[PATCH] gnu: jupyter: Fix python-ipython conflict that prevented installation

DoneSubmitted by Edouard Klein.
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2 participants
  • Edouard Klein
  • Ricardo Wurmus
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unassigned
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normal
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Edouard Klein wrote on 16 Jun 10:57 +0200
(address . guix-patches@gnu.org)
87o8pj9ymu.fsf@alice.lan
* 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 belowcan see them.(python-widgetsnbextension): Wrap inprompt-toolkit-2-instead-of-prompt-toolkit to satisfy an explicitdependency on python-prompt-toolkit-2.(python-ipywidgets): Likewise.(python-jupyter-console): Likewise.(jupyter): Likewise.
* gnu/packages/package-management.scm (guix-jupyter): Wrap somedependencies in prompt-toolkit-2-instead-of-prompt-toolkit to make thereverse bag graphs of python-prompt-toolkit-2 and python-prompt-toolkit-3disconnected graphs.
* gnu/packages/machine-learning.scm (python-iml): Wrap inprompt-toolkit-2-instead-of-prompt-toolkit to satisfy an explicitdependency 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(-)
Toggle diff (474 lines)diff --git a/gnu/packages/machine-learning.scm b/gnu/packages/machine-learning.scmindex 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 (packagediff --git a/gnu/packages/package-management.scm b/gnu/packages/package-management.scmindex 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.scmindex 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
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Edouard Klein wrote on 16 Jun 11:21 +0200
(address . 41889@debbugs.gnu.org)
87lfkn9xis.fsf@alice.lan
Hi all,
Here is my proposed correction for the breakage I introduced when Iupdated python-prompt-toolkit (bugs #41738, #41729 and 41730).
As you can see on the attached images, I disconnected all packages thatdepend on ppt2 from the packages that depend on ppt3.This should fix all reported problems. If it does not, this means thatthere is an undeclared dependency, which is a bug. Please do nothesitate to tell me about any problem you encounter that my be tied tothis change.
jupyter's &co dependency on ppt2 is still a mystery to me. It is computedby the setuptools when they run but nowhere in the source of thepackages that have an explicit dependency on ppt2 was I able to find anyreference to it.
I have no idea how setuptools comes to the conclusion that it needs"prompt_toolkit<2.1.0,>=2.0.0". I (grep -r -i)-ed, in the source code ofipywidgets and could not find anything. This is black magic to me.
I would have loved to bring all those packages to ppt3 and forget aboutppt2 altogether, but because nowhere in the source is the dependencywritten, I can't do it. Any help would be appreciated. In the meantimethis fix should do the trick.
I did not repair packages that were broken for reasons unrelated toppt, but I'm quite confident that once their brokenness is fixed, ppt3won't be a problem for them. For example in my dirty work tree I have afix for python-rpy2, but it is tied to a pandas upgrade, and too manypackages depend on pandas for me to handle right now.
Cheers,
Edouard.
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Ricardo Wurmus wrote on 16 Jun 18:16 +0200
[PATCH] Fix ipython/jupyter
(address . 41889@debbugs.gnu.org)(name . Ricardo Wurmus)(address . rekado@elephly.net)
20200616161617.28035-1-rekado@elephly.net
--- gnu/packages/machine-learning.scm | 3 +-- gnu/packages/python-xyz.scm | 15 ++++----------- 2 files changed, 5 insertions(+), 13 deletions(-)
Toggle diff (70 lines)diff --git a/gnu/packages/machine-learning.scm b/gnu/packages/machine-learning.scmindex 0e11da41ca..cc69aa3ec1 100644--- a/gnu/packages/machine-learning.scm+++ b/gnu/packages/machine-learning.scm@@ -1817,8 +1817,7 @@ advanced research.") "1k8szlpm19rcwcxdny9qdm3gmaqq8akb4xlvrzyz8c2d679aak6l")))) (build-system python-build-system) (propagated-inputs- `(("ipython" ,(prompt-toolkit-2-instead-of-prompt-toolkit- python-ipython))+ `(("ipython" ,python-ipython) ("numpy" ,python-numpy) ("pandas" ,python-pandas) ("scipy" ,python-scipy)))diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scmindex 7e0a738d51..5896764266 100644--- a/gnu/packages/python-xyz.scm+++ b/gnu/packages/python-xyz.scm@@ -6450,7 +6450,7 @@ callback signature using a prototype function.") (propagated-inputs `(("python-backcall" ,python-backcall) ("python-pyzmq" ,python-pyzmq)- ("python-prompt-toolkit" ,python-prompt-toolkit)+ ("python-prompt-toolkit" ,python-prompt-toolkit-2) ("python-terminado" ,python-terminado) ("python-matplotlib" ,python-matplotlib) ("python-numpy" ,python-numpy)@@ -9004,8 +9004,7 @@ interactive computing.") "1ismyaxbv9d56yqqqb8xl58hg0iq0bbyy014a53y1g3hfbc8g7q7")))) (build-system python-build-system) (propagated-inputs- `(("python-ipykernel"- ,(prompt-toolkit-2-instead-of-prompt-toolkit python-ipykernel))+ `(("python-ipykernel" ,python-ipykernel) ("python-notebook" ,python-notebook))) (native-inputs `(("python-certifi" ,python-certifi)@@ -9032,8 +9031,7 @@ notebooks.") "15sww2mvnkqlvx55gwa82v05062a8j1xpncnqna4k9sl53hgcig9")))) (build-system python-build-system) (propagated-inputs- `(("python-ipython" ,(prompt-toolkit-2-instead-of-prompt-toolkit- python-ipython))+ `(("python-ipython" ,python-ipython) ("python-traitlets" ,python-traitlets) ("python-widgetsnbextension" ,python-widgetsnbextension))) (native-inputs@@ -9063,8 +9061,7 @@ in the data.") "06s3kr5vx0l1y1b7fxb04dmrppscl7q69sl9yyfr0d057d1ssvkg")))) (build-system python-build-system) (propagated-inputs- `(("python-ipykernel" ,(prompt-toolkit-2-instead-of-prompt-toolkit- python-ipykernel))+ `(("python-ipykernel" ,python-ipykernel) ("python-jupyter-client" ,python-jupyter-client) ("python-prompt-toolkit" ,python-prompt-toolkit-2) ("python-pygments" ,python-pygments)))@@ -12192,10 +12189,6 @@ characters, mouse support, and auto suggestions.") ("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)) -- 2.26.2
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Ricardo Wurmus wrote on 16 Jun 19:37 +0200
Re: [bug#41889] [PATCH] gnu: jupyter: Fix python-ipython conflict that prevented installation
(name . Edouard Klein)(address . edk@beaver-labs.com)
874kravrnj.fsf@elephly.net
Hi Edouard,
thank you for providing a fix. I think it’s too complicated, though.Using prompt-toolkit-2-instead-of-prompt-toolkit everywhere does notseem like an elegant solution.
I pushed a different fix with commit 7146c8c75d.
-- Ricardo
Closed
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