Add glossary to documentation #3352
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max-sixty
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Sep 28, 2019
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Great—this is really helpful. Thanks @gwgundersen
I'm sure we'll go through some iteration on the exact language (I added a couple of comments), so all comments welcome. Let's merge our best effort fairly soon and continue iterating from there
doc/terminology.rst
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| **Coordinate:** A one-dimensional array that labels a dimension of another ``DataArray``. There are two types of coordinate arrays: *dimension coordinates* and *non-dimension coordinates* (see below). A coordinate named ``x`` can be retrieved from ``arr.coords[x]``. A ``DataArray`` can have more coordinates than dimensions because a single dimension can be assigned multiple coordinate arrays. However, only one coordinate array can be a assigned as a particular dimension's dimension coordinate array. As a consequence, ``len(arr.dims) <= len(arr.coords)`` in general. |
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non-dimensional coordinates can be multi-dimensional
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I thought "multi-dimensional coordinates" really just meant multiple one-dimensional coordinate arrays labeling the same dimension. I inferred that from this page. Is this what you mean or something else? Also, could you please show me an example? I've tried and failed to use assign_coords to add a multi-dimensional DataArray as a coordinate array.
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For example
In [8]: xr.DataArray(np.ones((2,3)), dims=['a','b'], coords=dict(c=(('a','b'), np.zeros((2,3)))))
Out[8]:
<xarray.DataArray (a: 2, b: 3)>
array([[1., 1., 1.],
[1., 1., 1.]])
Coordinates:
c (a, b) float64 0.0 0.0 0.0 0.0 0.0 0.0
Dimensions without coordinates: a, b
doc/terminology.rst
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| **Dimension / dimensions:** A *dimension* is a nonnegative number for the dimensionality of the underlying data, while an array's *dimensions* are a set of dimension names. The name of the ``i``-th dimension is ``arr.dims[i]``. If an array is created without dimensions, the default dimension names are ``dim_0``, ``dim_1``, and so forth. |
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I'm not sure about A *dimension* is a nonnegative number for the dimensionality —I think that's a good definition for dimensionality, but wouldn't think of a dimension as a number?
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I struggled with this because in math, a "dimension" is a number, but in common parlance and xarray, "dimension" is often used to refer to a dimension axis—or a locus in which all but one of the coordinates ("coordinates" in the math sense, not xarray sense) is fixed. I didn't want to define "coordinate" and "dimension" in the math sense and then re-define them, although I think that would be the clearest at the expense of brevity.
Anyway, how about this:
Dimension: In mathematics, the dimension of data is loosely the number of degrees of freedom for it. A dimension axis is a set of all points in which all but one of these degrees of freedom is fixed. We can think of each dimension axis as having a name, for example the "x dimension". In xarray, a
DataArray's dimensions are its named dimension axes, and the name of thei-th dimension isarr.dims[i]. If an array is created without dimensions, the default dimension names aredim_0,dim_1, and so forth.
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It might be worth borrowing the description from the netCDF data model documentation: https://www.unidata.ucar.edu/software/netcdf/docs/netcdf_data_model.html
Dimensions: describe the axes of the [DataArrays]. A dimension has a name and a length...
dcherian
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Sep 28, 2019
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This is epic.
Thanks, @gwgundersen. This is a great start. I've added a few comments but things are looking nice.
Other things we should add (but not required right now): alignment, broadcasting, merging, concatenating, combining
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Thanks for the feedback @max-sixty and @dcherian. I tried to incorporate your feedback and pushed some new changes. Here's a screenshot of the page. Happy to iterate more on this if needed. I do think getting this stuff right is really useful for new users.
