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Fix tests and update examples #36

Merged
merged 28 commits into from
Jun 8, 2018
Merged

Fix tests and update examples #36

merged 28 commits into from
Jun 8, 2018

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namurphy
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@namurphy namurphy commented Jun 7, 2018

I am going through and fixing tests, mostly in nei.py and eigenvaluetable.py. I am also about to make a few changes to how things are set up for Travis CI, so I'll need to keep this pull request open to make sure the test settings are correct.

namurphy added 5 commits June 7, 2018 12:56
@namurphy
Improve how _get_temperature_index treats boundary
e3b9319 
When EigenData2._get_temperature_index had an input that equals the
boundary, it had been issuing a warning.  I changed this so that the
warning is not issued when the temperature equals the minimum or
maximum temperature in the grid.  When I start a simulation at 10000
K, I no longer get a warning.
@namurphy
Removing comments no longer needed for Python 3
cbeaf8d
@namurphy
Update NEI example and formatting changes
362eced
@namurphy
Update EigenData2 docstring to pass doctest
de67972
@namurphy
Update example in NEI class
b543957
@namurphy namurphy added the Status: work in progress Pull requests that are currently being worked on label Jun 7, 2018
@pep8speaks
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pep8speaks commented Jun 7, 2018 •
edited
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Hello @namurphy! Thanks for updating the PR.

Line 281:5: E303 too many blank lines (2)

Line 91:18: E251 unexpected spaces around keyword / parameter equals
Line 91:20: E251 unexpected spaces around keyword / parameter equals
Line 92:20: E251 unexpected spaces around keyword / parameter equals
Line 92:22: E251 unexpected spaces around keyword / parameter equals
Line 383:80: E501 line too long (104 > 79 characters)
Line 454:20: E251 unexpected spaces around keyword / parameter equals
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Line 472:80: E501 line too long (85 > 79 characters)
Line 632:39: E225 missing whitespace around operator
Line 915:80: E501 line too long (82 > 79 characters)
Line 971:80: E501 line too long (89 > 79 characters)
Line 983:5: E303 too many blank lines (2)
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Line 1193:57: E225 missing whitespace around operator
Line 1194:9: E122 continuation line missing indentation or outdented
Line 1195:9: E122 continuation line missing indentation or outdented
Line 1199:1: E302 expected 2 blank lines, found 1
Line 1216:80: E501 line too long (82 > 79 characters)
Line 1222:9: E265 block comment should start with '# '
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Line 1233:9: E265 block comment should start with '# '
Line 1233:9: E303 too many blank lines (2)
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Line 1240:74: E231 missing whitespace after ','
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Line 1241:36: E231 missing whitespace after ','
Line 1241:62: E228 missing whitespace around modulo operator
Line 1241:80: E501 line too long (85 > 79 characters)
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Line 1248:70: E231 missing whitespace after ','
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Line 1252:63: E228 missing whitespace around modulo operator
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Line 1275:14: E225 missing whitespace around operator
Line 1281:13: E303 too many blank lines (2)
Line 1284:73: E231 missing whitespace after ','
Line 1284:80: E501 line too long (91 > 79 characters)
Line 1284:91: E502 the backslash is redundant between brackets
Line 1285:25: E127 continuation line over-indented for visual indent
Line 1295:76: E231 missing whitespace after ','
Line 1295:80: E501 line too long (103 > 79 characters)
Line 1313:1: W391 blank line at end of file

Line 8:1: E265 block comment should start with '# '
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Line 10:80: E501 line too long (80 > 79 characters)
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Line 17:1: E302 expected 2 blank lines, found 1
Line 23:54: E261 at least two spaces before inline comment
Line 23:80: E501 line too long (94 > 79 characters)
Line 30:25: E231 missing whitespace after ','
Line 52:1: E265 block comment should start with '# '
Line 53:1: E265 block comment should start with '# '
Line 79:1: E302 expected 2 blank lines, found 1
Line 134:17: E261 at least two spaces before inline comment
Line 135:17: E261 at least two spaces before inline comment
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Line 167:1: E265 block comment should start with '# '
Line 168:1: E302 expected 2 blank lines, found 1
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Line 64:28: E225 missing whitespace around operator
Line 87:80: E501 line too long (87 > 79 characters)
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Line 215:80: E501 line too long (91 > 79 characters)
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Line 13:1: E265 block comment should start with '# '
Line 50:23: E231 missing whitespace after ','
Line 54:9: E265 block comment should start with '# '
Line 54:80: E501 line too long (80 > 79 characters)
Line 55:61: E231 missing whitespace after ','
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Line 60:9: E265 block comment should start with '# '
Line 71:23: E231 missing whitespace after ','
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Line 75:80: E501 line too long (80 > 79 characters)
Line 76:61: E231 missing whitespace after ','
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Line 81:9: E265 block comment should start with '# '
Line 98:19: E231 missing whitespace after ','
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Line 101:8: E225 missing whitespace around operator
Line 105:1: E265 block comment should start with '# '
Line 107:1: E265 block comment should start with '# '
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  • In the file setup.py, following are the PEP8 issues :

