Merge branch 'master' into core-updates

1 files changed, 57 insertions, 110 deletions

diff --git a/gnu/packages/machine-learning.scm b/gnu/packages/machine-learning.scm
index afac56f6f7..509b9c7cdd 100644
--- a/gnu/packages/machine-learning.scm
+++ b/gnu/packages/machine-learning.scm
@@ -1,6 +1,6 @@
 ;;; GNU Guix --- Functional package management for GNU
 ;;; Copyright © 2015, 2016, 2017, 2018, 2019, 2020, 2021, 2022 Ricardo Wurmus <rekado@elephly.net>
-;;; Copyright © 2016, 2020, 2021 Efraim Flashner <efraim@flashner.co.il>
+;;; Copyright © 2016, 2020, 2021, 2022 Efraim Flashner <efraim@flashner.co.il>
 ;;; Copyright © 2016, 2017, 2020 Marius Bakke <mbakke@fastmail.com>
 ;;; Copyright © 2016 Hartmut Goebel <h.goebel@crazy-compilers.com>
 ;;; Copyright © 2018, 2019, 2020 Tobias Geerinckx-Rice <me@tobias.gr>
@@ -16,7 +16,7 @@
 ;;; Copyright © 2020 Konrad Hinsen <konrad.hinsen@fastmail.net>
 ;;; Copyright © 2020 Edouard Klein <edk@beaver-labs.com>
 ;;; Copyright © 2020, 2021, 2022 Vinicius Monego <monego@posteo.net>
-;;; Copyright © 2020, 2021 Maxim Cournoyer <maxim.cournoyer@gmail.com>
+;;; Copyright © 2020, 2021, 2022 Maxim Cournoyer <maxim.cournoyer@gmail.com>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -1095,8 +1095,13 @@ computing environments.")
     (arguments
      `(#:phases
        (modify-phases %standard-phases
+         (add-before 'build 'configure
+           (lambda _
+             (setenv "SKLEARN_BUILD_PARALLEL"
+                     (number->string (parallel-job-count)))))
          (add-after 'build 'build-ext
-           (lambda _ (invoke "python" "setup.py" "build_ext" "--inplace")))
+           (lambda _ (invoke "python" "setup.py" "build_ext" "--inplace"
+                             "-j" (number->string (parallel-job-count)))))
          (replace 'check
            (lambda* (#:key tests? #:allow-other-keys)
              (when tests?
@@ -1107,13 +1112,15 @@ computing environments.")
                (setenv "HOME" "/tmp")
 
                (invoke "pytest" "sklearn" "-m" "not network"
+                       "-n" (number->string (parallel-job-count))
                        ;; This test tries to access the internet.
                        "-k" "not test_load_boston_alternative")))))))
-    (inputs
-     (list openblas))
+    (inputs (list openblas))
     (native-inputs
-     (list python-pytest python-pandas ;for tests
-           python-cython))
+     (list python-cython
+           python-pandas
+           python-pytest
+           python-pytest-xdist))
     (propagated-inputs
      (list python-numpy python-threadpoolctl python-scipy python-joblib))
     (home-page "https://scikit-learn.org/")
@@ -1121,55 +1128,8 @@ computing environments.")
     (description
      "Scikit-learn provides simple and efficient tools for data mining and
 data analysis.")
-    (properties `((python2-variant . ,(delay python2-scikit-learn))))
     (license license:bsd-3)))
 
-;; scikit-learn 0.22 and later only supports Python 3, so we stick with
-;; an older version here.
-(define-public python2-scikit-learn
-  (let ((base (package-with-python2 (strip-python2-variant python-scikit-learn))))
-    (package
-      (inherit base)
-      (version "0.20.4")
-      (source (origin
-                (method git-fetch)
-                (uri (git-reference
-                      (url "https://github.com/scikit-learn/scikit-learn")
-                      (commit version)))
-                (file-name (git-file-name "python-scikit-learn" version))
-                (sha256
-                 (base32
-                  "08zbzi8yx5wdlxfx9jap61vg1malc9ajf576w7a0liv6jvvrxlpj"))))
-      (arguments
-       `(#:python ,python-2
-         #:phases
-         (modify-phases %standard-phases
-           (add-after 'build 'build-ext
-             (lambda _ (invoke "python" "setup.py" "build_ext" "--inplace")))
-           (replace 'check
-             (lambda* (#:key tests? #:allow-other-keys)
-               (when tests?
-                 ;; Restrict OpenBLAS threads to prevent segfaults while testing!
-                 (setenv "OPENBLAS_NUM_THREADS" "1")
-
-                 ;; Some tests require write access to $HOME.
-                 (setenv "HOME" "/tmp")
-
-                 (invoke "pytest" "sklearn" "-m" "not network"
-                         "-k"
-                         (string-append
-                          ;; This test tries to access the internet.
-                          "not test_load_boston_alternative"
-                          ;; This test fails for unknown reasons
-                          " and not test_rank_deficient_design"))))))))
-      (inputs
-       (list openblas))
-      (native-inputs
-       (list python2-pytest python2-pandas ;for tests
-             python2-cython))
-      (propagated-inputs
-       (list python2-numpy python2-scipy python2-joblib)))))
-
 (define-public python-threadpoolctl
   (package
     (name "python-threadpoolctl")
@@ -1203,13 +1163,13 @@ for scientific computing and data science (e.g. BLAS and OpenMP).")
 (define-public python-pynndescent
   (package
     (name "python-pynndescent")
-    (version "0.5.5")
+    (version "0.5.6")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "pynndescent" version))
        (sha256
-        (base32 "10pqqqc3jkpw03cyzy04slxmpgyhqnlgbyk0c1cv7kqr5d0zhzbs"))))
+        (base32 "0p3jsdcprjfzz7qf5674dsqfpvdn6p4wgqikg7b6ki5abf433yv1"))))
     (build-system python-build-system)
     (arguments
      `(#:phases
@@ -1217,12 +1177,16 @@ for scientific computing and data science (e.g. BLAS and OpenMP).")
          (replace 'check
            (lambda* (#:key inputs outputs tests? #:allow-other-keys)
              (when tests?
-               (add-installed-pythonpath inputs outputs)
-               (invoke "python" "-m" "pytest" "--pyargs" "pynndescent")))))))
-    (native-inputs
-     (list python-pytest))
+               (invoke "python" "-m" "pytest" "--pyargs" "pynndescent"
+                       ;; wminkowski no longer exists in scipy 1.8.0 (see:
+                       ;; https://github.com/lmcinnes/pynndescent/issues/177)
+                       "-k" "not test_weighted_minkowski")))))))
+    (native-inputs (list python-pytest))
     (propagated-inputs
-     (list python-joblib python-llvmlite python-numba python-scikit-learn
+     (list python-joblib
+           python-llvmlite
+           python-numba
+           python-scikit-learn
            python-scipy))
     (home-page "https://github.com/lmcinnes/pynndescent")
     (synopsis "Nearest neighbor descent for approximate nearest neighbors")
@@ -1362,9 +1326,6 @@ forward-mode differentiation, and the two can be composed arbitrarily.  The
 main intended application of Autograd is gradient-based optimization.")
       (license license:expat))))
 
