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Subject: bug#60545: Keras h5py Version Mismatch
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Date: Wed, 4 Jan 2023 01:37:34 +0000
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Hi Guix!


It would seem that the current keras version expects an earlier h5py versio=
n for loading models.  Specifically, running:

from tensorflow.keras.models import load_model
model =3D load_model("model.h5")

fails with:

  File "/gnu/store/idfn4l2kxil9id21v1yci4jcw6103fah-profile/lib/python3.9/s=
ite-packages/tensorflow/python/keras/engine/saving.py", line 228, in load_m=
odel
    model_config =3D json.loads(model_config.decode('utf-8'))
AttributeError: 'str' object has no attribute 'decode'

The above works fine in my local pip environment (see below).  A quick sear=
ch online indicates that this can be fixed by downgrading h5py to version 2=
.10.  The current h5py version in guix is 3.6.

My assumption is that this could also be fixed with an upgrade to keras, bu=
t upgrading keras sounds much more involved.  For a short-term fix, would i=
t be possible to add back a package definition for an earlier h5py in addit=
ion to the current version?  I'm sure an appropriate version exists somewhe=
re in guix's git history, though my git-foo is too weak for me to check.


Thanks,
Zacchae


P.S.
working (pip): keras 2.10.0, h5py 3.7.0
not working (current guix): keras 2.2.4, h5py 3.6.0

--_000_CY4PR03MB27591E805538BEE2A385256098F59CY4PR03MB2759namp_
Content-Type: text/html; charset="iso-8859-1"
Content-Transfer-Encoding: quoted-printable

<html>
<head>
<meta http-equiv=3D"Content-Type" content=3D"text/html; charset=3Diso-8859-=
1">
<style type=3D"text/css" style=3D"display:none;"> P {margin-top:0;margin-bo=
ttom:0;} </style>
</head>
<body dir=3D"ltr">
<div class=3D"elementToProof"><span style=3D"font-family: Calibri, Arial, H=
elvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0); background-colo=
r: rgb(255, 255, 255);">Hi Guix!</span></div>
<div class=3D"elementToProof"><span style=3D"font-family: Calibri, Arial, H=
elvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0); background-colo=
r: rgb(255, 255, 255);"><br>
</span></div>
<div class=3D"elementToProof"><span style=3D"font-family: Calibri, Arial, H=
elvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0); background-colo=
r: rgb(255, 255, 255);"><br>
</span></div>
<div class=3D"elementToProof"><span style=3D"font-family: Calibri, Arial, H=
elvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0); background-colo=
r: rgb(255, 255, 255);">It would seem that the current keras version expect=
s an earlier h5py version for loading
 models.&nbsp; Specifically, running:</span></div>
<div class=3D"elementToProof"><span style=3D"font-family: Calibri, Arial, H=
elvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0); background-colo=
r: rgb(255, 255, 255);"><br>
</span></div>
<div class=3D"elementToProof"><span style=3D"font-family: Calibri, Arial, H=
elvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0); background-colo=
r: rgb(255, 255, 255);">from tensorflow.keras.models import load_model</spa=
n></div>
<div class=3D"elementToProof"><span style=3D"font-family: Calibri, Arial, H=
elvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0); background-colo=
r: rgb(255, 255, 255);">model =3D load_model(&quot;model.h5&quot;)</span></=
div>
<div class=3D"elementToProof"><span style=3D"font-family: Calibri, Arial, H=
elvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0); background-colo=
r: rgb(255, 255, 255);"><br>
</span></div>
<div class=3D"elementToProof" style=3D"font-family: Calibri, Arial, Helveti=
ca, sans-serif; font-size: 12pt; color: rgb(0, 0, 0); background-color: rgb=
(255, 255, 255);">
fails with:</div>
<div class=3D"elementToProof ContentPasted0" style=3D"font-family: Calibri,=
 Arial, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0); backgr=
ound-color: rgb(255, 255, 255);">
<br>
</div>
<div class=3D"elementToProof ContentPasted0" style=3D"font-family: Calibri,=
 Arial, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0); backgr=
ound-color: rgb(255, 255, 255);">
&nbsp; File &quot;/gnu/store/idfn4l2kxil9id21v1yci4jcw6103fah-profile/lib/p=
ython3.9/site-packages/tensorflow/python/keras/engine/saving.py&quot;, line=
 228, in load_model
<div class=3D"FluidPluginCopy ContentPasted0">&nbsp; &nbsp; model_config =
=3D json.loads(model_config.decode('utf-8'))</div>
<div class=3D"FluidPluginCopy ContentPasted0">AttributeError: 'str' object =
has no attribute 'decode'</div>
<br>
</div>
<div class=3D"elementToProof ContentPasted0" style=3D"font-family: Calibri,=
 Arial, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0); backgr=
ound-color: rgb(255, 255, 255);">
The above works fine in my local pip environment (see below).&nbsp; A quick=
 search online indicates that this can be fixed by downgrading h5py to vers=
ion 2.10.&nbsp; The current h5py version in guix is 3.6.</div>
<div class=3D"elementToProof ContentPasted0" style=3D"font-family: Calibri,=
 Arial, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0); backgr=
ound-color: rgb(255, 255, 255);">
<br>
</div>
<div class=3D"elementToProof ContentPasted0" style=3D"font-family: Calibri,=
 Arial, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0); backgr=
ound-color: rgb(255, 255, 255);">
My assumption is that this could also be fixed with an upgrade to keras, bu=
t upgrading keras sounds much more involved.&nbsp; For a short-term fix, wo=
uld it be possible to add back a package definition for an earlier h5py in =
addition to the current version?&nbsp; I'm
 sure an appropriate version exists somewhere in guix's git history, though=
 my git-foo is too weak for me to check.</div>
<div class=3D"elementToProof ContentPasted0" style=3D"font-family: Calibri,=
 Arial, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0); backgr=
ound-color: rgb(255, 255, 255);">
<br>
</div>
<div class=3D"elementToProof ContentPasted0" style=3D"font-family: Calibri,=
 Arial, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0); backgr=
ound-color: rgb(255, 255, 255);">
<br>
</div>
<div class=3D"elementToProof ContentPasted0" style=3D"font-family: Calibri,=
 Arial, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0); backgr=
ound-color: rgb(255, 255, 255);">
Thanks,</div>
<div class=3D"elementToProof ContentPasted0" style=3D"font-family: Calibri,=
 Arial, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0); backgr=
ound-color: rgb(255, 255, 255);">
<div>Zacchae</div>
<div><br>
</div>
<div><br>
</div>
<div>P.S.</div>
<div>working (pip): keras 2.10.0, h5py 3.7.0</div>
<div>not working (current guix): keras 2.2.4, h5py 3.6.0</div>
</div>
</body>
</html>

