From 0cc843925d59093b70490ccbca5e18bc4174de9c Mon Sep 17 00:00:00 2001
From: Efraim Flashner
Date: Wed, 14 Jun 2023 19:49:27 +0300
Subject: gn: genecup: Use correct python-h5py.

* gn/packages/python.scm (python-h5py-2): New variable.
* gn/packages/machine-learning.scm (tensorflow-native): Remove comments.
* gn/packages/ratspub.scm (use-corrected-inputs): New procedure.
(genecup-with-tensorflow-native, genecup-latest-with-tensorflow-native):
Use use-corrected-inputs.
---
 gn/packages/machine-learning.scm | 12 ------------
 gn/packages/python.scm           | 33 +++++++++++++++++++++++++++++++++
 gn/packages/ratspub.scm          | 12 ++++++++++--
 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")))
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