GNU bug report logs - #49207
gnu: Add python-iris. (scitools)

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

From: Vinicius Monego <monego <at> posteo.net>
To: guix-patches <at> gnu.org
Subject: gnu: Add python-iris. (scitools)
Date: Thu, 24 Jun 2021 12:39:15 +0000

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

[0001-gnu-Add-python-imagehash.patch (text/x-patch, attachment)]

[0002-gnu-Add-python-xxhash.patch (text/x-patch, attachment)]

[0003-gnu-Add-python-antlr4.patch (text/x-patch, attachment)]

[0004-gnu-Add-python-cf-units.patch (text/x-patch, attachment)]

[0005-gnu-Add-python-pyke.patch (text/x-patch, attachment)]

[0006-gnu-Add-python-iris.patch (text/x-patch, attachment)]

Message #8 received at 49207 <at> debbugs.gnu.org (full text, mbox):

From: Vinicius Monego <monego <at> posteo.net>
To: 49207 <at> debbugs.gnu.org
Cc: Vinicius Monego <monego <at> posteo.net>
Subject: [PATCH 0/6] gnu: Add python-iris (scitools).
Date: Fri, 23 Jul 2021 23:25:23 +0000

Resending with send-email for convenience, without changes.

Vinicius Monego (6):
  gnu: Add python-imagehash.
  gnu: Add python-xxhash.
  gnu: Add python-antlr4.
  gnu: Add python-cf-units.
  gnu: Add python-pyke.
  gnu: Add python-iris.

 gnu/packages/geo.scm        | 114 ++++++++++++++++++++++++++++++++++
 gnu/packages/python-xyz.scm | 119 ++++++++++++++++++++++++++++++++++++
 2 files changed, 233 insertions(+)

-- 
2.30.2

Message #11 received at 49207 <at> debbugs.gnu.org (full text, mbox):

From: Vinicius Monego <monego <at> posteo.net>
To: 49207 <at> debbugs.gnu.org
Cc: Vinicius Monego <monego <at> posteo.net>
Subject: [PATCH 1/6] gnu: Add python-imagehash.
Date: Fri, 23 Jul 2021 23:25:24 +0000

* gnu/packages/python-xyz.scm (python-imagehash): New variable.
---
 gnu/packages/python-xyz.scm | 41 +++++++++++++++++++++++++++++++++++++
 1 file changed, 41 insertions(+)

diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index d8c3fbec07..eef180b720 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -12995,6 +12995,47 @@ The API is as much as possible the similar to jQuery.  pyquery uses lxml for
 fast xml and html manipulation.")
     (license license:bsd-3)))
 
+(define-public python-imagehash
+  (package
+    (name "python-imagehash")
+    (version "4.2.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "ImageHash" version))
+       (sha256
+        (base32 "0kgiksjggw2warfz5d04fr3iph47vwxcb8jrlj41ljkhrc3ahsd9"))))
+    (build-system python-build-system)
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases
+         (replace 'check
+           (lambda* (#:key inputs outputs tests? #:allow-other-keys)
+             (when tests?
+               (add-installed-pythonpath inputs outputs)
+               (invoke "pytest")))))))
+    (native-inputs
+     `(("python-pytest" ,python-pytest)))
+    (propagated-inputs
+     `(("python-numpy" ,python-numpy)
+       ("python-pillow" ,python-pillow)
+       ("python-pywavelets" ,python-pywavelets)
+       ("python-scipy" ,python-scipy)
+       ("python-six" ,python-six)))
+    (home-page "https://github.com/JohannesBuchner/imagehash")
+    (synopsis "Image hashing library")
+    (description "ImageHash is an Image hashing library.  It supports:
+
+@itemize
+@item Average hashing
+@item Perceptual hashing
+@item Difference hashing
+@item Wavelet hashing
+@item HSV color hashing (colorhash)
+@item Crop-resistant hashing
+@end itemize")
+    (license license:bsd-2)))
+
 (define-public python-anyjson
   (package
     (name "python-anyjson")
-- 
2.30.2

