From eff366b469218a0ad01cb40dcf64807e4f9cc4b8 Mon Sep 17 00:00:00 2001 From: Leo Famulari Date: Sun, 30 Dec 2018 12:45:09 -0500 Subject: gnu: python-lxml: Update to 4.2.5 [fixes CVE-2018-19787]. * gnu/packages/python.scm (python-lxml, python2-lxml): Update to 4.2.5. --- gnu/packages/python.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/python.scm') diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index 9ef0654cb8..00d60333a4 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -5190,14 +5190,14 @@ implementation of D-Bus.") (define-public python-lxml (package (name "python-lxml") - (version "4.2.4") + (version "4.2.5") (source (origin (method url-fetch) (uri (pypi-uri "lxml" version)) (sha256 (base32 - "1jk336k0kw616gfhqk1wwxsjjwz0flld0n294lz8kxch610bxbz2")))) + "0zw0y9hs0nflxhl9cs6ipwwh53szi3w2x06wl0k9cylyqac0cwin")))) (build-system python-build-system) (inputs `(("libxml2" ,libxml2) -- cgit v1.2.3 From cd70798a23750dba18266c0e551c68b7ef1b118b Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 2 Jan 2019 12:46:33 +0100 Subject: gnu: python-docopt: Use INVOKE. * gnu/packages/python.scm (python-docopt)[arguments]: Use INVOKE. --- gnu/packages/python.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to 'gnu/packages/python.scm') diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index 00d60333a4..ebf56326e1 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -7343,7 +7343,7 @@ automatically detect a wide range of file encodings.") `(#:phases (modify-phases %standard-phases (replace 'check - (lambda _ (zero? (system* "py.test"))))))) + (lambda _ (invoke "py.test")))))) (home-page "http://docopt.org") (synopsis "Command-line interface description language for Python") (description "This library allows the user to define a command-line -- cgit v1.2.3 From ec933e05a20cc70d23f576c5763d6c69eb8452eb Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 2 Jan 2019 12:47:03 +0100 Subject: gnu: python-configargparse: Use INVOKE. * gnu/packages/python.scm (python-configargparse)[arguments]: Use INVOKE. --- gnu/packages/python.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to 'gnu/packages/python.scm') diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index ebf56326e1..76ac5bc2fc 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -7455,7 +7455,7 @@ config files.") ;; NOTE: Many tests do not run because they rely on Python's ;; built-in test.test_argparse, but we remove the unit tests from ;; our Python installation. - (zero? (system* "python" "setup.py" "test"))))))) + (invoke "python" "setup.py" "test")))))) (synopsis "Replacement for argparse") (description "A drop-in replacement for argparse that allows options to also be set via config files and/or environment variables.") -- cgit v1.2.3 From 13e7c884c7e90d815e950127a06e81ecf35177d2 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 2 Jan 2019 12:47:43 +0100 Subject: gnu: python-clint: Use INVOKE. * gnu/packages/python.scm (python-clint)[arguments]: Use INVOKE. --- gnu/packages/python.scm | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) (limited to 'gnu/packages/python.scm') diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index 76ac5bc2fc..e51de2a201 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -7728,8 +7728,7 @@ Blog, News or Announcements section to a Sphinx website.") '(#:phases (modify-phases %standard-phases (replace 'check - (lambda _ - (zero? (system* "py.test" "-v"))))))) + (lambda _ (invoke "py.test" "-v")))))) (native-inputs `(("python-pytest" ,python-pytest))) (propagated-inputs -- cgit v1.2.3 From eecaf17086510ae68bc495b2d9a06a152347bd69 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 2 Jan 2019 12:48:09 +0100 Subject: gnu: python-hy: Use INVOKE. * gnu/packages/python.scm (python-hy)[arguments]: Use INVOKE. --- gnu/packages/python.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to 'gnu/packages/python.scm') diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index e51de2a201..27f78a2726 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -7807,7 +7807,7 @@ with a new public API, and RPython support.") (lambda _ ;; Tests require write access to HOME. (setenv "HOME" "/tmp") - (zero? (system* "nosetests"))))))) + (invoke "nosetests")))))) (native-inputs `(("python-coverage" ,python-coverage) ("python-nose" ,python-nose))) -- cgit v1.2.3 From 80486d6673c09bc350a79f9c9dc82d88019e8662 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 2 Jan 2019 12:48:39 +0100 Subject: gnu: python-prompt-toolkit: Update to 2.0.7. * gnu/packages/python.scm (python-prompt-toolkit): Update to 2.0.7. [arguments]: Enable tests; add phase "post-install-check" and delete "check" phase. [native-inputs]: Add python-pytest. --- gnu/packages/python.scm | 53 +++++++++++++++++++++++++++++-------------------- 1 file changed, 32 insertions(+), 21 deletions(-) (limited to 'gnu/packages/python.scm') diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index 27f78a2726..20b1ff69f0 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -9888,32 +9888,43 @@ collections of data.") (package-with-python2 python-backpack)) (define-public python-prompt-toolkit - (package - (name "python-prompt-toolkit") - (version "1.0.15") - (source - (origin - (method url-fetch) - (uri (pypi-uri "prompt_toolkit" version ".tar.gz")) - (sha256 + (package + (name "python-prompt-toolkit") + (version "2.0.7") + (source + (origin + (method url-fetch) + (uri (pypi-uri "prompt_toolkit" version ".tar.gz")) + (sha256 (base32 - "05v9h5nydljwpj5nm8n804ms0glajwfy1zagrzqrg91wk3qqi1c5")))) - (build-system python-build-system) - (arguments - '(#:tests? #f)) ; The test suite uses some Windows-specific data types. - (propagated-inputs - `(("python-wcwidth" ,python-wcwidth) - ("python-six" ,python-six) - ("python-pygments" ,python-pygments))) - (home-page "https://github.com/jonathanslenders/python-prompt-toolkit") - (synopsis "Library for building command line interfaces in Python") - (description - "Prompt-Toolkit is a library for building interactive command line + "0fgacqk73w7s932vy46pan2yp8rvjmlkag20xvaydh9mhf6h85zx")))) + (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) + ("python-six" ,python-six) + ("python-pygments" ,python-pygments))) + (native-inputs + `(("python-pytest" ,python-pytest))) + (home-page "https://github.com/jonathanslenders/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))) + (license license:bsd-3))) (define-public python2-prompt-toolkit (package-with-python2 python-prompt-toolkit)) -- cgit v1.2.3 From 464cb5b55de70a28e9c42ef6e8a1f84ba5918d90 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 2 Jan 2019 13:37:44 +0100 Subject: gnu: Add python-prompt-toolkit-1. * gnu/packages/python.scm (python-prompt-toolkit-1, python2-prompt-toolkit-1): New variables. --- gnu/packages/python.scm | 14 ++++++++++++++ 1 file changed, 14 insertions(+) (limited to 'gnu/packages/python.scm') diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index 20b1ff69f0..8c091c0fa3 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -9929,6 +9929,20 @@ characters, mouse support, and auto suggestions.") (define-public python2-prompt-toolkit (package-with-python2 python-prompt-toolkit)) +(define-public python-prompt-toolkit-1 + (package (inherit python-prompt-toolkit) + (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") -- cgit v1.2.3 From 92a9f93615b14fe684c9670f8c103687c308cff8 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 2 Jan 2019 13:45:35 +0100 Subject: gnu: python-ipython: Update to 5.8.0. * gnu/packages/python.scm (python-ipython): Update to 5.8.0. [propagated-inputs]: Replace python-prompt-toolkit with python-prompt-toolkit-1. [arguments]: Use INVOKE in the "check" phase; return #T from the "fix-tests" phase. --- gnu/packages/python.scm | 110 +++++++++++++++++++++++++----------------------- 1 file changed, 57 insertions(+), 53 deletions(-) (limited to 'gnu/packages/python.scm') diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index 8c091c0fa3..56234b7559 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -4879,21 +4879,24 @@ installing @code{kernelspec}s for use with Jupyter frontends.") (define-public python2-ipykernel (package-with-python2 python-ipykernel)) +;; This is the latest release of the LTS version of ipython with support for +;; Python 2.7 and Python 3.x. Later non-LTS versions starting from 6.0 have +;; dropped support for Python 2.7. We may want to rename this package. (define-public python-ipython (package (name "python-ipython") - (version "5.5.0") + (version "5.8.0") (source (origin (method url-fetch) (uri (pypi-uri "ipython" version ".tar.gz")) (sha256 - (base32 "03qmzpfy00if10i9k8fjkam1s4xg22j73f933x5d228z9n4rwik6")))) + (base32 "01l93i4hspf0lvhmycvc8j378bslm9rw30mwfspsl6v1ayc69b2b")))) (build-system python-build-system) (outputs '("out" "doc")) (propagated-inputs `(("python-pyzmq" ,python-pyzmq) - ("python-prompt-toolkit" ,python-prompt-toolkit) + ("python-prompt-toolkit" ,python-prompt-toolkit-1) ("python-terminado" ,python-terminado) ("python-matplotlib" ,python-matplotlib) ("python-numpy" ,python-numpy) @@ -4963,59 +4966,60 @@ installing @code{kernelspec}s for use with Jupyter frontends.") (arguments `(#:phases (modify-phases %standard-phases - (add-after - 'install 'install-doc - (lambda* (#:key inputs outputs #:allow-other-keys) - (let* ((data (string-append (assoc-ref outputs "doc") "/share")) - (doc (string-append data "/doc/" ,name "-" ,version)) - (html (string-append doc "/html")) - (man1 (string-append data "/man/man1")) - (info (string-append data "/info")) - (examples (string-append doc "/examples")) - (python-arg (string-append "PYTHON=" (which "python")))) - (setenv "LANG" "en_US.utf8") - ;; Make installed package available for running the tests - (add-installed-pythonpath inputs outputs) - (with-directory-excursion "docs" - ;; FIXME: pdf fails to build - ;;(system* "make" "pdf" "PAPER=a4") - (system* "make" python-arg "html") - (system* "make" python-arg "info")) - (copy-recursively "docs/man" man1) - (copy-recursively "examples" examples) - (copy-recursively "docs/build/html" html) - ;; (copy-file "docs/build/latex/ipython.pdf" - ;; (string-append doc "/ipython.pdf")) - (mkdir-p info) - (copy-file "docs/build/texinfo/ipython.info" - (string-append info "/ipython.info")) - (copy-file "COPYING.rst" (string-append doc "/COPYING.rst"))))) + (add-after 'install 'install-doc + (lambda* (#:key inputs outputs #:allow-other-keys) + (let* ((data (string-append (assoc-ref outputs "doc") "/share")) + (doc (string-append data "/doc/" ,name "-" ,version)) + (html (string-append doc "/html")) + (man1 (string-append data "/man/man1")) + (info (string-append data "/info")) + (examples (string-append doc "/examples")) + (python-arg (string-append "PYTHON=" (which "python")))) + (setenv "LANG" "en_US.utf8") + ;; Make installed package available for running the tests + (add-installed-pythonpath inputs outputs) + (with-directory-excursion "docs" + ;; FIXME: pdf fails to build + ;;(system* "make" "pdf" "PAPER=a4") + (system* "make" python-arg "html") + (system* "make" python-arg "info")) + (copy-recursively "docs/man" man1) + (copy-recursively "examples" examples) + (copy-recursively "docs/build/html" html) + ;; (copy-file "docs/build/latex/ipython.pdf" + ;; (string-append doc "/ipython.pdf")) + (mkdir-p info) + (copy-file "docs/build/texinfo/ipython.info" + (string-append info "/ipython.info")) + (copy-file "COPYING.rst" (string-append doc "/COPYING.rst"))) + #t)) ;; Tests can only be run after the library has been installed and not ;; within the source directory. (delete 'check) - (add-after - 'install 'check - (lambda* (#:key inputs outputs tests? #:allow-other-keys) - (if tests? - (with-directory-excursion "/tmp" - ;; Make installed package available for running the tests - (add-installed-pythonpath inputs outputs) - (setenv "HOME" "/tmp/") ;; required by a test - (zero? (system* (string-append (assoc-ref outputs "out") - "/bin/iptest")))) - #t))) - (add-before - 'install 'fix-tests - (lambda* (#:key inputs #:allow-other-keys) - (substitute* "./IPython/utils/_process_posix.py" - (("/usr/bin/env', 'which") (which "which"))) - (substitute* "./IPython/core/tests/test_inputtransformer.py" - (("#!/usr/bin/env python") - (string-append "#!" (which "python")))) - ;; Disable 1 failing test - (substitute* "./IPython/core/tests/test_magic.py" - (("def test_dirops\\(\\):" all) - (string-append "@dec.skipif(True)\n" all)))))))) + (add-after 'install 'check + (lambda* (#:key inputs outputs tests? #:allow-other-keys) + (if tests? + (begin + ;; Make installed package available for running the tests + (add-installed-pythonpath inputs outputs) + (setenv "HOME" "/tmp/") ;; required by a test + ;; These two tests throw errors. + (delete-file "IPython/extensions/tests/test_storemagic.py") + (delete-file "IPython/core/tests/test_displayhook.py") + (invoke "nosetests")) + #t))) + (add-before 'install 'fix-tests + (lambda* (#:key inputs #:allow-other-keys) + (substitute* "./IPython/utils/_process_posix.py" + (("/usr/bin/env', 'which") (which "which"))) + (substitute* "./IPython/core/tests/test_inputtransformer.py" + (("#!/usr/bin/env python") + (string-append "#!" (which "python")))) + ;; Disable 1 failing test + (substitute* "./IPython/core/tests/test_magic.py" + (("def test_dirops\\(\\):" all) + (string-append "@dec.skipif(True)\n" all))) + #t))))) (home-page "https://ipython.org") (synopsis "IPython is a tool for interactive computing in Python") (description -- cgit v1.2.3 From f0eb442c20466a256f1851522330baccb1afb287 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 2 Jan 2019 15:45:27 +0100 Subject: gnu: python-ipykernel: Update to 5.1.0. * gnu/packages/python.scm (python-ipykernel): Update to 5.1.0. [arguments]: Enable tests. [propagated-inputs]: Add python-ipython. [native-inputs]: Add python-pytest and python-nose. --- gnu/packages/python.scm | 23 ++++++++++++++++------- 1 file changed, 16 insertions(+), 7 deletions(-) (limited to 'gnu/packages/python.scm') diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index 56234b7559..ee51f2387c 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -4856,20 +4856,29 @@ installing @code{kernelspec}s for use with Jupyter frontends.") (define-public python-ipykernel (package (name "python-ipykernel") - (version "4.5.2") + (version "5.1.0") (source (origin (method url-fetch) (uri (pypi-uri "ipykernel" version)) (sha256 - (base32 "0qllv0k6zzv1r1cj1x2ygxmlrrqhbslzj8rc6r6fg3kc1rgz4m2s")))) + (base32 "0br95qhrd5k65g10djngiy27hs0642301hlf2q142i8djabvzh0g")))) (build-system python-build-system) - ;; The tests load a submodule of IPython. However, IPython itself depends - ;; on ipykernel. - (arguments `(#:tests? #f)) + (arguments + `(#:phases + (modify-phases %standard-phases + (replace 'check + (lambda _ + (setenv "HOME" "/tmp") + (invoke "pytest" "-v") + #t))))) (propagated-inputs - ;; imported at runtime during connect - `(("python-jupyter-client" ,python-jupyter-client))) + `(("python-ipython" ,python-ipython) + ;; imported at runtime during connect + ("python-jupyter-client" ,python-jupyter-client))) + (native-inputs + `(("python-pytest" ,python-pytest) + ("python-nose" ,python-nose))) (home-page "https://ipython.org") (synopsis "IPython Kernel for Jupyter") (description -- cgit v1.2.3 From 75246daff2754f925d3d63ca8995c8e635e17651 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 2 Jan 2019 15:46:44 +0100 Subject: gnu: python-ipython: Break dependency on python-ipykernel. * gnu/packages/python.scm (python-ipython)[propagated-inputs]: Remove python-ipykernel. [arguments]: Delete more broken tests. --- gnu/packages/python.scm | 20 ++++++++++++++------ 1 file changed, 14 insertions(+), 6 deletions(-) (limited to 'gnu/packages/python.scm') diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index ee51f2387c..4cf6936d03 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -4923,7 +4923,6 @@ installing @code{kernelspec}s for use with Jupyter frontends.") ("python-simplegeneric" ,python-simplegeneric) ("python-jsonschema" ,python-jsonschema) ("python-traitlets" ,python-traitlets) - ("python-ipykernel" ,python-ipykernel) ("python-nbformat" ,python-nbformat) ("python-pygments" ,python-pygments))) (inputs @@ -5012,12 +5011,12 @@ installing @code{kernelspec}s for use with Jupyter frontends.") ;; Make installed package available for running the tests (add-installed-pythonpath inputs outputs) (setenv "HOME" "/tmp/") ;; required by a test - ;; These two tests throw errors. - (delete-file "IPython/extensions/tests/test_storemagic.py") - (delete-file "IPython/core/tests/test_displayhook.py") - (invoke "nosetests")) + ;; We only test the core because one of the other tests + ;; tries to import ipykernel. + (invoke "python" "IPython/testing/iptest.py" + "-v" "IPython/core/tests")) #t))) - (add-before 'install 'fix-tests + (add-before 'check 'fix-tests (lambda* (#:key inputs #:allow-other-keys) (substitute* "./IPython/utils/_process_posix.py" (("/usr/bin/env', 'which") (which "which"))) @@ -5028,6 +5027,15 @@ installing @code{kernelspec}s for use with Jupyter frontends.") (substitute* "./IPython/core/tests/test_magic.py" (("def test_dirops\\(\\):" all) (string-append "@dec.skipif(True)\n" all))) + ;; This test introduces a circular dependency on ipykernel + ;; (which depends on ipython). + (delete-file "IPython/core/tests/test_display.py") + ;; These tests throw errors for unknown reasons. + (delete-file "IPython/extensions/tests/test_storemagic.py") + (delete-file "IPython/core/tests/test_displayhook.py") + (delete-file "IPython/core/tests/test_interactiveshell.py") + (delete-file "IPython/core/tests/test_pylabtools.py") + (delete-file "IPython/core/tests/test_paths.py") #t))))) (home-page "https://ipython.org") (synopsis "IPython is a tool for interactive computing in Python") -- cgit v1.2.3 From ffabccb22f2af42528d534a0150c5c69608f4942 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 2 Jan 2019 15:47:57 +0100 Subject: gnu: python-jupyter-client: Update to 5.2.4. * gnu/packages/python.scm (python-jupyter-client): Update to 5.2.4. --- gnu/packages/python.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/python.scm') diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index 4cf6936d03..8613edec9f 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -4824,14 +4824,14 @@ without using the configuration machinery.") (define-public python-jupyter-client (package (name "python-jupyter-client") - (version "4.4.0") + (version "5.2.4") (source (origin (method url-fetch) (uri (pypi-uri "jupyter_client" version)) (sha256 (base32 - "1vjjrpjw7k5sh982pbjnslv7byfbfazjw9g92jvs7dz5qbx556n9")))) + "0l9mh7ccrpl3lppym3dnky8n1nk7xarzzdcxf4q2s7aw203cpydm")))) (build-system python-build-system) ;; Tests fail because of missing native python kernel which I assume is ;; provided by the ipython package, which we cannot use because it would -- cgit v1.2.3 From abe50aa369d43e95966c12146f542f44d5fef8d1 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 2 Jan 2019 15:48:18 +0100 Subject: gnu: Add python-prometheus-client. * gnu/packages/python.scm (python-prometheus-client, python2-prometheus-client): New variables. --- gnu/packages/python.scm | 25 +++++++++++++++++++++++++ 1 file changed, 25 insertions(+) (limited to 'gnu/packages/python.scm') diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index 8613edec9f..f2b24481ef 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -7113,6 +7113,31 @@ convert an @code{.ipynb} notebook file into various static formats including: (define-public python2-nbconvert (package-with-python2 python-nbconvert)) +(define-public python-prometheus-client + (package + (name "python-prometheus-client") + (version "0.5.0") + (source + (origin + (method url-fetch) + (uri (pypi-uri "prometheus_client" version)) + (sha256 + (base32 + "0g7rpv1pq2lab1nfqdx98z9d3bqwc400alg1j4ynrpjkrbsizhg8")))) + (build-system python-build-system) + (arguments '(#:tests? #f)) ; tests are not included + (propagated-inputs + `(("python-twisted" ,python-twisted))) + (home-page "https://github.com/prometheus/client_python") + (synopsis "Python client for the Prometheus monitoring system") + (description + "This package provides a Python client for the Prometheus monitoring +system.") + (license license:asl2.0))) + +(define-public python2-prometheus-client + (package-with-python2 python-prometheus-client)) + (define-public python-notebook (package (name "python-notebook") -- cgit v1.2.3 From b6fc288e57883d835aef6da1608a17a5de6ef3c9 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 2 Jan 2019 15:49:01 +0100 Subject: gnu: Add python-send2trash. * gnu/packages/python.scm (python-send2trash, python2-send2trash): New variables. --- gnu/packages/python.scm | 22 ++++++++++++++++++++++ 1 file changed, 22 insertions(+) (limited to 'gnu/packages/python.scm') diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index f2b24481ef..59a3f1364b 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -4888,6 +4888,28 @@ installing @code{kernelspec}s for use with Jupyter frontends.") (define-public python2-ipykernel (package-with-python2 python-ipykernel)) +(define-public python-send2trash + (package + (name "python-send2trash") + (version "1.5.0") + (source + (origin + (method url-fetch) + (uri (pypi-uri "send2trash" version)) + (sha256 + (base32 + "1ci8vcwjmjlp11ljj1ckrfmml9fkq1mclx2gr53y4zvhgp01q030")))) + (build-system python-build-system) + (home-page "https://github.com/hsoft/send2trash") + (synopsis "Send files to trash") + (description + "This package provides a cross-platform mechanism to send files to the +trash.") + (license license:bsd-3))) + +(define-public python2-send2trash + (package-with-python2 python-send2trash)) + ;; This is the latest release of the LTS version of ipython with support for ;; Python 2.7 and Python 3.x. Later non-LTS versions starting from 6.0 have ;; dropped support for Python 2.7. We may want to rename this package. -- cgit v1.2.3 From fec14302d5b57fe94ebecb78933c6402ebe90414 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 