diff options
Diffstat (limited to 'gnu')
| -rw-r--r-- | gnu/packages/admin.scm | 4 | ||||
| -rw-r--r-- | gnu/packages/audio.scm | 2 | ||||
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 29 | ||||
| -rw-r--r-- | gnu/packages/fediverse.scm | 4 | ||||
| -rw-r--r-- | gnu/packages/guile-xyz.scm | 4 | ||||
| -rw-r--r-- | gnu/packages/machine-learning.scm | 43 | ||||
| -rw-r--r-- | gnu/packages/maths.scm | 6 | ||||
| -rw-r--r-- | gnu/packages/networking.scm | 27 | ||||
| -rw-r--r-- | gnu/packages/python-science.scm | 1 | ||||
| -rw-r--r-- | gnu/packages/python-xyz.scm | 37 | ||||
| -rw-r--r-- | gnu/packages/wm.scm | 4 | ||||
| -rw-r--r-- | gnu/services/cuirass.scm | 29 |
12 files changed, 143 insertions, 47 deletions
diff --git a/gnu/packages/admin.scm b/gnu/packages/admin.scm index bbb16b7a84..d549f41211 100644 --- a/gnu/packages/admin.scm +++ b/gnu/packages/admin.scm @@ -3034,7 +3034,7 @@ environment variable is set and output is to tty.") (define-public lr (package (name "lr") - (version "2.0") + (version "2.0.1") (source (origin (method git-fetch) @@ -3043,7 +3043,7 @@ environment variable is set and output is to tty.") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 - (base32 "05k971vf6080igfila8iav5d4j7sgh301123yng9lvsmr8frf8mf")))) + (base32 "0mqhcgi4v3zzic0ikf7ja4km1mik29gdp15q8qwjw5bmh22d74ff")))) (build-system gnu-build-system) (arguments (list #:tests? #f ; There are no tests. diff --git a/gnu/packages/audio.scm b/gnu/packages/audio.scm index 12b6eb91f2..b03d2d4fe5 100644 --- a/gnu/packages/audio.scm +++ b/gnu/packages/audio.scm @@ -6814,7 +6814,7 @@ default and preferred audio driver but also supports native drivers like ALSA.") (list cmake-minimal pkg-config)) (inputs (list bash-minimal - asio + asio-1.28 bitsery clap-1.1 dbus diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index e94fca2935..cab61ef45a 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -24552,48 +24552,45 @@ populations.") (license license:bsd-3))) (define-public scregseg + ;; 0.1.3 was released in 2023, there are a lot of comparability fixes on + ;; master branch, use the latest commit for now. + (let ((commit "78ebff8c3507752c3bfbc4db3f72f7e8a733e92f") + (revision "0")) (package (name "scregseg") - (version "0.1.3") + (version (git-version "0.1.3" revision commit)) (source (origin (method git-fetch) (uri (git-reference (url "https://github.com/BIMSBbioinfo/scregseg") - (commit (string-append "v" version)))) + (commit commit))) (file-name (git-file-name name version)) (sha256 (base32 - "07g2barywa1wi8mggbxkbxqjw1fzd0a0l9cjdbkx4s40imb1dbxb")) + "19iasx6zh305cn8p390ack78f4iklyk61xmnf99c2b8ibml7jmzj")) (snippet '(delete-file "src/scregseg/_utils.c")))) (build-system pyproject-build-system) (arguments (list + #:test-flags + #~(list "--pyargs" "scregseg") #:phases '(modify-phases %standard-phases ;; Numba needs a writable dir to cache functions. (add-before 'check 'set-numba-cache-dir (lambda _ (setenv "NUMBA_CACHE_DIR" "/tmp"))) - ;; Cython extensions have to be built before running the tests. - (add-before 'check 'build-extensions - (lambda _ - (invoke "python" "setup.py" "build_ext" "--inplace"))) ;; NumPy 1.20 deprecated the type wrappers for int and float. (add-after 'unpack 'compatibility (lambda _ (substitute* "src/scregseg/_utils.pyx" - (("np.float") "float")))) - (add-after 'unpack 'do-not-fail-to-find-sklearn - (lambda _ - ;; XXX: I have no idea why it cannot seem to find sklearn. - (substitute* "setup.py" - (("'sklearn',") ""))))))) + (("np.float") "float"))))))) (native-inputs (list python-cython - python-wheel)) + python-setuptools)) (propagated-inputs - (list python-scikit-learn + (list python-scikit-learn-1.6 python-scipy python-numpy python-hmmlearn @@ -24615,7 +24612,7 @@ Dirichlet-Multinomial emission probabilities to segment the genome either according to distinct relative cross-cell accessibility profiles or (after collapsing the