Line 28:80: E501 line too long (89 > 79 characters)
Line 29:80: E501 line too long (107 > 79 characters)
Line 34:1: E402 module level import not at top of file
Line 35:1: E402 module level import not at top of file
Line 44:1: E402 module level import not at top of file
Line 46:1: E402 module level import not at top of file
Line 47:1: E402 module level import not at top of file
Line 153:80: E501 line too long (99 > 79 characters)
Line 165:1: E124 closing bracket does not match visual indentation

Comment last updated on June 08, 2018 at 00:33 Hours UTC

namurphy added 19 commits June 7, 2018 14:08
@namurphy
Update MANIFEST.in to include data files
98b2a6b 
Non-Python files need to be included in MANIFEST.in so that they are
kept track of while running `python setup.py install` and `python
setup.py test`.  This should recursively include everything in the
data directory.
@namurphy
Fix typo in dens_ratio
51a7801
@namurphy
Include all HDF5 files in setup.py
1886387
@namurphy
Remove packagename folder
1625eba 
This snuck back in when I pulled in the latest changes from the
astropy affiliated package template.
@namurphy
Update MANIFEST.in
516d4c0
@namurphy
Update requirements/requirements.txt
94309a3
@namurphy
Add h5py to requirements
f41d0ad 
For many of the packages in requirements/requirements.txt, the minimum
required version is probably more recent that is necessary for most of
these.  The exceptions are NumPy (which had some io changes as of
1.14) and Cython (which had some bugs for ~0.27 that showed up in
PlasmaPy).
@namurphy
Require Astropy version >= 3.0.0
fe5253d 
There have been problems with some NumPy and SciPy functions dropping
units from Quantity instances.  More recent versions of Astropy with
NumPy 1.13 or 1.14ish can handle these special functions better.  This
will probably be important since users may use NumPy and SciPy
functions in the functions that define density and temperature
evolution.
@namurphy
Handle nei/tests/coveragerc in setup.py
3fb1e13 
For some reason I keep getting an error that the coveragerc file has
not been found.  Here I'm handling the coveragerc file (for code test
coverage checking) in the same way as the HDF5 files.
@namurphy
Use travis_wait in tests
152e48e 
Tests for test_eigenvaluetable.py were timing out in Travis CI because
there was no screen output for 10 minutes.  This now allows 30 minutes
for no screen output.  We will probably want to shorten the tests
though, if possible.
@namurphy
Use PlasmaPy pycodestyle and pydocstyle settings
4a08be3
@namurphy
Parametrize test_element_range
0de31a3
@namurphy
Modify test_eigenvalue.py for Travis CI problems
ae026c2 
I temporarily commented out a test that depended on ChiantiPy because
it might be causes Travis CI to get stalled and time out.  I also
parametrized another test so that there would be more frequent screen
output, and the tests would be performed independently of each other.
@namurphy
Remove command to make Travis wait for screen output
2421c97
@namurphy
Set max_steps in all NEI tests
da79f56
@namurphy
Temporarily shorten NEI class tests
4541cfc
@namurphy
Modify error message in tests
c7303ca
@namurphy
Use int around atomic_numb in test_eigenvaluetable
833c3bb 
There was a bug in PlasmaPy where there was a TypeError raised when an
int was expected and a numpy.dtype of something like int64 was used.
@namurphy
Shorten eigenvaluetable tests because of Travis CI delays
11fcaf2
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codecov-io commented Jun 7, 2018 •
edited
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Codecov Report

❗ No coverage uploaded for pull request base (master@3f3b078). Click here to learn what that means.
The diff coverage is 60%.

Impacted file tree graph

@@            Coverage Diff            @@
##             master      #36   +/-   ##
=========================================
  Coverage          ?   67.95%           
=========================================
  Files             ?        6           
  Lines             ?     1267           
  Branches          ?        0           
=========================================
  Hits              ?      861           
  Misses            ?      406           
  Partials          ?        0
Impacted Files Coverage Δ
nei/data/read_save_ir_rate.py 1.28% <ø> (ø)
nei/classes/nei.py 69.44% <57.14%> (ø)
nei/classes/eigenvaluetable.py 90.56% <62.5%> (ø)

Continue to review full report at Codecov.

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namurphy added 2 commits June 7, 2018 19:41
@namurphy
Add assert statements to EigenData2 tests
7ba0044 
I also parametrized this to check a few different elements.  For some
reason, there have been some problems with Travis CI in creating
EigenData2 instances for heavier elements (e.g., Fe).
@namurphy
Add memory checks to .travis.yml
0062337
@namurphy
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namurphy commented Jun 8, 2018

I finally got the tests to pass again on Travis CI, though I'm still having some problems with test_nei_class.py and test_eigenvaluetable.py. The main problem is that the tests time out when the tests include heavier elements like iron. The heavier elements work fine when running the tests on my workstation locally, but for some reason take a lot longer on Travis. I had started to think it may have been memory limitations, but the data files are each ~5 MB so I'm not sure.

@namurphy
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namurphy commented Jun 8, 2018

Closes #32. Closes #29. <-- These statements tell GitHub to close those issues once the current issue is merged.

@namurphy namurphy changed the title Fix tests and update examples (do not merge yet) Fix tests and update examples Jun 8, 2018
@namurphy namurphy added Status: ready for review PRs that are ready for code review testing and removed Status: work in progress Pull requests that are currently being worked on labels Jun 8, 2018
@namurphy namurphy merged commit 8026539 into NEI-modeling:master Jun 8, 2018
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