mpg-age-bioinformatics / bit Goto Github PK

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]

Suggested changes for style/grammar

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,"

References/bibliography

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.:

https://github.com/cytoscape/py2cytoscape/blob/0f7a6db76362f9c768e778528816c00f9978bcc2/py2cytoscape/cyrest/base.py#L80

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.

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

https://pypi.org/project/pyrsync2/
https://pypi.org/project/pyrsync/

can we replace git subprocess calls with a git python client:

https://github.com/mpg-age-bioinformatics/bit/blob/master/bit/git.py

Alternative:

https://gitpython.readthedocs.io/en/stable/tutorial.html

archive module for generating tars and moving to respective archive folder.