Merge branch 'master' into staging
Marius Bakke
commit
e5455bef85
|
|
@ -847,7 +847,7 @@ intended to behave exactly the same as the original BWK awk.")
|
|||
(define-public python-cellbender
|
||||
(package
|
||||
(name "python-cellbender")
|
||||
(version "0.2.1")
|
||||
(version "0.2.2")
|
||||
(source
|
||||
(origin
|
||||
(method git-fetch)
|
||||
|
|
@ -857,8 +857,8 @@ intended to behave exactly the same as the original BWK awk.")
|
|||
(file-name (git-file-name name version))
|
||||
(sha256
|
||||
(base32
|
||||
"1zav2q8nnss80i25y06fccagkvrqsy7lpylsl4dxv4qkj8p4fnv3"))))
|
||||
(build-system python-build-system)
|
||||
"12q22va7rbc3sx9ygc6p6hh6xw9wbqjmhba5h5gb836p5xplj5fa"))))
|
||||
(build-system pyproject-build-system)
|
||||
(arguments
|
||||
(list #:tests? #false)) ;there are none
|
||||
(propagated-inputs
|
||||
|
|
@ -885,14 +885,14 @@ from high-throughput single-cell RNA sequencing (scRNA-seq) data.")
|
|||
(define-public python-htsget
|
||||
(package
|
||||
(name "python-htsget")
|
||||
(version "0.2.5")
|
||||
(version "0.2.6")
|
||||
(source (origin
|
||||
(method url-fetch)
|
||||
(uri (pypi-uri "htsget" version))
|
||||
(sha256
|
||||
(base32
|
||||
"0ic07q85vhw9djf23k57b21my7i5xp400m8gfqgr5gcryqvdr0yk"))))
|
||||
(build-system python-build-system)
|
||||
"111q4pzkav26aa3hkgh948wqlyrq7dq6sjml9z63n3blw8s6b0c4"))))
|
||||
(build-system pyproject-build-system)
|
||||
(native-inputs
|
||||
(list python-setuptools-scm))
|
||||
(propagated-inputs
|
||||
|
|
@ -914,11 +914,12 @@ servers supporting the protocol.")
|
|||
(sha256
|
||||
(base32
|
||||
"18rhzk08d3rpxhi5xh6pqg64x6v5q3daw6y3v54k85v4swncjrwj"))))
|
||||
(build-system python-build-system)
|
||||
(build-system pyproject-build-system)
|
||||
(arguments
|
||||
`(#:modules ((srfi srfi-26)
|
||||
(guix build utils)
|
||||
(guix build python-build-system))
|
||||
(guix build python-build-system)
|
||||
(guix build pyproject-build-system))
|
||||
;; See https://github.com/daler/pybedtools/issues/192
|
||||
#:phases
|
||||
(modify-phases %standard-phases
|
||||
|
|
@ -978,7 +979,7 @@ which are widely used for genomic interval manipulation or \"genome algebra\".
|
|||
pybedtools extends BEDTools by offering feature-level manipulations from with
|
||||
Python.")
|
||||
;; pypi lists GPLv2 in the PKG-INFO and website, but was relicensed in
|
||||
;; version 0.9.0 and the LICENSE.txt is consistant with the source code.
|
||||
;; version 0.9.0 and the LICENSE.txt is consistent with the source code.
|
||||
;;
|
||||
;; pybedtools/include/gzstream.cpp and pybedtools/include/gzstream.h are
|
||||
;; licensed lgpl2.1+
|
||||
|
|
@ -1032,7 +1033,7 @@ use-case, we encourage users to compose functions to achieve their goals.")
|
|||
(define-public python-biom-format
|
||||
(package
|
||||
(name "python-biom-format")
|
||||
(version "2.1.10")
|
||||
(version "2.1.12")
|
||||
(source
|
||||
(origin
|
||||
(method git-fetch)
|
||||
|
|
@ -1044,25 +1045,22 @@ use-case, we encourage users to compose functions to achieve their goals.")
|
|||
(file-name (git-file-name name version))
|
||||
(sha256
|
||||
(base32
|
||||
"0i62j6ksmp78ap2dnl969gq6vprc3q87zc8ksj9if8g2603iq6i8"))
|
||||
"06x2d8fv80jp86kd66fm3ragmxrpa2j0lzsbm337ziqjnpsdwc0f"))
|
||||
(modules '((guix build utils)))
|
||||
;; Delete generated C files.
|
||||
(snippet
|
||||
'(for-each delete-file (find-files "." "\\.c")))))
|
||||
(build-system python-build-system)
|
||||
(arguments
|
||||
`(#:phases
|
||||
(modify-phases %standard-phases
|
||||
(list
|
||||
#:phases
|
||||
'(modify-phases %standard-phases
|
||||
(add-after 'unpack 'use-cython
|
||||
(lambda _ (setenv "USE_CYTHON" "1")))
|
||||
(add-after 'unpack 'relax
|
||||
(lambda _
|
||||
(substitute* "setup.py"
|
||||
(("pytest < 5.3.4") "pytest"))))
|
||||
(add-after 'unpack 'disable-broken-tests
|
||||
(lambda _
|
||||
(substitute* "biom/tests/test_cli/test_validate_table.py"
|
||||
(("^(.+)def test_invalid_hdf5" m indent)
|
||||
(substitute* "biom/tests/test_util.py"
|
||||
(("^(.+)def test_biom_open_hdf5_no_h5py" m indent)
|
||||
(string-append indent
|
||||
"@npt.dec.skipif(True, msg='Guix')\n"
|
||||
m)))
|
||||
|
|
@ -1073,13 +1071,14 @@ use-case, we encourage users to compose functions to achieve their goals.")
