From de911ce55da50172b51c662c44a7d1adff148dca Mon Sep 17 00:00:00 2001 From: Martin Yeo <40734014+trexfeathers@users.noreply.github.com> Date: Fri, 16 Sep 2022 14:23:32 +0100 Subject: [PATCH 1/9] Lockfile updates (#4968) * Updated environment lockfiles * Adjustments for Cartopy v0.21.0 (SciTools/cartopy@fcb784d). * Cartopy >=0.21 pin. * What's New entry. * WIP try netCDF4 pin. * Try pip installing netcdf4==1.6.1 as requested by @ocefpaf. * Revert "Try pip installing netcdf4==1.6.1 as requested by @ocefpaf." This reverts commit ce9f890980e32d7af9ef88c747e81b05fd5dea09. * netcdf4!=1.6.1 * Align Conda YAML formatting. Co-authored-by: Lockfile bot --- docs/src/whatsnew/latest.rst | 13 ++- lib/iris/analysis/cartography.py | 4 +- .../analysis/cartography/test_rotate_winds.py | 25 +++--- requirements/ci/nox.lock/py310-linux-64.lock | 84 +++++++++--------- requirements/ci/nox.lock/py38-linux-64.lock | 86 +++++++++---------- requirements/ci/nox.lock/py39-linux-64.lock | 86 +++++++++---------- requirements/ci/py310.yml | 4 +- requirements/ci/py38.yml | 4 +- requirements/ci/py39.yml | 4 +- setup.cfg | 4 +- 10 files changed, 164 insertions(+), 150 deletions(-) diff --git a/docs/src/whatsnew/latest.rst b/docs/src/whatsnew/latest.rst index a420494157..73f7e60351 100644 --- a/docs/src/whatsnew/latest.rst +++ b/docs/src/whatsnew/latest.rst @@ -50,7 +50,7 @@ This document explains the changes made to Iris for this release #. `@bjlittle`_ and `@lbdreyer`_ (reviewer) fixed the building of the CF Standard Names module ``iris.std_names`` for the ``setup.py`` commands ``develop`` and ``std_names``. (:issue:`4951`, :pull:`4952`) - + #. `@lbdreyer`_ and `@pp-mo`_ (reviewer) fixed the cube print out such that scalar ancillary variables are displayed in a dedicated section rather than being added to the vector ancillary variables section. Further, ancillary @@ -83,6 +83,13 @@ This document explains the changes made to Iris for this release #. `@rcomer`_ introduced the ``dask >=2.26`` minimum pin, so that Iris can benefit from Dask's support for `NEP13`_ and `NEP18`_. (:pull:`4905`) +#. `@trexfeathers`_ advanced the Cartopy pin to ``>=0.21``, as Cartopy's + change to default Transverse Mercator projection affects an Iris test. + See `SciTools/cartopy@fcb784d`_ and `SciTools/cartopy@8860a81`_ for more + details. + (:pull:`4968`) +#. `@trexfeathers`_ introduced the ``netcdf4!=1.6.1`` pin to avoid a problem + with segfaults. (:pull:`4968`) 📚 Documentation @@ -117,4 +124,6 @@ This document explains the changes made to Iris for this release .. _NEP13: https://numpy.org/neps/nep-0013-ufunc-overrides.html .. _NEP18: https://numpy.org/neps/nep-0018-array-function-protocol.html -.. _pypa/setuptools#1684: https://github.com/pypa/setuptools/issues/1684 \ No newline at end of file +.. _pypa/setuptools#1684: https://github.com/pypa/setuptools/issues/1684 +.. _SciTools/cartopy@fcb784d: https://github.com/SciTools/cartopy/commit/fcb784daa65d95ed9a74b02ca292801c02bc4108 +.. _SciTools/cartopy@8860a81: https://github.com/SciTools/cartopy/commit/8860a8186d4dc62478e74c83f3b2b3e8f791372e \ No newline at end of file diff --git a/lib/iris/analysis/cartography.py b/lib/iris/analysis/cartography.py index 44129ff175..f38e48354d 100644 --- a/lib/iris/analysis/cartography.py +++ b/lib/iris/analysis/cartography.py @@ -1008,8 +1008,8 @@ def _transform_distance_vectors_tolerance_mask( u_one_t, v_zero_t = _transform_distance_vectors(ones, zeros, ds, dx2, dy2) u_zero_t, v_one_t = _transform_distance_vectors(zeros, ones, ds, dx2, dy2) # Squared magnitudes should be equal to one within acceptable tolerance. - # A value of atol=2e-3 is used, which corresponds to a change in magnitude - # of approximately 0.1%. + # A value of atol=2e-3 is used, which masks any magnitude changes >0.5% + # (approx percentage - based on experimenting). sqmag_1_0 = u_one_t**2 + v_zero_t**2 sqmag_0_1 = u_zero_t**2 + v_one_t**2 mask = np.logical_not( diff --git a/lib/iris/tests/unit/analysis/cartography/test_rotate_winds.py b/lib/iris/tests/unit/analysis/cartography/test_rotate_winds.py index 7bd8fdb597..7952b3bb46 100644 --- a/lib/iris/tests/unit/analysis/cartography/test_rotate_winds.py +++ b/lib/iris/tests/unit/analysis/cartography/test_rotate_winds.py @@ -16,6 +16,7 @@ import cartopy.crs as ccrs import numpy as np import numpy.ma as ma +import pytest from iris.analysis.cartography import rotate_winds, unrotate_pole import iris.coord_systems @@ -410,7 +411,11 @@ def test_transposed(self): class TestMasking(tests.IrisTest): def test_rotated_to_osgb(self): # Rotated Pole data with large extent. - x = np.linspace(311.9, 391.1, 10) + # A 'correct' answer is not known for this test; it is therefore + # written as a 'benchmark' style test - a change in behaviour will + # cause a test failure, requiring developers to approve/reject the + # new behaviour. + x = np.linspace(221.9, 301.1, 10) y = np.linspace(-23.6, 24.8, 8) u, v = uv_cubes(x, y) ut, vt = rotate_winds(u, v, iris.coord_systems.OSGB()) @@ -422,14 +427,14 @@ def test_rotated_to_osgb(self): # Snapshot of mask with fixed tolerance of atol=2e-3 expected_mask = np.array( [ - [1, 1, 1, 0, 0, 0, 0, 0, 0, 1], - [1, 1, 1, 0, 0, 0, 0, 0, 0, 1], - [1, 1, 1, 1, 0, 0, 0, 0, 1, 1], - [1, 1, 1, 1, 0, 0, 0, 0, 1, 1], - [1, 1, 1, 1, 0, 0, 0, 0, 1, 1], - [1, 1, 1, 1, 1, 0, 0, 1, 1, 1], - [1, 1, 1, 1, 1, 0, 0, 1, 1, 1], - [1, 1, 1, 1, 1, 0, 0, 1, 1, 1], + [0, 0, 0, 1, 1, 1, 0, 0, 0, 1], + [0, 0, 0, 0, 1, 1, 1, 0, 1, 1], + [0, 0, 0, 0, 0, 1, 1, 1, 1, 1], + [0, 0, 0, 0, 1, 1, 1, 0, 0, 0], + [0, 0, 0, 1, 1, 1, 1, 1, 0, 0], + [0, 1, 1, 1, 1, 1, 1, 0, 0, 0], + [0, 1, 1, 1, 0, 1, 1, 1, 0, 0], + [0, 1, 0, 0, 0, 0, 1, 1, 1, 0], ], np.bool_, ) @@ -443,7 +448,7 @@ def test_rotated_to_osgb(self): # Calculate percentage error (note there are no zero magnitudes # so we can divide safely). anom = 100.0 * np.abs(res_mag - expected_mag) / expected_mag - self.assertTrue(anom[~ut.data.mask].max() < 0.1) + assert anom[~ut.data.mask].max() == pytest.approx(0.3227935) def test_rotated_to_unrotated(self): # Suffiently accurate so that no mask is introduced. diff --git a/requirements/ci/nox.lock/py310-linux-64.lock b/requirements/ci/nox.lock/py310-linux-64.lock index d88fd19a29..5a18284896 100644 --- a/requirements/ci/nox.lock/py310-linux-64.lock +++ b/requirements/ci/nox.lock/py310-linux-64.lock @@ -1,9 +1,9 @@ # Generated by conda-lock. # platform: 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https://conda.anaconda.org/conda-forge/linux-64/cf-units-3.1.1-py39hd257fcd_0.tar.bz2#e0f1f1d3013be31359d3ac635b288469 https://conda.anaconda.org/conda-forge/linux-64/esmf-8.2.0-mpi_mpich_h5a1934d_102.tar.bz2#bb8bdfa5e3e9e3f6ec861f05cd2ad441 https://conda.anaconda.org/conda-forge/linux-64/gtk2-2.24.33-h90689f9_2.tar.bz2#957a0255ab58aaf394a91725d73ab422 -https://conda.anaconda.org/conda-forge/noarch/identify-2.5.3-pyhd8ed1ab_0.tar.bz2#682f05a8e4b047ce4bdcec9d69c12551 -https://conda.anaconda.org/conda-forge/noarch/imagehash-4.2.1-pyhd8ed1ab_0.tar.bz2#01cc8698b6e1a124dc4f585516c27643 +https://conda.anaconda.org/conda-forge/noarch/identify-2.5.5-pyhd8ed1ab_0.tar.bz2#985ef0c4ed7a26731c419818080ef6ce +https://conda.anaconda.org/conda-forge/noarch/imagehash-4.3.0-pyhd8ed1ab_0.tar.bz2#aee564f0021a2a0ab12239fbdd28e209 https://conda.anaconda.org/conda-forge/linux-64/librsvg-2.54.4-h7abd40a_0.tar.bz2#921e53675ed5ea352f022b79abab076a https://conda.anaconda.org/conda-forge/linux-64/matplotlib-base-3.5.3-py39h19d6b11_2.tar.bz2#dc400bb297d8425b8b05367a21854b0b -https://conda.anaconda.org/conda-forge/linux-64/netcdf4-1.6.0-nompi_py39h71b8e10_101.tar.bz2#91e01aa93a2bcca96c9d64d2ce4f65f0 +https://conda.anaconda.org/conda-forge/linux-64/netcdf4-1.6.0-nompi_py39h6ced12a_102.tar.bz2#b92600d0fef7f12f426935d87d6413e6 https://conda.anaconda.org/conda-forge/noarch/pyopenssl-22.0.0-pyhd8ed1ab_0.tar.bz2#1d7e241dfaf5475e893d4b824bb71b44 https://conda.anaconda.org/conda-forge/linux-64/pyqt5-sip-12.11.0-py39h5a03fae_0.tar.bz2#1fd9112714d50ee5be3dbf4fd23964dc https://conda.anaconda.org/conda-forge/noarch/pytest-forked-1.4.0-pyhd8ed1ab_0.tar.bz2#95286e05a617de9ebfe3246cecbfb72f -https://conda.anaconda.org/conda-forge/linux-64/qt-main-5.15.4-ha5833f6_2.tar.bz2#dd3aa6715b9e9efaf842febf18ce4261 -https://conda.anaconda.org/conda-forge/linux-64/cartopy-0.20.3-py39hed214b2_2.tar.bz2#12964abb0bdcb4abb3c680b359560c1b 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b/requirements/ci/py310.yml index 8f730729b7..76ca9e4f58 100644 --- a/requirements/ci/py310.yml +++ b/requirements/ci/py310.yml @@ -11,12 +11,12 @@ dependencies: - setuptools-scm >=7 # Core dependencies. - - cartopy >=0.20 + - cartopy >=0.21 - cf-units >=3.1 - cftime >=1.5 - dask-core >=2.26 - matplotlib - - netcdf4 + - netcdf4 !=1.6.1 - numpy >=1.19 - python-xxhash - pyproj diff --git a/requirements/ci/py38.yml b/requirements/ci/py38.yml index d92a68076c..5a8c878ee1 100644 --- a/requirements/ci/py38.yml +++ b/requirements/ci/py38.yml @@ -11,12 +11,12 @@ dependencies: - setuptools-scm >=7 # Core dependencies. - - cartopy >=0.20 + - cartopy >=0.21 - cf-units >=3.1 - cftime >=1.5 - dask-core >=2.26 - matplotlib - - netcdf4 + - netcdf4 !=1.6.1 - numpy >=1.19 - python-xxhash - pyproj diff --git a/requirements/ci/py39.yml b/requirements/ci/py39.yml index 001d3565d5..7931e20336 100644 --- a/requirements/ci/py39.yml +++ b/requirements/ci/py39.yml @@ -11,12 +11,12 @@ dependencies: - setuptools-scm >=7 # Core dependencies. - - cartopy >=0.20 + - cartopy >=0.21 - cf-units >=3.1 - cftime >=1.5 - dask-core >=2.26 - matplotlib - - netcdf4 + - netcdf4 !=1.6.1 - numpy >=1.19 - python-xxhash - pyproj diff --git a/setup.cfg b/setup.cfg index e5f0bc5b46..92cbe4747c 100644 --- a/setup.cfg +++ b/setup.cfg @@ -47,12 +47,12 @@ version = attr: iris.__version__ [options] include_package_data = True install_requires = - cartopy>=0.20 + cartopy>=0.21 cf-units>=3.1 cftime>=1.5.0 dask[array]>=2.26 matplotlib - netcdf4 + netcdf4!=1.6.1 numpy>=1.19 scipy shapely!=1.8.3 From 0dea89741f6fbd979380312fec02f4ad916ec875 Mon Sep 17 00:00:00 2001 From: "scitools-ci[bot]" <107775138+scitools-ci[bot]@users.noreply.github.com> Date: Tue, 20 Sep 2022 09:51:03 +0100 Subject: [PATCH 2/9] Updated environment lockfiles (#4971) Co-authored-by: Lockfile bot --- requirements/ci/nox.lock/py310-linux-64.lock | 11 ++++++----- requirements/ci/nox.lock/py38-linux-64.lock | 11 ++++++----- requirements/ci/nox.lock/py39-linux-64.lock | 11 ++++++----- 3 files changed, 18 insertions(+), 15 deletions(-) diff --git a/requirements/ci/nox.lock/py310-linux-64.lock b/requirements/ci/nox.lock/py310-linux-64.lock index 5a18284896..4d1b238179 100644 --- a/requirements/ci/nox.lock/py310-linux-64.lock +++ b/requirements/ci/nox.lock/py310-linux-64.lock @@ -1,6 +1,6 @@ # Generated by conda-lock. # platform: linux-64 -# input_hash: 9d180dce74d2d2af2a3e377c05d03d2a00c603b6d46a9f39b9c92bfbc71e7d3e +# input_hash: 9bcbc5c76124fc238f88ac16184aebeb8fac11fe9d4df03e70a7f50e2d24aa9f @EXPLICIT https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81 https://conda.anaconda.org/conda-forge/linux-64/ca-certificates-2022.9.14-ha878542_0.tar.bz2#87c986dab320658abaf3e701406b665c @@ -76,7 +76,7 @@ https://conda.anaconda.org/conda-forge/linux-64/libedit-3.1.20191231-he28a2e2_2. https://conda.anaconda.org/conda-forge/linux-64/libevent-2.1.10-h9b69904_4.tar.bz2#390026683aef81db27ff1b8570ca1336 https://conda.anaconda.org/conda-forge/linux-64/libllvm14-14.0.6-he0ac6c6_0.tar.bz2#f5759f0c80708fbf9c4836c0cb46d0fe https://conda.anaconda.org/conda-forge/linux-64/libnghttp2-1.47.0-hdcd2b5c_1.tar.bz2#6fe9e31c2b8d0b022626ccac13e6ca3c -https://conda.anaconda.org/conda-forge/linux-64/libpng-1.6.37-h753d276_4.tar.bz2#6b611734b73d639c084ac4be2fcd996a +https://conda.anaconda.org/conda-forge/linux-64/libpng-1.6.38-h753d276_0.tar.bz2#575078de1d3a3114b3ce131bd1508d0c https://conda.anaconda.org/conda-forge/linux-64/libsqlite-3.39.3-h753d276_0.tar.bz2#ccb2457c73609f2622b8a4b3e42e5d8b https://conda.anaconda.org/conda-forge/linux-64/libssh2-1.10.0-haa6b8db_3.tar.bz2#89acee135f0809a18a1f4537390aa2dd https://conda.anaconda.org/conda-forge/linux-64/libvorbis-1.3.7-h9c3ff4c_0.tar.bz2#309dec04b70a3cc0f1e84a4013683bc0 @@ -206,8 +206,9 @@ https://conda.anaconda.org/conda-forge/linux-64/unicodedata2-14.0.0-py310h5764c6 