[bug#47022] [PATCH 1/3] gnu: Add python-pooch.

[bug#47022] [PATCH 1/3] gnu: Add python-pooch.

[Vinicius Monego]

* gnu/packages/python-xyz.scm (python-pooch): New variable.
---
 gnu/packages/python-xyz.scm | 25 +++++++++++++++++++++++++
 1 file changed, 25 insertions(+)

diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index 912b9db62b..c1b67bffc6 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -19248,6 +19248,31 @@ library: to minimize boilerplate code in traditional extension modules by
 inferring type information using compile-time introspection.")
     (license license:bsd-3)))
 
+(define-public python-pooch
+  (package
+    (name "python-pooch")
+    (version "1.3.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "pooch" version))
+       (sha256
+        (base32 "1618adsg9r8fsv422sv35z1i723q3a1iir5v7dv2sklh4pl4im1h"))))
+    (build-system python-build-system)
+    (arguments
+     `(#:tests? #f)) ;requires online data
+    (propagated-inputs
+     `(("python-appdirs" ,python-appdirs)
+       ("python-packaging" ,python-packaging)
+       ("python-requests" ,python-requests)))
+    (home-page "https://github.com/fatiando/pooch")
+    (synopsis "Manage your Python library's sample data files")
+    (description
+     "Pooch manages your Python library's sample data files: it automatically
+downloads and stores them in a local directory, with support for versioning
+and corruption checks.")
+    (license license:bsd-3)))
+
 (define-public python-fasteners
   (package
     (name "python-fasteners")
-- 
2.30.1

[bug#47022] [PATCH 2/3] gnu: python-scikit-image: Update to 0.18.1.

[Vinicius Monego]

* gnu/packages/python-science.scm (python-scikit-image): Update to 0.18.1.
[propagated-inputs]: Remove python-six.
---
 gnu/packages/python-science.scm | 9 ++++-----
 1 file changed, 4 insertions(+), 5 deletions(-)

diff --git a/gnu/packages/python-science.scm b/gnu/packages/python-science.scm
index a1e2b57669..250ab4a192 100644
--- a/gnu/packages/python-science.scm
+++ b/gnu/packages/python-science.scm
@@ -9,7 +9,7 @@
 ;;; Copyright © 2019 Maxim Cournoyer <maxim.cournoyer@gmail.com>
 ;;; Copyright © 2019 Giacomo Leidi <goodoldpaul@autistici.org>
 ;;; Copyright © 2020 Pierre Langlois <pierre.langlois@gmx.com>
-;;; Copyright © 2020 Vinicius Monego <monego@posteo.net>
+;;; Copyright © 2020, 2021 Vinicius Monego <monego@posteo.net>
 ;;; Copyright © 2021 Greg Hogan <code@greghogan.com>
 ;;;
 ;;; This file is part of GNU Guix.
@@ -240,18 +240,18 @@ logic, also known as grey logic.")
 (define-public python-scikit-image
   (package
     (name "python-scikit-image")
-    (version "0.17.2")
+    (version "0.18.1")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "scikit-image" version))
        (sha256
-        (base32 "1cyqqbcbrg3prc36wis0sm3q5rjhd7h9bp33jwfyixzhi02lr5dx"))))
+        (base32 "0wgisa03smhrphcjnhq7waa5vyyd32b67hblapjbqrqqj751idpv"))))
     (build-system python-build-system)
     (arguments
      ;; TODO: Some tests require running X11 server. Disable them?
      '(#:tests? #f))
-    ;; See DEPENDS.txt for the list of build and run time requiremnts
+    ;; See requirements/ for the list of build and run time requirements.
     (propagated-inputs
      `(("python-cloudpickle" ,python-cloudpickle)
        ("python-dask" ,python-dask)
@@ -262,7 +262,6 @@ logic, also known as grey logic.")
        ("python-pillow" ,python-pillow)
        ("python-pywavelets" ,python-pywavelets)
        ("python-scipy" ,python-scipy)
-       ("python-six" ,python-six)
        ("python-tifffile" ,python-tifffile)))
     (native-inputs
      `(("python-cython" ,python-cython)))
-- 
2.30.1

[bug#47022] [PATCH 3/3] gnu: scikit-image: Enable tests.

[Vinicius Monego]

* gnu/packages/python-science.scm (scikit-image)[arguments]: Add phases related to tests.
[native-inputs]: Add python-codecov, python-flake8, python-pytest,
python-pytest-cov, python-pytest-localserver, python-wheel.
---
 gnu/packages/python-science.scm | 30 +++++++++++++++++++++++++++---
 1 file changed, 27 insertions(+), 3 deletions(-)

