GNU bug report logs - #50813
[PATCH] gnu: python-pandas: Update to 1.3.3.

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Message #5 received at submit <at> debbugs.gnu.org (full text, mbox):

From: Felix Gruber <felgru <at> posteo.net>
To: guix-patches <at> gnu.org
Cc: Felix Gruber <felgru <at> posteo.net>
Subject: [PATCH] gnu: python-pandas: Update to 1.3.3.
Date: Sun, 26 Sep 2021 09:47:03 +0000

* gnu/packages/python-science.scm (python-pandas): Update to 1.3.3.
---
 gnu/packages/python-science.scm | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/python-science.scm b/gnu/packages/python-science.scm
index 738b504e3b..676ad00f5e 100644
--- a/gnu/packages/python-science.scm
+++ b/gnu/packages/python-science.scm
@@ -14,6 +14,7 @@
 ;;; Copyright © 2021 Roel Janssen <roel <at> gnu.org>
 ;;; Copyright © 2021 Paul Garlick <pgarlick <at> tourbillion-technology.com>
 ;;; Copyright © 2021 Arun Isaac <arunisaac <at> systemreboot.net>
+;;; Copyright © 2021 Felix Gruber <felgru <at> posteo.net>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -329,13 +330,13 @@ of the SGP4 satellite tracking algorithm.")
 (define-public python-pandas
   (package
     (name "python-pandas")
-    (version "1.3.0")
+    (version "1.3.3")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "pandas" version))
        (sha256
-        (base32 "1qi2cv450m05dwccx3p1s373k5b4ncvwi74plnms2pidrz4ycm65"))))
+        (base32 "1pq1nwj2kysy2g3p18wjb1xn8vk1jhcyisxilsnkwyd99aqqqb17"))))
     (build-system python-build-system)
     (arguments
      `(#:modules ((guix build utils)
-- 
2.30.2

Message #8 received at 50813 <at> debbugs.gnu.org (full text, mbox):

From: Ludovic Courtès <ludo <at> gnu.org>
To: Felix Gruber <felgru <at> posteo.net>
Cc: 50813 <at> debbugs.gnu.org
Subject: Re: bug#50813: [PATCH] gnu: python-pandas: Update to 1.3.3.
Date: Thu, 07 Oct 2021 11:07:11 +0200

Hi Felix,

Felix Gruber <felgru <at> 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?

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

Thanks in advance!

Ludo’.

Message #11 received at 50813 <at> debbugs.gnu.org (full text, mbox):

From: Felix Gruber <felgru <at> posteo.net>
To: 50813 <at> debbugs.gnu.org,
	Ludovic Courtès <ludo <at> gnu.org>
Cc: Felix Gruber <felgru <at> posteo.net>
Subject: [PATCH v2 0/6] gnu: python-pandas: Update to 1.3.3.
Date: Sun, 10 Oct 2021 15:04:28 +0000

Hi Ludo’,

On 10/7/21 11:07 AM, Ludovic Courtès wrote:
> 
> Felix Gruber <felgru <at> 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 >= 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 ‘guix refresh -l
> python-pandas’ 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 <at> 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 <at> 1.1.alpha19
  already failed on master due to unbuildable ocaml4.07-re <at> 1.10.3.
* python-scikit-rebate <at> 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 <at> 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 >= 2.8.0 which would entail
  rebuilding 561 dependent packages.
* imp <at> 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 <at> 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

Message #14 received at 50813 <at> debbugs.gnu.org (full text, mbox):

From: Felix Gruber <felgru <at> posteo.net>
To: 50813 <at> debbugs.gnu.org,
	Ludovic Courtès <ludo <at> gnu.org>
Cc: Felix Gruber <felgru <at> posteo.net>
Subject: [PATCH v2 1/6] gnu: python-pandas: Update to 1.3.3.
Date: Sun, 10 Oct 2021 15:04:29 +0000