https://conda.anaconda.org/conda-forge/linux-64/virtualenv-20.16.5-py310hff52083_0.tar.bz2#e572565848d8d19e74983f4d122734a8 https://conda.anaconda.org/conda-forge/linux-64/brotlipy-0.7.0-py310h5764c6d_1004.tar.bz2#6499bb11b7feffb63b26847fc9181319 https://conda.anaconda.org/conda-forge/linux-64/cftime-1.6.1-py310hde88566_0.tar.bz2#1f84cf065287d73aa0233d432d3a1ba9 +https://conda.anaconda.org/conda-forge/linux-64/contourpy-1.0.5-py310hbf28c38_0.tar.bz2#85565efb2bf44e8a5782e7c418d30cfe https://conda.anaconda.org/conda-forge/linux-64/cryptography-37.0.4-py310h597c629_0.tar.bz2#f285746449d16d92884f4ce0cfe26679 -https://conda.anaconda.org/conda-forge/noarch/dask-core-2022.9.0-pyhd8ed1ab_0.tar.bz2#859607d7a80dc90039b3d94cfa2b1931 +https://conda.anaconda.org/conda-forge/noarch/dask-core-2022.9.1-pyhd8ed1ab_0.tar.bz2#68bb7f24f75b9691c42fd50e178749f5 https://conda.anaconda.org/conda-forge/linux-64/fonttools-4.37.2-py310h5764c6d_0.tar.bz2#4a195cef7a7649b3c44efff3853e162c https://conda.anaconda.org/conda-forge/linux-64/gstreamer-1.20.3-hd4edc92_1.tar.bz2#34c6484852afee76e334c1f593dd8282 https://conda.anaconda.org/conda-forge/linux-64/harfbuzz-5.1.0-hf9f4e7c_0.tar.bz2#7c1f73a8f7864a202b126d82e88ddffc @@ -230,7 +231,7 @@ https://conda.anaconda.org/conda-forge/linux-64/cf-units-3.1.1-py310hde88566_0.t https://conda.anaconda.org/conda-forge/linux-64/gst-plugins-base-1.20.3-h57caac4_1.tar.bz2#4078c60fba5867ce6349b90c387170a2 https://conda.anaconda.org/conda-forge/noarch/identify-2.5.5-pyhd8ed1ab_0.tar.bz2#985ef0c4ed7a26731c419818080ef6ce https://conda.anaconda.org/conda-forge/noarch/imagehash-4.3.0-pyhd8ed1ab_0.tar.bz2#aee564f0021a2a0ab12239fbdd28e209 -https://conda.anaconda.org/conda-forge/linux-64/matplotlib-base-3.5.3-py310h8d5ebf3_2.tar.bz2#760bc53cc184c9d6eeca9a38099e5fa8 +https://conda.anaconda.org/conda-forge/linux-64/matplotlib-base-3.6.0-py310h8d5ebf3_0.tar.bz2#001fdef689e7cbcbbce6d5a6ebee90b6 https://conda.anaconda.org/conda-forge/linux-64/netcdf-fortran-4.6.0-mpi_mpich_hd09bd1e_0.tar.bz2#247c70ce54beeb3e60def44061576821 https://conda.anaconda.org/conda-forge/linux-64/netcdf4-1.6.0-nompi_py310h55e1e36_102.tar.bz2#588d5bd8f16287b766c509ef173b892d https://conda.anaconda.org/conda-forge/linux-64/pango-1.50.9-hc4f8a73_0.tar.bz2#b8e090dce29a036357552a009c770187 @@ -250,7 +251,7 @@ https://conda.anaconda.org/conda-forge/linux-64/esmpy-8.2.0-mpi_mpich_py310hd9c8 https://conda.anaconda.org/conda-forge/linux-64/graphviz-6.0.1-h5abf519_0.tar.bz2#123c55da3e9ea8664f73c70e13ef08c2 https://conda.anaconda.org/conda-forge/linux-64/pyqt-5.15.7-py310h29803b5_0.tar.bz2#b5fb5328cae86d0b1591fc4894e68238 https://conda.anaconda.org/conda-forge/noarch/requests-2.28.1-pyhd8ed1ab_1.tar.bz2#089382ee0e2dc2eae33a04cc3c2bddb0 -https://conda.anaconda.org/conda-forge/linux-64/matplotlib-3.5.3-py310hff52083_2.tar.bz2#46fb1538bf92de6d807feb81b462aa0f +https://conda.anaconda.org/conda-forge/linux-64/matplotlib-3.6.0-py310hff52083_0.tar.bz2#2db9d22cc226ef79d9cd87fc958c2b04 https://conda.anaconda.org/conda-forge/noarch/sphinx-4.5.0-pyh6c4a22f_0.tar.bz2#46b38d88c4270ff9ba78a89c83c66345 https://conda.anaconda.org/conda-forge/noarch/pydata-sphinx-theme-0.8.1-pyhd8ed1ab_0.tar.bz2#7d8390ec71225ea9841b276552fdffba https://conda.anaconda.org/conda-forge/noarch/sphinx-copybutton-0.5.0-pyhd8ed1ab_0.tar.bz2#4c969cdd5191306c269490f7ff236d9c diff --git a/requirements/ci/nox.lock/py38-linux-64.lock b/requirements/ci/nox.lock/py38-linux-64.lock index f916efefc8..a485b37ede 100644 --- a/requirements/ci/nox.lock/py38-linux-64.lock +++ b/requirements/ci/nox.lock/py38-linux-64.lock @@ -1,6 +1,6 @@ # Generated by conda-lock. # platform: linux-64 -# input_hash: 22508264922e791fc7a682c11aec4c066a925d74d292b7f7d868e2efd0023bdf +# input_hash: 34099f3b69d60b791c26fcde2961739ff7cb0f9c144a37335b9f2183abe0dda3 @EXPLICIT https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81 https://conda.anaconda.org/conda-forge/linux-64/ca-certificates-2022.9.14-ha878542_0.tar.bz2#87c986dab320658abaf3e701406b665c @@ -75,7 +75,7 @@ https://conda.anaconda.org/conda-forge/linux-64/libedit-3.1.20191231-he28a2e2_2. https://conda.anaconda.org/conda-forge/linux-64/libevent-2.1.10-h9b69904_4.tar.bz2#390026683aef81db27ff1b8570ca1336 https://conda.anaconda.org/conda-forge/linux-64/libllvm14-14.0.6-he0ac6c6_0.tar.bz2#f5759f0c80708fbf9c4836c0cb46d0fe https://conda.anaconda.org/conda-forge/linux-64/libnghttp2-1.47.0-hdcd2b5c_1.tar.bz2#6fe9e31c2b8d0b022626ccac13e6ca3c -https://conda.anaconda.org/conda-forge/linux-64/libpng-1.6.37-h753d276_4.tar.bz2#6b611734b73d639c084ac4be2fcd996a +https://conda.anaconda.org/conda-forge/linux-64/libpng-1.6.38-h753d276_0.tar.bz2#575078de1d3a3114b3ce131bd1508d0c https://conda.anaconda.org/conda-forge/linux-64/libsqlite-3.39.3-h753d276_0.tar.bz2#ccb2457c73609f2622b8a4b3e42e5d8b https://conda.anaconda.org/conda-forge/linux-64/libssh2-1.10.0-haa6b8db_3.tar.bz2#89acee135f0809a18a1f4537390aa2dd https://conda.anaconda.org/conda-forge/linux-64/libvorbis-1.3.7-h9c3ff4c_0.tar.bz2#309dec04b70a3cc0f1e84a4013683bc0 @@ -210,8 +210,9 @@ https://conda.anaconda.org/conda-forge/linux-64/unicodedata2-14.0.0-py38h0a891b7 https://conda.anaconda.org/conda-forge/linux-64/virtualenv-20.16.5-py38h578d9bd_0.tar.bz2#b2247bb2492e261c25fabbbb2c7a23b5 https://conda.anaconda.org/conda-forge/linux-64/brotlipy-0.7.0-py38h0a891b7_1004.tar.bz2#9fcaaca218dcfeb8da806d4fd4824aa0 https://conda.anaconda.org/conda-forge/linux-64/cftime-1.6.1-py38h71d37f0_0.tar.bz2#acf7ef1f057459e9e707142a4b92e481 +https://conda.anaconda.org/conda-forge/linux-64/contourpy-1.0.5-py38h43d8883_0.tar.bz2#0650a251fd701bbe5ac44e74cf632af8 https://conda.anaconda.org/conda-forge/linux-64/cryptography-37.0.4-py38h2b5fc30_0.tar.bz2#28e9acd6f13ed29f27d5550a1cf0554b -https://conda.anaconda.org/conda-forge/noarch/dask-core-2022.9.0-pyhd8ed1ab_0.tar.bz2#859607d7a80dc90039b3d94cfa2b1931 +https://conda.anaconda.org/conda-forge/noarch/dask-core-2022.9.1-pyhd8ed1ab_0.tar.bz2#68bb7f24f75b9691c42fd50e178749f5 https://conda.anaconda.org/conda-forge/linux-64/fonttools-4.37.2-py38h0a891b7_0.tar.bz2#5be9368f14f462705b69da737b11159d https://conda.anaconda.org/conda-forge/linux-64/gst-plugins-base-1.20.3-h57caac4_1.tar.bz2#4078c60fba5867ce6349b90c387170a2 https://conda.anaconda.org/conda-forge/noarch/jinja2-3.1.2-pyhd8ed1ab_1.tar.bz2#c8490ed5c70966d232fdd389d0dbed37 @@ -234,7 +235,7 @@ https://conda.anaconda.org/conda-forge/linux-64/gtk2-2.24.33-h90689f9_2.tar.bz2# https://conda.anaconda.org/conda-forge/noarch/identify-2.5.5-pyhd8ed1ab_0.tar.bz2#985ef0c4ed7a26731c419818080ef6ce https://conda.anaconda.org/conda-forge/noarch/imagehash-4.3.0-pyhd8ed1ab_0.tar.bz2#aee564f0021a2a0ab12239fbdd28e209 https://conda.anaconda.org/conda-forge/linux-64/librsvg-2.54.4-h7abd40a_0.tar.bz2#921e53675ed5ea352f022b79abab076a -https://conda.anaconda.org/conda-forge/linux-64/matplotlib-base-3.5.3-py38h38b5ce0_2.tar.bz2#0db5b110946be87a04643c1ba95c6ef9 +https://conda.anaconda.org/conda-forge/linux-64/matplotlib-base-3.6.0-py38hb021067_0.tar.bz2#315ee5c0fbee508e739ddfac2bf8f600 https://conda.anaconda.org/conda-forge/linux-64/netcdf4-1.6.0-nompi_py38h2a9f00d_102.tar.bz2#533ae5db3e2367d71a7890efb0aa3cdc https://conda.anaconda.org/conda-forge/noarch/pyopenssl-22.0.0-pyhd8ed1ab_0.tar.bz2#1d7e241dfaf5475e893d4b824bb71b44 https://conda.anaconda.org/conda-forge/linux-64/pyqt5-sip-12.11.0-py38hfa26641_0.tar.bz2#6ddbd9abb62e70243702c006b81c63e4 @@ -248,7 +249,7 @@ https://conda.anaconda.org/conda-forge/linux-64/pre-commit-2.20.0-py38h578d9bd_0 https://conda.anaconda.org/conda-forge/linux-64/pyqt-5.15.7-py38h7492b6b_0.tar.bz2#59ece9f652baf50ee6b842db833896ae https://conda.anaconda.org/conda-forge/noarch/pytest-xdist-2.5.0-pyhd8ed1ab_0.tar.bz2#1fdd1f3baccf0deb647385c677a1a48e https://conda.anaconda.org/conda-forge/noarch/urllib3-1.26.11-pyhd8ed1ab_0.tar.bz2#0738978569b10669bdef41c671252dd1 -https://conda.anaconda.org/conda-forge/linux-64/matplotlib-3.5.3-py38h578d9bd_2.tar.bz2#3b6f187bade8a47d05c8a74c6385a900 +https://conda.anaconda.org/conda-forge/linux-64/matplotlib-3.6.0-py38h578d9bd_0.tar.bz2#602eb908e81892115c1405c9d99abd56 https://conda.anaconda.org/conda-forge/noarch/requests-2.28.1-pyhd8ed1ab_1.tar.bz2#089382ee0e2dc2eae33a04cc3c2bddb0 https://conda.anaconda.org/conda-forge/noarch/sphinx-4.5.0-pyh6c4a22f_0.tar.bz2#46b38d88c4270ff9ba78a89c83c66345 https://conda.anaconda.org/conda-forge/noarch/pydata-sphinx-theme-0.8.1-pyhd8ed1ab_0.tar.bz2#7d8390ec71225ea9841b276552fdffba diff --git a/requirements/ci/nox.lock/py39-linux-64.lock b/requirements/ci/nox.lock/py39-linux-64.lock index e0faf9028b..ecab388f39 100644 --- a/requirements/ci/nox.lock/py39-linux-64.lock +++ b/requirements/ci/nox.lock/py39-linux-64.lock @@ -1,6 +1,6 @@ # Generated by conda-lock. # platform: linux-64 -# input_hash: 1e66fc8b152ee34808f52142e576752894895cd3d1c29a3a408d42ee4062ba51 +# input_hash: 44cf413042165b62fe105f738e80b926629f61c1763d74df419910081521225b @EXPLICIT https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81 https://conda.anaconda.org/conda-forge/linux-64/ca-certificates-2022.9.14-ha878542_0.tar.bz2#87c986dab320658abaf3e701406b665c @@ -76,7 +76,7 @@ https://conda.anaconda.org/conda-forge/linux-64/libedit-3.1.20191231-he28a2e2_2. https://conda.anaconda.org/conda-forge/linux-64/libevent-2.1.10-h9b69904_4.tar.bz2#390026683aef81db27ff1b8570ca1336 https://conda.anaconda.org/conda-forge/linux-64/libllvm14-14.0.6-he0ac6c6_0.tar.bz2#f5759f0c80708fbf9c4836c0cb46d0fe https://conda.anaconda.org/conda-forge/linux-64/libnghttp2-1.47.0-hdcd2b5c_1.tar.bz2#6fe9e31c2b8d0b022626ccac13e6ca3c -https://conda.anaconda.org/conda-forge/linux-64/libpng-1.6.37-h753d276_4.tar.bz2#6b611734b73d639c084ac4be2fcd996a +https://conda.anaconda.org/conda-forge/linux-64/libpng-1.6.38-h753d276_0.tar.bz2#575078de1d3a3114b3ce131bd1508d0c https://conda.anaconda.org/conda-forge/linux-64/libsqlite-3.39.3-h753d276_0.tar.bz2#ccb2457c73609f2622b8a4b3e42e5d8b https://conda.anaconda.org/conda-forge/linux-64/libssh2-1.10.0-haa6b8db_3.tar.bz2#89acee135f0809a18a1f4537390aa2dd https://conda.anaconda.org/conda-forge/linux-64/libvorbis-1.3.7-h9c3ff4c_0.tar.bz2#309dec04b70a3cc0f1e84a4013683bc0 @@ -211,8 +211,9 @@ https://conda.anaconda.org/conda-forge/linux-64/unicodedata2-14.0.0-py39hb9d737c https://conda.anaconda.org/conda-forge/linux-64/virtualenv-20.16.5-py39hf3d152e_0.tar.bz2#165e71a44187ac22e2e1669fd3ca2392 https://conda.anaconda.org/conda-forge/linux-64/brotlipy-0.7.0-py39hb9d737c_1004.tar.bz2#05a99367d885ec9990f25e74128a8a08 https://conda.anaconda.org/conda-forge/linux-64/cftime-1.6.1-py39hd257fcd_0.tar.bz2#0911339f31c5fa644c312e4b3af95ea5 +https://conda.anaconda.org/conda-forge/linux-64/contourpy-1.0.5-py39hf939315_0.tar.bz2#c9ff0dfb602033b1f1aaf323b58e04fa https://conda.anaconda.org/conda-forge/linux-64/cryptography-37.0.4-py39hd97740a_0.tar.bz2#edc3668e7b71657237f94cf25e286478 -https://conda.anaconda.org/conda-forge/noarch/dask-core-2022.9.0-pyhd8ed1ab_0.tar.bz2#859607d7a80dc90039b3d94cfa2b1931 +https://conda.anaconda.org/conda-forge/noarch/dask-core-2022.9.1-pyhd8ed1ab_0.tar.bz2#68bb7f24f75b9691c42fd50e178749f5 https://conda.anaconda.org/conda-forge/linux-64/fonttools-4.37.2-py39hb9d737c_0.tar.bz2#b47e528ae5d9e0a786896a21aa0b0307 https://conda.anaconda.org/conda-forge/linux-64/gst-plugins-base-1.20.3-h57caac4_1.tar.bz2#4078c60fba5867ce6349b90c387170a2 https://conda.anaconda.org/conda-forge/noarch/jinja2-3.1.2-pyhd8ed1ab_1.tar.bz2#c8490ed5c70966d232fdd389d0dbed37 @@ -235,7 +236,7 @@ https://conda.anaconda.org/conda-forge/linux-64/gtk2-2.24.33-h90689f9_2.tar.bz2# https://conda.anaconda.org/conda-forge/noarch/identify-2.5.5-pyhd8ed1ab_0.tar.bz2#985ef0c4ed7a26731c419818080ef6ce https://conda.anaconda.org/conda-forge/noarch/imagehash-4.3.0-pyhd8ed1ab_0.tar.bz2#aee564f0021a2a0ab12239fbdd28e209 https://conda.anaconda.org/conda-forge/linux-64/librsvg-2.54.4-h7abd40a_0.tar.bz2#921e53675ed5ea352f022b79abab076a -https://conda.anaconda.org/conda-forge/linux-64/matplotlib-base-3.5.3-py39h19d6b11_2.tar.bz2#dc400bb297d8425b8b05367a21854b0b +https://conda.anaconda.org/conda-forge/linux-64/matplotlib-base-3.6.0-py39hf9fd14e_0.tar.bz2#bdc55b4069ab9d2f938525c4cf90def0 https://conda.anaconda.org/conda-forge/linux-64/netcdf4-1.6.0-nompi_py39h6ced12a_102.tar.bz2#b92600d0fef7f12f426935d87d6413e6 