Futures netcdf no unlimited #2838
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@corinnebosley on the chance it's passed you by, I've updated the approximate list of things that need to be done in this PR on #2385 😄 |
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@dkillick Thanks, this one feels a little bit confusing. That list is going to be essential, and much appreciated. |
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Notes to self:
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@dkillick Well I'm stumped. I really don't know why the test files don't match up, and the bits inside the @@s are just confusing and don't really tell me anything. They seem to be suggesting that I may have moved things around in the cdl files, so now they don't match up with where things sit in the files produced in testing, but I haven't so they should. I am annoyed. |
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...maybe it's telling me that the files that are produced in the test seem to have an extra line or two at the top, so that's why they don't match up to the cdl reference files. Let me dig into this a bit... |
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@dkillick I will have to hand this over to you to finish. Sorry. It's got all complicated as well. The initial test results ended up only failing a whole load of cdl match-up tests (see https://github.com/SciTools/iris/blob/master/lib/iris/tests/test_pp_cf.py#L86), so after a bit of looking we decided that this was not a problem as the variables have bits in which tell Iris what dimensions to put where, so the cubes should come out the same. Well they don't. The very next bit of the test I've pointed to shows that the resultant cubes don't actually match up to the reference cml files, so that sucks, and it means that something is broken. Good luck with this one! |
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corinnebosley
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Oct 25, 2017
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Good changes so far @dkillick
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Thanks @corinnebosley! BTW I found why all the CDL files were changing – take a look at what assertCDL does to CDL output... |
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@dkillick Well that's sneaky. Good spot. Have you got Travis testing a fix for that now? |
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@corinnebosley that's the hope... |
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djkirkham
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Oct 26, 2017
| states = [True, False] | ||
| exp_emsg = '' | ||
| for state in states: | ||
| with self.assertRaisesRegexp(AttributeError, exp_emsg): |
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You can just use self.assertRaises() if you don't want to specify a message.
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No, that means I forgot to add the error message...
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Does this need a What's New entry? |
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Yes it does, thanks @djkirkham. Will this PR never die? |
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Oct 26, 2017
| @@ -0,0 +1,8 @@ | |||
| * Deprecated FUTURE flag :attr:`iris.Future.netcdf_no_unlimited`. | |||
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| * Removed deprecated behaviour that automatically set the length of the outer netCDF variable to 'UNLIMITED' on save. | |||
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Perhaps change 'on save' to 'when saving in netCDF format' or something similar, to give more context.
djkirkham
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Oct 26, 2017
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| * Removed deprecated behaviour that automatically set the length of the outer netCDF variable to 'UNLIMITED' on save. | ||
| This change means that no cube dimension coordinates will be automatically saved as netCDF variables with 'UNLIMITED' length. | ||
| You can manually specify cube dimension coordinates to save with 'UNLIMITED' length. |
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I find using the second-person a bit jarring in a technical context. Can you change this to the passive voice? Something like 'Cube dimension coordinates to save with 'UNLIMITED' length can be manually specified.'
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Or 'It's possible to manually specify...'
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Oct 26, 2017
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I'm going to merge this as-is if the tests pass, and we can look at rewording the documentation at a later stage
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Nothing but timeouts here @djkirkham. |
rhattersley
reviewed
Oct 27, 2017
| self.netcdf_no_unlimited, self.clip_latitudes) | ||
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| deprecated_options = {'cell_datetime_objects': 'warning', | ||
| 'netcdf_no_unlimited': 'error', |
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The "error" behaviour doesn't seem right. 😕
If I've been a Good User and taken account of the deprecation warnings then my current, v1.9 compatible code should look something like:
with iris.Future(netcdf_no_unlimited=True):
# Do clever stuff with netCDF files
With the behaviour proposed in this PR, when I upgrade to v2.0 my code will get an error. 👎 The whole point of deprecations is to allow seemless migration.
Instead, I should get a deprecation warning about setting netcdf_no_unlimited=True. This lets my code continue to run, and I can remove the now unnecessary with block in my own good time.
If I've been a Bad User and ignored the deprecation warnings from v1.9, my code might just be:
# Do clever stuff with netCDF files that relies on the old behaviour
In which case my code is now broken. That's my own silly fault.