|
|||
m))))))))
|
||||
(propagated-inputs
|
||||
(list python-anndata
|
||||
python-numpy
|
||||
python-scipy
|
||||
python-click
|
||||
python-flake8
|
||||
python-future
|
||||
python-click
|
||||
python-h5py
|
||||
python-pandas))
|
||||
python-numpy
|
||||
python-pandas
|
||||
python-scikit-bio
|
||||
python-scipy))
|
||||
(native-inputs
|
||||
(list python-cython python-pytest python-pytest-cov python-nose))
|
||||
(home-page "http://www.biom-format.org")
|
||||
|
|
@ -1094,42 +1093,45 @@ e.g. microbiome samples, genomes, metagenomes.")
|
|||
(define-public python-pairtools
|
||||
(package
|
||||
(name "python-pairtools")
|
||||
(version "0.3.0")
|
||||
(version "1.0.2")
|
||||
(source (origin
|
||||
(method git-fetch)
|
||||
(uri (git-reference
|
||||
(url "https://github.com/mirnylab/pairtools")
|
||||
(url "https://github.com/open2c/pairtools")
|
||||
(commit (string-append "v" version))))
|
||||
(file-name (git-file-name name version))
|
||||
(sha256
|
||||
(base32
|
||||
"0gr8y13q7sd6yai6df4aavl2470n1f9s3cib6r473z4hr8hcbwmc"))))
|
||||
"0xn4cg4jq3rfn42h8rfwg0k6xkvihjrv32gwldb9y0jp05lzw9cs"))))
|
||||
(build-system python-build-system)
|
||||
(arguments
|
||||
`(#:phases
|
||||
(modify-phases %standard-phases
|
||||
(add-after 'unpack 'fix-references
|
||||
(lambda _
|
||||
(substitute* '("pairtools/pairtools_merge.py"
|
||||
"pairtools/pairtools_sort.py")
|
||||
(("/bin/bash") (which "bash")))
|
||||
#t))
|
||||
(substitute* '("pairtools/cli/header.py"
|
||||
"pairtools/cli/merge.py"
|
||||
"pairtools/cli/sort.py")
|
||||
(("/bin/bash") (which "bash")))))
|
||||
(replace 'check
|
||||
(lambda* (#:key inputs outputs #:allow-other-keys)
|
||||
(add-installed-pythonpath inputs outputs)
|
||||
(with-directory-excursion "/tmp"
|
||||
(invoke "pytest" "-v")))))))
|
||||
(lambda* (#:key tests? #:allow-other-keys)
|
||||
(when tests?
|
||||
(with-directory-excursion "/tmp"
|
||||
(invoke "pytest" "-v"))))))))
|
||||
(native-inputs
|
||||
(list python-cython python-nose python-pytest))
|
||||
(inputs
|
||||
`(("python" ,python-wrapper)))
|
||||
(list python-cython python-pytest))
|
||||
(propagated-inputs
|
||||
(list htslib ; for bgzip, looked up in PATH
|
||||
samtools ; looked up in PATH
|
||||
lz4 ; for lz4c
|
||||
python-bioframe
|
||||
python-click
|
||||
python-numpy))
|
||||
(home-page "https://github.com/mirnylab/pairtools")
|
||||
python-numpy
|
||||
python-pandas
|
||||
python-pysam
|
||||
python-pyyaml
|
||||
python-scipy))
|
||||
(home-page "https://github.com/open2c/pairtools")
|
||||
(synopsis "Process mapped Hi-C data")
|
||||
(description "Pairtools is a simple and fast command-line framework to
|
||||
process sequencing data from a Hi-C experiment. Process pair-end sequence
|
||||
|
|
@ -2974,6 +2976,71 @@ generation, and transformation to RDF. Salad provides a bridge between document
|
|||
and record oriented data modeling and the Semantic Web.")
|
||||
(license license:asl2.0)))
|
||||
|
||||
(define-public python-scikit-bio
|
||||
(package
|
||||
(name "python-scikit-bio")
|
||||
(version "0.5.7")
|
||||
(source (origin
|
||||
(method url-fetch)
|
||||
(uri (pypi-uri "scikit-bio" version))
|
||||
(sha256
|
||||
(base32
|
||||
"1a8xbp3vrw8wfpm3pa2nb4rcar0643iqnb043ifwqbqyc86clhv3"))))
|
||||
(build-system pyproject-build-system)
|
||||
(arguments
|
||||
(list
|
||||
#:phases
|
||||
'(modify-phases %standard-phases
|
||||
;; See https://github.com/biocore/scikit-bio/pull/1826
|
||||
(add-after 'unpack 'compatibility
|
||||
(lambda _
|
||||
(substitute* "skbio/sequence/tests/test_sequence.py"
|
||||
(("def test_concat_strict_many")
|
||||
"def _do_not_test_concat_strict_many"))
|
||||
(substitute* "skbio/stats/distance/_mantel.py"
|
||||
(("from scipy.stats import PearsonRConstantInputWarning")
|
||||
"from scipy.stats import ConstantInputWarning")
|
||||
(("from scipy.stats import PearsonRNearConstantInputWarning")
|
||||
"from scipy.stats import NearConstantInputWarning")
|
||||
(("from scipy.stats import SpearmanRConstantInputWarning") "")
|
||||
(("warnings.warn\\(PearsonRConstantInputWarning\\(\\)\\)")
|
||||
"warnings.warn(ConstantInputWarning())")
|
||||
(("warnings.warn\\(PearsonRNearConstantInputWarning\\(\\)\\)")
|
||||
"warnings.warn(NearConstantInputWarning())")
|
||||
(("warnings.warn\\(SpearmanRConstantInputWarning\\(\\)\\)")
|
||||
"warnings.warn(ConstantInputWarning())"))
|
||||
(substitute* "skbio/diversity/alpha/tests/test_base.py"
|
||||
(("self.assertEqual\\(pielou_e")
|
||||
"self.assertAlmostEqual(pielou_e"))))
|
||||
(add-before 'check 'build-extensions
|
||||
(lambda _
|
||||
;; Cython extensions have to be built before running the tests.