https://conda.anaconda.org/conda-forge/noarch/pyopenssl-22.0.0-pyhd8ed1ab_0.tar.bz2#1d7e241dfaf5475e893d4b824bb71b44 https://conda.anaconda.org/conda-forge/linux-64/pyqt5-sip-12.11.0-py39h5a03fae_0.tar.bz2#1fd9112714d50ee5be3dbf4fd23964dc @@ -249,7 +250,7 @@ https://conda.anaconda.org/conda-forge/linux-64/pre-commit-2.20.0-py39hf3d152e_0 https://conda.anaconda.org/conda-forge/linux-64/pyqt-5.15.7-py39h18e9c17_0.tar.bz2#5ed8f83afff3b64fa91f7a6af8d7ff04 https://conda.anaconda.org/conda-forge/noarch/pytest-xdist-2.5.0-pyhd8ed1ab_0.tar.bz2#1fdd1f3baccf0deb647385c677a1a48e https://conda.anaconda.org/conda-forge/noarch/urllib3-1.26.11-pyhd8ed1ab_0.tar.bz2#0738978569b10669bdef41c671252dd1 -https://conda.anaconda.org/conda-forge/linux-64/matplotlib-3.5.3-py39hf3d152e_2.tar.bz2#98bf9bdfbac2ac73bbd1dc12a61519eb +https://conda.anaconda.org/conda-forge/linux-64/matplotlib-3.6.0-py39hf3d152e_0.tar.bz2#93f29e4d6f852de18384412b0e0d03b5 https://conda.anaconda.org/conda-forge/noarch/requests-2.28.1-pyhd8ed1ab_1.tar.bz2#089382ee0e2dc2eae33a04cc3c2bddb0 https://conda.anaconda.org/conda-forge/noarch/sphinx-4.5.0-pyh6c4a22f_0.tar.bz2#46b38d88c4270ff9ba78a89c83c66345 https://conda.anaconda.org/conda-forge/noarch/pydata-sphinx-theme-0.8.1-pyhd8ed1ab_0.tar.bz2#7d8390ec71225ea9841b276552fdffba From 46755facbffc025c16e8932633f42f6c18c3ea5d Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Wed, 21 Sep 2022 15:47:03 +0100 Subject: [PATCH 3/9] Bump peter-evans/create-pull-request from 4.1.1 to 4.1.2 (#4974) Bumps [peter-evans/create-pull-request](https://github.com/peter-evans/create-pull-request) from 4.1.1 to 4.1.2. - [Release notes](https://github.com/peter-evans/create-pull-request/releases) - [Commits](https://github.com/peter-evans/create-pull-request/compare/18f90432bedd2afd6a825469ffd38aa24712a91d...171dd555b9ab6b18fa02519fdfacbb8bf671e1b4) --- updated-dependencies: - dependency-name: peter-evans/create-pull-request dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> --- .github/workflows/refresh-lockfiles.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/refresh-lockfiles.yml b/.github/workflows/refresh-lockfiles.yml index 95b65acb8b..0f08743421 100644 --- a/.github/workflows/refresh-lockfiles.yml +++ b/.github/workflows/refresh-lockfiles.yml @@ -91,7 +91,7 @@ jobs: - name: Create Pull Request id: cpr - uses: peter-evans/create-pull-request@18f90432bedd2afd6a825469ffd38aa24712a91d + uses: peter-evans/create-pull-request@171dd555b9ab6b18fa02519fdfacbb8bf671e1b4 with: token: ${{ steps.generate-token.outputs.token }} commit-message: Updated environment lockfiles From d18b84c021ecb87d87700565bd47629114523c02 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Thu, 22 Sep 2022 11:05:41 +0100 Subject: [PATCH 4/9] Bump actions/stale from 5 to 6 (#4977) Bumps [actions/stale](https://github.com/actions/stale) from 5 to 6. - [Release notes](https://github.com/actions/stale/releases) - [Changelog](https://github.com/actions/stale/blob/main/CHANGELOG.md) - [Commits](https://github.com/actions/stale/compare/v5...v6) --- updated-dependencies: - dependency-name: actions/stale dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> --- .github/workflows/stale.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/stale.yml b/.github/workflows/stale.yml index 008fe56deb..c65f37284f 100644 --- a/.github/workflows/stale.yml +++ b/.github/workflows/stale.yml @@ -14,7 +14,7 @@ jobs: if: "github.repository == 'SciTools/iris'" runs-on: ubuntu-latest steps: - - uses: actions/stale@v5 + - uses: actions/stale@v6 with: repo-token: ${{ secrets.GITHUB_TOKEN }} From a131d86d4bb18fc1b484f380259f6af5efe959da Mon Sep 17 00:00:00 2001 From: stephenworsley <49274989+stephenworsley@users.noreply.github.com> Date: Thu, 22 Sep 2022 15:31:52 +0100 Subject: [PATCH 5/9] Update release guide (#4963) * update release guide * adress review comments --- docs/src/developers_guide/release.rst | 21 +++++++++++---------- 1 file changed, 11 insertions(+), 10 deletions(-) diff --git a/docs/src/developers_guide/release.rst b/docs/src/developers_guide/release.rst index 25a426e20b..37a17ed791 100644 --- a/docs/src/developers_guide/release.rst +++ b/docs/src/developers_guide/release.rst @@ -224,17 +224,14 @@ These steps assume a release for ``1.9.0`` is to be created. Release Steps ~~~~~~~~~~~~~ -#. Create the release feature branch ``v1.9.x`` on `SciTools/iris`_. - The only exception is for a point/bugfix release, as it should already exist -#. Update the ``iris.__init__.py`` version string e.g., to ``1.9.0`` #. Update the ``whatsnew`` for the release: * Use ``git`` to rename ``docs/src/whatsnew/latest.rst`` to the release version file ``v1.9.rst`` - * Update ``docs/src/whatsnews/index.rst`` to rename ``latest.rst`` in the - include statement and toctree. * Use ``git`` to delete the ``docs/src/whatsnew/latest.rst.template`` file * In ``v1.9.rst`` remove the ``[unreleased]`` caption from the page title. + Replace this with ``[release candidate]`` for the release candidate and + remove this for the actual release. Note that, the Iris version and release date are updated automatically when the documentation is built * Review the file for correctness @@ -253,6 +250,9 @@ Release Steps #. Once all the above steps are complete, the release is cut, using the :guilabel:`Draft a new release` button on the `Iris release page `_ + and targeting the release branch if it exists +#. Create the release feature branch ``v1.9.x`` on `SciTools/iris`_ if it doesn't + already exist. For point/bugfix releases use the branch which already exists Post Release Steps @@ -260,17 +260,18 @@ Post Release Steps #. Check the documentation has built on `Read The Docs`_. The build is triggered by any commit to ``main``. Additionally check that the versions - available in the pop out menu in the bottom left corner include the new + available in the pop out menu in the bottom right corner include the new release version. If it is not present you will need to configure the versions available in the **admin** dashboard in `Read The Docs`_. #. Review the `Active Versions`_ for the ``scitools-iris`` project on `Read The Docs`_ to ensure that the appropriate versions are ``Active`` and/or ``Hidden``. To do this ``Edit`` the appropriate version e.g., see `Editing v3.0.0rc0`_ (must be logged into Read the Docs). -#. Make a new ``latest.rst`` from ``latest.rst.template`` and update the include - statement and the toctree in ``index.rst`` to point at the new +#. Merge back to ``main``. This should be done after all releases, including + the release candidate, and also after major changes to the release branch. +#. On main, make a new ``latest.rst`` from ``latest.rst.template`` and update + the include statement and the toctree in ``index.rst`` to point at the new ``latest.rst``. -#. Merge back to ``main`` .. _SciTools/iris: https://github.com/SciTools/iris @@ -285,4 +286,4 @@ Post Release Steps .. _Generating Distribution Archives: https://packaging.python.org/tutorials/packaging-projects/#generating-distribution-archives .. _Packaging Your Project: https://packaging.python.org/guides/distributing-packages-using-setuptools/#packaging-your-project .. _latest CF standard names: http://cfconventions.org/standard-names.html -.. _setuptools-scm: https://github.com/pypa/setuptools_scm \ No newline at end of file +.. _setuptools-scm: https://github.com/pypa/setuptools_scm From 831816e73fb6edb76c43df16a6e9c0e0e18f3bcf Mon Sep 17 00:00:00 2001 From: lbdreyer Date: Fri, 23 Sep 2022 11:12:00 +0100 Subject: [PATCH 6/9] Add short entry to release guide about what to do with the whats new for point releases. (#4980) --- docs/src/developers_guide/release.rst | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/docs/src/developers_guide/release.rst b/docs/src/developers_guide/release.rst index 37a17ed791..de7aa6c719 100644 --- a/docs/src/developers_guide/release.rst +++ b/docs/src/developers_guide/release.rst @@ -209,6 +209,11 @@ branch, and then released by tagging ``v1.9.1``. New features shall not be included in a point release, these are for bug fixes. +``whatsnew`` entries should be added to the existing +``docs/src/whatsnew/v1.9.rst`` file in a new ``v1.9.1`` section. A template for +this bugfix patches section can be found in the +``docs/src/whatsnew/latest.rst.template`` file. + A point release does not require a release candidate, but the rest of the release process is to be followed, including the merge back of changes into ``main``. From 04e592006dbdc27d647782e151a2b36847b1311d Mon Sep 17 00:00:00 2001 From: "scitools-ci[bot]" <107775138+scitools-ci[bot]@users.noreply.github.com> Date: Mon, 26 Sep 2022 08:55:50 +0100 Subject: [PATCH 7/9] Updated environment lockfiles (#4991) Co-authored-by: Lockfile bot --- requirements/ci/nox.lock/py310-linux-64.lock | 52 ++++++++++---------- requirements/ci/nox.lock/py38-linux-64.lock | 44 ++++++++--------- requirements/ci/nox.lock/py39-linux-64.lock | 44 ++++++++--------- 3 files changed, 70 insertions(+), 70 deletions(-) diff --git a/requirements/ci/nox.lock/py310-linux-64.lock b/requirements/ci/nox.lock/py310-linux-64.lock index 4d1b238179..b73b8af3da 100644 --- a/requirements/ci/nox.lock/py310-linux-64.lock +++ b/requirements/ci/nox.lock/py310-linux-64.lock @@ -23,10 +23,11 @@ https://conda.anaconda.org/conda-forge/linux-64/alsa-lib-1.2.7.2-h166bdaf_0.tar. https://conda.anaconda.org/conda-forge/linux-64/attr-2.5.1-h166bdaf_1.tar.bz2#d9c69a24ad678ffce24c6543a0176b00 https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-h7f98852_4.tar.bz2#a1fd65c7ccbf10880423d82bca54eb54 https://conda.anaconda.org/conda-forge/linux-64/c-ares-1.18.1-h7f98852_0.tar.bz2#f26ef8098fab1f719c91eb760d63381a -https://conda.anaconda.org/conda-forge/linux-64/expat-2.4.8-h27087fc_0.tar.bz2#e1b07832504eeba765d648389cc387a9 +https://conda.anaconda.org/conda-forge/linux-64/expat-2.4.9-h27087fc_0.tar.bz2#493ac8b2503a949aebe33d99ea0c284f https://conda.anaconda.org/conda-forge/linux-64/fftw-3.3.10-nompi_hf0379b8_105.tar.bz2#9d3e01547ba04a57372beee01158096f https://conda.anaconda.org/conda-forge/linux-64/fribidi-1.0.10-h36c2ea0_0.tar.bz2#ac7bc6a654f8f41b352b38f4051135f8 https://conda.anaconda.org/conda-forge/linux-64/geos-3.11.0-h27087fc_0.tar.bz2#a583d0bc9a85c48e8b07a588d1ac8a80 +https://conda.anaconda.org/conda-forge/linux-64/gettext-0.19.8.1-h27087fc_1009.tar.bz2#17f91dc8bb7a259b02be5bfb2cd2395f https://conda.anaconda.org/conda-forge/linux-64/giflib-5.2.1-h36c2ea0_2.tar.bz2#626e68ae9cc5912d6adb79d318cf962d https://conda.anaconda.org/conda-forge/linux-64/graphite2-1.3.13-h58526e2_1001.tar.bz2#8c54672728e8ec6aa6db90cf2806d220 https://conda.anaconda.org/conda-forge/linux-64/icu-70.1-h27087fc_0.tar.bz2#87473a15119779e021c314249d4b4aed @@ -66,7 +67,6 @@ https://conda.anaconda.org/conda-forge/linux-64/xorg-xproto-7.0.31-h7f98852_1007 https://conda.anaconda.org/conda-forge/linux-64/xxhash-0.8.0-h7f98852_3.tar.bz2#52402c791f35e414e704b7a113f99605 https://conda.anaconda.org/conda-forge/linux-64/xz-5.2.6-h166bdaf_0.tar.bz2#2161070d867d1b1204ea749c8eec4ef0 https://conda.anaconda.org/conda-forge/linux-64/yaml-0.2.5-h7f98852_2.tar.bz2#4cb3ad778ec2d5a7acbdf254eb1c42ae -https://conda.anaconda.org/conda-forge/linux-64/gettext-0.19.8.1-h73d1719_1008.tar.bz2#af49250eca8e139378f8ff0ae9e57251 https://conda.anaconda.org/conda-forge/linux-64/hdf4-4.2.15-h9772cbc_4.tar.bz2#dd3e1941dd06f64cb88647d2f7ff8aaa https://conda.anaconda.org/conda-forge/linux-64/libblas-3.9.0-16_linux64_openblas.tar.bz2#d9b7a8639171f6c6fa0a983edabcfe2b https://conda.anaconda.org/conda-forge/linux-64/libbrotlidec-1.0.9-h166bdaf_7.tar.bz2#37a460703214d0d1b421e2a47eb5e6d0 @@ -74,6 +74,8 @@ https://conda.anaconda.org/conda-forge/linux-64/libbrotlienc-1.0.9-h166bdaf_7.ta https://conda.anaconda.org/conda-forge/linux-64/libcap-2.65-ha37c62d_0.tar.bz2#2c1c43f5442731b58e070bcee45a86ec https://conda.anaconda.org/conda-forge/linux-64/libedit-3.1.20191231-he28a2e2_2.tar.bz2#4d331e44109e3f0e19b4cb8f9b82f3e1 https://conda.anaconda.org/conda-forge/linux-64/libevent-2.1.10-h9b69904_4.tar.bz2#390026683aef81db27ff1b8570ca1336 +https://conda.anaconda.org/conda-forge/linux-64/libflac-1.3.4-h27087fc_0.tar.bz2#620e52e160fd09eb8772dedd46bb19ef +https://conda.anaconda.org/conda-forge/linux-64/libglib-2.72.1-h2d90d5f_0.tar.bz2#ebeadbb5fbc44052eeb6f96a2136e3c2 https://conda.anaconda.org/conda-forge/linux-64/libllvm14-14.0.6-he0ac6c6_0.tar.bz2#f5759f0c80708fbf9c4836c0cb46d0fe https://conda.anaconda.org/conda-forge/linux-64/libnghttp2-1.47.0-hdcd2b5c_1.tar.bz2#6fe9e31c2b8d0b022626ccac13e6ca3c https://conda.anaconda.org/conda-forge/linux-64/libpng-1.6.38-h753d276_0.tar.bz2#575078de1d3a3114b3ce131bd1508d0c @@ -91,14 +93,17 @@ https://conda.anaconda.org/conda-forge/linux-64/udunits2-2.2.28-hc3e0081_0.tar.b https://conda.anaconda.org/conda-forge/linux-64/xorg-libsm-1.2.3-hd9c2040_1000.tar.bz2#9e856f78d5c80d5a78f61e72d1d473a3 https://conda.anaconda.org/conda-forge/linux-64/zlib-1.2.12-h166bdaf_3.tar.bz2#76c717057865201aa2d24b79315645bb https://conda.anaconda.org/conda-forge/linux-64/zstd-1.5.2-h6239696_4.tar.bz2#adcf0be7897e73e312bd24353b613f74 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https://conda.anaconda.org/conda-forge/noarch/pockets-0.9.1-py_0.tar.bz2#1b52f0c42e8077e5a33e00fe72269364 https://conda.anaconda.org/conda-forge/linux-64/psutil-5.9.2-py39hb9d737c_0.tar.bz2#1e7ffe59e21862559e06b981817e5058 -https://conda.anaconda.org/conda-forge/linux-64/pulseaudio-14.0-h0868958_9.tar.bz2#5bca71f0cf9b86ec58dd9d6216a3ffaf https://conda.anaconda.org/conda-forge/noarch/pygments-2.13.0-pyhd8ed1ab_0.tar.bz2#9f478e8eedd301008b5f395bad0caaed https://conda.anaconda.org/conda-forge/linux-64/pyproj-3.4.0-py39h2c22827_1.tar.bz2#a1ca42c2a746601d42f27bbcb7f6acfc https://conda.anaconda.org/conda-forge/noarch/python-dateutil-2.8.2-pyhd8ed1ab_0.tar.bz2#dd999d1cc9f79e67dbb855c8924c7984 @@ -210,17 +210,17 @@ https://conda.anaconda.org/conda-forge/noarch/typing-extensions-4.3.0-hd8ed1ab_0 https://conda.anaconda.org/conda-forge/linux-64/unicodedata2-14.0.0-py39hb9d737c_1.tar.bz2#ef84376736d1e8a814ccb06d1d814e6f https://conda.anaconda.org/conda-forge/linux-64/virtualenv-20.16.5-py39hf3d152e_0.tar.bz2#165e71a44187ac22e2e1669fd3ca2392 https://conda.anaconda.org/conda-forge/linux-64/brotlipy-0.7.0-py39hb9d737c_1004.tar.bz2#05a99367d885ec9990f25e74128a8a08 -https://conda.anaconda.org/conda-forge/linux-64/cftime-1.6.1-py39hd257fcd_0.tar.bz2#0911339f31c5fa644c312e4b3af95ea5 +https://conda.anaconda.org/conda-forge/linux-64/cftime-1.6.2-py39h2ae25f5_0.tar.bz2#4b108127973b66b36edd6449aa6afde0 https://conda.anaconda.org/conda-forge/linux-64/contourpy-1.0.5-py39hf939315_0.tar.bz2#c9ff0dfb602033b1f1aaf323b58e04fa https://conda.anaconda.org/conda-forge/linux-64/cryptography-37.0.4-py39hd97740a_0.tar.bz2#edc3668e7b71657237f94cf25e286478 https://conda.anaconda.org/conda-forge/noarch/dask-core-2022.9.1-pyhd8ed1ab_0.tar.bz2#68bb7f24f75b9691c42fd50e178749f5 -https://conda.anaconda.org/conda-forge/linux-64/fonttools-4.37.2-py39hb9d737c_0.tar.bz2#b47e528ae5d9e0a786896a21aa0b0307 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+https://conda.anaconda.org/conda-forge/linux-64/pandas-1.5.0-py39h4661b88_0.tar.bz2#ae807099430cd22b09b869b0536425b7 +https://conda.anaconda.org/conda-forge/linux-64/pango-1.50.10-hc4f8a73_0.tar.bz2#fead2b3178129155c334c751df4daba6 https://conda.anaconda.org/conda-forge/linux-64/pytest-7.1.3-py39hf3d152e_0.tar.bz2#b807481ba94ec32bc742f2fe775d0bff https://conda.anaconda.org/conda-forge/linux-64/python-stratify-0.2.post0-py39hd257fcd_2.tar.bz2#644be766007a1dc7590c3277647f81a1 https://conda.anaconda.org/conda-forge/linux-64/pywavelets-1.3.0-py39hd257fcd_1.tar.bz2#c4b698994b2d8d2e659ae02202e6abe4 @@ -238,7 +238,7 @@ https://conda.anaconda.org/conda-forge/noarch/imagehash-4.3.0-pyhd8ed1ab_0.tar.b https://conda.anaconda.org/conda-forge/linux-64/librsvg-2.54.4-h7abd40a_0.tar.bz2#921e53675ed5ea352f022b79abab076a https://conda.anaconda.org/conda-forge/linux-64/matplotlib-base-3.6.0-py39hf9fd14e_0.tar.bz2#bdc55b4069ab9d2f938525c4cf90def0 https://conda.anaconda.org/conda-forge/linux-64/netcdf4-1.6.0-nompi_py39h6ced12a_102.tar.bz2#b92600d0fef7f12f426935d87d6413e6 -https://conda.anaconda.org/conda-forge/noarch/pyopenssl-22.0.0-pyhd8ed1ab_0.tar.bz2#1d7e241dfaf5475e893d4b824bb71b44 +https://conda.anaconda.org/conda-forge/noarch/pyopenssl-22.0.0-pyhd8ed1ab_1.tar.bz2#2e7e3630919d29c8216bfa2cd643d79e https://conda.anaconda.org/conda-forge/linux-64/pyqt5-sip-12.11.0-py39h5a03fae_0.tar.bz2#1fd9112714d50ee5be3dbf4fd23964dc https://conda.anaconda.org/conda-forge/noarch/pytest-forked-1.4.0-pyhd8ed1ab_0.tar.bz2#95286e05a617de9ebfe3246cecbfb72f https://conda.anaconda.org/conda-forge/linux-64/qt-main-5.15.6-hc525480_0.tar.bz2#abd0f27f5e84cd0d5ae14d22b08795d7 From e96a0536af4ce40b4cd385108ae824565236b6a4 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Wed, 28 Sep 2022 09:01:35 +0100 Subject: [PATCH 8/9] Bump peter-evans/create-pull-request from 4.1.2 to 4.1.3 (#4995) Bumps [peter-evans/create-pull-request](https://github.com/peter-evans/create-pull-request) from 4.1.2 to 4.1.3. - [Release notes](https://github.com/peter-evans/create-pull-request/releases) - [Commits](https://github.com/peter-evans/create-pull-request/compare/171dd555b9ab6b18fa02519fdfacbb8bf671e1b4...671dc9c9e0c2d73f07fa45a3eb0220e1622f0c5f) --- updated-dependencies: - dependency-name: peter-evans/create-pull-request dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> --- .github/workflows/refresh-lockfiles.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/refresh-lockfiles.yml b/.github/workflows/refresh-lockfiles.yml index 0f08743421..a45cccfeab 100644 --- a/.github/workflows/refresh-lockfiles.yml +++ b/.github/workflows/refresh-lockfiles.yml @@ -91,7 +91,7 @@ jobs: - name: Create Pull Request id: cpr - uses: peter-evans/create-pull-request@171dd555b9ab6b18fa02519fdfacbb8bf671e1b4 + uses: peter-evans/create-pull-request@671dc9c9e0c2d73f07fa45a3eb0220e1622f0c5f with: token: ${{ steps.generate-token.outputs.token }} commit-message: Updated environment lockfiles From d8f8dac7c69f765c75690ab540d8c961adbb921c Mon Sep 17 00:00:00 2001 From: Patrick Peglar Date: Wed, 28 Sep 2022 14:02:26 +0100 Subject: [PATCH 9/9] Netcdf separate loadsave (#4803) * Split iris.fileformats.netcdf into separate load+save submodules. * Fix mutable default. * Fixes. * Fix iris.fileformats.netdf.__all__. * Fix tests. * Fix license header. * Move unit tests for sub-module APIs. * Review changes. * Add whatsnew; slightly improved module docstrings. --- docs/src/whatsnew/latest.rst | 4 + lib/iris/experimental/ugrid/load.py | 13 +- lib/iris/experimental/ugrid/save.py | 3 +- .../fileformats/_nc_load_rules/helpers.py | 2 +- lib/iris/fileformats/netcdf/__init__.py | 49 ++ lib/iris/fileformats/netcdf/loader.py | 594 ++++++++++++++++++ .../{netcdf.py => netcdf/saver.py} | 590 +---------------- .../nc_load_rules/actions/__init__.py | 6 +- .../fileformats/netcdf/loader/__init__.py | 6 + .../{ => loader}/test__get_cf_var_data.py | 2 +- .../{ => loader}/test__load_aux_factory.py | 2 +- .../netcdf/{ => loader}/test__load_cube.py | 6 +- ...__translate_constraints_to_var_callback.py | 4 +- .../unit/fileformats/netcdf/saver/__init__.py | 6 + .../test__FillValueMaskCheckAndStoreTarget.py | 2 +- .../unit/fileformats/netcdf/test_Saver.py | 2 +- .../unit/fileformats/netcdf/test_save.py | 10 +- 17 files changed, 702 insertions(+), 599 deletions(-) create mode 100644 lib/iris/fileformats/netcdf/__init__.py create mode 100644 lib/iris/fileformats/netcdf/loader.py rename lib/iris/fileformats/{netcdf.py => netcdf/saver.py} (83%) create mode 100644 lib/iris/tests/unit/fileformats/netcdf/loader/__init__.py rename lib/iris/tests/unit/fileformats/netcdf/{ => loader}/test__get_cf_var_data.py (97%) rename lib/iris/tests/unit/fileformats/netcdf/{ => loader}/test__load_aux_factory.py (99%) rename lib/iris/tests/unit/fileformats/netcdf/{ => loader}/test__load_cube.py (96%) rename lib/iris/tests/unit/fileformats/netcdf/{ => loader}/test__translate_constraints_to_var_callback.py (97%) create mode 100644 lib/iris/tests/unit/fileformats/netcdf/saver/__init__.py rename lib/iris/tests/unit/fileformats/netcdf/{ => saver}/test__FillValueMaskCheckAndStoreTarget.py (97%) diff --git a/docs/src/whatsnew/latest.rst b/docs/src/whatsnew/latest.rst index 73f7e60351..d2eadb17d6 100644 --- a/docs/src/whatsnew/latest.rst +++ b/docs/src/whatsnew/latest.rst @@ -110,6 +110,10 @@ This document explains the changes made to Iris for this release package tests, see `pypa/setuptools#1684`_. Also performed assorted ``setup.py`` script hygiene. (:pull:`4948`, :pull:`4949`, :pull:`4950`) +#. `@pp-mo`_ split the module :mod:`iris.fileformats.netcdf` into separate + :mod:`~iris.fileformats.netcdf.loader` and :mod:`~iris.fileformats.netcdf.saver` + submodules, just to make the code easier to handle. + .. comment Whatsnew author names (@github name) in alphabetical order. Note that, diff --git a/lib/iris/experimental/ugrid/load.py b/lib/iris/experimental/ugrid/load.py index 6c802e00d4..a522d91313 100644 --- a/lib/iris/experimental/ugrid/load.py +++ b/lib/iris/experimental/ugrid/load.py @@ -8,8 +8,7 @@ Extensions to Iris' NetCDF loading to allow the construction of :class:`~iris.experimental.ugrid.mesh.Mesh`\\ es from UGRID data in the file. -Eventual destination: :mod:`iris.fileformats.netcdf` (plan to split that module -into ``load`` and ``save`` in future). +Eventual destination: :mod:`iris.fileformats.netcdf`. """ from contextlib import contextmanager @@ -19,8 +18,8 @@ from ...config import get_logger from ...coords import AuxCoord -from ...fileformats import netcdf from ...fileformats._nc_load_rules.helpers import get_attr_units, get_names +from ...fileformats.netcdf import loader as nc_loader from ...io import decode_uri, expand_filespecs from ...util import guess_coord_axis from .cf import ( @@ -202,7 +201,7 @@ def load_meshes(uris, var_name=None): else: handling_format_spec = FORMAT_AGENT.get_spec(source, None) - if handling_format_spec.handler == netcdf.load_cubes: + if handling_format_spec.handler == nc_loader.load_cubes: valid_sources.append(source) else: message = f"Ignoring non-NetCDF file: {source}" @@ -239,7 +238,7 @@ def _build_aux_coord(coord_var, file_path): assert isinstance(coord_var, CFUGridAuxiliaryCoordinateVariable) attributes = {} attr_units = get_attr_units(coord_var, attributes) - points_data = netcdf._get_cf_var_data(coord_var, file_path) + points_data = nc_loader._get_cf_var_data(coord_var, file_path) # Bounds will not be loaded: # Bounds may be present, but the UGRID conventions state this would @@ -293,7 +292,7 @@ def _build_connectivity(connectivity_var, file_path, element_dims): assert isinstance(connectivity_var, CFUGridConnectivityVariable) attributes = {} attr_units = get_attr_units(connectivity_var, attributes) - indices_data = netcdf._get_cf_var_data(connectivity_var, file_path) + indices_data = nc_loader._get_cf_var_data(connectivity_var, file_path) cf_role = connectivity_var.cf_role start_index = connectivity_var.start_index @@ -462,7 +461,7 @@ def _build_mesh(cf, mesh_var, file_path): ) mesh_elements = filter(None, mesh_elements) for iris_object in mesh_elements: - netcdf._add_unused_attributes( + nc_loader._add_unused_attributes( iris_object, cf.cf_group[iris_object.var_name] ) diff --git a/lib/iris/experimental/ugrid/save.py b/lib/iris/experimental/ugrid/save.py index 8a5934b939..3c42137905 100644 --- a/lib/iris/experimental/ugrid/save.py +++ b/lib/iris/experimental/ugrid/save.py @@ -8,8 +8,7 @@ Extensions to Iris' NetCDF saving to allow :class:`~iris.experimental.ugrid.mesh.Mesh` saving in UGRID format. -Eventual destination: :mod:`iris.fileformats.netcdf` (plan to split that module -into ``load`` and ``save`` in future). +Eventual destination: :mod:`iris.fileformats.netcdf`. """ from collections.abc import Iterable diff --git a/lib/iris/fileformats/_nc_load_rules/helpers.py b/lib/iris/fileformats/_nc_load_rules/helpers.py index d50d3f324a..c075a659ac 100644 --- a/lib/iris/fileformats/_nc_load_rules/helpers.py +++ b/lib/iris/fileformats/_nc_load_rules/helpers.py @@ -31,9 +31,9 @@ import iris.fileformats.netcdf from iris.fileformats.netcdf import ( UnknownCellMethodWarning, - _get_cf_var_data, parse_cell_methods, ) +from iris.fileformats.netcdf.loader import _get_cf_var_data import iris.std_names import iris.util diff --git a/lib/iris/fileformats/netcdf/__init__.py