* gnu/packages/python-science.scm (python-pandas): Update to 1.3.3.
---
 gnu/packages/python-science.scm | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/python-science.scm b/gnu/packages/python-science.scm
index cc6a759e82..d19d731f76 100644
--- a/gnu/packages/python-science.scm
+++ b/gnu/packages/python-science.scm
@@ -14,6 +14,7 @@
 ;;; Copyright © 2021 Roel Janssen <roel <at> gnu.org>
 ;;; Copyright © 2021 Paul Garlick <pgarlick <at> tourbillion-technology.com>
 ;;; Copyright © 2021 Arun Isaac <arunisaac <at> systemreboot.net>
+;;; Copyright © 2021 Felix Gruber <felgru <at> posteo.net>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -329,13 +330,13 @@ of the SGP4 satellite tracking algorithm.")
 (define-public python-pandas
   (package
     (name "python-pandas")
-    (version "1.3.0")
+    (version "1.3.3")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "pandas" version))
        (sha256
-        (base32 "1qi2cv450m05dwccx3p1s373k5b4ncvwi74plnms2pidrz4ycm65"))))
+        (base32 "1pq1nwj2kysy2g3p18wjb1xn8vk1jhcyisxilsnkwyd99aqqqb17"))))
     (build-system python-build-system)
     (arguments
      `(#:modules ((guix build utils)
-- 
2.30.2

Message #17 received at 50813 <at> debbugs.gnu.org (full text, mbox):

From: Felix Gruber <felgru <at> posteo.net>
To: 50813 <at> debbugs.gnu.org,
	Ludovic Courtès <ludo <at> gnu.org>
Cc: Felix Gruber <felgru <at> posteo.net>
Subject: [PATCH v2 2/6] gnu: python-dask: Update to 2021.9.1.
Date: Sun, 10 Oct 2021 15:04:30 +0000

* gnu/packages/python-xyz.scm (python-dask): Update to 2021.9.1.
---
 gnu/packages/python-xyz.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index 634cd5efec..b1678b2bda 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -22196,13 +22196,13 @@ decisions with any given backend.")
 (define-public python-dask
   (package
     (name "python-dask")
-    (version "2021.7.1")
+    (version "2021.9.1")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "dask" version))
        (sha256
-        (base32 "131c1bp193d7wp4gx09j6wark1c322c8sqjy22i0jaafl5rqfbz7"))))
+        (base32 "0p6nd8wi30l29g5hdwk0453w6fxg4zvxq1y1ix0fa2f8rbr2n7z1"))))
     (build-system python-build-system)
     (arguments
      `(#:phases
-- 
2.30.2

Message #20 received at 50813 <at> debbugs.gnu.org (full text, mbox):

From: Felix Gruber <felgru <at> posteo.net>
To: 50813 <at> debbugs.gnu.org,
	Ludovic Courtès <ludo <at> gnu.org>
Cc: Felix Gruber <felgru <at> posteo.net>
Subject: [PATCH v2 3/6] gnu: python-distributed: Update to 2021.09.1.
Date: Sun, 10 Oct 2021 15:04:31 +0000

* gnu/packages/python-science.scm (python-distributed): Update to
  2021.09.1.
  [arguments]: Disable failing test test_text.
---
 gnu/packages/python-science.scm | 10 ++++++----
 1 file changed, 6 insertions(+), 4 deletions(-)

diff --git a/gnu/packages/python-science.scm b/gnu/packages/python-science.scm
index d19d731f76..b68a2838fc 100644
--- a/gnu/packages/python-science.scm
+++ b/gnu/packages/python-science.scm
@@ -900,7 +900,7 @@ and more
 (define-public python-distributed
   (package
     (name "python-distributed")
-    (version "2021.07.1")
+    (version "2021.09.1")
     (source
      (origin
        ;; The test files are not included in the archive on pypi
@@ -911,7 +911,7 @@ and more
        (file-name (git-file-name name version))
        (sha256
         (base32
-         "0i55zf3k55sqjxnwlzsyj3h3v1588fn54ng4mj3dfiqzh3nlj0dg"))))
+         "05djzza3f72nw1i1c9qyamgaf93pbf6jxx0migpp1wvvfl0v2j9z"))))
     (build-system python-build-system)
     (arguments
      '(#:phases
@@ -940,9 +940,11 @@ and more
                        "-m" "not slow and not gpu and not ipython and not avoid_ci"
                        "-k"
                        ;; TODO: These tests fail for unknown reasons:
-                       ;; Assertion error.
                        (string-append
-                        "not test_version_option"
+                        ;; TimeoutExpired
+                        "not test_text"
+                        ;; AssertionError
+                        " and not test_version_option"
                         ;; "The 'distributed' distribution was not found"
                         " and not test_register_backend_entrypoint"
                         ;; "AttributeError: module 'distributed.dashboard' has no attribute 'scheduler'"
-- 
2.30.2