single-cell tracks to pseudo-bulk tracks) to capture distinct cross-cluster accessibility profiles.") - (license license:gpl3+))) + (license license:gpl3+)))) (define-public megadepth (package diff --git a/gnu/packages/fediverse.scm b/gnu/packages/fediverse.scm index e2bbb622ed..6cad92f38e 100644 --- a/gnu/packages/fediverse.scm +++ b/gnu/packages/fediverse.scm @@ -274,7 +274,7 @@ seamlessly with your desktop environment.") (define-public snac2 (package (name "snac") - (version "2.81") + (version "2.83") (source (origin (method git-fetch) @@ -283,7 +283,7 @@ seamlessly with your desktop environment.") (commit version))) (file-name (git-file-name name version)) (sha256 - (base32 "12wnd7r9k1fmf9yikczhiplbjjvpi66c7n22hs6xla3qqm7vwcm3")))) + (base32 "0xh108p148mqlj1da05yrng0d82rw34n1i97cjzz7p606ll4j6p4")))) (build-system gnu-build-system) (inputs (list curl openssl)) (arguments diff --git a/gnu/packages/guile-xyz.scm b/gnu/packages/guile-xyz.scm index 92b70b2318..9f393ef82d 100644 --- a/gnu/packages/guile-xyz.scm +++ b/gnu/packages/guile-xyz.scm @@ -7769,14 +7769,14 @@ application to open a given file or URL based on given configurations.") (define-public guile-goblins (package (name "guile-goblins") - (version "0.16.1") + (version "0.17.0") (source (origin (method url-fetch) (uri (string-append "https://files.spritely.institute/releases" "/guile-goblins/guile-goblins-" version ".tar.gz")) (sha256 - (base32 "10ffdr98nck05pnsq5qagp7wpyky5wdk83n3qrnh9aphm9qq5frh")))) + (base32 "16jkmfspsnza2fdk5jr05a5pfh7x856gpg031i21s1yvy43l8mi0")))) (build-system gnu-build-system) (arguments (list diff --git a/gnu/packages/machine-learning.scm b/gnu/packages/machine-learning.scm index 01b7c49de5..529841aad4 100644 --- a/gnu/packages/machine-learning.scm +++ b/gnu/packages/machine-learning.scm @@ -2133,6 +2133,49 @@ computing environments.") data analysis.") (license license:bsd-3))) +;; 1.7 intorduced breaking changes in API. +(define-public python-scikit-learn-1.6 + (package + (inherit python-scikit-learn) + (name "python-scikit-learn") + (version "1.6.1") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/scikit-learn/scikit-learn") + (commit version))) + (file-name (git-file-name name version)) + (sha256 + (base32 "08z1b58n31grfvl42wi6rdwrfhrdhnzkkxhg19iag3zkvkcvxqjl")))) + (arguments + (substitute-keyword-arguments (package-arguments python-scikit-learn) + ((#:test-flags flags) + #~(list "--numprocesses" (number->string (min 8 (parallel-job-count))) + "-m" "not network" + "-k" (string-join + (list "not test_ard_accuracy_on_easy_problem" + "test_check_inplace_ensure_writeable" + "test_check_is_fitted_with_attributes" + "test_covariance" + "test_estimators" + "test_ledoit_wolf" + "test_mcd" + "test_mcd_issue1127" + "test_mcd_support_covariance_is_zero" + "test_oas" + "test_shrunk_covariance" + "test_toy_ard_object") + " and not "))) + ((#:phases phases) + #~(modify-phases #$phases + (add-after 'unpack 'remove-broken-tests + (lambda _ + ;; ImportError: cannot import name 'ColMajor' from + ;; 'sklearn.utils._cython_blas' + ;; (<...>/_cython_blas.cpython-311-x86_64-linux-gnu.so) + (delete-file-recursively "sklearn/utils/tests/test_cython_blas.py"))))))))) + (define-public python-scikit-learn-extra ;; This commit fixes an incompatibility with newer versions of scikit-learn (let ((commit "0f95d8dda4c69f9de4fb002366041adcb1302f3b") diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm index c0987f699e..ae9e2a2553 100644 --- a/gnu/packages/maths.scm +++ b/gnu/packages/maths.scm @@ -2657,7 +2657,7 @@ scientific data storage.") (define-public n2p2 (package (name "n2p2") - (version "2.1.4") + (version "2.3.0") (source (origin (method git-fetch) (uri (git-reference @@ -2666,7 +2666,7 @@ scientific data storage.") (file-name (git-file-name name version)) (sha256 (base32 - "1lw195ihpxwh08387i4gamk1glhalpq888q6nj8l5vswbgnrv1pq")))) + "01090j477gh9zk7wj416fvv1hxdnnxwhzy67bn96a04zhnayzkkj")))) (build-system