|
||||
(invoke "python3" "setup.py" "build_ext" "--inplace")))
|
||||
(replace 'check
|
||||
(lambda* (#:key tests? #:allow-other-keys)
|
||||
(when tests? (invoke "python3" "-m" "skbio.test")))))))
|
||||
(propagated-inputs
|
||||
(list python-cachecontrol
|
||||
python-decorator
|
||||
python-h5py
|
||||
python-hdmedians
|
||||
python-ipython
|
||||
python-lockfile
|
||||
python-matplotlib
|
||||
python-natsort
|
||||
python-numpy
|
||||
python-pandas
|
||||
python-scikit-learn
|
||||
python-scipy))
|
||||
(native-inputs
|
||||
(list python-coverage python-pytest))
|
||||
(home-page "https://scikit-bio.org")
|
||||
(synopsis "Data structures, algorithms and educational resources for bioinformatics")
|
||||
(description
|
||||
"This package provides data structures, algorithms and educational
|
||||
resources for bioinformatics.")
|
||||
(license license:bsd-3)))
|
||||
|
||||
(define-public cwltool
|
||||
(package
|
||||
(name "cwltool")
|
||||
|
|
|
|||
|
|
@ -795,8 +795,31 @@ EUI-64, also known as MAC-48 media access control addresses.")
|
|||
#:cargo-development-inputs
|
||||
(("rust-glob" ,rust-glob-0.3))))))
|
||||
|
||||
(define-public rust-gl-0.14
|
||||
(package
|
||||
(name "rust-gl")
|
||||
(version "0.14.0")
|
||||
(source (origin
|
||||
(method url-fetch)
|
||||
(uri (crate-uri "gl" version))
|
||||
(file-name (string-append name "-" version ".tar.gz"))
|
||||
(sha256
|
||||
(base32
|
||||
"015lgy3qpzdw7mnh59a4y4hdjq1fhv7nkqlmh1h6fzc212qxlkm9"))))
|
||||
(build-system cargo-build-system)
|
||||
(arguments
|
||||
`(#:cargo-development-inputs
|
||||
(("rust-glutin" ,rust-glutin-0.21))
|
||||
#:cargo-inputs
|
||||
(("rust-gl-generator" ,rust-gl-generator-0.14))))
|
||||
(home-page "https://github.com/brendanzab/gl-rs/")
|
||||
(synopsis "OpenGL bindings for rust")
|
||||
(description "This package provides OpenGL bindings for rust.")
|
||||
(license license:asl2.0)))
|
||||
|
||||
(define-public rust-gl-0.11
|
||||
(package
|
||||
(inherit rust-gl-0.14)
|
||||
(name "rust-gl")
|
||||
(version "0.11.0")
|
||||
(source
|
||||
|
|
@ -808,15 +831,10 @@ EUI-64, also known as MAC-48 media access control addresses.")
|
|||
(sha256
|
||||
(base32
|
||||
"1wcqpyhck0xriffkmgmldy33lwk2044hb4l02d44vm4fbvicin6p"))))
|
||||
(build-system cargo-build-system)
|
||||
(arguments
|
||||
`(#:skip-build? #t
|
||||
#:cargo-inputs
|
||||
(("rust-gl-generator" ,rust-gl-generator-0.10))))
|
||||
(home-page "https://github.com/brendanzab/gl-rs/")
|
||||
(synopsis "OpenGL bindings for rust")
|
||||
(description "This package provides OpenGL bindings for rust.")
|
||||
(license license:asl2.0)))
|
||||
(("rust-gl-generator" ,rust-gl-generator-0.10))))))
|
||||
|
||||
(define-public rust-gl-generator-0.14
|
||||
(package
|
||||
|
|
|
|||
|
|
@ -4950,6 +4950,29 @@ methods.")
|
|||
(description "This package provides a safe abstraction around AtomicPtr.")
|
||||
(license license:asl2.0)))
|
||||
|
||||
(define-public rust-atomic-0.5
|
||||
(package
|
||||
(name "rust-atomic")
|
||||
(version "0.5.1")
|
||||
(source (origin
|
||||
(method url-fetch)
|
||||
(uri (crate-uri "atomic" version))
|
||||
(file-name (string-append name "-" version ".tar.gz"))
|
||||
(sha256
|
||||
(base32
|
||||
"0k135q1qfmxxyzrlhr47r0j38r5fnd4163rgl552qxyagrk853dq"))))
|
||||
(build-system cargo-build-system)
|
||||
(arguments
|
||||
`(#:cargo-inputs (("rust-autocfg" ,rust-autocfg-1))))
|
||||
(home-page "https://github.com/Amanieu/atomic-rs")
|
||||
(synopsis "Generic @code{Atomic<T>} wrapper type")
|
||||
(description
|
||||
"This package provides a generic @code{Atomic<T>} type for all
|
||||
@code{T: Copy} types, unlike the standard library which only provides a few
|
||||
fixed atomic types.")
|
||||
;; The user can choose either license.
