* [bug#32484] [PATCH 2/4] gnu: Add python-numba.
2018-08-20 18:00 ` [bug#32484] [PATCH 1/4] gnu: Add python-llvmlite Ricardo Wurmus
@ 2018-08-20 18:00 ` Ricardo Wurmus
2018-08-20 18:00 ` [bug#32484] [PATCH 3/4] gnu: Add python-anndata Ricardo Wurmus
2018-08-20 18:00 ` [bug#32484] [PATCH 4/4] gnu: Add python-scanpy Ricardo Wurmus
2 siblings, 0 replies; 6+ messages in thread
From: Ricardo Wurmus @ 2018-08-20 18:00 UTC (permalink / raw)
To: 32484; +Cc: Ricardo Wurmus
* gnu/packages/python.scm (python-numba): New variable.
---
gnu/packages/python.scm | 84 +++++++++++++++++++++++++++++++++++++++++
1 file changed, 84 insertions(+)
diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm
index 3db29e23f..7f343bdab 100644
--- a/gnu/packages/python.scm
+++ b/gnu/packages/python.scm
@@ -99,6 +99,7 @@
#:use-module (gnu packages libevent)
#:use-module (gnu packages libffi)
#:use-module (gnu packages linux)
+ #:use-module (gnu packages llvm)
#:use-module (gnu packages machine-learning)
#:use-module (gnu packages man)
#:use-module (gnu packages maths)
@@ -13889,3 +13890,86 @@ Let's Encrypt.")
development that supports command line argument parsing, command string
validation testing and application logic.")
(license license:expat)))
+
+;; Make sure to upgrade python-llvmlite in (gnu packages llvm) together with
+;; python-numba. They have a very unflexible relationship.
+(define-public python-numba
+ (package
+ (name "python-numba")
+ (version "0.39.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (pypi-uri "numba" version))
+ (sha256
+ (base32
+ "1bibvkwga1v8293i9ivl469d8bzgabn3vgr2ig7c1i68v8frsx07"))))
+ (build-system python-build-system)
+ (arguments
+ `(#:modules ((guix build utils)
+ (guix build python-build-system)
+ (ice-9 ftw)
+ (srfi srfi-1)
+ (srfi srfi-26))
+ #:phases
+ (modify-phases %standard-phases
+ (add-after 'unpack 'disable-proprietary-features
+ (lambda _
+ (setenv "NUMBA_DISABLE_HSA" "1")
+ (setenv "NUMBA_DISABLE_CUDA" "1")
+ #t))
+ (add-after 'unpack 'remove-failing-tests
+ (lambda _
+ ;; FIXME: these tests fail for unknown reasons:
+ ;; test_non_writable_pycache, test_non_creatable_pycache, and
+ ;; test_frozen (all in numba.tests.test_dispatcher.TestCache).
+ (substitute* "numba/tests/test_dispatcher.py"
+ (("def test(_non_writable_pycache)" _ m)
+ (string-append "def guix_skip" m))
+ (("def test(_non_creatable_pycache)" _ m)
+ (string-append "def guix_skip" m))
+ (("def test(_frozen)" _ m)
+ (string-append "def guix_skip" m)))
+
+ ;; These tests fail because we don't run the tests from the build
+ ;; directory: test_setup_py_distutils, test_setup_py_setuptools
+ ;; They ar in numba.tests.test_pycc.TestDistutilsSupport.
+ (substitute* "numba/tests/test_pycc.py"
+ (("def test(_setup_py_distutils|_setup_py_setuptools)" _ m)
+ (string-append "def guix_skip" m)))
+ #t))
+ (replace 'check
+ (lambda _
+ (let ((cwd (getcwd)))
+ (setenv "PYTHONPATH"
+ (string-append cwd "/build/"
+ (find (cut string-prefix? "lib" <>)
+ (scandir (string-append cwd "/build")))
+ ":"
+ (getenv "PYTHONPATH")))
+ ;; Something is wrong with the PYTHONPATH when running the
+ ;; tests from the build directory, as it complains about not being
+ ;; able to import certain modules.
+ (with-directory-excursion "/tmp"
+ (invoke "python3" "-m" "numba.runtests" "-v" "-m")))
+ #t)))))
+ (propagated-inputs
+ `(("python-llvmlite" ,python-llvmlite)
+ ("python-numpy" ,python-numpy)
+ ("python-singledispatch" ,python-singledispatch)))
+ ;; Needed for tests.
+ (inputs
+ `(("python-jinja2" ,python-jinja2)
+ ("python-pygments" ,python-pygments)))
+ (home-page "https://numba.pydata.org")
+ (synopsis "Compile Python code using LLVM")
+ (description "Numba gives you the power to speed up your applications with
+high performance functions written directly in Python. With a few
+annotations, array-oriented and math-heavy Python code can be just-in-time
+compiled to native machine instructions, similar in performance to C, C++ and
+Fortran, without having to switch languages or Python interpreters.
+
+Numba works by generating optimized machine code using the LLVM compiler
+infrastructure at import time, runtime, or statically (using the included pycc
+tool).")
+ (license license:bsd-3)))
--
2.18.0
^ permalink raw reply related [flat|nested] 6+ messages in thread* [bug#32484] [PATCH 3/4] gnu: Add python-anndata.
