Subject: [bug#41889] [PATCH] gnu: jupyter: Fix python-ipython conflict that prevented installation

From: Edouard Klein <[email-masked]>
Date: Tue, 16 Jun 2020 10:57:13 +0200

* gnu/packages/python-xyz.scm (python-prompt-toolkit, python-prompt-toolkit-2)
(prompt-toolkit-2-instead-of-prompt-toolkit, python2-prompt-toolkit)
(python-prompt-toolkit-1): Move up so that packages defined below
can see them.
(python-widgetsnbextension): Wrap in
prompt-toolkit-2-instead-of-prompt-toolkit to satisfy an explicit
dependency on python-prompt-toolkit-2.
(python-ipywidgets): Likewise.
(python-jupyter-console): Likewise.
(jupyter): Likewise.

* gnu/packages/package-management.scm (guix-jupyter): Wrap some
dependencies in prompt-toolkit-2-instead-of-prompt-toolkit to make the
reverse bag graphs of python-prompt-toolkit-2 and python-prompt-toolkit-3
disconnected graphs.

* gnu/packages/machine-learning.scm (python-iml): Wrap in
prompt-toolkit-2-instead-of-prompt-toolkit to satisfy an explicit
dependency on python-prompt-toolkit-2.
---
 gnu/packages/machine-learning.scm   |  46 ++--
 gnu/packages/package-management.scm |   4 +-
 gnu/packages/python-xyz.scm         | 345 ++++++++++++++--------------
 3 files changed, 198 insertions(+), 197 deletions(-)

diff --git a/gnu/packages/machine-learning.scm b/gnu/packages/machine-learning.scm
index 0e11da41ca..51bf2ad779 100644
--- a/gnu/packages/machine-learning.scm
+++ b/gnu/packages/machine-learning.scm
@@ -1805,33 +1805,33 @@ advanced research.")
     (license license:asl2.0)))
 
 (define-public python-iml
-  (package
-    (name "python-iml")
-    (version "0.6.2")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (pypi-uri "iml" version))
-       (sha256
-        (base32
-         "1k8szlpm19rcwcxdny9qdm3gmaqq8akb4xlvrzyz8c2d679aak6l"))))
-    (build-system python-build-system)
-    (propagated-inputs
-     `(("ipython" ,(prompt-toolkit-2-instead-of-prompt-toolkit
-                    python-ipython))
-       ("numpy" ,python-numpy)
-       ("pandas" ,python-pandas)
-       ("scipy" ,python-scipy)))
-    (native-inputs
-     `(("nose" ,python-nose)))
-    (home-page "https://github.com/interpretable-ml/iml")
-    (synopsis "Interpretable Machine Learning (iML) package")
-    (description "Interpretable ML (iML) is a set of data type objects,
+  (prompt-toolkit-2-instead-of-prompt-toolkit
+   (package
+     (name "python-iml")
+     (version "0.6.2")
+     (source
+      (origin
+        (method url-fetch)
+        (uri (pypi-uri "iml" version))
+        (sha256
+         (base32
+          "1k8szlpm19rcwcxdny9qdm3gmaqq8akb4xlvrzyz8c2d679aak6l"))))
+     (build-system python-build-system)
+     (propagated-inputs
+      `(("ipython" ,python-ipython)
+        ("numpy" ,python-numpy)
+        ("pandas" ,python-pandas)
+        ("scipy" ,python-scipy)))
+     (native-inputs
+      `(("nose" ,python-nose)))
+     (home-page "https://github.com/interpretable-ml/iml")
+     (synopsis "Interpretable Machine Learning (iML) package")
+     (description "Interpretable ML (iML) is a set of data type objects,
 visualizations, and interfaces that can be used by any method designed to
 explain the predictions of machine learning models (or really the output of
 any function).  It currently contains the interface and IO code from the Shap
 project, and it will potentially also do the same for the Lime project.")
-    (license license:expat)))
+     (license license:expat))))
 
 (define-public python-keras-applications
   (package
diff --git a/gnu/packages/package-management.scm b/gnu/packages/package-management.scm
index c1e6657dff..c282ecab40 100644
--- a/gnu/packages/package-management.scm
+++ b/gnu/packages/package-management.scm
@@ -976,8 +976,8 @@ environments.")
 
