diff --git a/.github/ISSUE_TEMPLATE/bug-report.md b/.github/ISSUE_TEMPLATE/bug-report.md new file mode 100644 index 00000000000..9bb783574f6 --- /dev/null +++ b/.github/ISSUE_TEMPLATE/bug-report.md @@ -0,0 +1,31 @@ +--- +name: "\U0001F41B Bug Report" +about: Submit a bug report to help us improve Iris +title: '' +labels: 'New: Issue, Type: Bug' +assignees: '' + +--- + +## 🐛 Bug Report + + +## How To Reproduce +Steps to reproduce the behaviour: + +1. +2. +3. + +## Expected behaviour + + +## Screenshots + + +## Environment + - OS & Version: [e.g., Ubuntu 20.04 LTS] + - Iris Version: [e.g., From the command line run `python -c "import iris; print(iris.__version__)"`] + +## Additional context + diff --git a/.github/ISSUE_TEMPLATE/config.yml b/.github/ISSUE_TEMPLATE/config.yml new file mode 100644 index 00000000000..6d8befbe3c1 --- /dev/null +++ b/.github/ISSUE_TEMPLATE/config.yml @@ -0,0 +1,2 @@ +# reference: https://docs.github.com/en/github/building-a-strong-community/configuring-issue-templates-for-your-repository#configuring-the-template-chooser +blank_issues_enabled: false diff --git a/.github/ISSUE_TEMPLATE/documentation.md b/.github/ISSUE_TEMPLATE/documentation.md new file mode 100644 index 00000000000..8caa62a1c7f --- /dev/null +++ b/.github/ISSUE_TEMPLATE/documentation.md @@ -0,0 +1,12 @@ +--- +name: "\U0001F4DA Documentation" +about: Report an issue with the Iris documentation +title: '' +labels: 'New: Documentation, Type: Documentation' +assignees: '' + +--- + +## 📚 Documentation + + diff --git a/.github/ISSUE_TEMPLATE/feature-request.md b/.github/ISSUE_TEMPLATE/feature-request.md new file mode 100644 index 00000000000..e8b1c3894c9 --- /dev/null +++ b/.github/ISSUE_TEMPLATE/feature-request.md @@ -0,0 +1,18 @@ +--- +name: "⚙ Feature Request" +about: Submit a request for a new feature in Iris +title: '' +labels: 'New: Feature' +assignees: '' + +--- + +## ⚙ Feature Request + + +## Motivation + + + +## Additional context + diff --git a/.github/ISSUE_TEMPLATE/issue.md b/.github/ISSUE_TEMPLATE/issue.md new file mode 100644 index 00000000000..e66042609c9 --- /dev/null +++ b/.github/ISSUE_TEMPLATE/issue.md @@ -0,0 +1,11 @@ +--- +name: "\U0001F4F0 Custom Issue" +about: Submit a generic issue to help us improve Iris +title: '' +labels: 'New: Issue' +assignees: '' + +--- + +## 📰 Custom Issue + diff --git a/ci/requirements/readthedocs.yml b/ci/requirements/readthedocs.yml index 4a1df9cc7b5..121f8a67226 100644 --- a/ci/requirements/readthedocs.yml +++ b/ci/requirements/readthedocs.yml @@ -14,12 +14,11 @@ dependencies: # Without these, iris won't even import. - - cartopy>=0.12 - - proj4<6 + - cartopy>=0.18 - cf-units>=2 - cftime - dask>=2 - - matplotlib<3.3 + - matplotlib - netcdf4 - numpy>=1.14 - scipy diff --git a/docs/iris/src/index.rst b/docs/iris/src/index.rst index 83392b3d65c..c3cd487de59 100644 --- a/docs/iris/src/index.rst +++ b/docs/iris/src/index.rst @@ -1,10 +1,16 @@ +.. note:: For **Iris 2.4** and earlier documentation please see the + `legacy documentation`_ + +.. _legacy documentation: https://scitools.org.uk/iris/docs/v2.4.0/ + + Iris Documentation ================== .. todolist:: -**A powerful, format-agnostic, community-driven Python library for analysing and -visualising Earth science data.** +**A powerful, format-agnostic, community-driven Python library for analysing +and visualising Earth science data.