[bug#47976] [PATCH 00/10] Add Orange

[bug#47976] [PATCH 00/10] Add Orange

[Vinicius Monego]

This patchset adds the Orange data mining / data visualization / machine learning toolkit.

I had to disable tests for the orange widget base because unittest failed to load a file. But all tests for orange itself are passing.

Vinicius Monego (10):
  gnu: Add python-anyqt.
  gnu: Add python-pyqtgraph.
  gnu: Add python-qasync.
  gnu: Add python-orange-canvas-core.
  gnu: Add python-orange-widget-base.
  gnu: Add python-serverfiles.
  gnu: Add python-python-louvain.
  gnu: python-pynndescent: Update to 0.5.2.
  gnu: python-opentsne: Update to 0.5.2.
  gnu: Add orange.

 gnu/local.mk                      |   1 +
 gnu/packages/graph.scm            |  22 ++++
 gnu/packages/machine-learning.scm |   8 +-
 gnu/packages/orange.scm           | 211 ++++++++++++++++++++++++++++++
 gnu/packages/python-xyz.scm       | 113 ++++++++++++++++
 5 files changed, 351 insertions(+), 4 deletions(-)
 create mode 100644 gnu/packages/orange.scm

-- 
2.31.1

[bug#47976] [PATCH 01/10] gnu: Add python-anyqt.

[Vinicius Monego]

* gnu/packages/python-xyz.scm (python-anyqt): 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 c01993ecd7..7366dd190c 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -12395,6 +12395,32 @@ ISO 8859, etc.).")
 (define-public python2-translitcodec
   (package-with-python2 python-translitcodec))
 
+(define-public python-anyqt
+  (package
+    (name "python-anyqt")
+    (version "0.0.11")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "AnyQt" version))
+       (sha256
+        (base32 "0gl2czirzjvhbq963i2awxp8kwbc1grh67lpcwfipyn9w3kdwdj4"))))
+    (build-system python-build-system)
+    (arguments
+     `(#:tests? #f ;there are no tests
+       #:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'delete-files
+           ;; Delete files related to other operating systems.
+           (lambda _
+             (delete-file "AnyQt/QtMacExtras.py")
+             (delete-file "AnyQt/QtWinExtras.py")
+             #t)))))
+    (home-page "https://github.com/ales-erjavec/anyqt")
+    (synopsis "PyQt4/PyQt5 compatibility layer")
+    (description "AnyQt is a PyQt4/PyQt5 compatibility layer.")
+    (license license:gpl3)))
+
 (define-public python-editor
   (package
   (name "python-editor")
-- 
2.31.1

[bug#47976] [PATCH 02/10] gnu: Add python-pyqtgraph.

[Vinicius Monego]

* gnu/packages/python-xyz.scm (python-pyqtgraph): New variable.
---
The homepage does not support https.

 gnu/packages/python-xyz.scm | 52 +++++++++++++++++++++++++++++++++++++
 1 file changed, 52 insertions(+)

diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index 7366dd190c..e3e55c010a 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -12421,6 +12421,58 @@ ISO 8859, etc.).")
     (description "AnyQt is a PyQt4/PyQt5 compatibility layer.")
     (license license:gpl3)))
 
+(define-public python-pyqtgraph
+  (package
+    (name "python-pyqtgraph")
+    (version "0.12.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "pyqtgraph" version))
+       (sha256
+        (base32 "0kc7ncv0lr3spni29i9g8nszyr4xinswqi2zzs6v8kqqi593pvyj"))))
+    (build-system python-build-system)
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases
+         (add-before 'check 'set-home-and-qpa
+           (lambda _
+             (setenv "HOME" "/tmp")
+             (setenv "QT_QPA_PLATFORM" "offscreen")
+             #t))
+         (replace 'check
+           (lambda* (#:key inputs outputs #:allow-other-keys)
+             (add-installed-pythonpath inputs outputs)
+             (invoke "pytest" "-vv" "-k"
+                     ;; These tests try to download online data.
+                     (string-append "not test_PolyLineROI"
+                                    " and not test_getArrayRegion_axisorder"
+                                    " and not test_getArrayRegion"
+                                    " and not test_PlotCurveItem"
+                                    " and not test_NonUniformImage_colormap"
+                                    " and not test_NonUniformImage_lut"
+                                    " and not test_ImageItem_axisorder"
+                                    " and not test_ImageItem")))))))
+    (native-inputs
+     `(("python-pytest" ,python-pytest)
+       ("python-pytest-cov" ,python-pytest-cov)
+       ("python-pytest-xdist" ,python-pytest-xdist)))
+    (inputs
+     `(("qtbase" ,qtbase)))
+    (propagated-inputs
+     `(("python-h5py" ,python-h5py)
+       ("python-numpy" ,python-numpy)
+       ("python-pyopengl" ,python-pyopengl)
+       ("python-scipy" ,python-scipy)
+       ("python-pyqt" ,python-pyqt)))
+    (home-page "http://www.pyqtgraph.org")
+    (synopsis "Scientific Graphics and GUI Library for Python")
+    (description
+     "PyQtGraph is a Pure-python graphics library for PyQt5, PyQt6, PySide2
+and PySide6.  It is intended for use in mathematics, scientific or engineering
+applications.")
+    (license license:expat)))
+
 (define-public python-editor
   (package
   (name "python-editor")
-- 
2.31.1

[bug#47976] [PATCH 03/10] gnu: Add python-qasync.

[Vinicius Monego]

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

diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index e3e55c010a..66f9a98091 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -12473,6 +12473,41 @@ and PySide6.  It is intended for use in mathematics, scientific or engineering
 applications.")
     (license license:expat)))
 
+(define-public python-qasync
+  (package
+    (name "python-qasync")
+    (version "0.15.0")
+    (source
+     (origin
+       ;; There are no tests in the PyPI tarball.
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/CabbageDevelopment/qasync/")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "0va9h6v102d7mxz608banjc0l0v02dq3ywhr5i4nqaxx3qkazc2l"))))
+    (build-system python-build-system)
+    (arguments
+     `(#:test-target "pytest"
+       #:phases
+       (modify-phases %standard-phases
+         (add-before 'check 'set-qpa
+           (lambda _
+             (setenv "QT_QPA_PLATFORM" "offscreen")
+             #t)))))
+    (native-inputs
+     `(("python-pytest" ,python-pytest)
+       ("python-pytest-runner" ,python-pytest-runner)))
+    (propagated-inputs
+     `(("python-pyqt" ,python-pyqt)))
+    (home-page "https://github.com/CabbageDevelopment/qasync")
+    (synopsis "Implementation of the PEP 3156 Event-Loop with Qt")
+    (description
+     "@code{qasync} allows coroutines to be used in PyQt/PySide applications
+by providing an implementation of the PEP 3156 event-loop.")
+    (license license:bsd-3)))
+
 (define-public python-editor
   (package
   (name "python-editor")
-- 
2.31.1

[bug#47976] [PATCH 04/10] gnu: Add python-orange-canvas-core.