Message #23 received at 50813 <at> debbugs.gnu.org (full text, mbox):

From: Felix Gruber <felgru <at> posteo.net>
To: 50813 <at> debbugs.gnu.org,
	Ludovic Courtès <ludo <at> gnu.org>
Cc: Felix Gruber <felgru <at> posteo.net>
Subject: [PATCH v2 4/6] gnu: python-eliot: Update to 1.13.0.
Date: Sun, 10 Oct 2021 15:04:32 +0000

* gnu/packages/python-xyz.scm (python-eliot): Update to 1.13.0.
  [arguments] Disable failing tests test_omitLoggerFromActionType and
  test_logCallsDefaultLoggerWrite.
---
 gnu/packages/python-xyz.scm | 15 +++++++++++++--
 1 file changed, 13 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index b1678b2bda..db7bfc9108 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -108,6 +108,7 @@
 ;;; Copyright © 2021 Simon Streit <simon <at> netpanic.org>
 ;;; Copyright © 2021 Daniel Meißner <daniel.meissner-i4k <at> ruhr-uni-bochum.de>
 ;;; Copyright © 2021 Pradana Aumars <paumars <at> courrier.dev>
+;;; Copyright © 2021 Felix Gruber <felgru <at> posteo.net>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -24776,13 +24777,13 @@ tbutils
 (define-public python-eliot
   (package
     (name "python-eliot")
-    (version "1.12.0")
+    (version "1.13.0")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "eliot" version))
        (sha256
-        (base32 "0wabv7hk63l12881f4zw02mmj06583qsx2im0yywdjlj8f56vqdn"))))
+        (base32 "1xzzhsjrrw430dc84vamf683bwp9i0nr86xf2iav6yla615ijq2p"))))
     (build-system python-build-system)
     (arguments
      `(#:phases
@@ -24798,6 +24799,16 @@ tbutils
            ;; be installed and these tests should pass.
            (lambda _
              (delete-file "eliot/tests/test_prettyprint.py")
+             #t))
+         (add-after 'remove-eliot-prettyprint-tests 'remove-failing-tests
+           (lambda _
+             ;; These tests started to fail after updating python-pandas to
+             ;; 1.3.3 and python-dask to 2021.9.1.
+             (substitute* "eliot/tests/test_validation.py"
+               (("test_omitLoggerFromActionType")
+                "_test_omitLoggerFromActionType")
+               (("test_logCallsDefaultLoggerWrite")
+                "_test_logCallsDefaultLoggerWrite"))
              #t)))))
     (propagated-inputs
      `(("python-boltons" ,python-boltons)
-- 
2.30.2

Message #26 received at 50813 <at> debbugs.gnu.org (full text, mbox):

From: Felix Gruber <felgru <at> posteo.net>
To: 50813 <at> debbugs.gnu.org,
	Ludovic Courtès <ludo <at> gnu.org>
Cc: Felix Gruber <felgru <at> posteo.net>
Subject: [PATCH v2 5/6] gnu: synapse: Update to 1.44.0.
Date: Sun, 10 Oct 2021 15:04:33 +0000

* gnu/packages/matrix.scm (synapse): Update to 1.44.0.
---
 gnu/packages/matrix.scm | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/matrix.scm b/gnu/packages/matrix.scm
index 5c2b194d07..e6b0b99630 100644
--- a/gnu/packages/matrix.scm
+++ b/gnu/packages/matrix.scm
@@ -3,6 +3,7 @@
 ;;; Copyright © 2020 Tobias Geerinckx-Rice <me <at> tobias.gr>
 ;;; Copyright © 2020, 2021 Michael Rohleder <mike <at> rohleder.de>
 ;;; Copyright © 2020 Giacomo Leidi <goodoldpaul <at> autistici.org>
+;;; Copyright © 2021 Felix Gruber <felgru <at> posteo.net>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -86,13 +87,13 @@ an LDAP server.")
 (define-public synapse
   (package
     (name "synapse")
-    (version "1.29.0")
+    (version "1.44.0")
     (source (origin
               (method url-fetch)
               (uri (pypi-uri "matrix-synapse" version))
               (sha256
                (base32
-                "0if2yhpz8psg0661401mvxznldbfhk2j9rhbs25jdaqm9jsv6907"))))
+                "1lgi1a4ksz4z78yb84bi29x4y080bx1dadib2wznvmwsfif0azx0"))))
     (build-system python-build-system)
     ;; TODO Run tests with ‘PYTHONPATH=. trial3 tests’.
     (propagated-inputs
-- 
2.30.2