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From: help-debbugs@HIDDEN (GNU bug Tracking System)
To: Zacchaeus Scheffer <Zacchaeus.Scheffer@HIDDEN>
Subject: bug#60545: Acknowledgement (Keras h5py Version Mismatch)
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Date: Wed, 04 Jan 2023 07:35:03 +0000

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Message sent to bug-guix@HIDDEN:

Subject: bug#60545: Keras h5py Version Mismatch
Resent-From: zimoun <zimon.toutoune@HIDDEN>
Original-Sender: "Debbugs-submit" <debbugs-submit-bounces <at> debbugs.gnu.org>
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Date: Fri, 06 Jan 2023 15:40:41 +0100
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Hi,

On Wed, 04 Jan 2023 at 01:37, Zacchaeus Scheffer <Zacchaeus.Scheffer@HIDDEN> wrote:

> working (pip): keras 2.10.0, h5py 3.7.0
> not working (current guix): keras 2.2.4, h5py 3.6.0

Indeed, it is collateral to ea403bf290f4bf8c7bae314e32dbb90653f92996

--8<---------------cut here---------------start------------->8---
gnu: python-h5py: Update to 3.6.0.

* gnu/packages/python-xyz.scm (python-h5py): Update to 3.6.0.
[arguments]: Set HDF5_DIR variable instead of patching files.
--8<---------------cut here---------------end--------------->8---

Well, the update of Keras to 2.11.0 (the current latest) requires some
work.  First, fetch from Github instead of PyPI because the sources are
not available after v2.6.0; e.g.,

    https://pypi.org/project/keras/2.11.0/#files

Then, second adapt the recipe.  Do you want to give a try?


Cheers,
simon

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merge 60608 60545
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