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-rw-r--r--gn/packages/machine-learning.scm12
-rw-r--r--gn/packages/python.scm33
-rw-r--r--gn/packages/ratspub.scm12
3 files changed, 43 insertions, 14 deletions
diff --git a/gn/packages/machine-learning.scm b/gn/packages/machine-learning.scm
index fbaffb2..8f9f1f0 100644
--- a/gn/packages/machine-learning.scm
+++ b/gn/packages/machine-learning.scm
@@ -11,18 +11,6 @@
(arguments
(substitute-keyword-arguments (package-arguments tensorflow)
((#:substitutable? _ #f) #f)
- ;((#:phases phases)
- ; `(modify-phases ,phases
- ; (add-after 'unpack 'hardcode-multicore-usage
- ; (lambda _
- ; (substitute* "tensorflow/core/protobuf/config.proto"
- ; ;(("num_threads = 1") "num_threads = 28") ; 56/2 for penguin2
- ; ;(("intra_op_parallelism_threads = 2")
- ; ; "intra_op_parallelism_threads = 0")
- ; ;(("inter_op_parallelism_threads = 5")
- ; ; "inter_op_parallelism_threads = 0")
- ; )
- ; #t))))
((#:configure-flags flags)
`(cons
"-Dtensorflow_OPTIMIZE_FOR_NATIVE_ARCH=ON"
diff --git a/gn/packages/python.scm b/gn/packages/python.scm
index 2c7ca86..510546d 100644
--- a/gn/packages/python.scm
+++ b/gn/packages/python.scm
@@ -9,8 +9,10 @@
#:use-module (gnu packages image)
#:use-module (gnu packages libffi)
#:use-module (gnu packages linux)
+ #:use-module (gnu packages maths)
#:use-module (gnu packages monitoring)
#:use-module (gnu packages pcre)
+ #:use-module (gnu packages pkg-config)
#:use-module (gnu packages protobuf)
#:use-module (gnu packages python)
#:use-module (gnu packages python-build)
@@ -1845,3 +1847,34 @@ file format spec.")
(synopsis "Shim for rdflib 5 and 6 incompatibilities")
(description "Shim for rdflib 5 and 6 incompatibilities")
(license license:cc0)))
+
+(define-public python-h5py-2
+ (package
+ (name "python-h5py")
+ (version "2.10.0")
+ (source (origin
+ (method url-fetch)
+ (uri (pypi-uri "h5py" version))
+ (sha256
+ (base32
+ "0baipzv8n93m0dq0riyi8rfhzrjrfrfh8zqhszzp1j2xjac2fhc4"))))
+ (build-system python-build-system)
+ (arguments
+ `(#:tests? #f ;no test target
+ #:phases (modify-phases %standard-phases
+ (add-after 'unpack 'fix-hdf5-paths
+ (lambda* (#:key inputs #:allow-other-keys)
+ (setenv "HDF5_DIR"
+ (assoc-ref inputs "hdf5")))))))
+ (propagated-inputs (list python-six python-numpy))
+ (inputs (list hdf5-1.10))
+ (native-inputs (list python-cython python-pkgconfig pkg-config))
+ (home-page "https://www.h5py.org/")
+ (synopsis "Read and write HDF5 files from Python")
+ (description
+ "The h5py package provides both a high- and low-level interface to the
+HDF5 library from Python. The low-level interface is intended to be a
+complete wrapping of the HDF5 API, while the high-level component supports
+access to HDF5 files, datasets and groups using established Python and NumPy
+concepts.")
+ (license license:bsd-3)))
diff --git a/gn/packages/ratspub.scm b/gn/packages/ratspub.scm
index af64365..726bc0b 100644
--- a/gn/packages/ratspub.scm
+++ b/gn/packages/ratspub.scm
@@ -17,6 +17,7 @@
#:use-module (gnu packages python-xyz)
#:use-module (gn packages javascript)
#:use-module (gn packages machine-learning)
+ #:use-module (gn packages python)
#:use-module (gn packages web))
(define-public ratspub
@@ -148,6 +149,13 @@ Association Studies}} catalog are also included in the search. These
gene-keyword relationships are presented as an interactive graph and a table.")
(license license:expat)))
+(define use-corrected-inputs
+ (package-input-rewriting/spec
+ ;; Tensorflow-native provides much improved speeds. python-h5py@2 provides
+ ;; compatibility with our version of tensorflow.
+ `(("tensorflow" . ,(const tensorflow-native))
+ ("python-h5py" . ,(const python-h5py-2)))))
+
(define-public ratspub-with-tensorflow-native
(package
(inherit
@@ -399,11 +407,11 @@ concepts and a list of keywords for each concept.")
(define-public genecup-with-tensorflow-native
(package
(inherit
- (tensowflow-native-instead-of-tensorflow genecup))
+ (use-corrected-inputs genecup))
(name "genecup-with-tensorflow-native")))
(define-public genecup-latest-with-tensorflow-native
(package
(inherit
- (tensowflow-native-instead-of-tensorflow genecup-master))
+ (use-corrected-inputs genecup-master))
(name "genecup-latest-with-tensorflow-native")))