|
||||
(license (list license:asl2.0 license:expat))))
|
||||
|
||||
(define-public rust-atomic-polyfill-1
|
||||
(package
|
||||
(name "rust-atomic-polyfill")
|
||||
|
|
@ -17146,7 +17169,7 @@ diff.")
|
|||
(define-public rust-digest-0.10
|
||||
(package
|
||||
(name "rust-digest")
|
||||
(version "0.10.1")
|
||||
(version "0.10.6")
|
||||
(source
|
||||
(origin
|
||||
(method url-fetch)
|
||||
|
|
@ -17155,7 +17178,7 @@ diff.")
|
|||
(string-append name "-" version ".tar.gz"))
|
||||
(sha256
|
||||
(base32
|
||||
"16wpqnwlzx0lbnwccwikns7dq8fblcc6kma2l7xz8anlh5hdd5xn"))))
|
||||
"0vz74785s96g727vg37iwkjvbkcfzp093j49ihhyf8sh9s7kfs41"))))
|
||||
(build-system cargo-build-system)
|
||||
(arguments
|
||||
`(#:skip-build? #t
|
||||
|
|
@ -29311,6 +29334,35 @@ kernel32.")
|
|||
"This package provides a Log macro for log's kv-unstable backend.")
|
||||
(license (list license:expat license:asl2.0))))
|
||||
|
||||
(define-public rust-k9-0.11
|
||||
(package
|
||||
(name "rust-k9")
|
||||
(version "0.11.6")
|
||||
(source (origin
|
||||
(method url-fetch)
|
||||
(uri (crate-uri "k9" version))
|
||||
(file-name (string-append name "-" version ".tar.gz"))
|
||||
(sha256
|
||||
(base32
|
||||
"1a8pxz6fygqzknxdlb4l835kqxgjk7snm4bjhhhn783r025vbp9j"))))
|
||||
(build-system cargo-build-system)
|
||||
(arguments
|
||||
`(#:skip-build? #t
|
||||
#:cargo-inputs (("rust-anyhow" ,rust-anyhow-1)
|
||||
("rust-colored" ,rust-colored-1)
|
||||
("rust-diff" ,rust-diff-0.1)
|
||||
("rust-lazy-static" ,rust-lazy-static-1)
|
||||
("rust-libc" ,rust-libc-0.2)
|
||||
("rust-proc-macro2" ,rust-proc-macro2-1)
|
||||
("rust-regex" ,rust-regex-1)
|
||||
("rust-syn" ,rust-syn-1)
|
||||
("rust-term-size" ,rust-term-size-0.3))))
|
||||
(home-page "https://github.com/aaronabramov/k9")
|
||||
(synopsis "Testing library")
|
||||
(description
|
||||
"This package contains helper macros for writing unit tests.")
|
||||
(license license:expat)))
|
||||
|
||||
(define-public rust-language-tags-0.3
|
||||
(package
|
||||
(name "rust-language-tags")
|
||||
|
|
@ -32372,8 +32424,33 @@ parallelize and optimize.")
|
|||
"This package provides MaybeUninit for friends of backwards compatibility.")
|
||||
(license (list license:asl2.0 license:expat))))
|
||||
|
||||
(define-public rust-md-5-0.10
|
||||
(package
|
||||
(name "rust-md-5")
|
||||
(version "0.10.5")
|
||||
(source (origin
|
||||
(method url-fetch)
|
||||
(uri (crate-uri "md-5" version))
|
||||
(file-name (string-append name "-" version ".tar.gz"))
|
||||
(sha256
|
||||
(base32
|
||||
"1jmrykh705dfclkgxwjysj5y8l1nyrn1gddw5xpgyjyla1l50rb3"))))
|
||||
(build-system cargo-build-system)
|
||||
(arguments
|
||||
`(#:skip-build? #t
|
||||
#:cargo-inputs
|
||||
(("rust-digest" ,rust-digest-0.10)
|
||||
("rust-md5-asm" ,rust-md5-asm-0.5))))
|
||||
(home-page "https://github.com/RustCrypto/hashes")
|
||||
(synopsis "MD5 hash function")
|
||||
(description
|
||||
"This library provides a MD5 hash function for Rust.")
|
||||
;; The user can choose either license.
|
||||
(license (list license:expat license:asl2.0))))
|
||||
|
||||
(define-public rust-md-5-0.9
|
||||
(package
|
||||
(inherit rust-md-5-0.10)
|
||||
(name "rust-md-5")
|
||||
(version "0.9.1")
|
||||
(source
|
||||
|
|
@ -32385,7 +32462,6 @@ parallelize and optimize.")
|
|||
(sha256
|
||||
(base32
|
||||
"059ajjacz1q3cms7vl6cvhdqs4qdw2nnwj9dq99ryzv0p6djfnkv"))))
|
||||
(build-system cargo-build-system)
|
||||
(arguments
|
||||
`(#:cargo-inputs
|
||||
(("rust-block-buffer" ,rust-block-buffer-0.9)
|
||||
|
|
@ -32394,11 +32470,7 @@ parallelize and optimize.")
|
|||
("rust-opaque-debug" ,rust-opaque-debug-0.3))
|
||||
#:cargo-development-inputs
|
||||
(("rust-digest" ,rust-digest-0.9)
|
||||
("rust-hex-literal" ,rust-hex-literal-0.2))))
|
||||
(home-page "https://github.com/RustCrypto/hashes")
|
||||
(synopsis "MD5 hash function")
|
||||
(description "MD5 hash function.")
|
||||
(license (list license:expat license:asl2.0))))
|
||||
("rust-hex-literal" ,rust-hex-literal-0.2))))))
|
||||
|
||||
(define-public rust-md-5-0.8
|
||||
(package
|
||||
|
|
@ -32472,8 +32544,31 @@ parallelize and optimize.")
