Re: ipython 7.7.0 install issues
John Dey <[email protected]> Mon, 12 Aug 2019 12:26:47 -0700
| Newsgroups | gmane.comp.python.ipython.devel |
|---|---|
| Message-ID | <CAAwU4WyEyVqoaxWhfKV6v+q-M5vJpSfajEPztgDfv5juS3xUUQ@mail.gmail.com> |
--===============2162868142359423182== Content-Type: multipart/alternative; boundary="000000000000f66f4e058ff08128" --000000000000f66f4e058ff08128 Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: quoted-printable 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/a0890cfb71bae7f08= 2325799b70513da2cdf661e/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 [email protected] On Fri, Aug 9, 2019 at 3:52 PM Nicholas Bollweg <[email protected]> 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 <[email protected]> wrote: > >> I am building everything from source, over 700 modules. >> >> John Dey >> [email protected] >> >> >> On Fri, Aug 9, 2019 at 2:28 PM Matthias Bussonnier < >> [email protected]> 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 <[email protected]> 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=E2=80=99t 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/sit= e-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/sit= e-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/sit= e-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/sit= e-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 >>>> [email protected] >>>> _______________________________________________ >>>> IPython-dev mailing list >>>> [email protected] >>>> https://mail.python.org/mailman/listinfo/ipython-dev >>>> >>> _______________________________________________ >>> IPython-dev mailing list >>> [email protected] >>> https://mail.python.org/mailman/listinfo/ipython-dev >>> >> _______________________________________________ >> IPython-dev mailing list >> [email protected] >> https://mail.python.org/mailman/listinfo/ipython-dev >> > _______________________________________________ > IPython-dev mailing list > [email protected] > https://mail.python.org/mailman/listinfo/ipython-dev > --000000000000f66f4e058ff08128 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable <div dir=3D"ltr"><div>Thanks for your comment about GenUtils it was very he= lpful. 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.</div><div><br></di= v><div>If you are curious; this is how I am building Python. I am using Eas= yBuild 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 gen= omic genetics tools. What is EasyBuild?=C2=A0 <a href=3D"https://easybuild.= readthedocs.io/en/latest/Introduction.html">https://easybuild.readthedocs.i= o/en/latest/Introduction.html</a></div><div>This is my recipe for building = 3.7.4: <a href=3D"https://github.com/FredHutch/easybuild-life-sciences/blob= /a0890cfb71bae7f082325799b70513da2cdf661e/fh_easyconfigs/p/Python/Python-3.= 7.4-foss-2016b-fh1.eb">https://github.com/FredHutch/easybuild-life-sciences= /blob/a0890cfb71bae7f082325799b70513da2cdf661e/fh_easyconfigs/p/Python/Pyth= on-3.7.4-foss-2016b-fh1.eb</a></div><div><br></div><div>Please don't as= k me why we do not use Conda. Notice that my recipe contains paths to all t= he dependencies that are not part of Python. This build process is complete= ly separate from the system libraries. This recipe can be built on many dif= ferent Linuxes.=C2=A0 <br></div><div>I have written two tools for documenti= ng/maintaining Python builds: EasyUpdate and EasyAnnotate. EasyUpdate queri= es Pypi for module version updates. <a href=3D"https://github.com/fizwit/ea= sy_update">https://github.com/fizwit/easy_update.<br></a></div><div><br></d= iv><div>The Scientific Software Inventory I am trying to maintain:</div><di= v><a href=3D"https://fredhutch.github.io/easybuild-life-sciences/">https://= fredhutch.github.io/easybuild-life-sciences/</a> </div><div><br></div><div>= thanks for the help,</div><div><br></div><div>John Dey<br></div><div><div><= div dir=3D"ltr" class=3D"gmail_signature" data-smartmail=3D"gmail_signature= "><div dir=3D"ltr"><a href=3D"mailto:[email protected]" target=3D"_blank">jo= [email protected]</a><br></div></div></div><br></div></div><br><div class=3D"g= mail_quote"><div dir=3D"ltr" class=3D"gmail_attr">On Fri, Aug 9, 2019 at 3:= 52 PM Nicholas Bollweg <<a href=3D"mailto:[email protected]">nick.b= [email protected]</a>> wrote:<br></div><blockquote class=3D"gmail_quote" = style=3D"margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);pa= dding-left:1ex"><div dir=3D"auto">Ipython, notebook, traitlets and genutils= used to all be distributed and developed together, and were split apart in= The Big Split.