Message #29 received at 50813 <at> debbugs.gnu.org (full text, mbox):

From: Felix Gruber <felgru <at> posteo.net>
To: 50813 <at> debbugs.gnu.org,
	Ludovic Courtès <ludo <at> gnu.org>
Cc: Felix Gruber <felgru <at> posteo.net>
Subject: [PATCH v2 6/6] gnu: clipper: Disable non-deterministic test.
Date: Sun, 10 Oct 2021 15:04:34 +0000

This test fails/succeeds non-deterministically.

* gnu/packages/bioinformatics.scm (clipper)[arguments]: Disable
  non-deterministic test test_get_FDR_cutoff_mean.
---
 gnu/packages/bioinformatics.scm | 9 ++++++++-
 1 file changed, 8 insertions(+), 1 deletion(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 082e47bf5b..7dec74f0c0 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -22,6 +22,7 @@
 ;;; Copyright © 2021 Tim Howes <timhowes <at> lavabit.com>
 ;;; Copyright © 2021 Hong Li <hli <at> mdc-berlin.de>
 ;;; Copyright © 2021 Simon Tournier <zimon.toutoune <at> gmail.com>
+;;; Copyright © 2021 Felix Gruber <felgru <at> posteo.net>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -2363,7 +2364,13 @@ databases.")
              (let ((out (assoc-ref outputs "out")))
                (for-each make-file-writable
                          (find-files out "\\.gz$"))
-               #t))))))
+               #t)))
+         (add-after 'unpack 'disable-nondeterministic-test
+           (lambda _
+             ;; This test fails/succeeds non-deterministically.
+             (substitute* "clipper/test/test_call_peak.py"
+               (("test_get_FDR_cutoff_mean") "_test_get_FDR_cutoff_mean"))
+             #t)))))
     (inputs
      `(("htseq" ,htseq)
        ("python-pybedtools" ,python-pybedtools)
-- 
2.30.2

Message #32 received at 50813 <at> debbugs.gnu.org (full text, mbox):

From: Greg Hogan <code <at> greghogan.com>
To: Felix Gruber <felgru <at> posteo.net>
Cc: Ludovic Courtès <ludo <at> gnu.org>, 50813 <at> debbugs.gnu.org
Subject: Re: [bug#50813] [PATCH v2 0/6] gnu: python-pandas: Update to 1.3.3.
Date: Tue, 12 Oct 2021 09:28:18 -0400

[Message part 1 (text/plain, inline)]

#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 <felgru <at> posteo.net> wrote:

> Hi Ludo’,
>
> On 10/7/21 11:07 AM, Ludovic Courtès wrote:
> >
> > Felix Gruber <felgru <at> 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 >= 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 ‘guix refresh -l
> > python-pandas’ 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 <at> 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 <at> 1.1.alpha19
>   already failed on master due to unbuildable ocaml4.07-re <at> 1.10.3.
> * python-scikit-rebate <at> 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 <at> 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 >= 2.8.0 which would entail
>   rebuilding 561 dependent packages.
> * imp <at> 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 <at> 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
>
>
>
>
>

[Message part 2 (text/html, inline)]

Message #37 received at 50813-done <at> debbugs.gnu.org (full text, mbox):

From: Ludovic Courtès <ludo <at> gnu.org>
To: Felix Gruber <felgru <at> posteo.net>
Cc: 50813-done <at> debbugs.gnu.org
Subject: Re: bug#50813: [PATCH] gnu: python-pandas: Update to 1.3.3.
Date: Tue, 12 Oct 2021 16:52:13 +0200

Hi Felix,

Felix Gruber <felgru <at> posteo.net> skribis:

> On 10/7/21 11:07 AM, Ludovic Courtès wrote:
>> 
>> Felix Gruber <felgru <at> 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 >= 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.

