Use cftime instead of netcdftime #3016

ocefpaf · 2018-05-11T17:23:25Z

This is pending a new cf_units release.

stickler-ci · 2018-05-11T17:23:53Z

lib/iris/tests/test_pp_module.py

@@ -176,7 +176,7 @@ def test_lbproc_access(self):
        self.assertEqual(warn.call_count, 3)

    def test_t1_t2_access(self):
-        self.assertEqual(self.r[0].t1.timetuple(), netcdftime.datetime(1994, 12, 1, 0, 0).timetuple())
+        self.assertEqual(self.r[0].t1.timetuple(), cftime.datetime(1994, 12, 1, 0, 0).timetuple())


E501 line too long (98 > 79 characters)

@ocefpaf Just need to clip this line, thanks

bjlittle · 2018-05-14T08:58:23Z

requirements/core.txt

@@ -6,6 +6,7 @@
 cartopy
 matplotlib<1.9
 netcdf4
+cftime


@ocefpaf We're keeping these is alphabetical order, so could you move this to be after cartopy instead, thanks.

I'm looking at the fixes we need to cut cf_units 2.0, but once that is done, cftime will be pulled in by cf_units, but let's keep it as an explicit dependency here in order to keep things moving along

bjlittle · 2018-05-14T13:07:52Z

👍 Nice one, thanks @ocefpaf ... I'll wait for travis-ci to do it's thing before merging.

ocefpaf · 2018-05-14T13:15:37Z

I'll wait for travis-ci to do it's thing before merging.

I would wait for the next cf_units first. (Also, we are working on a stable release for cftime that should be out soon.)

ocefpaf · 2018-05-14T13:17:54Z

requirements/core.txt

@@ -4,10 +4,11 @@
 # Without these, iris won't even import.

 cartopy
+cf_units>=1.2


@bjlittle this needs to be cf_units >=2.

PS: I tested with a git install of latest cf_units and we still have some failures to fix here too.

Yup, I've raised an issue on cf_units, see SciTools/cf-units#97, I'm working on that now 😉

What is it that means we need to pin this? Seems like it is causing us a bit of an impasse (the travis tests are currently failing on master) that I'd love to be able to resolve quickly by merging this without the cf_units release.

I guess that with your new tests this can be either 1 or 2, right?

pelson

Could do with a rebase. Happy in principle though.

pelson · 2018-05-16T11:42:22Z

requirements/core.txt

@@ -4,10 +4,11 @@
 # Without these, iris won't even import.

 cartopy
+cf_units>=1.2


What is it that means we need to pin this? Seems like it is causing us a bit of an impasse (the travis tests are currently failing on master) that I'd love to be able to resolve quickly by merging this without the cf_units release.

ocefpaf · 2018-05-22T18:57:47Z

lib/iris/tests/results/netcdf/int64_data_netcdf3.cml

@@ -6,6 +6,6 @@
    </attributes>
    <coords/>
    <cellMethods/>
-    <data checksum="0xecbb4b55" dtype="int32" shape="(2, 2)"/>
+    <data checksum="0xecbb4b55" dtype="int32" mask_checksum="no-masked-elements" shape="(2, 2)"/>


I guess that this change is needed due to Unidata/netcdf4-python#787

ocefpaf · 2018-05-22T19:01:33Z

Only two failures remain:

