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author | Shepherd on Tux02 | 2024-06-20 08:37:15 -0500 |
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committer | Shepherd on Tux02 | 2024-06-20 08:37:15 -0500 |
commit | fe5fd5cb23907f8e37edafda96bafa608a3e0e7f (patch) | |
tree | 0b4cec2038dde07fe26f1c6882369f36a9545a19 /gn/packages/python.scm | |
parent | f0f8dc84eca7088177797f84db05314537615c77 (diff) | |
parent | 0362ee068a39ce9a5fd6f0fba9cd5586211f07f1 (diff) | |
download | guix-bioinformatics-fe5fd5cb23907f8e37edafda96bafa608a3e0e7f.tar.gz |
Merge branch 'master' of /home/git/public/guix-bioinformatics
Diffstat (limited to 'gn/packages/python.scm')
-rw-r--r-- | gn/packages/python.scm | 165 |
1 files changed, 121 insertions, 44 deletions
diff --git a/gn/packages/python.scm b/gn/packages/python.scm index 510546d..e7cfdd7 100644 --- a/gn/packages/python.scm +++ b/gn/packages/python.scm @@ -3,6 +3,7 @@ #:use-module (gnu packages) #:use-module (gnu packages check) #:use-module (gnu packages compression) + #:use-module (gnu packages databases) #:use-module (gnu packages fontutils) #:use-module (gnu packages ghostscript) #:use-module (gnu packages icu4c) @@ -32,8 +33,10 @@ #:use-module (guix packages) #:use-module (guix download) #:use-module (guix git-download) + #:use-module (guix hg-download) #:use-module (guix gexp) #:use-module (guix utils) + #:use-module (guix build-system pyproject) #:use-module (guix build-system python) #:use-module (srfi srfi-1)) @@ -862,50 +865,6 @@ spreadsheets without the need for COM objects.") (description "Extensions to the standard Python datetime module") (license license:bsd-3))) -(define-public python-arvados-python-client - (package - (name "python-arvados-python-client") - (version "2.5.0") - (source - (origin - (method url-fetch) - (uri (pypi-uri "arvados-python-client" version)) - (sha256 - (base32 "1j08aykj0v2z2bqwr5nfnbjgc1yzdnfdafcnxbf2jbwqh8kx7zc9")) - (modules '((guix build utils))) - (snippet - '(begin - (substitute* "setup.py" - ;; Don't set a maximum version of pycurl. - (("(pycurl >=([[:digit:]]+\\.?)+),.*" _ pycurl) - (string-append pycurl "',\n"))))))) - (build-system python-build-system) - (arguments - `(#:tests? #f)) ; tests not included? - (propagated-inputs - (list python-ciso8601 - python-future - python-google-api-client - python-google-api-core-1 - python-google-auth-1 - python-httplib2 - python-protobuf - python-pycurl - python-pyparsing-2.4.7 ; < 3 - python-ruamel.yaml - python-ws4py)) - (native-inputs - (list python-mock - python-pbr-1.6.0 - python-pyyaml)) - (home-page "https://arvados.org") - (synopsis "Arvados client library") - (description "This package provides the arvados module, an API client for -Arvados. It also includes higher-level functions to help you write Crunch -scripts, and command-line tools to store and retrieve data in the Keep storage -server.") - (license license:asl2.0))) - (define-public python-pyshex (package (name "python-pyshex") @@ -1815,6 +1774,30 @@ file format spec.") (license:fsf-free (string-append "https://web.archive.org/web/20190211105114/" "http://www.repoze.org/LICENSE.txt"))))) +;; Note: This package is only needed for rdflib < 6.0; supersede when +;; the above are removed. +(define-public python-rdflib-jsonld + (package + (name "python-rdflib-jsonld") + (version "0.6.2") + (source + (origin + (method url-fetch) + (uri (pypi-uri "rdflib-jsonld" version)) + (sha256 + (base32 + "0qrshlqzv5g5bign7kjja3xf7hyk7xgayr3yd0qlqda1kl0x6z0h")))) + (build-system python-build-system) + (native-inputs + (list python-nose)) + (propagated-inputs + (list python-rdflib)) + (home-page "https://github.com/RDFLib/rdflib-jsonld") + (synopsis "rdflib extension adding JSON-LD