Neat.

>> For the record, I tried to build everything reported by ‘guix refresh -l
>> python-pandas’ 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 <at> 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 <at> 1.1.alpha19
>   already failed on master due to unbuildable ocaml4.07-re <at> 1.10.3.
> * python-scikit-rebate <at> 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 <at> 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 >= 2.8.0 which would entail
>   rebuilding 561 dependent packages.
> * imp <at> 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 <at> 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.

Awesome.

>   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.

python-dask and pigx-rnaseq build fine for me with this patch series,
along with everything in between.

Applied, thank you!

Ludo’.

Message #40 received at 50813 <at> debbugs.gnu.org (full text, mbox):

From: Michael Rohleder <mike <at> rohleder.de>
To: Felix Gruber <felgru <at> posteo.net>
Cc: 50813 <at> debbugs.gnu.org
Subject: Re: [bug#50813] [PATCH v2 5/6] gnu: synapse: Update to 1.44.0.
Date: Wed, 13 Oct 2021 14:01:32 +0200

[Message part 1 (text/plain, inline)]

Hello Felix,

Thank you for the patch!

Did you try running this version?

I think, synapse > 1.30 needs a newer python-cryptography (I think >=3.4) at
runtime, which we dont have currently...
(See also bug #48655)

-- 
Windows without the X is like making love without a partner.

[signature.asc (application/pgp-signature, inline)]

Message #43 received at 50813 <at> debbugs.gnu.org (full text, mbox):

From: Felix Gruber <felgru <at> posteo.net>
To: Michael Rohleder <mike <at> rohleder.de>
Cc: 50813 <at> debbugs.gnu.org
Subject: Re: [bug#50813] [PATCH v2 5/6] gnu: synapse: Update to 1.44.0.
Date: Wed, 13 Oct 2021 16:33:09 +0000

Hi Michael,

On 10/13/21 2:01 PM, Michael Rohleder wrote:
> Thank you for the patch!
> 
> Did you try running this version?
> 
> I think, synapse > 1.30 needs a newer python-cryptography (I think >=3.4) at
> runtime, which we dont have currently...
> (See also bug #48655)

I didn't try to run synapse after the update. Sorry if I broke it. :-(

Message #46 received at 50813 <at> debbugs.gnu.org (full text, mbox):

From: Michael Rohleder <mike <at> rohleder.de>
To: Felix Gruber <felgru <at> posteo.net>
Cc: 50813 <at> debbugs.gnu.org
Subject: Re: [bug#50813] [PATCH v2 5/6] gnu: synapse: Update to 1.44.0.
Date: Thu, 14 Oct 2021 06:25:52 +0200

[Message part 1 (text/plain, inline)]

Hi Felix,

Felix Gruber <felgru <at> posteo.net> writes:
> On 10/13/21 2:01 PM, Michael Rohleder wrote:
>> Thank you for the patch!
>> 
>> Did you try running this version?
>> 
>> I think, synapse > 1.30 needs a newer python-cryptography (I think >=3.4) at
>> runtime, which we dont have currently...
>> (See also bug #48655)
>
> I didn't try to run synapse after the update. Sorry if I broke it. :-(

Maybe it's possible to revert this patch?!

I think, a non working synapse is useless, no?


-- 
Software is like sex: it is better when it is free. - Linus Torvalds

[signature.asc (application/pgp-signature, inline)]

Message #49 received at 50813 <at> debbugs.gnu.org (full text, mbox):

From: Felix Gruber <felgru <at> posteo.net>
To: Michael Rohleder <mike <at> rohleder.de>
Cc: 50813 <at> debbugs.gnu.org
Subject: Re: [bug#50813] [PATCH v2 5/6] gnu: synapse: Update to 1.44.0.
Date: Thu, 14 Oct 2021 19:08:48 +0000

Hi Michael,

On 10/14/21 6:25 AM, Michael Rohleder wrote:
> Maybe it's possible to revert this patch?!
> 
> I think, a non working synapse is useless, no?

I've opened bug #51211 to revert my update of synapse.

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