======================================================================
FAIL: test_period_of_interest (iris.tests.test_nimrod.TestLoad)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/travis/miniconda/envs/test-environment/lib/python3.6/site-packages/scitools_iris-2.1.0.dev0-py3.6.egg/iris/tests/test_nimrod.py", line 107, in test_period_of_interest
    self.assertCML(cube, ("nimrod", "period_of_interest.cml"))
  File "/home/travis/miniconda/envs/test-environment/lib/python3.6/site-packages/scitools_iris-2.1.0.dev0-py3.6.egg/iris/tests/__init__.py", line 406, in assertCML
    self._check_same(xml, reference_path)
  File "/home/travis/miniconda/envs/test-environment/lib/python3.6/site-packages/scitools_iris-2.1.0.dev0-py3.6.egg/iris/tests/__init__.py", line 496, in _check_same
    type_comparison_name)
  File "/home/travis/miniconda/envs/test-environment/lib/python3.6/site-packages/scitools_iris-2.1.0.dev0-py3.6.egg/iris/tests/__init__.py", line 235, in _assert_str_same
    self.fail("%s do not match: %s\n%s" % (type_comparison_name, reference_filename, diff))
AssertionError: CML do not match: /home/travis/miniconda/envs/test-environment/lib/python3.6/site-packages/scitools_iris-2.1.0.dev0-py3.6.egg/iris/tests/results/nimrod/period_of_interest.cml
--- Reference
+++ Test result
@@ -6 +6 @@
-        <dimCoord bounds="[[379973.0, 379974.0]]" id="cb784457" points="[379974.0]" shape="(1,)" standard_name="time" units="Unit('hours since 1970-01-01 00:00:00', calendar='standard')" value_type="float64"/>
+        <dimCoord bounds="[[379973.0, 379974.0]]" id="cb784457" points="[379974.0]" shape="(1,)" standard_name="time" units="Unit('hours since 1970-01-01 00:00:00', calendar='gregorian')" value_type="float64"/>
======================================================================
FAIL: test_repr_pass_1 (iris.tests.test_unit.TestStringify)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/travis/miniconda/envs/test-environment/lib/python3.6/site-packages/scitools_iris-2.1.0.dev0-py3.6.egg/iris/tests/test_unit.py", line 502, in test_repr_pass_1
    self.assertEqual(repr(u), "Unit('hours since 2007-01-15 12:06:00', calendar='standard')")
AssertionError: "Unit('hours since 2007-01-15 12:06:00', calendar='gregorian')" != "Unit('hours since 2007-01-15 12:06:00', calendar='standard')"
- Unit('hours since 2007-01-15 12:06:00', calendar='gregorian')
?                                                   ^^^^^^^
+ Unit('hours since 2007-01-15 12:06:00', calendar='standard')
?                                                   ^^  ++++

Should I updated those 'standard' calendars to 'gregorian'?

pelson · 2018-05-23T09:04:04Z

Could we add a what's new to give users a heads up about the change? I've done a similar thing in https://github.com/SciTools/iris/pull/3023/files#diff-4edce611793e498bf2483d76b404e733.

pelson · 2018-05-23T09:04:45Z

@ocefpaf - let's try to separate the cf_units from the cftime updates. #3023 relates for cf_units.

stickler-ci · 2018-05-23T13:35:20Z

lib/iris/tests/test_unit.py

@@ -499,7 +499,7 @@ def test_repr_pass_0(self):
    def test_repr_pass_1(self):
        u = Unit("hours since 2007-01-15 12:06:00", calendar=unit.CALENDAR_STANDARD)
        #self.assertEqual(repr(u), "Unit('hour since 2007-01-15 12:06:00.00000000 UTC', calendar='standard')")
-        self.assertEqual(repr(u), "Unit('hours since 2007-01-15 12:06:00', calendar='standard')")
+        self.assertEqual(repr(u), "Unit('hours since 2007-01-15 12:06:00', calendar='gregorian')")


E501 line too long (98 > 79 characters)

ocefpaf · 2018-05-23T13:41:57Z

@ocefpaf - let's try to separate the cf_units from the cftime updates. #3023 relates for cf_units.

