From john at fuzzdog.com  Fri Aug  9 15:58:55 2019
From: john at fuzzdog.com (John Dey)
Date: Fri, 9 Aug 2019 12:58:55 -0700
Subject: [IPython-dev] ipython 7.7.0 install issues
Message-ID: <CAAwU4Wytt+XgONb+cZoTHQxd356TDJAfXygvRHVPDh5+y_bk7w@mail.gmail.com>

I'm building Python 3.7.4 with ipython7.7.0.

Issue:  Ipython depends on traitlets, and traitlets depends on
ipython_genutils.
ipython_genutils has been depreciated. pypi ipython_genutils: "Pretend this
doesn?t exist. Nobody should use it."

what am I doing wrong?  How to install traitlets?  jgraph also depends on
traitlets.

```
>>> import IPython
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File
"/app/easybuild/software/Python/3.7.4-foss-2016b-fh1/lib/python3.7/site-packages/IPython/__init__.py",
line 54, in <module>
    from .core.application import Application
  File
"/app/easybuild/software/Python/3.7.4-foss-2016b-fh1/lib/python3.7/site-packages/IPython/core/application.py",
line 23, in <module>
    from traitlets.config.application import Application, catch_config_error
ModuleNotFoundError: No module named 'traitlets'
>>> import IPython
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File
"/app/easybuild/software/Python/3.7.4-foss-2016b-fh1/lib/python3.7/site-packages/IPython/__init__.py",
line 54, in <module>
    from .core.application import Application
  File
"/app/easybuild/software/Python/3.7.4-foss-2016b-fh1/lib/python3.7/site-packages/IPython/core/application.py",
line 23, in <module>
    from traitlets.config.application import Application, catch_config_error
ModuleNotFoundError: No module named 'traitlets'
```

John Dey
john at fuzzdog.com
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From bussonniermatthias at gmail.com  Fri Aug  9 17:27:49 2019
From: bussonniermatthias at gmail.com (Matthias Bussonnier)
Date: Fri, 9 Aug 2019 14:27:49 -0700
Subject: [IPython-dev] ipython 7.7.0 install issues
In-Reply-To: <CAAwU4Wytt+XgONb+cZoTHQxd356TDJAfXygvRHVPDh5+y_bk7w@mail.gmail.com>
References: <CAAwU4Wytt+XgONb+cZoTHQxd356TDJAfXygvRHVPDh5+y_bk7w@mail.gmail.com>
Message-ID: <CANJQusVNUuJ7CE-Vjt3CyHNMQpp0+DJRPej5-z8hCcUvPZ=dQA@mail.gmail.com>

How are you installing IPython ?

When installing with pip or conda; it should pull all the dependencies
automatically.
-- 
Matthias


On Fri, 9 Aug 2019 at 12:59, John Dey <john at fuzzdog.com> wrote:

