taskSavannah Administration - Tasks: task #14571, Submission of Comparison Plotter...

 
 

task #14571: Submission of Comparison Plotter to visually evaluate ocean model simulations

Submitter:  Marco van Hulten <hulten>
Submitted:  Sat 24 Jun 2017 08:19:12 PM UTC
   
 
Should Start On:  Fri 23 Jun 2017 10:00:00 PM UTC Should be Finished on:  Mon 03 Jul 2017 10:00:00 PM UTC
Category:  Project Approval Priority:  * 5 - Normal
Status:  Done Privacy:  Public
Assigned to:  ineiev Open/Closed:  Closed
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Thu 13 Jul 2017 06:08:36 PM UTC, comment #14: 

Thank you, approving.

Ineiev <ineiev>
Site Administrator
Wed 12 Jul 2017 06:10:51 PM UTC, comment #13: 

I uploaded a new version of the library at http://klimato.org/pub/complot_v0.1_rc4.tar.gz (md5: 53ed78fc888fec03931078fc4f01ac0a).

I asked the the permissions, and most I got, to include it under free licence.  Copyright notices and licences are now included for all files in the package.

I wrote I would start a new repository, but the version history does not go as far back as I thought: it's fine like this, so I left the full hg history.  I also didn't remove any of the c2d_*.jnl front-end scripts, because they may be useful to users.

Marco van Hulten <hulten>
Tue 11 Jul 2017 05:02:40 PM UTC, comment #12: 

Getting confirmations from copyright holders is sufficient; for GNU  people, it would be impractical to repeat all those checks, even in a reduced form.

Ineiev <ineiev>
Site Administrator
Tue 11 Jul 2017 02:35:15 PM UTC, comment #11: 

Right now I am sending requests to copyright holders of auxiliary data that I want to use in the package.  I am asking them if I may include their data in this package under the CC-BY-SA-3.0 licence.  Is this enough, or do I need, for instance, send the confirmation e-mails to some address @gnu.org such that the rights can be easier checked if and when this is needed?

Marco van Hulten <hulten>
Thu 06 Jul 2017 06:17:45 PM UTC, comment #10: 

I'm not so familiar with the fair use doctrine to judge about using limited amount of data; I guess that the analogy with citation is not complete: the purpose of citation is to discuss the work, and in your case data would be used for your package.

When you change coordinates, you make a derivative work, and in order to make a derivative work, you need a permission from the copyright holder, so this doesn't resolve the issue.

In principle, plots are derivative works, too, but the data license seems to allow them implicitly ("please cite all relevant publications from researchers that made the measurements you use in your work", that is, they allow making works that cite those relevant publications).

I'd suggest asking -email is unavailable- (please be ready to wait for a long time, re-ask after no response and wait again...)---unless you can avoid those data completely.

Ineiev <ineiev>
Site Administrator
Thu 06 Jul 2017 09:11:23 AM UTC, comment #9: 

I did receive your message, and my message got probably submitted two times by accident.

I intend to work on this package and finish the submission next week.  There are two types of issues I want to address then:

1. A little bit of refactoring and making faster of the code.  I also intend to start a clean repository with a reduced number of scripts.  Over the last two years I have developed and used ComPlot only for my own purposes, which brings along a lot of silly commits, as well as a number of unnecessary c2d_*.jnl front-end scripts that I may add over time such that they are usable for more users.

2. On the copyright issues of the auxiliary data, I think I will be able to manage this.  I have the following questions and issues:

- The "Download Agreement" of the GEOTRACES data (which is the dataset I mostly rely on) <http://www.bodc.ac.uk/data/documents/nodb/325181/> states that one "shall not distribute downloaded data to any third party", so we cannot include it as a whole in the package.  Assuming that I do not get the right permissions of the copyright holders, I believe that there are two ways I can still use it; possibly this falls under "fair use".  One would be the use of a limited number of data points which would be akin to a citation.  In that case I should make clear not only the copyright but also that it is a small exemplary sample of the dataset.  The other would be providing the plots on the website and/or in the package (possibly linked from README.md) with a much larger number of data points.  In principle one could get a part of the dataset, to a smaller precision than the raw data, from reading the colour values, comparing those with the colour key bar.  However, as I have published those type of plots at big publishers before, without any request from copyright holders of the original data, I do not think that this is a problem.

- About the coordinate files, following basic copyright rules, you are probably right that they are copyrighted.  However, it would be truly bizarre if anyone makes an issue of treating them as if they are in the public domain.  Or it may fall under fair use.  I cannot give any legal argumentation.  If you really think there is an issue here, I could alter the coordinates: I only need to define a path that approximates the cruise transect.

Marco van Hulten <hulten>
Tue 04 Jul 2017 06:35:37 AM UTC, comment #8: 

You sent me two messages via Savannah interface; I replied to both via email; do you get my replies?

Ineiev <ineiev>
Site Administrator
Fri 30 Jun 2017 12:11:19 PM UTC, comment #7: 

I'm sorry, I'm not a scientist, and I'm not quite familiar with the situation.

> I would think a list of coordinates is not copyrightable.


A list of coordinates is a kind of map; maps are copyrightable.

> as I note in the README_data.md, it is a practice to use the data for any (scientific?) purpose


...until Elsevier sues Sci-Hub.