Ah, these would be great to have. I've created #3355 so I/we remember. |
max-sixty
reviewed
Sep 29, 2019
max-sixty
reviewed
Sep 29, 2019
max-sixty
reviewed
Sep 29, 2019
max-sixty
reviewed
Sep 29, 2019
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Shall we merge now and take the other items as follow-ups? |
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Let's wait till tonight for other comments? Also we should push all the recent documentation work to stable |
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Since the current wording of the "Coordinate" definition seems to imply only one dimension, should the multidimensional coordinate issue that remains be cleared up here or in a follow-up PR? If it's a follow-up, I'd be glad to submit one for it. |
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Ok thanks for being so prompt! I'll merge now so all our excited contributors can chip in :) |
max-sixty
reviewed
Sep 30, 2019
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* upstream/master: Revisit # noqa annotations (pydata#3359) Fix codecov.io upload on Windows (pydata#3360) Add how do I ... section (pydata#3357) Add glossary to documentation (pydata#3352) Documentation improvements (pydata#3328) Remove `complex.nc` from built docs (pydata#3353) Fix DataArray.to_netcdf type annotation (pydata#3325)
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* upstream/master: Remove setting of universal wheels (pydata#3367) Revisit # noqa annotations (pydata#3359) Fix codecov.io upload on Windows (pydata#3360) Add how do I ... section (pydata#3357) Add glossary to documentation (pydata#3352) Documentation improvements (pydata#3328) Remove `complex.nc` from built docs (pydata#3353) Fix DataArray.to_netcdf type annotation (pydata#3325) CI test suites with pinned minimum dependencies (pydata#3346) Bugfix/plot accept coord dim (pydata#3345) CI environments overhaul (pydata#3340) Add hypothesis support to related projects (pydata#3335) More doc fixes (pydata#3333) Improve the documentation of swap_dims (pydata#3331) fix the doc names of the return value of swap_dims (pydata#3329)
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commit b0c336f Author: Maximilian Roos <[email protected]> Date: Mon Oct 21 04:52:36 2019 -0400 Whatsnew for #3419 (#3422) * pyupgrade --py36-plus * Update xarray/core/nputils.py Co-Authored-By: crusaderky <[email protected]> * Update xarray/core/parallel.py Co-Authored-By: crusaderky <[email protected]> * Update xarray/tests/test_cftime_offsets.py Co-Authored-By: crusaderky <[email protected]> * Update xarray/tests/test_cftime_offsets.py Co-Authored-By: crusaderky <[email protected]> * whatsnew commit 2984415 Author: Rhys Doyle <[email protected]> Date: Mon Oct 21 01:17:47 2019 +0100 Revert changes made in #3358 (#3411) * Revert #3358 * Revision * Code review * Merge from master * Obsolescence note commit 3c462b9 Author: Maximilian Roos <[email protected]> Date: Sun Oct 20 20:16:58 2019 -0400 Python3.6 idioms (#3419) * pyupgrade --py36-plus * Update xarray/core/nputils.py Co-Authored-By: crusaderky <[email protected]> * Update xarray/core/parallel.py Co-Authored-By: crusaderky <[email protected]> * Update xarray/tests/test_cftime_offsets.py Co-Authored-By: crusaderky <[email protected]> * Update xarray/tests/test_cftime_offsets.py Co-Authored-By: crusaderky <[email protected]> commit 9886e3c Author: crusaderky <[email protected]> Date: Sun Oct 20 23:42:36 2019 +0100 Temporarily mark pseudonetcdf-3.1 as incompatible (#3420) commit 0f7ab0e Author: Dan Nowacki <[email protected]> Date: Thu Oct 17 14:13:44 2019 -0700 Fix and add test for groupby_bins() isnan TypeError. (#3405) * Fix and add test for groupby_bins() isnan TypeError. * Better testing * black commit 6cd50cc Author: pmallas <[email protected]> Date: Thu Oct 17 10:15:47 2019 -0400 Update where docstring to make return value type more clear (#3408) * Update where docstring to make return value type more clear The where docstring was a little confusing to me. I misunderstood "Same type as caller' to mean the values in the xarray not the xarray itself. I think this small change will clean it up for most users. Thanks. * Update xarray/core/common.py Co-Authored-By: Maximilian Roos <[email protected]> commit 55b1ac0 Author: keewis <[email protected]> Date: Thu Oct 17 05:13:39 2019 +0200 tests for arrays with units (#3238) * create the empty test file * add tests for data array aggregation functions * include pint in