** Iris implements a data model based on the `CF conventions `_ giving you a powerful, format-agnostic interface for working with your data. @@ -23,18 +29,19 @@ associated metadata as first-class objects includes: * subsetting and extraction, * merge and concatenate, * aggregations and reductions (including min, max, mean and weighted averages), -* interpolation and regridding (including nearest-neighbor, linear and area-weighted), and +* interpolation and regridding (including nearest-neighbor, linear and + area-weighted), and * operator overloads (``+``, ``-``, ``*``, ``/``, etc.). -A number of file formats are recognised by Iris, including CF-compliant NetCDF, GRIB, -and PP, and it has a plugin architecture to allow other formats to be added seamlessly. +A number of file formats are recognised by Iris, including CF-compliant NetCDF, +GRIB, and PP, and it has a plugin architecture to allow other formats to be +added seamlessly. Building upon `NumPy `_ and -`dask `_, -Iris scales from efficient single-machine workflows right through to multi-core -clusters and HPC. -Interoperability with packages from the wider scientific Python ecosystem comes from Iris' -use of standard NumPy/dask arrays as its underlying data storage. +`dask `_, Iris scales from efficient +single-machine workflows right through to multi-core clusters and HPC. +Interoperability with packages from the wider scientific Python ecosystem comes +from Iris' use of standard NumPy/dask arrays as its underlying data storage. .. toctree:: diff --git a/docs/iris/src/userguide/cube_maths.rst b/docs/iris/src/userguide/cube_maths.rst index e42af10ea22..69273b45b96 100644 --- a/docs/iris/src/userguide/cube_maths.rst +++ b/docs/iris/src/userguide/cube_maths.rst @@ -219,6 +219,8 @@ The result could now be plotted using the guidance provided in the A very similar example to this can be found in the examples section, with the title "Deriving Exner Pressure and Air Temperature". +.. _cube_maths_combining_units: + Combining units --------------- diff --git a/docs/iris/src/whatsnew/contributions_3.0.0/bugfix_2019-Nov-21_cell_measure_attributes.txt b/docs/iris/src/whatsnew/contributions_3.0.0/bugfix_2019-Nov-21_cell_measure_attributes.txt deleted file mode 100644 index 577e193fe56..00000000000 --- a/docs/iris/src/whatsnew/contributions_3.0.0/bugfix_2019-Nov-21_cell_measure_attributes.txt +++ /dev/null @@ -1,2 +0,0 @@ -* Fixed a bug where the attributes of cell measures in netcdf-CF files were discarded on - loading. They now appear on the CellMeasure in the loaded cube. diff --git a/docs/iris/src/whatsnew/contributions_3.0.0/docchange_2020-Aug-25_clarify_unit_handling.txt b/docs/iris/src/whatsnew/contributions_3.0.0/docchange_2020-Aug-25_clarify_unit_handling.txt deleted file mode 100644 index a9d953dfbe6..00000000000 --- a/docs/iris/src/whatsnew/contributions_3.0.0/docchange_2020-Aug-25_clarify_unit_handling.txt +++ /dev/null @@ -1 +0,0 @@ -* Added an explanation to the user guide of how units are handled by cube arithmetic. \ No newline at end of file diff --git a/docs/iris/src/whatsnew/contributions_3.0.0/incompatiblechange_2020-May-15_change_default_unit_loading.txt b/docs/iris/src/whatsnew/contributions_3.0.0/incompatiblechange_2020-May-15_change_default_unit_loading.txt deleted file mode 100644 index be048990f3a..00000000000 --- a/docs/iris/src/whatsnew/contributions_3.0.0/incompatiblechange_2020-May-15_change_default_unit_loading.txt +++ /dev/null @@ -1 +0,0 @@ -* When loading data from netcdf-CF files, where a variable has no "units" property, the corresponding Iris object will have "units='unknown'". Prior to Iris 3.0, these cases defaulted to "units='1'". \ No newline at end of file diff --git a/docs/iris/src/whatsnew/contributions_3.0.0/newfeature_2019-Nov-21_netcdf_ancillary_data.txt b/docs/iris/src/whatsnew/contributions_3.0.0/newfeature_2019-Nov-21_netcdf_ancillary_data.txt deleted file mode 100644 index 26f01c16c2e..00000000000 --- a/docs/iris/src/whatsnew/contributions_3.0.0/newfeature_2019-Nov-21_netcdf_ancillary_data.txt +++ /dev/null @@ -1,2 +0,0 @@ -* CF Ancillary Variables are now loaded from and saved to netcdf-CF files. Support for `quality flags `_ is also provided to ensure they load and save with appropriate units. - diff --git a/lib/iris/analysis/cartography.py b/lib/iris/analysis/cartography.py index f103549d4ed..8d047203ce6 100644 --- a/lib/iris/analysis/cartography.py +++ b/lib/iris/analysis/cartography.py @@ -599,6 +599,12 @@ def project(cube, target_proj, nx=None, ny=None): on the statistics of the data e.g. the mean and standard deviation will not be preserved. + .. warning:: + + If the target projection is non-rectangular, e.g. Robinson, the target + grid may include points outside the boundary of the projection. The + latitude/longitude of such points may be unpredictable. + """ try: lon_coord, lat_coord = _get_lon_lat_coords(cube) diff --git a/lib/iris/plot.py b/lib/iris/plot.py index 36afe906dc8..0500c3d8906 100644 --- a/lib/iris/plot.py +++ b/lib/iris/plot.py @@ -441,6 +441,11 @@ def _draw_2d_from_bounds(draw_method_name, cube, *args, **kwargs): values = np.arange(data.shape[data_dim] + 1) - 0.5 else: values = coord.contiguous_bounds() + values = _fixup_dates(coord, values) + if values.dtype == np.dtype(object) and isinstance( + values[0], datetime.datetime + ): + values = mpl_dates.date2num(values) plot_arrays.append(values) diff --git a/lib/iris/quickplot.py b/lib/iris/quickplot.py index 147f119fd3b..42c0dba46ab 100644 --- a/lib/iris/quickplot.py +++ b/lib/iris/quickplot.py @@ -13,7 +13,10 @@ """ +from packaging import version + import cf_units +from matplotlib import __version__ as _mpl_version import matplotlib.pyplot as plt import iris.config @@ -46,6 +49,13 @@ def _title(cube_or_coord, with_units): if _use_symbol(units): units = units.symbol + if units.is_time_reference(): + # iris.plot uses matplotlib.dates.date2num, which is fixed to the below unit. + if version.parse(_mpl_version) >= version.parse("3.3"): + days_since = "1970-01-01" + else: + days_since = "0001-01-01" + units = "days since {}".format(days_since) title += " / {}".format(units) return title diff --git a/lib/iris/tests/experimental/test_raster.py b/lib/iris/tests/experimental/test_raster.py index 44a28576459..80ff7251206 100644 --- a/lib/iris/tests/experimental/test_raster.py +++ b/lib/iris/tests/experimental/test_raster.py @@ -77,6 +77,10 @@ def _check_tiff_export(self, masked, inverted=False): 339, 33550, 33922, + 42113, + # Don't add a check entry for this, as coding changed between gdal + # version 1 and 2. + # tif_header_entries[42113] = (u'1e+20',) ] tif_header_entries = { 256: (160,), @@ -130,12 +134,6 @@ def _check_tiff_export(self, masked, inverted=False): # Mask some of the data + expect a slightly different header... cube.data = np.ma.masked_where(cube.data <= 380, cube.data) - # There is an additional key.. - tif_header_keys += [42113] - # Don't add a check entry for this, as coding changed between gdal - # version 1 and 2, *and* between Python2 and Python3. - # tif_header_entries[42113] = (u'1e+20',) - if inverted: # Check with the latitude coordinate (and the corresponding # cube.data) inverted. diff --git a/lib/iris/tests/integration/plot/test_plot_2d_coords.py b/lib/iris/tests/integration/plot/test_plot_2d_coords.py index 7883fd713a8..00543409765 100644 --- a/lib/iris/tests/integration/plot/test_plot_2d_coords.py +++ b/lib/iris/tests/integration/plot/test_plot_2d_coords.py @@ -43,14 +43,14 @@ def test_2d_coord_bounds_platecarree(self): cube = simple_cube_w_2d_coords()[0, 0] ax = plt.axes(projection=ccrs.PlateCarree(central_longitude=180)) qplt.pcolormesh(cube) - ax.coastlines(color="red") + ax.coastlines(resolution="110m", color="red") self.check_graphic() def test_2d_coord_bounds_northpolarstereo(self): cube = simple_cube_w_2d_coords()[0, 0] ax = plt.axes(projection=ccrs.NorthPolarStereo()) qplt.pcolormesh(cube) - ax.coastlines(color="red") + ax.coastlines(resolution="110m", color="red") self.check_graphic() @@ -71,7 +71,7 @@ def test_2d_coords_contour(self): cube.add_aux_coord(co_x, (0, 1)) ax = plt.axes(projection=ccrs.PlateCarree()) qplt.contourf(cube) - ax.coastlines(color="red") + ax.coastlines(resolution="110m", color="red") ax.gridlines(draw_labels=True) ax.set_extent((0, 180, 0, 90)) self.check_graphic() diff --git a/lib/iris/tests/integration/plot/test_vector_plots.py b/lib/iris/tests/integration/plot/test_vector_plots.py index 19a5a60c2d6..e811efd0150 100644 --- a/lib/iris/tests/integration/plot/test_vector_plots.py +++ b/lib/iris/tests/integration/plot/test_vector_plots.py @@ -121,7 +121,7 @@ def test_2d_plain_latlon(self): self.plot( "latlon_2d", u_cube, v_cube, coords=("longitude", "latitude") ) - ax.coastlines(color="red") + ax.coastlines(resolution="110m", color="red") ax.set_global() self.check_graphic() @@ -132,7 +132,7 @@ def test_2d_plain_latlon_on_polar_map(self): self.plot( "latlon_2d_polar", u_cube, v_cube, coords=("longitude", "latitude") ) - ax.coastlines(color="red") + ax.coastlines(resolution="110m", color="red") self.check_graphic() def test_2d_rotated_latlon(self): @@ -142,7 +142,7 @@ def test_2d_rotated_latlon(self): self.plot( "2d_rotated", u_cube, v_cube, coords=("longitude", "latitude") ) - ax.coastlines(color="red") + ax.coastlines(resolution="110m", color="red") ax.set_global() self.check_graphic() diff --git a/lib/iris/tests/results/imagerepo.json b/lib/iris/tests/results/imagerepo.json index a353507d12a..f9430ae9f58 100644 --- a/lib/iris/tests/results/imagerepo.json +++ b/lib/iris/tests/results/imagerepo.json @@ -6,7 +6,8 @@ "gallery_tests.test_plot_COP_maps.TestCOPMaps.test_plot_cop_maps.0": [ "https://scitools.github.io/test-iris-imagehash/images/v4/ea9138db95668524913e6ac168997e85957e917e876396b96a81b5ce3c496935.png", "https://scitools.github.io/test-iris-imagehash/images/v4/ea9130db95668524913c6ac178995b0d956e917ec76396b96a853dcf94696935.png", - "https://scitools.github.io/test-iris-imagehash/images/v4/ea9130db95668524913e6ac168991f0d956e917ec76396b96a853dcf94796931.png" + "https://scitools.github.io/test-iris-imagehash/images/v4/ea9130db95668524913e6ac168991f0d956e917ec76396b96a853dcf94796931.png", + "https://scitools.github.io/test-iris-imagehash/images/v4/ea9130db95668524913d6ac168991f0d956e917ec76396b96a853dcf94696935.png" ], "gallery_tests.test_plot_SOI_filtering.TestSOIFiltering.test_plot_soi_filtering.0": [ "https://scitools.github.io/test-iris-imagehash/images/v4/fac460b9c17b78723e05a5a9954edaf062332799954e9ca5c63b9a52d24e5a95.png", @@ -21,7 +22,8 @@ ], "gallery_tests.test_plot_anomaly_log_colouring.TestAnomalyLogColouring.test_plot_anomaly_log_colouring.0": [ "https://scitools.github.io/test-iris-imagehash/images/v4/ec4464e185a39f93931e9b1e91696d2949dde6e63e26a47a5ad391938d9a5a0c.png", - "https://scitools.github.io/test-iris-imagehash/images/v4/ecc164e78e979b19b3789b0885a564a56cc2c65e3ec69469db1bdb9a853c1e24.png" + "https://scitools.github.io/test-iris-imagehash/images/v4/ecc164e78e979b19b3789b0885a564a56cc2c65e3ec69469db1bdb9a853c1e24.png", + "https://scitools.github.io/test-iris-imagehash/images/v4/ece164e68e979b19b3781b0885a564a56ccac65e3ec69469db1bdb9a853c1e24.png" ], "gallery_tests.test_plot_atlantic_profiles.TestAtlanticProfiles.test_plot_atlantic_profiles.0": [ "https://scitools.github.io/test-iris-imagehash/images/v4/9f8260536bd28e1320739437b5f437b0a51d66f4cc5d08fcd00fdb1c93fcb21c.png", @@ -35,7 +37,7 @@ "https://scitools.github.io/test-iris-imagehash/images/v4/eeea64dd6ea8cd99991f1322b3761e06845718d89995b3131f32a4765ec2a1cd.png", "https://scitools.github.io/test-iris-imagehash/images/v4/eeea64dd6ea8cd99991d1322b3741e2684571cd89995b3131f32a4765ee2a1cc.png" ], - "gallery_tests.test_plot_coriolis.TestCoriolisPlot.test_plot_coriolis.0": [ + "gallery_tests.test_plot_coriolis.TestCoriolisPlot.test_plot_coriolis.0": [ "https://scitools.github.io/test-iris-imagehash/images/v4/e78665de9a699659e55e9965886979966986c5e63e98c19e3a256679e1981a24.png", "https://scitools.github.io/test-iris-imagehash/images/v4/e68665de9a699659c1fe99a5896965966996c46e3e19c1da3a652669c51e1a26.png" ], @@ -48,8 +50,7 @@ "https://scitools.github.io/test-iris-imagehash/images/v4/ea9521fb956a394068931e9be07e4aa5856cc47e4a91957a1ba55bb5b17a3b81.png" ], "gallery_tests.test_plot_custom_aggregation.TestCustomAggregation.test_plot_custom_aggregation.0": [ - "https://scitools.github.io/test-iris-imagehash/images/v4/fe816e81917e907eb43e873f85677ac190f0703c6a95811f1ac33ce1a57a6f18.png", - "https://scitools.github.io/test-iris-imagehash/images/v4/fe816e81817e907eb43e873f85637ac198d8703c6a94811f1ac73ee1a57a6f90.png" + "https://scitools.github.io/test-iris-imagehash/images/v4/ee816f81917e907eb03ec73f856f7ac198d070186e90811f1be33ee1a57a6e18.png" ], "gallery_tests.test_plot_custom_file_loading.TestCustomFileLoading.test_plot_custom_file_loading.0": [ "https://scitools.github.io/test-iris-imagehash/images/v4/faa0cbf1845e34be913787416edcc8bc3bc81f9b63332662a4ed30cdc1b2cd21.png", @@ -107,9 +108,7 @@ "https://scitools.github.io/test-iris-imagehash/images/v4/be817a87845ea56cec79817a919e338436a5c1e73fa16c736c4a3e816a1e6b1c.png" ], "gallery_tests.test_plot_polar_stereo.TestPolarStereo.test_plot_polar_stereo.0": [ - "https://scitools.github.io/test-iris-imagehash/images/v4/e168317a92d36d89c5bb9e94c55e6f0c9a93c15a6ec584763b21716791de3a81.png", - "https://scitools.github.io/test-iris-imagehash/images/v4/b9e16079971e9e93c8ce0f84c31e3b929f92c0ff3ca1c17e39e03961c07e3f80.png", - "https://scitools.github.io/test-iris-imagehash/images/v4/ba1e615ec7e097a9961f9cb190f838e091c2c1e73f07c11f6f386b3cc1783e11.png" + "https://scitools.github.io/test-iris-imagehash/images/v4/ba1e615ec7e097ad961f9cb190f038e091c2c1e73f07c11f6f386b3cc1793e01.png" ], "gallery_tests.test_plot_polynomial_fit.TestPolynomialFit.test_plot_polynomial_fit.0": [ "https://scitools.github.io/test-iris-imagehash/images/v4/abff4a9df26435886520c97f12414695c4b69d23934bc86adc969237d68ccc6f.png", @@ -124,12 +123,7 @@ "https://scitools.github.io/test-iris-imagehash/images/v4/fa854f19851a30e4cc76cd0bb0f932dca7c665b1c92ccb4b4ed19e9c3721b5c8.png" ], "gallery_tests.test_plot_projections_and_annotations.TestProjectionsAndAnnotations.test_plot_projections_and_annotations.1": [ - "https://scitools.github.io/test-iris-imagehash/images/v4/e385699d9c3896627243318fcdad5a7dc6dba492e9b69964936dc21974b18592.png", - "https://scitools.github.io/test-iris-imagehash/images/v4/e385699d9c3896727243318f8dad5a7dc65ba492b93699649b6dc25b64938592.png", - 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"https://scitools.github.io/test-iris-imagehash/images/v4/e85a636c86a597a791c9349b94b79969c396c95bccc69a64db38c9b039a58ca6.png" + "https://scitools.github.io/test-iris-imagehash/images/v4/e85a636c86a597a791c9349b94b79969c396c95bccc69a64db38c9b039a58ca6.png", + "https://scitools.github.io/test-iris-imagehash/images/v4/e85a634c86a597a793c9349b94b79969c396c95bcce69a64d938c9b039a58ca6.png" ], "iris.tests.test_quickplot.TestQuickplotCoordinatesGiven.test_yx.4": [ "https://scitools.github.io/test-iris-imagehash/images/v4/ad2f6d2fd2d09295c2d1c3d33c1bc2d67d2c696ce0653c3ac2b1d976da05c2c4.png", @@ -1034,4 +1022,4 @@ "https://scitools.github.io/test-iris-imagehash/images/v4/82fe81987fdf77ffe0002addd4002805dd28df67d9a9d4625bfddc209841de20.png", "https://scitools.github.io/test-iris-imagehash/images/v4/82fa80997f547799a0037a00d52f0956ddaf9f7e98a1816e09f5d8260bfffe00.png" ] -} \ No newline at end of file +} diff --git a/lib/iris/tests/results/unit/analysis/cartography/project/TestAll/cube.cml b/lib/iris/tests/results/unit/analysis/cartography/project/TestAll/cube.cml index 6c192a10063..5504f2a91fb 100644 --- a/lib/iris/tests/results/unit/analysis/cartography/project/TestAll/cube.cml +++ b/lib/iris/tests/results/unit/analysis/cartography/project/TestAll/cube.cml @@ -9,24 +9,21 @@ - + [84.2615071705, 54.8444503701, 26.7572382165, + ..., 30.1637424823, 58.6051855118, + 86.9541974993], + [inf, 62.6851802716, 39.629088106, ..., + 42.3249307728, 64.8680485778, inf], + [inf, inf, 46.2669891845, ..., 47.2804926757, + inf, inf]]" shape="(10, 10)" standard_name="latitude" units="Unit('degrees')" value_type="float64"> @@ -40,23 +37,20 @@ - + [-58.34983089, -70.8813785605, -58.2031036304, + ..., 60.1459645527, 72.0019781785, + 20.6956240803], + [inf, -35.1608514733, -42.5369291003, ..., + 43.052784475, 31.4703511243, inf], + [inf, inf, -15.3083916055, ..., 14.2709222711, + inf, inf]]" shape="(10, 10)" standard_name="longitude" units="Unit('degrees')" value_type="float64"> @@ -74,10 +68,10 @@ 15305249.9975]" shape="(10,)" standard_name="projection_x_coordinate" units="Unit('m')" value_type="float64"/> - + =0.12 -#conda: proj4<6 +cartopy>=0.18 cf-units>=2 cftime dask[array]>=2 #conda: dask>=2 -matplotlib<3.3 +matplotlib netcdf4 numpy>=1.14 scipy diff --git a/requirements/extensions.txt b/requirements/extensions.txt index 8e8e847f889..220fb562ec0 100644 --- a/requirements/extensions.txt +++ b/requirements/extensions.txt @@ -6,4 +6,3 @@ # first. iris-grib #conda: -gdal