changes in the way of initialization Project from dict and pandas df

pepkit / peppy

Project metadata manager for PEPs in Python

https://pep.databio.org/peppy

BSD 2-Clause "Simplified" License

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changes in the way of initialization Project from dict and pandas df #405

Closed khoroshevskyi closed 2 years ago

khoroshevskyi commented 2 years ago

Address #402 Also addresses #401

Big changes in functions:

to_dict (returning only crucial object variables. This method is more efficient, than returning all variables)
from_dict (initialization of the object from dict of variables that were generated by to_dict function)
from_pandas (added possibility to initialize project also by using subsample table and config file )
new equal function (Now equal function will check only samples. - previous version was checking all variables. If any path to the file was not the same it would return that this projects were not the same. Now it's fixed)

nsheff commented 2 years ago

Is the purpose of this to simplify inserting into the database with pepdbagent?

I mean, what prompted the change?

khoroshevskyi commented 2 years ago

Is the purpose of this to simplify inserting into the database with pepdbagent?

Not simplifying, I would say make it more efficient (especially storage efficient) and more reasonable to store one sample table, then 3 sample tables in different configurations. I assume, now it will take 3x less space in pepdb.

nsheff commented 2 years ago

and will this also make it possible to use simplified projects, because they are unprocessed? like, I mean collapsed constant rows to the project level?

khoroshevskyi commented 2 years ago

and will this also make it possible to use simplified projects, because they are unprocessed? like, I mean collapsed constant rows to the project level?

Do you mean projects, such as geofetch is producing (e.g. where config file contains append)? - then Yes!

nsheff commented 2 years ago

Do you mean projects, such as geofetch is producing (e.g. where config file contains append)? - then Yes!

Yes, that's what I mean. Great!

Can you rename this Pull Request to something more clear? Why does it say "402" ?

rafalstepien commented 2 years ago

Do you mean projects, such as geofetch is producing (e.g. where config file contains append)? - then Yes!

Yes, that's what I mean. Great!

Can you rename this Pull Request to something more clear? Why does it say "402" ?

I think because it originated from issue number 402

nsheff commented 2 years ago

I think because it originated from issue number 402

Indeed. @Khoroshevskyi you have to use the # sign to link to the issue and indicate it as an issue number. Also, this probably belongs in the description of the PR

rafalstepien commented 2 years ago

So after changing the name of PR are we good to go?

nsheff commented 2 years ago

~I made 1 request for a change, this still is not addressed (see above)~

Nevermind, I was wrong.

khoroshevskyi commented 2 years ago

Do you mean projects, such as geofetch is producing (e.g. where config file contains append)? - then Yes!

Yes, that's what I mean. Great!

Can you rename this Pull Request to something more clear? Why does it say "402" ?

As Rafal mentioned above, the name was originated from the issue number 402. All 4 changes are related to this problem. eq function is related to functionality to_dict; from_dict is dependent from to_dict ; And from_pandas has similar function as from_dict . That's why all this changes were made here. Is there something else to change @nsheff ?

khoroshevskyi commented 2 years ago

I have chenged the names of the dict keys, could you check it please? @nsheff --> https://github.com/pepkit/peppy/pull/405/commits/802ea1a112635f1f233a5faa12e0716bf13d8157