Message #14 received at 49207 <at> debbugs.gnu.org (full text, mbox):

From: Vinicius Monego <monego <at> posteo.net>
To: 49207 <at> debbugs.gnu.org
Cc: Vinicius Monego <monego <at> posteo.net>
Subject: [PATCH 2/6] gnu: Add python-xxhash.
Date: Fri, 23 Jul 2021 23:25:25 +0000

* gnu/packages/python-xyz.scm (python-xxhash): New variable.
---
 gnu/packages/python-xyz.scm | 26 ++++++++++++++++++++++++++
 1 file changed, 26 insertions(+)

diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index eef180b720..2b4ce0cba3 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -136,6 +136,7 @@
   #:use-module (gnu packages crypto)
   #:use-module (gnu packages databases)
   #:use-module (gnu packages dbm)
+  #:use-module (gnu packages digest)
   #:use-module (gnu packages djvu)
   #:use-module (gnu packages docker)
   #:use-module (gnu packages enchant)
@@ -13036,6 +13037,31 @@ fast xml and html manipulation.")
 @end itemize")
     (license license:bsd-2)))
 
+(define-public python-xxhash
+  (package
+    (name "python-xxhash")
+    (version "2.0.2")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "xxhash" version))
+       (sha256
+        (base32 "0jbvz19acznq00544gcsjg05fkvrmwbnwdfgrvwss3i1ys6avgmp"))))
+    (build-system python-build-system)
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'use-system-xxhash
+           (lambda _
+             (setenv "XXHASH_LINK_SO" "1"))))))
+    (inputs
+     `(("xxhash" ,xxhash)))
+    (home-page "https://github.com/ifduyue/python-xxhash")
+    (synopsis "Python binding for xxHash")
+    (description "This package provides a Python interface binding for the
+xxHash non-cryptographic hash algorithm.")
+    (license license:bsd-2)))
+
 (define-public python-anyjson
   (package
     (name "python-anyjson")
-- 
2.30.2

Message #17 received at 49207 <at> debbugs.gnu.org (full text, mbox):

From: Vinicius Monego <monego <at> posteo.net>
To: 49207 <at> debbugs.gnu.org
Cc: Vinicius Monego <monego <at> posteo.net>
Subject: [PATCH 3/6] gnu: Add python-antlr4.
Date: Fri, 23 Jul 2021 23:25:26 +0000

* gnu/packages/python-xyz.scm (python-antlr4): New variable.
---
 gnu/packages/python-xyz.scm | 19 +++++++++++++++++++
 1 file changed, 19 insertions(+)

diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index 2b4ce0cba3..61b1b7d29c 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -13062,6 +13062,25 @@ fast xml and html manipulation.")
 xxHash non-cryptographic hash algorithm.")
     (license license:bsd-2)))
 
+(define-public python-antlr4
+  (package
+    (name "python-antlr4")
+    (version "4.7.2")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "antlr4-python3-runtime" version))
+       (sha256
+        (base32 "02xm7ccsf51vh4xsnhlg6pvchm1x3ckgv9kwm222w5drizndr30n"))))
+    (arguments
+     `(#:tests? #f)) ; there are no tests
+    (build-system python-build-system)
+    (home-page "https://www.antlr.org")
+    (synopsis "ANTLR runtime for Python")
+    (description
+     "This package provides a ANTLR runtime for Python.")
+    (license license:bsd-3)))
+
 (define-public python-anyjson
   (package
     (name "python-anyjson")
-- 
2.30.2

Message #20 received at 49207 <at> debbugs.gnu.org (full text, mbox):

From: Vinicius Monego <monego <at> posteo.net>
To: 49207 <at> debbugs.gnu.org
Cc: Vinicius Monego <monego <at> posteo.net>
Subject: [PATCH 4/6] gnu: Add python-cf-units.
Date: Fri, 23 Jul 2021 23:25:27 +0000