> I'm building Python 3.7.4 with ipython7.7.0.
>
> Issue:  Ipython depends on traitlets, and traitlets depends on
> ipython_genutils.
> ipython_genutils has been depreciated. pypi ipython_genutils: "Pretend
> this doesn?t exist. Nobody should use it."
>
> what am I doing wrong?  How to install traitlets?  jgraph also depends on
> traitlets.
>
> ```
> >>> import IPython
> Traceback (most recent call last):
>   File "<stdin>", line 1, in <module>
>   File
> "/app/easybuild/software/Python/3.7.4-foss-2016b-fh1/lib/python3.7/site-packages/IPython/__init__.py",
> line 54, in <module>
>     from .core.application import Application
>   File
> "/app/easybuild/software/Python/3.7.4-foss-2016b-fh1/lib/python3.7/site-packages/IPython/core/application.py",
> line 23, in <module>
>     from traitlets.config.application import Application,
> catch_config_error
> ModuleNotFoundError: No module named 'traitlets'
> >>> import IPython
> Traceback (most recent call last):
>   File "<stdin>", line 1, in <module>
>   File
> "/app/easybuild/software/Python/3.7.4-foss-2016b-fh1/lib/python3.7/site-packages/IPython/__init__.py",
> line 54, in <module>
>     from .core.application import Application
>   File
> "/app/easybuild/software/Python/3.7.4-foss-2016b-fh1/lib/python3.7/site-packages/IPython/core/application.py",
> line 23, in <module>
>     from traitlets.config.application import Application,
> catch_config_error
> ModuleNotFoundError: No module named 'traitlets'
> ```
>
> John Dey
> john at fuzzdog.com
> _______________________________________________
> IPython-dev mailing list
> IPython-dev at python.org
> https://mail.python.org/mailman/listinfo/ipython-dev
>
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From john at fuzzdog.com  Fri Aug  9 18:27:09 2019
From: john at fuzzdog.com (John Dey)
Date: Fri, 9 Aug 2019 15:27:09 -0700
Subject: [IPython-dev] ipython 7.7.0 install issues
In-Reply-To: <CANJQusVNUuJ7CE-Vjt3CyHNMQpp0+DJRPej5-z8hCcUvPZ=dQA@mail.gmail.com>
References: <CAAwU4Wytt+XgONb+cZoTHQxd356TDJAfXygvRHVPDh5+y_bk7w@mail.gmail.com>
 <CANJQusVNUuJ7CE-Vjt3CyHNMQpp0+DJRPej5-z8hCcUvPZ=dQA@mail.gmail.com>
Message-ID: <CAAwU4WwmExoQc1d7W_PY4iyY4yNB6Wh7dWapk55a1srzLXR+7w@mail.gmail.com>

I am building everything from source, over 700 modules.

John Dey
john at fuzzdog.com


On Fri, Aug 9, 2019 at 2:28 PM Matthias Bussonnier <
bussonniermatthias at gmail.com> wrote:

> How are you installing IPython ?
>
> When installing with pip or conda; it should pull all the dependencies
> automatically.
> --
> Matthias
>
>
