GNU bug report logs - #60545
Keras h5py Version Mismatch

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Package: guix; Reported by: Zacchaeus Scheffer <Zacchaeus.Scheffer@HIDDEN>; merged with #60608; Done: Andreas Enge <andreas@HIDDEN>; Maintainer for guix is bug-guix@HIDDEN.

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Closing this, as we have moved on to newer versions.
If you still see problems, please open an issue on codeberg.

Andreas
Notification sent to Ricardo Wurmus <rekado@HIDDEN>:
bug acknowledged by developer. Full text available.
Reply sent to Andreas Enge <andreas@HIDDEN>:
You have taken responsibility. Full text available.

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Closing this, as we have moved on to newer versions.
If you still see problems, please open an issue on codeberg.

Andreas
Notification sent to Zacchaeus Scheffer <Zacchaeus.Scheffer@HIDDEN>:
bug acknowledged by developer. Full text available.
Reply sent to Andreas Enge <andreas@HIDDEN>:
You have taken responsibility. Full text available.

Message received at 60545 <at> debbugs.gnu.org:


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From: Zacchaeus Scheffer <Zacchaeus.Scheffer@HIDDEN>
To: zimoun <zimon.toutoune@HIDDEN>, "60545 <at> debbugs.gnu.org"
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Subject: Re: bug#60545: Keras h5py Version Mismatch
Thread-Topic: bug#60545: Keras h5py Version Mismatch
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Hi,

I should probably mention that I am not looking into this.  I want to learn=
 more guix, but keras and the additional dependencies required for later ve=
rsions is kind of a monster to me at the moment.

Thanks,
Zacchae
________________________________
From: zimoun <zimon.toutoune@HIDDEN>
Sent: Friday, January 6, 2023 6:40 AM
To: Zacchaeus Scheffer <Zacchaeus.Scheffer@HIDDEN>; 60545@HIDDEN=
u.org <60545 <at> debbugs.gnu.org>
Subject: Re: bug#60545: Keras h5py Version Mismatch

CAUTION: Email originated externally, do not click links or open attachment=
s unless you recognize the sender and know the content is safe.


Hi,

On Wed, 04 Jan 2023 at 01:37, Zacchaeus Scheffer <Zacchaeus.Scheffer@synapt=
ics.com> 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://urldefense.proofpoint.com/v2/url?u=3Dhttps-3A__pypi.org_project=
_keras_2.11.0_-23files&d=3DDwIBAg&c=3D7dfBJ8cXbWjhc0BhImu8wVIoUFmBzj1s88r8E=
GyM0UY&r=3D1moyBSYvgSFmdTYHNEHEwakZGFkPl3pixLezH1qWWXFZPpSXOvpoeGr4XIg6G8V0=
&m=3DNqD4egq46utBpoyT-8Gr6A3lESGvdg2j7CIMrB0r_y4I-pFRV2Gxn2-Lb7s7tsyD&s=3DR=
o23h-Sd5x7VKOXeIYl4j5KGqDMAyZprruKUgdacbCo&e=3D

