From d41199a56fb56f4258026960bff2a5b0c052f907 Mon Sep 17 00:00:00 2001 From: Patrick Peglar Date: Fri, 7 May 2021 19:55:10 +0100 Subject: [PATCH 1/6] Widen cube printout for long ancil or cell-measure names. --- lib/iris/cube.py | 8 +++-- lib/iris/tests/unit/cube/test_Cube.py | 52 +++++++++++++++++++++++++++ 2 files changed, 58 insertions(+), 2 deletions(-) diff --git a/lib/iris/cube.py b/lib/iris/cube.py index f0c9dca166..54c70baab4 100644 --- a/lib/iris/cube.py +++ b/lib/iris/cube.py @@ -2420,7 +2420,7 @@ def vector_summary( delta = max_line_offset - min_alignment + 5 cube_header = "%-*s (%s)" % ( int(name_padding + delta), - self.name() or "unknown", + nameunit, dimension_header, ) alignment += delta @@ -2477,7 +2477,11 @@ def vector_summary( # Calculate the maximum line offset. max_line_offset = 0 - for coord in all_coords: + for coord in ( + list(all_coords) + + self.ancillary_variables() + + self.cell_measures() + ): max_line_offset = max( max_line_offset, len( diff --git a/lib/iris/tests/unit/cube/test_Cube.py b/lib/iris/tests/unit/cube/test_Cube.py index 9713cd0191..3378f25e35 100644 --- a/lib/iris/tests/unit/cube/test_Cube.py +++ b/lib/iris/tests/unit/cube/test_Cube.py @@ -596,6 +596,58 @@ def test_similar_coords(self): self.cube.add_aux_coord(coord) self.assertIn("baz", self.cube.summary()) + def test_long_components(self): + # Check that components with long names 'stretch' the printout correctly. + cube = Cube(np.zeros((20, 20, 20)), units=1) + dimco = DimCoord(np.arange(20), long_name="dimco") + auxco = AuxCoord(np.zeros(20), long_name="auxco") + ancil = AncillaryVariable(np.zeros(20), long_name="ancil") + cellm = CellMeasure(np.zeros(20), long_name="cellm") + cube.add_dim_coord(dimco, 0) + cube.add_aux_coord(auxco, 0) + cube.add_cell_measure(cellm, 1) + cube.add_ancillary_variable(ancil, 2) + + original_summary = cube.summary() + long_name = "long_name______________________________________" + for component in (dimco, auxco, ancil, cellm): + # For each (type of) component, set a long name so the header columns get shifted. + old_name = component.name() + component.rename(long_name) + new_summary = cube.summary() + component.rename( + old_name + ) # Put each back the way it was afterwards + + # Check that the resulting 'stretched' output has dimension columns aligned correctly. + lines = new_summary.split("\n") + header = lines[0] + colon_inds = [ + i_char for i_char, char in enumerate(header) if char == ":" + ] + for line in lines[1:]: + # Replace all '-' with 'x' to make checking easier, and add a final buffer space. + line = line.replace("-", "x") + " " + if " x " in line: + # For lines with any columns : check that columns are where expected + for col_ind in colon_inds: + # Chop out chars before+after each expected column. + self.assertEqual( + line[col_ind - 1 : col_ind + 2], " x " + ) + + # Finally also: compare old with new, but replacing new name and ignoring spacing differences + def collapse_space(string): + # Replace all multiple spaces with a single space. + while " " in string: + string = string.replace(" ", " ") + return string + + self.assertEqual( + collapse_space(new_summary).replace(long_name, old_name), + collapse_space(original_summary), + ) + class Test_is_compatible(tests.IrisTest): def setUp(self): From e9d548084c2f8553a7277cbdbdcb5e2c8584773e Mon Sep 17 00:00:00 2001 From: Patrick Peglar Date: Fri, 7 May 2021 20:57:03 +0100 Subject: [PATCH 2/6] Adjust result for fixed cube-units printout. --- lib/iris/tests/results/cdm/str_repr/simple.__str__.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/lib/iris/tests/results/cdm/str_repr/simple.__str__.txt b/lib/iris/tests/results/cdm/str_repr/simple.__str__.txt index b174d346d2..59e3aba236 100644 --- a/lib/iris/tests/results/cdm/str_repr/simple.__str__.txt +++ b/lib/iris/tests/results/cdm/str_repr/simple.__str__.txt @@ -1,4 +1,4 @@ -thingness (foo: 11) +thingness / (1) (foo: 11) Dimension coordinates: foo x Auxiliary coordinates: From f3e47709576be756b537a3112475bf7e8f1ae996 Mon Sep 17 00:00:00 2001 From: Patrick Peglar Date: Wed, 7 Jul 2021 17:05:02 +0100 Subject: [PATCH 3/6] Added whatsnew. --- docs/iris/src/whatsnew/3.0.4.rst | 592 +++++++++++++++++++++++++++++++ 1 file changed, 592 insertions(+) create mode 100644 docs/iris/src/whatsnew/3.0.4.rst diff --git a/docs/iris/src/whatsnew/3.0.4.rst b/docs/iris/src/whatsnew/3.0.4.rst new file mode 100644 index 0000000000..cfbd609f03 --- /dev/null +++ b/docs/iris/src/whatsnew/3.0.4.rst @@ -0,0 +1,592 @@ +.. include:: ../common_links.inc + +v3.0.4 (?? ??August 