b/lib/iris/fileformats/netcdf/__init__.py new file mode 100644 index 0000000000..505e173b0b --- /dev/null +++ b/lib/iris/fileformats/netcdf/__init__.py @@ -0,0 +1,49 @@ +# Copyright Iris contributors +# +# This file is part of Iris and is released under the LGPL license. +# See COPYING and COPYING.LESSER in the root of the repository for full +# licensing details. +""" +Module to support the loading and saving of NetCDF files, also using the CF conventions +for metadata interpretation. + +See : `NetCDF User's Guide `_ +and `netCDF4 python module `_. + +Also : `CF Conventions `_. + +""" +import iris.config + +# Note: *must* be done before importing from submodules, as they also use this ! +logger = iris.config.get_logger(__name__) + +from .loader import DEBUG, NetCDFDataProxy, load_cubes +from .saver import ( + CF_CONVENTIONS_VERSION, + MESH_ELEMENTS, + SPATIO_TEMPORAL_AXES, + CFNameCoordMap, + Saver, + UnknownCellMethodWarning, + parse_cell_methods, + save, +) + +# Export all public elements from the loader and saver submodules. +# NOTE: the separation is purely for neatness and developer convenience; from +# the user point of view, it is still all one module. +__all__ = ( + "CFNameCoordMap", + "CF_CONVENTIONS_VERSION", + "DEBUG", + "MESH_ELEMENTS", + "NetCDFDataProxy", + "SPATIO_TEMPORAL_AXES", + "Saver", + "UnknownCellMethodWarning", + "load_cubes", + "logger", + "parse_cell_methods", + "save", +) diff --git a/lib/iris/fileformats/netcdf/loader.py b/lib/iris/fileformats/netcdf/loader.py new file mode 100644 index 0000000000..95f394c70d --- /dev/null +++ b/lib/iris/fileformats/netcdf/loader.py @@ -0,0 +1,594 @@ +# Copyright Iris contributors +# +# This file is part of Iris and is released under the LGPL license. +# See COPYING and COPYING.LESSER in the root of the repository for full +# licensing details. +""" +Module to support the loading of Iris cubes from NetCDF files, also using the CF +conventions for metadata interpretation. + +See : `NetCDF User's Guide `_ +and `netCDF4 python module `_. + +Also : `CF Conventions `_. + +""" +import warnings + +import netCDF4 +import numpy as np + +from iris._lazy_data import as_lazy_data +from iris.aux_factory import ( + AtmosphereSigmaFactory, + HybridHeightFactory, + HybridPressureFactory, + OceanSFactory, + OceanSg1Factory, + OceanSg2Factory, + OceanSigmaFactory, + OceanSigmaZFactory, +) +import iris.config +import iris.coord_systems +import iris.coords +import iris.exceptions +import iris.fileformats.cf +from iris.fileformats.netcdf.saver import _CF_ATTRS +import iris.io +import iris.util + +# Show actions activation statistics. +DEBUG = False + +# Get the logger : shared logger for all in 'iris.fileformats.netcdf'. +from . import logger + + +def _actions_engine(): + # Return an 'actions engine', which provides a pyke-rules-like interface to + # the core cf translation code. + # Deferred import to avoid circularity. + import iris.fileformats._nc_load_rules.engine as nc_actions_engine + + engine = nc_actions_engine.Engine() + return engine + + +class NetCDFDataProxy: + """A reference to the data payload of a single NetCDF file variable.""" + + __slots__ = ("shape", "dtype", "path", "variable_name", "fill_value") + + def __init__(self, shape, dtype, path, variable_name, fill_value): + self.shape = shape + self.dtype = dtype + self.path = path + self.variable_name = variable_name + self.fill_value = fill_value + + @property + def ndim(self): + return len(self.shape) + + def __getitem__(self, keys): + dataset = netCDF4.Dataset(self.path) + try: + variable = dataset.variables[self.variable_name] + # Get the NetCDF variable data and slice. + var = variable[keys] + finally: + dataset.close() + return np.asanyarray(var) + + def __repr__(self): + fmt = ( + "<{self.__class__.__name__} shape={self.shape}" + " dtype={self.dtype!r} path={self.path!r}" + " variable_name={self.variable_name!r}>" + ) + return fmt.format(self=self) + + def __getstate__(self): + return {attr: getattr(self, attr) for attr in self.__slots__} + + def __setstate__(self, state): + for key, value in state.items(): + setattr(self, key, value) + + +def _assert_case_specific_facts(engine, cf, cf_group): + # Initialise a data store for built cube elements. + # This is used to patch element attributes *not* setup by the actions + # process, after the actions code has run. + engine.cube_parts["coordinates"] = [] + engine.cube_parts["cell_measures"] = [] + engine.cube_parts["ancillary_variables"] = [] + + # Assert facts for CF coordinates. + for cf_name in cf_group.coordinates.keys(): + engine.add_case_specific_fact("coordinate", (cf_name,)) + + # Assert facts for CF auxiliary coordinates. + for cf_name in cf_group.auxiliary_coordinates.keys(): + engine.add_case_specific_fact("auxiliary_coordinate", (cf_name,)) + + # Assert facts for CF cell measures. + for cf_name in cf_group.cell_measures.keys(): + engine.add_case_specific_fact("cell_measure", (cf_name,)) + + # Assert facts for CF ancillary variables. + for cf_name in cf_group.ancillary_variables.keys(): + engine.add_case_specific_fact("ancillary_variable", (cf_name,)) + + # Assert facts for CF grid_mappings. + for cf_name in cf_group.grid_mappings.keys(): + engine.add_case_specific_fact("grid_mapping", (cf_name,)) + + # Assert facts for CF labels. + for cf_name in cf_group.labels.keys(): + engine.add_case_specific_fact("label", (cf_name,)) + + # Assert facts for CF formula terms associated with the cf_group + # of the CF data variable. + + # Collect varnames of formula-root variables as we go. + # NOTE: use dictionary keys as an 'OrderedSet' + # - see: https://stackoverflow.com/a/53657523/2615050 + # This is to ensure that we can handle the resulting facts in a definite + # order, as using a 'set' led to indeterminate results. + formula_root = {} + for cf_var in cf.cf_group.formula_terms.values(): + for cf_root, cf_term in cf_var.cf_terms_by_root.items(): + # Only assert this fact if the formula root variable is + # defined in the CF group of the CF data variable. + if cf_root in cf_group: + formula_root[cf_root] = True + engine.add_case_specific_fact( + "formula_term", + (cf_var.cf_name, cf_root, cf_term), + ) + + for cf_root in formula_root.keys(): + engine.add_case_specific_fact("formula_root", (cf_root,)) + + +def _actions_activation_stats(engine, cf_name): + print("-" * 80) + print("CF Data Variable: %r" % cf_name) + + engine.print_stats() + + print("Rules Triggered:") + + for rule in sorted(list(engine.rules_triggered)): + print("\t%s" % rule) + + print("Case Specific Facts:") + kb_facts = engine.get_kb() + + for key in kb_facts.entity_lists.keys(): + for arg in kb_facts.entity_lists[key].case_specific_facts: + print("\t%s%s" % (key, arg)) + + +def _set_attributes(attributes, key, value): + """Set attributes dictionary, converting unicode strings appropriately.""" + + if isinstance(value, str): + try: + attributes[str(key)] = str(value) + except UnicodeEncodeError: + attributes[str(key)] = value + else: + attributes[str(key)] = value + + +def _add_unused_attributes(iris_object, cf_var): + """ + Populate the attributes of a cf element with the "unused" attributes + from the associated CF-netCDF variable. That is, all those that aren't CF + reserved terms. + + """ + + def attribute_predicate(item): + return item[0] not in _CF_ATTRS + + tmpvar = filter(attribute_predicate, cf_var.cf_attrs_unused()) + for attr_name, attr_value in tmpvar: + _set_attributes(iris_object.attributes, attr_name, attr_value) + + +def _get_actual_dtype(cf_var): + # Figure out what the eventual data type will be after any scale/offset + # transforms. + dummy_data = np.zeros(1, dtype=cf_var.dtype) + if hasattr(cf_var, "scale_factor"): + dummy_data = cf_var.scale_factor * dummy_data + if hasattr(cf_var, "add_offset"): + dummy_data = cf_var.add_offset + dummy_data + return dummy_data.dtype + + +def _get_cf_var_data(cf_var, filename): + # Get lazy chunked data out of a cf variable. + dtype = _get_actual_dtype(cf_var) + + # Create cube with deferred data, but no metadata + fill_value = getattr( + cf_var.cf_data, + "_FillValue", + netCDF4.default_fillvals[cf_var.dtype.str[1:]], + ) + proxy = NetCDFDataProxy( + cf_var.shape, dtype, filename, cf_var.cf_name, fill_value + ) + # Get the chunking specified for the variable : this is either a shape, or + # maybe the string "contiguous". + chunks = cf_var.cf_data.chunking() + # In the "contiguous" case, pass chunks=None to 'as_lazy_data'. + if chunks == "contiguous": + chunks = None + return as_lazy_data(proxy, chunks=chunks) + + +class _OrderedAddableList(list): + """ + A custom container object for actions recording. + + Used purely in actions debugging, to accumulate a record of which actions + were activated. + + It replaces a set, so as to preserve the ordering of operations, with + possible repeats, and it also numbers the entries. + + The actions routines invoke an 'add' method, so this effectively replaces + a set.add with a list.append. + + """ + + def __init__(self, *args, **kwargs): + super().__init__(*args, **kwargs) + self._n_add = 0 + + def add(self, msg): + self._n_add += 1 + n_add = self._n_add + self.append(f"#{n_add:03d} : {msg}") + + +def _load_cube(engine, cf, cf_var, filename): + from iris.cube import Cube + + """Create the cube associated with the CF-netCDF data variable.""" + data = _get_cf_var_data(cf_var, filename) + cube = Cube(data) + + # Reset the actions engine. + engine.reset() + + # Initialise engine rule processing hooks. + engine.cf_var = cf_var + engine.cube = cube + engine.cube_parts = {} + engine.requires = {} + engine.rules_triggered = _OrderedAddableList() + engine.filename = filename + + # Assert all the case-specific facts. + # This extracts 'facts' specific to this data-variable (aka cube), from + # the info supplied in the CFGroup object. + _assert_case_specific_facts(engine, cf, cf_var.cf_group) + + # Run the actions engine. + # This creates various cube elements and attaches them to the cube. + # It also records various other info on the engine, to be processed later. + engine.activate() + + # Having run the rules, now add the "unused" attributes to each cf element. + def fix_attributes_all_elements(role_name): + elements_and_names = engine.cube_parts.get(role_name, []) + + for iris_object, cf_var_name in elements_and_names: + _add_unused_attributes(iris_object, cf.cf_group[cf_var_name]) + + # Populate the attributes of all coordinates, cell-measures and ancillary-vars. + fix_attributes_all_elements("coordinates") + fix_attributes_all_elements("ancillary_variables") + fix_attributes_all_elements("cell_measures") + + # Also populate attributes of the top-level cube itself. + _add_unused_attributes(cube, cf_var) + + # Work out reference names for all the coords. + names = { + coord.var_name: coord.standard_name or coord.var_name or "unknown" + for coord in cube.coords() + } + + # Add all the cube cell methods. + cube.cell_methods = [ + iris.coords.CellMethod( + method=method.method, + intervals=method.intervals, + comments=method.comments, + coords=[ + names[coord_name] if coord_name in names else coord_name + for coord_name in method.coord_names + ], + ) + for method in cube.cell_methods + ] + + if DEBUG: + # Show activation statistics for this data-var (i.e. cube). + _actions_activation_stats(engine, cf_var.cf_name) + + return cube + + +def _load_aux_factory(engine, cube): + """ + Convert any CF-netCDF dimensionless coordinate to an AuxCoordFactory. + + """ + formula_type = engine.requires.get("formula_type") + if formula_type in [ + "atmosphere_sigma_coordinate", + "atmosphere_hybrid_height_coordinate", + "atmosphere_hybrid_sigma_pressure_coordinate", + "ocean_sigma_z_coordinate", + "ocean_sigma_coordinate", + "ocean_s_coordinate", + "ocean_s_coordinate_g1", + "ocean_s_coordinate_g2", + ]: + + def coord_from_term(term): + # Convert term names to coordinates (via netCDF variable names). + name = engine.requires["formula_terms"].get(term, None) + if name is not None: + for coord, cf_var_name in engine.cube_parts["coordinates"]: + if cf_var_name == name: + return coord + warnings.warn( + "Unable to find coordinate for variable " + "{!r}".format(name) + ) + + if formula_type == "atmosphere_sigma_coordinate": + pressure_at_top = coord_from_term("ptop") + sigma = coord_from_term("sigma") + surface_air_pressure = coord_from_term("ps") + factory = AtmosphereSigmaFactory( + pressure_at_top, sigma, surface_air_pressure + ) + elif formula_type == "atmosphere_hybrid_height_coordinate": + delta = coord_from_term("a") + sigma = coord_from_term("b") + orography = coord_from_term("orog") + factory = HybridHeightFactory(delta, sigma, orography) + elif formula_type == "atmosphere_hybrid_sigma_pressure_coordinate": + # Hybrid pressure has two valid versions of its formula terms: + # "p0: var1 a: var2 b: var3 ps: var4" or + # "ap: var1 b: var2 ps: var3" where "ap = p0 * a" + # Attempt to get the "ap" term. + delta = coord_from_term("ap") + if delta is None: + # The "ap" term is unavailable, so try getting terms "p0" + # and "a" terms in order to derive an "ap" equivalent term. + coord_p0 = coord_from_term("p0") + if coord_p0 is not None: + if coord_p0.shape != (1,): + msg = ( + "Expecting {!r} to be a scalar reference " + "pressure coordinate, got shape {!r}".format( + coord_p0.var_name, coord_p0.shape + ) + ) + raise ValueError(msg) + if coord_p0.has_bounds(): + msg = ( + "Ignoring atmosphere hybrid sigma pressure " + "scalar coordinate {!r} bounds.".format( + coord_p0.name() + ) + ) + warnings.warn(msg) + coord_a = coord_from_term("a") + if coord_a is not None: + if coord_a.units.is_unknown(): + # Be graceful, and promote unknown to dimensionless units. + coord_a.units = "1" + delta = coord_a * coord_p0.points[0] + delta.units = coord_a.units * coord_p0.units + delta.rename("vertical pressure") + delta.var_name = "ap" + cube.add_aux_coord(delta, cube.coord_dims(coord_a)) + + sigma = coord_from_term("b") + surface_air_pressure = coord_from_term("ps") + factory = HybridPressureFactory(delta, sigma, surface_air_pressure) + elif formula_type == "ocean_sigma_z_coordinate": + sigma = coord_from_term("sigma") + eta = coord_from_term("eta") + depth = coord_from_term("depth") + depth_c = coord_from_term("depth_c") + nsigma = coord_from_term("nsigma") + zlev = coord_from_term("zlev") + factory = OceanSigmaZFactory( + sigma, eta, depth, depth_c, nsigma, zlev + ) + elif formula_type == "ocean_sigma_coordinate": + sigma = coord_from_term("sigma") + eta = coord_from_term("eta") + depth = coord_from_term("depth") + factory = OceanSigmaFactory(sigma, eta, depth) + elif formula_type == "ocean_s_coordinate": + s = coord_from_term("s") + eta = coord_from_term("eta") + depth = coord_from_term("depth") + a = coord_from_term("a") + depth_c = coord_from_term("depth_c") + b = coord_from_term("b") + factory = OceanSFactory(s, eta, depth, a, b, depth_c) + elif formula_type == "ocean_s_coordinate_g1": + s = coord_from_term("s") + c = coord_from_term("c") + eta = coord_from_term("eta") + depth = coord_from_term("depth") + depth_c = coord_from_term("depth_c") + factory = OceanSg1Factory(s, c, eta, depth, depth_c) + elif formula_type == "ocean_s_coordinate_g2": + s = coord_from_term("s") + c = coord_from_term("c") + eta = coord_from_term("eta") + depth = coord_from_term("depth") + depth_c = coord_from_term("depth_c") + factory = OceanSg2Factory(s, c, eta, depth, depth_c) + cube.add_aux_factory(factory) + + +def _translate_constraints_to_var_callback(constraints): + """ + Translate load constraints into a simple data-var filter function, if possible. + + Returns: + * function(cf_var:CFDataVariable): --> bool, + or None. + + For now, ONLY handles a single NameConstraint with no 'STASH' component. + + """ + import iris._constraints + + constraints = iris._constraints.list_of_constraints(constraints) + result = None + if len(constraints) == 1: + (constraint,) = constraints + if ( + isinstance(constraint, iris._constraints.NameConstraint) + and constraint.STASH == "none" + ): + # As long as it doesn't use a STASH match, then we can treat it as + # a testing against name properties of cf_var. + # That's just like testing against name properties of a cube, except that they may not all exist. + def inner(cf_datavar): + match = True + for name in constraint._names: + expected = getattr(constraint, name) + if name != "STASH" and expected != "none": + attr_name = "cf_name" if name == "var_name" else name + # Fetch property : N.B. CFVariable caches the property values + # The use of a default here is the only difference from the code in NameConstraint. + if not hasattr(cf_datavar, attr_name): + continue + actual = getattr(cf_datavar, attr_name, "") + if actual != expected: + match = False + break + return match + + result = inner + return result + + +def load_cubes(filenames, callback=None, constraints=None): + """ + Loads cubes from a list of NetCDF filenames/OPeNDAP URLs. + + Args: + + * filenames (string/list): + One or more NetCDF filenames/OPeNDAP URLs to load from. + + Kwargs: + + * callback (callable function): + Function which can be passed on to :func:`iris.io.run_callback`. + + Returns: + Generator of loaded NetCDF :class:`iris.cube.Cube`. + + """ + # TODO: rationalise UGRID/mesh handling once experimental.ugrid is folded + # into standard behaviour. + # Deferred import to avoid circular imports. + from iris.experimental.ugrid.cf import CFUGridReader + from iris.experimental.ugrid.load import ( + PARSE_UGRID_ON_LOAD, + _build_mesh_coords, + _meshes_from_cf, + ) + from iris.io import run_callback + + # Create a low-level data-var filter from the original load constraints, if they are suitable. + var_callback = _translate_constraints_to_var_callback(constraints) + + # Create an actions engine. + engine = _actions_engine() + + if isinstance(filenames, str): + filenames = [filenames] + + for filename in filenames: + # Ingest the netCDF file. + meshes = {} + if PARSE_UGRID_ON_LOAD: + cf = CFUGridReader(filename) + meshes = _meshes_from_cf(cf) + else: + cf = iris.fileformats.cf.CFReader(filename) + + # Process each CF data variable. + data_variables = list(cf.cf_group.data_variables.values()) + list( + cf.cf_group.promoted.values() + ) + for cf_var in data_variables: + if var_callback and not var_callback(cf_var): + # Deliver only selected results. + continue + + # cf_var-specific mesh handling, if a mesh is present. + # Build the mesh_coords *before* loading the cube - avoids + # mesh-related attributes being picked up by + # _add_unused_attributes(). + mesh_name = None + mesh = None + mesh_coords, mesh_dim = [], None + if PARSE_UGRID_ON_LOAD: + mesh_name = getattr(cf_var, "mesh", None) + if mesh_name is not None: + try: + mesh = meshes[mesh_name] + except KeyError: + message = ( + f"File does not contain mesh: '{mesh_name}' - " + f"referenced by variable: '{cf_var.cf_name}' ." + ) + logger.debug(message) + if mesh is not None: + mesh_coords, mesh_dim = _build_mesh_coords(mesh, cf_var) + + cube = _load_cube(engine, cf, cf_var, filename) + + # Attach the mesh (if present) to the cube. + for mesh_coord in mesh_coords: + cube.add_aux_coord(mesh_coord, mesh_dim) + + # Process any associated formula terms and attach + # the corresponding AuxCoordFactory. + try: + _load_aux_factory(engine, cube) + except ValueError as e: + warnings.warn("{}".format(e)) + + # Perform any user registered callback function. + cube = run_callback(callback, cube, cf_var, filename) + + # Callback mechanism may return None, which must not be yielded + if cube is None: + continue + + yield cube diff --git a/lib/iris/fileformats/netcdf.py b/lib/iris/fileformats/netcdf/saver.py similarity index 83% rename from lib/iris/fileformats/netcdf.py rename to lib/iris/fileformats/netcdf/saver.py index 6a7b37a1cc..650c5e3338 100644 --- a/lib/iris/fileformats/netcdf.py +++ b/lib/iris/fileformats/netcdf/saver.py @@ -4,16 +4,16 @@ # See COPYING and COPYING.LESSER in the root of the repository for full # licensing details. """ -Module to support the loading of a NetCDF file into an Iris cube. +Module to support the saving of Iris cubes to a NetCDF file, also using the CF +conventions for metadata interpretation. -See also: `netCDF4 python `_ +See : `NetCDF User's Guide `_ +and `netCDF4 python module `_. -Also refer to document 'NetCDF Climate and Forecast (CF) Metadata Conventions'. +Also : `CF Conventions `_. """ - import collections -import collections.abc from itertools import repeat, zip_longest import os import os.path @@ -28,7 +28,7 @@ import numpy as np import numpy.ma as ma -from iris._lazy_data import _co_realise_lazy_arrays, as_lazy_data, is_lazy_data +from iris._lazy_data import _co_realise_lazy_arrays, is_lazy_data from iris.aux_factory import ( AtmosphereSigmaFactory, HybridHeightFactory, @@ -48,28 +48,17 @@ import iris.io import iris.util -# Show actions activation statistics. -DEBUG = False +# Get the logger : shared logger for all in 'iris.fileformats.netcdf'. +from . import logger -# Configure the logger. -logger = iris.config.get_logger(__name__) +# Avoid warning about unused import. +# We could use an __all__, but we don't want to maintain one here +logger # Standard CML spatio-temporal axis names. SPATIO_TEMPORAL_AXES = ["t", "z", "y", "x"] -# Pass through CF attributes: -# - comment -# - Conventions -# - flag_masks -# - flag_meanings -# - flag_values -# - history -# - institution -# - reference -# - source -# - title -# - positive -# +# The CF-meaningful attributes which may appear on a data variable. _CF_ATTRS = [ "add_offset", "ancillary_variables", @@ -447,555 +436,6 @@ def coord(self, name): return result -def _actions_engine(): - # Return an 'actions engine', which provides a pyke-rules-like interface to - # the core cf translation code. - # Deferred import to avoid circularity. - import iris.fileformats._nc_load_rules.engine as nc_actions_engine - - engine = nc_actions_engine.Engine() - return engine - - -class NetCDFDataProxy: - """A reference to the data payload of a single NetCDF file variable.""" - - __slots__ = ("shape", "dtype", "path", "variable_name", "fill_value") - - def __init__(self, shape, dtype, path, variable_name, fill_value): - self.shape = shape - self.dtype = dtype - self.path = path - self.variable_name = variable_name - self.fill_value = fill_value - - @property - def ndim(self): - return len(self.shape) - - def __getitem__(self, keys): - dataset = netCDF4.Dataset(self.path) - try: - variable = dataset.variables[self.variable_name] - # Get the NetCDF variable data and slice. - var = variable[keys] - finally: - dataset.close() - return np.asanyarray(var) - - def __repr__(self): - fmt = ( - "<{self.__class__.__name__} shape={self.shape}" - " dtype={self.dtype!r} path={self.path!r}" - " variable_name={self.variable_name!r}>" - ) - return fmt.format(self=self) - - def __getstate__(self): - return {attr: getattr(self, attr) for attr in self.