diff options
Diffstat (limited to 'gnu/packages/python-xyz.scm')
| -rw-r--r-- | gnu/packages/python-xyz.scm | 347 |
1 files changed, 269 insertions, 78 deletions
diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 50a586d773..98abf038a5 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -156,12 +156,14 @@ (define-module (gnu packages python-xyz) #:use-module ((guix licenses) #:prefix license:) #:use-module (gnu packages) - #:use-module (gnu packages algebra) #:use-module (gnu packages adns) #:use-module (gnu packages aidc) + #:use-module (gnu packages algebra) #:use-module (gnu packages attr) #:use-module (gnu packages backup) + #:use-module (gnu packages base) #:use-module (gnu packages bash) + #:use-module (gnu packages bdw-gc) #:use-module (gnu packages check) #:use-module (gnu packages cmake) #:use-module (gnu packages compression) @@ -177,28 +179,28 @@ #:use-module (gnu packages documentation) #:use-module (gnu packages enchant) #:use-module (gnu packages file) - #:use-module (gnu packages fontutils) #:use-module (gnu packages fonts) + #:use-module (gnu packages fontutils) #:use-module (gnu packages freedesktop) - #:use-module (gnu packages gdb) #:use-module (gnu packages gcc) + #:use-module (gnu packages gdb) #:use-module (gnu packages geo) #:use-module (gnu packages ghostscript) #:use-module (gnu packages gl) #:use-module (gnu packages glib) #:use-module (gnu packages gnome) #:use-module (gnu packages gnupg) - #:use-module (gnu packages graphviz) #:use-module (gnu packages graphics) + #:use-module (gnu packages graphviz) #:use-module (gnu packages gsasl) #:use-module (gnu packages gstreamer) #:use-module (gnu packages gtk) #:use-module (gnu packages haskell-xyz) #:use-module (gnu packages icu4c) - #:use-module (gnu packages inkscape) #:use-module (gnu packages image) #:use-module (gnu packages image-processing) #:use-module (gnu packages imagemagick) + #:use-module (gnu packages inkscape) #:use-module (gnu packages java) #:use-module (gnu packages jupyter) #:use-module (gnu packages kerberos) @@ -214,10 +216,10 @@ #:use-module (gnu packages maths) #:use-module (gnu packages monitoring) #:use-module (gnu packages multiprecision) - #:use-module (gnu packages networking) #:use-module (gnu packages ncurses) - #:use-module (gnu packages node) + #:use-module (gnu packages networking) #:use-module (gnu packages ninja) + #:use-module (gnu packages node) #:use-module (gnu packages openstack) #:use-module (gnu packages pcre) #:use-module (gnu packages pdf) @@ -236,14 +238,15 @@ #:use-module (gnu packages rdf) #:use-module (gnu packages readline) #:use-module (gnu packages regex) - #:use-module (gnu packages sdl) #:use-module (gnu packages scanner) + #:use-module (gnu packages sdl) #:use-module (gnu packages search) #:use-module (gnu packages serialization) #:use-module (gnu packages shells) #:use-module (gnu packages sphinx) #:use-module (gnu packages ssh) #:use-module (gnu packages swig) + #:use-module (gnu packages tcl) #:use-module (gnu packages terminals) #:use-module (gnu packages tex) #:use-module (gnu packages texinfo) @@ -254,24 +257,20 @@ #:use-module (gnu packages video) #:use-module (gnu packages web) #:use-module (gnu packages wxwidgets) - #:use-module (gnu packages base) #:use-module (gnu packages xml) - #:use-module (gnu packages xorg) #:use-module (gnu packages xdisorg) - #:use-module (gnu packages tcl) - #:use-module (gnu packages bdw-gc) - #:use-module (gnu packages serialization) + #:use-module (gnu packages xorg) #: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 gnu) #:use-module (guix build-system cargo) #:use-module (guix build-system cmake) + #:use-module (guix build-system gnu) #:use-module (guix build-system pyproject) #:use-module (guix build-system python) + #:use-module (guix download) + #:use-module (guix hg-download) + #:use-module (guix git-download) + #:use-module (guix gexp) + #:use-module (guix utils) #:use-module (srfi srfi-1) #:use-module (srfi srfi-26)) @@ -1342,15 +1341,10 @@ threads.") (sha256 (base32 "0bwkvjpjfyi9dgszzad9aww2vc00w3bczjnbifi92cp7wch2l923")))) - (build-system python-build-system) + (build-system pyproject-build-system) (native-inputs - (list python-setuptools-scm