diff --git a/gnu/packages/python-science.scm b/gnu/packages/python-science.scm
index 250ab4a192..552c4c50cd 100644
--- a/gnu/packages/python-science.scm
+++ b/gnu/packages/python-science.scm
@@ -36,6 +36,8 @@
   #:use-module (gnu packages maths)
   #:use-module (gnu packages perl)
   #:use-module (gnu packages python)
+  #:use-module (gnu packages python-build)
+  #:use-module (gnu packages python-check)
   #:use-module (gnu packages python-web)
   #:use-module (gnu packages python-xyz)
   #:use-module (gnu packages sphinx)
@@ -249,9 +251,25 @@ logic, also known as grey logic.")
         (base32 "0wgisa03smhrphcjnhq7waa5vyyd32b67hblapjbqrqqj751idpv"))))
     (build-system python-build-system)
     (arguments
-     ;; TODO: Some tests require running X11 server. Disable them?
-     '(#:tests? #f))
+     `(#:phases
+       (modify-phases %standard-phases
+         (add-before 'build 'change-home-dir
+           (lambda _
+             ;; Change from /homeless-shelter to /tmp for write permission.
+             (setenv "HOME" "/tmp")
+             #t))
+         (replace 'build
+           (lambda _
+             (invoke "make")))
+         (replace 'check
+           (lambda _
+             ;; The following tests require online data.
+             (invoke "python" "-m" "pytest" "skimage" "--doctest-modules" "-k"
+                     (string-append "not test_ndim"
+                                    " and not test_skin")))))))
     ;; See requirements/ for the list of build and run time requirements.
+    ;; NOTE: scikit-image has an optional dependency on python-pooch, however
+    ;; propagating it would enable many more tests that require online data.
     (propagated-inputs
      `(("python-cloudpickle" ,python-cloudpickle)
        ("python-dask" ,python-dask)
@@ -264,7 +282,13 @@ logic, also known as grey logic.")
        ("python-scipy" ,python-scipy)
        ("python-tifffile" ,python-tifffile)))
     (native-inputs
-     `(("python-cython" ,python-cython)))
+     `(("python-codecov" ,python-codecov)
+       ("python-cython" ,python-cython)
+       ("python-flake8" ,python-flake8)
+       ("python-pytest" ,python-pytest)
+       ("python-pytest-cov" ,python-pytest-cov)
+       ("python-pytest-localserver" ,python-pytest-localserver)
+       ("python-wheel" ,python-wheel)))
     (home-page "https://scikit-image.org/")
     (synopsis "Image processing in Python")
     (description
-- 
2.30.1

[bug#47022] [PATCH v2 3/3] gnu: python-scikit-image: Enable tests.

[Vinicius Monego]

* gnu/packages/python-science.scm (python-scikit-image)[arguments]: Add phases
related to tests.
[native-inputs]: Add python-codecov, python-flake8, python-pytest,
python-pytest-cov, python-pytest-localserver, python-wheel.
---
Same patch, only changed commit message.

 gnu/packages/python-science.scm | 30 +++++++++++++++++++++++++++---
 1 file changed, 27 insertions(+), 3 deletions(-)

diff --git a/gnu/packages/python-science.scm b/gnu/packages/python-science.scm
index 250ab4a192..552c4c50cd 100644
--- a/gnu/packages/python-science.scm
+++ b/gnu/packages/python-science.scm
@@ -36,6 +36,8 @@
   #:use-module (gnu packages maths)
   #:use-module (gnu packages perl)
   #:use-module (gnu packages python)
+  #:use-module (gnu packages python-build)
+  #:use-module (gnu packages python-check)
   #:use-module (gnu packages python-web)
   #:use-module (gnu packages python-xyz)
   #:use-module (gnu packages sphinx)
@@ -249,9 +251,25 @@ logic, also known as grey logic.")
         (base32 "0wgisa03smhrphcjnhq7waa5vyyd32b67hblapjbqrqqj751idpv"))))
     (build-system python-build-system)
     (arguments
-     ;; TODO: Some tests require running X11 server. Disable them?
-     '(#:tests? #f))
+     `(#:phases
+       (modify-phases %standard-phases
+         (add-before 'build 'change-home-dir
+           (lambda _
+             ;; Change from /homeless-shelter to /tmp for write permission.
+             (setenv "HOME" "/tmp")
+             #t))
+         (replace 'build
+           (lambda _
+             (invoke "make")))
+         (replace 'check
+           (lambda _
+             ;; The following tests require online data.
+             (invoke "python" "-m" "pytest" "skimage" "--doctest-modules" "-k"
+                     (string-append "not test_ndim"
+                                    " and not test_skin")))))))
     ;; See requirements/ for the list of build and run time requirements.
+    ;; NOTE: scikit-image has an optional dependency on python-pooch, however
+    ;; propagating it would enable many more tests that require online data.
     (propagated-inputs
      `(("python-cloudpickle" ,python-cloudpickle)
        ("python-dask" ,python-dask)
@@ -264,7 +282,13 @@ logic, also known as grey logic.")
        ("python-scipy" ,python-scipy)
        ("python-tifffile" ,python-tifffile)))
     (native-inputs
-     `(("python-cython" ,python-cython)))
+     `(("python-codecov" ,python-codecov)
+       ("python-cython" ,python-cython)
+       ("python-flake8" ,python-flake8)
+       ("python-pytest" ,python-pytest)
+       ("python-pytest-cov" ,python-pytest-cov)
+       ("python-pytest-localserver" ,python-pytest-localserver)
+       ("python-wheel" ,python-wheel)))
     (home-page "https://scikit-image.org/")
     (synopsis "Image processing in Python")
     (description
-- 
2.30.1

bug#47022: [PATCH 1/3] gnu: Add python-pooch.

[Nicolas Goaziou]

Hello,

Vinicius Monego <monego@posteo.net> writes:

> * gnu/packages/python-xyz.scm (python-pooch): New variable.

Applied all three patches (v2 for the last one).

Thank you.

Regards,
-- 
Nicolas Goaziou