* gnu/packages/geo.scm (python-cf-units): New variable.
---
 gnu/packages/geo.scm | 47 ++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 47 insertions(+)

diff --git a/gnu/packages/geo.scm b/gnu/packages/geo.scm
index 37be78edbf..314165062c 100644
--- a/gnu/packages/geo.scm
+++ b/gnu/packages/geo.scm
@@ -58,6 +58,7 @@
   #:use-module (gnu packages bash)
   #:use-module (gnu packages bison)
   #:use-module (gnu packages boost)
+  #:use-module (gnu packages c)
   #:use-module (gnu packages check)
   #:use-module (gnu packages compression)
   #:use-module (gnu packages curl)
@@ -898,6 +899,52 @@ Shapely capabilities
 @end itemize")
     (license license:lgpl3+)))
 
+(define-public python-cf-units
+  (package
+    (name "python-cf-units")
+    (version "2.1.5")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "cf-units" version))
+       (sha256
+        (base32 "0cswphn1cw0qyzglcn4xinr3pfhvbsdyll4hnb702fsfxv9q2cyl"))))
+    (build-system python-build-system)
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'disable-doctest
+           (lambda _
+             ;; Two doctests fail.
+             (substitute* "setup.cfg" (("--doctest-modules") ""))))
+         (replace 'check
+           (lambda* (#:key inputs outputs tests? #:allow-other-keys)
+             (when tests?
+               (add-installed-pythonpath inputs outputs)
+               (invoke "pytest" "--pyargs" "cf_units" "-ra"
+                       ;; This test failed.
+                       "-k" "not test_masked_ndarray")))))))
+    (native-inputs
+     `(("python-coveralls" ,python-coveralls)
+       ("python-cython" ,python-cython)
+       ("python-jinja2" ,python-jinja2)
+       ("python-pep8" ,python-pep8)
+       ("python-pytest" ,python-pytest)
+       ("python-pytest-cov" ,python-pytest-cov)
+       ("python-pytest-runner" ,python-pytest-runner)))
+    (inputs
+     `(("udunits" ,udunits)))
+    (propagated-inputs
+     `(("python-antlr4" ,python-antlr4)
+       ("python-cftime" ,python-cftime)
+       ("python-numpy" ,python-numpy)
+       ("python-six" ,python-six)))
+    (home-page "https://github.com/SciTools/cf-units")
+    (synopsis "Units of measure as required by the CF metadata conventions")
+    (description "This package provides units of measure as required by the
+Climate and Forecast (CF) metadata conventions.")
+    (license license:lgpl3)))
+
 (define-public postgis
   (package
     (name "postgis")
-- 
2.30.2

Message #23 received at 49207 <at> debbugs.gnu.org (full text, mbox):

From: Vinicius Monego <monego <at> posteo.net>
To: 49207 <at> debbugs.gnu.org
Cc: Vinicius Monego <monego <at> posteo.net>
Subject: [PATCH 5/6] gnu: Add python-pyke.
Date: Fri, 23 Jul 2021 23:25:28 +0000

* gnu/packages/python-xyz.scm (python-pyke): New variable.
---
 gnu/packages/python-xyz.scm | 33 +++++++++++++++++++++++++++++++++
 1 file changed, 33 insertions(+)

diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index 61b1b7d29c..360650332e 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -6009,6 +6009,39 @@ operators such as union, intersection, and difference.")
 search in Python.")
     (license license:lgpl3+)))
 
