Oliver Beckstein
Oliver Beckstein
AttributeDict does not support hasattr() but it should: ```python import gromacs ad = gromacs.utilities.AttributeDict(a=1, b=2) assert hasattr(ad, "a") assert not hasattr(ad, "x") # raises AttributeError from KeyError ``` Using ``in``...
JOSS paper
Write a short software paper on GromacsWrapper for [JOSS](http://joss.theoj.org/). - [Author instructions](https://joss.readthedocs.io/en/latest/submitting.html) – create a repo and then submit, ~1000 words, see examples - authors? - any contributor (name on...
As pointed out in PR #164 , the `edit_mdp()` function should use the MDP parser. This would also reduce extremely cryptic errors such as `gmx grompp: -include is not an...
Short software paper for submission to the [Journal of Open Source Software](http://joss.theoj.org/). The paper will be part of the GromacsWrapper repository; this appears to be the common pattern with other...
For the paper #147 it would be very beneficial to demonstrate that GromacsWrapper has been used elsewhere, especially in software or work that can be cited. Please add to this...
The docs should start with a small tutorial that shows how to use GromacsWrapper. This is also important for the paper #147 because they will review docs together with installability...
Add the analysis of converging fraction R_c from the paper S. Fan, B. I. Iorga, and O. Beckstein. Prediction of octanol-water partition coefficients for the SAMPL6- log P molecules using...
In the context of #201 it became apparent that the order of columns in a DataFrame can become important if care is not taken to access the correct columns via...
pymbar 4 has been released and pymbar 3 will not be maintained anymore (see Discussion #205 ). (Addendum: there now seems to be LTS for 3.x, see #205 ) alchemlyb...
From the tests ``` src/alchemlyb/tests/parsing/test_gmx.py: 61 warnings /home/runner/work/alchemlyb/alchemlyb/src/alchemlyb/parsing/gmx.py:210: FutureWarning: pandas.Float64Index is deprecated and will be removed from pandas in a future version. Use pandas.Index with the appropriate dtype instead. index=pd.Float64Index(times.values,...