Upcoming releases, breaking changes...?

[Björn Johansson]

Dear Pydna users,

I would like to make a couple of changes in the release after the next one.

I would like to remove the import statements in the __init__.py file. This means that one would have to do

from pydna.XYZ import abc

instead of using

 

import pydna
pydna.abc

directly.

I would also like to remove the following modules:

pydna.design.print_primer_pair
pydna.design.cloning_primers
pydna.design.integration_primers
pydna.design.assembly_primers

all of which should be replaced by:

pydna.design.assembly_fragments
pydna.design.primer_design

The two last functions have an interface that is much more logical and easier to remember.

Have a look at some examples for how this is supposed to work (gibson and gibson2 examples).

There are also new docstrings for the design module.

This would be a version 2.X.X since this breaks backwards compatibility. 

Thoughts about this? Any other suggestions are welcome.

/bjorn

[Mark Budde]

I agree with all these changes. The init statement sometimes makes it difficult to find the where a function is located.

On an unrelated note - is there a simple way to disable shelving with amplify? I have run into a number of issues with this. 

(1) I have twice been amplifying lots of large fragments, which causes python to crash (probably a memory issue on my side). However, this permanently breaks the amplify functionality until I delete the shelve file. 

(2) A more pernicious problem manifests as such: (a) I amplify from a genbank file. (b) I edit the original genbank file. (c) When I try to amplify again, the changes I made to the genbank file are missing. After a ton of troubleshooting, I realize that the shelve is stuck on the previous version of the genbank file. (d) I delete the shelve and the files are updated.

Thanks,

Mark

[Björn Johansson]

Hi Mark,

There is a simple way that should work. I do not know which version you run but the latest 1.2.0

allows you to 

import pydna

pydna.open_config_folder()

Which should open the config folder in the file browser.

Inside is the pydna.ini file.

Mine currently has this content:

[main]

loglevel=30

email=bjor...@gmail.com

data_dir=/home/bjorn/.local/share/pydna

log_dir=/home/bjorn/.cache/pydna/log

ape=tclsh /home/bjorn/.ApE/apeextractor/ApE.vfs/lib/app-AppMain/AppMain.tcl

cache=nocache       

primers=/home/bjorn/Dropbox/wikidata/Primers.txt

 The line that says cache=nocache should turn off the cache.

Please let me know if this works for you.

/bjorn

[Björn Johansson]

Please have a look at the 1.2.0 release.

It does not have the import statements removed yet, this will be only in 2.0.0.

cheers,

Bjorn