=C2=A0<div dir=3D"auto"><br></div><div dir=3D"auto"><a href= =3D"https://blog.jupyter.org/the-big-split" target=3D"_blank">https://blog.= jupyter.org/the-big-split</a><br><div dir=3D"auto"><br></div><div dir=3D"au= to">The wording on genutils is overly harsh, should more mean "don'= ;t start using it as a dependency". It is perfectly fine code in pract= ice.</div></div></div><br><div class=3D"gmail_quote"><div dir=3D"ltr" class= =3D"gmail_attr">On Fri, Aug 9, 2019, 18:27 John Dey <<a href=3D"mailto:j= [email protected]" rel=3D"noreferrer" target=3D"_blank">[email protected]</a>&= gt; wrote:<br></div><blockquote class=3D"gmail_quote" style=3D"margin:0px 0= px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div = dir=3D"ltr"><div>I am building everything from source, over 700 modules.<br= ></div><div><br></div><div><div><div dir=3D"ltr" class=3D"gmail-m_-91991180= 99132424151m_-767643489238911617m_578556805080774943gmail_signature"><div d= ir=3D"ltr"><div>John Dey<br></div><a href=3D"mailto:[email protected]" rel= =3D"noreferrer noreferrer" target=3D"_blank">[email protected]</a><br></div>= </div></div><br></div></div><br><div class=3D"gmail_quote"><div dir=3D"ltr"= class=3D"gmail_attr">On Fri, Aug 9, 2019 at 2:28 PM Matthias Bussonnier &l= t;<a href=3D"mailto:[email protected]" rel=3D"noreferrer norefer= rer" target=3D"_blank">[email protected]</a>> wrote:<br></div= ><blockquote class=3D"gmail_quote" style=3D"margin:0px 0px 0px 0.8ex;border= -left:1px solid rgb(204,204,204);padding-left:1ex"><div dir=3D"ltr">How are= you installing IPython ?=C2=A0<div><br></div><div>When installing with pip= or conda; it should pull all the dependencies automatically.=C2=A0</div><d= iv>--=C2=A0</div><div>Matthias</div><div><br></div></div><br><div class=3D"= gmail_quote"><div dir=3D"ltr" class=3D"gmail_attr">On Fri, 9 Aug 2019 at 12= :59, John Dey <<a href=3D"mailto:[email protected]" rel=3D"noreferrer nor= eferrer" target=3D"_blank">[email protected]</a>> wrote:<br></div><blockq= uote class=3D"gmail_quote" style=3D"margin:0px 0px 0px 0.8ex;border-left:1p= x solid rgb(204,204,204);padding-left:1ex"><div dir=3D"ltr"><div>I'm bu= ilding Python 3.7.4 with ipython7.7.0.</div><div><br></div><div>Issue:=C2= =A0 Ipython depends on traitlets, and traitlets depends on ipython_genutils= .</div><div>ipython_genutils has been depreciated. pypi ipython_genutils: <= font size=3D"2">"<span style=3D"color:rgb(70,70,70);font-family:"= Source Sans Pro",Helvetica,Arial,sans-serif;font-style:normal;font-var= iant-ligatures:normal;font-variant-caps:normal;font-weight:400;letter-spaci= ng:normal;text-align:start;text-indent:0px;text-transform:none;white-space:= normal;word-spacing:0px;background-color:rgb(253,253,253);text-decoration-s= tyle:initial;text-decoration-color:initial;display:inline;float:none">Prete= nd this doesn=E2=80=99t exist. Nobody should use it."</span></font></d= iv><div><font size=3D"2"><span style=3D"color:rgb(70,70,70);font-family:&qu= ot;Source Sans Pro",Helvetica,Arial,sans-serif;font-style:normal;font-= variant-ligatures:normal;font-variant-caps:normal;font-weight:400;letter-sp= acing:normal;text-align:start;text-indent:0px;text-transform:none;white-spa= ce:normal;word-spacing:0px;background-color:rgb(253,253,253);text-decoratio= n-style:initial;text-decoration-color:initial;display:inline;float:none"><b= r></span></font></div><div><font size=3D"2"><span style=3D"color:rgb(70,70,= 70);font-family:"Source Sans Pro",Helvetica,Arial,sans-serif;font= -style:normal;font-variant-ligatures:normal;font-variant-caps:normal;font-w= eight:400;letter-spacing:normal;text-align:start;text-indent:0px;text-trans= form:none;white-space:normal;word-spacing:0px;background-color:rgb(253,253,= 253);text-decoration-style:initial;text-decoration-color:initial;display:in= line;float:none">what am I doing wrong?=C2=A0 How to install traitlets?=C2= =A0 jgraph also depends on traitlets.</span></font></div><div><font size=3D= "2"><span style=3D"color:rgb(70,70,70);font-family:"Source Sans Pro&qu= ot;,Helvetica,Arial,sans-serif;font-style:normal;font-variant-ligatures:nor= mal;font-variant-caps:normal;font-weight:400;letter-spacing:normal;text-ali= gn:start;text-indent:0px;text-transform:none;white-space:normal;word-spacin= g:0px;background-color:rgb(253,253,253);text-decoration-style:initial;text-= decoration-color:initial;display:inline;float:none"><br></span></font></div= ><div><font size=3D"2"><span style=3D"color:rgb(70,70,70);font-family:"= ;Source Sans Pro",Helvetica,Arial,sans-serif;font-style:normal;font-va= riant-ligatures:normal;font-variant-caps:normal;font-weight:400;letter-spac= ing:normal;text-align:start;text-indent:0px;text-transform:none;white-space= :normal;word-spacing:0px;background-color:rgb(253,253,253);text-decoration-= style:initial;text-decoration-color:initial;display:inline;float:none">```<= /span></font></div><div><font