the ci * ignore missing type annotations for pint * really skip the tests if pint is not available * remove the reason from the importorskip call * test that the dataarray constructor does not strip the unit * convert every unit stripped warning to an error * work around pint not implementing np.allclose yet * remove the now unnecessary filterwarnings decorator * xfail all tests that depend on pint having a __array_function__ * treat nans as equal * implement tests for simple arithmetic operations * use param's id argument to assign readable names * add tests for sel() and isel() * add more readable names for the unary arithmetics * xfail every test that is not yet xfailing These don't pass because the constructor raises a unit stripped warning - fixed in pint#764. * only xfail if pint is not the current development version This is test is not really reliable, but sufficient for now. * always use lists instead of tuples for indexing * add tests for loc and squeeze * black * add names and xfail marks to the parameters * add tests for interp and interp_like * implement tests for reindex * remove the xfail marks where it is not clear yet that pint is to blame * add tests for reindex_like * don't pass the new DataArray to a kwarg * xfail if not on pint dev * refactor the tests * add tests for univariate and bivariate ufuncs * black * xfail aggregation only if pint does not implement __array_function__ yet * remove the global filterwarnings mark apparently, this caused the tests to change behavior, resulting in different errors, or causing tests to pass that should actually fail. * add a test case for the repr * create a pytest mark that explicitly requires pint's __array_function__ * also check the string representation in addition to the repr * add helpers for creating method tests * check that simple aggregation methods work * use format() instead of format strings * make sure the repr of method calls is different from functions * merge the two aggregation tests * explicitly check whether pint supports __array_function__ relying on versions is somewhat fragile. * provide a fallback for the new base quantity * check that no warning is raised for both with and without coords * also check that the repr works both with and without coords * wrap all aggregation function calls * xfail every call that fails because of something outside xarray * xfail tests related to dimension coordinates and indexes * use the dimensions from the original array * allow passing arguments to the method on call * add tests for comparisons * add tests for detecting, filling and dropping missing values * mark the missing value tests as requiring pint to support duck arrays * add tests for isin, where and interpolate_na * reformat unit ids and add a test parameter for compatible units * remove an unnecessary xfail * add tests for the top-level replication functions (*_like) * check for whatever pint does with *_like functions * add tests for combine_first * xfail the bivariate ufunc tests * xfail the call to np.median * move the top-level function tests out of the DataArray namespace class * add cumsum and cumprod to the list of aggregation functions * add tests for the numpy methods * check for equal units directly after checking the magnitude * add tests for content manipulation methods * add tests for comparing DataArrays (equals, indentical) * add a test for broadcast_equals * refactor the comparison operation tests * rewrite the strip, attach and assert_equal functions and add extract * preserve multiindex in strip and attach * attach the unit from element "data" as fallback * fix some small typos * compare QuantityScalar and QuantitySequence based on their values * make the isel test more robust * add tests for reshaping and reordering * unify the structure of the tests * mark the remaining tests as requiring a recent pint version, too * explicitly handle quantities as parameters * change the repr of the function / method wrappers * check whether __init__ and repr / str handle units in data and coords * generalize array_attach_units * move the redefinition of DimensionalityError * identify quantities using isinstance * typo * skip tests with a pint version without __array_function__ * compare DataArrays where possible * mark only the compatible unit as xfailing * preserve the name of data arrays * also attach units to x_mm * Test in more CI environments; documentation * What's New * remove a stale function * use Quantity directly for