0 =C2=A0I'm not sure if this is the right solution.)
* orange@3.28.0
=C2=A0 Already failed to build on mater, because its dependency
=C2=A0 python-orange-canvas-core.
=C2=A0 I've looked into updating both to their latest version, but that=
=C2=A0 would require updating python-pygments to >=3D 2.8.0 which would = entail
=C2=A0 rebuilding 561 dependent packages.
* imp@2.13.0
=C2=A0 I was running out of memory while building imp, which in the end
=C2=A0 killed the build process. It seems that my 8GB of RAM are not
=C2=A0 sufficient to build imp, so I cannot tell if the update of
=C2=A0 python-pandas might break imp.
* tadbit@1.0.1
=C2=A0 depends on imp, so I couldn't build it either.

I've prepared patches for those packages that I was able to fix.

Best,
Felix

Felix Gruber (6):
=C2=A0 gnu: python-pandas: Update to 1.3.3.
=C2=A0 gnu: python-dask: Update to 2021.9.1.
=C2=A0 gnu: python-distributed: Update to 2021.09.1.
=C2=A0 gnu: python-eliot: Update to 1.13.0.
=C2=A0 gnu: synapse: Update to 1.44.0.
=C2=A0 gnu: clipper: Disable non-deterministic test.

=C2=A0gnu/packages/bioinformatics.scm |=C2=A0 9 ++++++++-
=C2=A0gnu/packages/matrix.scm=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0|=C2=A0 5 ++= +--
=C2=A0gnu/packages/python-science.scm | 15 +++++++++------
=C2=A0gnu/packages/python-xyz.scm=C2=A0 =C2=A0 =C2=A0| 19 +++++++++++++++--= --
=C2=A04 files changed, 35 insertions(+), 13 deletions(-)

--
2.30.2




--0000000000002c9f2305ce27d24f--