I'll work on this later today. (I'll be in meeting all morning 😒)

pelson · 2018-05-23T13:42:49Z

No worries. Would you mind rebasing when you're out of that meeting? 😄

ocefpaf · 2018-05-23T23:31:41Z

lib/iris/tests/test_pandas.py

@@ -31,6 +31,11 @@
 import netCDF4
 import numpy as np

+# TODO Remove this if statement as we move to cftime


Moved this here to make it easier to remove it later.

ocefpaf · 2018-05-23T23:34:10Z

requirements/core.txt

 cftime
+dask>=0.17.1
+matplotlib<1.9
+netcdf4<1.4


All the dependencies are now in alphabetical order and kept netcdf4<1.4 to avoid putting the netcdf4>=1.4 fixes in the same PR.

I have another PR ready once this is merged that should get all the tests, but those depending on nc-time-axis, to pass.

ocefpaf · 2018-05-24T12:20:58Z

@pelson everything should pass with the latest nc-time-axis.

pelson

LGTM. Looks like we are blocked on another dependency though... 😞

The entanglement is real. 😄

pelson · 2018-05-24T13:12:07Z

lib/iris/tests/test_pandas.py

 import numpy as np

+# TODO Remove this if statement as we move to cftime
+if cf_units.__version__ > '1':


Is this necessary? Do you expect the tests to be passing with netcdftime still?

Is this necessary? Do you expect the tests to be passing with netcdftime still?

Probably not. Let me remove that...

bjlittle · 2018-05-31T11:56:24Z

Needs SciTools/nc-time-axis#34

pelson · 2018-06-01T07:49:31Z

Should now be unblocked.

ocefpaf · 2018-06-01T11:10:55Z

Should now be unblocked.

I hope I did not messed up the rebase 😬

bjlittle · 2018-06-01T11:50:08Z

Bingo!

Awesome, thanks @ocefpaf 👍

@corinnebosley

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(SciTools#3156) * Add integration graphics tests for pcolormesh with 2d coords (SciTools#3149) * Vector plots 4 (SciTools#3158) * Fix contig_ tolerance kwarg bug (SciTools#3162) * Add simple lazy aggregations * Lazy SUM and COUNT, tests improved * Add tests for MAX and MIN * Update tests for STD_DEV * Use NetCDF variable's chunks on load (SciTools#3131) Preserve NetCDF chunks on dataset load * Iteration and less duplication * Attempt to fix Matplotlib issue by resticting to 2.x * Non-test review actions * Make COUNT tests truer unit tests * Convert MAX and MIN tests to truer unit tests * Convert COUNT and SUM agg tests to truer unit tests * Tests for new _lazy_data function * Fix for netCDF4 1.4 behaviour change. (SciTools#3177) * Improve gracefully filling warning (SciTools#3171) * Realise that running the tests is simpler than I thought * Make Gracefully warning only appear when filling is required * Add tests of warnings * Get rid of install changes, they are in SciTools#3170 * Update after review * Add whatsnew entry * Minor clarification to entry via a little more punctuation * Revert nc vars masking fix (temporarily). (SciTools#3178) * fix for pandas column object bug (SciTools#3176) * turn columns object into pandas array, plus test included cml this time * made things the way pandas like it; bambooish * regenerated cml to match output * Update module headers and installation instructions (SciTools#3170) * Update module headers and installation instructions * Realise that running the tests is simpler than I thought * Update install instructions for developers * Update INSTALL to be consistent * Correct some failing tests * Update tests.rst (SciTools#3082) Added one line on how to test. This is mentioned in the Iris Check List in pulls.rst list, but would be good to have it here as well (useful for new contributors like me). * Add link to developer guide. (SciTools#3093) * Combine identical test routines for pcolor + pcolormesh. * Test 'contiguity_tolerance' use in iris.plot.pcolor and pcolormesh. * Unpin dask * Handle printing bounds of long time interval coords (SciTools#3140) * Handle printing time bounds * Whatsnew, whitespace fix for test result * iris.util.reverse on cubes (SciTools#3155) * make cube reversing official * review: test conventions, etc. * review: enable coord specification * add whatsnew * review: AssertRaises --> AssertRaisesRegexp * cube error handling * Improved Aux factory error handling: better message, delivered earlier (SciTools#3182) * Tests for expected behaviour * Raise error if aux factory relies on a coordinate external to cube * Include coordinate name in error message * Don't check whether dependencies that are "None" are in the coords. * Review changes: check cube name in error and variable rename * Truncated variable for flake8 * Correct cube collapse code * Provide info on pp-field indices in the file for structured um loads. (SciTools#2977) * Field locations for structured um loads. * Remove unused import. * Fix test for new implementation. * Added whatsnew. * Review changes. * simplify dev guide * Integration test for iris.plot.contour with 2d coords. (SciTools#3189) * Integration test for iris.plot.contour with 2d coords. * Review changes. * pinned numpy to not 1.15.2 in core requirements * Public contiguity checking (SciTools#3144) :champagne: :1st_place_medal: for sticking with it @corinnebosley * Populate whatsnew 2.2 (SciTools#3192) * started adding entries to whatsnew * more updates to whatsnew * first complete draft of 2.2 whatsnew * some small corrections * made corrections suggested in review * Update version str * Update CF standard name table to v59 * Fix docstring re structured text warnings (SciTools#3073) (SciTools#3197) * updated version string to 2.3.0dev0 * add contact options to README removed gitter from contact list * Add stash mapping changes to v2.1.0 changelog replaced list with link of stash mappings * expanded name of dev group * added an n for better flow * Fix broken link to dask docs (SciTools#3204)

