* [bug#44819] [PATCH 1/2] gnu: Add python-pynndescent.
@ 2020-11-23 15:38 Vinicius Monego
2020-11-23 15:40 ` [bug#44819] [PATCH 2/2] gnu: Add python-opentsne Vinicius Monego
2020-11-25 23:38 ` [bug#44819] [PATCH 1/2] gnu: Add python-pynndescent Leo Famulari
0 siblings, 2 replies; 3+ messages in thread
From: Vinicius Monego @ 2020-11-23 15:38 UTC (permalink / raw)
To: 44819; +Cc: Vinicius Monego
* 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
^ permalink raw reply related [flat|nested] 3+ messages in thread
* [bug#44819] [PATCH 2/2] gnu: Add python-opentsne.
2020-11-23 15:38 [bug#44819] [PATCH 1/2] gnu: Add python-pynndescent Vinicius Monego
@ 2020-11-23 15:40 ` Vinicius Monego
2020-11-25 23:38 ` [bug#44819] [PATCH 1/2] gnu: Add python-pynndescent Leo Famulari
1 sibling, 0 replies; 3+ messages in thread
From: Vinicius Monego @ 2020-11-23 15:40 UTC (permalink / raw)
To: 44819; +Cc: Vinicius Monego
* 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
^ permalink raw reply related [flat|nested] 3+ messages in thread
* [bug#44819] [PATCH 1/2] gnu: Add python-pynndescent.
2020-11-23 15:38 [bug#44819] [PATCH 1/2] gnu: Add python-pynndescent Vinicius Monego
2020-11-23 15:40 ` [bug#44819] [PATCH 2/2] gnu: Add python-opentsne Vinicius Monego
@ 2020-11-25 23:38 ` Leo Famulari
1 sibling, 0 replies; 3+ messages in thread
From: Leo Famulari @ 2020-11-25 23:38 UTC (permalink / raw)
To: Vinicius Monego; +Cc: 44819
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
^ permalink raw reply [flat|nested] 3+ messages in thread
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2020-11-23 15:38 [bug#44819] [PATCH 1/2] gnu: Add python-pynndescent Vinicius Monego
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2020-11-25 23:38 ` [bug#44819] [PATCH 1/2] gnu: Add python-pynndescent Leo Famulari
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