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Alexander Pashuk edited this page Aug 27, 2017 · 1 revision

exe Bug

No notebooks was found for this paper

Reason 1. Page was not parsed or downloaded

R: we need to make changes in Exe to be notified and to fix parser.

Example, http://msystems.asm.org/content/2/2/e00191-16

Reason 2. Notebook is in archive.

R: we need to implement decompressor. S: there might be many archives, how can we easily check which of them contains notebook?

Example, ...

Reason 3. Shortened / With redirects Links.

Extension is not installed

?Double check this case

A data set with kinematic and ground reaction forces of human balance https://github.com/demotu/datasets/blob/master/PDS/notebooks/PostureDataset.ipynb

#!pip install version_information
%load_ext version_information

Not whole repository is cloned

R: tbd https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5534162/

https://github.com/ajouary/VR_Zebrafish/blob/master/Code/FishTracking.ipynb

Too big data / Timeout on download

https://dx.doi.org/10.12688/f1000research.9110.1

Didn't define Kernel / Old notebook format

http://nbviewer.jupyter.org/github/biocore/American-Gut/blob/master/ipynb/module2_v1.0.ipynb https://github.com/DCPROGS/SCALCS/blob/master/notebooks/Calculate_Popen_SynapticCurrent_alpha1GlyR_Flip.ipynb

Paper issues

No notebooks was found for this paper

Actually, no notebooks, indeed

Not direct link mentioned in the paper

Example, http://nbviewer.ipython.org/urls/raw.github.com/cschin/Write_A_Genome_Assembler_With_IPython/master/Write_An_Assembler.ipynb vs http://nbviewer.jupyter.org/github/cschin/Write_A_Genome_Assembler_With_IPython/blob/master/Write_An_Assembler.ipynb (in this case platform changed URL)

Dependencies issue

Library can't be installed automatically or installed with errors

Example, https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4670004/ automatic error log: ImportError: No module named 'py2cytoscape' Explanation: 'C core' lib of 'igraph', which is lib of 'py2cytoscape' can't be installed. Look for details in the full log.

Installation in Python should include validation

Correct declaration:

import pkgutil
import pip
if not pkgutil.find_loader("YourModuleName"):
   pip.main(['install', 'YourModuleName'])
import YourModuleName

It would be nice to note versions of the modules in the comments for preservation purposes or use '==' and pip freeze. For example,

pip install -I MySQL_python==1.2.2

https://stackoverflow.com/questions/5226311/installing-specific-package-versions-with-pip https://pip.pypa.io/en/stable/reference/pip_freeze/

Example of wrong declaration:

Installation in R should include validation

if("RMySQL" %in% rownames(installed.packages()) == FALSE) {
  install.packages("RMySQL")
}
library(RMySQL)

Outdated/deprecated mode

Not working / buggy library

Example, https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5395614/ https://github.com/BlueBrain/nat/blob/master/notebooks/ThalamusStereology.ipynb There is already issue: https://github.com/python-quantities/python-quantities/issues/128

Not working external API

Example, https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5395614/ https://github.com/christian-oreilly/NIP_FENS2016/blob/master/Part3-Ontologies.ipynb "KeyError: 'curie' Try to reproduce manually in Jupyter: in response really no 'curie' attribute"

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