__slots__} - - def __setstate__(self, state): - for key, value in state.items(): - setattr(self, key, value) - - -def _assert_case_specific_facts(engine, cf, cf_group): - # Initialise a data store for built cube elements. - # This is used to patch element attributes *not* setup by the actions - # process, after the actions code has run. - engine.cube_parts["coordinates"] = [] - engine.cube_parts["cell_measures"] = [] - engine.cube_parts["ancillary_variables"] = [] - - # Assert facts for CF coordinates. - for cf_name in cf_group.coordinates.keys(): - engine.add_case_specific_fact("coordinate", (cf_name,)) - - # Assert facts for CF auxiliary coordinates. - for cf_name in cf_group.auxiliary_coordinates.keys(): - engine.add_case_specific_fact("auxiliary_coordinate", (cf_name,)) - - # Assert facts for CF cell measures. - for cf_name in cf_group.cell_measures.keys(): - engine.add_case_specific_fact("cell_measure", (cf_name,)) - - # Assert facts for CF ancillary variables. - for cf_name in cf_group.ancillary_variables.keys(): - engine.add_case_specific_fact("ancillary_variable", (cf_name,)) - - # Assert facts for CF grid_mappings. - for cf_name in cf_group.grid_mappings.keys(): - engine.add_case_specific_fact("grid_mapping", (cf_name,)) - - # Assert facts for CF labels. - for cf_name in cf_group.labels.keys(): - engine.add_case_specific_fact("label", (cf_name,)) - - # Assert facts for CF formula terms associated with the cf_group - # of the CF data variable. - - # Collect varnames of formula-root variables as we go. - # NOTE: use dictionary keys as an 'OrderedSet' - # - see: https://stackoverflow.com/a/53657523/2615050 - # This is to ensure that we can handle the resulting facts in a definite - # order, as using a 'set' led to indeterminate results. - formula_root = {} - for cf_var in cf.cf_group.formula_terms.values(): - for cf_root, cf_term in cf_var.cf_terms_by_root.items(): - # Only assert this fact if the formula root variable is - # defined in the CF group of the CF data variable. - if cf_root in cf_group: - formula_root[cf_root] = True - engine.add_case_specific_fact( - "formula_term", - (cf_var.cf_name, cf_root, cf_term), - ) - - for cf_root in formula_root.keys(): - engine.add_case_specific_fact("formula_root", (cf_root,)) - - -def _actions_activation_stats(engine, cf_name): - print("-" * 80) - print("CF Data Variable: %r" % cf_name) - - engine.print_stats() - - print("Rules Triggered:") - - for rule in sorted(list(engine.rules_triggered)): - print("\t%s" % rule) - - print("Case Specific Facts:") - kb_facts = engine.get_kb() - - for key in kb_facts.entity_lists.keys(): - for arg in kb_facts.entity_lists[key].case_specific_facts: - print("\t%s%s" % (key, arg)) - - -def _set_attributes(attributes, key, value): - """Set attributes dictionary, converting unicode strings appropriately.""" - - if isinstance(value, str): - try: - attributes[str(key)] = str(value) - except UnicodeEncodeError: - attributes[str(key)] = value - else: - attributes[str(key)] = value - - -def _add_unused_attributes(iris_object, cf_var): - """ - Populate the attributes of a cf element with the "unused" attributes - from the associated CF-netCDF variable. That is, all those that aren't CF - reserved terms. - - """ - - def attribute_predicate(item): - return item[0] not in _CF_ATTRS - - tmpvar = filter(attribute_predicate, cf_var.cf_attrs_unused()) - for attr_name, attr_value in tmpvar: - _set_attributes(iris_object.attributes, attr_name, attr_value) - - -def _get_actual_dtype(cf_var): - # Figure out what the eventual data type will be after any scale/offset - # transforms. - dummy_data = np.zeros(1, dtype=cf_var.dtype) - if hasattr(cf_var, "scale_factor"): - dummy_data = cf_var.scale_factor * dummy_data - if hasattr(cf_var, "add_offset"): - dummy_data = cf_var.add_offset + dummy_data - return dummy_data.dtype - - -def _get_cf_var_data(cf_var, filename): - # Get lazy chunked data out of a cf variable. - dtype = _get_actual_dtype(cf_var) - - # Create cube with deferred data, but no metadata - fill_value = getattr( - cf_var.cf_data, - "_FillValue", - netCDF4.default_fillvals[cf_var.dtype.str[1:]], - ) - proxy = NetCDFDataProxy( - cf_var.shape, dtype, filename, cf_var.cf_name, fill_value - ) - # Get the chunking specified for the variable : this is either a shape, or - # maybe the string "contiguous". - chunks = cf_var.cf_data.chunking() - # In the "contiguous" case, pass chunks=None to 'as_lazy_data'. - if chunks == "contiguous": - chunks = None - return as_lazy_data(proxy, chunks=chunks) - - -class _OrderedAddableList(list): - """ - A custom container object for actions recording. - - Used purely in actions debugging, to accumulate a record of which actions - were activated. - - It replaces a set, so as to preserve the ordering of operations, with - possible repeats, and it also numbers the entries. - - The actions routines invoke an 'add' method, so this effectively replaces - a set.add with a list.append. - - """ - - def __init__(self, *args, **kwargs): - super().__init__(*args, **kwargs) - self._n_add = 0 - - def add(self, msg): - self._n_add += 1 - n_add = self._n_add - self.append(f"#{n_add:03d} : {msg}") - - -def _load_cube(engine, cf, cf_var, filename): - from iris.cube import Cube - - """Create the cube associated with the CF-netCDF data variable.""" - data = _get_cf_var_data(cf_var, filename) - cube = Cube(data) - - # Reset the actions engine. - engine.reset() - - # Initialise engine rule processing hooks. - engine.cf_var = cf_var - engine.cube = cube - engine.cube_parts = {} - engine.requires = {} - engine.rules_triggered = _OrderedAddableList() - engine.filename = filename - - # Assert all the case-specific facts. - # This extracts 'facts' specific to this data-variable (aka cube), from - # the info supplied in the CFGroup object. - _assert_case_specific_facts(engine, cf, cf_var.cf_group) - - # Run the actions engine. - # This creates various cube elements and attaches them to the cube. - # It also records various other info on the engine, to be processed later. - engine.activate() - - # Having run the rules, now add the "unused" attributes to each cf element. - def fix_attributes_all_elements(role_name): - elements_and_names = engine.cube_parts.get(role_name, []) - - for iris_object, cf_var_name in elements_and_names: - _add_unused_attributes(iris_object, cf.cf_group[cf_var_name]) - - # Populate the attributes of all coordinates, cell-measures and ancillary-vars. - fix_attributes_all_elements("coordinates") - fix_attributes_all_elements("ancillary_variables") - fix_attributes_all_elements("cell_measures") - - # Also populate attributes of the top-level cube itself. - _add_unused_attributes(cube, cf_var) - - # Work out reference names for all the coords. - names = { - coord.var_name: coord.standard_name or coord.var_name or "unknown" - for coord in cube.coords() - } - - # Add all the cube cell methods. - cube.cell_methods = [ - iris.coords.CellMethod( - method=method.method, - intervals=method.intervals, - comments=method.comments, - coords=[ - names[coord_name] if coord_name in names else coord_name - for coord_name in method.coord_names - ], - ) - for method in cube.cell_methods - ] - - if DEBUG: - # Show activation statistics for this data-var (i.e. cube). - _actions_activation_stats(engine, cf_var.cf_name) - - return cube - - -def _load_aux_factory(engine, cube): - """ - Convert any CF-netCDF dimensionless coordinate to an AuxCoordFactory. - - """ - formula_type = engine.requires.get("formula_type") - if formula_type in [ - "atmosphere_sigma_coordinate", - "atmosphere_hybrid_height_coordinate", - "atmosphere_hybrid_sigma_pressure_coordinate", - "ocean_sigma_z_coordinate", - "ocean_sigma_coordinate", - "ocean_s_coordinate", - "ocean_s_coordinate_g1", - "ocean_s_coordinate_g2", - ]: - - def coord_from_term(term): - # Convert term names to coordinates (via netCDF variable names). - name = engine.requires["formula_terms"].get(term, None) - if name is not None: - for coord, cf_var_name in engine.cube_parts["coordinates"]: - if cf_var_name == name: - return coord - warnings.warn( - "Unable to find coordinate for variable " - "{!r}".format(name) - ) - - if formula_type == "atmosphere_sigma_coordinate": - pressure_at_top = coord_from_term("ptop") - sigma = coord_from_term("sigma") - surface_air_pressure = coord_from_term("ps") - factory = AtmosphereSigmaFactory( - pressure_at_top, sigma, surface_air_pressure - ) - elif formula_type == "atmosphere_hybrid_height_coordinate": - delta = coord_from_term("a") - sigma = coord_from_term("b") - orography = coord_from_term("orog") - factory = HybridHeightFactory(delta, sigma, orography) - elif formula_type == "atmosphere_hybrid_sigma_pressure_coordinate": - # Hybrid pressure has two valid versions of its formula terms: - # "p0: var1 a: var2 b: var3 ps: var4" or - # "ap: var1 b: var2 ps: var3" where "ap = p0 * a" - # Attempt to get the "ap" term. - delta = coord_from_term("ap") - if delta is None: - # The "ap" term is unavailable, so try getting terms "p0" - # and "a" terms in order to derive an "ap" equivalent term. - coord_p0 = coord_from_term("p0") - if coord_p0 is not None: - if coord_p0.shape != (1,): - msg = ( - "Expecting {!r} to be a scalar reference " - "pressure coordinate, got shape {!r}".format( - coord_p0.var_name, coord_p0.shape - ) - ) - raise ValueError(msg) - if coord_p0.has_bounds(): - msg = ( - "Ignoring atmosphere hybrid sigma pressure " - "scalar coordinate {!r} bounds.".format( - coord_p0.name() - ) - ) - warnings.warn(msg) - coord_a = coord_from_term("a") - if coord_a is not None: - if coord_a.units.is_unknown(): - # Be graceful, and promote unknown to dimensionless units. - coord_a.units = "1" - delta = coord_a * coord_p0.points[0] - delta.units = coord_a.units * coord_p0.units - delta.rename("vertical pressure") - delta.var_name = "ap" - cube.add_aux_coord(delta, cube.coord_dims(coord_a)) - - sigma = coord_from_term("b") - surface_air_pressure = coord_from_term("ps") - factory = HybridPressureFactory(delta, sigma, surface_air_pressure) - elif formula_type == "ocean_sigma_z_coordinate": - sigma = coord_from_term("sigma") - eta = coord_from_term("eta") - depth = coord_from_term("depth") - depth_c = coord_from_term("depth_c") - nsigma = coord_from_term("nsigma") - zlev = coord_from_term("zlev") - factory = OceanSigmaZFactory( - sigma, eta, depth, depth_c, nsigma, zlev - ) - elif formula_type == "ocean_sigma_coordinate": - sigma = coord_from_term("sigma") - eta = coord_from_term("eta") - depth = coord_from_term("depth") - factory = OceanSigmaFactory(sigma, eta, depth) - elif formula_type == "ocean_s_coordinate": - s = coord_from_term("s") - eta = coord_from_term("eta") - depth = coord_from_term("depth") - a = coord_from_term("a") - depth_c = coord_from_term("depth_c") - b = coord_from_term("b") - factory = OceanSFactory(s, eta, depth, a, b, depth_c) - elif formula_type == "ocean_s_coordinate_g1": - s = coord_from_term("s") - c = coord_from_term("c") - eta = coord_from_term("eta") - depth = coord_from_term("depth") - depth_c = coord_from_term("depth_c") - factory = OceanSg1Factory(s, c, eta, depth, depth_c) - elif formula_type == "ocean_s_coordinate_g2": - s = coord_from_term("s") - c = coord_from_term("c") - eta = coord_from_term("eta") - depth = coord_from_term("depth") - depth_c = coord_from_term("depth_c") - factory = OceanSg2Factory(s, c, eta, depth, depth_c) - cube.add_aux_factory(factory) - - -def _translate_constraints_to_var_callback(constraints): - """ - Translate load constraints into a simple data-var filter function, if possible. - - Returns: - * function(cf_var:CFDataVariable): --> bool, - or None. - - For now, ONLY handles a single NameConstraint with no 'STASH' component. - - """ - import iris._constraints - - constraints = iris._constraints.list_of_constraints(constraints) - result = None - if len(constraints) == 1: - (constraint,) = constraints - if ( - isinstance(constraint, iris._constraints.NameConstraint) - and constraint.STASH == "none" - ): - # As long as it doesn't use a STASH match, then we can treat it as - # a testing against name properties of cf_var. - # That's just like testing against name properties of a cube, except that they may not all exist. - def inner(cf_datavar): - match = True - for name in constraint._names: - expected = getattr(constraint, name) - if name != "STASH" and expected != "none": - attr_name = "cf_name" if name == "var_name" else name - # Fetch property : N.B. CFVariable caches the property values - # The use of a default here is the only difference from the code in NameConstraint. - if not hasattr(cf_datavar, attr_name): - continue - actual = getattr(cf_datavar, attr_name, "") - if actual != expected: - match = False - break - return match - - result = inner - return result - - -def load_cubes(filenames, callback=None, constraints=None): - """ - Loads cubes from a list of NetCDF filenames/OPeNDAP URLs. - - Args: - - * filenames (string/list): - One or more NetCDF filenames/OPeNDAP URLs to load from. - - Kwargs: - - * callback (callable function): - Function which can be passed on to :func:`iris.io.run_callback`. - - Returns: - Generator of loaded NetCDF :class:`iris.cube.Cube`. - - """ - # TODO: rationalise UGRID/mesh handling once experimental.ugrid is folded - # into standard behaviour. - # Deferred import to avoid circular imports. - from iris.experimental.ugrid.cf import CFUGridReader - from iris.experimental.ugrid.load import ( - PARSE_UGRID_ON_LOAD, - _build_mesh_coords, - _meshes_from_cf, - ) - from iris.io import run_callback - - # Create a low-level data-var filter from the original load constraints, if they are suitable. - var_callback = _translate_constraints_to_var_callback(constraints) - - # Create an actions engine. - engine = _actions_engine() - - if