GNU bug report logs - #68609
[PATCH 0/2] gnu: python-pandera: Fix build.

Previous Next

To add a comment to this bug, you must first unarchive it, by sending
a message to control AT debbugs.gnu.org, with unarchive 68609 in the body.
You can then email your comments to 68609 AT debbugs.gnu.org in the normal way.

Toggle the display of automated, internal messages from the tracker.

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

From: Troy Figiel <troy <at> troyfigiel.com>
To: guix-patches <at> gnu.org
Subject: [PATCH 0/2] gnu: python-pandera: Fix build.
Date: Sat, 20 Jan 2024 14:42:29 +0100

With the 1.5.3 upgrade of python-pandas, python-modin is broken. I tried
fixing it by upgrading it to a compatible version, but this has a ripple
effect on a variety of packages such as python-boto3, python-fsspec,
etc.

For now, I would suggest to simply remove python-modin as a native-input from python-pandera. Since it is an optional dependency in the first place, not much is lost as long as python-modin is broken on master.

Troy Figiel (2):
  gnu: python-pandas-stubs: Update to 1.5.3.230321.
  gnu: python-pandera: Fix build.

 gnu/packages/python-science.scm | 35 +++++++++++++++++++++++----------
 1 file changed, 25 insertions(+), 10 deletions(-)


base-commit: 0eadd486484fcf9a234758842f74ba28361640db
-- 
2.42.0

Message #8 received at 68609 <at> debbugs.gnu.org (full text, mbox):

From: Troy Figiel <troy <at> troyfigiel.com>
To: 68609 <at> debbugs.gnu.org
Subject: [PATCH 1/2] gnu: python-pandas-stubs: Update to 1.5.3.230321.
Date: Sat, 20 Jan 2024 14:10:40 +0100

* gnu/packages/python-science.scm (python-pandas-stubs): Update to
1.5.3.230321.
[arguments]<#:test-flags>: Ignore tests that require a version of
python-pyarrow with ORC integration.
[native-inputs]: Add python-odfpy.
---
 gnu/packages/python-science.scm | 20 ++++++++++++++++----
 1 file changed, 16 insertions(+), 4 deletions(-)

diff --git a/gnu/packages/python-science.scm b/gnu/packages/python-science.scm
index 3c131fe730..4eb0195889 100644
--- a/gnu/packages/python-science.scm
+++ b/gnu/packages/python-science.scm
@@ -580,8 +580,8 @@ (define-public python-pandas-stubs
     (name "python-pandas-stubs")
     ;; The versioning follows that of Pandas and uses the date of the
     ;; python-pandas-stubs release. This is the latest version of
-    ;; python-pandas-stubs for python-pandas 1.4.4.
-    (version "1.4.4.220919")
+    ;; python-pandas-stubs for python-pandas 1.5.3.
+    (version "1.5.3.230321")
     (source
      (origin
        ;; No tests in the PyPI tarball.
@@ -591,10 +591,21 @@ (define-public python-pandas-stubs
              (commit (string-append "v" version))))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "14fhj1y71akwl41ws7cpazsbq5b8wf4rwaydqq2h39q7gylpcp99"))))
+        (base32 "1blwlq5053pxnmx721zdd6v8njiybz4azribx2ygq33jcpmknda6"))))
     (build-system pyproject-build-system)
     (arguments
-     '(#:phases (modify-phases %standard-phases
+     (list
+      #:test-flags #~(list "-k"
+                           (string-append
+                            ;; The python-pyarrow package in Guix is not built
+                            ;; with ORC integration, causing these tests to
+                            ;; fail.
+                            "not test_orc"
+                            " and not test_orc_path"
+                            " and not test_orc_buffer"
+                            " and not test_orc_columns"
+                            " and not test_orc_bytes"))
+      #:phases '(modify-phases %standard-phases
                   (add-before 'check 'prepare-x
                     (lambda _
                       (system "Xvfb &")
@@ -607,6 +618,7 @@ (define-public python-pandas-stubs
     ;; tests will be skipped for now.
     (native-inputs (list python-lxml
                          python-matplotlib
+                         python-odfpy
                          python-pandas
                          python-poetry-core
                          python-pyarrow
-- 
2.42.0

Message #11 received at 68609 <at> debbugs.gnu.org (full text, mbox):

From: Troy Figiel <troy <at> troyfigiel.com>
To: 68609 <at> debbugs.gnu.org
Subject: [PATCH 2/2] gnu: python-pandera: Fix build.
Date: Sat, 20 Jan 2024 14:55:28 +0100

* gnu/packages/python-science.scm (python-pandera): Fix build.
[source]: Delete tests/modin directory.
[native-inputs]: Remove python-modin.
---
 gnu/packages/python-science.scm | 15 +++++++++------
 1 file changed, 9 insertions(+), 6 deletions(-)

diff --git a/gnu/packages/python-science.scm b/gnu/packages/python-science.scm
index 4eb0195889..3422302a87 100644
--- a/gnu/packages/python-science.scm
+++ b/gnu/packages/python-science.scm
@@ -661,16 +661,20 @@ (define-public python-pandera
        (sha256
         (base32 "1mnqk583z90k1n0z3lfa4rd0ng40v7hqfk7phz5gjmxlzfjbxa1x"))
        (modules '((guix build utils)))
-       ;; These tests require PySpark. We need to remove the entire directory,
-       ;; since the conftest.py in this directory contains a PySpark import.
-       ;; (See: https://github.com/pytest-dev/pytest/issues/7452)
-       (snippet '(delete-file-recursively "tests/pyspark"))))
+       ;; These tests require PySpark and Modin. We need to remove the entire
+       ;; directory, since the conftest.py in these directories contain
+       ;; imports.  (See: https://github.com/pytest-dev/pytest/issues/7452)
+       (snippet '(begin
+                   (delete-file-recursively "tests/pyspark")
+                   (delete-file-recursively "tests/modin")))))
     (build-system pyproject-build-system)
     (arguments
      (list
       #:test-flags '(list "-k"
                           (string-append
-                           ;; Needs python-pandas >= 1.5
+                           ;; Mypy functionality is experimental and relying
+                           ;; on pandas-stubs can lead to false
+                           ;; positives. These tests currently fail.
                            "not test_python_std_list_dict_generics"
                            " and not test_python_std_list_dict_empty_and_none"
                            " and not test_pandas_modules_importable"))))
@@ -692,7 +696,6 @@ (define-public python-pandera
     (native-inputs (list python-dask ;dask extra
                          python-fastapi ;fastapi extra
                          python-geopandas ;geopandas extra
-                         python-modin ;modin extra
                          python-pyarrow ;needed to run fastapi tests
                          python-pytest
                          python-pytest-asyncio
-- 
2.42.0

Message #16 received at 68609-done <at> debbugs.gnu.org (full text, mbox):

From: Sharlatan Hellseher <sharlatanus <at> gmail.com>
To: 68609-done <at> debbugs.gnu.org
Subject: [PATCH 0/2] gnu: python-pandera: Fix build.
Date: Sat, 20 Jan 2024 22:11:09 +0000

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

Pushed as e1d3be4113c854d6efdfda6a8c3e5757753425ad

Thanks,
Oleg

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

Previous Next

GNU bug tracking system
Copyright (C) 1999 Darren O. Benham, 1997,2003 nCipher Corporation Ltd, 1994-97 Ian Jackson.