diff options
Diffstat (limited to 'gnu/packages/statistics.scm')
| -rw-r--r-- | gnu/packages/statistics.scm | 317 |
1 files changed, 250 insertions, 67 deletions
diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index e025653338..f28e60362c 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -81,6 +81,7 @@ #:use-module (gnu packages perl) #:use-module (gnu packages pkg-config) #:use-module (gnu packages python) + #:use-module (gnu packages python-build) #:use-module (gnu packages python-science) #:use-module (gnu packages python-xyz) #:use-module (gnu packages readline) @@ -622,14 +623,14 @@ for reading and writing some dBase files.") (define-public r-kernsmooth (package (name "r-kernsmooth") - (version "2.23-21") + (version "2.23-22") (source (origin (method url-fetch) (uri (cran-uri "KernSmooth" version)) (sha256 (base32 - "12qsy90cmcg8pdvcpasdskh82x9d83xdznibi9b7z1hkw8ccnqrx")))) + "1sblhl7b9d3m6034xd3254ddkj9ssqxawknzksfbgjh68s849q3n")))) (properties `((upstream-name . "KernSmooth"))) (build-system r-build-system) (native-inputs @@ -666,14 +667,14 @@ also flexible enough to handle most nonstandard requirements.") (define-public r-matrix (package (name "r-matrix") - (version "1.5-4.1") + (version "1.6-0") (source (origin (method url-fetch) (uri (cran-uri "Matrix" version)) (sha256 (base32 - "0bh87f6yll06q0068wavwmagvsc0p95g7071zsjr2yzb2dr5i2b5")))) + "17dpfqyr68dldlj4v26rjrwv6pv87czj9szqqp64fwczyy0fdszb")))) (properties `((upstream-name . "Matrix"))) (build-system r-build-system) (propagated-inputs @@ -955,19 +956,20 @@ effects of different types of color-blindness.") (define-public r-digest (package (name "r-digest") - (version "0.6.31") + (version "0.6.33") (source (origin (method url-fetch) (uri (cran-uri "digest" version)) (sha256 - (base32 "1f9isi4i2502f88c2sh4l461hgyary2aa02zd47pb9mc1r4lya2s")))) + (base32 "06bq696wpmn8ivbrpxw0qlcf835kc515m8jfv9zbwf8ndf42qw5y")))) (build-system r-build-system) ;; Vignettes require r-knitr, which requires r-digest, so we have to ;; disable them and the tests. (arguments `(#:tests? #f #:configure-flags (list "--no-build-vignettes"))) + (native-inputs (list r-simplermarkdown)) (home-page "https://dirk.eddelbuettel.com/code/digest.html") (synopsis "Create cryptographic hash digests of R objects") (description @@ -1717,13 +1719,13 @@ R packages that praise their users.") (define-public r-testthat (package (name "r-testthat") - (version "3.1.8") + (version "3.1.10") (source (origin (method url-fetch) (uri (cran-uri "testthat" version)) (sha256 (base32 - "09y8gdzssb41m8j2ph12g6nlwxm02075aiyc5bb6lsqgvnpzi4rl")))) + "1xh80rxv0whz618kpwzlzg0jg2vhm4073nyx03hd4xpg0ifhhd9i")))) (build-system r-build-system) (propagated-inputs (list r-brio @@ -1862,14 +1864,14 @@ database.") (define-public r-dbplyr (package (name "r-dbplyr") - (version "2.3.2") + (version "2.3.3") (source (origin (method url-fetch) (uri (cran-uri "dbplyr" version)) (sha256 (base32 - "1b3zf2ai4kp96wd6i4jg9b3n37bwbw7lfvxvs1i1kcn6brch1p0d")))) + "1d3m7bhd8n5l0x1phfwzgrw2kwfyahb9yd61bbcnryd6m8c8kr3w")))) (build-system r-build-system) (propagated-inputs (list r-blob @@ -1945,14 +1947,14 @@ side.") (define-public r-locfit (package (name "r-locfit") - (version "1.5-9.7") + (version "1.5-9.8") (source (origin (method url-fetch) (uri (cran-uri "locfit" version)) (sha256 (base32 - "1zvsa7hvnp0pvjyy0nnrg8bdv8gv4l23jb66wkc0kipvi78grra8")))) + "1qqxw69p42l4szr2fl73bdydpcbxn68iyxyyjy7qy3p56bxrn2hd")))) (build-system r-build-system) (propagated-inputs (list r-lattice)) @@ -2026,6 +2028,74 @@ and fast file reading.") "This package provides tools to export R data as LaTeX and HTML tables.") (license license:gpl2+))) +(define-public python-vega-datasets + (package + (name "python-vega-datasets") + (version "0.9.0") + (source + (origin + (method url-fetch) + (uri (pypi-uri "vega_datasets" version)) + (sha256 + (base32 "1h1zv607mars2j73v8fdwihjh479blqxyw29nhmc73lf40s9iglx")) + (modules '((guix build utils))) + (patches + (search-patches "python-vega-datasets-remove-la-riots-code.patch")))) + (build-system pyproject-build-system) + (arguments + (list #:phases + #~(modify-phases %standard-phases + (add-after 'unpack 'remove-la-riots-dataset + ;; Remove dataset with unclear license. + (lambda _ + (delete-file "vega_datasets/_data/la-riots.csv")))))) + (native-inputs (list python-pytest)) + (propagated-inputs (list python-pandas)) + (home-page "https://github.com/altair-viz/vega_datasets") + (synopsis "Example datasets used by Vega-related projects") + (description "This package provides a collection of datasets used in Vega +and Vega-Lite examples.") + (license license:expat))) + +(define-public python-altair + (package + (name "python-altair") + (version "5.0.1") + (source (origin + (method git-fetch) ; no tests in PyPI + (uri (git-reference + (url "https://github.com/altair-viz/altair") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1r74v5n51br9pjhxdzrr62cdgnwkapci93aifnl8dqmfpizfpd7d")))) + (build-system pyproject-build-system) + (arguments + ;; First two open an external connection. + ;; Last introduces a circular dependency on altair-viewer. + (list #:test-flags #~(list "-k" (string-append + "not test_from_and_to_json_roundtrip" + " and not test_render_examples_to_chart" + " and not test_save_html")))) + (propagated-inputs (list python-jinja2 + python-jsonschema + python-numpy + python-pandas + python-toolz + python-typing-extensions)) + (native-inputs (list python-black + python-hatchling + python-ipython + python-m2r + python-pytest + python-vega-datasets)) + (home-page "https://altair-viz.github.io/") + (synopsis "Declarative statistical visualization library for Python") + (description + "Vega-Altair is a declarative statistical visualization library for Python.") + (license license:expat))) + (define-public python-hdmedians (package (name "python-hdmedians") @@ -2056,6 +2126,111 @@ 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-arviz + (package + (name "python-arviz") + (version "0.15.1") + (source (origin + (method git-fetch) ; PyPI misses some test files + (uri (git-reference + (url "https://github.com/arviz-devs/arviz") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "0nqr4v927r9kc50z7rwlk2m8nw3dnnmmwmwcfijzd93gbg53wc4f")))) + (build-system pyproject-build-system) + (arguments + ;; FIXME: matplotlib tests fail because of the "--save" test flag. + (list #:test-flags #~'("--ignore" + "arviz/tests/base_tests/test_plots_matplotlib.py") + #:phases + #~(modify-phases %standard-phases + (add-after 'unpack 'remove-radon + (lambda _ + (delete-file + ;; This dataset is loaded remotely, it's not supposed to + ;; be copied locally. + "arviz/data/example_data/code/radon/radon.json"))) + (add-before 'check 'write-permission + (lambda _ + ;; 3 tests require write permission. + (setenv "HOME" "/tmp")))))) + (native-inputs (list python-cloudpickle python-pytest)) + (propagated-inputs (list python-h5netcdf + python-matplotlib + python-numpy + python-packaging + python-pandas + python-scipy + python-typing-extensions + python-xarray + python-xarray-einstats)) + (home-page "https://github.com/arviz-devs/arviz") + (synopsis "Exploratory analysis of Bayesian models") + (description + "ArviZ is a Python package for exploratory analysis of Bayesian models. +It includes functions for posterior analysis, data storage, model checking, +comparison and diagnostics.") + (license license:asl2.0))) + +(define-public