2021) +************************* + +This document explains the changes made to Iris for this release +(:doc:`View all changes `.) + + +.. dropdown:: :opticon:`alert` v3.0.4 Patches + :container: + shadow + :title: text-primary text-center font-weight-bold + :body: bg-light + :animate: fade-in + :open: + + The patches included in this release include: + + 🐛 **Bugs Fixed** + + #. `@lbdreyer`_ modified :meth:`~iris.cube.Cube.intersection` to use a tolerant + equality check, when looking for cells that straddle the wrapping point. + (:pull:`4220`) + + +.. dropdown:: :opticon:`alert` v3.0.2 Patches + :container: + shadow + :title: text-primary text-center font-weight-bold + :body: bg-light + :animate: fade-in + + The patches included in this release include: + + 🐛 **Bugs Fixed** + + #. `@jonseddon`_ handled a malformed ``um_stash_source`` CF variable attribute in + a netCDF file rather than raising a ``ValueError``. (:pull:`4035`) + + #. `@rcomer`_ fixed :meth:`~iris.cube.Cube.intersection` for special cases + where one cell's bounds align with the requested maximum and minimum, as + reported in :issue:`3391`. (:pull:`4059`) + + #. `@bjlittle`_ resolved a regression in arithmetic behaviour between a coordinate + and a cube which resulted in a ``NotYetImplementedError`` being raised, as reported + in :issue:`4000`. This fix supports ``+``, ``-``, ``*``, and ``/`` operations + between a coordinate and a cube, and for convenience additionally includes + :meth:`iris.cube.Cube.__neg__` support. (:pull:`4159`) + + #. `@pp-mo`_ fixed 2 bugs in cube printout: + Firstly, ancillary-variables or cell-measures with long names can now widen the cube "dimensions map" to fit, + whereas previously printing these cases caused an Exception. + Secondly, cube units are now always printed, whereas previously they were missed out any time that the + "dimensions map" was widened to accomodate long coordinate names. + + 📚 **Documentation** + + #. `@bjlittle`_ updated the ``intersphinx_mapping`` and fixed documentation + to use ``stable`` URLs for `matplotlib`_. (:pull:`4003`) [``pre-v3.1.0``] + + 💼 **Internal** + + #. `@jamesp`_ updated a test to the latest numpy version (:pull:`3977`) [``pre-v3.1.0``] + + #. `@bjlittle`_ enabled `cirrus-ci`_ compute credits for non-draft pull-requests + from collaborators targeting the Iris ``master`` branch. (:pull:`4007`) + [``pre-v3.1.0``] + + #. `@bjlittle`_ added conditional task execution to `.cirrus.yml`_ to allow + developers to easily disable `cirrus-ci`_ tasks. See + :ref:`skipping Cirrus-CI tasks`. (:pull:`4019`) [``pre-v3.1.0``] + + #. `@pp-mo`_ adjusted the use of :func:`dask.array.from_array` in :func:`iris._lazy_data.as_lazy_data`, + to avoid the dask 'test access'. This makes loading of netcdf files with a + large number of variables significantly faster. (:pull:`4135`) + + #. `@pp-mo`_ reverted a change made previously in (:pull:`3659`) to + :meth:`iris.fileformats.pp.PPDataProxy.__getitem__`. The check for empty slicings + is no longer needed since (:pull:`4135`) was added. (:pull:`4141`) + + Note that, the above contributions labelled with ``pre-v3.1.0`` are part of the forthcoming + Iris v3.1.0 release, but require to be included in this patch release. + + +.. dropdown:: :opticon:`alert` v3.0.1 Patches + :container: + shadow + :title: text-primary text-center font-weight-bold + :body: bg-light + :animate: fade-in + + The patches included in this release include: + + 💼 **Internal** + + #. `@bjlittle`_ gracefully promote formula terms within :mod:`~iris.aux_factory` that have ``units`` of ``unknown`` + to ``units`` of ``1`` (dimensionless), where the formula term **must** have dimensionless ``units``. Without this + graceful treatment of ``units`` the resulting :class:`~iris.cube.Cube` will **not** contain the expected auxiliary + factory, and the associated derived coordinate will be missing. (:pull:`3965`) + + +.. dropdown:: :opticon:`report` v3.0.0 Release Highlights + :container: + shadow + :title: text-primary text-center font-weight-bold + :body: bg-light + :animate: fade-in + + The highlights for this major release of Iris include: + + * We've finally dropped support for ``Python 2``, so welcome to ``Iris 3`` + and ``Python 3``! + * We've extended our coverage of the `CF Conventions and Metadata`_ by + introducing support for `CF Ancillary Data`_ and `Quality Flags`_, + * Lazy regridding is now available for several regridding schemes, + * Managing and manipulating metadata within Iris is now easier and more + consistent thanks to the introduction of a new common metadata API, + * :ref:`Cube