gnu-build-system) (arguments `(#:make-flags '("MODE=shared" "-C" "src") @@ -2674,6 +2674,8 @@ scientific data storage.") (modify-phases %standard-phases (add-after 'unpack 'post-unpack (lambda* (#:key inputs #:allow-other-keys) + (substitute* "src/makefile" + (("shell") "bash")) (substitute* "src/makefile.gnu" (("PROJECT_EIGEN=/usr/include/eigen3") (string-append "PROJECT_EIGEN=" diff --git a/gnu/packages/networking.scm b/gnu/packages/networking.scm index b31350b145..fb585008c2 100644 --- a/gnu/packages/networking.scm +++ b/gnu/packages/networking.scm @@ -977,7 +977,7 @@ publish/subscribe, RPC-style request/reply, or service discovery.") (define-public nanomsg (package (name "nanomsg") - (version "1.2.1") + (version "1.2.2") (source (origin (method git-fetch) @@ -987,7 +987,7 @@ publish/subscribe, RPC-style request/reply, or service discovery.") (commit version))) (file-name (git-file-name name version)) (sha256 - (base32 "0dnnz054czajkdq60z5xw28iiv2qwqhigv9wj54388rk4ak0y3ya")))) + (base32 "1vd7kgmljbifa61y6by4ywk4pfxv9kwwcls87iyr32grfyd0v0yl")))) (build-system cmake-build-system) (arguments `(#:configure-flags @@ -1967,7 +1967,7 @@ of the same name.") libssh libxml2 lz4 - lua-5.2 + lua-5.4 mit-krb5 `(,nghttp2 "lib") minizip @@ -2884,7 +2884,7 @@ that block port 22.") (define-public iperf (package (name "iperf") - (version "3.19") + (version "3.19.1") (source (origin (method git-fetch) @@ -2893,7 +2893,7 @@ that block port 22.") (commit version))) (file-name (git-file-name name version)) (sha256 - (base32 "0hddhjzcr6j5sbsb2dllhn4f7pazvh0h3zykalky5m1gnh1virgw")))) + (base32 "1kj2p3dprxv1r77whd5g1wak2k71c7khhrkkx60lcnkf70qy5q67")))) (build-system gnu-build-system) (arguments `(#:configure-flags @@ -3414,7 +3414,7 @@ updates to the zebra daemon.") (define-public bgpq3 (package (name "bgpq3") - (version "0.1.36.1") + (version "0.1.38") (source (origin (method git-fetch) @@ -3423,7 +3423,7 @@ updates to the zebra daemon.") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 - (base32 "0768hihx7idmn2dk8ii21m0dm052amlnfpqq53vsfaapb60n1smc")))) + (base32 "11zm2z2cxazzr1x6mwmjc167cclkgaah7b1k8pfpfm555bpli9mf")))) (build-system gnu-build-system) (arguments '(#:tests? #f)) ; no test suite @@ -3770,6 +3770,17 @@ low-level I/O programming that provides developers with a consistent asynchronous model using a modern C++ approach.") (license license:boost1.0))) +(define-public asio-1.28 + (package/inherit asio + (version "1.28.2") + (source + (origin + (method url-fetch) + (uri (string-append "mirror://sourceforge/asio/asio/" + version " (Stable)/asio-" version ".tar.bz2")) + (sha256 + (base32 "1479z0pa9781dx1crsyaa9fvlcmyhb22m355f8cil77jjh13xf7i")))))) + (define-public shadowsocks (package (name "shadowsocks") @@ -4194,7 +4205,7 @@ and targeted primarily for asynchronous processing of HTTP-requests.") (string-append "extra_link_args=[" args ", '-Wl,-rpath=" #$output "/lib']"))))) ;; This is due to an upstream issue: - ;; https://git.jami.net/savoirfairelinux/opendht/-/issues/69 + ;; https://git.jami.net/savoirfairelinux/opendht/-/issues/69 (add-after 'unpack 'fix-llhttp-lib-substitution (lambda _ (substitute* "configure.ac" diff --git a/gnu/packages/python-science.scm b/gnu/packages/python-science.scm index 65f385d494..22ee57c4b1 100644 --- a/gnu/packages/python-science.scm +++ b/gnu/packages/python-science.scm @@ -318,6 +318,7 @@ possibility to differentiate functions that contain matrix functions as python-boltons python-dask python-distributed + python-filelock python-hatch-vcs python-hatchling python-joblib diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 1841903e60..f16aff83aa 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -28985,12 +28985,10 @@ tool).") (list c-blosc lz4 zlib `(,zstd "lib"))) (propagated-inputs - (list python-coverage - python-google-crc32c + (list python-google-crc32c