python-pymc + (package + (name "python-pymc") + (version "5.5.0") + (source (origin + (method git-fetch) ; no tests in PyPI + (uri (git-reference + (url "https://github.com/pymc-devs/pymc") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "077xigv3lfcn9fqc14rsnam4v95fmqk2wpzfrgj08vg8m7f69wdj")))) + (build-system pyproject-build-system) + (arguments + (list #:tests? #f ; tests are too computationally intensive + #:phases #~(modify-phases %standard-phases + (add-after 'unpack 'versioneer + (lambda _ + (with-output-to-file "setup.cfg" + (lambda () + (display "\ +[versioneer] +VCS = git +style = pep440 +versionfile_source = pymc/_version.py +versionfile_build = pymc/_version.py +tag_prefix = +parentdir_prefix = pymc- +"))) + (invoke "versioneer" "install") + (substitute* "setup.py" + (("versioneer.get_version\\(\\)") + (string-append "\"" #$version "\""))))) + ;; To create the compiledir for tests. + (add-before 'check 'write-permissions + (lambda* (#:key tests? #:allow-other-keys) + (when tests? + (setenv "HOME" "/tmp"))))))) + (native-inputs (list python-pytest-cov python-versioneer)) + (propagated-inputs (list python-arviz + python-cachetools + python-cloudpickle + python-fastprogress + python-numpy + python-pandas + python-pytensor + python-scipy + python-typing-extensions)) + (home-page "https://github.com/pymc-devs/pymc") + (synopsis "Library for probabilistic programming in Python") + (description + "PyMC (formerly PyMC3) is a Python package for Bayesian statistical +modeling focusing on advanced Markov chain Monte Carlo (MCMC) and variational +inference (VI) algorithms.") + (license license:asl2.0))) + (define-public python-patsy (package (name "python-patsy") @@ -2090,41 +2265,49 @@ building design matrices.") (define-public python-statsmodels (package (name "python-statsmodels") - (version "0.13.1") + (version "0.14.0") (source (origin (method url-fetch) (uri (pypi-uri "statsmodels" version)) (sha256 - (base32 "0sbsyxgpzhys5padhkhrj71z4i1q41sm938pz0x8ff6jjvcchvh0")) + (base32 "1927ysv7m46m1x3wz05i0s3r5x0nasmidf2yy54djrp9i7bcfxb8")) (modules '((guix build utils))) (snippet - '(begin - (for-each delete-file (find-files "." "\\.c$")))))) - (build-system python-build-system) + '(for-each delete-file (find-files "." "\\.c$"))))) + (build-system pyproject-build-system) (arguments - `(;; The test suite is very large and rather brittle. Tests often fail - ;; because of minor changes in dependencies that upstream hasn't fixed - ;; in a new release. - #:tests? #f - #:phases - (modify-phases %standard-phases - (add-after 'unpack 'set-matplotlib-backend-to-agg - (lambda _ - ;; Set the matplotlib backend to Agg to avoid problems using the - ;; GTK backend without a display. - (substitute* (append (find-files "statsmodels/graphics/tests" "\\.py") - '("statsmodels/tsa/vector_ar/tests/test_var.py" - "statsmodels/duration/tests/test_survfunc.py")) - (("import matplotlib\\.pyplot as plt" line) - (string-append "import matplotlib;matplotlib.use('Agg');" - line))) - #t))))) + (list + ;; The test suite is very large and rather brittle. Tests often fail + ;; because of minor changes in dependencies that upstream hasn't fixed + ;; in a new release. + #:tests? #f + #:phases + #~(modify-phases %standard-phases + (add-after 'unpack 'set-matplotlib-backend-to-agg + (lambda _ + ;; Set the matplotlib backend to Agg to avoid problems using the + ;; GTK backend without a display. + (substitute* (append (find-files "statsmodels/graphics/tests" "\\.py") + '("statsmodels/tsa/vector_ar/tests/test_var.py" + "statsmodels/duration/tests/test_survfunc.py")) + (("import matplotlib\\.pyplot as plt" line) + (string-append "import matplotlib;matplotlib.use('Agg');" + line)))))))) (propagated-inputs - (list python-numpy python-scipy python-pandas python-patsy - python-matplotlib)) + (list python-numpy python-packaging python-pandas python-patsy + python-scipy)) (native-inputs - (list python-cython python-nose python-sphinx)) + (list python-colorama + python-cython + python-flake8 + python-isort + python-joblib + python-matplotlib + python-pytest + python-pytest-randomly + python-pytest-xdist + python-setuptools-scm)) (home-page "https://statsmodels.sourceforge.net/") (synopsis "Statistical modeling and econometrics in Python") (description @@ -2178,14 +2361,14 @@ and environmental data in the framework of Euclidean exploratory methods.") (define-public r-xml2 (package (name "r-xml2") - (version "1.3.4") + (version "1.3.5") (source (origin (method url-fetch) (uri (cran-uri "xml2" version)) (sha256 (base32 - "0c1h7fvkrcqcgnky6hhp9ysaraxhqdqjvsdlq0450fk4ishv22rl")))) + "10p214gzzcy2zzcq2xkh1vz2wrjsys5gplvk9c1crq3nmfki0six")))) (build-system r-build-system) (inputs (list libxml2 zlib)) @@ -2576,13 +2759,13 @@ pure C implementation of the Git core methods.") (define-public r-rstudioapi (package (name "r-rstudioapi") - (version "0.14") + (version "0.15.0") (source (origin (method url-fetch) (uri (cran-uri "rstudioapi" version)) (sha256 (base32 - "1i5g9l2739mlaglzg98iifycx98jlzxj5933qfb8lwmdn63hk7a6")))) + "1kvc870gx02cpb800zjvdrhfhyfpzgkydgw2g7kxdlrpr8fwhnwk")))) (build-system r-build-system) (native-inputs (list r-knitr)) @@ -2774,13 +2957,13 @@ well as additional utilities such as panel and axis annotation functions.") (define-public r-rcpparmadillo (package (name "r-rcpparmadillo") - (version "0.12.4.0.0") + (version "0.12.4.1.0") (source (origin (method url-fetch) (uri (cran-uri "RcppArmadillo" version)) (sha256 (base32 - "1jw2fhbva0qrgd4cwddjgwl8f8fzkxyp6vysl1qabh5bcp259nzn")))) + "1mf5dpsbjhfwalf4k3yhzgh0j1f40v1g7a3p6crm6xfp0k85jhq3")))) (properties `((upstream-name . "RcppArmadillo"))) (build-system r-build-system) (propagated-inputs @@ -2866,13 +3049,13 @@ certain criterion, e.g., it contains a certain regular file.") (define-public r-rmarkdown (package (name "r-rmarkdown") - (version "2.22") + (version "2.23") (source (origin (method url-fetch) (uri (cran-uri "rmarkdown" version)) (sha256 - (base32 "1f47ccph09ilqlr0bnyrxkadja4ddp4klvb933aws3rya0cmaqy6")))) + (base32 "09f8gfa4cfjwqb44xdr832blbgknn4ciyisvcrpyz5x51iphi3b6")))) (properties `((upstream-name . "rmarkdown") (updater-extra-propagated-inputs . ("pandoc")))) @@ -4174,13 +4357,13 @@ vignettes.") (define-public r-mvtnorm (package (name "r-mvtnorm") - (version "1.2-0") + (version "1.2-2") (source (origin (method url-fetch) (uri (cran-uri "mvtnorm" version)) (sha256 (base32 - "1q1bmsvd10iz003xlsd40dj5bhmy2069p88ydf9f4gj56mysnlpm")))) + "047y4sv1ydvszmzrssywhqfhx2mcrlbkypczgbh380wk7yrncmbg")))) (build-system r-build-system) (native-inputs (list gfortran)) @@ -4384,13 +4567,13 @@ features present in other programming languages.") (define-public r-plotly (package (name "r-plotly") - (version "4.10.1") + (version "4.10.2") (source (origin (method url-fetch) (uri (cran-uri "plotly" version)) (sha256 (base32 - "0yin1kid3a69fcwrrajwzqbhx4xc81x8p8m0yfh1fkm2rfhj22dc")) + "0y2jiyfx895f15wcpizybssic4draw1vgvqz2b7f82z73319m01b")) (modules '((guix build utils))) (snippet '(with-directory-excursion "inst/htmlwidgets/lib/" @@ -4434,8 +4617,8 @@ features present in other programming languages.") (propagated-inputs (list r-base64enc r-crosstalk - r-digest r-data-table + r-digest r-dplyr r-ggplot2 r-htmltools @@ -5400,14 +5583,14 @@ data for species delimitation, nearest neighbor based noise detection.") (define-public r-deoptimr (package (name "r-deoptimr") - (version "1.0-13") + (version "1.0-14") (source (origin (method url-fetch) (uri (cran-uri "DEoptimR" version)) (sha256 (base32 - "1wpqg659vpcd6cgy4sa9qygf0s0w44n46yma8990awkgnbxjmfxa")))) + "0d2ij0ncwjp9kh5bv7nvha8p1g73y620pw62c1q5chvjpjvxshfp")))) (properties `((upstream-name . "DEoptimR"))) (build-system r-build-system) (home-page "https://cran.r-project.org/web/packages/DEoptimR") @@ -5423,14 +5606,14 @@ can be efficiently implemented directly in the R language.") (define-public r-robustbase (package (name "r-robustbase") - (version "0.95-1") + (version "0.99-0") (source (origin (method url-fetch) (uri (cran-uri "robustbase" version)) (sha256 (base32 - "1sm37gqs35cvkacigsla8kzvpzjzsrgkabf58ymk9pzcndnx4b46")))) + "0xshwfv6vq47857xfhwnlxcl1511ghn6pyjylrg39i19xhp44za3")))) (build-system r-build-system) (native-inputs (list gfortran)) @@ -5468,14 +5651,14 @@ analysis} (PCA) by projection pursuit.") (define-public r-rrcov (package (name "r-rrcov") - (version "1.7-3") + (version "1.7-4") (source (origin (method url-fetch) (uri (cran-uri "rrcov" version)) (sha256 (base32 - "0shcsfxgb37ggys9d4cyfjs1p2szj52lfkva746fqsx64cvkcfw5")))) + "0jkm2w38kbzicfx2542rb90r7kcrbm7hiaasajw1zq8gb7ffshb3")))) (build-system r-build-system) (propagated-inputs (list r-lattice r-mvtnorm r-pcapp r-robustbase)) @@ -5519,14 +5702,14 @@ generally.") (define-public r-robust (package (name "r-robust") - (version "0.7-1") + (version "0.7-2") (source (origin (method url-fetch) (uri (cran-uri "robust" version)) (sha256 (base32 - "1pv5xvns3p8dpaadf6v0fqz099ml768ahgp271wpiclrcc6cgapg")))) + "1kryflq2p0c78pggnj5yghjivy4npxfkzcqhxh9jvrngkpxhsrb6")))) (build-system r-build-system) (propagated-inputs (list r-fit-models r-lattice r-mass r-robustbase r-rrcov)) @@ -5620,14 +5803,14 @@ VGLMs can be loosely thought of as multivariate generalised linear models.") (define-public r-pbapply (package (name "r-pbapply") - (version "1.7-0") + (version "1.7-2") (source (origin (method url-fetch) (uri (cran-uri "pbapply" version)) (sha256 (base32 - "1h06nz312si2hsy2klrmy6w46q341bl3q5v61g133450w0qykf34")))) + "04xf1p7c0066cwnxfmzaikbc322bxnw022ziv8kkhzlc6268rvdf")))) (build-system r-build-system) (home-page "https://github.com/psolymos/pbapply") (synopsis "Adding progress bar to apply functions") @@ -5790,14 +5973,14 @@ algorithms.") (define-public r-lme4 (package (name "r-lme4") - (version "1.1-33") + (version "1.1-34") (source (origin (method url-fetch) (uri (cran-uri "lme4" version)) (sha256 (base32 - "0409nhvdkkh571gdi9w21z6szkgnmj4sssw3988idh5wgknsamnr")))) + "1bbaxkrd5m3d40y6jdyrdr4vsjyzkfixbqjwj6c8inmks98f2wp8")))) (build-system r-build-system) (propagated-inputs (list r-boot @@ -5805,8 +5988,8 @@ algorithms.") r-mass r-matrix r-minqa - r-nloptr r-nlme + r-nloptr r-rcpp r-rcppeigen)) (native-inputs @@ -6837,14 +7020,14 @@ or eta squared effect size.") (define-public r-logspline (package (name "r-logspline") - (version "2.1.19") + (version "2.1.20") (source (origin (method url-fetch) (uri (cran-uri "logspline" version)) (sha256 (base32 - "1527cnnn5qdjp8gr4yls0jp0aachjz5s2v79vs79vrfyvxp9w89p")))) + "1nsrgz9sh9qg2fj0x7k48lqhpgzq1z78jfz89ckzp5xm4r8lpgcb")))) (properties `((upstream-name . "logspline"))) (build-system r-build-system) (native-inputs (list gfortran)) @@ -6929,13 +7112,13 @@ designs, one-way designs, general ANOVA designs, and linear regression.") (define-public r-norm (package (name "r-norm") - (version "1.0-11.0") + (version "1.0-11.1") (source (origin (method url-fetch) (uri (cran-uri "norm" version)) (sha256 (base32 - "0bj0d518c5cld1h2ymm7sjhd6b3v2h3w8rcn9b5mki1fg20lx2nd")))) + "1g33g721c0f2b275b334ir6n0h81fh567vs9vrxk60y21z1ydzy2")))) (build-system r-build-system) (native-inputs (list gfortran)) |