PyTables Error-handling #1307

skoudoro · 2017-07-24T17:38:44Z

The goal of this PR is to resolve #1306.

@arokem @aarya22, can you have a look ?

Thanks !

aarya22 · 2017-07-24T18:19:00Z

Nice job on fixing the NameError.

arokem

LGTM overall. A couple of small questions regarding the error that gets raised.

arokem · 2017-07-24T18:18:14Z

dipy/io/peaks.py

-        odf = None
+    affine = pam.affine if hasattr(pam, 'affine') else affine
+    shm_coeff = pam.shm_coeff if hasattr(pam, 'shm_coeff') else None
+    odf = pam.odf if hasattr(pam, 'odf') else None


arokem · 2017-07-24T18:19:22Z

dipy/io/tests/test_io_peaks.py

+        pam.odf = np.zeros((10, 10, 10, sphere.vertices.shape[0]))
+
+        if not have_tables:
+            npt.assert_raises(TripWireError, save_peaks, fname, pam)


Looks like this might raise an ImportError?

save_peaks raise TripWireError , however _safe_save raise ImportError, so it is ok here. To be more consistent, I generate a TripWireError via a fake call in _safe_save now.

Is the error handling in _safe_save tested elsewhere? Would you mind writing a test, if it isn't?

👍 test added

arokem · 2017-07-24T18:20:04Z

dipy/io/peaks.py

-    else:
-        func_create_carray = f.create_carray
+    if not have_tables:
+        raise ImportError('PyTables is not installed')


Is there some way to get the TripWireError here (instead of an ImportError?)

coveralls · 2017-07-24T19:14:10Z

Coverage decreased (-0.01%) to 85.425% when pulling d3d017b on skoudoro:issue_1306_pytables into 08d8d90 on nipy:master.

coveralls · 2017-07-24T19:14:10Z

Coverage decreased (-0.01%) to 85.425% when pulling d3d017b on skoudoro:issue_1306_pytables into 08d8d90 on nipy:master.

codecov-io · 2017-07-24T19:14:30Z

Codecov Report

Merging #1307 into master will decrease coverage by 0.03%.
The diff coverage is 75.51%.

@@            Coverage Diff            @@
##           master   #1307      +/-   ##
=========================================
- Coverage   87.13%   87.1%   -0.04%     
=========================================
  Files         228     228              
  Lines       28800   28816      +16     
  Branches     3093    3092       -1     
=========================================
+ Hits        25094   25099       +5     
- Misses       3003    3014      +11     
  Partials      703     703

Impacted Files	Coverage Δ
dipy/io/dpy.py	`94.02% <100%> (+1.38%)`	⬆️
dipy/io/tests/test_io_peaks.py	`89.81% <73.68%> (-7.66%)`	⬇️
dipy/io/peaks.py	`89.79% <80%> (-2.66%)`	⬇️

Continue to review full report at Codecov.

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coveralls · 2017-07-24T20:21:12Z

Coverage decreased (-0.01%) to 85.425% when pulling d3d017b on skoudoro:issue_1306_pytables into 08d8d90 on nipy:master.

coveralls · 2017-07-24T20:21:12Z

Coverage decreased (-0.01%) to 85.425% when pulling d3d017b on skoudoro:issue_1306_pytables into 08d8d90 on nipy:master.

arokem

This is converging. Just one more question about the test.

arokem · 2017-07-24T23:03:52Z

dipy/io/peaks.py

-        func_create_carray = f.create_carray
+    if not have_tables:
+        # We generate a TripWireError via this call
+        _ = tables.any_attributes


👍

This seems fine to me.

arokem · 2017-07-24T23:05:44Z

dipy/io/tests/test_io_peaks.py

+        pam.odf = np.zeros((10, 10, 10, sphere.vertices.shape[0]))
+
+        if not have_tables:
+            npt.assert_raises(TripWireError, save_peaks, fname, pam)


Is the error handling in _safe_save tested elsewhere? Would you mind writing a test, if it isn't?

coveralls · 2017-07-25T14:59:13Z

Coverage decreased (-0.03%) to 85.405% when pulling 2b0af87 on skoudoro:issue_1306_pytables into 08d8d90 on nipy:master.

arokem · 2017-07-25T23:59:27Z

+1 for the merge from me. Anyone else want to take a look?

If not, I will merge in a couple of days.

PyTables Error-handling

skoudoro added 4 commits July 24, 2017 19:07

cryptic NameError correction for PyTables

55b73a3

PEP8 correction

ff7377a

replace class attribute tests : try/except -> hasattr

4bf2818

assign a role to the unused function parameter "affine"

998e58c

arokem reviewed Jul 24, 2017

View reviewed changes

To be more consistent, raise a TripWireError instead of ImportError

d3d017b

arokem reviewed Jul 24, 2017

View reviewed changes

adding a test to _safe_save function

2b0af87

arokem merged commit 0c10a43 into dipy:master Jul 30, 2017

skoudoro deleted the issue_1306_pytables branch July 31, 2017 13:35

ShreyasFadnavis pushed a commit to ShreyasFadnavis/dipy that referenced this pull request Sep 20, 2018

Merge pull request dipy#1307 from skoudoro/issue_1306_pytables

4222c6c

PyTables Error-handling

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PyTables Error-handling #1307

PyTables Error-handling #1307

skoudoro commented Jul 24, 2017

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PyTables Error-handling #1307

PyTables Error-handling #1307

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coveralls commented Jul 25, 2017 • edited

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