python-importlib-metadata python-msgpack - python-numpy - python-numpydoc)) + python-numpy)) (native-inputs (list python-cython python-py-cpuinfo @@ -37154,6 +37152,31 @@ other.") nested data structures in Python like lists and dictionaries.") (license license:expat))) +(define-public python-durationpy + (package + (name "python-durationpy") + (version "0.10") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/icholy/durationpy") + (commit version))) + (file-name (git-file-name name version)) + (sha256 + (base32 "1617wg77j68z7v4rbjrhv6n7bchznhgjn21qrmb034sf4hwg77dl")))) + (build-system pyproject-build-system) + (arguments + (list #:test-backend #~'custom + #:test-flags #~(list "test.py"))) + (native-inputs (list python-setuptools)) + (home-page "https://github.com/icholy/durationpy") + (synopsis "Python <-> Golang time duration formats converter") + (description + "This package implements a functionality to convert between +Python's @code{datetime.timedelta} and Golang's @code{time.Duration} formats.") + (license license:expat))) + (define-public python-murmurhash3 (let ((commit "01f1128a2c5ea08e6dc33515e140bedd68393a2d") (revision "0")) @@ -40444,12 +40467,8 @@ and XML respectively. The processing is done through @command{jq}, (propagated-inputs (list python-asciitree python-fasteners - python-ipywidgets - python-notebook python-numcodecs - python-numpy - python-numpydoc - python-pydata-sphinx-theme)) + python-numpy)) (native-inputs (list python-pytest python-pytest-xdist diff --git a/gnu/packages/wm.scm b/gnu/packages/wm.scm index bc3e55ad70..07cb4e8dfd 100644 --- a/gnu/packages/wm.scm +++ b/gnu/packages/wm.scm @@ -3954,7 +3954,7 @@ read and write, and compatible with JSON.") (define-public labwc (package (name "labwc") - (version "0.9.1") + (version "0.9.2") (source (origin (method git-fetch) (uri (git-reference @@ -3963,7 +3963,7 @@ read and write, and compatible with JSON.") (file-name (git-file-name name version)) (sha256 (base32 - "0p475vjn9gg314spf89di6i1l2lr9xx59mz4hq4shvbh64hr48pi")))) + "1qgjfc9glynpd39qdsdfznmn7ggki1kgxnhi1vlc54ianmpdxa38")))) (build-system meson-build-system) (native-inputs (list pkg-config gettext-minimal scdoc)) diff --git a/gnu/services/cuirass.scm b/gnu/services/cuirass.scm index 27ff87ca56..e813b7cfdb 100644 --- a/gnu/services/cuirass.scm +++ b/gnu/services/cuirass.scm @@ -134,6 +134,28 @@ (web-extra-options cuirass-configuration-web-extra-options (default '()))) +(define (cuirass-configuration->specification-file config) + "Return a specification file built from CONFIG and validate it." + (define cuirass + (cuirass-configuration-cuirass config)) + + (define build + #~(begin + (use-modules (ice-9 pretty-print)) + + (call-with-output-file #$output + (lambda (port) + (pretty-print '#$(cuirass-configuration-specifications config) + port))) + + ;; Validate the spec file upfront. + (unless (zero? + (system* #$(file-append cuirass "/bin/cuirass") "register" + "--check" "-S" #$output)) + (exit 1)))) + + (computed-file "cuirass-specs.scm" build)) + (define (cuirass-shepherd-service config) "Return a <shepherd-service> for the Cuirass service with CONFIG." (define (endpoint name) @@ -162,9 +184,7 @@ (database (cuirass-configuration-database config)) (port (cuirass-configuration-port config)) (host (cuirass-configuration-host config)) - (config-file (scheme-file - "cuirass-specs.scm" - (cuirass-configuration-specifications config))) + (config-file (cuirass-configuration->specification-file config)) (one-shot? (cuirass-configuration-one-shot? config)) (fallback? (cuirass-configuration-fallback? config)) (extra-options (cuirass-configuration-extra-options config)) @@ -223,6 +243,9 @@ (list #$(endpoint "bridge") #$(endpoint "remote-builds")) + ;; Start working right away. + #:lazy-start? #f + #:environment-variables (list "LC_ALL=C.UTF-8" ;for proper file name decoding "GIT_SSL_CAINFO=/etc/ssl/certs/ca-certificates.crt" |