Enable duecredit for magdir by mtb-za · Pull Request #293 · fatiando/fatiando

mtb-za · 2016-07-08T15:09:18Z

Fixes #222 and test for general rollout of #292

Adds the ability to easily get the citation of a function that was used.

To test:

Install duecredit: pip install duecredit

(This should be doable without installing it globally, but that is not working
for me. I may be missing something here with importing the module, because
this is what our_duecredit.py is supposed to enable, if I understand their
docs correctly.)

Then, either:

Call the script with python -m duecredit gravmag_magdir_dipolemagdir.py.

OR

Set an environment variable: DUECREDIT_ENABLE=yes.
Run python cookbook\gravmag_magdir_dipolemagdir.py.

Any output from the script will be shown first, followed by something like:

DueCredit Report:
- Estimates total mag. dir. of approx. spherical bodies /
fatiando.gravmag.magdir:DipoleMagDir (v 0.4-21-gcb9ce97-dirty) [1]
- Scientific tools library / numpy (v 1.10.4) [2]

1 package cited
0 modules cited
1 function cited

References
----------

[1] Oliveira, V.C. et al., 2015. Estimation of the total magnetization direction
of approximately spherical bodies. Nonlin. Processes Geophys., 22(2),
pp.215-232.

Checklist:

Make tests for new code (at least 80% coverage)
Create/update docstrings
Include relevant equations and citations in docstrings
Docstrings follow the style conventions
Code follows PEP8 style conventions
Code and docs have been spellchecked
Include new dependencies in doc/install.rst, requirements.txt, environment.yml, ci/requirements-conda.txt and ci/requirements-pip.txt.
Documentation builds properly (run cd doc; make locally)
Changelog entry (leave for last to avoid conflicts)

Closes fatiando#222 Adds the ability to easily get the citation of a function that was used. To test: 1. Install duecredit: `pip install duecredit` Then, either: 1. Call the script with `python -m duecredit gravmag_magdir_dipolemagdir.py`. OR 1. Set an environment variable: `DUECREDIT_ENABLE=yes`. 2. Run `python cookbook\gravmag_magdir_dipolemagdir.py`. Either method should output something like the following on the command line. Any output from the script will be shown first. =========== DueCredit Report: - Estimates total mag. dir. of approx. spherical bodies / fatiando.gravmag.magdir:DipoleMagDir (v 0.4-21-gcb9ce97-dirty) [1] - Scientific tools library / numpy (v 1.10.4) [2] 1 package cited 0 modules cited 1 function cited References ---------- [1] Oliveira, V.C. et al., 2015. Estimation of the total magnetization direction of approximately spherical bodies. Nonlin. Processes Geophys., 22(2), pp.215-232.

leouieda · 2016-07-08T16:09:01Z

@mtb-za wow thanks for this! That was very quick.

From what I understood of their docs, you can only get the citation information if you have duecredit installed. The stub that we commit to our repository only does something if it can import duecredit [1]. If not, then it does nothing and doesn't bother us. That is a good thing because it doesn't add yet another dependency for us.

leouieda · 2016-07-08T16:11:28Z

While you're at it, could you also please add the following to the docstring of DipoleMagDir?

After the first line of the docstring add the line:

Implements the method of Oliveira Jr. et al. (2015).

and place the reference after Blakely:

Oliveira Jr., V. C., D. P. Sales, V. C. F. Barbosa, and L. Uieda (2015), 
Estimation of the total magnetization direction of approximately spherical bodies, 
Nonlin. Processes Geophys., 22(2), 215–232, doi:10.5194/npg-22-215-2015.

That way we are complete with #222

leouieda · 2016-07-08T16:14:06Z

One more thing, maybe we should rename our_duecredit.py to _our_duecredit.py so that it is hidden from users (this is only meant to be used internally). You can rename in git with git mv.

Added reference to the docstring as usual. Renamed duecredit's stub to be internal for us, not public facing.

Forgot to change the import after moving the duecredit stub.

mtb-za · 2016-07-12T10:32:54Z

This should be pretty much done now. If someone gives it the OK, I will edit the changelog and it can be merged.

leouieda · 2016-07-12T12:15:15Z

This is perfect, thanks Martin! You can add the changelog entry (please provide a link to the duecredit.org website there). Also, make sure the documentation builds properly after the change. Let me know when it's done and I'll merge this.

mtb-za · 2016-07-13T10:40:57Z

I am having trouble running make on this computer. The last commit fixed an error in the Travis build for the docs, so I think it is working now.

I will try and check this in the next couple days on a *nix machine. But if someone else can check before then, that would be good.

The output for the docs from Travis is here:

building [mo]: targets for 0 po files that are out of date
building [html]: targets for 122 source files that are out of date
updating environment: 135 added, 0 changed, 0 removed
reading sources... [100%] news                                                  
looking for now-outdated files... none found
pickling environment... done
checking consistency... done
preparing documents... done
writing output... [100%] news                                                   
generating indices... genindex py-modindex
highlighting module code... [100%] fatiando.gravmag.basin2d                     
writing additional pages... search
copying images... [100%] gallery/5-seismic/images/thumb/sphx_glr_convolutional_model_thumb.png
copying downloadable files... [100%] _static/cookbook/mesher_prismmesh.py       
copying static files... WARNING: favicon file u'favicon.ico' does not exist
done
copying extra files... done
dumping search index in English (code: en) ... done
dumping object inventory... done
build succeeded, 1 warning.
Embedding documentation hyperlinks in examples..
    processing: index.html
    processing: point_scatter.html
    processing: regular_grid.html
    processing: mayavi-exaggerate.html
    processing: seismic-wiggle.html
    processing: prism_mesh.html
    processing: prism_model.html
    processing: eqlayer_mag_transform.html
    processing: eqlayer_transform.html
    processing: euler_expanding_window.html
    processing: euler_moving_window.html
    processing: convolutional_model.html
    processing: srtomo_regularized.html
[done]

Build finished. The HTML pages are in _build/html.
make: Leaving directory `/home/travis/build/fatiando/fatiando/doc'
Finished building documentation

leouieda · 2016-07-13T13:38:14Z

  to subsections.
  (`PR 275 <https://github.com/fatiando/fatiando/pull/275>`__)
+* Added back-end support for decorators from duecredit
+  (`<https://github.com/duecredit/duecredit/>`__) to be added to methods. This


Please replace

duecredit (`<https://github.com/duecredit/duecredit/>`__)`

with

`duecredit <https://github.com/duecredit/duecredit/>`__

The syntax

text <target>__

in rst is equivalent to

[Text](target)

In Markdown. I get this wrong all the time. That's one of the reasons i added "build the docs locally" to the check list 😄

leouieda · 2016-07-13T13:40:44Z

Are you getting an error running make or don't have it installed?

Unicode support is one the reasons I really want to move to Python 3. That - in the page numbers of the reference always gets me.

mtb-za · 2016-07-13T14:46:00Z

It is installed, but is giving me an error when I run make all:

sh: C:\Program: No such file or directory
Makefile:30: recipe for target 'cookbook' failed
make: *** [cookbook] Error 127

This seems to be something related to a space in the path to sh, since the one it is using is C:\Program Files (x86)\Git\bin\sh.exe. cf: http://stackoverflow.com/questions/5999507/mingw-make-cant-handle-spaces-in-path
I will run it locally on a *nix machine tomorrow though, which should not have this issue. :)

Having trouble running make on this computer: it is complaining about the path to `sh`. The travis build suggests that there is a problem here though: building [html]: targets for 122 source files that are out of date updating environment: 135 added, 0 changed, 0 removed reading sources... [ 9%] api/gravmag.magdir Encoding error: 'ascii' codec can't decode byte 0xe2 in position 2846: ordinal not in range(128) The full traceback has been saved in /tmp/sphinx-err-5FAnuX.log, if you want to report the issue to the developers. make: *** [html] Error 1 make: Leaving directory `/home/travis/build/fatiando/fatiando/doc' Finished building documentation This commit should remove the only non-ASCII character that I introduced. Fixed syntax in changelog.rst file

leouieda · 2016-07-13T15:27:11Z

@mtb-za using command-line tools in Windows is always a pain. OK, I'll run it here as well and see if I catch anything.

leouieda · 2016-07-13T20:43:26Z

@mtb-za Travis seems to be OK and the docs build perfectly on my machine, so I'll merge this now.

Thanks again for doing this so quickly!

leouieda added the docs label Jul 8, 2016

leouieda added this to the 0.5 milestone Jul 8, 2016

mtb-za added 2 commits July 11, 2016 11:18

Changes to add reference to docstring proper

88652b2

Added reference to the docstring as usual. Renamed duecredit's stub to be internal for us, not public facing.

Fixed import

f006079

Forgot to change the import after moving the duecredit stub.

mtb-za mentioned this pull request Jul 12, 2016

Provide citation information for all functions/classes/modules #292

Open

Edited changelog

ad39566

leouieda reviewed Jul 13, 2016
View reviewed changes

mtb-za force-pushed the duecredit_testing branch from 036c028 to 1bb59fe Compare July 13, 2016 15:09

leouieda merged commit a57522f into fatiando:master Jul 13, 2016

mtb-za deleted the duecredit_testing branch July 14, 2016 08:19

mtb-za mentioned this pull request Jan 31, 2018

Adding duecredit decorators to all relevant functions #423

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Enable duecredit for magdir#293

Enable duecredit for magdir#293
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