|
|||
(base32
|
||||
"0j2s8aqdkhwhy7awga2bmv5n8qq8bgy8672iha9f3y871dm6vibr"))))))
|
||||
|
||||
(define-public rust-md5-asm-0.5
|
||||
(package
|
||||
(name "rust-md5-asm")
|
||||
(version "0.5.0")
|
||||
(source (origin
|
||||
(method url-fetch)
|
||||
(uri (crate-uri "md5-asm" version))
|
||||
(file-name (string-append name "-" version ".tar.gz"))
|
||||
(sha256
|
||||
(base32
|
||||
"1ixmkg8j7sqy9zln6pz9xi2dl2d9zpm8pz6p49za47n1bvradfbk"))))
|
||||
(build-system cargo-build-system)
|
||||
(arguments
|
||||
`(#:cargo-inputs (("rust-cc" ,rust-cc-1))))
|
||||
(home-page "https://github.com/RustCrypto/asm-hashes")
|
||||
(synopsis "Assembly implementation of MD5 compression function")
|
||||
(description
|
||||
"This package contains an assembly implementation of the MD5
|
||||
compression function.")
|
||||
(supported-systems '("x86_64-linux" "i686-linux"))
|
||||
(license license:expat)))
|
||||
|
||||
(define-public rust-md5-asm-0.4
|
||||
(package
|
||||
(inherit rust-md5-asm-0.5)
|
||||
(name "rust-md5-asm")
|
||||
(version "0.4.3")
|
||||
(source
|
||||
|
|
@ -32485,16 +32580,9 @@ parallelize and optimize.")
|
|||
(sha256
|
||||
(base32
|
||||
"0gpk5647js1k084jc7pg2gji0cvl6hjkkbfia6lnpk8y4shyairv"))))
|
||||
(build-system cargo-build-system)
|
||||
(arguments
|
||||
`(#:cargo-inputs
|
||||
(("rust-cc" ,rust-cc-1))))
|
||||
(home-page "https://github.com/RustCrypto/asm-hashes")
|
||||
(synopsis "Assembly implementation of MD5 compression function")
|
||||
(description "This package contains an assembly implementation of MD5
|
||||
compression function.")
|
||||
(supported-systems '("x86_64-linux" "i686-linux"))
|
||||
(license license:expat)))
|
||||
(("rust-cc" ,rust-cc-1))))))
|
||||
|
||||
(define-public rust-measureme-0.7
|
||||
(package
|
||||
|
|
@ -32718,8 +32806,33 @@ file IO.")
|
|||
(sha256
|
||||
(base32 "0nmymqy9q62x577ydja0ysfyir7h5qa0n5fwcnvchfhhlsi0rdyr"))))))
|
||||
|
||||
(define-public rust-memoffset-0.7
|
||||
(package
|
||||
(name "rust-memoffset")
|
||||
(version "0.7.1")
|
||||
(source
|
||||
(origin
|
||||
(method url-fetch)
|
||||
(uri (crate-uri "memoffset" version))
|
||||
(file-name (string-append name "-" version ".tar.gz"))
|
||||
(sha256
|
||||
(base32 "1x2zv8hv9c9bvgmhsjvr9bymqwyxvgbca12cm8xkhpyy5k1r7s2x"))))
|
||||
(build-system cargo-build-system)
|
||||
(arguments
|
||||
`(#:cargo-inputs
|
||||
(("rust-autocfg" ,rust-autocfg-1))
|
||||
#:cargo-development-inputs
|
||||
(("rust-doc-comment" ,rust-doc-comment-0.3))))
|
||||
(home-page "https://github.com/Gilnaa/memoffset")
|
||||
(synopsis "C-like offset_of functionality for Rust structs")
|
||||
(description
|
||||
"This package provides C-like @code{offset_of} functionality
|
||||
for Rust structs.")
|
||||
(license license:expat)))
|
||||
|
||||
(define-public rust-memoffset-0.6
|
||||
(package
|
||||
(inherit rust-memoffset-0.7)
|
||||
(name "rust-memoffset")
|
||||
(version "0.6.5")
|
||||
(source
|
||||
|
|
@ -32736,13 +32849,7 @@ file IO.")
|
|||
(("rust-autocfg" ,rust-autocfg-1))
|
||||
#:cargo-development-inputs
|
||||
(("rust-doc-comment" ,rust-doc-comment-0.3))))
|
||||
(inputs (list rust-autocfg-1))
|
||||
(home-page "https://github.com/Gilnaa/memoffset")
|
||||
(synopsis "C-like offset_of functionality for Rust structs")
|
||||
(description
|
||||
"This package provides C-like @code{offset_of} functionality
|
||||
for Rust structs.")
|
||||
(license license:expat)))
|
||||
(inputs (list rust-autocfg-1))))
|
||||
|
||||
(define-public rust-memoffset-0.5
|
||||
(package
|
||||
|
|
@ -52346,6 +52453,28 @@ functionality and without weak references.")