> On Fri, 9 Aug 2019 at 12:59, John Dey <john at fuzzdog.com> wrote:
>
>> I'm building Python 3.7.4 with ipython7.7.0.
>>
>> Issue:  Ipython depends on traitlets, and traitlets depends on
>> ipython_genutils.
>> ipython_genutils has been depreciated. pypi ipython_genutils: "Pretend
>> this doesn?t exist. Nobody should use it."
>>
>> what am I doing wrong?  How to install traitlets?  jgraph also depends on
>> traitlets.
>>
>> ```
>> >>> import IPython
>> Traceback (most recent call last):
>>   File "<stdin>", line 1, in <module>
>>   File
>> "/app/easybuild/software/Python/3.7.4-foss-2016b-fh1/lib/python3.7/site-packages/IPython/__init__.py",
>> line 54, in <module>
>>     from .core.application import Application
>>   File
>> "/app/easybuild/software/Python/3.7.4-foss-2016b-fh1/lib/python3.7/site-packages/IPython/core/application.py",
>> line 23, in <module>
>>     from traitlets.config.application import Application,
>> catch_config_error
>> ModuleNotFoundError: No module named 'traitlets'
>> >>> import IPython
>> Traceback (most recent call last):
>>   File "<stdin>", line 1, in <module>
>>   File
>> "/app/easybuild/software/Python/3.7.4-foss-2016b-fh1/lib/python3.7/site-packages/IPython/__init__.py",
>> line 54, in <module>
>>     from .core.application import Application
>>   File
>> "/app/easybuild/software/Python/3.7.4-foss-2016b-fh1/lib/python3.7/site-packages/IPython/core/application.py",
>> line 23, in <module>
>>     from traitlets.config.application import Application,
>> catch_config_error
>> ModuleNotFoundError: No module named 'traitlets'
>> ```
>>
>> John Dey
>> john at fuzzdog.com
>> _______________________________________________
>> IPython-dev mailing list
>> IPython-dev at python.org
>> https://mail.python.org/mailman/listinfo/ipython-dev
>>
> _______________________________________________
> IPython-dev mailing list
> IPython-dev at python.org
> https://mail.python.org/mailman/listinfo/ipython-dev
>
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From bussonniermatthias at gmail.com  Fri Aug  9 18:52:09 2019
From: bussonniermatthias at gmail.com (Matthias Bussonnier)
Date: Fri, 9 Aug 2019 15:52:09 -0700
Subject: [IPython-dev] ipython 7.7.0 install issues
In-Reply-To: <CAAwU4WwmExoQc1d7W_PY4iyY4yNB6Wh7dWapk55a1srzLXR+7w@mail.gmail.com>
References: <CAAwU4Wytt+XgONb+cZoTHQxd356TDJAfXygvRHVPDh5+y_bk7w@mail.gmail.com>
 <CANJQusVNUuJ7CE-Vjt3CyHNMQpp0+DJRPej5-z8hCcUvPZ=dQA@mail.gmail.com>
 <CAAwU4WwmExoQc1d7W_PY4iyY4yNB6Wh7dWapk55a1srzLXR+7w@mail.gmail.com>
Message-ID: <CANJQusXjVdsQQeEC=3fd0emAkE1PpCbbSFSfavG+MEdP2dxsXQ@mail.gmail.com>