arithmetic ` has been significantly improved with + regards to extended broadcasting, auto-transposition and a more lenient + behaviour towards handling metadata and coordinates, + * Our :ref:`documentation ` has been refreshed, + restructured, revitalised and rehosted on `readthedocs`_, + * It's now easier than ever to :ref:`install Iris ` + as a user or a developer, and the newly revamped developers guide walks + you though how you can :ref:`get involved ` + and contribute to Iris, + * Also, this is a major release of Iris, so please be aware of the + :ref:`incompatible changes ` and + :ref:`deprecations `. + + And finally, get in touch with us on `GitHub`_ if you have any issues or + feature requests for improving Iris. Enjoy! + + +📢 Announcements +================ + +#. Congratulations to `@bouweandela`_, `@jvegasbsc`_, and `@zklaus`_ who + recently became Iris core developers. They bring a wealth of expertise to the + team, and are using Iris to underpin `ESMValTool`_ - "*A community diagnostic + and performance metrics tool for routine evaluation of Earth system models + in CMIP*". Welcome aboard! 🎉 + +#. Congratulations also goes to `@jonseddon`_ who recently became an Iris core + developer. We look forward to seeing more of your awesome contributions! 🎉 + + +✨ Features +=========== + +#. `@MoseleyS`_ greatly enhanced the :mod:`~iris.fileformats.nimrod` + module to provide richer meta-data translation when loading ``Nimrod`` data + into cubes. This covers most known operational use-cases. (:pull:`3647`) + +#. `@stephenworsley`_ improved the handling of + :class:`iris.coords.CellMeasure`\ s in the :class:`~iris.cube.Cube` + statistical operations :meth:`~iris.cube.Cube.collapsed`, + :meth:`~iris.cube.Cube.aggregated_by` and + :meth:`~iris.cube.Cube.rolling_window`. These previously removed every + :class:`~iris.coords.CellMeasure` attached to the cube. Now, a + :class:`~iris.coords.CellMeasure` will only be removed if it is associated + with an axis over which the statistic is being run. (:pull:`3549`) + +#. `@stephenworsley`_, `@pp-mo`_ and `@abooton`_ added support for + `CF Ancillary Data`_ variables. These are created as + :class:`iris.coords.AncillaryVariable`, and appear as components of cubes + much like :class:`~iris.coords.AuxCoord`\ s, with the new + :class:`~iris.cube.Cube` methods + :meth:`~iris.cube.Cube.add_ancillary_variable`, + :meth:`~iris.cube.Cube.remove_ancillary_variable`, + :meth:`~iris.cube.Cube.ancillary_variable`, + :meth:`~iris.cube.Cube.ancillary_variables` and + :meth:`~iris.cube.Cube.ancillary_variable_dims`. + They are loaded from and saved to NetCDF-CF files. Special support for + `Quality Flags`_ is also provided, to ensure they load and save with + appropriate units. (:pull:`3800`) + +#. `@bouweandela`_ implemented lazy regridding for the + :class:`~iris.analysis.Linear`, :class:`~iris.analysis.Nearest`, and + :class:`~iris.analysis.AreaWeighted` regridding schemes. (:pull:`3701`) + +#. `@bjlittle`_ added `logging`_ support within :mod:`iris.analysis.maths`, + :mod:`iris.common.metadata`, and :mod:`iris.common.resolve`. Each module + defines a :class:`logging.Logger` instance called ``logger`` with a default + ``level`` of ``INFO``. To enable ``DEBUG`` logging use + ``logger.setLevel("DEBUG")``. (:pull:`3785`) + +#. `@bjlittle`_ added the :mod:`iris.common.resolve` module, which provides + infrastructure to support the analysis, identification and combination + of metadata common between two :class:`~iris.cube.Cube` operands into a + single resultant :class:`~iris.cube.Cube` that will be auto-transposed, + and with the appropriate broadcast shape. (:pull:`3785`) + +#. `@bjlittle`_ added the :ref:`common metadata API `, which provides + a unified treatment of metadata across Iris, and allows users to easily + manage and manipulate their metadata in a consistent way. (:pull:`3785`) + +#. `@bjlittle`_ added :ref:`lenient metadata ` support, to + allow users to control **strict** or **lenient** metadata equivalence, + difference and combination. (:pull:`3785`) + +#. `@bjlittle`_ added :ref:`lenient cube maths ` support and + resolved several long standing major issues with cube arithmetic regarding + a more robust treatment of cube broadcasting, cube dimension auto-transposition, + and preservation of common metadata and coordinates during cube math operations. + Resolves :issue:`1887`, :issue:`2765`, and :issue:`3478`. (:pull:`3785`) + +#. `@pp-mo`_ and `@TomekTrzeciak`_ enhanced :meth:`~iris.cube.Cube.collapse` to allow a 1-D weights array when + collapsing