        ;; For testing.
        ("jupyter" ,jupyter)
-       ("python-ipython" ,python-ipython)
-       ("python-ipykernel" ,python-ipykernel)))
+       ("python-ipython" ,(prompt-toolkit-2-instead-of-prompt-toolkit python-ipython))
+       ("python-ipykernel" ,(prompt-toolkit-2-instead-of-prompt-toolkit python-ipykernel))))
     (inputs
      `(("guix" ,guix)
        ("guile" ,guile-3.0)))
diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index 7e0a738d51..ebe21a3754 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -8872,6 +8872,81 @@ functions to find and load entry points.")
 from elisp.")
     (license license:gpl3)))
 
+(define-public python-prompt-toolkit
+  (package
+    (name "python-prompt-toolkit")
+    (version "3.0.5")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "prompt_toolkit" version))
+       (sha256
+        (base32
+         "1j3x5s4gp4ih73sbcni0a0vffbzvrxbrbnkvb3fzjgxn810ilgan"))))
+    (build-system python-build-system)
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases
+         (delete 'check)
+         (add-after 'install 'post-install-check
+           (lambda* (#:key inputs outputs #:allow-other-keys)
+             ;; HOME is needed for the test
+             ;; "test_pathcompleter_can_expanduser".
+             (setenv "HOME" "/tmp")
+             (add-installed-pythonpath inputs outputs)
+             (invoke "py.test"))))))
+    (propagated-inputs
+     `(("python-wcwidth" ,python-wcwidth)))
+    (native-inputs
+     `(("python-pytest" ,python-pytest)))
+    (home-page
+     "https://github.com/prompt-toolkit/python-prompt-toolkit")
+    (synopsis "Library for building command line interfaces in Python")
+    (description
+     "Prompt-Toolkit is a library for building interactive command line
+interfaces in Python.  It's like GNU Readline but it also features syntax
+highlighting while typing, out-of-the-box multi-line input editing, advanced
+code completion, incremental search, support for Chinese double-width
+characters, mouse support, and auto suggestions.")
+    (license license:bsd-3)))
+
+(define-public python-prompt-toolkit-2
+  (package (inherit python-prompt-toolkit)
+    (name "python-prompt-toolkit")
+    (version "2.0.7")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "prompt_toolkit" version))
+       (sha256
+        (base32
+         "0fgacqk73w7s932vy46pan2yp8rvjmlkag20xvaydh9mhf6h85zx"))))
+    (propagated-inputs
+     `(("python-wcwidth" ,python-wcwidth)
+       ("python-six" ,python-six)
+       ("python-pygments" ,python-pygments)))))
+
+(define-public prompt-toolkit-2-instead-of-prompt-toolkit
+  (package-input-rewriting/spec
+   `(("python-prompt-toolkit" . ,(const python-prompt-toolkit-2)))))
+
+(define-public python2-prompt-toolkit
+  (package-with-python2 python-prompt-toolkit-2))
+
+(define-public python-prompt-toolkit-1
+  (package (inherit python-prompt-toolkit-2)
+    (version "1.0.15")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "prompt_toolkit" version ".tar.gz"))
+       (sha256
+        (base32
+         "05v9h5nydljwpj5nm8n804ms0glajwfy1zagrzqrg91wk3qqi1c5"))))))
+
+(define-public python2-prompt-toolkit-1
+  (package-with-python2 python-prompt-toolkit-1))
+
 (define-public python-nbconvert
   (package
     (name "python-nbconvert")
@@ -8992,91 +9067,91 @@ interactive computing.")
                   (("formats = self.nbconvert_api") "return #")))))))))))
 