[Vinicius Monego]

* gnu/packages/orange.scm: New file.
* gnu/packages/local.mk (GNU_SYSTEM_MODULES): Add it.
---
 gnu/local.mk            |  1 +
 gnu/packages/orange.scm | 67 +++++++++++++++++++++++++++++++++++++++++
 2 files changed, 68 insertions(+)
 create mode 100644 gnu/packages/orange.scm

diff --git a/gnu/local.mk b/gnu/local.mk
index 50b11a8ca2..e8b6effb36 100644
--- a/gnu/local.mk
+++ b/gnu/local.mk
@@ -420,6 +420,7 @@ GNU_SYSTEM_MODULES =				\
   %D%/packages/openldap.scm			\
   %D%/packages/openpgp.scm			\
   %D%/packages/openstack.scm			\
+  %D%/packages/orange.scm			\
   %D%/packages/orpheus.scm			\
   %D%/packages/ots.scm				\
   %D%/packages/package-management.scm		\
diff --git a/gnu/packages/orange.scm b/gnu/packages/orange.scm
new file mode 100644
index 0000000000..9f30befde2
--- /dev/null
+++ b/gnu/packages/orange.scm
@@ -0,0 +1,67 @@
+;;; GNU Guix --- Functional package management for GNU
+;;; Copyright © 2021 Vinicius Monego <monego@posteo.net>
+;;;
+;;; This file is part of GNU Guix.
+;;;
+;;; GNU Guix is free software; you can redistribute it and/or modify it
+;;; under the terms of the GNU General Public License as published by
+;;; the Free Software Foundation; either version 3 of the License, or (at
+;;; your option) any later version.
+;;;
+;;; GNU Guix is distributed in the hope that it will be useful, but
+;;; WITHOUT ANY WARRANTY; without even the implied warranty of
+;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+;;; GNU General Public License for more details.
+;;;
+;;; You should have received a copy of the GNU General Public License
+;;; along with GNU Guix.  If not, see <http://www.gnu.org/licenses/>.
+
+(define-module (gnu packages orange)
+  #:use-module ((guix licenses) #:prefix license:)
+  #:use-module (guix packages)
+  #:use-module (guix download)
+  #:use-module (guix build-system python)
+  #:use-module (gnu packages)
+  #:use-module (gnu packages python-web)
+  #:use-module (gnu packages python-xyz)
+  #:use-module (gnu packages qt))
+
+(define-public python-orange-canvas-core
+  (package
+    (name "python-orange-canvas-core")
+    (version "0.1.19")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "orange-canvas-core" version))
+       (sha256
+        (base32 "03wav2msfm32y8zwq69v1v6qyh1ld76xla2z60avf49yhbwjgwal"))))
+    (build-system python-build-system)
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases
+         (add-before 'check 'check-setup
+           (lambda _
+             ;; This test fails with: RuntimeError: Event loop is closed.
+             (substitute* "orangecanvas/application/tests/test_mainwindow.py"
+               (("test_help_requests") "_test_help_requests"))
+             (setenv "HOME" "/tmp")
+             (setenv "QT_QPA_PLATFORM" "offscreen")
+             #t)))))
+    (propagated-inputs
+     `(("python-anyqt" ,python-anyqt)
+       ("python-cachecontrol" ,python-cachecontrol)
+       ("python-commonmark" ,python-commonmark)
+       ("python-dictdiffer" ,python-dictdiffer)
+       ("python-docutils" ,python-docutils)
+       ("python-pyqt" ,python-pyqt)
+       ("python-qasync" ,python-qasync)
+       ("python-requests" ,python-requests)
+       ("python-setuptools" ,python-setuptools)))
+    (home-page "https://github.com/biolab/orange-canvas-core")
+    (synopsis "Core component of Orange Canvas")
+    (description
+     "Orange Canvas Core is a framework for building graphical user interfaces
+for editing workflows.  It is a component used to build the Orange Canvas
+data-mining application.")
+    (license license:gpl3+)))
-- 
2.31.1

[bug#47976] [PATCH 05/10] gnu: Add python-orange-widget-base.

[Vinicius Monego]

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

diff --git a/gnu/packages/orange.scm b/gnu/packages/orange.scm
index 9f30befde2..1788163721 100644
--- a/gnu/packages/orange.scm
+++ b/gnu/packages/orange.scm
@@ -65,3 +65,38 @@
 for editing workflows.  It is a component used to build the Orange Canvas
 data-mining application.")
     (license license:gpl3+)))
+
+(define-public python-orange-widget-base
+  (package
+    (name "python-orange-widget-base")
+    (version "4.12.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "orange-widget-base" version))
+       (sha256
+        (base32 "13sy3s8rdqs3i3ghixljpqvnfz81qmbb0kqlasw39zvf39qc22kz"))))
+    (build-system python-build-system)
+    (arguments
+     `(;; unittest fails to load one test, all other tests are passing:
+       ;; AttributeError: module 'orangewidget' has no attribute 'version'.
+       #:tests? #f
+       #:phases
+       (modify-phases %standard-phases
+         (add-before 'check 'check-setup
+           (lambda _
+             (setenv "HOME" "/tmp")
+             (setenv "QT_QPA_PLATFORM" "offscreen")
+             #t)))))
+    (propagated-inputs
+     `(("python-anyqt" ,python-anyqt)
+       ("python-matplotlib" ,python-matplotlib)
+       ("python-orange-canvas-core"
+        ,python-orange-canvas-core)
+       ("python-pyqtgraph" ,python-pyqtgraph)))
+    (home-page "https://github.com/biolab/orange-widget-base")
+    (synopsis "Base Widget for Orange Canvas")
+    (description
+     "Orange Widget Base provides a base widget component for a interactive
+GUI based workflow.  It is primarily used in the Orange framework.")
+    (license license:gpl3+)))
-- 
2.31.1

[bug#47976] [PATCH 05/10] gnu: Add python-orange-widget-base.

[Leo Famulari]

On Fri, Apr 23, 2021 at 05:28:11PM +0000, Vinicius Monego wrote:
> * gnu/packages/orange.scm (python-orange-widget-base): New variable.

> +     `(;; unittest fails to load one test, all other tests are passing:
> +       ;; AttributeError: module 'orangewidget' has no attribute 'version'.
> +       #:tests? #f

Sometimes I see this similar errors caused by removal of the ".git"
metadata repository. The build scripts try to use Git to check the
version and fail. Anyways, it's not a big deal.

[bug#47976] [PATCH 06/10] gnu: Add python-serverfiles.