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


Cheers,
simon


--_000_CY4PR03MB27599F8ABE114B8822E4ABFF98D09CY4PR03MB2759namp_
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<html>
<head>
<meta http-equiv=3D"Content-Type" content=3D"text/html; charset=3Dus-ascii"=
>
<style type=3D"text/css" style=3D"display:none;"> P {margin-top:0;margin-bo=
ttom:0;} </style>
</head>
<body dir=3D"ltr">
<div style=3D"font-family: Calibri, Arial, Helvetica, sans-serif; font-size=
: 12pt; color: rgb(0, 0, 0); background-color: rgb(255, 255, 255);" class=
=3D"elementToProof">
Hi,</div>
<div style=3D"font-family: Calibri, Arial, Helvetica, sans-serif; font-size=
: 12pt; color: rgb(0, 0, 0); background-color: rgb(255, 255, 255);" class=
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<br>
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<div style=3D"font-family: Calibri, Arial, Helvetica, sans-serif; font-size=
: 12pt; color: rgb(0, 0, 0); background-color: rgb(255, 255, 255);" class=
=3D"elementToProof">
I should probably mention that I am not looking into this.&nbsp; I want to =
learn more guix, but keras and the additional dependencies required for lat=
er versions is kind of a monster to me at the moment.</div>
<div style=3D"font-family: Calibri, Arial, Helvetica, sans-serif; font-size=
: 12pt; color: rgb(0, 0, 0); background-color: rgb(255, 255, 255);" class=
=3D"elementToProof">
<br>
</div>
<div style=3D"font-family: Calibri, Arial, Helvetica, sans-serif; font-size=
: 12pt; color: rgb(0, 0, 0); background-color: rgb(255, 255, 255);" class=
=3D"elementToProof">
Thanks,
<div>Zacchae</div>
</div>
<div style=3D"font-family: Calibri, Arial, Helvetica, sans-serif; font-size=
: 12pt; color: rgb(0, 0, 0); background-color: rgb(255, 255, 255);" class=
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<div id=3D"divRplyFwdMsg" dir=3D"ltr"><font face=3D"Calibri, sans-serif" st=
yle=3D"font-size:11pt" color=3D"#000000"><b>From:</b> zimoun &lt;zimon.tout=
oune@HIDDEN&gt;<br>
<b>Sent:</b> Friday, January 6, 2023 6:40 AM<br>
<b>To:</b> Zacchaeus Scheffer &lt;Zacchaeus.Scheffer@HIDDEN&gt;; 605=
45 <at> debbugs.gnu.org &lt;60545 <at> debbugs.gnu.org&gt;<br>
<b>Subject:</b> Re: bug#60545: Keras h5py Version Mismatch</font>
<div>&nbsp;</div>
</div>
<div class=3D"BodyFragment"><font size=3D"2"><span style=3D"font-size:11pt;=
">
<div class=3D"PlainText">CAUTION: Email originated externally, do not click=
 links or open attachments unless you recognize the sender and know the con=
tent is safe.<br>
<br>
<br>
Hi,<br>
<br>
On Wed, 04 Jan 2023 at 01:37, Zacchaeus Scheffer &lt;Zacchaeus.Scheffer@syn=
aptics.com&gt; wrote:<br>
<br>
&gt; working (pip): keras 2.10.0, h5py 3.7.0<br>
&gt; not working (current guix): keras 2.2.4, h5py 3.6.0<br>
<br>
Indeed, it is collateral to ea403bf290f4bf8c7bae314e32dbb90653f92996<br>
<br>
--8&lt;---------------cut here---------------start-------------&gt;8---<br>
gnu: python-h5py: Update to 3.6.0.<br>
<br>
* gnu/packages/python-xyz.scm (python-h5py): Update to 3.6.0.<br>
[arguments]: Set HDF5_DIR variable instead of patching files.<br>
--8&lt;---------------cut here---------------end---------------&gt;8---<br>
<br>
Well, the update of Keras to 2.11.0 (the current latest) requires some<br>
work.&nbsp; First, fetch from Github instead of PyPI because the sources ar=
e<br>
not available after v2.6.0; e.g.,<br>
<br>
&nbsp;&nbsp;&nbsp; <a href=3D"https://urldefense.proofpoint.com/v2/url?u=3D=
https-3A__pypi.org_project_keras_2.11.0_-23files&amp;d=3DDwIBAg&amp;c=3D7df=
BJ8cXbWjhc0BhImu8wVIoUFmBzj1s88r8EGyM0UY&amp;r=3D1moyBSYvgSFmdTYHNEHEwakZGF=
kPl3pixLezH1qWWXFZPpSXOvpoeGr4XIg6G8V0&amp;m=3DNqD4egq46utBpoyT-8Gr6A3lESGv=
dg2j7CIMrB0r_y4I-pFRV2Gxn2-Lb7s7tsyD&amp;s=3DRo23h-Sd5x7VKOXeIYl4j5KGqDMAyZ=
prruKUgdacbCo&amp;e=3D">
https://urldefense.proofpoint.com/v2/url?u=3Dhttps-3A__pypi.org_project_ker=
as_2.11.0_-23files&amp;d=3DDwIBAg&amp;c=3D7dfBJ8cXbWjhc0BhImu8wVIoUFmBzj1s8=
8r8EGyM0UY&amp;r=3D1moyBSYvgSFmdTYHNEHEwakZGFkPl3pixLezH1qWWXFZPpSXOvpoeGr4=
XIg6G8V0&amp;m=3DNqD4egq46utBpoyT-8Gr6A3lESGvdg2j7CIMrB0r_y4I-pFRV2Gxn2-Lb7=
s7tsyD&amp;s=3DRo23h-Sd5x7VKOXeIYl4j5KGqDMAyZprruKUgdacbCo&amp;e=3D</a><br>
<br>
Then, second adapt the recipe.&nbsp; Do you want to give a try?<br>
<br>
<br>
Cheers,<br>
simon<br>
<br>
</div>
</span></font></div>
</body>
</html>

--_000_CY4PR03MB27599F8ABE114B8822E4ABFF98D09CY4PR03MB2759namp_--
Information forwarded to bug-guix@HIDDEN:
bug#60545; Package guix. Full text available.
Merged 60545 60608. Request was from Simon Tournier <zimon.toutoune@HIDDEN> to control <at> debbugs.gnu.org. Full text available.

Message received at 60545 <at> debbugs.gnu.org:


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From: zimoun <zimon.toutoune@HIDDEN>
To: Zacchaeus Scheffer <Zacchaeus.Scheffer@HIDDEN>,
 60545 <at> debbugs.gnu.org
Subject: Re: bug#60545: Keras h5py Version Mismatch
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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
Information forwarded to bug-guix@HIDDEN:
bug#60545; Package guix. Full text available.

Message received at submit <at> debbugs.gnu.org:


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From: Zacchaeus Scheffer <Zacchaeus.Scheffer@HIDDEN>
To: "bug-guix@HIDDEN" <bug-guix@HIDDEN>
Subject: Keras h5py Version Mismatch
Thread-Topic: Keras h5py Version Mismatch
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--_000_CY4PR03MB27591E805538BEE2A385256098F59CY4PR03MB2759namp_
Content-Type: text/plain; charset="iso-8859-1"
Content-Transfer-Encoding: quoted-printable

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>

--_000_CY4PR03MB27591E805538BEE2A385256098F59CY4PR03MB2759namp_--
Acknowledgement sent to Zacchaeus Scheffer <Zacchaeus.Scheffer@HIDDEN>:
New bug report received and forwarded. Copy sent to bug-guix@HIDDEN. Full text available.
Report forwarded to bug-guix@HIDDEN:
bug#60545; Package guix. Full text available.
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