Comments (10)
I like the idea of a separate pdb2pqr
repo. The only downside I see is that git history will be lost, but I think the benefits you listed will outweigh this.
from apbs-pdb2pqr.
That works for me too. I have started moving pdb2pqr issues to the new repo.
from apbs-pdb2pqr.
I like the idea of a separate
pdb2pqr
repo. The only downside I see is that git history will be lost, but I think the benefits you listed will outweigh this.
There may be a way to move over the git history and prune out the APBS history to keep the archive size reasonable.
from apbs-pdb2pqr.
Following the instructions on https://help.github.com/en/github/using-git/splitting-a-subfolder-out-into-a-new-repository, we could create a repository for apbs and pdb2pqr by splitting them. They would each have their respective histories intact (at least from their top level directory).
I created a new empty repository for pdb2pqr (https://github.com/Electrostatics/pdb2pqr) using the following:
mkdir split && cd split/
git clone https://github.com/Electrostatics/apbs-pdb2pqr.git
cd apbs-pdb2pqr/
git filter-branch --prune-empty --subdirectory-filter pdb2pqr/ master
git remote add origin https://github.com/Electrostatics/pdb2pqr.git
git remote set-url origin https://github.com/Electrostatics/pdb2pqr.git
git push -u origin master
@sobolevnrm and @kozlac can you set the new repository and see if it has everything we need to make pdb2pqr a release on PyPI?
from apbs-pdb2pqr.
Hi @intendo -- wow! Thanks for moving this over. However, now I'm confused: was this an existence proof or an actual migration of the repo? If the latter, we need to figure out what to do with the code in the main apbs-pdb2pqr repo. We can transfer issues but I'm unsure how to move branches given the differences between repositories. However, these repos are going to get out of sync very quickly. Can you make the new repo read-only while we figure this out?
from apbs-pdb2pqr.
This was proof that it can be done. Branches on apbs-pdb2pqr can be pushed to the new pdb2pqr repo and then deleted.
I think the procedure is:
# go to your directory where your current apbs-pdb2pqr repo is
# checkout the branch you want to push (e.g. nathan/pdb2pka)
git remote add pdb2pqr https://github.com/Electrostatics/pdb2pqr
git push pdb2pqr
# repeat for all your branches you want to move to the new repository
I can only make the pdb2pqr read only for 24 hours at a time.
If you want, we can delete this and we can do it again. It only takes about 10 minutes.
from apbs-pdb2pqr.
I love the forward-leaning nature of this and think we should proceed -- you took a huge jump I was hesitating on and made the right move.
Here are my thoughts on some next steps:
- @sobolevnrm and @intendo transfer relevant issues to the new repo
- @sobolevnrm and @intendo make sure the relevant people have the similar roles on the new repo
- @sobolevnrm squats on pdb2pqr PyPI package name -- moved to Electrostatics/pdb2pqr#48
- @sobolevnrm moves any remaining branches to the new repo (probably with manual diffs because he doesn't believe that the procedure @intendo outlined will work) -- moved to Electrostatics/pdb2pqr#49
- @sobolevnrm and @intendo
git delete
(but notgit filter-branch
) pdb2pqr code fromapbs-pdb2pqr
repo -- moved to #624 - @sobolevnrm and @intendo rename
apbs-pdb2pqr
repo toapbs
- @sobolevnrm updates documentation for
apbs
,pdb2pqr
, and http://www.poissonboltzmann.org/ - @sobolevnrm continues to fix PDB2PKA -- moved to Electrostatics/pdb2pqr#50
- @intendo makes a PyPI package for APBS to satisfy PDB2PKA dependencies
- @sobolevnrm updates the PDB2PQR PyPI package with APBS package dependency
What do you think?
from apbs-pdb2pqr.
My thoughts were to:
- split out pdb2pqr into a new repository for new organization/development.
- split out (or duplicate and then git delete) apbs into a new repository for new organization/development
- leave apbs-pdb2pqr for maintenance of APBS-PDB2PQR 3.0 release
from apbs-pdb2pqr.
That works for me if we leave the apbs-pdb2pqr
repo HEAD mostly empty with a README.md that points to the new locations. The release was tagged and will still be available in the archive but I don't want to create confusion by duplicating code in different repos. What do you think?
from apbs-pdb2pqr.
This thread is too messy: I've put the APBS-specific tasks in #626 and moved the PDB2PQR-specific tasks over to https://github.com/Electrostatics/pdb2pqr/issues
from apbs-pdb2pqr.
Related Issues (20)
- Add testing for extensions
- PDB2PQR tests don't actually work HOT 1
- PDB2PQR --assign-only does not assign charges or radii
- PDB2PQR doesn't recognize HETATM with --drop-water HOT 2
- Problem with pdb2pqr.utilities.getFFfile HOT 1
- Please fix really ugly code HOT 1
- Replace C++ clique-finding with Python
- Double-check Cmake build HOT 4
- Possibly reinstate PDB2PKA ligand support
- Large apbs .dx file downloads fail from web server due to server-side error? HOT 8
- APBS and Python3 HOT 7
- PyMOL 2.4.0 APBS plug-in not recognising PDB2PQR HOT 4
- Remove binaries from Git repo HOT 9
- NotImplementedError: PDB2PKA not implemented. HOT 12
- Positive potential on hydrophobic protein interfaces HOT 3
- Remove PDB2PQR code from this repo
- Create separate apbs repo
- Update README.md and documentation for this repo HOT 1
- Remove APBS code from this repo
Recommend Projects
-
React
A declarative, efficient, and flexible JavaScript library for building user interfaces.
-
Vue.js
🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
-
Typescript
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
-
TensorFlow
An Open Source Machine Learning Framework for Everyone
-
Django
The Web framework for perfectionists with deadlines.
-
Laravel
A PHP framework for web artisans
-
D3
Bring data to life with SVG, Canvas and HTML. 📊📈🎉
-
Recommend Topics
-
javascript
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
-
web
Some thing interesting about web. New door for the world.
-
server
A server is a program made to process requests and deliver data to clients.
-
Machine learning
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
-
Visualization
Some thing interesting about visualization, use data art
-
Game
Some thing interesting about game, make everyone happy.
Recommend Org
-
Facebook
We are working to build community through open source technology. NB: members must have two-factor auth.
-
Microsoft
Open source projects and samples from Microsoft.
-
Google
Google ❤️ Open Source for everyone.
-
Alibaba
Alibaba Open Source for everyone
-
D3
Data-Driven Documents codes.
-
Tencent
China tencent open source team.
from apbs-pdb2pqr.