+(define-public python-pyke
+  (package
+    (name "python-pyke")
+    (version "1.1.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "scitools-pyke" version))
+       (sha256
+        (base32 "0q7nxd0gw135922ck155w2nj2vf47k7cgzdqipxlyrgq6q3lkinl"))))
+    (build-system python-build-system)
+    ;; FIXME: two tests are failing with:
+    ;; "AttributeError: 'fc_tests' object has no attribute 'engine'.".
+    (arguments
+     `(#:tests? #f))
+    (home-page "https://sourceforge.net/projects/pyke/")
+    (synopsis "Python Knowledge Engine")
+    (description "Pyke is a Python Knowledge Engine and automatic Python
+program generator.  Both forward-chaining and backward-chaining rules (which
+may include Python code) are compiled into Python.  It can also automatically
+assemble Python programs out of Python functions which are attached to
+backward-chaining rules.
+
+Features:
+
+@itemize
+@item Automatic programming: generates Python programs.
+@item Forward and backward chaining.
+@item Multiple knowledge engines and rule bases.
+@item Rule-based inheritance.
+@end itemize")
+    (license license:expat)))
+
 (define-public python-wurlitzer
   (package
     (name "python-wurlitzer")
-- 
2.30.2

Message #26 received at 49207 <at> debbugs.gnu.org (full text, mbox):

From: Vinicius Monego <monego <at> posteo.net>
To: 49207 <at> debbugs.gnu.org
Cc: Vinicius Monego <monego <at> posteo.net>
Subject: [PATCH 6/6] gnu: Add python-iris.
Date: Fri, 23 Jul 2021 23:25:29 +0000

* gnu/packages/geo.scm (python-iris): New variable.
---
 gnu/packages/geo.scm | 67 ++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 67 insertions(+)

diff --git a/gnu/packages/geo.scm b/gnu/packages/geo.scm
index 314165062c..36c020e31d 100644
--- a/gnu/packages/geo.scm
+++ b/gnu/packages/geo.scm
@@ -92,6 +92,7 @@
   #:use-module (gnu packages protobuf)
   #:use-module (gnu packages pulseaudio)
   #:use-module (gnu packages python)
+  #:use-module (gnu packages python-build)
   #:use-module (gnu packages python-check)
   #:use-module (gnu packages python-science)
   #:use-module (gnu packages python-web)
@@ -945,6 +946,72 @@ Shapely capabilities
 Climate and Forecast (CF) metadata conventions.")
     (license license:lgpl3)))
 
+(define-public python-iris
+  (package
+    (name "python-iris")
+    (version "3.0.2")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "scitools-iris" version))
+       (sha256
+        (base32 "1zqicscnnfqpck960xdjng38qk0w0spmcysl89l3smagdsagzxkr"))))
+    (build-system python-build-system)
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases
+         (add-before 'check 'pre-check
+           (lambda _
+             ;; Some tests require a writable home.
+             (setenv "HOME" "/tmp")
+             ;; Iris will check for "scitools-iris[test]" before running the
+             ;; tests.  The complete test set weighs 150MB.  Skip this check.
+             (substitute* "setup.py"
+               ((".*tests_require.*") ""))
+             ;; The tests below open external connections.
+             (substitute*
+                 "lib/iris/tests/integration/plot/test_vector_plots.py"
+               (("test_2d_plain_latlon") "_test_2d_plain_latlon")
+               (("test_2d_plain_latlon_on_polar_map")
+                "_test_2d_plain_latlon_on_polar_map")
+               (("test_2d_rotated_latlon") "_test_2d_rotated_latlon"))
+             (substitute*
+                 "lib/iris/tests/integration/plot/test_plot_2d_coords.py"
+               (("test_2d_coords_contour") "_test_2d_coords_contour"))
+             ;; This one fails with AssertionError.
+             (substitute* "lib/iris/tests/experimental/test_animate.py"
+               (("test_cube_animation") "_test_cube_animation"))
+             ;; Compile Pyke rules before running the tests.
+             (invoke "python" "setup.py" "pyke_rules"))))))
+    (propagated-inputs
+     `(("python-cartopy" ,python-cartopy)
+       ("python-cf-units" ,python-cf-units)
+       ("python-cftime" ,python-cftime)
+       ("python-dask" ,python-dask)
+       ("python-matplotlib" ,python-matplotlib)
+       ("python-netcdf4" ,python-netcdf4)
+       ("python-numpy" ,python-numpy)
+       ("python-scipy" ,python-scipy)
+       ("python-xxhash" ,python-xxhash)))
+    (native-inputs
+     `(("netcdf" ,netcdf)
+       ("python-black" ,python-black)
+       ("python-filelock" ,python-filelock)
+       ("python-imagehash" ,python-imagehash)
+       ("python-nose" ,python-nose)
+       ("python-pillow" ,python-pillow)
+       ("python-pyke" ,python-pyke)
+       ("python-requests" ,python-requests)
+       ("python-wheel" ,python-wheel)))
+    (home-page "https://github.com/SciTools/iris")
+    (synopsis "Library for analysing and visualising Earth science data")
+    (description "Iris is a Python library for analysing and visualising Earth
+science data.  It excels when working with multi-dimensional Earth Science
+data, where tabular representations become unwieldy and inefficient.  Iris
+implements a data model based on the CF conventions.")
+    ;; See iris/docs/src/copyright.rst.
+    (license license:lgpl3+)))
+
 (define-public postgis
   (package
     (name "postgis")
-- 
2.30.2