Or perhaps my code looks like:
with iris.Future(netcdf_no_unlimited=False):
# Do clever stuff with netCDF files that relies on the old behaviour
In which case I should now get an error because I'm trying to set the context to an unsupported value. Again, this is my own silly fault.
In other words, setting netcdf_no_unlimited to True should provoke a warning, but setting it to False should raise an error.
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Indeed it should. I notice that is what is documented in the what's new too...
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Discussed offline with @pelson: I'll put up a separate PR to change the behaviour of the Future object so that the 'error' behaviour is to raise an exception if the flag is set to False and raise a warning when it is set to True.
This was referenced Oct 27, 2017
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Oct 22, 2018
* Fix coord_comparison when coords are the same object * Added what's new items for SciTools#2730 and SciTools#2325. (SciTools#2852) * Added what's new items for SciTools#2730 and SciTools#2325. [skip ci] * Moved the bugfix docs to enhancement for the 3x speedup of area weights. [skip ci] * Add unit test * Add workaround * Add test of current dask behaviour * Ammended cube.var_name documentation. (SciTools#2874) Ammended cube.var_name documentation to refer to it as NetCDF. * Futures netcdf no unlimited (SciTools#2838) * switched boolean operator and altered docstring * raised error on future flag and tweaked functionality * small change to deprecation warning message * Code changes * remake cdl results * More CDL updates (cherry picked from commit 47272b3) * Review actions * Use default Dask scheduler settings (SciTools#2879) Disable dask.set_options call on _lazy_data import. * Fix doctest failing due to change in 'netcdf_promote' future behaviour (SciTools#2883) * Remove unneeded image repo url (SciTools#2885) * Updated 2.0 release notes. (SciTools#2884) * Add iris-grib as a testing dependency; Python 3 included. * Fix requirements for iris_grib>=0.12, assuming it will have eccodes + thus work with Python 3 * Made the iris extensions not install by default. * Reduced the number of processes used by default when testing. * Set the documentation build to use viridis as the default colormap (rather than Jet as we are using matplotlib 1 still). * Change behaviour of 'error' level (SciTools#2881) * Change behaviour of 'error' level * Change Future netcdf_no_unlimited tests * Fix tests testing the wrong thing * Dask processing options docs updates * Added some what's new information about SciTools#2435 and SciTools#2810. * Use the cube dimension order to determine the plot axes. * Small update to experimental-FF whatsnew statement (SciTools#2898) * Move some whatsnew items, remove spurious list * Move nc-no-unlim text to whatsnew * Fill value handling on save notes * Netcdf scalar cube loading bugfix Previously Iris used to simply ignore scalar cubes. * Corrected usage context in description of PointInCell regrid scheme. (SciTools#2735) * Re-worked setup.py to avoid the need for separate/non-standard build commands (SciTools#2891) Re-worked setup.py to avoid the need for separate/non-standard build commands. * Missing data whitepaper (SciTools#2906) * Ensure lon/lat return order is consistent throughout (SciTools#2238) * Updated to v46 of the CF standard-name table. (SciTools#2908) * Updated to v46 of the CF standard-name table. * Updated the area-type table to v6. * Use viridis cmap for doc images (SciTools#2909) * Stickler config (SciTools#2896) * Added a flake8 config. * Added a stickler-ci config. * Handled the recent update to conda-forge for testing, perhaps relating to GEOS update. (SciTools#2912) * Bumped master to the v2.1 stream. (SciTools#2910) * Stickler config (SciTools#2896) * Added a flake8 config. * Added a stickler-ci config. * Improved the way requirements are handled, ensuring that pip gets all the information it needs. (SciTools#2890) Improved the way requirements are handled, ensuring that pip gets all the information it needs. * Further docs refinement for v2.0.0 (SciTools#2916) Some minor documentation tweaks for v2.0.0 * Remove obsolete reference from Userguide. (SciTools#2915) * Reverse 2878 (SciTools#2926) * Remove dask issue workaround; wrap computed MaskedConstant as array * Reduce exception message for loading missing files. (SciTools#2925) * reduce