[Vinicius Monego]

* gnu/packages/orange.scm (python-serverfiles): New variable.
---
 gnu/packages/orange.scm | 21 +++++++++++++++++++++
 1 file changed, 21 insertions(+)

diff --git a/gnu/packages/orange.scm b/gnu/packages/orange.scm
index 1788163721..5713516e58 100644
--- a/gnu/packages/orange.scm
+++ b/gnu/packages/orange.scm
@@ -100,3 +100,24 @@ data-mining application.")
      "Orange Widget Base provides a base widget component for a interactive
 GUI based workflow.  It is primarily used in the Orange framework.")
     (license license:gpl3+)))
+
+(define-public python-serverfiles
+  (package
+    (name "python-serverfiles")
+    (version "0.3.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "serverfiles" version))
+       (sha256
+        (base32 "1qgbzgnaxj4wsp2rdas53qxsh0j7xpibq25w6lviwyaqwwrgq42y"))))
+    (build-system python-build-system)
+    (propagated-inputs
+     `(("python-requests" ,python-requests)))
+    (home-page "https://github.com/biolab/serverfiles")
+    (synopsis "Utility to access files on a HTTP server and store them locally")
+    (description
+     "This package provides an utility that accesses files on a HTTP server
+and stores them locally for reuse.  It is primarily used by the Orange
+framework.")
+    (license license:gpl3+)))
-- 
2.31.1

[bug#47976] [PATCH 07/10] gnu: Add python-python-louvain.

[Vinicius Monego]

* gnu/packages/graph.scm (python-python-louvain): New variable.
---
 gnu/packages/graph.scm | 22 ++++++++++++++++++++++
 1 file changed, 22 insertions(+)

diff --git a/gnu/packages/graph.scm b/gnu/packages/graph.scm
index d2e4c875a1..7b61c8f103 100644
--- a/gnu/packages/graph.scm
+++ b/gnu/packages/graph.scm
@@ -6,6 +6,7 @@
 ;;; Copyright © 2019 Andreas Enge <andreas@enge.fr>
 ;;; Copyright © 2020 Alexander Krotov <krotov@iitp.ru>
 ;;; Copyright © 2020 Pierre Langlois <pierre.langlos@gmx.com>
+;;; Copyright © 2021 Vinicius Monego <monego@posteo.net>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -228,6 +229,27 @@ subplots, multiple-axes, polar charts, and bubble charts. ")
 (define-public python2-plotly
   (package-with-python2 python-plotly-2.4.1))
 
+(define-public python-python-louvain
+  (package
+    (name "python-python-louvain")
+    (version "0.15")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "python-louvain" version))
+       (sha256
+        (base32 "1sqp97fwh4asx0jr72x8hil8z8fcg2xq92jklmh2m599pvgnx19a"))))
+    (build-system python-build-system)
+    (propagated-inputs
+     `(("python-networkx" ,python-networkx)
+       ("python-numpy" ,python-numpy)))
+    (home-page "https://github.com/taynaud/python-louvain")
+    (synopsis "Louvain algorithm for community detection")
+    (description
+     "This package provides a pure Python implementation of the Louvain
+algorithm for community detection in large networks.")
+    (license license:bsd-3)))
+
 (define-public python-louvain
   (package
     (name "python-louvain")
-- 
2.31.1

[bug#47976] [PATCH 08/10] gnu: python-pynndescent: Update to 0.5.2.

[Vinicius Monego]

* gnu/packages/machine-learning.scm (python-pynndescent): Update to 0.5.2.
---
 gnu/packages/machine-learning.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/machine-learning.scm b/gnu/packages/machine-learning.scm
index ddd600d0f0..fd4e55f30a 100644
--- a/gnu/packages/machine-learning.scm
+++ b/gnu/packages/machine-learning.scm
@@ -915,13 +915,13 @@ for scientific computing and data science (e.g. BLAS and OpenMP).")
 (define-public python-pynndescent
   (package
     (name "python-pynndescent")
-    (version "0.4.8")
+    (version "0.5.2")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "pynndescent" version))
        (sha256
-        (base32 "0li1fclif50v6xrq7wh3lif9vv5jpj7xhrb0z6g89wwjnp9b9833"))))
+        (base32 "0w87c2v0li2rdbx6qfc2lb6y6bxpdy3jwfgzfs1kcr4d1chj5zfr"))))
     (build-system python-build-system)
     (native-inputs
      `(("python-nose" ,python-nose)))
-- 
2.31.1

[bug#47976] [PATCH 09/10] gnu: python-opentsne: Update to 0.5.2.

[Vinicius Monego]

* gnu/packages/machine-learning.scm (python-opentsne): Update to 0.5.2.
---
 gnu/packages/machine-learning.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/machine-learning.scm b/gnu/packages/machine-learning.scm
index fd4e55f30a..837ebbba67 100644
--- a/gnu/packages/machine-learning.scm
+++ b/gnu/packages/machine-learning.scm
@@ -941,7 +941,7 @@ for k-neighbor-graph construction and approximate nearest neighbor search.")
 (define-public python-opentsne
   (package
     (name "python-opentsne")
-    (version "0.4.4")
+    (version "0.5.2")
     (source
      (origin
        ;; No tests in the PyPI tarball.
@@ -951,7 +951,7 @@ for k-neighbor-graph construction and approximate nearest neighbor search.")
              (commit (string-append "v" version))))
        (file-name (string-append name "-" version "-checkout"))
        (sha256
-        (base32 "08wamsssmyf6511cbmglm67dp48i6xazs89m1cskdk219v90bc76"))))
+        (base32 "1hl42wmafydk4fxdx05l180k3canmqw8h9r20fsqq2aq440b09gh"))))
     (build-system python-build-system)
     (arguments
      `(#:phases
-- 
2.31.1

[bug#47976] [PATCH 10/10] gnu: Add orange.

[Vinicius Monego]

* gnu/packages/orange.scm (orange): New variable.
---
 gnu/packages/orange.scm | 88 +++++++++++++++++++++++++++++++++++++++++
 1 file changed, 88 insertions(+)

diff --git a/gnu/packages/orange.scm b/gnu/packages/orange.scm
index 5713516e58..f70bd83c47 100644
--- a/gnu/packages/orange.scm
+++ b/gnu/packages/orange.scm
@@ -22,6 +22,11 @@
   #:use-module (guix download)
   #:use-module (guix build-system python)
   #:use-module (gnu packages)
+  #:use-module (gnu packages freedesktop)
+  #:use-module (gnu packages graph)
+  #:use-module (gnu packages machine-learning)
+  #:use-module (gnu packages python-crypto)
+  #:use-module (gnu packages python-science)
   #:use-module (gnu packages python-web)
   #:use-module (gnu packages python-xyz)
   #:use-module (gnu packages qt))
@@ -101,6 +106,89 @@ data-mining application.")
 GUI based workflow.  It is primarily used in the Orange framework.")
     (license license:gpl3+)))
 