Message #31 received at 49207 <at> debbugs.gnu.org (full text, mbox):

From: Vinicius Monego <monego <at> posteo.net>
To: 49207 <at> debbugs.gnu.org
Cc: Vinicius Monego <monego <at> posteo.net>
Subject: [PATCH v2 1/5] gnu: Add python-imagehash.
Date: Fri,  9 Jun 2023 14:58:50 +0000

* gnu/packages/digest.scm (python-imagehash): New variable.
---
 gnu/packages/digest.scm | 35 +++++++++++++++++++++++++++++++++++
 1 file changed, 35 insertions(+)

diff --git a/gnu/packages/digest.scm b/gnu/packages/digest.scm
index 481771804b..405c1769d3 100644
--- a/gnu/packages/digest.scm
+++ b/gnu/packages/digest.scm
@@ -2,6 +2,7 @@
 ;;; Copyright © 2017, 2019, 2020 Tobias Geerinckx-Rice <me <at> tobias.gr>
 ;;; Copyright © 2021 Ryan Prior <rprior <at> protonmail.com>
 ;;; Copyright © 2021, 2022 Ricardo Wurmus <rekado <at> elephly.net>
+;;; Copyright © 2023 Vinicius Monego <monego <at> posteo.net>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -29,7 +30,10 @@ (define-module (gnu packages digest)
   #:use-module (guix build-system python)
   #:use-module (guix build-system trivial)
   #:use-module (guix utils)
+  #:use-module (gnu packages check)
   #:use-module (gnu packages python-build)
+  #:use-module (gnu packages python-science)
+  #:use-module (gnu packages python-xyz)
   #:use-module (ice-9 match))
 
 (define-public wyhash
@@ -129,3 +133,34 @@ (define-public python-xxhash
     (description "This package provides Python bindings for the xxHash hash
 algorithm.")
     (license license:bsd-3)))
+
+(define-public python-imagehash
+  (package
+    (name "python-imagehash")
+    (version "4.3.1")
+    (source
+     (origin
+       (method git-fetch) ;no tests in PyPI
+       (uri (git-reference
+             (url "https://github.com/JohannesBuchner/imagehash")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "1lw9lxzrzy9s5v3xc35vmh97hlyavnla087fp19k77va6v8vbjjf"))))
+    (build-system pyproject-build-system)
+    (native-inputs (list python-pytest))
+    (propagated-inputs (list python-numpy python-pillow python-pywavelets
+                             python-scipy))
+    (home-page "https://github.com/JohannesBuchner/imagehash")
+    (synopsis "Image hashing library")
+    (description "ImageHash is an image hashing library.  It supports:
+
+@itemize
+@item Average hashing
+@item Perceptual hashing
+@item Difference hashing
+@item Wavelet hashing
+@item HSV color hashing (colorhash)
+@item Crop-resistant hashing
+@end itemize")
+    (license license:bsd-2)))
-- 
2.34.1