over a single dimension. + Previously, the weights had to be the same shape as the whole cube, which could cost a lot of memory in some cases. + The 1-D form is supported by most weighted array statistics (such as :meth:`np.average`), so this now works + with the corresponding Iris schemes (in that case, :const:`~iris.analysis.MEAN`). (:pull:`3943`) + + +🐛 Bugs Fixed +============= + +#. `@stephenworsley`_ fixed :meth:`~iris.cube.Cube.remove_coord` to now also + remove derived coordinates by removing aux_factories. (:pull:`3641`) + +#. `@jonseddon`_ fixed ``isinstance(cube, collections.Iterable)`` to now behave + as expected if a :class:`~iris.cube.Cube` is iterated over, while also + ensuring that ``TypeError`` is still raised. (Fixed by setting the + ``__iter__()`` method in :class:`~iris.cube.Cube` to ``None``). + (:pull:`3656`) + +#. `@stephenworsley`_ enabled cube concatenation along an axis shared by cell + measures; these cell measures are now concatenated together in the resulting + cube. Such a scenario would previously cause concatenation to inappropriately + fail. (:pull:`3566`) + +#. `@stephenworsley`_ newly included :class:`~iris.coords.CellMeasure`\ s in + :class:`~iris.cube.Cube` copy operations. Previously copying a + :class:`~iris.cube.Cube` would ignore any attached + :class:`~iris.coords.CellMeasure`. (:pull:`3546`) + +#. `@bjlittle`_ set a :class:`~iris.coords.CellMeasure`'s + ``measure`` attribute to have a default value of ``area``. + Previously, the ``measure`` was provided as a keyword argument to + :class:`~iris.coords.CellMeasure` with a default value of ``None``, which + caused a ``TypeError`` when no ``measure`` was provided, since ``area`` or + ``volume`` are the only accepted values. (:pull:`3533`) + +#. `@trexfeathers`_ set **all** plot types in :mod:`iris.plot` to now use + :obj:`matplotlib.dates.date2num` to format date/time coordinates for use on a plot + axis (previously :meth:`~iris.plot.pcolor` and :meth:`~iris.plot.pcolormesh` + did not include this behaviour). (:pull:`3762`) + +#. `@trexfeathers`_ changed date/time axis labels in :mod:`iris.quickplot` to + now **always** be based on the ``epoch`` used in :obj:`matplotlib.dates.date2num` + (previously would take the unit from a time coordinate, if present, even + though the coordinate's value had been changed via ``date2num``). + (:pull:`3762`) + +#. `@pp-mo`_ newly included attributes of cell measures in NETCDF-CF + file loading; they were previously being discarded. They are now available on + the :class:`~iris.coords.CellMeasure` in the loaded :class:`~iris.cube.Cube`. + (:pull:`3800`) + +#. `@pp-mo`_ fixed the netcdf loader to now handle any grid-mapping + variables with missing ``false_easting`` and ``false_northing`` properties, + which was previously failing for some coordinate systems. See :issue:`3629`. + (:pull:`3804`) + +#. `@stephenworsley`_ changed the way tick labels are assigned from string coords. + Previously, the first tick label would occasionally be duplicated. This also + removes the use of the deprecated `matplotlib`_ ``IndexFormatter``. (:pull:`3857`) + +#. `@znicholls`_ fixed :meth:`~iris.quickplot._title` to only check + ``units.is_time_reference`` if the ``units`` symbol is not used. (:pull:`3902`) + +#. `@rcomer`_ fixed a bug whereby numpy array type attributes on a cube's + coordinates could prevent printing it. See :issue:`3921`. (:pull:`3922`) + +.. _whatsnew 3.0.4 changes: + +💣 Incompatible Changes +======================= + +#. `@pp-mo`_ rationalised :class:`~iris.cube.CubeList` extraction + methods: + + The former method ``iris.cube.CubeList.extract_strict``, and the ``strict`` + keyword of the :meth:`~iris.cube.CubeList.extract` method have been removed, + and are replaced by the new routines :meth:`~iris.cube.CubeList.extract_cube` + and :meth:`~iris.cube.CubeList.extract_cubes`. + The new routines perform the same operation, but in a style more like other + ``Iris`` functions such as :meth:`~iris.load_cube` and :meth:`~iris.load_cubes`. + Unlike ``strict`` extraction, the type of return value is now completely + consistent : :meth:`~iris.cube.CubeList.extract_cube` always returns a + :class:`~iris.cube.Cube`, and :meth:`~iris.cube.CubeList.extract_cubes` + always returns an :class:`iris.cube.CubeList` of a length equal to the + number of constraints. (:pull:`3715`) + +#. `@pp-mo`_ removed the former function + ``iris.analysis.coord_comparison``. (:pull:`3562`) + +#. `@bjlittle`_ moved the + :func:`iris.experimental.equalise_cubes.equalise_attributes` function from + the :mod:`iris.experimental` module into the :mod:`iris.util` module. Please + use the :func:`iris.util.equalise_attributes` function instead. + (:pull:`3527`) + +#. `@bjlittle`_ removed the module ``iris.experimental.concatenate``. In + ``v1.6.0`` the experimental ``concatenate`` functionality was moved to the + :meth:`iris.cube.CubeList.concatenate` method. Since then, calling the + :func:`iris.experimental.concatenate.concatenate` function raised an + exception. (:pull:`3523`) + +#. `@stephenworsley`_ changed the default units of :class:`~iris.coords.DimCoord` + and :class:`~iris.coords.AuxCoord` from `"1"` to `"unknown"`. (:pull:`3795`) + +#. `@stephenworsley`_ changed Iris objects loaded from NetCDF-CF files to have + ``units='unknown'`` where the corresponding NetCDF variable has no ``units`` + property. Previously these cases defaulted to ``units='1'``. + This affects loading of coordinates whose file variable has no "units" + attribute (not valid, under `CF units rules`_): These will now have units + of `"unknown"`, rather than `"1"`, which **may prevent the creation of + a hybrid vertical coordinate**. While these cases used to "work", this was + never really correct behaviour. (:pull:`3795`) + +#. `@SimonPeatman`_ added attribute ``var_name`` to coordinates created by the + :func:`iris.analysis.trajectory.interpolate` function. This prevents + duplicate coordinate errors in certain circumstances. (:pull:`3718`) + +#. `@bjlittle`_ aligned the :func:`iris.analysis.maths.apply_ufunc` with the + rest of the :mod:`iris.analysis.maths` API by changing its keyword argument + from ``other_cube`` to ``other``. (:pull:`3785`) + +#. `@bjlittle`_ changed the :meth:`iris.analysis.maths.IFunc.__call__` to ignore + any surplus ``other`` keyword argument for a ``data_func`` that requires + **only one** argument. This aligns the behaviour of + :meth:`iris.analysis.maths.IFunc.__call__` with + :func:`~iris.analysis.maths.apply_ufunc`. Previously a ``ValueError`` + exception was raised. (:pull:`3785`) + + +.. _whatsnew 3.0.4 deprecations: + +🔥 Deprecations +=============== + +#. `@stephenworsley`_ removed the deprecated :class:`iris.Future` flags + ``cell_date_time_objects``, ``netcdf_promote``, ``netcdf_no_unlimited`` and + ``clip_latitudes``. (:pull:`3459`) + +#. `@stephenworsley`_ changed :attr:`iris.fileformats.pp.PPField.lbproc` to be an + ``int``. The deprecated attributes ``flag1``, ``flag2`` etc. have been + removed from it. (:pull:`3461`) + +#. `@bjlittle`_ deprecated :func:`~iris.util.as_compatible_shape` in preference + for :class:`~iris.common.resolve.Resolve` e.g., ``Resolve(src, tgt)(tgt.core_data())``. + The :func:`~iris.util.as_compatible_shape` function will be removed in a future + release of Iris. (:pull:`3892`) + + +🔗 Dependencies +=============== + +#. `@stephenworsley`_, `@trexfeathers`_ and `@bjlittle`_ removed ``Python2`` + support, modernising the codebase by switching to exclusive ``Python3`` + support. (:pull:`3513`) + +#. `@bjlittle`_ improved the developer set up process. Configuring Iris and + :ref:`installing_from_source` as a developer with all the required package + dependencies is now easier with our curated conda environment YAML files. + (:pull:`3812`) + +#. `@stephenworsley`_ pinned Iris to require `Dask`_ ``>=2.0``. (:pull:`3460`) + +#. `@stephenworsley`_ and `@trexfeathers`_ pinned Iris to require + `Cartopy`_ ``>=0.18``, in order to remain compatible with the latest version + of `matplotlib`_. (:pull:`3762`) + +#. `@bjlittle`_ unpinned Iris to use the latest version of `matplotlib`_. + Supporting ``Iris`` for both ``Python2`` and ``Python3`` had resulted in + pinning our dependency on `matplotlib`_ at ``v2.x``. But this is no longer + necessary now that ``Python2`` support has been dropped. (:pull:`3468`) + +#. `@stephenworsley`_ and `@trexfeathers`_ unpinned Iris to use the latest version + of `Proj`_. (:pull:`3762`) + +#. `@stephenworsley`_ and `@trexfeathers`_ removed GDAL from the extensions + dependency group. We no longer consider it to be an extension. (:pull:`3762`) + + +.. _whatsnew 3.0.4 docs: + +📚 Documentation +================ + +#. `@tkknight`_ moved the + :ref:`sphx_glr_generated_gallery_oceanography_plot_orca_projection.py` + from the general part of the gallery to oceanography. (:pull:`3761`) + +#. `@tkknight`_ updated documentation to use a modern sphinx theme and be + served from https://scitools-iris.readthedocs.io/en/latest/. (:pull:`3752`) + +#. `@bjlittle`_ added support for the `black`_ code formatter. This is + now automatically checked on GitHub PRs, replacing