error message * update file not found tests * clearer message * Allow missing value (SciTools#2892) * Allow missing_value as a user set attribute This allows the user to set missing_value as an attribute on a cube while ensuring that it is saved as local attribute in the netcdf file. * Added the what's new and updated the copyright years for SciTools#2892. * Fix some header dates. * Add note on using intersection (SciTools#2931) * CML changes for cf_units v1.2.0 (SciTools#2936) * CML changes for cf-units v1.2.0 * Add whatsnew entry * [DOC]: Update userguide note on intersection (SciTools#2933) * Update userguide note on intersection * Update with concrete boundary examples * Prepare master for v2.0.x branch (SciTools#2934) * Converted the contributions into the whatsnew. * Updated to a dev version string. * Tweaked what's new, bumped version string, and updated the MANIFEST for pypi. * Perserve dtype of source cube with area weighted regridder (SciTools#2203) Perserve dtype of source cube with area weighted regridder & add what's new * Update license headers to handle the merge of a PR from 2017 in 2018 (SciTools#2948) * DOC: lazy data docstring made clearer (SciTools#2947) * DOC: lazy data docstring made clearer * Clarify "view" * Remove gdal from 'all' to 'extensions' depedency group. * Remove gdal from 'all' to 'extensions' depedency group. * DOC: lazy data docstring made clearer (SciTools#2947) * DOC: lazy data docstring made clearer * Clarify "view" * No docs are better than wrong docs on dask * Add a general zenodo link to the readme. (SciTools#2955) * Improved the pip installability of scitools-iris. (SciTools#2956) * Release of iris v2.0.0 🎉 * Merge v2.0.x into master (SciTools#2957) * Tweaked what's new, bumped version string, and updated the MANIFEST for pypi. * Remove gdal from 'all' to 'extensions' depedency group. * DOC: lazy data docstring made clearer (SciTools#2947) * DOC: lazy data docstring made clearer * Clarify "view" * No docs are better than wrong docs on dask * Add a general zenodo link to the readme. (SciTools#2955) * Improved the pip installability of scitools-iris. (SciTools#2956) * Release of iris v2.0.0 🎉 * Move v2.0.x branch into development mode. * Fix the documentation building for latest version of sphinx. (SciTools#2958) * Remove FutureWarning from use of np.issubdtype(obj, np.str) (SciTools#2954) * Add cube co-realisation. (SciTools#2967) * Fix for changed API of cartopy.crs.Stereographic (SciTools#2971) * Fix for changed API of cartopy.crs.Stereographic; fixes tests.test_coordsystem. * License header fix. * remove site.cfg exclude from manifest.in (SciTools#2978) * Save calendar attribute for cube data (SciTools#2984) * Fix bug with aux coords with scalefactor/add_offset (SciTools#2975) Fix bug with aux coords with scalefactor/add_offset * Rename to correct package name * Fix imagehash hex_to_hash (SciTools#2989) * Fix imagehash hex_to_hash * expose hamming distance vector * fix idiff * update imagerepo * fix repo hashes (bjlittle) * fix repo hashed (scitools) * fix test_image_json * test_pearsonr: use compatible cubes for testing compatible cubes (SciTools#2960) Pearsonr test using compatible cubes * Use unittest.mock for Python 3 (SciTools#3003) * reflect new latitude guess_bounds behaviour (SciTools#3006) * Pin Dask to >=0.17.1 (SciTools#2965) * Fill a usability gap in iris.analysis.Trajectory (SciTools#2770) * Fill a usability hole in Trajectory * Remove iris.experimental.um module (SciTools#2781) * Remove iris.experimental.um module * Replace use of sphinx's status_iterator function, which has moved * Lazy unit conversions for cube and coord data. (SciTools#2964) * Gracefully handle long time intervals (SciTools#2354) Gracefully handle long time intervals (months & years) when plotting * Prevent creation of invalid CF variable names. (SciTools#3009) Prevent creation of invalid CF variable names. * Add stash check to name() (SciTools#2930) Try the STASH attribute when checking for possible names (as is already done in the summary method) * Attempts to fix docs-build error reporting. (SciTools#2983) Remove final semicolon to report docs-build error. * Phenomenon translation updates (SciTools#3011) * Netcdftime dep (SciTools#3017) Pin to netcdf4 1.3 or below while we await netdftime updates Correct deprecated pandas use in v0.23 * add 'axes' kwarg to _label when called from contourf * Replace iris.co_realise_cubes with