instance tests * explicitly set roll_coords to silence a deprecation warning * skip the whole module if pint does not implement __array_function__ the advantage is that now forgetting to decorate a test case is not possible. * allow to attach units using the mapping from extract_units * add tests for computation methods resampling fails until I figure out how to use it with non-datetime coords. * add tests for grouped operations * add a test for rolling_exp * add a todo note for the module level skip on __array_function__ * add a test for dot * use attach_units instead of manually attaching * modify the resample test to actually work * add a test for to_unstacked_dataset * update whats-new.rst and installing.rst * reformat the whats-new.rst entry * What's New commit 1f81338 Author: keewis <[email protected]> Date: Wed Oct 16 20:54:27 2019 +0200 Fixes to the resample docs (#3400) * add a missing newline to make sphinx detect the code block * update the link to the pandas documentation * explicitly state that this only works with datetime dimensions * also put the datetime dim requirement into the function description * add Series.resample and DataFrame.resample as reference * add the changes to whats-new.rst * move references to the bottom of the docstring commit 3f9069b Author: Joseph Hamman <[email protected]> Date: Mon Oct 14 14:22:08 2019 -0700 Revert to dev version commit 62943e2 Author: Joseph Hamman <[email protected]> Date: Mon Oct 14 12:51:46 2019 -0700 Release v0.14.0 commit 30472ec Author: Joseph Hamman <[email protected]> Date: Mon Oct 14 12:24:05 2019 -0700 updates for 0.14 release [black only] commit 4519843 Author: Joseph Hamman <[email protected]> Date: Mon Oct 14 12:18:54 2019 -0700 updates for 0.14 release commit 4f5ca73 Author: Deepak Cherian <[email protected]> Date: Mon Oct 14 18:06:53 2019 +0000 Make concat more forgiving with variables that are being merged. (#3364) * Make concat more forgiving with variables that are being merged. * rename test. * simplify test. * make diff smaller. commit ae1d8c7 Author: Crypto Jerônimo <[email protected]> Date: Sun Oct 13 15:38:36 2019 +0100 Fix documentation typos (#3396) commit 863e490 Author: Joe Hamman <[email protected]> Date: Sat Oct 12 17:33:33 2019 -0400 OrderedDict --> dict, some python3.5 cleanup too (#3389) * OrderedDict --> dict, some python3.5 cleanup too * respond to part of @shoyer's review * fix set attr syntax on netcdf4 vars * fix typing errors * update whats new and todo comments * Typing annotations * Typing annotations * Fix regression * More substantial changes * More polish * Typing annotations * Rerun notebooks commit 6851e3e Author: crusaderky <[email protected]> Date: Sat Oct 12 21:05:32 2019 +0100 Annotate LRUCache (#3395) commit 4c05d38 Author: Stephan Hoyer <[email protected]> Date: Fri Oct 11 08:47:57 2019 -0700 BUG: overrides to a dimension coordinate do not get aligned (#3393) Fixes GH3377 commit 3f29551 Author: Deepak Cherian <[email protected]> Date: Thu Oct 10 23:44:19 2019 +0000 map_blocks (#3276) * map_block attempt 2 * Address reviews: errors, args + kwargs support. * Works with datasets! * remove wrong comment. * Support chunks. * infer template. * cleanup * cleanup2 * api.rst * simple shape change error check. * Make test more complicated. * Fix for when user function doesn't set DataArray.name * Now _to_temp_dataset works. * Add whats-new * chunks kwarg makes no sense right now. * review feedback: 1. skip index graph nodes. 2. var → name 3. quicker dataarray creation. 4. Add restrictions to docstring. 5. rename chunk construction task. 6. error when non-xarray object is returned. 7. restore non-coord dims. review * Support nondim coords in make_meta. * Add Dataset.unify_chunks * doc updates. * minor. * update comment. * More complicated test dataset. Tests fail :X * Don't know why compute is needed. * work with DataArray nondim coords. * fastpath unify_chunks * comment. * much improved tests. * Change args, kwargs syntax. * Add dataset, dataarray methods. * api.rst * docstrings. * Fix unify_chunks. * Move assert_chunks_equal to xarray.testing. * minor changes. * Better error handling when inferring returned object * wip * wip * better to_array * Docstrings + nicer error message. * remove unify_chunks in map_blocks + better tests. * typing for unify_chunks * address more review comments. * more unify_chunks tests. * Just use dask.core.utils.meta_from_array * get tests working. assert_equal needs a lot of fixing. * more