Message #34 received at 49207 <at> debbugs.gnu.org (full text, mbox):

From: Vinicius Monego <monego <at> posteo.net>
To: 49207 <at> debbugs.gnu.org
Cc: Vinicius Monego <monego <at> posteo.net>
Subject: [PATCH v2 2/5] gnu: Add python-cf-units.
Date: Fri,  9 Jun 2023 14:58:51 +0000

* gnu/packages/geo.scm (python-cf-units): New variable.
---
 gnu/packages/geo.scm | 46 ++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 46 insertions(+)

diff --git a/gnu/packages/geo.scm b/gnu/packages/geo.scm
index 25805fe2e5..2c15df18cc 100644
--- a/gnu/packages/geo.scm
+++ b/gnu/packages/geo.scm
@@ -1380,6 +1380,52 @@ (define-public postgis
                ;; doc
                license:cc-by-sa3.0))))
 
+(define-public python-cf-units
+  (package
+    (name "python-cf-units")
+    (version "3.2.0")
+    (source (origin
+              (method url-fetch)
+              (uri (pypi-uri "cf-units" version))
+              (sha256
+               (base32
+                "0kq76p13ndm8033m0jfbfryhlk3c0iwy1d92sg1f8zqmwi0g3ac8"))))
+    (build-system pyproject-build-system)
+    (arguments
+     ;; FIXME: 'ImportError: cannot import name '_udunits2' from partially
+     ;; initialized module 'cf_units' (most likely due to a circular import)'.
+     ;; Importing works after the package is built.
+     (list #:tests? #f
+           #:phases
+           #~(modify-phases %standard-phases
+               (add-after 'unpack 'udunits-path
+                 (lambda _
+                   (setenv "UDUNITS2_XML_PATH"
+                           (string-append
+                            #$(this-package-input "udunits")
+                            "/share/udunits/udunits2.xml"))))
+               ;; cf-units has a hard dependency on antlr4 4.7.2 and
+               ;; doesn't work with newer versions.  Upstream is trying
+               ;; to change it or make antlr4 optional, see
+               ;; https://github.com/SciTools/cf-units/issues/313
+               (delete 'sanity-check))))
+    (propagated-inputs (list java-antlr4-runtime-python
+                             python-cftime
+                             python-jinja2
+                             python-numpy))
+    (inputs (list udunits))
+    (native-inputs (list python-codecov
+                         python-cython
+                         python-jinja2
+                         python-pytest
+                         python-pytest-cov
+                         python-setuptools-scm))
+    (home-page "https://github.com/SciTools/cf-units")
+    (synopsis "Units of measure as required by the CF metadata conventions")
+    (description "This package provids units of measure as required by the
+ Climate and Forecast (CF) metadata conventions.")
+    (license license:lgpl3+)))
+
 (define-public tegola
   (package
     (name "tegola")
-- 
2.34.1

Message #37 received at 49207 <at> debbugs.gnu.org (full text, mbox):

From: Vinicius Monego <monego <at> posteo.net>
To: 49207 <at> debbugs.gnu.org
Cc: Vinicius Monego <monego <at> posteo.net>
Subject: [PATCH v2 3/5] gnu: python-dask: Propagate python-importlib-metadata.
Date: Fri,  9 Jun 2023 14:58:52 +0000

* gnu/packages/python-xyz.scm (python-dask)[native-inputs]: Move
python-importlib-metadata to...
[propagated-inputs]: ...here.
---
 gnu/packages/python-xyz.scm | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index 9036246bfb..7d5128911f 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -25146,6 +25146,7 @@ (define-public python-dask
     (propagated-inputs
      (list python-cloudpickle
            python-fsspec
+           python-importlib-metadata
            python-numpy
            python-packaging
            python-pandas
@@ -25154,7 +25155,6 @@ (define-public python-dask
            python-pyyaml))
     (native-inputs
      (list python-click
-           python-importlib-metadata
            python-pytest python-pytest-runner python-pytest-rerunfailures
            python-versioneer))
     (home-page "https://github.com/dask/dask/")
-- 
2.34.1

