[bug#68609] [PATCH 1/2] gnu: python-pandas-stubs: Update to 1.5.3.230321.

[bug#68609] [PATCH 1/2] gnu: python-pandas-stubs: Update to 1.5.3.230321.

[Troy Figiel]

* 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

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

[Troy Figiel]

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

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

[Troy Figiel]

* 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

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

[Sharlatan Hellseher]

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Pushed as e1d3be4113c854d6efdfda6a8c3e5757753425ad

Thanks,
Oleg

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