2 Jan 2019 15:49:29 +0100 Subject: gnu: python-widgetsnbextension: Update to 3.4.2. * gnu/packages/python.scm (python-widgetsnbextension): Update to 3.4.2. [propagated-inputs]: Add python-ipykernel. --- gnu/packages/python.scm | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) (limited to 'gnu/packages/python.scm') diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index 59a3f1364b..b80ea0ba1f 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -7219,17 +7219,18 @@ interactive computing.") (define-public python-widgetsnbextension (package (name "python-widgetsnbextension") - (version "1.2.6") + (version "3.4.2") (source (origin (method url-fetch) (uri (pypi-uri "widgetsnbextension" version)) (sha256 (base32 - "0lff2mrwrgsa1mxmwx3phl9xvy0jqfpg6khbmxy53jbq56rwy666")))) + "0rc2nivdy7k4m3vljx7wdh2jh11djapcgwhvzlbs0isl8gl8nqgs")))) (build-system python-build-system) (propagated-inputs - `(("python-notebook" ,python-notebook))) + `(("python-ipykernel" ,python-ipykernel) + ("python-notebook" ,python-notebook))) (native-inputs `(("python-certifi" ,python-certifi) ("python-nose" ,python-nose))) -- cgit v1.2.3 From 88bf9be38e32787393cb4c71d79d73c1d1971754 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 2 Jan 2019 15:51:57 +0100 Subject: gnu: python-ipywidgets: Enable tests. * gnu/packages/python.scm (python-ipywidgets)[arguments]: Remove. [native-inputs]: Add python-nose and python-pytest. [propagated-inputs]: Remove python-ipykernel. --- gnu/packages/python.scm | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) (limited to 'gnu/packages/python.scm') diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index b80ea0ba1f..52fa59329c 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -7255,13 +7255,13 @@ notebooks.") (base32 "1lk0qrr5l9a0z7qkkn30hv5832whxwxymf1l576fmmad0n7hkxms")))) (build-system python-build-system) - ;; FIXME: it's not clear how to run the tests. - (arguments `(#:tests? #f)) (propagated-inputs - `(("python-ipykernel" ,python-ipykernel) - ("python-ipython" ,python-ipython) + `(("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 -- cgit v1.2.3 From 4fc112b452b6ac086bd93efc2ba137990a44d34a Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 2 Jan 2019 16:06:55 +0100 Subject: gnu: python-ipython: Remove dependency on python-jupyter-core-minimal. * gnu/packages/python.scm (python-ipython)[propagated-inputs]: Remove python-jupyter-core-minimal. --- gnu/packages/python.scm | 6 ------ 1 file changed, 6 deletions(-) (limited to 'gnu/packages/python.scm') diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index 52fa59329c..1c5b163041 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -4933,12 +4933,6 @@ trash.") ("python-numpy" ,python-numpy) ("python-numpydoc" ,python-numpydoc) ("python-jinja2" ,python-jinja2) - ("python-jupyter-console" - ;; The python-ipython and python-jupyter-console require each - ;; other. To get the functionality in both packages working, strip - ;; down the python-jupyter-console package when using it as an input - ;; to python-ipython. - ,python-jupyter-console-minimal) ("python-mistune" ,python-mistune) ("python-pexpect" ,python-pexpect) ("python-pickleshare" ,python-pickleshare) -- cgit v1.2.3 From 493e5e6daa058b7eb5e2ffbeccad2a5bd47dc60d Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 2 Jan 2019 16:07:56 +0100 Subject: gnu: python-jupyter-console: Fix inputs. * gnu/packages/python.scm (python-jupyter-console)[propagated-inputs]: Remove python-ipython; replace python-prompt-toolkit with python-prompt-toolkit-1. [native-inputs]: Add python-nose. --- gnu/packages/python.scm | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) (limited to 'gnu/packages/python.scm') diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index 1c5b163041..e15f6f6a8e 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -7279,14 +7279,15 @@ in the data.") (base32 "1kam1qzgwr7srhm5r6aj90di5sws4bq0jmiw15452ddamb9yspal")))) (build-system python-build-system) - ;; FIXME: it's not clear how to run the tests. + ;; Tests only run in an TTY. (arguments `(#:tests? #f)) (propagated-inputs `(("python-ipykernel" ,python-ipykernel) - ("python-ipython" ,python-ipython) ("python-jupyter-client" ,python-jupyter-client) - ("python-prompt-toolkit" ,python-prompt-toolkit) + ("python-prompt-toolkit" ,python-prompt-toolkit-1) ("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 -- cgit v1.2.3 From 91dd8b368703ab0d183839fbe9fa8a3d23bf5001 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 2 Jan 2019 16:27:18 +0100 Subject: gnu: python-notebook: Update to 5.7.4. * gnu/packages/python.scm (python-notebook): Update to 5.7.4. [arguments]: Use INVOKE for tests. [propagated-inputs]: Remove python-ipython; add python-prometheus-client, python-send2trash, and python-terminado. --- gnu/packages/python.scm | 19 ++++++++++++++----- 1 file changed, 14 insertions(+), 5 deletions(-) (limited to 'gnu/packages/python.scm') diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index e15f6f6a8e..f68062a481 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -7157,27 +7157,36 @@ system.") (define-public python-notebook (package (name "python-notebook") - (version "4.2.3") + (version "5.7.4") (source (origin (method url-fetch) (uri (pypi-uri "notebook" version)) (sha256 (base32 - "0laq5c2f21frq6xcdckgq7raqhznbjb0qs0357g612z87wyn1a9r")))) + "0jm7324mbxljmn9hgapj66q7swyz5ai92blmr0jpcy0h80x6f26r")))) (build-system python-build-system) (arguments `(#:phases (modify-phases %standard-phases (replace 'check (lambda _ - ;; HOME must be set for tests + ;; These tests require a browser + (delete-file-recursively "notebook/tests/selenium") + ;; Some tests need HOME (setenv "HOME" "/tmp") - (zero? (system* "nosetests"))))))) + ;; This file contains "warningfilters", which are not supported + ;; by this version of nose. + (delete-file "setup.cfg") + (with-directory-excursion "/tmp" + (invoke "nosetests" "-v")) + #t))))) (propagated-inputs `(("python-jupyter-core" ,python-jupyter-core) ("python-nbformat" ,python-nbformat) ("python-nbconvert" ,python-nbconvert) - ("python-ipython" ,python-ipython))) + ("python-prometheus-client" ,python-prometheus-client) + ("python-send2trash" ,python-send2trash) + ("python-terminado" ,python-terminado))) (native-inputs `(("python-nose" ,python-nose) ("python-sphinx" ,python-sphinx) -- cgit v1.2.3 From 38306e11685b18e9fff5766252b39942da0d75d9 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 2 Jan 2019 16:28:27 +0100 Subject: gnu: Add python-qtconsole. * gnu/packages/python.scm (python-qtconsole): New variable. --- gnu/packages/python.scm | 36 ++++++++++++++++++++++++++++++++++++ 1 file changed, 36 insertions(+) (limited to 'gnu/packages/python.scm') diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index f68062a481..8bc2935761 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -7333,6 +7333,42 @@ Jupyter kernels such as IJulia and IRKernel.") "python-ipython" (package-propagated-inputs python-jupyter-console))))) +(define-public python-qtconsole + (package + (name "python-qtconsole") + (version "4.4.3") + (source + (origin + (method url-fetch) + (uri (pypi-uri "qtconsole" version)) + (sha256 + (base32 + "1b03n1ixzscm0jw97l4dq5iy4fslnqxq5bb8287xb7n2a1gs26xw")))) + (build-system python-build-system) + (arguments + ;; XXX: Tests are disabled, because this package needs python-ipython 7, + ;; but we only have the LTS version 5.x. This means that there might be + ;; runtime errors, but since this is a dependency of the Jupyter package, + ;; and Jupyter can be used without the qtconsole we can overlook this for + ;; now. + `(#:tests? #f + #:phases + (modify-phases %standard-phases + (add-before 'check 'pre-check + (lambda _ + (setenv "QT_QPA_PLATFORM" "offscreen") + #t))))) + (propagated-inputs + `(("python-ipykernel" ,python-ipykernel) + ("python-ipython" ,python-ipython))) + (native-inputs + `(("python-pytest" ,python-pytest))) + (home-page "http://jupyter.org") + (synopsis "Jupyter Qt console") + (description "This package provides a Qt-based console for Jupyter with +support for rich media output.") + (license license:bsd-3))) + (define-public jupyter (package (name "jupyter") -- cgit v1.2.3 From 9fb5771af76123cfecee83da677cb7fb7a6c810c Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 2 Jan 2019 16:29:51 +0100 Subject: gnu: jupyter: Add missing dependency. * gnu/packages/python.scm (jupyter)[propagated-inputs]: Add python-qtconsole. [home-page]: Use https URL. [arguments]: Update comment on why tests are disabled. --- gnu/packages/python.scm | 12 +++++------- 1 file changed, 5 insertions(+), 7 deletions(-) (limited to 'gnu/packages/python.scm') diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index 8bc2935761..ad5c564278 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -7,7 +7,7 @@ ;;; Copyright © 2014, 2015 Federico Beffa ;;; Copyright © 2015 Omar Radwan ;;; Copyright © 2015 Pierre-Antoine Rault -;;; Copyright © 2015, 2016, 2017, 2018 Ricardo Wurmus +;;; Copyright © 2015, 2016, 2017, 2018, 2019 Ricardo Wurmus ;;; Copyright © 2015, 2016 Christopher Allan Webber ;;; Copyright © 2015 Eric Dvorsak ;;; Copyright © 2015, 2016 David Thompson @@ -7381,21 +7381,19 @@ support for rich media output.") (base32 "0pwf3pminkzyzgx5kcplvvbvwrrzd3baa7lmh96f647k30rlpp6r")))) (build-system python-build-system) - ;; FIXME: it's not clear how to run the tests. - (arguments `(#:tests? #f)) + (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-notebook" ,python-notebook) + ("python-qtconsole" ,python-qtconsole))) (native-search-paths (list (search-path-specification (variable "JUPYTER_PATH") (files '("share/jupyter"))))) - - (home-page "http://jupyter.org") + (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 -- cgit v1.2.3 From 46930b7ea9792caf8bb75994240b8dd6470648ff Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Sun, 6 Jan 2019 09:43:36 +0200 Subject: gnu: python-sphinx-alabaster-theme: Update to 0.7.12. * gnu/packages/python.scm (python-sphinx-alabaster-theme): Update to 0.7.12. --- gnu/packages/python.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) (limited to 'gnu/packages/python.scm') diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index ad5c564278..f2f27f5626 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -14,7 +14,7 @@ ;;; Copyright © 2015, 2016, 2017 Leo Famulari ;;; Copyright © 2015, 2017 Ben Woodcroft ;;; Copyright © 2015, 2016 Erik Edrosa -;;; Copyright © 2015, 2016, 2017, 2018 Efraim Flashner +;;; Copyright © 2015, 2016, 2017, 2018, 2019 Efraim Flashner ;;; Copyright © 2015, 2017 Kyle Meyer ;;; Copyright © 2015, 2016 Chris Marusich ;;; Copyright © 2016 Danny Milosavljevic @@ -10706,13 +10706,13 @@ related extensions.") (define-public python-sphinx-alabaster-theme (package (name "python-sphinx-alabaster-theme") - (version "0.7.9") + (version "0.7.12") (source (origin (method url-fetch) (uri (pypi-uri "alabaster" version)) (sha256 (base32 - "027anxzcb951gjlcc43y3rbn9qrw36d16vj9wd2smv5410xx9bs7")))) + "00nwwjj2d2ym4s2kk217x7jkx1hnczc3fvm8yxbqmsp6b0nxfqd6")))) (build-system python-build-system) (propagated-inputs `(("python-pygments" ,python-pygments))) -- cgit v1.2.3 From 36df69d6fe3b254572075292b93a49b2118ba2a3 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Sun, 6 Jan 2019 09:46:19 +0200 Subject: gnu: python-imagesize: Update to 1.1.0. * gnu/packages/python.scm (python-imagesize): Update to 1.1.0. --- gnu/packages/python.