+(define-public orange
+  (package
+    (name "orange")
+    (version "3.28.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "Orange3" version))
+       (sha256
+        (base32 "1ac4xjjkx06z10hl7k0zh1z3qhkl5vng15l9jkpkmck9spinbzil"))))
+    (build-system python-build-system)
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'preparations
+           (lambda _
+             ;; Delete test that opens an outgoing connection.
+             (delete-file "Orange/tests/test_url_reader.py")
+             ;; This is a binary file and it breaks runpath validation.
+             (delete-file "Orange/tests/datasets/binary-blob.tab")
+             ;; Skip the test which uses that binary file.
+             (substitute* "Orange/tests/test_txt_reader.py"
+               (("test_read_nonutf8_encoding") "_test_read_nonutf8_encoding"))
+             ;; Relax some dependency versions.
+             (substitute* "requirements-gui.txt" (("PyQtWebEngine>=5.12") ""))
+             (substitute* "requirements-core.txt"
+               (("httpx>=0.14.0,<0.17") "httpx"))
+             #t))
+         (add-before 'check 'set-HOME
+           ;; Tests need a writable home.
+           (lambda _ (setenv "HOME" "/tmp") #t))
+         (add-after 'install 'wrap-executable
+           ;; Ensure that icons are found at runtime.
+           (lambda* (#:key inputs outputs #:allow-other-keys)
+             (let ((out (assoc-ref outputs "out")))
+               (wrap-program (string-append out "/bin/orange-canvas")
+                 `("QT_PLUGIN_PATH" prefix
+                   ,(list (string-append (assoc-ref inputs "qtsvg")
+                                         "/lib/qt5/plugins/")))))
+             #t)))))
+    (native-inputs
+     `(("python-cython" ,python-cython)))
+    (inputs
+     `(("python-anyqt" ,python-anyqt)
+       ("python-baycomp" ,python-baycomp)
+       ("python-bottleneck" ,python-bottleneck)
+       ("python-chardet" ,python-chardet)
+       ("python-httpx" ,python-httpx)
+       ("python-joblib" ,python-joblib)
+       ("python-keyring" ,python-keyring)
+       ("python-keyrings.alt" ,python-keyrings.alt)
+       ("python-louvain" ,python-python-louvain)
+       ("python-matplotlib" ,python-matplotlib)
+       ("python-networkx" ,python-networkx)
+       ("python-numpy" ,python-numpy)
+       ("python-openpyxl" ,python-openpyxl)
+       ("python-opentsne" ,python-opentsne)
+       ("python-orange-canvas-core"
+        ,python-orange-canvas-core)
+       ("python-orange-widget-base"
+        ,python-orange-widget-base)
+       ("python-pandas" ,python-pandas)
+       ("python-pyqt" ,python-pyqt)
+       ("python-pyqtgraph" ,python-pyqtgraph)
+       ("python-pyqtwebengine" ,python-pyqtwebengine)
+       ("python-pyyaml" ,python-pyyaml)
+       ("python-requests" ,python-requests)
+       ("python-scikit-learn" ,python-scikit-learn)
+       ("python-scipy" ,python-scipy)
+       ("python-serverfiles" ,python-serverfiles)
+       ("python-xlrd" ,python-xlrd)
+       ("python-xlsxwriter" ,python-xlsxwriter)
+       ("qtbase" ,qtbase)
+       ("qtsvg" ,qtsvg)
+       ("xdg-utils" ,xdg-utils)))
+    (home-page "https://orangedatamining.com/")
+    (synopsis "Component-based data mining framework")
+    (description
+     "Orange is a graphical toolkit for machine learning, data analysis and
+visualization based on the Qt framework.  It is easy to use and enables rapid
+experimenting with its tools.")
+    (license license:gpl3+)))
+
 (define-public python-serverfiles
   (package
     (name "python-serverfiles")
-- 
2.31.1

[bug#47976] [PATCH 10/10] gnu: Add orange.

[Leo Famulari]

On Fri, Apr 23, 2021 at 05:28:16PM +0000, Vinicius Monego wrote:
> * gnu/packages/orange.scm (orange): New variable.
> +         (add-after 'unpack 'preparations
> +           (lambda _
> +             ;; Delete test that opens an outgoing connection.
> +             (delete-file "Orange/tests/test_url_reader.py")

Okay.

> +             ;; This is a binary file and it breaks runpath validation.
> +             (delete-file "Orange/tests/datasets/binary-blob.tab")
> +             ;; Skip the test which uses that binary file.
> +             (substitute* "Orange/tests/test_txt_reader.py"
> +               (("test_read_nonutf8_encoding") "_test_read_nonutf8_encoding"))

If 'binary-blob.tab' is software, we should remove it in an origin
snippet. If it's just data, then it's fine to do it like this.

> +             ;; Relax some dependency versions.
> +             (substitute* "requirements-gui.txt" (("PyQtWebEngine>=5.12") ""))

Isn't this unecessary? We have PyQtWebEngine 5.15.2.

> +             (substitute* "requirements-core.txt"
> +               (("httpx>=0.14.0,<0.17") "httpx"))

And for this, we have 0.16.1.

[bug#47976] [PATCH 10/10] gnu: Add orange.

[Vinicius Monego]

Leo Famulari writes:

>> +             ;; This is a binary file and it breaks runpath validation.
>> +             (delete-file "Orange/tests/datasets/binary-blob.tab")
>> +             ;; Skip the test which uses that binary file.
>> +             (substitute* "Orange/tests/test_txt_reader.py"
>> +               (("test_read_nonutf8_encoding") "_test_read_nonutf8_encoding"))
>
> If 'binary-blob.tab' is software, we should remove it in an origin
> snippet. If it's just data, then it's fine to do it like this.
>

It is just data.

>> +             ;; Relax some dependency versions.
>> +             (substitute* "requirements-gui.txt" (("PyQtWebEngine>=5.12") ""))
>
> Isn't this unecessary? We have PyQtWebEngine 5.15.2.
>

There's something with pyqtwebengine not being found. The check phase
will fail to find it if I don't remove it from requirements. The same
happened in the Spyder package, but in that case the executable would
complain. I'm not sure why this happens.

>> +             (substitute* "requirements-core.txt"
>> +               (("httpx>=0.14.0,<0.17") "httpx"))
>
> And for this, we have 0.16.1.

Ok, 0.17 has been out for a while now and I have an update for it, but
did not submit yet. I will leave this substitution for later then.

[bug#47976] [PATCH 10/10] gnu: Add orange.

[Leo Famulari]

On Fri, Apr 23, 2021 at 09:04:22PM +0000, Vinicius Monego wrote:
> Ok, 0.17 has been out for a while now and I have an update for it, but
> did not submit yet. I will leave this substitution for later then.

We don't usually relax version restrictions to use non-approved
versions. The program will have to be changed upstream to work with
httpx 0.17. So, this substitution should be removed from the patch.

