ChrisMoth
commented
6 years ago Solved with the 9 commits by ChrisMoth on May 24 and May 28 of 2018.
Closed ChrisMoth closed 6 years ago
ChrisMoth
commented
6 years ago Solved with the 9 commits by ChrisMoth on May 24 and May 28 of 2018.
Going forward, the master branch of CapraLab/pdbmap will be official, and will be mirrred to psbadmin's /dors/capra_lab/users/pdbadmin/pdbmap to run the pipeline.
Backstory emails - read bottom up:
The copy of pdbmap in the CapraLab GitHub is a fork the pdbmap repo in my personal github. I don’t think we ever switched the local repositories to push/pull to/from that GitHub, so its likely that it is very out of date. Without knowing any of the details, I would suggest that whatever repository and branch you’ve been working on is the pdbmap master branch now and should replace any existing master branch. Also, the active development of pdbmap (and the other tools) should move from my GitHub to the CapraLab GitHub. So, I would suggest replacing the master branch with the aspackage branch and pushing all repos to CapraLab. If the current CapraLab/pdbmap is out of date, it could be (archived then) deleted and replaced.
Mike
From: Chris Moth Sent: Monday, May 21, 2018 9:14 PM To: Robert Michael Sivley Cc: Gregory Richard Sliwoski Subject: Trying to check in pdbmap... but CapraLab and MikeSivley versionsvery different
Mike,
Greg and Tony introduced me to the CapraLab github
https://github.com/CapraLab/pdbmap
and I am checking in everything there.
It seems CapraLab's pdbmap seems to have a different branch philosophy of pdbmap checked in, which lacks the aspackage branch of your
https://github.com/mikesivley/pdbmap/tree/aspackage
It feels a little wrong that CapraLab does not have an obvious branch containing your scripts and Jupyter notebooks, though I can find still these when I look back through the history, and those commits are pretty clear.
I have about decided that I need to re-checkin everything that I just pushed to your "aspackage" branch, to the "master" branch at CapraLab.
Does this seem right to you? And, what commands can I use to do this very quickly?
Thanks Chris.
(For reference, below is your August 11 intro discussion on pdbmap.
Q1: You will also likely work with /dors/capra_lab/projects/pathprox/
Prologue to Q2: To my knowledge, the copy of pdbmap in /dors/capra_lab/projects/psb_collab/ is not currently in use by anyone, and may not be up-to-date. The git project for pdbmap also has two major branches. The copy of pdbmap in my personal directory is the original development branch for pdbmap (master). This project over time suffered much scope creep and included many partially-developed features, and included much of the code that is now contained in the pathprox and psb_pipeline projects. A while back I made an effort to separate these into separate projects that interacted with one another. While doing so, I also worked to clean out all but the core functionality of pdbmap. I did this in a new git branch (aspackage). The copy of pdbmap at /dors/capra_lab/projects/pdbmap is on this branch and is the copy that all other projects should refer to. It also includes the most detailed README file, since I've been trying to get it into shape for public distribution.
Answer to Q2: The most important files in each of the projects are: pdbmap/pdbmap.py, pathprox/pathprox.py, and psb_pipeline/bin/psb_pipeline.py. For PDBMap, I would also recommend pdbmap/lib/.py and .sql, which contains all class and database definitions for the PDBMap project. It may also be easier to review these before trying to parse pdbmap.py.
Q3: The best README file for pdbmap is at /dors/capra_lab/projects/pdbmap/README.md. It is best viewed with markup on github.
I have invited mothcw as a collaborator for all three projects on github.
Mike