unify_chunks test. * assert_chunks_equal fixes. * copy over meta_from_array. * minor fixes. * raise chunks error earlier and test for map_blocks raising chunk error * fix. * Type annotations * py35 compat * make sure unify_chunks does not compute. * Make tests functional by call compute before assert_equal * Update whats-new * Work with attributes. * Support attrs and name changes. * more assert_equal * test changing coord attribute * fix whats new * rework tests to use fixtures (kind of) * more review changes. * cleanup * more review feedback. * fix unify_chunks. * read dask_array_compat :) * Dask 1.2.0 compat. * documentation polish * make_meta reflow * cosmetic * polish * Fix tests * isort * isort * Add func call to docstrings. commit 291cb80 Author: Deepak Cherian <[email protected]> Date: Thu Oct 10 18:23:20 2019 +0000 Add groupby.dims & Fix groupby reduce for DataArray (#3338) * Fix groupby reduce for DataArray * bugfix. * another bugfix. * bugfix unique_and_monotonic for object indexes (uniqueness is enough) * Add groupby.dims property. * update reduce docstring to point to xarray.ALL_DIMS * test for object index dims. * test reduce dimensions error. * Add whats-new * fix docs build * sq whats-new * one more test. * fix test. * undo monotonic change. * Add dimensions to repr. * Raise error if no bins. * Raise nice error if no groups were formed. * Some more error raising and testing. * Add dataset tests. * update whats-new. * fix tests. * make dims a cached lazy property. * fix whats-new. * whitespace * fix whats-new commit 3f0049f Author: crusaderky <[email protected]> Date: Wed Oct 9 19:01:29 2019 +0100 Speed up isel and __getitem__ (#3375) * Variable.isel cleanup/speedup * Dataset.isel code cleanup * Speed up isel * What's New * Better error checks * Speedup * type annotations * Update doc/whats-new.rst Co-Authored-By: Maximilian Roos <[email protected]> * What's New * What's New * Always shallow-copy variables commit 132733a Author: Deepak Cherian <[email protected]> Date: Tue Oct 8 22:13:47 2019 +0000 Fix concat bug when concatenating unlabeled dimensions. (#3362) * Fix concat bug when concatenating unlabeled dimensions. * Add whats-new * Add back older test. * fix test * Revert "fix test" This reverts commit c33ca34. * better fix commit 6fb272c Author: crusaderky <[email protected]> Date: Tue Oct 8 22:23:46 2019 +0100 Rolling minimum dependency versions policy (#3358) * - Downgrade numpy to 1.14, pandas to 0.20, scipy to 0.19 (24 months old) - Downgrade dask to 1.1 (6 months old) - Don't pin patch versions * Apply rolling policy (see #3222) * Automated tool to verify the minimum versions * Drop Python 3.5 * lint * Trivial cosmetic * Cosmetic * (temp) debug CI failure * Parallelize versions check script * Remove hacks for legacy dask * Documentation * Assorted cleanup * Assorted cleanup * Fix regression * Cleanup * type annotations upgraded to Python 3.6 * count_not_none backport * pd.Index.equals on legacy pandas returned False when comparing vs. a ndarray * Documentation * pathlib cleanup * Slide deprecations from 0.14 to 0.15 * More cleanups * More cleanups * Fix min_deps_check * Fix min_deps_check * Set policy of 12 months for pandas and scipy * Cleanup * Cleanup * Sphinx fix * Overhaul readthedocs environment * Fix test crash * Fix test crash * Prune readthedocs environment * Cleanup * Hack around versioneer bug on readthedocs CI * Code review * Prevent random timeouts in the readthedocs CI * What's New polish * Merge from Master * Trivial cosmetic * Reimplement pandas.core.common.count_not_none commit 3e2a754 Author: Alan D. Snow <[email protected]> Date: Tue Oct 8 09:36:52 2019 -0500 added geocube and rioxarray to related projects (#3383) commit 4254b4a Author: crusaderky <[email protected]> Date: Fri Oct 4 23:17:56 2019 +0100 Lint (#3373) * raise exception instance, not class * isort * isort * Bump mypy version commit 283b4fe Author: Deepak Cherian <[email protected]> Date: Fri Oct 4 17:04:36 2019 +0000 Docs/more fixes (#2934) * Move netcdf to beginning of io.rst * Better indexing example. * Start de-emphasizing pandas * misc. * compute, load, persist docstrings + text. * split-apply-combine. * np.newaxis. * misc. * some dask stuff. * Little more dask. * undo index.rst changes. * link to dask docs on chunks * Fix io.rst. * small changes. * rollingupdate. * joe's review commit dfdeef7 Author: Stephan Hoyer <[email protected]> Date: Thu Oct 3 21:42:50 2019 -0700 Explicitly keep track of