Message #40 received at 49207 <at> debbugs.gnu.org (full text, mbox):

From: Vinicius Monego <monego <at> posteo.net>
To: 49207 <at> debbugs.gnu.org
Cc: Vinicius Monego <monego <at> posteo.net>
Subject: [PATCH v2 4/5] gnu: python-cartopy: Add dependencies.
Date: Fri,  9 Jun 2023 14:58:53 +0000

* gnu/packages/geo.scm (python-cartopy)[native-inputs]: Add
python-setuptools-scm, python-wheel.
---
 gnu/packages/geo.scm | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/gnu/packages/geo.scm b/gnu/packages/geo.scm
index 2c15df18cc..c1b028104c 100644
--- a/gnu/packages/geo.scm
+++ b/gnu/packages/geo.scm
@@ -1303,7 +1303,9 @@ (define-public python-cartopy
      (list python-cython
            python-flufl-lock
            python-pytest
-           python-pytest-mpl))
+           python-pytest-mpl
+           python-setuptools-scm
+           python-wheel))
     (home-page "https://scitools.org.uk/cartopy/docs/latest/")
     (synopsis "Cartographic library for visualisation")
     (description
-- 
2.34.1

Message #43 received at 49207 <at> debbugs.gnu.org (full text, mbox):

From: Vinicius Monego <monego <at> posteo.net>
To: 49207 <at> debbugs.gnu.org
Cc: Vinicius Monego <monego <at> posteo.net>
Subject: [PATCH v2 5/5] gnu: Add python-scitools-iris.
Date: Fri,  9 Jun 2023 14:58:54 +0000

* gnu/packages/geo.scm (python-scitools-iris): New variable.
---
 gnu/packages/geo.scm | 69 ++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 69 insertions(+)

diff --git a/gnu/packages/geo.scm b/gnu/packages/geo.scm
index c1b028104c..eb58781591 100644
--- a/gnu/packages/geo.scm
+++ b/gnu/packages/geo.scm
@@ -73,6 +73,7 @@ (define-module (gnu packages geo)
   #:use-module (gnu packages curl)
   #:use-module (gnu packages databases)
   #:use-module (gnu packages datastructures)
+  #:use-module (gnu packages digest)
   #:use-module (gnu packages docbook)
   #:use-module (gnu packages documentation)
   #:use-module (gnu packages elf)
@@ -1428,6 +1429,74 @@ (define-public python-cf-units
  Climate and Forecast (CF) metadata conventions.")
     (license license:lgpl3+)))
 