python-tornado python-typeguard + (list python-setuptools-scm python-tornado-6 python-typeguard python-pytest)) - (arguments - (list #:phases - #~(modify-phases %standard-phases - (replace 'check - (lambda _ (invoke "pytest" "-vv")))))) (home-page "https://github.com/jd/tenacity") (synopsis "Retrying library for python") (description "Tenacity is a general-purpose python library to simplify the @@ -2693,48 +2687,32 @@ class.") (define-public python-can (package (name "python-can") - (version "4.0.0") + (version "4.2.0") (source (origin (method url-fetch) (uri (pypi-uri "python-can" version)) (sha256 (base32 - "0pcbdgdw94lc2sxd56w6wdsshrs9dd5d3wp0x4sfd0drzx32inar")))) - (build-system python-build-system) + "1w5sdzxivpd3pw4pypwnjlksvfimdb93qnlddbrh5f13flhsgg8g")))) + (build-system pyproject-build-system) (arguments - `(#:phases (modify-phases %standard-phases - (add-after 'unpack 'relax-version-requirements - (lambda _ - (substitute* "setup.py" - (("mock~=2\\.0") "mock") - (("coverage<5") "coverage") - (("pytest~=4\\.6") "pytest") - (("pytest-timeout~=1\\.3") "pytest-timeout") - (("pytest-cov.*") "pytest-cov\n") - (("hypothesis~=4\\.56") "hypothesis")))) - (add-after 'unpack 'fix-broken-tests - ;; The tests try to run two scripts it expects should be - ;; in PATH, but they aren't at this time (see: - ;; https://github.com/hardbyte/python-can/issues/805). - (lambda _ - (substitute* "test/test_scripts.py" - (("\"can_logger\\.py --help\"") "") - (("\"can_player\\.py --help\"") "")))) - (replace 'check - (lambda* (#:key tests? #:allow-other-keys) - (when tests? - (invoke "pytest" "-vv" "test" - ;; Disable tests which require specific CAN - ;; drivers we have no package for in Guix. - "--ignore" "test/test_interface_canalystii.py" - ;; These tests fail with "OSError: [Errno 19] - ;; No such device". - "-k" "not BasicTestUdpMulticastBusIPv"))))))) + (list + #:test-flags + #~(list + ;; TODO: Check if it could be packed: + ;; https://github.com/projectgus/python-canalystii + ;; + ;; Disable tests which require specific CAN drivers we have no + ;; package for in Guix. + "--ignore" "test/test_interface_canalystii.py" + ;; These tests fail with "OSError: [Errno 19] No such device". + "-k" "not BasicTestUdpMulticastBusIPv"))) (propagated-inputs (list python-msgpack python-typing-extensions python-wrapt)) (native-inputs - (list python-codecov + (list ;; python-canalystii ; Not packed yet + python-codecov python-coverage python-future python-hypothesis @@ -4419,6 +4397,58 @@ with sensible defaults out of the box.") clickgen is using @code{anicursorgen} and @code{xcursorgen} under the hood.") (license license:expat))) +(define-public python-clickhouse-connect + (package + (name "python-clickhouse-connect") + (version "0.6.1") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/ClickHouse/clickhouse-connect") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1s0lk7xdq8f351cmpbp6jidqi5zdazrdba7w7fxph0w8sd74amry")))) + (build-system pyproject-build-system) + (arguments + (list + #:test-flags + ;; All these tests require docker-compose + '(list "--ignore-glob=tests/integration_tests/*") + #:phases + '(modify-phases %standard-phases + (add-after 'unpack 'patch-pyproject + (lambda _ + ;; Our version of pytest is confused by this field. + (substitute* "pyproject.toml" + (("^env_files.*") "")))) + (add-before 'check 'build-extensions + (lambda _ + ;; Cython extensions have to be built before running the tests. + (invoke "python" "setup.py" "build_ext" "--inplace")))))) + (propagated-inputs + (list python-arrow + python-certifi + python-lz4 + python-numpy + python-orjson + python-pandas + python-pytz + python-sqlalchemy + python-urllib3 + python-zstandard)) + (native-inputs + (list python-cython + python-pytest)) + (home-page "https://github.com/ClickHouse/clickhouse-connect") + (synopsis + "ClickHouse database core driver for Python, Pandas, and Superset") + (description + "This package provides a high performance core database driver for +connecting ClickHouse to Python, Pandas, and Superset.") + (license license:asl2.0))) + (define-public python-cligj (package (name "python-cligj") @@ -9411,6 +9441,28 @@ all the newest features of the