-(define-public python2-autograd
-  (package-with-python2 python-autograd))
-
 (define-public lightgbm
   (package
     (name "lightgbm")
@@ -1451,38 +1412,6 @@ such as online, hashing, allreduce, reductions, learning2search, active, and
 interactive learning.")
     (license license:bsd-3)))
 
-(define-public python2-fastlmm
-  (package
-    (name "python2-fastlmm")
-    (version "0.2.21")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (pypi-uri "fastlmm" version ".zip"))
-       (sha256
-        (base32
-         "1q8c34rpmwkfy3r4d5172pzdkpfryj561897z9r3x22gq7813x1m"))))
-    (build-system python-build-system)
-    (arguments
-     `(#:tests? #f ; some test files are missing
-       #:python ,python-2)) ; only Python 2.7 is supported
-    (propagated-inputs
-     (list python2-numpy
-           python2-scipy
-           python2-matplotlib
-           python2-pandas
-           python2-scikit-learn
-           python2-pysnptools))
-    (native-inputs
-     (list unzip python2-cython python2-mock python2-nose))
-    (home-page "http://research.microsoft.com/en-us/um/redmond/projects/mscompbio/fastlmm/")
-    (synopsis "Perform genome-wide association studies on large data sets")
-    (description
-     "FaST-LMM, which stands for Factored Spectrally Transformed Linear Mixed
-Models, is a program for performing both single-SNP and SNP-set genome-wide
-association studies (GWAS) on extremely large data sets.")
-    (license license:asl2.0)))
-
 (define-public python-hyperopt
   (package
     (name "python-hyperopt")
@@ -2785,26 +2714,40 @@ These include a barrier, broadcast, and allreduce.")
 (define-public python-umap-learn
   (package
     (name "python-umap-learn")
-    (version "0.3.10")
+    (version "0.5.3")
     (source
      (origin
-       (method url-fetch)
-       (uri (pypi-uri "umap-learn" version))
+       (method git-fetch)               ;no tests in pypi release
+       (uri (git-reference
+             (url "https://github.com/lmcinnes/umap")
+             (commit version)))
+       (file-name (git-file-name name version))
        (sha256
         (base32
-         "02ada2yy6km6zgk2836kg1c97yrcpalvan34p8c57446finnpki1"))))
+         "1315jkb0h1b579y9m59632f0nnpksilm01nxx46in0rq8zna8vsb"))))
     (build-system python-build-system)
-    (native-inputs
-     (list python-joblib python-nose))
+    (arguments
+     (list
+      #:phases
+      #~(modify-phases %standard-phases
+          (replace 'check
+            (lambda* (#:key tests? #:allow-other-keys)
+              (when tests?
+                (setenv "HOME" "/tmp")
+                (invoke "pytest" "-vv" "umap")))))))
+    (native-inputs (list python-pytest))
     (propagated-inputs
-     (list python-numba python-numpy python-scikit-learn python-scipy))
+     (list python-numba
+           python-numpy
+           python-pynndescent
+           python-scikit-learn
+           python-scipy
+           python-tqdm))
     (home-page "https://github.com/lmcinnes/umap")
-    (synopsis
-     "Uniform Manifold Approximation and Projection")
-    (description
-     "Uniform Manifold Approximation and Projection is a dimension reduction
-technique that can be used for visualisation similarly to t-SNE, but also for
-general non-linear dimension reduction.")
+    (synopsis "Uniform Manifold Approximation and Projection")
+    (description "Uniform Manifold Approximation and Projection is a dimension
+reduction technique that can be used for visualization similarly to t-SNE, but
+also for general non-linear dimension reduction.")
     (license license:bsd-3)))
 
 (define-public nnpack
@@ -3046,7 +2989,11 @@ Note: currently this package does not provide GPU support.")
        (uri (pypi-uri "hmmlearn" version))
        (sha256
         (base32
-         "1my0j3rzp17438idr32ssh0j969a98yjblx5igx5kgiiigr9qa1a"))))
+         "1my0j3rzp17438idr32ssh0j969a98yjblx5igx5kgiiigr9qa1a"))
+       (snippet
+        #~(begin
+            (use-modules ((guix build utils)))
+            (delete-file "lib/hmmlearn/_hmmc.c")))))
     (build-system python-build-system)
     (arguments
      `(#:phases