+(define-public python-scitools-iris
+  (package
+    (name "python-scitools-iris")
+    (version "3.6.0")
+    (source (origin
+              (method url-fetch)
+              (uri (pypi-uri "scitools-iris" version))
+              (sha256
+               (base32
+                "08r13aans17qgv93m0hwzwmiqvbgkn5rhp9r5szyv4i99xz62igj"))))
+    (build-system pyproject-build-system)
+    (arguments
+     ;; Tests below fail because of URL open errors and missing data (which is
+     ;; probably being downloaded).
+     (list #:test-flags
+           #~(list "--ignore" "lib/iris/tests/test_cf.py"
+                   "--ignore" "lib/iris/tests/integration/netcdf/test_delayed_save.py"
+                   "--ignore" "lib/iris/tests/integration/netcdf/test_thread_safety.py"
+                   "--ignore" "lib/iris/tests/integration/plot/test_vector_plots.py"
+                   "--ignore" "lib/iris/tests/unit/analysis/regrid/test__CurvilinearRegridder.py"
+                   "-k" (string-append "not test_python_versions"
+                                       " and not test_2d_coords_contour"
+                                       " and not test_grouped_dim"
+                                       " and not test_ungrouped_dim"))
+           #:phases #~(modify-phases %standard-phases
+                        (add-before 'check 'build-std-names
+                          (lambda _
+                            ;; Need to build lib/iris/std_names.py before
+                            ;; running the tests.
+                            (invoke "python" "setup.py" "std_names")
+                            ;; Replace some executable paths.
+                            (let ((nc #$(this-package-native-input "netcdf")))
+                              (substitute* "lib/iris/tests/stock/netcdf.py"
+                                (("env_bin_path\\(\"ncgen\"\\)")
+                                 (format #f "\"~a/bin/ncgen\"" nc)))
+                              (substitute* "lib/iris/tests/__init__.py"
+                                (("env_bin_path\\(\"ncdump\"\\)")
+                                 (format #f "\"~a/bin/ncdump\"" nc))))))
+                        ;; To avoid the antlr4 error from cf-units.
+                        (delete 'sanity-check))))
+    (native-inputs (list netcdf
+                         python-click
+                         python-filelock
+                         python-imagehash
+                         python-pytest
+                         python-setuptools-scm
+                         python-wheel))
+    (propagated-inputs (list python-cartopy
+                             python-cf-units
+                             python-cftime
+                             python-dask
+                             python-distributed
+                             python-matplotlib
+                             python-netcdf4
+                             python-numpy
+                             python-pyproj
+                             python-scipy
+                             python-shapely
+                             python-xxhash))
+    (home-page "https://github.com/SciTools/iris")
+    (synopsis "Library for analysing and visualising Earth science data")
+    (description
+     "Iris is a Python library for analysing and visualising Earth
++science data.  It excels when working with multi-dimensional Earth Science
++data, where tabular representations become unwieldy and inefficient.  Iris
++implements a data model based on the CF conventions.")
+    (license license:lgpl3+)))
+
 (define-public tegola
   (package
     (name "tegola")
-- 
2.34.1

Message #48 received at 49207-done <at> debbugs.gnu.org (full text, mbox):

From: Sharlatan Hellseher <sharlatanus <at> gmail.com>
To: 49207-done <at> debbugs.gnu.org
Subject: gnu: Add python-iris. (scitools)
Date: Tue, 11 Feb 2025 16:07:37 +0000

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

Hi,

Thank you for the patches.

The list of some applied modifications:
- patches [5/5]
  - [X] [PATCH v2 1/5] gnu: Add python-imagehash.
    - move to python-science to reduce number of inputs in digest.
    - extend description, taken from project's README
    - add missing native inputs: python-setuptools, python-wheel
  - [X] [PATCH v2 2/5] gnu: Add python-cf-units.
    - refresh to 3.3.0
    - fix uri cf-units -> cf_units as seen in PyPI for source archive name
    - remove from native inputs: python-codecov, python-pytest-cov, python-jinja2
    - swap python-cython to python-cython as seen in project's pyproject.toml
    - add to native inptus: python-setuptools, python-wheel
    - enable tests
    - preserver snatity-check phase
  - [X] [PATCH v2 3/5] gnu: python-dask: Propagate python-importlib-metadata.
    - skip, not required.
  - [X] [PATCH v2 4/5] gnu: python-cartopy: Add dependencies.
    - skip, not required.
  - [X] [PATCH v2 5/5] gnu: Add python-scitools-iris.
    - re-imported and set author to Vinicius Monego <monego <at> posteo.net>
      as patch failed to apply, no base commit
    - refresh to 3.11.1
    - adjust uri name according to PyPI source archive
    - preserver snatity-check phase
    - skip all tests requring data files from
      https://github.com/SciTools/iris-test-data
    - enable parallel tests with pytest-xdist

Pushed 3 to master as:
ca0dc61a871 * master gnu: Add python-scitools-iris.
f1397f2f499 * gnu: Add python-cf-units.
5ff5a2b2cf5 * gnu: Add python-imagehash.

--
Oleg

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