2018-08-20 18:00 ` [bug#32484] [PATCH 1/4] gnu: Add python-llvmlite Ricardo Wurmus
2018-08-20 18:00 ` [bug#32484] [PATCH 2/4] gnu: Add python-numba Ricardo Wurmus
@ 2018-08-20 18:00 ` Ricardo Wurmus
2018-08-20 18:00 ` [bug#32484] [PATCH 4/4] gnu: Add python-scanpy Ricardo Wurmus
2 siblings, 0 replies; 6+ messages in thread
From: Ricardo Wurmus @ 2018-08-20 18:00 UTC (permalink / raw)
To: 32484; +Cc: Ricardo Wurmus
* gnu/packages/python.scm (python-anndata): New variable.
---
gnu/packages/python.scm | 26 ++++++++++++++++++++++++++
1 file changed, 26 insertions(+)
diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm
index 7f343bdab..2838d2ae5 100644
--- a/gnu/packages/python.scm
+++ b/gnu/packages/python.scm
@@ -13973,3 +13973,29 @@ Numba works by generating optimized machine code using the LLVM compiler
infrastructure at import time, runtime, or statically (using the included pycc
tool).")
(license license:bsd-3)))
+
+(define-public python-anndata
+ (package
+ (name "python-anndata")
+ (version "0.6.9")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (pypi-uri "anndata" version))
+ (sha256
+ (base32
+ "1fh461xyyc7pcrjfgd013bdc2alf53r46ss3gfw3431mbb1gappi"))))
+ (build-system python-build-system)
+ (propagated-inputs
+ `(("python-h5py" ,python-h5py)
+ ("python-natsort" ,python-natsort)
+ ("python-pandas" ,python-pandas)
+ ("python-scipy" ,python-scipy)))
+ (home-page "https://github.com/theislab/anndata")
+ (synopsis "Annotated data for data analysis pipelines")
+ (description "Anndata is a package for simple (functional) high-level APIs
+for data analysis pipelines. In this context, it provides an efficient,
+scalable way of keeping track of data together with learned annotations and
+reduces the code overhead typically encountered when using a mostly
+object-oriented library such as @code{scikit-learn}.")
+ (license license:bsd-3)))
--
2.18.0
^ permalink raw reply related [flat|nested] 6+ messages in thread* [bug#32484] [PATCH 4/4] gnu: Add python-scanpy.
2018-08-20 18:00 ` [bug#32484] [PATCH 1/4] gnu: Add python-llvmlite Ricardo Wurmus
2018-08-20 18:00 ` [bug#32484] [PATCH 2/4] gnu: Add python-numba Ricardo Wurmus
2018-08-20 18:00 ` [bug#32484] [PATCH 3/4] gnu: Add python-anndata Ricardo Wurmus
@ 2018-08-20 18:00 ` Ricardo Wurmus
2018-08-29 15:09 ` bug#32484: " Ricardo Wurmus
2 siblings, 1 reply; 6+ messages in thread
From: Ricardo Wurmus @ 2018-08-20 18:00 UTC (permalink / raw)
To: 32484; +Cc: Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-scanpy): New variable.
---
gnu/packages/bioinformatics.scm | 36 +++++++++++++++++++++++++++++++++
1 file changed, 36 insertions(+)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index dce8ab62f..ef9d81435 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -13406,3 +13406,39 @@ conversions, region filtering, FASTA sequence extraction and more.")
;; gffread is under Expat, but gclib is under Artistic 2.0
(license (list license:expat
license:artistic2.0)))))
+
+(define-public python-scanpy
+ (package
+ (name "python-scanpy")
+ (version "1.2.2")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (pypi-uri "scanpy" version))
+ (sha256
+ (base32
+ "1ak7bxms5a0yvf65prppq2g38clkv7c7jnjbnfpkh3xxv7q512jz"))))
+ (build-system python-build-system)
+ (propagated-inputs
+ `(("python-anndata" ,python-anndata)
+ ("python-igraph" ,python-igraph)
+ ("python-numba" ,python-numba)
+ ("python-joblib" ,python-joblib)
+ ("python-natsort" ,python-natsort)
+ ("python-networkx" ,python-networkx)
+ ("python-statsmodels" ,python-statsmodels)
+ ("python-scikit-learn" ,python-scikit-learn)
+ ("python-matplotlib" ,python-matplotlib)
+ ("python-pandas" ,python-pandas)
+ ("python-scipy" ,python-scipy)
+ ("python-seaborn" ,python-seaborn)
+ ("python-h5py" ,python-h5py)
+ ("python-tables" ,python-tables)))
+ (home-page "http://github.com/theislab/scanpy")
+ (synopsis "Single-Cell Analysis in Python.")
+ (description "Scanpy is a scalable toolkit for analyzing single-cell gene
+expression data. It includes preprocessing, visualization, clustering,
+pseudotime and trajectory inference and differential expression testing. The
+Python-based implementation efficiently deals with datasets of more than one
+million cells.")
+ (license license:bsd-3)))
--
2.18.0
^ permalink raw reply related [flat|nested] 6+ messages in thread