indexes with merging (#3234) * Explicitly keep track of indexes in merge.py * Typing fixes * More tying fixes * more typing fixes * fixup commit 86fb71d Author: Deepak Cherian <[email protected]> Date: Thu Oct 3 15:41:50 2019 +0000 groupby repr (#3344) * groupby repr * add test. * test datetime and nondim coord * rename test_da → repr_da * Add whats-new * Update doc/whats-new.rst commit dd2b803 Author: Ryan May <[email protected]> Date: Wed Oct 2 15:43:44 2019 -0600 Remove setting of universal wheels (#3367) Universal wheels indicate that one wheel supports Python 2 and 3. This is no longer the case for xarray. This causes builds to generate files with names like xarray-0.13.0-py2.py3-none-any.whl, which can cause pip to incorrectly install the wheel when installing from a list of wheel files. commit 21705e6 Author: crusaderky <[email protected]> Date: Tue Oct 1 19:13:55 2019 +0100 Revisit # noqa annotations (#3359) commit fb575eb Author: crusaderky <[email protected]> Date: Tue Oct 1 15:11:21 2019 +0100 Fix codecov.io upload on Windows (#3360) commit 1ab2279 Author: Deepak Cherian <[email protected]> Date: Mon Sep 30 21:12:22 2019 +0000 Add how do I ... section (#3357) * Add how do I ... section * Bbugfix. * Update doc/howdoi.rst Co-Authored-By: Maximilian Roos <[email protected]> * Update doc/howdoi.rst Co-Authored-By: Maximilian Roos <[email protected]> * small updates. * Add more. commit bd1069b Author: Gregory Gundersen <[email protected]> Date: Sun Sep 29 19:39:53 2019 -0400 Add glossary to documentation (#3352) * First draft at terminology glossary. * Made name matching rules more explicit and hopefully clearer. * Amended what's new. * Changes based on feedback. * More changed based on feedback. commit b51683f Author: Anderson Banihirwe <[email protected]> Date: Sun Sep 29 07:50:21 2019 -0600 Documentation improvements (#3328) * Add examples for full_like, zeros_like, ones_like * Add examples for xr.align * Add examples for xr.merge * Update xr.where docstring * Update xr.dot docstring * Update xarray/core/common.py Co-Authored-By: Deepak Cherian <[email protected]> * Update xarray/core/common.py Co-Authored-By: Deepak Cherian <[email protected]> * Update xr.combine_by_coords docstring * Apply black formatting only * More black formatting * Remove unnecessary pandas bits * Fix indentation issues * Update assign and pipe * Update `Dataset.reindex` with examples * Update `Dataset.fillna` with examples * Address styling issues * Update docstring Co-Authored-By: Deepak Cherian <[email protected]> commit f3c7da6 Author: Gregory Gundersen <[email protected]> Date: Sat Sep 28 15:57:36 2019 -0400 Remove `complex.nc` from built docs (#3353) * Rolling back to prevent a different issue from leaking into this one. * Amended what's new. commit 6ece6a1 Author: Tony Tung <[email protected]> Date: Thu Sep 26 22:45:26 2019 -0700 Fix DataArray.to_netcdf type annotation (#3325) It calls DataSet.to_netcdf, which returns Union[bytes, "Delayed", None]. So this should as well. commit 16fdac9 Author: crusaderky <[email protected]> Date: Thu Sep 26 10:38:46 2019 +0100 CI test suites with pinned minimum dependencies (#3346) * CI test suites with pinned minimum dependencies * code review * Clarity re lxml commit ea101f5 Author: Tom Nicholas <[email protected]> Date: Thu Sep 26 10:51:58 2019 +0200 Bugfix/plot accept coord dim (#3345) Bug in plot.line fixed by ensuring 1D coords are cast down to their associated dims. There was previously two particular cases where this would not happen. commit 85c9a40 Author: crusaderky <[email protected]> Date: Wed Sep 25 02:40:54 2019 +0100 CI environments overhaul (#3340) * Rationalize and align CI environments. Add many optional dependencies to individual CI suites. * pynio and cdms2 are not available on Windows * cfgrib causes Python interpreter crash on Windows * dtype of np.arange defaults to int64 on Linux and int32 on Windows * Suppress failure to delete file on Windows * Mark hypotesis tests as @slow
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This is my attempt at closing #2410. I've borrowed a bit of text from that PR (thanks @horta), from #1295, and from the xarray docs. I avoided verbose examples—it makes quickly searching and reading the glossary difficult—and put most of the effort into explaining dimension vs non-dimension coordinates, which in my experience opens the door to true xarray enlightenment.
Corrections, comments, or suggestions for additional terminology welcome.