Then how are you building ?

If you don't give at least some of the commands you are running it's going
to be hard to tell you what's wrong.

Also IPython is pure Python, there should not be any building necessary.

Installing ipython_genutils is fine; deprecated mean it should not be used
for new functionality and that we'e slowly going to remove it; but if you
have to build and install it it's ok.
-- 
Matthias

On Fri, 9 Aug 2019 at 15:27, John Dey <john at fuzzdog.com> wrote:

> I am building everything from source, over 700 modules.
>
> John Dey
> john at fuzzdog.com
>
>
> On Fri, Aug 9, 2019 at 2:28 PM Matthias Bussonnier <
> bussonniermatthias at gmail.com> wrote:
>
>> How are you installing IPython ?
>>
>> When installing with pip or conda; it should pull all the dependencies
>> automatically.
>> --
>> Matthias
>>
>>
>> On Fri, 9 Aug 2019 at 12:59, John Dey <john at fuzzdog.com> wrote:
>>
>>> I'm building Python 3.7.4 with ipython7.7.0.
>>>
>>> Issue:  Ipython depends on traitlets, and traitlets depends on
>>> ipython_genutils.
>>> ipython_genutils has been depreciated. pypi ipython_genutils: "Pretend
>>> this doesn?t exist. Nobody should use it."
>>>
>>> what am I doing wrong?  How to install traitlets?  jgraph also depends
>>> on traitlets.
>>>
>>> ```
>>> >>> import IPython
>>> Traceback (most recent call last):
>>>   File "<stdin>", line 1, in <module>
>>>   File
>>> "/app/easybuild/software/Python/3.7.4-foss-2016b-fh1/lib/python3.7/site-packages/IPython/__init__.py",
>>> line 54, in <module>
>>>     from .core.application import Application
>>>   File
>>> "/app/easybuild/software/Python/3.7.4-foss-2016b-fh1/lib/python3.7/site-packages/IPython/core/application.py",
>>> line 23, in <module>
>>>     from traitlets.config.application import Application,
>>> catch_config_error
>>> ModuleNotFoundError: No module named 'traitlets'
>>> >>> import IPython
>>> Traceback (most recent call last):
>>>   File "<stdin>", line 1, in <module>
>>>   File
>>> "/app/easybuild/software/Python/3.7.4-foss-2016b-fh1/lib/python3.7/site-packages/IPython/__init__.py",
>>> line 54, in <module>
>>>     from .core.application import Application
>>>   File
>>> "/app/easybuild/software/Python/3.7.4-foss-2016b-fh1/lib/python3.7/site-packages/IPython/core/application.py",
>>> line 23, in <module>
>>>     from traitlets.config.application import Application,
>>> catch_config_error
>>> ModuleNotFoundError: No module named 'traitlets'
>>> ```
>>>
>>> John Dey
>>> john at fuzzdog.com
>>> _______________________________________________
>>> IPython-dev mailing list
>>> IPython-dev at python.org
>>> https://mail.python.org/mailman/listinfo/ipython-dev
>>>
>> _______________________________________________
>> IPython-dev mailing list
>> IPython-dev at python.org
>> https://mail.python.org/mailman/listinfo/ipython-dev
>>
> _______________________________________________
> IPython-dev mailing list
> IPython-dev at python.org
> https://mail.python.org/mailman/listinfo/ipython-dev
>
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From nick.bollweg at gmail.com  Fri Aug  9 18:51:54 2019
From: nick.bollweg at gmail.com (Nicholas Bollweg)
Date: Fri, 9 Aug 2019 18:51:54 -0400
Subject: [IPython-dev] ipython 7.7.0 install issues
In-Reply-To: <CAAwU4WwmExoQc1d7W_PY4iyY4yNB6Wh7dWapk55a1srzLXR+7w@mail.gmail.com>
References: <CAAwU4Wytt+XgONb+cZoTHQxd356TDJAfXygvRHVPDh5+y_bk7w@mail.gmail.com>
 <CANJQusVNUuJ7CE-Vjt3CyHNMQpp0+DJRPej5-z8hCcUvPZ=dQA@mail.gmail.com>
 <CAAwU4WwmExoQc1d7W_PY4iyY4yNB6Wh7dWapk55a1srzLXR+7w@mail.gmail.com>
Message-ID: <CACejjWzE+zDoJAxCmhUXGxj8s3FqfVgPLh44iCOy-B1Ojh2P8w@mail.gmail.com>