[bug#47976] [PATCH 00/10] Add Orange

[Leo Famulari]

On Fri, Apr 23, 2021 at 05:25:47PM +0000, Vinicius Monego wrote:
> This patchset adds the Orange data mining / data visualization / machine learning toolkit.
> 
> I had to disable tests for the orange widget base because unittest failed to load a file. But all tests for orange itself are passing.
> 
> Vinicius Monego (10):
>   gnu: Add python-anyqt.
>   gnu: Add python-pyqtgraph.
>   gnu: Add python-qasync.
>   gnu: Add python-orange-canvas-core.
>   gnu: Add python-orange-widget-base.
>   gnu: Add python-serverfiles.
>   gnu: Add python-python-louvain.
>   gnu: python-pynndescent: Update to 0.5.2.
>   gnu: python-opentsne: Update to 0.5.2.
>   gnu: Add orange.

Thanks! I sent some comments.

Otherwise, the patches look good to me, based on these standard
assumptions:

1) You linted and built the packages
2) The packages are using the latest upstream versions
3) You checked that the licenses are correct

[bug#47976] [PATCH 00/10] Add Orange

[Vinicius Monego]

Leo Famulari writes:

> On Fri, Apr 23, 2021 at 05:25:47PM +0000, Vinicius Monego wrote:
>> This patchset adds the Orange data mining / data visualization / machine learning toolkit.
>> 
>> I had to disable tests for the orange widget base because unittest failed to load a file. But all tests for orange itself are passing.
>> 
>> Vinicius Monego (10):
>>   gnu: Add python-anyqt.
>>   gnu: Add python-pyqtgraph.
>>   gnu: Add python-qasync.
>>   gnu: Add python-orange-canvas-core.
>>   gnu: Add python-orange-widget-base.
>>   gnu: Add python-serverfiles.
>>   gnu: Add python-python-louvain.
>>   gnu: python-pynndescent: Update to 0.5.2.
>>   gnu: python-opentsne: Update to 0.5.2.
>>   gnu: Add orange.
>
> Thanks! I sent some comments.
>
> Otherwise, the patches look good to me, based on these standard
> assumptions:
>
> 1) You linted and built the packages
> 2) The packages are using the latest upstream versions
> 3) You checked that the licenses are correct

Thanks for the reminder. I spotted some issues.

- python-setuptools can be removed from the inputs of
  python-orange-canvas-core. The linter will also complain about
  python-docutils being propagated, but that is how it should be.
- python-qasync's license is bsd-2, not bsd-3.
- httpx doesn't need version substitution in orange (already commented
in the other reply).

Orange also states in the website that "non-code" parts are licensed
under CC-BY-SA (version not specified), if that's relevant:

https://orangedatamining.com/license/

All versions are up to date and all packages were built.

Should I send a v2 only for the affected patches?

[bug#47976] [PATCH 00/10] Add Orange

[Leo Famulari]

On Fri, Apr 23, 2021 at 09:20:08PM +0000, Vinicius Monego wrote:
> Should I send a v2 only for the affected patches?

Can you send the full patch series as v2?

If that's not convenient, I can pick between v1 and v2.

[bug#47976] [PATCH v2 01/10] gnu: Add python-anyqt.

[Vinicius Monego]

* gnu/packages/python-xyz.scm (python-anyqt): New variable.
---
No changes.

 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 c01993ecd7..7366dd190c 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -12395,6 +12395,32 @@ ISO 8859, etc.).")
 (define-public python2-translitcodec
   (package-with-python2 python-translitcodec))
 
+(define-public python-anyqt
+  (package
+    (name "python-anyqt")
+    (version "0.0.11")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "AnyQt" version))
+       (sha256
+        (base32 "0gl2czirzjvhbq963i2awxp8kwbc1grh67lpcwfipyn9w3kdwdj4"))))
+    (build-system python-build-system)
+    (arguments
+     `(#:tests? #f ;there are no tests
+       #:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'delete-files
+           ;; Delete files related to other operating systems.
+           (lambda _
+             (delete-file "AnyQt/QtMacExtras.py")
+             (delete-file "AnyQt/QtWinExtras.py")
+             #t)))))
+    (home-page "https://github.com/ales-erjavec/anyqt")
+    (synopsis "PyQt4/PyQt5 compatibility layer")
+    (description "AnyQt is a PyQt4/PyQt5 compatibility layer.")
+    (license license:gpl3)))
+
 (define-public python-editor
   (package
   (name "python-editor")
-- 
2.31.1

[bug#47976] [PATCH v2 02/10] gnu: Add python-pyqtgraph.

[Vinicius Monego]

* gnu/packages/python-xyz.scm (python-pyqtgraph): New variable.
---
Changed casing in synopsis.

 gnu/packages/python-xyz.scm | 52 +++++++++++++++++++++++++++++++++++++
 1 file changed, 52 insertions(+)

diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index 7366dd190c..9bd78986bd 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -12421,6 +12421,58 @@ ISO 8859, etc.).")
     (description "AnyQt is a PyQt4/PyQt5 compatibility layer.")
     (license license:gpl3)))
 
+(define-public python-pyqtgraph
+  (package
+    (name "python-pyqtgraph")
+    (version "0.12.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "pyqtgraph" version))
+       (sha256
+        (base32 "0kc7ncv0lr3spni29i9g8nszyr4xinswqi2zzs6v8kqqi593pvyj"))))
+    (build-system python-build-system)
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases
+         (add-before 'check 'set-home-and-qpa
+           (lambda _
+             (setenv "HOME" "/tmp")
+             (setenv "QT_QPA_PLATFORM" "offscreen")
+             #t))
+         (replace 'check
+           (lambda* (#:key inputs outputs #:allow-other-keys)
+             (add-installed-pythonpath inputs outputs)
+             (invoke "pytest" "-vv" "-k"
+                     ;; These tests try to download online data.
+                     (string-append "not test_PolyLineROI"
+                                    " and not test_getArrayRegion_axisorder"
+                                    " and not test_getArrayRegion"
+                                    " and not test_PlotCurveItem"
+                                    " and not test_NonUniformImage_colormap"
+                                    " and not test_NonUniformImage_lut"
+                                    " and not test_ImageItem_axisorder"
+                                    " and not test_ImageItem")))))))
+    (native-inputs
+     `(("python-pytest" ,python-pytest)
+       ("python-pytest-cov" ,python-pytest-cov)
+       ("python-pytest-xdist" ,python-pytest-xdist)))
+    (inputs
+     `(("qtbase" ,qtbase)))
+    (propagated-inputs
+     `(("python-h5py" ,python-h5py)
+       ("python-numpy" ,python-numpy)
+       ("python-pyopengl" ,python-pyopengl)
+       ("python-scipy" ,python-scipy)
+       ("python-pyqt" ,python-pyqt)))
+    (home-page "http://www.pyqtgraph.org")
+    (synopsis "Scientific graphics and GUI library for Python")
+    (description
+     "PyQtGraph is a Pure-python graphics library for PyQt5, PyQt6, PySide2
+and PySide6.  It is intended for use in mathematics, scientific or engineering
+applications.")
+    (license license:expat)))
+
 (define-public python-editor
   (package
   (name "python-editor")
-- 
2.31.1

[bug#47976] [PATCH v2 03/10] gnu: Add python-qasync.

