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View Code? Open in Web Editor NEWThe [b]ermuda [i]nformation [t]riangle is a git-based tool for the management of code and data.
License: MIT License
The [b]ermuda [i]nformation [t]riangle is a git-based tool for the management of code and data.
License: MIT License
Backup raw option
(I've put paper issues in this issue tracker rather than leave comments on the review page as per the JOSS guidelines openjournals/joss-reviews#549)
[Line numbers refer to line breaks when opened in text editor]
l.21
In the increasing world of data
Change to something like: "With the increasing amount of data in the world..."
the mingles of data
Change to "mingling of data"
l.23
proficient tools have emerged along the last years
Change to: "emerged in recent years"
a unified tool is still in the need for many.
Change to something like: "...is still a need for many [researchers]"
l.24 - not quite clear what this means - could do with rewording.
l.26
remove first "for example"
eg.
-> e.g.
l.28
Project metadata and data can like this be kept in different instances.
Remove "like this" or reword to "can be kept like this in different instances"
l.30
Using rsync, it allows seamless multiple rsync calls for efficient synchronisations
Suggested change to "Using rsync bit allows seamless multiple rsync calls...".
l.32
Add punctuation somewhere to break long sentence, suggest comma after "HPC clusters,"
There are no references/citations in the paper and the .bib
file is blank (on master - it is not present in the tagged release version). Check that there are no references that can be added. (I assume this is OK if there is actually nothing to be cited, but maybe check with the JOSS editors)
auto comment on issue with commit and links to data
curl commands can be replaced by urllib2 calls in python 3
eg.:
Issue as part of JOSS review process (openjournals/joss-reviews#549).
bit
currently uses username and password for github.com or enterprise github authentication. This will likely fail for me because I've enabled two-factor authentication for my accounts. bit
should switch to personal access tokens which is also safer and allows to tweak permissions.
PYTHON_VERSION=sys.version_info[0]
if PYTHON_VERSION == 2:
import urllib2
elif PYTHON_VERSION == 3:
import urllib.request as urllib2
Issue as part of JOSS review process (openjournals/joss-reviews#549)
The bit --config
part of the Example usage section worked fine for me.
After this step I feel there should be some more information available on which folders need to be set up in owncloud and how the folder structure should look on the HPC. I cannot make the bit --start
work as I get the following output with nothing happening:
The bermuda information triangle works on the basis that all your projects are located in the same path and have a parent subpath in your local machine ie.
/file_system_a
|
'- data
|
'- projects
|
|- Company_A
| |
| |- CA_project_y
| |
| '- CA_project_x
| |
| |- results
| |- models
| |- scripts
| |- tmp
| |- slurm_logs
| '- wiki
|
'- Company_B
|
'- CB_project_n
Please expand the documentation here or allow bit to scaffold of a example structure.
Discovered through the JOSS review process over at: openjournals/joss-reviews#549
Downloaded and run setup.py as per the instructions in the README, but on running bit --config
in the first example given I get Traceback:
(The error is the same for bit --start
, i.e. TabError
)
$ bit --config
Traceback (most recent call last):
File "/home/dav/.local/bin/bit", line 11, in <module>
load_entry_point('bit==0.1.0', 'console_scripts', 'bit')()
File "/home/dav/anaconda3/lib/python3.5/site-packages/setuptools-27.2.0-py3.5.egg/pkg_resources/__init__.py", line 565, in load_entry_point
File "/home/dav/anaconda3/lib/python3.5/site-packages/setuptools-27.2.0-py3.5.egg/pkg_resources/__init__.py", line 2598, in load_entry_point
File "/home/dav/anaconda3/lib/python3.5/site-packages/setuptools-27.2.0-py3.5.egg/pkg_resources/__init__.py", line 2258, in load
File "/home/dav/anaconda3/lib/python3.5/site-packages/setuptools-27.2.0-py3.5.egg/pkg_resources/__init__.py", line 2264, in resolve
File "/home/dav/.local/lib/python3.5/site-packages/bit-0.1.0-py3.5.egg/bit/__init__.py", line 11, in <module>
import bit.config as config
File "/home/dav/.local/lib/python3.5/site-packages/bit-0.1.0-py3.5.egg/bit/config.py", line 112
return user_group
^
TabError: inconsistent use of tabs and spaces in indentation
can we replace git subprocess calls with a git python client:
https://github.com/mpg-age-bioinformatics/bit/blob/master/bit/git.py
Alternative:
archive module for generating tars and moving to respective archive folder.
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