GNU bug report logs - #44819
[PATCH 1/2] gnu: Add python-pynndescent.

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Message #5 received at submit <at> debbugs.gnu.org (full text, mbox):

From: Vinicius Monego <monego <at> posteo.net>
To: guix-patches <at> gnu.org
Cc: Vinicius Monego <monego <at> posteo.net>
Subject: [PATCH 1/2] gnu: Add python-pynndescent.
Date: Mon, 23 Nov 2020 12:38:13 -0300

* gnu/packages/machine-learning.scm (python-pynndescent): New variable.
---
Version 0.5.x was released days ago but it changes the API and breaks OpenTSNE tests.

 gnu/packages/machine-learning.scm | 27 +++++++++++++++++++++++++++
 1 file changed, 27 insertions(+)

diff --git a/gnu/packages/machine-learning.scm b/gnu/packages/machine-learning.scm
index 34b522c99b..2ad148b48e 100644
--- a/gnu/packages/machine-learning.scm
+++ b/gnu/packages/machine-learning.scm
@@ -65,6 +65,7 @@
   #:use-module (gnu packages gstreamer)
   #:use-module (gnu packages image)
   #:use-module (gnu packages linux)
+  #:use-module (gnu packages llvm)
   #:use-module (gnu packages maths)
   #:use-module (gnu packages mpi)
   #:use-module (gnu packages ocaml)
@@ -869,6 +870,32 @@ data analysis.")
                  (base32
                   "08zbzi8yx5wdlxfx9jap61vg1malc9ajf576w7a0liv6jvvrxlpj")))))))
 
+(define-public python-pynndescent
+  (package
+    (name "python-pynndescent")
+    (version "0.4.8")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "pynndescent" version))
+       (sha256
+        (base32 "0li1fclif50v6xrq7wh3lif9vv5jpj7xhrb0z6g89wwjnp9b9833"))))
+    (build-system python-build-system)
+    (native-inputs
+     `(("python-nose" ,python-nose)))
+    (propagated-inputs
+     `(("python-joblib" ,python-joblib)
+       ("python-llvmlite" ,python-llvmlite)
+       ("python-numba" ,python-numba)
+       ("python-scikit-learn" ,python-scikit-learn)
+       ("python-scipy" ,python-scipy)))
+    (home-page "https://github.com/lmcinnes/pynndescent")
+    (synopsis "Nearest neighbor descent for approximate nearest neighbors")
+    (description
+     "PyNNDescent provides a Python implementation of Nearest Neighbor Descent
+for k-neighbor-graph construction and approximate nearest neighbor search.")
+    (license license:bsd-2)))
+
 (define-public python-scikit-rebate
   (package
     (name "python-scikit-rebate")
-- 
2.20.1

Message #8 received at 44819 <at> debbugs.gnu.org (full text, mbox):

From: Vinicius Monego <monego <at> posteo.net>
To: 44819 <at> debbugs.gnu.org
Cc: Vinicius Monego <monego <at> posteo.net>
Subject: [PATCH 2/2] gnu: Add python-opentsne.
Date: Mon, 23 Nov 2020 12:40:32 -0300

* gnu/packages/machine-learning.scm (python-opentsne): New variable.
---
 gnu/packages/machine-learning.scm | 45 +++++++++++++++++++++++++++++++
 1 file changed, 45 insertions(+)

diff --git a/gnu/packages/machine-learning.scm b/gnu/packages/machine-learning.scm
index 2ad148b48e..2e5af23f0f 100644
--- a/gnu/packages/machine-learning.scm
+++ b/gnu/packages/machine-learning.scm
@@ -896,6 +896,51 @@ data analysis.")
 for k-neighbor-graph construction and approximate nearest neighbor search.")
     (license license:bsd-2)))
 
+(define-public python-opentsne
+  (package
+    (name "python-opentsne")
+    (version "0.4.4")
+    (source
+     (origin
+       ;; No tests in the PyPI tarball.
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/pavlin-policar/openTSNE")
+             (commit (string-append "v" version))))
+       (file-name (string-append name "-" version "-checkout"))
+       (sha256
+        (base32 "08wamsssmyf6511cbmglm67dp48i6xazs89m1cskdk219v90bc76"))))
+    (build-system python-build-system)
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases
+         ;; Benchmarks require the 'macosko2015' data files.
+         (add-after 'unpack 'delete-benchmark
+           (lambda _
+             (delete-file-recursively "benchmarks")
+             #t))
+         ;; Numba needs a writable dir to cache functions.
+         (add-before 'check 'set-numba-cache-dir
+           (lambda _
+             (setenv "NUMBA_CACHE_DIR" "/tmp")
+             #t)))))
+    (native-inputs
+     `(("python-cython" ,python-cython)))
+    (inputs
+     `(("fftw" ,fftw)))
+    (propagated-inputs
+     `(("python-numpy" ,python-numpy)
+       ("python-pynndescent" ,python-pynndescent)
+       ("python-scikit-learn" ,python-scikit-learn)
+       ("python-scipy" ,python-scipy)))
+    (home-page "https://github.com/pavlin-policar/openTSNE")
+    (synopsis "Extensible, parallel implementations of t-SNE")
+    (description
+     "This is a modular Python implementation of t-Distributed Stochastic
+Neighbor Embedding (t-SNE), a popular dimensionality-reduction algorithm for
+visualizing high-dimensional data sets.")
+    (license license:bsd-3)))
+             
 (define-public python-scikit-rebate
   (package
     (name "python-scikit-rebate")
-- 
2.20.1

Message #11 received at 44819 <at> debbugs.gnu.org (full text, mbox):

From: Leo Famulari <leo <at> famulari.name>
To: Vinicius Monego <monego <at> posteo.net>
Cc: 44819 <at> debbugs.gnu.org
Subject: Re: [bug#44819] [PATCH 1/2] gnu: Add python-pynndescent.
Date: Wed, 25 Nov 2020 18:38:46 -0500

On Mon, Nov 23, 2020 at 12:38:13PM -0300, Vinicius Monego wrote:
> * gnu/packages/machine-learning.scm (python-pynndescent): New variable.

Thanks! Pushed as 6a5da0d0342641c935451152b39df34b4f1ac680

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