[Vinicius Monego]

* gnu/packages/python-xyz.scm (python-qasync): New variable.
---
Changed license from bsd-3 to bsd-2.

 gnu/packages/python-xyz.scm | 35 +++++++++++++++++++++++++++++++++++
 1 file changed, 35 insertions(+)

diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index 9bd78986bd..d77599d53d 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -12473,6 +12473,41 @@ and PySide6.  It is intended for use in mathematics, scientific or engineering
 applications.")
     (license license:expat)))
 
+(define-public python-qasync
+  (package
+    (name "python-qasync")
+    (version "0.15.0")
+    (source
+     (origin
+       ;; There are no tests in the PyPI tarball.
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/CabbageDevelopment/qasync/")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "0va9h6v102d7mxz608banjc0l0v02dq3ywhr5i4nqaxx3qkazc2l"))))
+    (build-system python-build-system)
+    (arguments
+     `(#:test-target "pytest"
+       #:phases
+       (modify-phases %standard-phases
+         (add-before 'check 'set-qpa
+           (lambda _
+             (setenv "QT_QPA_PLATFORM" "offscreen")
+             #t)))))
+    (native-inputs
+     `(("python-pytest" ,python-pytest)
+       ("python-pytest-runner" ,python-pytest-runner)))
+    (propagated-inputs
+     `(("python-pyqt" ,python-pyqt)))
+    (home-page "https://github.com/CabbageDevelopment/qasync")
+    (synopsis "Implementation of the PEP 3156 Event-Loop with Qt")
+    (description
+     "@code{qasync} allows coroutines to be used in PyQt/PySide applications
+by providing an implementation of the PEP 3156 event-loop.")
+    (license license:bsd-2)))
+
 (define-public python-editor
   (package
   (name "python-editor")
-- 
2.31.1

[bug#47976] [PATCH v2 04/10] gnu: Add python-orange-canvas-core.

[Vinicius Monego]

* gnu/packages/orange.scm: New file.
* gnu/packages/local.mk (GNU_SYSTEM_MODULES): Add it.
---
Removed python-setuptools from propagated-inputs.
Changed license from gpl3+ to gpl3 (setup.py does not mention any later versions).

 gnu/local.mk            |  1 +
 gnu/packages/orange.scm | 66 +++++++++++++++++++++++++++++++++++++++++
 2 files changed, 67 insertions(+)
 create mode 100644 gnu/packages/orange.scm

diff --git a/gnu/local.mk b/gnu/local.mk
index 50b11a8ca2..e8b6effb36 100644
--- a/gnu/local.mk
+++ b/gnu/local.mk
@@ -420,6 +420,7 @@ GNU_SYSTEM_MODULES =				\
   %D%/packages/openldap.scm			\
   %D%/packages/openpgp.scm			\
   %D%/packages/openstack.scm			\
+  %D%/packages/orange.scm			\
   %D%/packages/orpheus.scm			\
   %D%/packages/ots.scm				\
   %D%/packages/package-management.scm		\
diff --git a/gnu/packages/orange.scm b/gnu/packages/orange.scm
new file mode 100644
index 0000000000..fb273cbbec
--- /dev/null
+++ b/gnu/packages/orange.scm
@@ -0,0 +1,66 @@
+;;; GNU Guix --- Functional package management for GNU
+;;; Copyright © 2021 Vinicius Monego <monego@posteo.net>
+;;;
+;;; This file is part of GNU Guix.
+;;;
+;;; GNU Guix is free software; you can redistribute it and/or modify it
+;;; under the terms of the GNU General Public License as published by
+;;; the Free Software Foundation; either version 3 of the License, or (at
+;;; your option) any later version.
+;;;
+;;; GNU Guix is distributed in the hope that it will be useful, but
+;;; WITHOUT ANY WARRANTY; without even the implied warranty of
+;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+;;; GNU General Public License for more details.
+;;;
+;;; You should have received a copy of the GNU General Public License
+;;; along with GNU Guix.  If not, see <http://www.gnu.org/licenses/>.
+
+(define-module (gnu packages orange)
+  #:use-module ((guix licenses) #:prefix license:)
+  #:use-module (guix packages)
+  #:use-module (guix download)
+  #:use-module (guix build-system python)
+  #:use-module (gnu packages)
+  #:use-module (gnu packages python-web)
+  #:use-module (gnu packages python-xyz)
+  #:use-module (gnu packages qt))
+
+(define-public python-orange-canvas-core
+  (package
+    (name "python-orange-canvas-core")
+    (version "0.1.19")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "orange-canvas-core" version))
+       (sha256
+        (base32 "03wav2msfm32y8zwq69v1v6qyh1ld76xla2z60avf49yhbwjgwal"))))
+    (build-system python-build-system)
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases
+         (add-before 'check 'check-setup
+           (lambda _
+             ;; This test fails with: RuntimeError: Event loop is closed.
+             (substitute* "orangecanvas/application/tests/test_mainwindow.py"
+               (("test_help_requests") "_test_help_requests"))
+             (setenv "HOME" "/tmp")
+             (setenv "QT_QPA_PLATFORM" "offscreen")
+             #t)))))
+    (propagated-inputs
+     `(("python-anyqt" ,python-anyqt)
+       ("python-cachecontrol" ,python-cachecontrol)
+       ("python-commonmark" ,python-commonmark)
+       ("python-dictdiffer" ,python-dictdiffer)
+       ("python-docutils" ,python-docutils)
+       ("python-pyqt" ,python-pyqt)
+       ("python-qasync" ,python-qasync)
+       ("python-requests" ,python-requests)))
+    (home-page "https://github.com/biolab/orange-canvas-core")
+    (synopsis "Core component of Orange Canvas")
+    (description
+     "Orange Canvas Core is a framework for building graphical user interfaces
+for editing workflows.  It is a component used to build the Orange Canvas
+data-mining application.")
+    (license license:gpl3)))
-- 
2.31.1

[bug#47976] [PATCH v2 05/10] gnu: Add python-orange-widget-base.