|
|||
(base32
|
||||
"1i1i8viy6y30mv9v5hwhg9w6b722qkyh9c6n8bn4d27jpv14pg0s"))))))
|
||||
|
||||
(define-public rust-sha1-smol-1
|
||||
(package
|
||||
(name "rust-sha1-smol")
|
||||
(version "1.0.0")
|
||||
(source (origin
|
||||
(method url-fetch)
|
||||
(uri (crate-uri "sha1_smol" version))
|
||||
(file-name (string-append name "-" version ".tar.gz"))
|
||||
(sha256
|
||||
(base32
|
||||
"04nhbhvsk5ms1zbshs80iq5r1vjszp2xnm9f0ivj38q3dhc4f6mf"))))
|
||||
(build-system cargo-build-system)
|
||||
(arguments
|
||||
`(#:skip-build? #t
|
||||
#:cargo-inputs (("rust-serde" ,rust-serde-1))))
|
||||
(home-page "https://github.com/mitsuhiko/sha1-smol")
|
||||
(synopsis "Dependency free SHA1 implementation")
|
||||
(description
|
||||
"This package provides a minimal dependency free implementation of
|
||||
SHA1 for Rust.")
|
||||
(license license:bsd-3)))
|
||||
|
||||
(define-public rust-sha1collisiondetection-0.2
|
||||
(package
|
||||
(name "rust-sha1collisiondetection")
|
||||
|
|
@ -68008,8 +68137,31 @@ for locating fonts.")
|
|||
(description "This package provides an implementation of zbase32.")
|
||||
(license license:lgpl3+)))
|
||||
|
||||
(define-public rust-zerocopy-0.6
|
||||
(package
|
||||
(name "rust-zerocopy")
|
||||
(version "0.6.1")
|
||||
(source (origin
|
||||
(method url-fetch)
|
||||
(uri (crate-uri "zerocopy" version))
|
||||
(file-name (string-append name "-" version ".tar.gz"))
|
||||
(sha256
|
||||
(base32
|
||||
"0dpj4nd9v56wy93ahjkp95znjzj91waqvidqch8gxwdwq661hbrk"))))
|
||||
(build-system cargo-build-system)
|
||||
(arguments
|
||||
`(#:skip-build? #t
|
||||
#:cargo-inputs
|
||||
(("rust-byteorder" ,rust-byteorder-1)
|
||||
("rust-zerocopy-derive" ,rust-zerocopy-derive-0.3))))
|
||||
(home-page "https://github.com/google/zerocopy")
|
||||
(synopsis "Utilities for zero-copy parsing and serialization")
|
||||
(description "Utilities for zero-copy parsing and serialization")
|
||||
(license license:bsd-2)))
|
||||
|
||||
(define-public rust-zerocopy-0.3
|
||||
(package
|
||||
(inherit rust-zerocopy-0.6)
|
||||
(name "rust-zerocopy")
|
||||
(version "0.3.1")
|
||||
(source
|
||||
|
|
@ -68019,21 +68171,41 @@ for locating fonts.")
|
|||
(file-name (string-append name "-" version ".tar.gz"))
|
||||
(sha256
|
||||
(base32 "00nbb6yal8f74bkpn7msjcnhisimw8s5777a63206rfnn3br45zh"))))
|
||||
(build-system cargo-build-system)
|
||||
(arguments
|
||||
`(#:skip-build? #t
|
||||
#:cargo-inputs
|
||||
(("rust-byteorder" ,rust-byteorder-1)
|
||||
("rust-zerocopy-derive" ,rust-zerocopy-derive-0.2))))
|
||||
(home-page "https://fuchsia.googlesource.com/fuchsia/+/HEAD/src/lib/zerocopy")
|
||||
(synopsis "Utilities for zero-copy parsing and serialization")
|
||||
(description
|
||||
"This package provides utilities for zero-copy parsing and
|
||||
serialization.")
|
||||
(license license:bsd-3)))
|
||||
|
||||
(define-public rust-zerocopy-derive-0.3
|
||||
(package
|
||||
(name "rust-zerocopy-derive")
|
||||
(version "0.3.2")
|
||||
(source (origin
|
||||
(method url-fetch)
|
||||
(uri (crate-uri "zerocopy-derive" version))
|
||||
(file-name (string-append name "-" version ".tar.gz"))
|
||||
(sha256
|
||||
(base32
|
||||
"18qr7dqlj89v1xl1g58l2xd6jidv0sbccscgl131gpppba0yc1b5"))))
|
||||
(build-system cargo-build-system)
|
||||
(arguments
|
||||
`(#:skip-build? #t
|
||||
#:cargo-inputs
|
||||
(("rust-proc-macro2" ,rust-proc-macro2-1)
|
||||
("rust-syn" ,rust-syn-1)
|
||||
("rust-synstructure" ,rust-synstructure-0.12))))
|
||||
(home-page "https://github.com/google/zerocopy")
|
||||
(synopsis "Custom derive for traits from the zerocopy Rust crate")
|
||||
(description
|
||||
"This package provides custom derive for traits from the zerocopy Rust
|
||||
crate.")
|
||||
(license license:bsd-2)))
|
||||
|
||||
(define-public rust-zerocopy-derive-0.2
|
||||
(package
|
||||
(inherit rust-zerocopy-derive-0.3)
|
||||
(name "rust-zerocopy-derive")
|
||||
(version "0.2.1")
|
||||
(source
|
||||
|
|
@ -68043,18 +68215,12 @@ serialization.")
|
|||
(file-name (string-append name "-" version ".tar.gz"))
|
||||
(sha256
|
||||
(base32 "1594sf9wwgpbavl1hb1avyz6n7km9apm8afc03x9y8h3spk3k76w"))))
|
||||
(build-system cargo-build-system)
|
||||
(arguments
|
||||
`(#:skip-build? #t
|
||||
#:cargo-inputs
|
||||
(("rust-proc-macro2" ,rust-proc-macro2-1)
|
||||
("rust-syn" ,rust-syn-1)
|
||||
("rust-synstructure" ,rust-synstructure-0.12))))
|
||||
(home-page "https://fuchsia.googlesource.com/fuchsia/+/HEAD/src/lib/zerocopy/zerocopy-derive")
|
||||
(synopsis "Custom derive for traits from the zerocopy Rust crate")
|
||||
(description
|
||||
"This package provides custom derive for traits from the zerocopy Rust
|
||||
crate.")
