<div dir="ltr"><div dir="ltr">On Mon, Jan 20, 2020 at 2:18 PM Benson Muite <<a href="mailto:benson_muite@emailplus.org">benson_muite@emailplus.org</a>> wrote:<br></div><div class="gmail_quote"><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-style:solid;border-left-color:rgb(204,204,204);padding-left:1ex">
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<p>Packaging is probably important. In many beginner tutorials, "sudo
apt-get install gromacs" is commonly used to avoid compilation
issues.</p></div></blockquote><div>That is fine when the version of GROMACS is not so important. For the next few years, the version of gmxapi will be pretty important. If the Python package included the necessary GROMACS code, wouldn't "pip install gmxapi" be just as easy as "sudo apt-get-install gromacs"?</div><div> </div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-style:solid;border-left-color:rgb(204,204,204);padding-left:1ex"><div><p> That being said, it would be helpful if developers could
completely turn off python and still have a usable installation
solely in a relatively low level language so that adding new
features and testing on new hardware is possible.</p></div></blockquote><div>Agreed. This point should be orthogonal to the present issue. </div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-style:solid;border-left-color:rgb(204,204,204);padding-left:1ex"><div><p>Ensuring
compatibility between Python packaging and Linux distribution
packaging can be a pain.</p></div></blockquote><div>I would say "impossible" as the complexity of a researcher's Python-driven toolkit grows. I don't see much point in packaging Python-driven scientific software for Linux distributions. <br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-style:solid;border-left-color:rgb(204,204,204);padding-left:1ex"><div><p>One might consider having a Python version
on Pypi so that beginners still have an easy way to install.</p></div></blockquote><div>There are gmxapi source distributions on PyPI. My proposal in this email thread would make it easier to install from PyPI by allowing the GROMACS dependency to be wrapped into the same package. </div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-style:solid;border-left-color:rgb(204,204,204);padding-left:1ex"><div><p>App
images (or other similar portable installable linux versions) are
another possible alternative to avoid beginners needing to compile.</p></div></blockquote><div>We have Docker and Singularity recipes for gmxapi 0.0.7. I have received feedback from HPC support staff that they find Spack useful in helping users to assemble their software tool kits. I am looking into technologies like Yarn to help provision execution environments. I welcome further discussion, especially regarding specific use cases.<br></div><div><br></div></div></div>