Rename and refactor package

[sdhutchins]

Before the official release, we need to decide on renaming the package and refactoring it.

• Rename repository from Datasnakes-Scripts to OrthoEvolution
• Refactor Datasnakes to OrthoEvol

Feel free to change the name of this.

[grabear]

I like OrthoEvol! Lets discuss this tomorrow during our meeting.

[grabear]

I like OrthoEvol. It sounds good, and it's on point for this project. If we link to this package in a publication, then it will make more sense for people as well. But we could also give at more general name and a more general function, and add more to it as we develop our other projects. What do you think? @sdhutchins.

For the short term I really like OrthoEvol, especially for publication. But if we decide to keep developing this package, we may pigeon hole ourselves with the name, and it could become confusing for users. So for the long term, the question remains.. How will we continue developing this package, and how will our future projects use it?

[grabear]

• OrthoEvol
• BioPipe
• SnakePipe (LOL)
• GenePipe
• GenieInAFlask
• Genie

[sdhutchins]

lol at Genie in a flask. That made my day. I needed to smile.

[sdhutchins]

I like OrthoEvol. It sounds good, and it's on point for this project. If we link to this package in a publication, then it will make more sense for people as well. But we could also give at more general name and a more general function, and add more to it as we develop our other projects. What do you think? @sdhutchins.
For the short term I really like OrthoEvol, especially for publication. But if we decide to keep developing this package, we may pigeon hole ourselves with the name, and it could become confusing for users. So for the long term, the question remains.. How will we continue developing this package, and how will our future projects use it?

I'll say this much...I agree about it for making the process of publishing a paper about the software easy. I think it's key we decide what we ultimately want out of this. For the GPCR and KARG projects, this is perfect and it's also perfect for other subsequent genomics or phylogenomics projects.

I think it's always possible to create a new package for other projects and/or turn something like the tools, manager, or cookies module of this project also into pypi projects...It'd actually be easy to do that and could garner more attention as well as allow us to use those packages in subsequent projects. It just all depends on how you see it.

We could have a genomics-project-manager package that includes Manager and Cookies. I'm just spitballing here. I see it a number of ways...all of which I'm cool with.

I've been looking over ete's paper and repo for some guidance. I'm not the biggest fan of the actual code in the project, but I enjoy the functionalities and their website.

[grabear]

Ok. I mean you're right. We could make a sort of utilities/tools PyPi package that includes:

• Cookies
• Manager
• Pipeline
• Tools

And a separate package for everything else:

• Orthologs
• RNA-seq
• Microbiome
• Etc...

This would allow us to develop our BioInformatics stuff outside of our Tools/Utilities stuff that we (and others) could develop for a wide genre of projects.

If we make that split we have got to do ASAP. But first we need to get our package stable:

• Integrate LogIt into package #88
• Create a Pull Request Template #85
• Finish Tools Module #83
• Documentation #77
• Rename and refactor package #76
• Abstract the configuration code in the Orthologs submodules #75
• new_basic_project Cookie for standalone projects. #74
• python 3.4 compatibility #59
• Find a pipeline workflow package and integrate it #38
• Alignment Class #37
• ETE3PAML - Clean and polish #35
• Integrate full pipeline #32
• Module Testing #25
• Works Cited #21
• Convert pathlib calls. #20

[grabear]

We could call the Utilities/Tools:

• Plumber
• PiedPiper
• Drano
• Yoshi
• Wario
• Mario
• PipeLabyrinth

Idk lol. Ideas @sdhutchins

[sdhutchins]

I can think we can keep this package as is and still make packages for the tools. Yes, I'm being lazy lol

[grabear]

Lol. Alright. So keep everything inside, and when we get ready, we can basically carbon copy our "Plumber" modules into a new package. We'll just have to make sure those tools only depend on each other. I think that's how they are functioning at the moment as far as I'm aware.

[sdhutchins]

lol Yes, if that's okay. I mean, we can do that at any time if wanted.

We could call the Utilities/Tools:
Plumber
PiedPiper
Drano
Yoshi
Wario
Mario
PipeLabyrinth
Idk lol. Ideas @sdhutchins

LMAO

[sdhutchins]

I love all those names though.

[sdhutchins]

@grabear Thought about this a few days ago. I really do think we should keep it designed for orthology inference or phylogenetics.

I think trying to incorporate rnaseq (and likely R) would be more complex. Also, I think we've created tools within this tool that we can offer as standalone tools from the Manager module to sge to the Cookies template to ftp. It'd improve our skills to develop more packages, and we'd also improve our resumes. By all means, we could take on these packages as individuals which would also be something to tout on our resumes or in future interviews (showing we can develop software in a collaborative manner and independent manner).

Just my thoughts.

I also think for the science community...having more and simpler tools that do great things can be more valuable than 1 big-complex tool (which can scare people off).

Let me know what you think. It'd be also great to get input from others about it as well.

[grabear]

Yea I can see that. BioPython for instance was pretty confusing at first.. I still like this idea though...

We could make a sort of utilities/tools PyPi package that includes:

Cookies
Manager
Tools

And a separate package for everything else:

Orthologs
RNA-seq
Microbiome
Etc...

What if we do a "bio-utilities" package and then an "ortho-evol" package that takes bio-utilities as a dependency?

[grabear]

For above though ortho-evol would be separate from anything we did with RNA-seq data or micro-biome data.

[sdhutchins]

Yeah, I think we can keep the current package as is and convert it to ortho-evol.

We can make those utilities you mentioned (Cookies, Manager, Tools) still separate or we can do it how you laid out. I really think each deserves their own pypi package or multiple ones - particularly the concepts.

I'm all for us having like 5 packages that we can use and put out there into the world. It was sort of where I was going with the py3utils and biosnips repos.

Manager could be designed as such that you could port in multiple projects into one project manager. You could call it bioproject or biomanager. Idk. We can get creative.

I mean the BioSQL stuff you've done should for sure be a pypi package. It can still be in this, but a package as well would be great.

One of the features of this package is project management and I think it's important it stays, but remains more specific to what we need to finish this project.

[grabear]

Ok. I'm going to think about this. I'll look at the dependencies for everything tomorrow.

[sdhutchins]

Addressed by #128

[sdhutchins]

#127