|
||||
(license license:bsd-3)))
|
||||
|
||||
(define-public rust-zeroize-1
|
||||
|
|
|
|||
|
|
@ -2998,6 +2998,40 @@ updates to the zebra daemon.")
|
|||
(home-page "https://www.nongnu.org/quagga/")
|
||||
(license license:gpl2+)))
|
||||
|
||||
(define-public bgpq3
|
||||
(package
|
||||
(name "bgpq3")
|
||||
(version "0.1.36.1")
|
||||
(source
|
||||
(origin
|
||||
(method git-fetch)
|
||||
(uri (git-reference
|
||||
(url "https://github.com/snar/bgpq3")
|
||||
(commit (string-append "v" version))))
|
||||
(file-name (git-file-name name version))
|
||||
(sha256
|
||||
(base32 "0768hihx7idmn2dk8ii21m0dm052amlnfpqq53vsfaapb60n1smc"))))
|
||||
(build-system gnu-build-system)
|
||||
(arguments
|
||||
'(#:tests? #f)) ; no test suite
|
||||
(native-inputs (list python-markdown))
|
||||
(home-page "http://snar.spb.ru/prog/bgpq3/")
|
||||
(synopsis
|
||||
"Generate BGP filters from the @acronym{IRR, Internet Routing Registry}")
|
||||
(description
|
||||
"This program helps automate the creation and maintenance of @acronym{BGP,
|
||||
Border Gateway Protocol} routing filters used for peering trough Internet
|
||||
exchanges.
|
||||
|
||||
It generates prefix lists, (extended) access lists, policy-statement terms, and
|
||||
AS paths from data in the @acronym{IRR, Internet Routing Registry}, including
|
||||
the @acronym{RADB, Routing Assets Database} operated by the Merit Network at the
|
||||
University of Michigan.
|
||||
|
||||
The filters can be aggregated and exported in the most common formats.")
|
||||
(license (list license:bsd-3 ; strlcpy.c, sys_queue.h
|
||||
license:bsd-2)))) ; everything else, but missing headers
|
||||
|
||||
(define-public thc-ipv6
|
||||
(let ((revision "0")
|
||||
(commit "4bb72573e0950ce6f8ca2800a10748477020029e"))
|
||||
|
|
|
|||
|
|
@ -2745,14 +2745,22 @@ and binaries removed, and adds modular support for using system libraries.")
|
|||
"third_party/devtools-frontend/src/third_party/typescript"
|
||||
"third_party/emoji-segmenter"
|
||||
"third_party/fdlibm"
|
||||
"third_party/ffmpeg"
|
||||
"third_party/ffmpeg/libavcodec/avcodec.h"
|
||||
"third_party/ffmpeg/libavcodec/packet.h"
|
||||
"third_party/ffmpeg/libavformat/avformat.h"
|
||||
"third_party/ffmpeg/libavformat/avio.h"
|
||||
"third_party/ffmpeg/libavutil/avutil.h"
|
||||
"third_party/ffmpeg/libavutil/imgutils.h"
|
||||
"third_party/ffmpeg/libavutil/log.h"
|
||||
"third_party/ffmpeg/libavutil/mathematics.h"
|
||||
"third_party/ffmpeg/libavutil/opt.h"
|
||||
"third_party/freetype"
|
||||
"third_party/googletest"
|
||||
"third_party/harfbuzz-ng"
|
||||
"third_party/highway"
|
||||
"third_party/hunspell"
|
||||
"third_party/iccjpeg"
|
||||
"third_party/icu"
|
||||
"third_party/icu" ;TODO: make pdfium use system version
|
||||
"third_party/inspector_protocol"
|
||||
"third_party/jinja2"
|
||||
"third_party/jsoncpp"
|
||||
|
|
@ -2770,18 +2778,23 @@ and binaries removed, and adds modular support for using system libraries.")
|
|||
"third_party/libjingle_xmpp"
|
||||
"third_party/libjpeg_turbo"
|
||||
"third_party/libjxl"
|
||||
"third_party/libpng"
|
||||
"third_party/libpng" ;TODO: make pdfium use system version
|
||||
"third_party/libsrtp"
|
||||
"third_party/libsync"
|
||||
"third_party/libudev"
|
||||
"third_party/liburlpattern"
|
||||
"third_party/libvpx"
|
||||
"third_party/libwebm"
|
||||
"third_party/libwebp"
|
||||
"third_party/libwebp/src/webp/decode.h"
|
||||
"third_party/libwebp/src/webp/demux.h"
|
||||
"third_party/libwebp/src/webp/encode.h"
|
||||
"third_party/libwebp/src/webp/format_constants.h"
|
||||
"third_party/libwebp/src/webp/mux.h"
|
||||
"third_party/libwebp/src/webp/mux_types.h"
|
||||
"third_party/libwebp/src/webp/types.h"
|
||||
"third_party/libx11"
|
||||
"third_party/libxcb-keysyms"
|
||||
"third_party/libxml"
|
||||
"third_party/libxslt"
|
||||
"third_party/libxml/chromium"
|
||||
"third_party/libyuv"
|
||||
"third_party/lottie"
|
||||
"third_party/lss"
|
||||
|
|
@ -2794,7 +2807,11 @@ and binaries removed, and adds modular support for using system libraries.")
