https://pfspipe.ipmu.jp/jira This file is an XML representation of an issue en-us 8.3.4 803005 13-09-2019 https://pfspipe.ipmu.jp/jira/browse/INFRA-290 Software Development Infrastructure <p>Please install ipympl into the stack conda environment on tiger for use in notebooks.</p> INFRA-290

Please install ipympl on tiger

Story Normal Done Done price rhl Tue, 16 Mar 2021 15:25:31 +0000 Wed, 1 Dec 2021 00:41:07 +0000 Wed, 1 Dec 2021 00:41:07 +0000 0 5 <p><a href="https://pfspipe.ipmu.jp/jira/secure/ViewProfile.jspa?name=ncaplar" class="user-hover" rel="ncaplar">ncaplar</a> has some things to add too.</p> <p>I apologize for the delay. </p> <p>I am using few notebook extensions (e.g., see here : <a href="https://towardsdatascience.com/jupyter-notebook-extensions-517fa69d2231)." class="external-link" rel="nofollow">https://towardsdatascience.com/jupyter-notebook-extensions-517fa69d2231</a> or <a href="https://jupyter-contrib-nbextensions.readthedocs.io/en/latest/install.html" class="external-link" rel="nofollow">https://jupyter-contrib-nbextensions.readthedocs.io/en/latest/install.html)</a> .Particular extensions I am using are code_prettify, collapsible_headings, codefolding, execute_time and toc2. If those would be available that would be lovely (but these can be installed by user only without touching the main part, I think)- but at least support for extensions would be very valuable.</p> <p>Also, module tqdm is nice, for monitoring progress of calculations.</p> <p>Please add pandas too.</p> <p>Add psycopg2.</p> <p>Please add ginga. More completely, my (old?) instructions read:</p> <div class="code panel" style="border-width: 1px;"><div class="codeContent panelContent"> <pre class="code-java"> Quick Start Instructions ------------------------ Install, via e.g. conda or pip: - ipywidgets - ipyevents - ginga Register the Jupyter extensions with:: jupyter nbextension enable --py --sys-prefix widgetsnbextension jupyter nbextension enable --py --sys-prefix ipyevents </pre> </div></div> <p>I have installed jupyter, astroplan, ipython jupyter_contrib_nbextensions, and ginga on the Hilo cluster, and added them to the standard install script.</p> <p>I have not been able to <tt>conda install</tt> on the tiger cluster, because I get <tt>Permission denied</tt> errors. I think <a href="https://pfspipe.ipmu.jp/jira/secure/ViewProfile.jspa?name=ncaplar" class="user-hover" rel="ncaplar">ncaplar</a> needs to fix the permissions (and double-check his <tt>umask</tt>), e.g.:</p> <div class="code panel" style="border-width: 1px;"><div class="codeContent panelContent"> <pre class="code-java"> drwxr-sr-x. 3 ncaplar hsc 4096 Mar 3 2020 /projects/HSC/PFS/stack/20190925/python/miniconda3-4.5.12/lib/python3.7/site-packages/backcall/ </pre> </div></div> <p>The lines to install the packages:</p> <div class="code panel" style="border-width: 1px;"><div class="codeContent panelContent"> <pre class="code-java"> conda install -y --no-update-dependencies jupyter ipython ipympl psycopg2 <span class="code-quote">'sqlalchemy&gt;=1.4'</span> ipywidgets conda install -y --no-update-dependencies -c conda-forge jupyter_contrib_nbextensions astroplan ipyevents ginga </pre> </div></div> <p>Changes look fine to me.</p> <p>Merged the changes.</p> <p>Will wait until we can actually implement on tiger before closing this ticket, but that's blocked on <a href="https://pfspipe.ipmu.jp/jira/secure/ViewProfile.jspa?name=ncaplar" class="user-hover" rel="ncaplar">ncaplar</a>.</p> <p>With thanks to <a href="https://pfspipe.ipmu.jp/jira/secure/ViewProfile.jspa?name=ncaplar" class="user-hover" rel="ncaplar">ncaplar</a> and <a href="https://pfspipe.ipmu.jp/jira/secure/ViewProfile.jspa?name=arnaud.lefur" class="user-hover" rel="arnaud.lefur">arnaud.lefur</a>, I managed to get this installed on tiger. I needed to remove some existing files (<tt>conda</tt> said it didn't recognise them, so they "may have been created by another package manager"), but I believe we're in business now.</p> <p>Please let me know if you notice any problems, or have further package requests for the pipeline.</p> Development Rank 0|zzs4o0: Reviewers hassan