isinstance(filenames, str): - filenames = [filenames] - - for filename in filenames: - # Ingest the netCDF file. - meshes = {} - if PARSE_UGRID_ON_LOAD: - cf = CFUGridReader(filename) - meshes = _meshes_from_cf(cf) - else: - cf = iris.fileformats.cf.CFReader(filename) - - # Process each CF data variable. - data_variables = list(cf.cf_group.data_variables.values()) + list( - cf.cf_group.promoted.values() - ) - for cf_var in data_variables: - if var_callback and not var_callback(cf_var): - # Deliver only selected results. - continue - - # cf_var-specific mesh handling, if a mesh is present. - # Build the mesh_coords *before* loading the cube - avoids - # mesh-related attributes being picked up by - # _add_unused_attributes(). - mesh_name = None - mesh = None - mesh_coords, mesh_dim = [], None - if PARSE_UGRID_ON_LOAD: - mesh_name = getattr(cf_var, "mesh", None) - if mesh_name is not None: - try: - mesh = meshes[mesh_name] - except KeyError: - message = ( - f"File does not contain mesh: '{mesh_name}' - " - f"referenced by variable: '{cf_var.cf_name}' ." - ) - logger.debug(message) - if mesh is not None: - mesh_coords, mesh_dim = _build_mesh_coords(mesh, cf_var) - - cube = _load_cube(engine, cf, cf_var, filename) - - # Attach the mesh (if present) to the cube. - for mesh_coord in mesh_coords: - cube.add_aux_coord(mesh_coord, mesh_dim) - - # Process any associated formula terms and attach - # the corresponding AuxCoordFactory. - try: - _load_aux_factory(engine, cube) - except ValueError as e: - warnings.warn("{}".format(e)) - - # Perform any user registered callback function. - cube = run_callback(callback, cube, cf_var, filename) - - # Callback mechanism may return None, which must not be yielded - if cube is None: - continue - - yield cube - - def _bytes_if_ascii(string): """ Convert the given string to a byte string (str in py2k, bytes in py3k) @@ -1837,7 +1277,9 @@ def _get_dim_names(self, cube_or_mesh): """ - def record_dimension(names_list, dim_name, length, matching_coords=[]): + def record_dimension( + names_list, dim_name, length, matching_coords=None + ): """ Record a file dimension, its length and associated "coordinates" (which may in fact also be connectivities). @@ -1846,6 +1288,8 @@ def record_dimension(names_list, dim_name, length, matching_coords=[]): matches the earlier finding. """ + if matching_coords is None: + matching_coords = [] if dim_name not in self._existing_dim: self._existing_dim[dim_name] = length else: diff --git a/lib/iris/tests/unit/fileformats/nc_load_rules/actions/__init__.py b/lib/iris/tests/unit/fileformats/nc_load_rules/actions/__init__.py index c18bdb8399..0cc3d09426 100644 --- a/lib/iris/tests/unit/fileformats/nc_load_rules/actions/__init__.py +++ b/lib/iris/tests/unit/fileformats/nc_load_rules/actions/__init__.py @@ -15,7 +15,7 @@ import iris.fileformats._nc_load_rules.engine from iris.fileformats.cf import CFReader import iris.fileformats.netcdf -from iris.fileformats.netcdf import _load_cube +from iris.fileformats.netcdf.loader import _load_cube from iris.tests.stock.netcdf import ncgen_from_cdl """ @@ -83,11 +83,11 @@ def load_cube_from_cdl(self, cdl_string, cdl_path, nc_path): # Grab a data variable : FOR NOW always grab the 'phenom' variable. cf_var = cf.cf_group.data_variables["phenom"] - engine = iris.fileformats.netcdf._actions_engine() + engine = iris.fileformats.netcdf.loader._actions_engine() # If debug enabled, switch on the activation summary debug output. # Use 'patch' so it is restored after the test. - self.patch("iris.fileformats.netcdf.DEBUG", self.debug) + self.patch("iris.fileformats.netcdf.loader.DEBUG", self.debug) with warnings.catch_warnings(): warnings.filterwarnings( diff --git a/lib/iris/tests/unit/fileformats/netcdf/loader/__init__.py b/lib/iris/tests/unit/fileformats/netcdf/loader/__init__.py new file mode 100644 index 0000000000..7c2ae96158 --- /dev/null +++ b/lib/iris/tests/unit/fileformats/netcdf/loader/__init__.py @@ -0,0 +1,6 @@ +# Copyright Iris contributors +# +# This file is part of Iris and is released under the LGPL license. +# See COPYING and COPYING.LESSER in the root of the repository for full +# licensing details. +"""Unit tests for the :mod:`iris.fileformats.netcdf.loader` module.""" diff --git a/lib/iris/tests/unit/fileformats/netcdf/test__get_cf_var_data.py b/lib/iris/tests/unit/fileformats/netcdf/loader/test__get_cf_var_data.py similarity index 97% rename from lib/iris/tests/unit/fileformats/netcdf/test__get_cf_var_data.py rename to lib/iris/tests/unit/fileformats/netcdf/loader/test__get_cf_var_data.py index 1bf39591d2..054c8e2db1 100644 --- a/lib/iris/tests/unit/fileformats/netcdf/test__get_cf_var_data.py +++ b/lib/iris/tests/unit/fileformats/netcdf/loader/test__get_cf_var_data.py @@ -16,7 +16,7 @@ from iris._lazy_data import _optimum_chunksize import iris.fileformats.cf -from iris.fileformats.netcdf import _get_cf_var_data +from iris.fileformats.netcdf.loader import _get_cf_var_data class Test__get_cf_var_data(tests.IrisTest): diff --git a/lib/iris/tests/unit/fileformats/netcdf/test__load_aux_factory.py b/lib/iris/tests/unit/fileformats/netcdf/loader/test__load_aux_factory.py similarity index 99% rename from lib/iris/tests/unit/fileformats/netcdf/test__load_aux_factory.py rename to lib/iris/tests/unit/fileformats/netcdf/loader/test__load_aux_factory.py index eb9da6b5d6..841935cc81 100644 --- a/lib/iris/tests/unit/fileformats/netcdf/test__load_aux_factory.py +++ b/lib/iris/tests/unit/fileformats/netcdf/loader/test__load_aux_factory.py @@ -16,7 +16,7 @@ from iris.coords import DimCoord from iris.cube import Cube -from iris.fileformats.netcdf import _load_aux_factory +from iris.fileformats.netcdf.loader import _load_aux_factory class TestAtmosphereHybridSigmaPressureCoordinate(tests.IrisTest): diff --git a/lib/iris/tests/unit/fileformats/netcdf/test__load_cube.py b/lib/iris/tests/unit/fileformats/netcdf/loader/test__load_cube.py similarity index 96% rename from lib/iris/tests/unit/fileformats/netcdf/test__load_cube.py rename to lib/iris/tests/unit/fileformats/netcdf/loader/test__load_cube.py index 0e98eec916..6e28a2f8e4 100644 --- a/lib/iris/tests/unit/fileformats/netcdf/test__load_cube.py +++ b/lib/iris/tests/unit/fileformats/netcdf/loader/test__load_cube.py @@ -15,7 +15,7 @@ from iris.coords import DimCoord import iris.fileformats.cf -from iris.fileformats.netcdf import _load_cube +from iris.fileformats.netcdf.loader import _load_cube class TestCoordAttributes(tests.IrisTest): @@ -28,7 +28,7 @@ def _patcher(engine, cf, cf_group): engine.cube_parts["coordinates"] = coordinates def setUp(self): - this = "iris.fileformats.netcdf._assert_case_specific_facts" + this = "iris.fileformats.netcdf.loader._assert_case_specific_facts" patch = mock.patch(this, side_effect=self._patcher) patch.start() self.addCleanup(patch.stop) @@ -112,7 +112,7 @@ def test_flag_pass_thru_multi(self): class TestCubeAttributes(tests.IrisTest): def setUp(self): - this = "iris.fileformats.netcdf._assert_case_specific_facts" + this = "iris.fileformats.netcdf.loader._assert_case_specific_facts" patch = mock.patch(this) patch.start() self.addCleanup(patch.stop) diff --git a/lib/iris/tests/unit/fileformats/netcdf/test__translate_constraints_to_var_callback.py b/lib/iris/tests/unit/fileformats/netcdf/loader/test__translate_constraints_to_var_callback.py similarity index 97% rename from lib/iris/tests/unit/fileformats/netcdf/test__translate_constraints_to_var_callback.py rename to lib/iris/tests/unit/fileformats/netcdf/loader/test__translate_constraints_to_var_callback.py index fb08ffda2b..77bb0d3950 100644 --- a/lib/iris/tests/unit/fileformats/netcdf/test__translate_constraints_to_var_callback.py +++ b/lib/iris/tests/unit/fileformats/netcdf/loader/test__translate_constraints_to_var_callback.py @@ -13,7 +13,9 @@ import iris from iris.fileformats.cf import CFDataVariable -from iris.fileformats.netcdf import _translate_constraints_to_var_callback +from iris.fileformats.netcdf.loader import ( + _translate_constraints_to_var_callback, +) # import iris tests first so that some things can be initialised before # importing anything else diff --git a/lib/iris/tests/unit/fileformats/netcdf/saver/__init__.py b/lib/iris/tests/unit/fileformats/netcdf/saver/__init__.py new file mode 100644 index 0000000000..a68d5fc5d0 --- /dev/null +++ b/lib/iris/tests/unit/fileformats/netcdf/saver/__init__.py @@ -0,0 +1,6 @@ +# Copyright Iris contributors +# +# This file is part of Iris and is released under the LGPL license. +# See COPYING and COPYING.LESSER in the root of the repository for full +# licensing details. +"""Unit tests for the :mod:`iris.fileformats.netcdf.saver` module.""" diff --git a/lib/iris/tests/unit/fileformats/netcdf/test__FillValueMaskCheckAndStoreTarget.py b/lib/iris/tests/unit/fileformats/netcdf/saver/test__FillValueMaskCheckAndStoreTarget.py similarity index 97% rename from lib/iris/tests/unit/fileformats/netcdf/test__FillValueMaskCheckAndStoreTarget.py rename to lib/iris/tests/unit/fileformats/netcdf/saver/test__FillValueMaskCheckAndStoreTarget.py index 01ba7ff38d..77209efafc 100644 --- a/lib/iris/tests/unit/fileformats/netcdf/test__FillValueMaskCheckAndStoreTarget.py +++ b/lib/iris/tests/unit/fileformats/netcdf/saver/test__FillValueMaskCheckAndStoreTarget.py @@ -17,7 +17,7 @@ import numpy as np -from iris.fileformats.netcdf import _FillValueMaskCheckAndStoreTarget +from iris.fileformats.netcdf.saver import _FillValueMaskCheckAndStoreTarget class Test__FillValueMaskCheckAndStoreTarget(tests.IrisTest): diff --git a/lib/iris/tests/unit/fileformats/netcdf/test_Saver.py b/lib/iris/tests/unit/fileformats/netcdf/test_Saver.py index e17082b5e9..174a46fdb7 100644 --- a/lib/iris/tests/unit/fileformats/netcdf/test_Saver.py +++ b/lib/iris/tests/unit/fileformats/netcdf/test_Saver.py @@ -203,7 +203,7 @@ def test_big_endian(self): def test_zlib(self): cube = self._simple_cube(">f4") - api = self.patch("iris.fileformats.netcdf.netCDF4") + api = self.patch("iris.fileformats.netcdf.saver.netCDF4") # Define mocked default fill values to prevent deprecation warning (#4374). api.default_fillvals = collections.defaultdict(lambda: -99.0) with Saver("/dummy/path", "NETCDF4") as saver: diff --git a/lib/iris/tests/unit/fileformats/netcdf/test_save.py b/lib/iris/tests/unit/fileformats/netcdf/test_save.py index 669a3c4137..030edbfce2 100644 --- a/lib/iris/tests/unit/fileformats/netcdf/test_save.py +++ b/lib/iris/tests/unit/fileformats/netcdf/test_save.py @@ -143,7 +143,7 @@ def test_None(self): # Test that when no fill_value argument is passed, the fill_value # argument to Saver.write is None or not present. cubes = self._make_cubes() - with mock.patch("iris.fileformats.netcdf.Saver") as Saver: + with mock.patch("iris.fileformats.netcdf.saver.Saver") as Saver: save(cubes, "dummy.nc") # Get the Saver.write mock @@ -161,7 +161,7 @@ def test_single(self): # that value is passed to each call to Saver.write cubes = self._make_cubes() fill_value = 12345.0 - with mock.patch("iris.fileformats.netcdf.Saver") as Saver: + with mock.patch("iris.fileformats.netcdf.saver.Saver") as Saver: save(cubes, "dummy.nc", fill_value=fill_value) # Get the Saver.write mock @@ -178,7 +178,7 @@ def test_multiple(self): # each element is passed to separate calls to Saver.write cubes = self._make_cubes() fill_values = [123.0, 456.0, 789.0] - with mock.patch("iris.fileformats.netcdf.Saver") as Saver: + with mock.patch("iris.fileformats.netcdf.saver.Saver") as Saver: save(cubes, "dummy.nc", fill_value=fill_values) # Get the Saver.write mock @@ -195,7 +195,7 @@ def test_single_string(self): # that value is passed to calls to Saver.write cube = Cube(["abc", "def", "hij"]) fill_value = "xyz" - with mock.patch("iris.fileformats.netcdf.Saver") as Saver: + with mock.patch("iris.fileformats.netcdf.saver.Saver") as Saver: save(cube, "dummy.nc", fill_value=fill_value) # Get the Saver.write mock @@ -211,7 +211,7 @@ def test_multi_wrong_length(self): # is passed as the fill_value argument, an error is raised cubes = self._make_cubes() fill_values = [1.0, 2.0, 3.0, 4.0] - with mock.patch("iris.fileformats.netcdf.Saver"): + with mock.patch("iris.fileformats.netcdf.saver.Saver"): with self.assertRaises(ValueError): save(cubes, "dummy.nc", fill_value=fill_values)