From 9f882daf1194993716b3064f549a9f8d3a97277e Mon Sep 17 00:00:00 2001 From: Lars-Dominik Braun Date: Tue, 21 Mar 2023 13:54:06 +0100 Subject: gnu: Add python-pylems. * gnu/packages/python-science.scm (python-pylems): New variable. --- gnu/packages/python-science.scm | 20 ++++++++++++++++++++ 1 file changed, 20 insertions(+) (limited to 'gnu/packages/python-science.scm') diff --git a/gnu/packages/python-science.scm b/gnu/packages/python-science.scm index 58d127277c..6061b432a7 100644 --- a/gnu/packages/python-science.scm +++ b/gnu/packages/python-science.scm @@ -1687,6 +1687,26 @@ (define-public python-vaex-core tabular datasets. This package provides the core modules of Vaex.") (license license:expat))) +(define-public python-pylems + (package + (name "python-pylems") + (version "0.6.0") + (source (origin + (method url-fetch) + (uri (pypi-uri "PyLEMS" version)) + (sha256 + (base32 + "074azbyivjbwi61fs5p8z9n6d8nk8xw6fmln1www13z1dccb3740")))) + (build-system python-build-system) + (propagated-inputs (list python-lxml)) + (home-page "https://github.com/LEMS/pylems") + (synopsis + "Python support for the Low Entropy Model Specification language (LEMS)") + (description + "A LEMS simulator written in Python which can be used to run +NeuroML2 models.") + (license license:lgpl3))) + ;;; ;;; Avoid adding new packages to the end of this file. To reduce the chances ;;; of a merge conflict, place them above by existing packages with similar -- cgit v1.2.3 From 34f684371ee1bc4c16d46cd660207be97c5df321 Mon Sep 17 00:00:00 2001 From: Lars-Dominik Braun Date: Tue, 21 Mar 2023 13:54:32 +0100 Subject: gnu: Add python-libneuroml. * gnu/packages/python-science.scm (python-libneuroml): New variable. --- gnu/packages/python-science.scm | 27 ++++++++++++++++++++++++++- 1 file changed, 26 insertions(+), 1 deletion(-) (limited to 'gnu/packages/python-science.scm') diff --git a/gnu/packages/python-science.scm b/gnu/packages/python-science.scm index 6061b432a7..073243b63d 100644 --- a/gnu/packages/python-science.scm +++ b/gnu/packages/python-science.scm @@ -76,7 +76,8 @@ (define-module (gnu packages python-science) #:use-module (guix download) #:use-module (guix git-download) #:use-module (guix utils) - #:use-module (guix build-system python)) + #:use-module (guix build-system python) + #:use-module (guix build-system pyproject)) (define-public python-scipy (package @@ -1707,6 +1708,30 @@ (define-public python-pylems NeuroML2 models.") (license license:lgpl3))) +(define-public python-libneuroml + (package + (name "python-libneuroml") + (version "0.4.1") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/NeuralEnsemble/libNeuroML.git") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "0mrm4rd6x1sm6hkvhk20mkqp9q53sl3lbvq6hqzyymkw1iqq6bhy")))) + (build-system pyproject-build-system) + (propagated-inputs (list python-lxml python-six)) + (native-inputs (list python-pytest python-numpy python-tables)) + (home-page "https://libneuroml.readthedocs.org/en/latest/") + (synopsis + "Python library for working with NeuroML descriptions of neuronal models") + (description + "This package provides a Python library for working with NeuroML descriptions of +neuronal models") + (license license:bsd-3))) + ;;; ;;; Avoid adding new packages to the end of this file. To reduce the chances ;;; of a merge conflict, place them above by existing packages with similar -- cgit v1.2.3 From 6d132c5ebf51205decf75377a33c82c113688b02 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Fri, 24 Mar 2023 17:58:44 +0100 Subject: gnu: Add python-scikit-optimize. * gnu/packages/python-science.scm (python-scikit-optimize): New