hn2016_falwa release 0.6.1 + remarks on GitHub CLI and repo management

Great thanks to Christopher Polster who submitted a pull request to include Xarray interface to the QGField class of the local wave activity package. 😄 Please find here the release note for version 0.6.1.

I learned something new cleaning up the GitHub repo and I’m gonna write about it.

1. Untrack changes in the repo

There are actually two places which you can define the files to be ignored by git:

• .gitignore: I used to have this locally. Christopher suggested I include that in the GitHub repo for everyone’s use, and I think that’s a better idea.
• .git/info/exclude: This is indeed the right place to specify personal files to be excluded (not shared on the repo).

2. Skip unit test when optional packages are not installed

In test_xarrayinterface.py, I modified the xarray import statement:

try:
    import xarray as xr
except ImportError:
    pytest.skip("Optional package Xarray is not installed.", allow_module_level=True)

Given that xarray is an optional package, even if it is not installed, unit test for this package shall still run through.

3. Move fortran modules into the package directory

The .f90 files that contain the f2py modules were located in hn2016_falwa/ before. Now it is moved to hn2016_falwa/f90_modules/. The modifications done are:

(1) In setpy.py, the extension is changed to something like:

ext4 = Extension(name='interpolate_fields_direct_inv',
                 sources=['hn2016_falwa/f90_modules/interpolate_fields_dirinv.f90'],
                 f2py_options=['--quiet'])

The compiled modules of suffix .so will be located in hn2016_falwa/ with this change.

(2) Add in hn2016_falwa/__init__.py:

from .interpolate_fields import interpolate_fields
...
from .compute_lwa_and_barotropic_fluxes import compute_lwa_and_barotropic_fluxes

4. Fix the display of documentation on readthedocs.org

To debug, go to https://readthedocs.org/projects/hn2016-falwa/ and look at the Builds. Even if it passes, the document may not be compiled properly. Go to View raw and check out all warnings/errors to see if you have a clue.

The fix I have done are:

• In docs/source/conf.py:
  • Fix the appended sys path
  • Add modules/packages that causes the compilation to fail/raise warning to autodoc_mock_imports in
• Add docs/requirements.txt and specify all external packages imported (i.e. numpy, scipy, xarray) in the package

5. Compare commits using GitHub’s interface

To display the difference between two commits using GitHub’s web interface, put in the following URL:

https://github.com/csyhuang/hn2016_falwa/compare/OLD-COMMIT-HASH..NEW-COMMIT-HASH

6. To pull a branch which other forked your repo to local