[Vinicius Monego]

* gnu/packages/orange.scm (python-orange-widget-base): New variable.
---
No changes.

 gnu/packages/orange.scm | 35 +++++++++++++++++++++++++++++++++++
 1 file changed, 35 insertions(+)

diff --git a/gnu/packages/orange.scm b/gnu/packages/orange.scm
index fb273cbbec..8cb8159594 100644
--- a/gnu/packages/orange.scm
+++ b/gnu/packages/orange.scm
@@ -64,3 +64,38 @@
 for editing workflows.  It is a component used to build the Orange Canvas
 data-mining application.")
     (license license:gpl3)))
+
+(define-public python-orange-widget-base
+  (package
+    (name "python-orange-widget-base")
+    (version "4.12.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "orange-widget-base" version))
+       (sha256
+        (base32 "13sy3s8rdqs3i3ghixljpqvnfz81qmbb0kqlasw39zvf39qc22kz"))))
+    (build-system python-build-system)
+    (arguments
+     `(;; unittest fails to load one test, all other tests are passing:
+       ;; AttributeError: module 'orangewidget' has no attribute 'version'.
+       #:tests? #f
+       #:phases
+       (modify-phases %standard-phases
+         (add-before 'check 'check-setup
+           (lambda _
+             (setenv "HOME" "/tmp")
+             (setenv "QT_QPA_PLATFORM" "offscreen")
+             #t)))))
+    (propagated-inputs
+     `(("python-anyqt" ,python-anyqt)
+       ("python-matplotlib" ,python-matplotlib)
+       ("python-orange-canvas-core"
+        ,python-orange-canvas-core)
+       ("python-pyqtgraph" ,python-pyqtgraph)))
+    (home-page "https://github.com/biolab/orange-widget-base")
+    (synopsis "Base Widget for Orange Canvas")
+    (description
+     "Orange Widget Base provides a base widget component for a interactive
+GUI based workflow.  It is primarily used in the Orange framework.")
+    (license license:gpl3+)))
-- 
2.31.1

[bug#47976] [PATCH v2 06/10] gnu: Add python-serverfiles.

[Vinicius Monego]

* gnu/packages/orange.scm (python-serverfiles): New variable.
---
No changes.

 gnu/packages/orange.scm | 21 +++++++++++++++++++++
 1 file changed, 21 insertions(+)

diff --git a/gnu/packages/orange.scm b/gnu/packages/orange.scm
index 8cb8159594..97be36e489 100644
--- a/gnu/packages/orange.scm
+++ b/gnu/packages/orange.scm
@@ -99,3 +99,24 @@ data-mining application.")
      "Orange Widget Base provides a base widget component for a interactive
 GUI based workflow.  It is primarily used in the Orange framework.")
     (license license:gpl3+)))
+
+(define-public python-serverfiles
+  (package
+    (name "python-serverfiles")
+    (version "0.3.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "serverfiles" version))
+       (sha256
+        (base32 "1qgbzgnaxj4wsp2rdas53qxsh0j7xpibq25w6lviwyaqwwrgq42y"))))
+    (build-system python-build-system)
+    (propagated-inputs
+     `(("python-requests" ,python-requests)))
+    (home-page "https://github.com/biolab/serverfiles")
+    (synopsis "Utility to access files on a HTTP server and store them locally")
+    (description
+     "This package provides an utility that accesses files on a HTTP server
+and stores them locally for reuse.  It is primarily used by the Orange
+framework.")
+    (license license:gpl3+)))
-- 
2.31.1

[bug#47976] [PATCH v2 07/10] gnu: Add python-python-louvain.

[Vinicius Monego]

* gnu/packages/graph.scm (python-python-louvain): New variable.
---
No changes.

 gnu/packages/graph.scm | 22 ++++++++++++++++++++++
 1 file changed, 22 insertions(+)

diff --git a/gnu/packages/graph.scm b/gnu/packages/graph.scm
index d2e4c875a1..7b61c8f103 100644
--- a/gnu/packages/graph.scm
+++ b/gnu/packages/graph.scm
@@ -6,6 +6,7 @@
 ;;; Copyright © 2019 Andreas Enge <andreas@enge.fr>
 ;;; Copyright © 2020 Alexander Krotov <krotov@iitp.ru>
 ;;; Copyright © 2020 Pierre Langlois <pierre.langlos@gmx.com>
+;;; Copyright © 2021 Vinicius Monego <monego@posteo.net>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -228,6 +229,27 @@ subplots, multiple-axes, polar charts, and bubble charts. ")
 (define-public python2-plotly
   (package-with-python2 python-plotly-2.4.1))
 
+(define-public python-python-louvain
+  (package
+    (name "python-python-louvain")
+    (version "0.15")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "python-louvain" version))
+       (sha256
+        (base32 "1sqp97fwh4asx0jr72x8hil8z8fcg2xq92jklmh2m599pvgnx19a"))))
+    (build-system python-build-system)
+    (propagated-inputs
+     `(("python-networkx" ,python-networkx)
+       ("python-numpy" ,python-numpy)))
+    (home-page "https://github.com/taynaud/python-louvain")
+    (synopsis "Louvain algorithm for community detection")
+    (description
+     "This package provides a pure Python implementation of the Louvain
+algorithm for community detection in large networks.")
+    (license license:bsd-3)))
+
 (define-public python-louvain
   (package
     (name "python-louvain")
-- 
2.31.1

[bug#47976] [PATCH v2 08/10] gnu: python-pynndescent: Update to 0.5.2.

[Vinicius Monego]

* gnu/packages/machine-learning.scm (python-pynndescent): Update to 0.5.2.
---
No changes.

 gnu/packages/machine-learning.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/machine-learning.scm b/gnu/packages/machine-learning.scm
index ddd600d0f0..fd4e55f30a 100644
--- a/gnu/packages/machine-learning.scm
+++ b/gnu/packages/machine-learning.scm
@@ -915,13 +915,13 @@ for scientific computing and data science (e.g. BLAS and OpenMP).")
 (define-public python-pynndescent
   (package
     (name "python-pynndescent")
-    (version "0.4.8")
+    (version "0.5.2")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "pynndescent" version))
        (sha256
-        (base32 "0li1fclif50v6xrq7wh3lif9vv5jpj7xhrb0z6g89wwjnp9b9833"))))
+        (base32 "0w87c2v0li2rdbx6qfc2lb6y6bxpdy3jwfgzfs1kcr4d1chj5zfr"))))
     (build-system python-build-system)
     (native-inputs
      `(("python-nose" ,python-nose)))
-- 
2.31.1

[bug#47976] [PATCH v2 09/10] gnu: python-opentsne: Update to 0.5.2.