variable. --- gnu/packages/python-science.scm | 66 +++++++++++++++++++++++++++++------------ 1 file changed, 47 insertions(+), 19 deletions(-) (limited to 'gnu/packages/python-science.scm') diff --git a/gnu/packages/python-science.scm b/gnu/packages/python-science.scm index 073243b63d..e932d6f74c 100644 --- a/gnu/packages/python-science.scm +++ b/gnu/packages/python-science.scm @@ -245,33 +245,61 @@ (define-public python-scikit-image "Scikit-image is a collection of algorithms for image processing.") (license license:bsd-3))) +(define-public python-scikit-optimize + (package + (name "python-scikit-optimize") + (version "0.9.0") + (source (origin + (method url-fetch) + (uri (pypi-uri "scikit-optimize" version)) + (sha256 + (base32 + "0230ya8bwrzxjwcy2vz23a3hg6caggnnmg2vq1f9zz2797kckn3p")))) + (build-system pyproject-build-system) + (propagated-inputs + (list python-joblib + python-matplotlib + python-numpy + python-pyaml + python-scikit-learn + python-scipy)) + (native-inputs + (list python-pytest)) + (home-page "https://scikit-optimize.github.io/") + (synopsis "Sequential model-based optimization toolbox") + (description "Scikit-Optimize, or @code{skopt}, is a simple and efficient +library to minimize (very) expensive and noisy black-box functions. It +implements several methods for sequential model-based optimization. +@code{skopt} aims to be accessible and easy to use in many contexts.") + (license license:bsd-3))) + (define-public python-scikit-allel (package (name "python-scikit-allel") (version "1.3.5") (source - (origin - (method url-fetch) - (uri (pypi-uri "scikit-allel" version)) - (sha256 - (base32 "1vg88ng6gd175gzk39iz1drxig5l91dyx398w2kbw3w8036zv8gj")))) + (origin + (method url-fetch) + (uri (pypi-uri "scikit-allel" version)) + (sha256 + (base32 "1vg88ng6gd175gzk39iz1drxig5l91dyx398w2kbw3w8036zv8gj")))) (build-system python-build-system) (arguments (list - #:phases - #~(modify-phases %standard-phases - (replace 'check - (lambda* (#:key tests? #:allow-other-keys) - (when tests? - (invoke "python" "setup.py" "build_ext" "--inplace") - (invoke "python" "-m" "pytest" "-v" "allel" - ;; AttributeError: 'Dataset' object has no attribute 'asstr' - "-k" (string-append - "not test_vcf_to_hdf5" - " and not test_vcf_to_hdf5_exclude" - " and not test_vcf_to_hdf5_rename" - " and not test_vcf_to_hdf5_group" - " and not test_vcf_to_hdf5_ann")))))))) + #:phases + #~(modify-phases %standard-phases + (replace 'check + (lambda* (#:key tests? #:allow-other-keys) + (when tests? + (invoke "python" "setup.py" "build_ext" "--inplace") + (invoke "python" "-m" "pytest" "-v" "allel" + ;; AttributeError: 'Dataset' object has no attribute 'asstr' + "-k" (string-append + "not test_vcf_to_hdf5" + " and not test_vcf_to_hdf5_exclude" + " and not test_vcf_to_hdf5_rename" + " and not test_vcf_to_hdf5_group" + " and not test_vcf_to_hdf5_ann")))))))) (propagated-inputs (list python-dask python-numpy)) -- cgit v1.2.3 From 896982f357034e3e53fe05f86c416835adffda0c Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Fri, 24 Mar 2023 18:23:01 +0100 Subject: gnu: python-scikit-allel: Use pyproject-build-system. * gnu/packages/python-science.scm (python-scikit-allel): Move up to create alphabetic order. [build-system]: Use pyproject-build-system. [arguments]: Provide test flags instead of overriding 'check phase; split out build step into new 'build-ext phase. Disable roh_mhmm tests. --- gnu/packages/python-science.scm | 101 +++++++++++++++++++++------------------- 1 file changed, 52 insertions(+), 49 deletions(-) (limited to 'gnu/packages/python-science.scm') diff --git a/gnu/packages/python-science.scm