 (define-public python-widgetsnbextension
-  (package
-    (name "python-widgetsnbextension")
-    (version "3.5.1")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (pypi-uri "widgetsnbextension" version))
-       (sha256
-        (base32
-         "1ismyaxbv9d56yqqqb8xl58hg0iq0bbyy014a53y1g3hfbc8g7q7"))))
-    (build-system python-build-system)
-    (propagated-inputs
-     `(("python-ipykernel"
-        ,(prompt-toolkit-2-instead-of-prompt-toolkit python-ipykernel))
-       ("python-notebook" ,python-notebook)))
-    (native-inputs
-     `(("python-certifi" ,python-certifi)
-       ("python-nose" ,python-nose)))
-    (home-page "https://ipython.org")
-    (synopsis "IPython HTML widgets for Jupyter")
-    (description "This package provides interactive HTML widgets for Jupyter
+  (prompt-toolkit-2-instead-of-prompt-toolkit
+   (package
+     (name "python-widgetsnbextension")
+     (version "3.5.1")
+     (source
+      (origin
+        (method url-fetch)
+        (uri (pypi-uri "widgetsnbextension" version))
+        (sha256
+         (base32
+          "1ismyaxbv9d56yqqqb8xl58hg0iq0bbyy014a53y1g3hfbc8g7q7"))))
+     (build-system python-build-system)
+     (propagated-inputs
+      `(("python-ipykernel" ,python-ipykernel)
+        ("python-notebook" ,python-notebook)))
+     (native-inputs
+      `(("python-certifi" ,python-certifi)
+        ("python-nose" ,python-nose)))
+     (home-page "https://ipython.org")
+     (synopsis "IPython HTML widgets for Jupyter")
+     (description "This package provides interactive HTML widgets for Jupyter
 notebooks.")
-    (license license:bsd-3)))
+     (license license:bsd-3))))
 
 (define-public python2-widgetsnbextension
   (package-with-python2 python-widgetsnbextension))
 
 (define-public python-ipywidgets
-  (package
-    (name "python-ipywidgets")
-    (version "7.5.1")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (pypi-uri "ipywidgets" version))
-       (sha256
-        (base32
-         "15sww2mvnkqlvx55gwa82v05062a8j1xpncnqna4k9sl53hgcig9"))))
-    (build-system python-build-system)
-    (propagated-inputs
-     `(("python-ipython" ,(prompt-toolkit-2-instead-of-prompt-toolkit
-                           python-ipython))
-       ("python-traitlets" ,python-traitlets)
-       ("python-widgetsnbextension" ,python-widgetsnbextension)))
-    (native-inputs
-     `(("python-nose" ,python-nose)
-       ("python-pytest" ,python-pytest)))
-    (home-page "https://ipython.org")
-    (synopsis "IPython HTML widgets for Jupyter")
-    (description "Ipywidgets are interactive HTML widgets for Jupyter
+  (prompt-toolkit-2-instead-of-prompt-toolkit
+   (package
+     (name "python-ipywidgets")
+     (version "7.5.1")
+     (source
+      (origin
+        (method url-fetch)
+        (uri (pypi-uri "ipywidgets" version))
+        (sha256
+         (base32
+          "15sww2mvnkqlvx55gwa82v05062a8j1xpncnqna4k9sl53hgcig9"))))
+     (build-system python-build-system)
+     (propagated-inputs
+      `(("python-ipython" ,python-ipython)
+        ("python-traitlets" ,python-traitlets)
+        ("python-widgetsnbextension" ,python-widgetsnbextension)))
+     (native-inputs
+      `(("python-nose" ,python-nose)
+        ("python-pytest" ,python-pytest)))
+     (home-page "https://ipython.org")
+     (synopsis "IPython HTML widgets for Jupyter")
+     (description "Ipywidgets are interactive HTML widgets for Jupyter
 notebooks and the IPython kernel.  Notebooks come alive when interactive
 widgets are used.  Users gain control of their data and can visualize changes
 in the data.")
-    (license license:bsd-3)))
+     (license license:bsd-3))))
 
 (define-public python2-ipywidgets
   (package-with-python2 python-ipywidgets))
 