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) (limited to 'gnu/packages/python.scm') diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index f2f27f5626..b610cea8cf 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -10895,14 +10895,14 @@ Record Format (DWARF).") (define-public python-imagesize (package (name "python-imagesize") - (version "1.0.0") + (version "1.1.0") (source (origin (method url-fetch) (uri (pypi-uri "imagesize" version)) (sha256 - (base32 - "05b3p62r7rbcvvbk5vknr3bhcq9b2airysn6ric534mng136wcjv")))) + (base32 + "1dg3wn7qpwmhgqc0r9na2ding1wif9q5spz3j9zn2riwphc2k0zk")))) (build-system python-build-system) (home-page "https://github.com/shibukawa/imagesize_py") (synopsis "Gets image size of files in various formats in Python") -- cgit v1.2.3 From 3cf324665d0358240492ce560826f11fbce17a60 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Sun, 6 Jan 2019 09:51:10 +0200 Subject: gnu: python-astroid: Update to 2.1.0. * gnu/packages/python.scm (python-astroid): Update to 2.1.0. --- gnu/packages/python.scm | 18 +++++++++--------- 1 file changed, 9 insertions(+), 9 deletions(-) (limited to 'gnu/packages/python.scm') diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index b610cea8cf..fd72e05cdb 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -11730,14 +11730,14 @@ clone, while other processes access the original tree.") (define-public python-astroid (package (name "python-astroid") - (version "2.0.4") + (version "2.1.0") (source (origin (method url-fetch) (uri (pypi-uri "astroid" version)) (sha256 (base32 - "138svbm88w5k0y2nvl4svyas1jfhcc5iy0d2ywkbcpn9kq8ks0f7")))) + "08hz675knh4294bancdapql392fmbjyimhbyrmfkz1ka7l035c1m")))) (build-system python-build-system) (propagated-inputs `(("python-lazy-object-proxy" ,python-lazy-object-proxy) @@ -11751,13 +11751,13 @@ clone, while other processes access the original tree.") (arguments `(#:phases (modify-phases %standard-phases - (add-after 'unpack 'remove-spurious-test - (lambda _ - ;; This can be removed after upgrading from python-3.7 - ;; https://github.com/PyCQA/astroid/issues/593 - ;; https://bugs.python.org/issue34056 - (delete-file "astroid/tests/unittest_modutils.py") - #t)) + (add-after 'unpack 'remove-spurious-test + (lambda _ + ;; This can be removed after upgrading from python-3.7 + ;; https://github.com/PyCQA/astroid/issues/593 + ;; https://bugs.python.org/issue34056 + (delete-file "astroid/tests/unittest_modutils.py") + #t)) (replace 'check (lambda _ (invoke "pytest" "astroid")))))) -- cgit v1.2.3 From 1fb68eefa1df49c34b6937256b58e1b2e176802c Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Sun, 6 Jan 2019 10:08:34 +0200 Subject: gnu: python-packaging: Update to 18.0. * gnu/packages/python.scm (python-packaging): Update to 18.0. --- gnu/packages/python.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/python.scm') diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index fd72e05cdb..c93edca806 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -12231,14 +12231,14 @@ several utilities, as well as an API for building localization tools.") (define-public python-packaging (package (name "python-packaging") - (version "17.1") + (version "18.0") (source (origin (method url-fetch) (uri (pypi-uri "packaging" version)) (sha256 (base32 - "0nrpayk8kij1zm9sjnk38ldz3a6705ggvw8ljylqbrb4vmqbf6gh")))) + "01wq9c53ix5rz6qg2c98gy8n4ff768rmanifm8m5jpjiaizj51h8")))) (build-system python-build-system) (arguments `(#:phases (modify-phases %standard-phases -- cgit v1.2.3 From a0bb4af21578a790185b12812cf709971a0c9fb1 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Sun, 6 Jan 2019 10:45:46 +0200 Subject: gnu: python-pysocks: Update to 1.6.8. * gnu/packages/python.scm (python-pysocks): Update to 1.6.8. --- gnu/packages/python.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/python.scm') diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index c93edca806..4ad8669e62 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -12992,14 +12992,14 @@ requirements is not met.") (define-public python-pysocks (package (name "python-pysocks") - (version "1.6.7") + (version "1.6.8") (source (origin (method url-fetch) (uri (pypi-uri "PySocks" version)) (sha256 (base32 - "1krkiss578zqwcg4c8iqz1hwscwhsvy2djp3xyvps5gsgvr2j0yh")))) + "0wn6xafwy9c1gamwljw3fyvih5w19qy9xp39zmv8c90ai5ajrr9z")))) (build-system python-build-system) (arguments `(#:tests? #f)) (home-page "https://github.com/Anorov/PySocks") -- cgit v1.2.3 From 99e61f302265569de64f0a4af9e33ade7df62158 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Sun, 6 Jan 2019 10:53:07 +0200 Subject: gnu: python-pyicu: Update to 2.2. * gnu/packages/python.scm (python-pyicu): Update to 2.2. --- gnu/packages/python.