Ipython, notebook, traitlets and genutils used to all be distributed and
developed together, and were split apart in The Big Split.

https://blog.jupyter.org/the-big-split

The wording on genutils is overly harsh, should more mean "don't start
using it as a dependency". It is perfectly fine code in practice.

On Fri, Aug 9, 2019, 18:27 John Dey <john at fuzzdog.com> wrote:

> I am building everything from source, over 700 modules.
>
> John Dey
> john at fuzzdog.com
>
>
> On Fri, Aug 9, 2019 at 2:28 PM Matthias Bussonnier <
> bussonniermatthias at gmail.com> wrote:
>
>> How are you installing IPython ?
>>
>> When installing with pip or conda; it should pull all the dependencies
>> automatically.
>> --
>> Matthias
>>
>>
>> On Fri, 9 Aug 2019 at 12:59, John Dey <john at fuzzdog.com> wrote:
>>
>>> I'm building Python 3.7.4 with ipython7.7.0.
>>>
>>> Issue:  Ipython depends on traitlets, and traitlets depends on
>>> ipython_genutils.
>>> ipython_genutils has been depreciated. pypi ipython_genutils: "Pretend
>>> this doesn?t exist. Nobody should use it."
>>>
>>> what am I doing wrong?  How to install traitlets?  jgraph also depends
>>> on traitlets.
>>>
>>> ```
>>> >>> import IPython
>>> Traceback (most recent call last):
>>>   File "<stdin>", line 1, in <module>
>>>   File
>>> "/app/easybuild/software/Python/3.7.4-foss-2016b-fh1/lib/python3.7/site-packages/IPython/__init__.py",
>>> line 54, in <module>
>>>     from .core.application import Application
>>>   File
>>> "/app/easybuild/software/Python/3.7.4-foss-2016b-fh1/lib/python3.7/site-packages/IPython/core/application.py",
>>> line 23, in <module>
>>>     from traitlets.config.application import Application,
>>> catch_config_error
>>> ModuleNotFoundError: No module named 'traitlets'
>>> >>> import IPython
>>> Traceback (most recent call last):
>>>   File "<stdin>", line 1, in <module>
>>>   File
>>> "/app/easybuild/software/Python/3.7.4-foss-2016b-fh1/lib/python3.7/site-packages/IPython/__init__.py",
>>> line 54, in <module>
>>>     from .core.application import Application
>>>   File
>>> "/app/easybuild/software/Python/3.7.4-foss-2016b-fh1/lib/python3.7/site-packages/IPython/core/application.py",
>>> line 23, in <module>
>>>     from traitlets.config.application import Application,
>>> catch_config_error
>>> ModuleNotFoundError: No module named 'traitlets'
>>> ```
>>>
>>> John Dey
>>> john at fuzzdog.com
>>> _______________________________________________
>>> IPython-dev mailing list
>>> IPython-dev at python.org
>>> https://mail.python.org/mailman/listinfo/ipython-dev
>>>
>> _______________________________________________
>> IPython-dev mailing list
>> IPython-dev at python.org
>> https://mail.python.org/mailman/listinfo/ipython-dev
>>
> _______________________________________________
> IPython-dev mailing list
> IPython-dev at python.org
> https://mail.python.org/mailman/listinfo/ipython-dev
>
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From john at fuzzdog.com  Mon Aug 12 15:26:47 2019
From: john at fuzzdog.com (John Dey)
Date: Mon, 12 Aug 2019 12:26:47 -0700
Subject: [IPython-dev] ipython 7.7.0 install issues
In-Reply-To: <CACejjWzE+zDoJAxCmhUXGxj8s3FqfVgPLh44iCOy-B1Ojh2P8w@mail.gmail.com>
References: <CAAwU4Wytt+XgONb+cZoTHQxd356TDJAfXygvRHVPDh5+y_bk7w@mail.gmail.com>
 <CANJQusVNUuJ7CE-Vjt3CyHNMQpp0+DJRPej5-z8hCcUvPZ=dQA@mail.gmail.com>
 <CAAwU4WwmExoQc1d7W_PY4iyY4yNB6Wh7dWapk55a1srzLXR+7w@mail.gmail.com>
 <CACejjWzE+zDoJAxCmhUXGxj8s3FqfVgPLh44iCOy-B1Ojh2P8w@mail.gmail.com>
Message-ID: <CAAwU4WyEyVqoaxWhfKV6v+q-M5vJpSfajEPztgDfv5juS3xUUQ@mail.gmail.com>

Thanks for your comment about GenUtils it was very helpful. I thought I was
not following some new build model correctly. I have added genutils back
into my build and that has fixed (most) of my issues. The big split does
not seem to be fully implemented yet.

If you are curious; this is how I am building Python. I am using EasyBuild
to create a custom Python built that contains modules that users at our
site have requested. EasyBuild is not as easy as it sounds, but neither is
making science reproducible. Our Python build is heavily focused on genomic
genetics tools. What is EasyBuild?
https://easybuild.readthedocs.io/en/latest/Introduction.html
This is my recipe for building 3.7.4:
https://github.com/FredHutch/easybuild-life-sciences/blob/a0890cfb71bae7f082325799b70513da2cdf661e/fh_easyconfigs/p/Python/Python-3.7.4-foss-2016b-fh1.eb

Please don't ask me why we do not use Conda. Notice that my recipe contains
paths to all the dependencies that are not part of Python. This build
process is completely separate from the system libraries. This recipe can
be built on many different Linuxes.
I have written two tools for documenting/maintaining Python builds:
EasyUpdate and EasyAnnotate. EasyUpdate queries Pypi for module version
updates. https://github.com/fizwit/easy_update.
<https://github.com/fizwit/easy_update>