CubeList.realise_data. (SciTools#3013) * Replace iris.co_realise_cubes with CubeList.realise_data. * Avoid exposing lazy-data functions in iris.cube and iris.coord modules. * Tidy lazy_data imports in cube + coords modules. * Amend var_name documentation (SciTools#3020) Amend documentation to be explicit that var_name is a netCDF quantity, not necessarily a CF one. * Updated tests for cf_units 2 (SciTools#3023) Updated tests for cf_units>=2 This change: * Removes the redundant ``iris/tests/test_unit.py`` tests. They are all migrated to cf_units. * Makes use of CALENDAR_GREGORIAN, rather than CALENDAR_STANDARD. These calendars are implemented as aliases in cf_units 2, and the "STANDARD" concept is not preserved/round-tripped. Added a what's new to help reduce possible impact for users. * Use ConfigParser for py>=3.2 (SciTools#3025) * WIP: Unpin mpl (SciTools#3019) * unpin mpl * Add _repr_html_ for Iris cubes (SciTools#2918) Add cube _repr_html_ functionality * Partial collapse of multi-dimensional coordinates (SciTools#3028) Adding support for partial collapse of multi-dimensional coordinates * Tidy up the root of the repository for v2.1 (SciTools#3034) A bunch of miscellaneous changes in preparation for the v2.1 release: * Move CONTRIBUTING.md to a .github/ folder. See also: https://help.github.com/articles/setting-guidelines-for-repository-contributors/ * Updated the .gitignore to reflect what gets produce in day-to-day iris development * Reduced the amount of redundancy in INSTALL. It now points to the requirements/ directory which is what we actually test. * Updated minimum dependencies in requirements (because that is all we test): * Numpy>=1.14 * Matplotlib>=2 * cf_units>=2 * Remove the CODING matrix item. (SciTools#3036) * Add Albers Equal Area Projection and some test as per SciTools#2496 (SciTools#2943) Add Albers Equal Area Projection and NetCDF rules to handle it * Improve the appeal of the landing pages (docs and README) (SciTools#3040) * Update the Iris README markdown to be consistent with other SciTools projects. * Gave the package a description (for pypi). * Minor spruce of the Iris docs layout to include the tagline and the forkme button * Use the correct pypi name for nc-time-axis. (SciTools#3039) * Use cftime instead of netcdftime (SciTools#3016) * use cftime instead of netcdftime * fix the docs too * fix license year * review actions * simplify test_pandas * what's new * remove cf_units check * Fixed the intermittent test in SciTools#3035. (SciTools#3037) * Fixed the intermittent test in SciTools#3035. The problem was that iris.util.format_array was stateful (via np.set_printoptions). * Fix stateful tests (SciTools#26) * Add dask-array as a requirement when pip installing. (SciTools#3033) * Unpin netcdf4 (SciTools#3031) * unpin netcdf4 * adapt for netcdf4 >=1.4 * fix userguide doctests * Metarelate updates in the UM 2 CF mapping (SciTools#3043) * Updated the README, and copied that over to the iris docs homepage. (SciTools#3045) * Added the what's new for iris 2.1 (SciTools#3044) Added the what's new for iris 2.1 * Updated the cf-standard names to v54. (SciTools#3046) Achieved with: $ wget http://cfconventions.org/Data/cf-standard-names/54/src/cf-standard-name-table.xml -O etc/cf-standard-name-table.xml ... --2018-06-02 06:32:17-- http://cfconventions.org/Data/cf-standard-names/54/src/cf-standard-name-table.xml ... * iris.quickplot: Ensure labels and plot use the same axes Allow iris.quickplot to accept an axes kwarg to which title and axes labels can be attached. This is done without using the matplotlib state machine. Closes SciTools#2946 * sticklering * Full-featured Mercator coord system (SciTools#3041) Add ``standard_parallel`` to the Mercator Coord System * Updated the branding and execution of Iris docs (SciTools#3050) * Updated the branding and execution of Iris This includes: * removing the "easy-to-use" statement in Iris' strapline. Let's let users be the judge of that. * improved the styling of the homepage, including re-instating the search bar. * Added a what's new for SciTools#3010. * Added a extlinks section for convenient linking to github issues with :issue:`number` and :pr:`number`. * Added a favicon for the docs. * Improve strapline style, content (SciTools#27) * Further improvements to Iris docs * Improved font (noto-sans) * Removed old CSS * Fixed a few what's new entries * [DOC] Iris Introduction updates (SciTools#3052) Update the introduction of Iris