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/python.scm') diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index 4ad8669e62..2fa510067b 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -1395,14 +1395,14 @@ Python 3.3+.") (define-public python-pyicu (package (name "python-pyicu") - (version "1.9.8") + (version "2.2") (source (origin (method url-fetch) (uri (pypi-uri "PyICU" version)) (sha256 (base32 - "05nz4p2dpkhwj6y9kik24xbvmfxji39nl0xw0sc0nvp9fgzf6xnd")))) + "0wq9y5fi1ighgf5aws9nr87vi1w44p7q1k83rx2y3qj5d2xyhspa")))) (build-system python-build-system) (inputs `(("icu4c" ,icu4c))) -- cgit v1.2.3 From 915c6bf60cd6bd69fafc3acc69fac1242c3d96a3 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= Date: Mon, 7 Jan 2019 14:14:50 +0100 Subject: gnu: python2-fastlmm: Move to machine-learning.scm. This is a step towards removing OCaml modules from the closure of (gnu packages python). * gnu/packages/python.scm (python2-fastlmm): Move to... * gnu/packages/machine-learning.scm (python2-fastlmm): ... here. --- gnu/packages/python.scm | 35 ----------------------------------- 1 file changed, 35 deletions(-) (limited to 'gnu/packages/python.scm') diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index 2fa510067b..a1a9b44dc4 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -103,7 +103,6 @@ #:use-module (gnu packages libffi) #:use-module (gnu packages linux) #:use-module (gnu packages llvm) - #:use-module (gnu packages machine-learning) #:use-module (gnu packages man) #:use-module (gnu packages maths) #:use-module (gnu packages multiprecision) @@ -3228,40 +3227,6 @@ color scales, and color space conversion easy. It has support for: (define-public python2-spectra (package-with-python2 python-spectra)) -(define-public python2-fastlmm - (package - (name "python2-fastlmm") - (version "0.2.21") - (source - (origin - (method url-fetch) - (uri (pypi-uri "fastlmm" version ".zip")) - (sha256 - (base32 - "1q8c34rpmwkfy3r4d5172pzdkpfryj561897z9r3x22gq7813x1m")))) - (build-system python-build-system) - (arguments - `(#:python ,python-2)) ; only Python 2.7 is supported - (propagated-inputs - `(("python2-numpy" ,python2-numpy) - ("python2-scipy" ,python2-scipy) - ("python2-matplotlib" ,python2-matplotlib) - ("python2-pandas" ,python2-pandas) - ("python2-scikit-learn" ,python2-scikit-learn) - ("python2-pysnptools" ,python2-pysnptools))) - (native-inputs - `(("unzip" ,unzip) - ("python2-cython" ,python2-cython) - ("python2-mock" ,python2-mock) - ("python2-nose" ,python2-nose))) - (home-page "http://research.microsoft.com/en-us/um/redmond/projects/mscompbio/fastlmm/") - (synopsis "Perform genome-wide association studies on large data sets") - (description - "FaST-LMM, which stands for Factored Spectrally Transformed Linear Mixed -Models, is a program for performing both single-SNP and SNP-set genome-wide -association studies (GWAS) on extremely large data sets.") - (license license:asl2.0))) - (define-public python-numpy-documentation (package (name "python-numpy-documentation") -- cgit v1.2.3 From 61f2587db98284ec555c2b3899ff6998f9bd91d3 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 7 Jan 2019 15:41:18 +0100 Subject: gnu: python-rpy2: Move to (gnu packages statistics). * gnu/packages/python.scm (python-rpy2): Move from here... * gnu/packages/statistics.scm (python-rpy2): ...to here. --- gnu/packages/python.scm | 59 ------------------------------------------------- 1 file changed, 59 deletions(-) (limited to 'gnu/packages/python.scm') diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index a1a9b44dc4..5a32681643 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -120,7 +120,6 @@ #:use-module (gnu packages search) #:use-module (gnu packages shells) #:use-module (gnu packages ssh) - #:use-module (gnu packages statistics) #:use-module (gnu packages terminals) #:use-module (gnu packages tex) #:use-module (gnu packages texinfo) @@ -3731,64 +3730,6 @@ those files. It can also efficiently manipulate ranges of integers using set operators such as union, intersection, and difference.") (license license:asl2.0))) -(define-public python-rpy2 - (package - (name "python-rpy2") - (version "2.9.4") - (source - (origin - (method url-fetch) - (uri (pypi-uri "rpy2" version)) - (sha256 - (base32 - "0bl1d2qhavmlrvalir9hmkjh74w21vzkvc2sg3cbb162s10zfmxy")))) - (build-system python-build-system) - (arguments - '(#:modules ((ice-9 ftw) - (srfi srfi-1) - (srfi srfi-26) - (guix build utils) - (guix build python-build-system)) - #:phases - (modify-phases %standard-phases - (replace 'check - (lambda* (#:key outputs inputs #:allow-other-keys) - (let ((cwd (getcwd))) - (setenv "PYTHONPATH" - (string-append cwd "/build/" - (find (cut string-prefix? "lib" <>) - (scandir (string-append cwd "/build"))) - ":" - (getenv "PYTHONPATH")))) - (invoke "python" "-m" "rpy2.tests" "-v")))))) - (propagated-inputs - `(("python-six" ,python-six) - ("python-jinja2" ,python-jinja2) - ("python-pytz" ,python-pytz))) - (inputs - `(("readline" ,readline) - ("icu4c" ,icu4c) - ("pcre" ,pcre) - ("r-minimal" ,r-minimal) - ("r-survival" ,r-survival) - ("r-ggplot2" ,r-ggplot2) - ("r-rsqlite" ,r-rsqlite) - ("r-dplyr" ,r-dplyr) - ("r-dbplyr" ,r-dbplyr) - ("python-numpy" ,python-numpy))) - (native-inputs - `(("zlib" ,zlib))) - (home-page "https://rpy2.bitbucket.io/") - (synopsis "Python interface to the R language") - (description "rpy2 is a redesign and rewrite of rpy. It is providing a -low-level interface to R from Python, a proposed high-level interface, -including wrappers to graphical libraries, as well as R-like structures and -functions.") - ;; Any of these licenses can be picked for the R interface. The whole - ;; project is released under GPLv2+ according to the license declaration - ;; in "setup.py". - (license (list license:mpl2.0 license:gpl2+ license:lgpl2.1+)))) - (define-public python-scipy (package (name "python-scipy") -- cgit v1.2.3