 (define-public python-jupyter-console
-  (package
-    (name "python-jupyter-console")
-    (version "6.1.0")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (pypi-uri "jupyter_console" version))
-       (sha256
-        (base32
-         "06s3kr5vx0l1y1b7fxb04dmrppscl7q69sl9yyfr0d057d1ssvkg"))))
-    (build-system python-build-system)
-    (propagated-inputs
-     `(("python-ipykernel" ,(prompt-toolkit-2-instead-of-prompt-toolkit
-        python-ipykernel))
-       ("python-jupyter-client" ,python-jupyter-client)
-       ("python-prompt-toolkit" ,python-prompt-toolkit-2)
-       ("python-pygments" ,python-pygments)))
-    (native-inputs
-     `(("python-nose" ,python-nose)))
-    (home-page "https://jupyter.org")
-    (synopsis "Jupyter terminal console")
-    (description "This package provides a terminal-based console frontend for
+  (prompt-toolkit-2-instead-of-prompt-toolkit
+   (package
+     (name "python-jupyter-console")
+     (version "6.1.0")
+     (source
+      (origin
+        (method url-fetch)
+        (uri (pypi-uri "jupyter_console" version))
+        (sha256
+         (base32
+          "06s3kr5vx0l1y1b7fxb04dmrppscl7q69sl9yyfr0d057d1ssvkg"))))
+     (build-system python-build-system)
+     (propagated-inputs
+      `(("python-ipykernel" ,python-ipykernel)
+        ("python-jupyter-client" ,python-jupyter-client)
+        ("python-prompt-toolkit" ,python-prompt-toolkit)
+        ("python-pygments" ,python-pygments)))
+     (native-inputs
+      `(("python-nose" ,python-nose)))
+     (home-page "https://jupyter.org")
+     (synopsis "Jupyter terminal console")
+     (description "This package provides a terminal-based console frontend for
 Jupyter kernels.  It also allows for console-based interaction with non-Python
 Jupyter kernels such as IJulia and IRKernel.")
-    (properties `((python2-variant . ,(delay python2-jupyter-console))))
-    (license license:bsd-3)))
+     (properties `((python2-variant . ,(delay python2-jupyter-console))))
+     (license license:bsd-3))))
 
 (define-public python2-jupyter-console
   (package
@@ -9209,37 +9284,38 @@ popular online obfuscators.")
     (license license:expat)))
 
 (define-public jupyter
-  (package
-    (name "jupyter")
-    (version "1.0.0")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (pypi-uri "jupyter" version))
-       (sha256
-        (base32
-         "0pwf3pminkzyzgx5kcplvvbvwrrzd3baa7lmh96f647k30rlpp6r"))))
-    (build-system python-build-system)
-    (arguments '(#:tests? #f)) ; there are none.
-    (propagated-inputs
-     `(("python-ipykernel" ,python-ipykernel)
-       ("python-ipywidgets" ,python-ipywidgets)
-       ("python-jupyter-console" ,python-jupyter-console)
-       ("python-nbconvert" ,python-nbconvert)
-       ("python-notebook" ,python-notebook)
-       ("python-qtconsole" ,python-qtconsole)))
-    (native-search-paths
-     (list (search-path-specification
-            (variable "JUPYTER_PATH")
-            (files '("share/jupyter")))))
-    (home-page "https://jupyter.org")
-    (synopsis "Web application for interactive documents")
-    (description
-     "The Jupyter Notebook is a web application that allows you to create and
+  (prompt-toolkit-2-instead-of-prompt-toolkit
+   (package
+     (name "jupyter")
+     (version "1.0.0")
+     (source
+      (origin
+        (method url-fetch)
+        (uri (pypi-uri "jupyter" version))
+        (sha256
+         (base32
+          "0pwf3pminkzyzgx5kcplvvbvwrrzd3baa7lmh96f647k30rlpp6r"))))
+     (build-system python-build-system)
+     (arguments '(#:tests? #f)) ; there are none.
+     (propagated-inputs
+      `(("python-ipykernel" ,python-ipykernel)
+        ("python-ipywidgets" ,python-ipywidgets)
+        ("python-jupyter-console" ,python-jupyter-console)
+        ("python-nbconvert" ,python-nbconvert)
+        ("python-notebook" ,python-notebook)
+        ("python-qtconsole" ,python-qtconsole)))
+     (native-search-paths
+      (list (search-path-specification
+             (variable "JUPYTER_PATH")
+             (files '("share/jupyter")))))
+     (home-page "https://jupyter.org")
+     (synopsis "Web application for interactive documents")
+     (description
+      "The Jupyter Notebook is a web application that allows you to create and
 share documents that contain live code, equations, visualizations and
 explanatory text.  Uses include: data cleaning and transformation, numerical
 simulation, statistical modeling, machine learning and much more.")
-    (license license:bsd-3)))
+     (license license:bsd-3))))
 