size=3D"2"><span style=3D"color:rgb(70,70,70)= ;font-family:"Source Sans Pro",Helvetica,Arial,sans-serif;font-st= yle:normal;font-variant-ligatures:normal;font-variant-caps:normal;font-weig= ht:400;letter-spacing:normal;text-align:start;text-indent:0px;text-transfor= m:none;white-space:normal;word-spacing:0px;background-color:rgb(253,253,253= );text-decoration-style:initial;text-decoration-color:initial;display:inlin= e;float:none">>>> import IPython<br>Traceback (most recent call la= st):<br>=C2=A0 File "<stdin>", line 1, in <module><br= >=C2=A0 File "/app/easybuild/software/Python/3.7.4-foss-2016b-fh1/lib/= python3.7/site-packages/IPython/__init__.py", line 54, in <module&g= t;<br>=C2=A0 =C2=A0 from .core.application import Application<br>=C2=A0 Fil= e "/app/easybuild/software/Python/3.7.4-foss-2016b-fh1/lib/python3.7/s= ite-packages/IPython/core/application.py", line 23, in <module><= br>=C2=A0 =C2=A0 from traitlets.config.application import Application, catc= h_config_error<br>ModuleNotFoundError: No module named 'traitlets'<= br>>>> import IPython<br>Traceback (most recent call last):<br>=C2= =A0 File "<stdin>", line 1, in <module><br>=C2=A0 Fil= e "/app/easybuild/software/Python/3.7.4-foss-2016b-fh1/lib/python3.7/s= ite-packages/IPython/__init__.py", line 54, in <module><br>=C2= =A0 =C2=A0 from .core.application import Application<br>=C2=A0 File "/= app/easybuild/software/Python/3.7.4-foss-2016b-fh1/lib/python3.7/site-packa= ges/IPython/core/application.py", line 23, in <module><br>=C2=A0= =C2=A0 from traitlets.config.application import Application, catch_config_= error<br>ModuleNotFoundError: No module named 'traitlets'</span></f= ont></div><div><font size=3D"2"><span style=3D"color:rgb(70,70,70);font-fam= ily:"Source Sans Pro",Helvetica,Arial,sans-serif;font-style:norma= l;font-variant-ligatures:normal;font-variant-caps:normal;font-weight:400;le= tter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;wh= ite-space:normal;word-spacing:0px;background-color:rgb(253,253,253);text-de= coration-style:initial;text-decoration-color:initial;display:inline;float:n= one">```<br></span> </font></div><div><br> </div><div><div><div dir=3D"ltr"= class=3D"gmail-m_-9199118099132424151m_-767643489238911617m_57855680508077= 4943gmail-m_-8398271743843641764gmail-m_-4206514537216111676gmail_signature= "><div dir=3D"ltr"><div>John Dey<br></div><a href=3D"mailto:[email protected]= m" rel=3D"noreferrer noreferrer" target=3D"_blank">[email protected]</a><br>= </div></div></div></div></div> _______________________________________________<br> IPython-dev mailing list<br> <a href=3D"mailto:[email protected]" rel=3D"noreferrer noreferrer" tar= get=3D"_blank">[email protected]</a><br> <a href=3D"https://mail.python.org/mailman/listinfo/ipython-dev" rel=3D"nor= eferrer noreferrer noreferrer" target=3D"_blank">https://mail.python.org/ma= ilman/listinfo/ipython-dev</a><br> </blockquote></div> _______________________________________________<br> IPython-dev mailing list<br> <a href=3D"mailto:[email protected]" rel=3D"noreferrer noreferrer" tar= get=3D"_blank">[email protected]</a><br> <a href=3D"https://mail.python.org/mailman/listinfo/ipython-dev" rel=3D"nor= eferrer noreferrer noreferrer" target=3D"_blank">https://mail.python.org/ma= ilman/listinfo/ipython-dev</a><br> </blockquote></div> _______________________________________________<br> IPython-dev mailing list<br> <a href=3D"mailto:[email protected]" rel=3D"noreferrer noreferrer" tar= get=3D"_blank">[email protected]</a><br> <a href=3D"https://mail.python.org/mailman/listinfo/ipython-dev" rel=3D"nor= eferrer noreferrer noreferrer" target=3D"_blank">https://mail.python.org/ma= ilman/listinfo/ipython-dev</a><br> </blockquote></div> _______________________________________________<br> IPython-dev mailing list<br> <a href=3D"mailto:[email protected]" target=3D"_blank">IPython-dev@pyt= hon.org</a><br> <a href=3D"https://mail.python.org/mailman/listinfo/ipython-dev" rel=3D"nor= eferrer" target=3D"_blank">https://mail.python.org/mailman/listinfo/ipython= -dev</a><br> </blockquote></div> --000000000000f66f4e058ff08128-- --===============2162868142359423182== Content-Type: text/plain; charset="us-ascii" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit Content-Disposition: inline _______________________________________________ IPython-dev mailing list [email protected] https://mail.python.org/mailman/listinfo/ipython-dev --===============2162868142359423182==--