GNU bug report logs - #76578
[PATCH 0/3] update python-dask

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

From: Benoit Martin <bmartin <at> cea.fr>
To: guix-patches <at> gnu.org
Cc: Benoit Martin <bmartin <at> cea.fr>
Subject: [PATCH 0/3] update python-dask
Date: Wed, 26 Feb 2025 09:00:52 +0100

This patch series updates python-dask and related packages.

Benoit Martin (3):
  gnu: python-dask-expr: Update to 1.1.21.
  gnu: python-distributed: Update to 2024.12.1.
  gnu: python-dask: Update to 2024.12.1.

 gnu/packages/python-science.scm | 14 ++++++++++----
 gnu/packages/python-xyz.scm     |  9 ++++++---
 2 files changed, 16 insertions(+), 7 deletions(-)


base-commit: 651f8765b657e35baf85ac74a1f6b09ff71691cb
-- 
2.34.1

Message #8 received at 76578 <at> debbugs.gnu.org (full text, mbox):

From: Benoit Martin <bmartin <at> cea.fr>
To: 76578 <at> debbugs.gnu.org
Cc: Benoit Martin <bmartin <at> cea.fr>
Subject: [PATCH 1/3] gnu: python-dask-expr: Update to 1.1.21.
Date: Wed, 26 Feb 2025 10:57:34 +0100

* gnu/packages/python-science.scm (python-dask-expr): Update to 1.1.21.

Change-Id: Iaee50368ffafc473164865249e2a51732b1ea54f
---
 gnu/packages/python-science.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/python-science.scm b/gnu/packages/python-science.scm
index 127e9e378a..9357d5ed10 100644
--- a/gnu/packages/python-science.scm
+++ b/gnu/packages/python-science.scm
@@ -2709,7 +2709,7 @@ (define-public python-pyglm
 (define-public python-dask-expr
   (package
     (name "python-dask-expr")
-    (version "1.0.14")
+    (version "1.1.21")
     (source
      (origin
        (method git-fetch)
@@ -2718,7 +2718,7 @@ (define-public python-dask-expr
              (commit (string-append "v" version))))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "0c2q8w8wl5d2hycbjp9vavkl5f36kaz390wxlis2d8d43jnqhf0d"))))
+        (base32 "0m920db2asmqf4w2dncpnkccdhx4c9sfcsd96bh1jfdh8sw2wf6z"))))
     (build-system pyproject-build-system)
     (arguments
      (list
-- 
2.34.1

Message #11 received at 76578 <at> debbugs.gnu.org (full text, mbox):

From: Benoit Martin <bmartin <at> cea.fr>
To: 76578 <at> debbugs.gnu.org
Cc: Benoit Martin <bmartin <at> cea.fr>
Subject: [PATCH 2/3] gnu: python-distributed: Update to 2024.12.1.
Date: Wed, 26 Feb 2025 10:57:35 +0100

* gnu/packages/python-science.scm (python-distributed): Update to 2024.12.1.

Change-Id: Ia557e7d87e48a709298bf7024ee01b08098f5842
---
 gnu/packages/python-science.scm | 10 ++++++++--
 1 file changed, 8 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/python-science.scm b/gnu/packages/python-science.scm
index 9357d5ed10..b6aa495941 100644
--- a/gnu/packages/python-science.scm
+++ b/gnu/packages/python-science.scm
@@ -2762,7 +2762,7 @@ (define-public python-dask-expr
 (define-public python-distributed
   (package
     (name "python-distributed")
-    (version "2024.4.2")
+    (version "2024.12.1")
     (source
      (origin
        ;; The test files are not included in the archive on pypi
@@ -2773,7 +2773,7 @@ (define-public python-distributed
        (file-name (git-file-name name version))
        (sha256
         (base32
-         "0sy9mqa8qlxsagbz8xn304csrlxhxj4b6k84yrjxdcmkp9pkx166"))))
+         "1k0kmzd48mvaaizbf3b6lk84s0fw88x9v7hfgiddyyv6mf4x7h27"))))
     (build-system pyproject-build-system)
     (arguments
      (list
@@ -2784,6 +2784,10 @@ (define-public python-distributed
                             " and not gpu"
                             " and not ipython"
                             " and not avoid_ci")
+             ;; This disables FutureWarning that are caught as error,
+             ;; related to the merge of python-dask-expr in python-dask.
+             "-W"
+             (string-append "ignore::FutureWarning")
              "-k"
              (string-append
               ;; These fail because they require network access,
@@ -2849,6 +2853,7 @@ (define-public python-distributed
                 "test_rebalance_sync"
                 "test_repr_localcluster"
                 "test_require_encryption"
+                "test_rpc_closed_exception"
                 "test_rpc_default"
                 "test_rpc_inproc"
                 "test_rpc_message_lifetime_default"
@@ -2880,6 +2885,7 @@ (define-public python-distributed
                 "test_threadpoolworkers_pick_correct_ioloop"
                 "test_tls_listen_connect"
                 "test_tls_temporary_credentials_functional"
+                "test_transition_failure_triggers_log_event"
                 "test_variable_in_task"
                 "test_worker_preload_text"
                 "test_worker_uses_same_host_as_nanny"
-- 
2.34.1

Message #14 received at 76578 <at> debbugs.gnu.org (full text, mbox):

From: Benoit Martin <bmartin <at> cea.fr>
To: 76578 <at> debbugs.gnu.org
Cc: Benoit Martin <bmartin <at> cea.fr>
Subject: [PATCH 3/3] gnu: python-dask: Update to 2024.12.1.
Date: Wed, 26 Feb 2025 10:57:36 +0100

* gnu/packages/python-xyz.scm (python-dask): Update to 2024.12.1.

Change-Id: I776e9dd3d4a12d33e89e4d48a5e637cb9d6f465e
---
 gnu/packages/python-xyz.scm | 9 ++++++---
 1 file changed, 6 insertions(+), 3 deletions(-)

diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index bb0ab777d5..5ac44db4b8 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -30507,7 +30507,7 @@ (define-public python-fsspec
 (define-public python-dask
   (package
     (name "python-dask")
-    (version "2024.4.2")
+    (version "2024.12.1")
     (source
      (origin
        (method git-fetch)
@@ -30516,7 +30516,7 @@ (define-public python-dask
              (commit version)))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "1kaxlvqd5hknlb0awck5vcw9b18nl8rpxx4j78js8p9d0y5rsgw8"))))
+        (base32 "17iqfyjphyn72xdr8fmynzvixskbq16pwmsknwc6anq7s2axvas2"))))
     (build-system pyproject-build-system)
     (arguments
      (list
@@ -30544,7 +30544,10 @@ (define-public python-dask
                     " and not test_to_delayed_optimize_graph"
                     ;; This one expects a deprecation warning that never
                     ;; comes.
-                    " and not test_RandomState_only_funcs")
+                    " and not test_RandomState_only_funcs"
+                    ;; This test expects a RuntimeWarning that is never
+                    ;; raised.
+                    " and not test_nanquantile_all_nan")
               ;; Tests must run from the output directory, because otherwise
               ;; it complains about the difference between the target
               ;; directory embedded in the pyc files and the source directory
-- 
2.34.1

Message #17 received at 76578 <at> debbugs.gnu.org (full text, mbox):

From: Ludovic Courtès <ludovic.courtes <at> inria.fr>
To: Benoit Martin <bmartin <at> cea.fr>
Cc: 76578 <at> debbugs.gnu.org
Subject: Re: [bug#76578] [PATCH 0/3] update python-dask
Date: Mon, 10 Mar 2025 13:55:34 +0100

Hi Benoit,

Benoit Martin <bmartin <at> cea.fr> skribis:

> This patch series updates python-dask and related packages.
>
> Benoit Martin (3):
>   gnu: python-dask-expr: Update to 1.1.21.
>   gnu: python-distributed: Update to 2024.12.1.
>   gnu: python-dask: Update to 2024.12.1.

This patch series breaks python-arboreto:

--8<---------------cut here---------------start------------->8---
starting phase `sanity-check'
validating 'arboreto' /gnu/store/k1rsw0q58s6d82bz7swp9qn5aba0j03n-python-arboreto-0.1.6/lib/python3.10/site-packages
...checking requirements: ERROR: arboreto==0.1.6 ContextualVersionConflict(bokeh 2.4.3 (/gnu/store/hm1anf9fnl635p07rgjr7vj0qg18cr06-python-bokeh-2.4.3/lib/python3.10/site-packages), Requirement.parse('bokeh>=3.1.0; extra == "diagnostics"'), {'dask'})
error: in phase 'sanity-check': uncaught exception:
%exception #<&invoke-error program: "python" arguments: ("/gnu/store/iqsjkp55pcx5bfcp2jm9yj5rlx9a0whd-sanity-check.py" "/gnu/store/k1rsw0q58s6d82bz7swp9qn5aba0j03n-python-arboreto-0.1.6/lib/python3.10/site-packages") exit-status: 1 term-signal: #f stop-signal: #f> 
phase `sanity-check' failed after 0.7 seconds
command "python" "/gnu/store/iqsjkp55pcx5bfcp2jm9yj5rlx9a0whd-sanity-check.py" "/gnu/store/k1rsw0q58s6d82bz7swp9qn5aba0j03n-python-arboreto-0.1
--8<---------------cut here---------------end--------------->8---

… and triggers one test failure in python-scitools-iris:

--8<---------------cut here---------------start------------->8---
SKIPPED [1] ../../../gnu/store/v685kxa0pv5xzss1sjina70vpkk418ad-python-scitools-iris-3.11.1/lib/python3.10/site-packages/iris/tests/test_abf.py:33: Test(s) require external data.
SKIPPED [1] ../../../gnu/store/v685kxa0pv5xzss1sjina70vpkk418ad-python-scitools-iris-3.11.1/lib/python3.10/site-packages/iris/tests/test_abf.py:21: Test(s) require external data.
FAILED tests/test_pickling.py::TestPickle::test_cube_with_deferred_unit_conversion - TypeError: cannot pickle 'Task' object: a class that defines __slots__ without defining __getstate__ cannot be pickled with protocol 0
========= 1 failed, 8680 passed, 966 skipped, 1101 warnings in 39.78s ==========
error: in phase 'check': uncaught exception:
%exception #<&invoke-error program: "/gnu/store/i65m7m87830mbw56p9gckfmk27vjrs56-python-pytest-8.3.3/bin/pytest" arguments: ("-vv" "--numprocesses" "34" "--pyargs" "iris" "-k" "not test_both_transposed and not test_2d_coords_contour and not test_2d_plain_latlon and not test_2d_plain_latlon_on_polar_map and not test_2d_rotated_latlon and not test_2d_rotated_latlon and not test_ancillary_variables_pass_0 and not test_auxiliary_coordinates_pass_0 and not test_bounds and not test_bounds_pass_0 and not test_broadcast_cubes and not test_broadcast_cubes_weighted and not test_broadcast_transpose_cubes_weighted and not test_cell_measures_pass_0 and not test_common_mask_broadcast and not test_common_mask_simple and not test_compatible_cubes and not test_compatible_cubes_weighted and not test_coord_transposed and not test_coordinates_pass_0 and not test_cube_transposed and not test_data_pass_0 and not test_destructor and not test_formula_terms_pass_0 and not test_global_attributes_pass_0 and not test_grid_mapping_pass_0 and not test_grouped_dim and not test_incompatible_cubes and not test_izip_different_shaped_coords and not test_izip_different_valued_coords and not test_izip_extra_coords_both_slice_dims and not test_izip_extra_coords_slice_dim and not test_izip_extra_coords_step_dim and not test_izip_extra_dim and not test_izip_input_collections and not test_izip_missing_slice_coords and not test_izip_nd_non_ortho and not test_izip_nd_ortho and not test_izip_no_args and not test_izip_no_common_coords_on_step_dim and not test_izip_onecube_height_lat_long and not test_izip_onecube_lat and not test_izip_onecube_lat_lon and not test_izip_onecube_no_coords and not test_izip_ordered and not test_izip_returns_iterable and not test_izip_same_cube_lat and not test_izip_same_cube_lat_lon and not test_izip_same_cube_no_coords and not test_izip_same_dims_single_coord and not test_izip_same_dims_two_coords and not test_izip_subcube_of_same and not test_izip_unequal_slice_coords and not test_izip_use_in_analysis and not test_label_dim_end and not test_label_dim_start and not test_lenient_handling and not test_load_pp_timevarying_orography and not test_mdtol and not test_netcdf_v3 and not test_no_delayed_writes and not test_no_transpose and not test_non_existent_coord and not test_perfect_corr and not test_perfect_corr_all_dims and not test_python_versions and not test_realfile_loadsave_equivalence and not test_realise_data and not test_realise_data_multisource and not test_scheduler_types and not test_single_coord and not test_stream and not test_stream_multisource and not test_stream_multisource__manychunks and not test_time_of_writing and not test_ungrouped_dim and not test_variable_attribute_touch_pass_0 and not test_variable_cf_group_pass_0 and not test_weight_error") exit-status: 1 term-signal: #f stop-signal: #f> 
phase `check' failed after 40.9 seconds
--8<---------------cut here---------------end--------------->8---

Do you think you could take a look?

For the record, I checked with:

  ./pre-inst-env guix build -P1 python-dask -P1 python-distributed \
      -P1 python-dask-expr --no-grafts

Thanks for your work!

Ludo’.

Message #20 received at 76578 <at> debbugs.gnu.org (full text, mbox):

From: Ludovic Courtès <ludovic.courtes <at> inria.fr>
To: Ludovic Courtès <ludovic.courtes <at> inria.fr>
Cc: sharlatanus <at> gmail.com, me <at> bonfacemunyoki.com,
 Benoit Martin <bmartin <at> cea.fr>, lars <at> 6xq.net, 76578 <at> debbugs.gnu.org,
 tanguy <at> bioneland.org
Subject: Re: [bug#76578] [PATCH 0/3] update python-dask
Date: Thu, 15 May 2025 09:36:30 +0200

Hello,

Ludovic Courtès <ludovic.courtes <at> inria.fr> writes:

> Benoit Martin <bmartin <at> cea.fr> skribis:
>
>> This patch series updates python-dask and related packages.
>>
>> Benoit Martin (3):
>>   gnu: python-dask-expr: Update to 1.1.21.
>>   gnu: python-distributed: Update to 2024.12.1.
>>   gnu: python-dask: Update to 2024.12.1.
>
> This patch series breaks python-arboreto:

[...]

> … and triggers one test failure in python-scitools-iris:

Python team, how would you suggest going forward with this ‘python-dask’
upgrade?

  https://issues.guix.gnu.org/76578

Perhaps updating ‘python-scitools-iris’ would help, but
‘python-arboreto’ is already the latest versions.

Thoughts?

Thanks,
Ludo’.

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