Ideally, you could generate sample data; if it's too hard, you could keep them out of your package and add references.

Ineiev <ineiev>
Site Administrator
Thu 29 Jun 2017 08:11:49 PM UTC, comment #6: 

I can add a copyright notice with licence for the logo (GPL-3+).

The data/coords_*.csv files are station coordinates.  Even though it is derived from datasets, I would think a list of coordinates is not copyrightable.

The other data files may be more difficult.  As I note in the README_data.md, it is a practice to use the data for any (scientific?) purpose.  It is a huge problem in science (at least in my field) that my colleges don't understand the importance of copyright.  I do not know how to handle this.

Maybe I can refer to a tar ball on my own website.  This would mean that already when running the demo (scripts/complot_demo.jnl) users would need to download this third-party data.  We could create the Savannah repository in such a way (so not non-free stuff in the repository but referring to those data), and figure out the best solution after that.

Marco van Hulten <hulten>
Thu 29 Jun 2017 07:45:33 AM UTC, comment #5: 

Thank you!

I still see two issues with lacking notices: logo.png and third-party files in data/. The former is minor, the latter to my mind is essential.


Ineiev <ineiev>
Site Administrator
Wed 28 Jun 2017 12:58:11 PM UTC, comment #4: 

I just uploaded a new version here:

http://klimato.org/pub/complot_v0.1_rc3.tar.gz

Marco van Hulten <hulten>
Tue 27 Jun 2017 07:24:03 AM UTC, comment #3: 

Thank you; unfortunately, some issues remained.

After reading data/README_data.md, the license of some files
in that directory remains unclear (and it would be desirable
to have explicit copyright notices for them).

scripts/put_colourbar.jnl scripts/put_text.jnl still lack notices.

Files like TODO.txt, tracers.txt and logo.png also should have
notices (for formats like images, such notices are usually put
in a README file in the same directory).

Having CC SA-BY in disjunction is fine; the requirement is to be free to use it under the FDL.

Ineiev <ineiev>
Site Administrator
Mon 26 Jun 2017 09:19:11 PM UTC, comment #2: 

I have added a licence header to all the *.jnl files.  It is not all the way at the top, because at least the description, usage and example should be visible to the user on the first page when using GO/HELP.  It is now consistently at the end of the comment header.

I changed the documentation licence for the README files to FDL 1.3 or higher.  Maybe I'll later add the CC SA-BY as a second licence.  I think that's okay, but I don't know if it would be useful.

I uploaded a new version of the package: http://klimato.org/pub/complot_v0.1_rc2.tar.gz

Marco van Hulten <hulten>
Mon 26 Jun 2017 12:51:49 PM UTC, comment #1: 

Thank you for submitting your package!

On Ferret licensing: first, OSD is not a license, it's a set of criteria for licenses, then, Ferret is a work of the US, it's public domain.  It's true that page you pointed at is confusing.

On notices in scripts: those scripts already contain description, author, requirements, and history; it doesn't seem to me that adding copyright and license notices would make the comments crucially longer.

On CC BY-SA: it's compatible with GPLv3, but not with further versions (and not with the FDL). Savannah's requirements for software is to be GPLv3+-compatible, and for manuals to be FDL1.3+-compatible.

Ineiev <ineiev>
Site Administrator
Sat 24 Jun 2017 08:19:12 PM UTC, original submission:  

A new project has been registered at Savannah
This project account will remain inactive until a site admin approves or discards the registration.


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While this item will be useful to track the registration process, approving or discarding the registration must be done using the specific Group Administration page, accessible only to site administrators, effectively logged as site administrators (superuser):



Registration Details


  • Name: Comparison Plotter to visually evaluate ocean model simulations
  • System Name:  complot
  • Type: non-GNU software and documentation
  • License: GNU General Public License v3 or later (The project is licensed under the GNU GPLv3 (or later).

Documentation is licensed under Creative Commons BY-SA.)




Description:

ComPlot is a collection of Ferret scripts, or package in short, that makes creating comparison plots in Ferret a bit more easy.  Ferret is a visualisation and analysis environment for oceanographers and meteorologists (ferret-vis in Debian).
The main purpose of ComPlot is to compare model results with data by plotting the data onto the model output as dots.  It is meant for oceanographers who want to compare ocean model output with observations.
It is programmed almost exclusively in the classic Ferret scripting language, but several standard Unix commands (like sed) are used to overcome limitations in the Ferret language.


Other Software Required:

- Ferret, Open Source Definition (sic), http://ferret.pmel.noaa.gov/Ferret/
- awk(1), sed(1), printf(1)


Other Comments:

The source files do not include a license header, because this would be somewhat of a problem.  This program exists of Ferret scripts that are typically first ran through GO/HELP script.jnl before issuing the actual command (without HELP and with other arguments).  Through this command the script is displayed through a pager.  In this way the user would be presented very often with the license header.  That is not useful.  As an alternative I have included a file called "HEADER" in the scripts directory, but I am open to other suggestions.


Tarball URL:

http://klimato.org/pub/complot_v0.1_rc1.tar.gz


Marco van Hulten <hulten>

 

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    Date Changed by Updated Field Previous Value => Replaced by
    2017-07-13 ineiev StatusIn Progress Done
        Open/ClosedOpen Closed
    2017-06-26 ineiev StatusNone In Progress
        Assigned toNone ineiev

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