stickler-ci reviewed May 11, 2018

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bjlittle reviewed May 14, 2018

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bjlittle self-assigned this May 14, 2018

bjlittle mentioned this pull request May 14, 2018

Add netcdftime as a dependency #3014

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bjlittle added the Release: Minor label May 14, 2018

ocefpaf commented May 14, 2018

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bjlittle added the Status: Blocked label May 14, 2018

pelson reviewed May 21, 2018

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pelson mentioned this pull request May 21, 2018

Updated tests for cf_units 2 #3023

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ocefpaf force-pushed the use_cftime branch 2 times, most recently from 42ea83f to 829dbbf Compare May 22, 2018 18:25

ocefpaf commented May 22, 2018

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ocefpaf force-pushed the use_cftime branch from 2ce3bbe to 6768f0f Compare May 23, 2018 13:34

stickler-ci reviewed May 23, 2018

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pelson removed the Status: Blocked label May 23, 2018

ocefpaf added 5 commits May 23, 2018 17:57

use cftime instead of netcdftime

930c6cd

fix the docs too

4629f21

fix license year

aa9c249

review actions

791f741

simplify test_pandas

e34942f

ocefpaf force-pushed the use_cftime branch from 6768f0f to e34942f Compare May 23, 2018 23:29

ocefpaf commented May 23, 2018

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what's new

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pelson approved these changes May 24, 2018

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remove cf_units check

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This was referenced May 28, 2018

New release SciTools/nc-time-axis#35

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Remove netcdf pin, and iris-grib dependency. conda-forge/iris-feedstock#29

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Unpin netcdf4 #3031

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bjlittle added the Status: Blocked label May 31, 2018

pelson removed the Status: Blocked label Jun 1, 2018

Merge branch 'master' into use_cftime

1a39a41

ocefpaf force-pushed the use_cftime branch from 4deeebe to 1a39a41 Compare June 1, 2018 11:29

bjlittle merged commit 243bb31 into SciTools:master Jun 1, 2018

ocefpaf deleted the use_cftime branch June 1, 2018 12:35

QuLogic added this to the v2.1.0 milestone Jun 2, 2018

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Use cftime instead of netcdftime #3016

Use cftime instead of netcdftime #3016

ocefpaf commented May 11, 2018

stickler-ci May 11, 2018

bjlittle May 14, 2018

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Use cftime instead of netcdftime #3016

Use cftime instead of netcdftime #3016

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