The Scientific Software Inventory I am trying to maintain:
https://fredhutch.github.io/easybuild-life-sciences/

thanks for the help,

John Dey
john at fuzzdog.com


On Fri, Aug 9, 2019 at 3:52 PM Nicholas Bollweg <nick.bollweg at gmail.com>
wrote:

> Ipython, notebook, traitlets and genutils used to all be distributed and
> developed together, and were split apart in The Big Split.
>
> https://blog.jupyter.org/the-big-split
>
> The wording on genutils is overly harsh, should more mean "don't start
> using it as a dependency". It is perfectly fine code in practice.
>
> On Fri, Aug 9, 2019, 18:27 John Dey <john at fuzzdog.com> wrote:
>
>> I am building everything from source, over 700 modules.
>>
>> John Dey
>> john at fuzzdog.com
>>
>>
>> On Fri, Aug 9, 2019 at 2:28 PM Matthias Bussonnier <
>> bussonniermatthias at gmail.com> wrote:
>>
>>> How are you installing IPython ?
>>>
>>> When installing with pip or conda; it should pull all the dependencies
>>> automatically.
>>> --
>>> Matthias
>>>
>>>
>>> On Fri, 9 Aug 2019 at 12:59, John Dey <john at fuzzdog.com> wrote:
>>>
>>>> I'm building Python 3.7.4 with ipython7.7.0.
>>>>
>>>> Issue:  Ipython depends on traitlets, and traitlets depends on
>>>> ipython_genutils.
>>>> ipython_genutils has been depreciated. pypi ipython_genutils: "Pretend
>>>> this doesn?t exist. Nobody should use it."
>>>>
>>>> what am I doing wrong?  How to install traitlets?  jgraph also depends
>>>> on traitlets.
>>>>
>>>> ```
>>>> >>> import IPython
>>>> Traceback (most recent call last):
>>>>   File "<stdin>", line 1, in <module>
>>>>   File
>>>> "/app/easybuild/software/Python/3.7.4-foss-2016b-fh1/lib/python3.7/site-packages/IPython/__init__.py",
>>>> line 54, in <module>
>>>>     from .core.application import Application
>>>>   File
>>>> "/app/easybuild/software/Python/3.7.4-foss-2016b-fh1/lib/python3.7/site-packages/IPython/core/application.py",
>>>> line 23, in <module>
>>>>     from traitlets.config.application import Application,
>>>> catch_config_error
>>>> ModuleNotFoundError: No module named 'traitlets'
>>>> >>> import IPython
>>>> Traceback (most recent call last):
>>>>   File "<stdin>", line 1, in <module>
>>>>   File
>>>> "/app/easybuild/software/Python/3.7.4-foss-2016b-fh1/lib/python3.7/site-packages/IPython/__init__.py",
>>>> line 54, in <module>
>>>>     from .core.application import Application
>>>>   File
>>>> "/app/easybuild/software/Python/3.7.4-foss-2016b-fh1/lib/python3.7/site-packages/IPython/core/application.py",
>>>> line 23, in <module>
>>>>     from traitlets.config.application import Application,
>>>> catch_config_error
>>>> ModuleNotFoundError: No module named 'traitlets'
>>>> ```
>>>>
>>>> John Dey
>>>> john at fuzzdog.com
>>>> _______________________________________________
>>>> IPython-dev mailing list
>>>> IPython-dev at python.org
>>>> https://mail.python.org/mailman/listinfo/ipython-dev
>>>>
>>> _______________________________________________
>>> IPython-dev mailing list
>>> IPython-dev at python.org
>>> https://mail.python.org/mailman/listinfo/ipython-dev
>>>
>> _______________________________________________
>> IPython-dev mailing list
>> IPython-dev at python.org
>> https://mail.python.org/mailman/listinfo/ipython-dev
>>
> _______________________________________________
> IPython-dev mailing list
> IPython-dev at python.org
> https://mail.python.org/mailman/listinfo/ipython-dev
>
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