 (define-public python-chardet
   (package
@@ -12138,81 +12214,6 @@ collections of data.")
 (define-public python2-backpack
   (package-with-python2 python-backpack))
 
-(define-public python-prompt-toolkit
-  (package
-    (name "python-prompt-toolkit")
-    (version "3.0.5")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (pypi-uri "prompt_toolkit" version))
-       (sha256
-        (base32
-         "1j3x5s4gp4ih73sbcni0a0vffbzvrxbrbnkvb3fzjgxn810ilgan"))))
-    (build-system python-build-system)
-    (arguments
-     `(#:phases
-       (modify-phases %standard-phases
-         (delete 'check)
-         (add-after 'install 'post-install-check
-           (lambda* (#:key inputs outputs #:allow-other-keys)
-             ;; HOME is needed for the test
-             ;; "test_pathcompleter_can_expanduser".
-             (setenv "HOME" "/tmp")
-             (add-installed-pythonpath inputs outputs)
-             (invoke "py.test"))))))
-    (propagated-inputs
-     `(("python-wcwidth" ,python-wcwidth)))
-    (native-inputs
-     `(("python-pytest" ,python-pytest)))
-    (home-page
-     "https://github.com/prompt-toolkit/python-prompt-toolkit")
-    (synopsis "Library for building command line interfaces in Python")
-    (description
-     "Prompt-Toolkit is a library for building interactive command line
-interfaces in Python.  It's like GNU Readline but it also features syntax
-highlighting while typing, out-of-the-box multi-line input editing, advanced
-code completion, incremental search, support for Chinese double-width
-characters, mouse support, and auto suggestions.")
-    (license license:bsd-3)))
-
-(define-public python-prompt-toolkit-2
-  (package (inherit python-prompt-toolkit)
-    (name "python-prompt-toolkit")
-    (version "2.0.7")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (pypi-uri "prompt_toolkit" version))
-       (sha256
-        (base32
-         "0fgacqk73w7s932vy46pan2yp8rvjmlkag20xvaydh9mhf6h85zx"))))
-    (propagated-inputs
-     `(("python-wcwidth" ,python-wcwidth)
-       ("python-six" ,python-six)
-       ("python-pygments" ,python-pygments)))))
-
-(define-public prompt-toolkit-2-instead-of-prompt-toolkit
-  (package-input-rewriting/spec
-   `(("python-prompt-toolkit" . ,(const python-prompt-toolkit-2)))))
-
-(define-public python2-prompt-toolkit
-  (package-with-python2 python-prompt-toolkit-2))
-
-(define-public python-prompt-toolkit-1
-  (package (inherit python-prompt-toolkit-2)
-    (version "1.0.15")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (pypi-uri "prompt_toolkit" version ".tar.gz"))
-       (sha256
-        (base32
-         "05v9h5nydljwpj5nm8n804ms0glajwfy1zagrzqrg91wk3qqi1c5"))))))
-
-(define-public python2-prompt-toolkit-1
-  (package-with-python2 python-prompt-toolkit-1))
-
 (define-public python-jedi
   (package
     (name "python-jedi")
-- 
2.26.2