rinikerlab / PyGromosTools

This package is a python library with tools for the Molecular Simulation - Software Gromos. It allows you to easily set up, manage and analyze simulations in python.

https://rinikerlab.github.io/PyGromosTools/

MIT License

16 stars 14 forks source link

Addresses issue #293 #294

Closed LaurianeJD closed 2 years ago

LaurianeJD commented 2 years ago

Description

correct typo in setup.py
modify installation procedure in README.md
fix minimal example Question: emin_gromos_system, jobID = emin didn't return a tuple, is that a bug? conda develop seems deprecated -> use pip instead

pultar commented 2 years ago

Looks good to me. Not sure why emin not always returns a jobID but I guess it makes sense for local submission. What do you think @MTLehner ?

MTLehner commented 2 years ago

Looks good to me. Not sure why emin not always returns a jobID but I guess it makes sense for local submission. What do you think @MTLehner ?

this was a change in the last release. It does not return the jobID anymore. It's always only a gromos_sytsem. And the JobID is saved as an attribute

codecov[bot] commented 2 years ago

Codecov Report

Merging #294 (554368c) into main (a21ab63) will not change coverage. The diff coverage is n/a.

@@           Coverage Diff           @@
##             main     #294   +/-   ##
=======================================
  Coverage   54.38%   54.38%           
=======================================
  Files          93       93           
  Lines       14355    14355           
=======================================
  Hits         7807     7807           
  Misses       6548     6548

Flag	Coverage Δ
unittests	`54.38% <ø> (ø)`

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Impacted Files	Coverage Δ
pygromos/files/gromos_system/gromos_system.py	`68.97% <ø> (ø)`

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pultar commented 2 years ago

@MTLehner we addressed your concerns vis-a-vis conda develop. however, since we both cannot install pygromos with this command, we also added the option to install with pip as a back up for users.

also, @LaurianeJD found an outdated comment in Gromos_System which is now fixed.

Could you please double check the changes?

LaurianeJD commented 2 years ago

The INSTALL.md file was updated to contain conda_env.yaml name with the correct extension. The other files that were changed are probably auto-generated by sphinx according to @pultar. Do we need to rebuild documentation @MTLehner ?