b/gnu/packages/python-science.scm index e932d6f74c..e53dded72a 100644 --- a/gnu/packages/python-science.scm +++ b/gnu/packages/python-science.scm @@ -1,5 +1,5 @@ ;;; GNU Guix --- Functional package management for GNU -;;; Copyright © 2015, 2016, 2020, 2021, 2022 Ricardo Wurmus +;;; Copyright © 2015, 2016, 2020, 2021, 2022, 2023 Ricardo Wurmus ;;; Copyright © 2015 Federico Beffa ;;; Copyright © 2016 Ben Woodcroft ;;; Copyright © 2016 Hartmut Goebel @@ -169,6 +169,57 @@ (define-public python-scipy routines such as routines for numerical integration and optimization.") (license license:bsd-3))) +(define-public python-scikit-allel + (package + (name "python-scikit-allel") + (version "1.3.5") + (source + (origin + (method url-fetch) + (uri (pypi-uri "scikit-allel" version)) + (sha256 + (base32 "1vg88ng6gd175gzk39iz1drxig5l91dyx398w2kbw3w8036zv8gj")))) + (build-system pyproject-build-system) + (arguments + (list + #:test-flags + '(list "-k" + (string-append + ;; AttributeError: 'Dataset' object has no attribute 'asstr' + "not test_vcf_to_hdf5" + " and not test_vcf_to_hdf5_exclude" + " and not test_vcf_to_hdf5_rename" + " and not test_vcf_to_hdf5_group" + " and not test_vcf_to_hdf5_ann" + ;; Does not work with recent hmmlearn + " and not test_roh_mhmm_0pct" + " and not test_roh_mhmm_100pct")) + #:phases + '(modify-phases %standard-phases + (add-before 'check 'build-ext + (lambda _ + (invoke "python" "setup.py" "build_ext" "--inplace")))))) + (propagated-inputs + (list python-dask + python-numpy)) + (native-inputs + (list python-cython + ;; The following are all needed for the tests + htslib + python-h5py + python-hmmlearn + python-numexpr + python-pytest + python-scipy + python-setuptools-scm + python-zarr)) + (home-page "https://github.com/cggh/scikit-allel") + (synopsis "Explore and analyze genetic variation data") + (description + "This package provides utilities for exploratory analysis of large scale +genetic variation data.") + (license license:expat))) + (define-public python-scikit-fuzzy (package (name "python-scikit-fuzzy") @@ -273,54 +324,6 @@ (define-public python-scikit-optimize @code{skopt} aims to be accessible and easy to use in many contexts.") (license license:bsd-3))) -(define-public python-scikit-allel - (package - (name "python-scikit-allel") - (version "1.3.5") - (source - (origin - (method url-fetch) - (uri (pypi-uri "scikit-allel" version)) - (sha256 - (base32 "1vg88ng6gd175gzk39iz1drxig5l91dyx398w2kbw3w8036zv8gj")))) - (build-system python-build-system) - (arguments - (list - #:phases - #~(modify-phases %standard-phases - (replace 'check - (lambda* (#:key tests? #:allow-other-keys) - (when tests? - (invoke "python" "setup.py" "build_ext" "--inplace") - (invoke "python" "-m" "pytest" "-v" "allel" - ;; AttributeError: 'Dataset' object has no attribute 'asstr' - "-k" (string-append - "not test_vcf_to_hdf5" - " and not test_vcf_to_hdf5_exclude" - " and not test_vcf_to_hdf5_rename" - " and not test_vcf_to_hdf5_group" - " and not test_vcf_to_hdf5_ann")))))))) - (propagated-inputs - (list python-dask - python-numpy)) - (native-inputs - (list python-cython - ;; The following are all needed for the tests - htslib - python-h5py - python-hmmlearn - python-numexpr - python-pytest - python-scipy - python-setuptools-scm - python-zarr)) - (home-page "https://github.com/cggh/scikit-allel") - (synopsis "Explore and analyze genetic variation data") - (description - "This package provides utilities for exploratory analysis of large scale -genetic variation data.") - (license license:expat))) - (define-public python-trimesh (package (name "python-trimesh") -- cgit v1.2.3