parser and serializer") + (description "This package provides an rdflib extension adding JSON-LD +parser and serializer.") + (license license:bsd-3))) + (define-public python-rdflib-shim (package (name "python-rdflib-shim") @@ -1878,3 +1861,97 @@ complete wrapping of the HDF5 API, while the high-level component supports access to HDF5 files, datasets and groups using established Python and NumPy concepts.") (license license:bsd-3))) + +(define-public python-typing-extensions-4.10 + (package + (inherit python-typing-extensions) + (version "4.10.0") + (source (origin + (method url-fetch) + (uri (pypi-uri "typing_extensions" version)) + (sha256 + (base32 + "1jxkj4pni8pdyrn79sq441lsp40xzw363n0qvfc6zfcgkv4dgaxh")))))) + +(define-public python-addict + (package + (name "python-addict") + (version "2.4.0") + (source (origin + (method url-fetch) + (uri (pypi-uri "addict" version)) + (sha256 + (base32 + "1574sicy5ydx9pvva3lbx8qp56z9jbdwbj26aqgjhyh61q723cmk")))) + (build-system pyproject-build-system) + (home-page "https://github.com/mewwts/addict") + (synopsis "Python dictionary with attribute accessible values") + (description "@code{python-addict} provides dictionaries whose items can +be get and set using both attribute and item syntax.") + (license license:expat))) + +(define-public python-enlighten + (package + (name "python-enlighten") + (version "1.12.4") + (source (origin + (method url-fetch) + (uri (pypi-uri "enlighten" version)) + (sha256 + (base32 + "0psvglhi0c7d7pdk9rfb8scnv3xbq2fz78619x2mxvz094mxkwvm")))) + (build-system pyproject-build-system) + (propagated-inputs + (list python-blessed python-prefixed)) + (home-page "https://github.com/Rockhopper-Technologies/enlighten") + (synopsis "Console progress bar library") + (description "@code{python-enlighten} is a console progress bar library +for Python. The main advantage of Enlighten is that it allows writing to +stdout and stderr without any redirection or additional code---just print or +log as you normally would. Enlighten also includes experimental support for +Jupyter Notebooks.") + (license license:mpl2.0))) + +(define-public python-pypubsub + (package + (name "python-pypubsub") + (version "4.0.3") + ;; There is no source tarball on PyPI. + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/schollii/pypubsub") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "02j74w28wzmdvxkk8i561ywjgizjifq3hgcl080yj0rvkd3wivlb")))) + (build-system python-build-system) + (home-page "https://github.com/schollii/pypubsub") + (synopsis "Python publish-subscribe library") + (description "@code{python-pypubsub} provides a pure Python +publish-subscribe API to facilitate event-based or message-based architecture +in a single-process application. It is centered on the notion of a topic; +senders publish messages of a given topic, and listeners subscribe to messages +of a given topic, all inside the same process. The package also supports a +variety of advanced features that facilitate debugging and maintaining topics +and messages in larger desktop or server-based applications.") + (license license:bsd-2))) + +(define-public python-prefixed + (package + (name "python-prefixed") + (version "0.7.0") + (source (origin + (method url-fetch) + (uri (pypi-uri "prefixed" version)) + (sha256 + (base32 + "1sdvxwy4kvcxvnq1nx70j1ccx5ga6wdb478vqd5azf1fc1gd2m0b")))) + (build-system pyproject-build-system) + (home-page "https://github.com/Rockhopper-Technologies/prefixed") + (synopsis "Prefixed alternative numeric library") + (description "@code{python-prefixed} provides an alternative +implementation of the built-in float which supports formatted output with +SI (decimal) and IEC (binary) prefixes.") + (license license:mpl2.0))) |