standard @code{pathlib} can be used also on older Python versions.") (license license:expat))) +(define-public python-pathy + (package + (name "python-pathy") + (version "0.10.1") + (source (origin + (method url-fetch) + (uri (pypi-uri "pathy" version)) + (sha256 + (base32 + "12v196q3rai33cfzrmb9pqfqv7ailngssjdrzdf8gzym9hdygmjc")))) + (build-system pyproject-build-system) + (propagated-inputs + (list python-dataclasses python-smart-open python-typer)) + (native-inputs (list python-mock python-pytest)) + (home-page "https://github.com/justindujardin/pathy") + (synopsis "Path interface for local and cloud bucket storage") + (description "Pathy is a python package (with type annotations) for +working with Cloud Bucket storage providers using a @code{pathlib} interface. +It provides @code{pathlib.Path} subclasses for local and cloud bucket +storage.") + (license license:asl2.0))) + (define-public python-importlib-resources (package (name "python-importlib-resources") @@ -10305,6 +10357,36 @@ you're careful. The @code{backcall} package provides a way of specifying the callback signature using a prototype function.") (license license:bsd-3))) +(define-public python-pubmed-parser + (package + (name "python-pubmed-parser") + (version "0.3.1") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/titipata/pubmed_parser") + (commit version))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "195cmjjg7xdwjj5455h78q7jnxnccia07a19xwndhlkxv7vk9v60")))) + (build-system pyproject-build-system) + (propagated-inputs + (list python-lxml + python-numpy + python-requests + python-six + python-unidecode)) + (native-inputs + (list python-pytest + python-pytest-cov)) + (home-page "https://github.com/titipata/pubmed_parser") + (synopsis "Parser for Pubmed Open-Access Subset and MEDLINE XML repository") + (description + "This package provides a Python parser for Pubmed Open-Access Subset and +MEDLINE XML repository.") + (license license:expat))) + (define-public python-pure-eval (package (name "python-pure-eval") @@ -15351,6 +15433,27 @@ provide an easy to use, pythonic and comprehensive Python interface to dialog. This allows one to make simple text-mode user interfaces on Unix-like systems") (license license:lgpl2.1))) +(define-public python-confection + (package + (name "python-confection") + (version "0.0.4") + (source (origin + (method url-fetch) + (uri (pypi-uri "confection" version)) + (sha256 + (base32 + "1ksfn10zhnpkcj3y0c3xs4dznvc062bk62x4c3ig0dd6bn4gbpdi")))) + (build-system pyproject-build-system) + (propagated-inputs (list python-pydantic python-srsly + python-typing-extensions)) + (native-inputs (list python-pytest)) + (home-page "https://github.com/explosion/confection") + (synopsis "Config system for Python") + (description "Confection is a lightweight library that offers a +configuration system letting you conveniently describe arbitrary trees of +objects.") + (license license:expat))) + (define-public python-configobj (package (name "python-configobj") @@ -16408,7 +16511,7 @@ enhancements to optimization and data fitting problems.") python-packaging python-pillow python-pyyaml - python-tornado + python-tornado-6 python-typing-extensions)) (native-inputs (list python-beautifulsoup4 @@ -17235,19 +17338,23 @@ checking library.") (define-public python-codespell (package (name "python-codespell") - (version "2.1.0") + (version "2.2.4") (source (origin (method url-fetch) (uri (pypi-uri "codespell" version)) (sha256 - (base32 "1r9y714cz8m894rxp7pyvicr1lw2iid24vz6fxbl5wzy8ibgxlqr")))) - (build-system python-build-system) + (base32 "0fp8ihlj8q23qdfryj5pq8srl85vn8k8p6gq3zg9qz957i3j0ihb")))) + (build-system pyproject-build-system) (inputs (list python-chardet)) (native-inputs - (list python-check-manifest python-flake8 python-pytest - python-pytest-cov python-pytest-dependency)) + (list python-flake8 + python-pygments + python-pytest + python-pytest-cov + python-pytest-dependency + python-tomli)) (arguments `(#:phases (modify-phases %standard-phases @@ -20481,6 +20588,59 @@ from the header, as well as section details and data available.") Mustache templating language renderer.") (license license:expat))) +(define-public python-duckdb + (package + (name "python-duckdb") + (version "0.8.0") + (source (origin + (method url-fetch) + (uri (pypi-uri "duckdb" version)) + (sha256 + (base32 + "13y1gs565q51li5fi9m7fpf0sqns8frsaii6v95acwjhmdds73f6")))) + (build-system pyproject-build-system) + (arguments + (list + #:test-flags + '(list "--ignore=tests/slow/test_h2oai_arrow.py" + ;; Don't install anything, thank you. + "-k" "not test_install_non_existent_extension") + #:phases + #~(modify-phases %standard-phases + ;; Tests need this + (add-before 'check 'set-HOME + (lambda _ (setenv "HOME" "/tmp"))) + (add-before 'build 'set-version + (lambda _ + (setenv "SETUPTOOLS_SCM_PRETEND_VERSION" #$version) + (substitute* "setup.py" + (("\"setuptools_scm<7.0.0\",") "")))) + ;; Later versions of pybind replace "_" with "const_name". + (add-after 'unpack 'pybind-compatibility + (lambda _ + (with-directory-excursion "src/include/duckdb_python" + (substitute* '("python_objects.hpp" + "pyfilesystem.hpp" + "pybind11/conversions/pyconnection_default.hpp") + (("const_name") "_")))))))) + (native-inputs + (list pybind11 + python-fsspec + python-google-cloud-storage + python-mypy + python-numpy + python-pandas + python-psutil + python-pyarrow + python-pytest + python-pytest-runner + python-setuptools-scm)) + (home-page "https://www.duckdb.org") + (synopsis "DuckDB embedded database") + (description "DuckDB is an in-process SQL OLAP database management +system.") + (license license:expat))) + (define-public python-dulwich (package (name "python-dulwich") @@ -26647,32 +26807,29 @@ the syntactic logic to configure and launch jobs in an execution environment.") (define-public python-flit (package (name "python-flit") - (version "3.5.1") + (version "3.8.0") ;same as python-flit-core (source (origin (method url-fetch) (uri (pypi-uri "flit" version)) (sha256 - (base32 "04152qj46sqbnlrj7ch9p7svjrrlpzbk0qr39g2yr0s4f5vp6frf")))) - (build-system python-build-system) + (base32 "0dz9sp2zlhkmk6sm5gapbbb30f7xq3n3jn5zxx5pkp25ppsaiwnh")))) + (build-system pyproject-build-system) (arguments (list + #:test-flags + ;; These tests fail when FLIT_NO_NETWORK is set + '(list "-k" "not test_invalid_classifier \ +and not test_install_requires \ +and not test_install_requires_extra \ +and not test_validate_classifiers_private") #:phases #~(modify-phases %standard-phases - ;; XXX: PEP 517 manual build copied from python-isort. - (replace 'build - (lambda _ - (invoke "python" "-m" "build" "--wheel" "--no-isolation" "."))) - (replace 'check + (add-before 'check 'pre-check (lambda* (#:key tests? inputs outputs #:allow-other-keys) (when tests? (setenv "HOME" "/tmp") - (setenv "FLIT_NO_NETWORK" "1")))) - (replace 'install - (lambda _ - (let ((whl (car (find-files "dist" "\\.whl$")))) - (invoke "pip" "--no-cache-dir" "--no-input" - "install" "--no-deps" "--prefix" #$output whl))))))) + (setenv "FLIT_NO_NETWORK" "1"))))))) (propagated-inputs (list python-pypa-build python-tomli-w @@ -31767,6 +31924,40 @@ uses the parsed regular expression, so you get a much more accurate result than trying to just split strings.") (license license:asl2.0))) +(define-public python-srsly + (package + (name "python-srsly") + (version "2.4.6") + (source (origin + (method url-fetch) + (uri (pypi-uri "srsly" version)) + (sha256 + (base32 + "0vsafkvk4g0p5m0dqrczqvlyza837i20xxmb24rrqk5s78r1zd27")))) + (build-system pyproject-build-system) + (arguments + (list + #:phases + #~(modify-phases %standard-phases + (add-before 'check 'build-extensions + (lambda _ + ;; Cython extensions have to be built before running the tests. + (invoke "python" "setup.py" "build_ext" "--inplace")))))) + (propagated-inputs (list python-catalogue)) + (native-inputs + (list python-cython + python-pytest + python-pytest-timeout + python-mock + python-numpy + python-psutil)) + (home-page "https://github.com/explosion/srsly") + (synopsis "Serialization utilities for Python") + (description "This package bundles some of the best Python serialization +libraries into one standalone package, with a high-level API that makes it +easy to write code that's correct across platforms and Pythons.") + (license license:expat))) + (define-public python-pyperf (package (name "python-pyperf") |