content. * Updated to v2.1.0. (SciTools#3051) * Move into development mode for v2.1.1 * Move into development mode for v2.2.0 * remove first 'and' from tagline to make it read easier * Notebook repr whatsnew update * remove first 'and' from tagline to make it read easier * minor requirements tidy * http -> https for copybutton.js (SciTools#3066) * Explain use of saver='string' in iris.save (SciTools#3062) * Fix reStructuredText warnings in documentation (SciTools#3069) * Add information about comparing STASH objects with strings (SciTools#3072) * Doc: Fallback to no syntax hightlighting without warning. (SciTools#3071) Fixes: iris/docs/iris/src/developers_guide/gitwash/development_workflow.rst:317: WARNING: Could not lex literal_block as "python". Highlighting skipped. http://www.sphinx-doc.org/en/stable/config.html#confval-highlight_language * Quick fix to get tests passing by pinning dask version (SciTools#3086) * ENH: Working zonal mean linear regridding for circular sources or with use of extrapolation (SciTools#3085) * Working zonal mean from circular/extrapolated source to target * MAINT: Refactor of zonal mean testing * MAINT: Documentation changes from review * Avoid pandas deprecation warning. (SciTools#3079) Avoid pandas deprecation warning. This also simplifies code by being explicit about usage of "base" and "values" for numpy and pandas objects, and removes legacy code that may no longer be valid. * Workaround for dask array copy bug (SciTools#3088) * add contact options to README * Add stash mapping changes to v2.1.0 changelog * Pin Dask for avoid 0.18.2 bug with masked arrays. * Tiny fix for dask, Python3 only? * Disable doctests for Python 2. * Ignore warnings and update array printouts. * Better way to disable Python2 doctests. * Support plotting 2D bounded coords * Add gridcell_angles and rotate_grid_vectors to iris.analysis.cartography, with tests: INCOMPLETE WIP * Roughly working, snapshotted with complex test plot code, to be reduced. * Small improvements. * First working quiver+streamplot. * Handle custom coords correctly * some words for docs, WIP probably * suggested tweaks and corrections * Update docs to included 2.2 versions (SciTools#3110) * Provide a test skipper for 2d coords WIP. (SciTools#3099) * Change version number (SciTools#3118) * re-added bounds definition for contiguity check, removed unnecessary test * Ensure Sphinx autodocs for grid_angles routines. * Codestyle fixes. * Whatsnew entries for 2d vector support. * Pin Dask to avoid 0.18.2 bug with masked arrays. (SciTools#3127) * Put orca_util routines in subpackage of iris.test.stock, to get existing iris.tests.unit.plot.test_2d_coords working. * Disable broken misused testcode in test_gridcell_angles. * Ditch test_gridcell_angles, none of it is functional. * Further style fixes. * Skip tests using iris-test-data, for Travis TEST_MINIMAL phases. * Codestyle fix (though this code obsolete anyway). * Fix unused imports. * Made-up test cube replaces use of iris-test-data. * Renamed keyword; improved docstring. * Change 'co' to 'coord' for clarity. * Review changes. * Update pp save rules to handle time means (SciTools#3132) * Vector plots 2 (SciTools#3120) * Small improvements; first sensible tests. * Enhanced testing; better checking and crs awareness in grid_angles routine. * Remove crud from test_gridcell_angles. * Use degree units for everything in _grid_angles. * Make assertArrayAllClose print details when it fails. * Rework and extend testing for gridcell_angles. * Fix assertArrayAllClose; remove debug code from test_gridcell_angles. * Remove obsolete assignments. * Remove obsolete code. * Small comment improvements. * Attempt to clarify docstrings of low-level routines. * More tests, and some functional fixes. * Codestyle fixes. * Review changes + fixes. * Avoid using sample data. * Temporary pin to avoid problems caused by Proj4 v5.1. (SciTools#3150) * Extending ORCA blockplotting (w/ tests) (SciTools#3135) * Tests for rotate_grid_vectors (SciTools#3148) * Tests for rotate_grid_vectors. * Small fix to assertArrayAllClose for values near 0. * Small tweaks. * Fix test method. * Fix 1 test for 'equal_nans' no longer the default. * Review changes. * Remove 'skip_2d' test decorator. (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)
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Closes #2835
WIP: This is only the first few steps of the change, more to come (with appropriate fixes).