|
|||
"third_party/node"
|
||||
"third_party/one_euro_filter"
|
||||
"third_party/openh264"
|
||||
"third_party/opus"
|
||||
"third_party/opus/src/include/opus.h"
|
||||
"third_party/opus/src/include/opus_custom.h"
|
||||
"third_party/opus/src/include/opus_defines.h"
|
||||
"third_party/opus/src/include/opus_multistream.h"
|
||||
"third_party/opus/src/include/opus_types.h"
|
||||
"third_party/ots"
|
||||
"third_party/pdfium"
|
||||
"third_party/pdfium/third_party/agg23"
|
||||
|
|
@ -2850,7 +2867,7 @@ and binaries removed, and adds modular support for using system libraries.")
|
|||
"third_party/woff2"
|
||||
"third_party/wuffs"
|
||||
"third_party/x11proto"
|
||||
"third_party/zlib"
|
||||
"third_party/zlib" ;TODO: make pdfium use system version
|
||||
"url/third_party/mozilla"
|
||||
"v8/src/third_party/utf8-decoder"
|
||||
"v8/src/third_party/valgrind"
|
||||
|
|
@ -2914,15 +2931,29 @@ linux/libcurl_wrapper.h"
|
|||
"-DQT_FEATURE_webengine_printing_and_pdf=OFF"
|
||||
"-DQT_FEATURE_webengine_pepper_plugins=OFF" ;widevine
|
||||
"-DQT_FEATURE_system_ffmpeg=ON"
|
||||
|
||||
;; Do not artificially limit codec support; video decoding is
|
||||
;; done by ffmpeg.
|
||||
"-DQT_FEATURE_webengine_proprietary_codecs=ON"
|
||||
|
||||
;; Use system libraries where possible (see src/core/CMakeLists.txt).
|
||||
"-DQT_FEATURE_webengine_system_alsa=ON"
|
||||
"-DQT_FEATURE_webengine_system_ffmpeg=ON"
|
||||
"-DQT_FEATURE_webengine_system_freetype=ON"
|
||||
"-DQT_FEATURE_webengine_system_harfbuzz=ON"
|
||||
"-DQT_FEATURE_webengine_system_icu=ON"
|
||||
"-DQT_FEATURE_webengine_system_libxml=ON"
|
||||
"-DQT_FEATURE_webengine_system_lcms2=ON"
|
||||
"-DQT_FEATURE_webengine_system_libevent=ON"
|
||||
"-DQT_FEATURE_webengine_system_libjpeg=ON"
|
||||
"-DQT_FEATURE_webengine_system_libpci=ON"
|
||||
"-DQT_FEATURE_webengine_system_libpng=ON"
|
||||
"-DQT_FEATURE_webengine_system_libwebp=ON"
|
||||
"-DQT_FEATURE_webengine_system_libxml=ON"
|
||||
"-DQT_FEATURE_webengine_system_libxslt=ON"
|
||||
"-DQT_FEATURE_webengine_system_minizip=ON"
|
||||
"-DQT_FEATURE_webengine_system_opus=ON"
|
||||
"-DQT_FEATURE_webengine_system_pulseaudio=ON"
|
||||
"-DQT_FEATURE_webengine_system_re2=ON"
|
||||
"-DQT_FEATURE_webengine_system_zlib=ON")
|
||||
#:phases
|
||||
#~(modify-phases %standard-phases
|
||||
|
|
@ -2989,6 +3020,7 @@ linux/libcurl_wrapper.h"
|
|||
(inputs
|
||||
(modify-inputs (package-inputs qtwebengine-5)
|
||||
(replace "qtmultimedia" qtmultimedia)
|
||||
(replace "harfbuzz" harfbuzz-5)
|
||||
(append libxkbfile xkeyboard-config)))
|
||||
(propagated-inputs
|
||||
(modify-inputs (package-propagated-inputs qtwebengine-5)
|
||||
|
|
|
|||
|
|
@ -45,6 +45,7 @@
|
|||
#:use-module (guix build-system emacs)
|
||||
#:use-module (guix build-system gnu)
|
||||
#:use-module (guix build-system r)
|
||||
#:use-module (guix build-system pyproject)
|
||||
#:use-module (guix build-system python)
|
||||
#:use-module (guix build-system trivial)
|
||||
#:use-module (gnu packages)
|
||||
|
|
@ -2010,6 +2011,36 @@ and fast file reading.")
|
|||
"This package provides tools to export R data as LaTeX and HTML tables.")
|
||||
(license license:gpl2+)))
|
||||
|
||||
(define-public python-hdmedians
|
||||
(package
|
||||
(name "python-hdmedians")
|
||||
(version "0.14.2")
|
||||
(source (origin
|
||||
(method url-fetch)
|
||||
(uri (pypi-uri "hdmedians" version))
|
||||
(sha256
|
||||
(base32
|
||||
"1mn2k8srnmfy451l7zvb2l4hn9701bc5awjm6q3vmqbicyqyqyml"))))
|
||||
(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-cython python-numpy))
|
||||
(native-inputs (list python-nose))
|
||||
(home-page "http://github.com/daleroberts/hdmedians")
|
||||
(synopsis "High-dimensional medians")
|
||||
(description "Various definitions for a high-dimensional median exist and
|
||||
this Python package provides a number of fast implementations of these
|
||||
definitions. Medians are extremely useful due to their high breakdown
|
||||
point (up to 50% contamination) and have a number of nice applications in
|
||||
machine learning, computer vision, and high-dimensional statistics.")
|
||||
(license license:asl2.0)))
|
||||
|
||||
(define-public python-patsy
|
||||
(package
|
||||
(name "python-patsy")
|
||||
|
|
|
|||
Reference in New Issue