[Vinicius Monego]

* gnu/packages/machine-learning.scm (python-opentsne): Update to 0.5.2.
---
No changes.

 gnu/packages/machine-learning.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/machine-learning.scm b/gnu/packages/machine-learning.scm
index fd4e55f30a..837ebbba67 100644
--- a/gnu/packages/machine-learning.scm
+++ b/gnu/packages/machine-learning.scm
@@ -941,7 +941,7 @@ for k-neighbor-graph construction and approximate nearest neighbor search.")
 (define-public python-opentsne
   (package
     (name "python-opentsne")
-    (version "0.4.4")
+    (version "0.5.2")
     (source
      (origin
        ;; No tests in the PyPI tarball.
@@ -951,7 +951,7 @@ for k-neighbor-graph construction and approximate nearest neighbor search.")
              (commit (string-append "v" version))))
        (file-name (string-append name "-" version "-checkout"))
        (sha256
-        (base32 "08wamsssmyf6511cbmglm67dp48i6xazs89m1cskdk219v90bc76"))))
+        (base32 "1hl42wmafydk4fxdx05l180k3canmqw8h9r20fsqq2aq440b09gh"))))
     (build-system python-build-system)
     (arguments
      `(#:phases
-- 
2.31.1

[bug#47976] [PATCH v2 10/10] gnu: Add orange.

[Vinicius Monego]

* gnu/packages/orange.scm (orange): New variable.
---
Removed httpx version substitution, rewritten description.

 gnu/packages/orange.scm | 85 +++++++++++++++++++++++++++++++++++++++++
 1 file changed, 85 insertions(+)

diff --git a/gnu/packages/orange.scm b/gnu/packages/orange.scm
index 97be36e489..19014c748d 100644
--- a/gnu/packages/orange.scm
+++ b/gnu/packages/orange.scm
@@ -22,6 +22,11 @@
   #:use-module (guix download)
   #:use-module (guix build-system python)
   #:use-module (gnu packages)
+  #:use-module (gnu packages freedesktop)
+  #:use-module (gnu packages graph)
+  #:use-module (gnu packages machine-learning)
+  #:use-module (gnu packages python-crypto)
+  #:use-module (gnu packages python-science)
   #:use-module (gnu packages python-web)
   #:use-module (gnu packages python-xyz)
   #:use-module (gnu packages qt))
@@ -100,6 +105,86 @@ data-mining application.")
 GUI based workflow.  It is primarily used in the Orange framework.")
     (license license:gpl3+)))
 
+(define-public orange
+  (package
+    (name "orange")
+    (version "3.28.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "Orange3" version))
+       (sha256
+        (base32 "1ac4xjjkx06z10hl7k0zh1z3qhkl5vng15l9jkpkmck9spinbzil"))))
+    (build-system python-build-system)
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'preparations
+           (lambda _
+             ;; Delete test that opens an outgoing connection.
+             (delete-file "Orange/tests/test_url_reader.py")
+             ;; This is a binary data file and it breaks runpath validation.
+             (delete-file "Orange/tests/datasets/binary-blob.tab")
+             ;; Skip the test which uses that binary file.
+             (substitute* "Orange/tests/test_txt_reader.py"
+               (("test_read_nonutf8_encoding") "_test_read_nonutf8_encoding"))
+             ;; Relax some dependency versions.
+             (substitute* "requirements-gui.txt" (("PyQtWebEngine>=5.12") ""))
+             #t))
+         (add-before 'check 'set-HOME
+           ;; Tests need a writable home.
+           (lambda _ (setenv "HOME" "/tmp") #t))
+         (add-after 'install 'wrap-executable
+           ;; Ensure that icons are found at runtime.
+           (lambda* (#:key inputs outputs #:allow-other-keys)
+             (let ((out (assoc-ref outputs "out")))
+               (wrap-program (string-append out "/bin/orange-canvas")
+                 `("QT_PLUGIN_PATH" prefix
+                   ,(list (string-append (assoc-ref inputs "qtsvg")
+                                         "/lib/qt5/plugins/")))))
+             #t)))))
+    (native-inputs
+     `(("python-cython" ,python-cython)))
+    (inputs
+     `(("python-anyqt" ,python-anyqt)
+       ("python-baycomp" ,python-baycomp)
+       ("python-bottleneck" ,python-bottleneck)
+       ("python-chardet" ,python-chardet)
+       ("python-httpx" ,python-httpx)
+       ("python-joblib" ,python-joblib)
+       ("python-keyring" ,python-keyring)
+       ("python-keyrings.alt" ,python-keyrings.alt)
+       ("python-louvain" ,python-python-louvain)
+       ("python-matplotlib" ,python-matplotlib)
+       ("python-networkx" ,python-networkx)
+       ("python-numpy" ,python-numpy)
+       ("python-openpyxl" ,python-openpyxl)
+       ("python-opentsne" ,python-opentsne)
+       ("python-orange-canvas-core"
+        ,python-orange-canvas-core)
+       ("python-orange-widget-base"
+        ,python-orange-widget-base)
+       ("python-pandas" ,python-pandas)
+       ("python-pyqt" ,python-pyqt)
+       ("python-pyqtgraph" ,python-pyqtgraph)
+       ("python-pyqtwebengine" ,python-pyqtwebengine)
+       ("python-pyyaml" ,python-pyyaml)
+       ("python-requests" ,python-requests)
+       ("python-scikit-learn" ,python-scikit-learn)
+       ("python-scipy" ,python-scipy)
+       ("python-serverfiles" ,python-serverfiles)
+       ("python-xlrd" ,python-xlrd)
+       ("python-xlsxwriter" ,python-xlsxwriter)
+       ("qtbase" ,qtbase)
+       ("qtsvg" ,qtsvg)
+       ("xdg-utils" ,xdg-utils)))
+    (home-page "https://orangedatamining.com/")
+    (synopsis "Component-based data mining framework")
+    (description
+     "Orange is a component-based, graphical framework for machine learning,
+data analysis, data mining and data visualization.")
+    (license license:gpl3+)))
+
 (define-public python-serverfiles
   (package
     (name "python-serverfiles")
-- 
2.31.1

bug#47976: [PATCH v2 10/10] gnu: Add orange.

[Leo Famulari]

On Sun, Apr 25, 2021 at 03:26:08AM +0000, Vinicius Monego wrote:
> * gnu/packages/orange.scm (orange): New variable.

Thanks for the v2 patches.

I pushed as 5461efe81f680b577cb12ba7d003e38009628b81 after making the
following changes:

> +             ;; Relax some dependency versions.
> +             (substitute* "requirements-gui.txt" (("PyQtWebEngine>=5.12") ""))

I rewrote this comment to explain the reason for the substitution.

Like I said, we do not change version constraints that are chosen by
upstream developers without a good reason, and so this comment was not
sufficient.

> +       ("python-louvain" ,python-python-louvain)

I missed this in the first round of review but, as specified in our
manual section Python Modules, we don't name packages
"python-python-foo", but instead just "python-foo".

After I changed it, I realized that we already have a python-louvain
package.

Anyways, I changed the pre-existing python-louvain package to be called
python-louvain-0.6, adjusted its user, and renamed your package to
python-louvain.

It would be nice to check if python-scanpy, which uses
python-louvain-0.6, can instead use python-louvain.

Let us know if you want advice about how to handle this situation in the
future.