the older, unittest-based + ``iris.tests.test_coding_standards.TestCodeFormat``. Black provides automatic + code format correction for most IDEs. See the new developer guide section on + :ref:`code_formatting`. (:pull:`3518`) + +#. `@tkknight`_ and `@trexfeathers`_ refreshed the :ref:`whats_new_contributions` + for the :ref:`iris_whatsnew`. This includes always creating the ``latest`` + what's new page so it appears on the latest documentation at + https://scitools-iris.readthedocs.io/en/latest/whatsnew. This resolves + :issue:`2104`, :issue:`3451`, :issue:`3818`, :issue:`3837`. Also updated the + :ref:`iris_development_releases_steps` to follow when making a release. + (:pull:`3769`, :pull:`3838`, :pull:`3843`) + +#. `@tkknight`_ enabled the PDF creation of the documentation on the + `Read the Docs`_ service. The PDF may be accessed by clicking on the version + at the bottom of the side bar, then selecting ``PDF`` from the ``Downloads`` + section. (:pull:`3765`) + +#. `@stephenworsley`_ added a warning to the + :func:`iris.analysis.cartography.project` function regarding its behaviour on + projections with non-rectangular boundaries. (:pull:`3762`) + +#. `@stephenworsley`_ added the :ref:`cube_maths_combining_units` section to the + user guide to clarify how ``Units`` are handled during cube arithmetic. + (:pull:`3803`) + +#. `@tkknight`_ overhauled the :ref:`developers_guide` including information on + getting involved in becoming a contributor and general structure of the + guide. This resolves :issue:`2170`, :issue:`2331`, :issue:`3453`, + :issue:`314`, :issue:`2902`. (:pull:`3852`) + +#. `@rcomer`_ added argument descriptions to the :class:`~iris.coords.DimCoord` + docstring. (:pull:`3681`) + +#. `@tkknight`_ added two url's to be ignored for the ``make linkcheck``. This + will ensure the Iris github project is not repeatedly hit during the + linkcheck for issues and pull requests as it can result in connection + refused and thus travis-ci_ job failures. For more information on linkcheck, + see :ref:`contributing.documentation.testing`. (:pull:`3873`) + +#. `@tkknight`_ enabled the napolean_ package that is used by sphinx_ to cater + for the existing google style docstrings and to also allow for `numpy`_ + docstrings. This resolves :issue:`3841`. (:pull:`3871`) + +#. `@tkknight`_ configured ``sphinx-build`` to promote warnings to errors when + building the documentation via ``make html``. This will minimise technical + debt accruing for the documentation. (:pull:`3877`) + +#. `@tkknight`_ updated :ref:`installing_iris` to include a reference to + Windows Subsystem for Linux. (:pull:`3885`) + +#. `@tkknight`_ updated the :ref:`iris_docs` homepage to include panels so the + links are more visible to users. This uses the sphinx-panels_ extension. + (:pull:`3884`) + +#. `@bjlittle`_ created the :ref:`Further topics ` section and + included documentation for :ref:`metadata`, :ref:`lenient metadata`, and + :ref:`lenient maths`. (:pull:`3890`) + +#. `@jonseddon`_ updated the CF version of the netCDF saver in the + :ref:`saving_iris_cubes` section and in the equivalent function docstring. + (:pull:`3925`) + +#. `@bjlittle`_ applied `Title Case Capitalization`_ to the documentation. + (:pull:`3940`) + + +💼 Internal +=========== + +#. `@pp-mo`_ and `@lbdreyer`_ removed all Iris test dependencies on `iris-grib`_ + by transferring all relevant content to the `iris-grib`_ repository. (:pull:`3662`, + :pull:`3663`, :pull:`3664`, :pull:`3665`, :pull:`3666`, :pull:`3669`, + :pull:`3670`, :pull:`3671`, :pull:`3672`, :pull:`3742`, :pull:`3746`) + +#. `@lbdreyer`_ and `@pp-mo`_ overhauled the handling of dimensional + metadata to remove duplication. (:pull:`3422`, :pull:`3551`) + +#. `@trexfeathers`_ simplified the standard license header for all files, which + removes the need to repeatedly update year numbers in the header. + (:pull:`3489`) + +#. `@stephenworsley`_ changed the numerical values in tests involving the + Robinson projection due to improvements made in + `Proj`_. (:pull:`3762`) (see also `Proj#1292`_ and `Proj#2151`_) + +#. `@stephenworsley`_ changed tests to account for more detailed descriptions of + projections in `GDAL`_. (:pull:`3762`) (see also `GDAL#1185`_) + +#. `@stephenworsley`_ changed tests to account for `GDAL`_ now saving fill values + for data without masked points. (:pull:`3762`) + +#. `@trexfeathers`_ changed every graphics test that includes `Cartopy's coastlines`_ + to account for new adaptive coastline scaling. (:pull:`3762`) + (see also `Cartopy#1105`_) + +#. `@trexfeathers`_ changed graphics tests to account for some new default + grid-line spacing in `Cartopy`_. (:pull:`3762`) (see also `Cartopy#1117`_) + +#. `@trexfeathers`_ added additional acceptable graphics test targets to account + for very minor changes in `matplotlib`_ version ``3.3`` (colormaps, fonts and + axes borders). (:pull:`3762`) + +#. `@rcomer`_ corrected the `matplotlib`_ backend in Iris tests to ignore + :obj:`matplotlib.rcdefaults`, instead the tests will **always** use ``agg``. + (:pull:`3846`) + +#. `@bjlittle`_ migrated the `black`_ support from ``19.10b0`` to ``20.8b1``. + (:pull:`3866`) + +#. `@lbdreyer`_ updated the CF standard name table to the latest version: `v75`_. + (:pull:`3867`) + +#. `@bjlittle`_ added :pep:`517` and :pep:`518` support for building and + installing Iris, in particular to handle the `PyKE`_ package dependency. + (:pull:`3812`) + +#. `@bjlittle`_ added metadata support for comparing :attr:`~iris.cube.Cube.attributes` + dictionaries that contain `numpy`_ arrays using `xxHash`_, an extremely fast + non-cryptographic hash algorithm, running at RAM speed limits. + +#. `@bjlittle`_ added the ``iris.tests.assertDictEqual`` method to override + :meth:`unittest.TestCase.assertDictEqual` in order to cope with testing + metadata :attr:`~iris.cube.Cube.attributes` dictionary comparison where + the value of a key may be a `numpy`_ array. (:pull:`3785`) + +#. `@bjlittle`_ added the :func:`~iris.config.get_logger` function for creating + a generic :class:`logging.Logger` with a :class:`logging.StreamHandler` and + custom :class:`logging.Formatter`. (:pull:`3785`) + +#. `@owena11`_ identified and optimised a bottleneck in ``FieldsFile`` header + loading due to the use of :func:`numpy.fromfile`. (:pull:`3791`) + +#. `@znicholls`_ added a test for plotting with the label being taken from the unit's symbol, + see :meth:`~iris.tests.test_quickplot.TestLabels.test_pcolormesh_str_symbol` (:pull:`3902`). + +#. `@znicholls`_ made :func:`~iris.tests.idiff.step_over_diffs` robust to hyphens (``-``) in + the input path (i.e. the ``result_dir`` argument) (:pull:`3902`). + +#. `@bjlittle`_ migrated the CIaaS from `travis-ci`_ to `cirrus-ci`_, and removed `stickler-ci`_ + support. (:pull:`3928`) + +#. `@bjlittle`_ introduced `nox`_ as a common and easy entry-point for test automation. + It can be used both from `cirrus-ci`_ in the cloud, and locally by the developer to + run the Iris tests, the doc-tests, the gallery doc-tests, and lint Iris + with `flake8`_ and `black`_. (:pull:`3928`) + +.. _Read the Docs: https://scitools-iris.readthedocs.io/en/latest/ +.. _CF units rules: https://cfconventions.org/Data/cf-conventions/cf-conventions-1.8/cf-conventions.html#units +.. _CF Ancillary Data: https://cfconventions.org/Data/cf-conventions/cf-conventions-1.8/cf-conventions.html#ancillary-data +.. _Quality Flags: https://cfconventions.org/Data/cf-conventions/cf-conventions-1.8/cf-conventions.html#flags +.. _iris-grib: https://github.com/SciTools/iris-grib +.. _Cartopy: https://github.com/SciTools/cartopy +.. _Cartopy's coastlines: https://scitools.org.uk/cartopy/docs/latest/matplotlib/geoaxes.html?highlight=coastlines#cartopy.mpl.geoaxes.GeoAxes.coastlines +.. _Cartopy#1105: https://github.com/SciTools/cartopy/pull/1105 +.. _Cartopy#1117: https://github.com/SciTools/cartopy/pull/1117 +.. _Dask: https://github.com/dask/dask +.. _Proj: https://github.com/OSGeo/PROJ +.. _black: https://black.readthedocs.io/en/stable/ +.. _Proj#1292: https://github.com/OSGeo/PROJ/pull/1292 +.. _Proj#2151: https://github.com/OSGeo/PROJ/pull/2151 +.. _GDAL: https://github.com/OSGeo/gdal +.. _GDAL#1185: https://github.com/OSGeo/gdal/pull/1185 +.. _@MoseleyS: https://github.com/MoseleyS +.. _@stephenworsley: https://github.com/stephenworsley +.. _@pp-mo: https://github.com/pp-mo +.. _@abooton: https://github.com/abooton +.. _@bouweandela: https://github.com/bouweandela +.. _@bjlittle: https://github.com/bjlittle +.. _@trexfeathers: https://github.com/trexfeathers +.. _@jonseddon: https://github.com/jonseddon +.. _@tkknight: https://github.com/tkknight +.. _@lbdreyer: https://github.com/lbdreyer +.. _@SimonPeatman: https://github.com/SimonPeatman +.. _@TomekTrzeciak: https://github.com/TomekTrzeciak +.. _@rcomer: https://github.com/rcomer +.. _@jvegasbsc: https://github.com/jvegasbsc +.. _@zklaus: https://github.com/zklaus +.. _@znicholls: https://github.com/znicholls +.. _ESMValTool: https://github.com/ESMValGroup/ESMValTool +.. _v75: https://cfconventions.org/Data/cf-standard-names/75/build/cf-standard-name-table.html +.. _sphinx-panels: https://sphinx-panels.readthedocs.io/en/latest/ +.. _logging: https://docs.python.org/3/library/logging.html +.. _numpy: https://github.com/numpy/numpy +.. _xxHash: https://github.com/Cyan4973/xxHash +.. _PyKE: https://pypi.org/project/scitools-pyke/ +.. _@owena11: https://github.com/owena11 +.. _GitHub: https://github.com/SciTools/iris/issues/new/choose +.. _readthedocs: https://readthedocs.org/ +.. _CF Conventions and Metadata: https://cfconventions.org/ +.. _flake8: https://flake8.pycqa.org/en/stable/ +.. _nox: https://nox.thea.codes/en/stable/ +.. _Title Case Capitalization: https://apastyle.apa.org/style-grammar-guidelines/capitalization/title-case +.. _travis-ci: https://travis-ci.org/github/SciTools/iris +.. _stickler-ci: https://stickler-ci.com/ +.. _@jamesp: https://github.com/jamesp From 54dc6c8d0972619be49172b2d18b848ce5880a6d Mon Sep 17 00:00:00 2001 From: Patrick Peglar Date: Thu, 8 Jul 2021 10:34:31 +0100 Subject: [PATCH 4/6] Include newest whatsnew in index. --- docs/iris/src/whatsnew/index.rst | 1 + 1 file changed, 1 insertion(+) diff --git a/docs/iris/src/whatsnew/index.rst b/docs/iris/src/whatsnew/index.rst index e7cfc3073b..e61ced3922 100644 --- a/docs/iris/src/whatsnew/index.rst +++ b/docs/iris/src/whatsnew/index.rst @@ -10,6 +10,7 @@ Iris versions. .. toctree:: :maxdepth: 1 + 3.0.4.rst 3.0.3.rst 3.0.2.rst 3.0.1.rst From dafcf1fc2d5b9c19dcab3be92a22127d7a293ee0 Mon Sep 17 00:00:00 2001 From: Patrick Peglar Date: Thu, 8 Jul 2021 14:41:24 +0100 Subject: [PATCH 5/6] Review: fix whatsnew structure. --- docs/iris/src/whatsnew/3.0.4.rst | 26 ++++++++++++++++---------- 1 file changed, 16 insertions(+), 10 deletions(-) diff --git a/docs/iris/src/whatsnew/3.0.4.rst b/docs/iris/src/whatsnew/3.0.4.rst index cfbd609f03..7c5c11032f 100644 --- a/docs/iris/src/whatsnew/3.0.4.rst +++ b/docs/iris/src/whatsnew/3.0.4.rst @@ -18,6 +18,22 @@ This document explains the changes made to Iris for this release 🐛 **Bugs Fixed** + #. `@pp-mo`_ reverted a change made previously in (:pull:`3659`) to + :meth:`iris.fileformats.pp.PPDataProxy.__getitem__`. The check for empty slicings + is no longer needed since (:pull:`4135`) was added. (:pull:`4141`) + + +.. dropdown:: :opticon:`alert` v3.0.3 Patches + :container: + shadow + :title: text-primary text-center font-weight-bold + :body: bg-light + :animate: fade-in + :open: + + The patches included in this release include: + + 🐛 **Bugs Fixed** + #. `@lbdreyer`_ modified :meth:`~iris.cube.Cube.intersection` to use a tolerant equality check, when looking for cells that straddle the wrapping point. (:pull:`4220`) @@ -46,12 +62,6 @@ This document explains the changes made to Iris for this release between a coordinate and a cube, and for convenience additionally includes :meth:`iris.cube.Cube.__neg__` support. (:pull:`4159`) - #. `@pp-mo`_ fixed 2 bugs in cube printout: - Firstly, ancillary-variables or cell-measures with long names can now widen the cube "dimensions map" to fit, - whereas previously printing these cases caused an Exception. - Secondly, cube units are now always printed, whereas previously they were missed out any time that the - "dimensions map" was widened to accomodate long coordinate names. - 📚 **Documentation** #. `@bjlittle`_ updated the ``intersphinx_mapping`` and fixed documentation @@ -73,10 +83,6 @@ This document explains the changes made to Iris for this release to avoid the dask 'test access'. This makes loading of netcdf files with a large number of variables significantly faster. (:pull:`4135`) - #. `@pp-mo`_ reverted a change made previously in (:pull:`3659`) to - :meth:`iris.fileformats.pp.PPDataProxy.__getitem__`. The check for empty slicings - is no longer needed since (:pull:`4135`) was added. (:pull:`4141`) - Note that, the above contributions labelled with ``pre-v3.1.0`` are part of the forthcoming Iris v3.1.0 release, but require to be included in this patch release. From 1070a505c29dd93887664b1a91e1237bda073efc Mon Sep 17 00:00:00 2001 From: Patrick Peglar Date: Thu, 8 Jul 2021 14:47:05 +0100 Subject: [PATCH 6/6] Fix initial sections display. --- docs/iris/src/whatsnew/3.0.4.rst | 1 - 1 file changed, 1 deletion(-) diff --git a/docs/iris/src/whatsnew/3.0.4.rst b/docs/iris/src/whatsnew/3.0.4.rst index 7c5c11032f..f43ce0d057 100644 --- a/docs/iris/src/whatsnew/3.0.4.rst +++ b/docs/iris/src/whatsnew/3.0.4.rst @@ -28,7 +28,6 @@ This document explains the changes made to Iris for this release :title: text-primary text-center font-weight-bold :body: bg-light :animate: fade-in - :open: The patches included in this release include: