diff --git a/MANIFEST.in b/MANIFEST.in index ff8e330fd5..ea5744519a 100644 --- a/MANIFEST.in +++ b/MANIFEST.in @@ -6,6 +6,9 @@ recursive-include lib/iris/tests/results *.cml *.cdl *.txt *.xml *.json recursive-include lib/iris/etc * include lib/iris/fileformats/_pyke_rules/*.k?b include lib/iris/tests/stock*.npz +exclude lib/iris/etc/site.cfg + +include requirements/*.txt # File required to build docs recursive-include docs Makefile *.js *.png *.py *.rst diff --git a/README.md b/README.md index c94da1ad9b..fe869f0461 100644 --- a/README.md +++ b/README.md @@ -3,7 +3,7 @@ Iris [![Join the chat at https://gitter.im/SciTools/iris](https://badges.gitter.im/SciTools/iris.svg)](https://gitter.im/SciTools/iris?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge&utm_content=badge) [![Build Status](https://api.travis-ci.org/repositories/SciTools/iris.svg?branch=master)](https://travis-ci.org/SciTools/iris/branches) -[![DOI](https://zenodo.org/badge/doi/10.5281/zenodo.51860.svg)](https://dx.doi.org/10.5281/zenodo.51860) +[![DOI](https://zenodo.org/badge/5312648.svg)](https://zenodo.org/badge/latestdoi/5312648) [![Documentation for master branch ](https://img.shields.io/badge/docs-master-blue.svg)](https://scitools-docs.github.io/iris/master/index.html) (C) British Crown Copyright 2010 - 2018, Met Office diff --git a/docs/iris/src/developers_guide/dask_interface.rst b/docs/iris/src/developers_guide/dask_interface.rst deleted file mode 100644 index ff25b39051..0000000000 --- a/docs/iris/src/developers_guide/dask_interface.rst +++ /dev/null @@ -1,35 +0,0 @@ -Iris Dask Interface -******************* - -Iris uses `dask `_ to manage lazy data interfaces and processing graphs. -The key principles that define this interface are: - -* A call to :attr:`cube.data` will always load all of the data. - -* Once this has happened: - - * :attr:`cube.data` is a mutable NumPy masked array or ``ndarray``, and - * ``cube._numpy_array`` is a private NumPy masked array, accessible via :attr:`cube.data`, which may strip off the mask and return a reference to the bare ``ndarray``. - -* You can use :attr:`cube.data` to set the data. This accepts: - - * a NumPy array (including masked array), which is assigned to ``cube._numpy_array``, or - * a dask array, which is assigned to ``cube._dask_array``, while ``cube._numpy_array`` is set to None. - -* ``cube._dask_array`` may be None, otherwise it is expected to be a dask array: - - * this may wrap a proxy to a file collection, or - * this may wrap the NumPy array in ``cube._numpy_array``. - -* All dask arrays wrap array-like objects where missing data are represented by ``nan`` values: - - * Masked arrays derived from these dask arrays create their mask using the locations of ``nan`` values. - * Where dask-wrapped arrays of ``int`` require masks, these arrays will first be cast to ``float``. - -* In order to support this mask conversion, cubes have a ``fill_value`` defined as part of their metadata, which may be ``None``. - -* Array copying is kept to an absolute minimum: - - * array references should always be passed, not new arrays created, unless an explicit copy operation is requested. - -* To test for the presence of a dask array of any sort, we use :func:`iris._lazy_data.is_lazy_data`. This is implemented as ``hasattr(data, 'compute')``. diff --git a/docs/iris/src/developers_guide/index.rst b/docs/iris/src/developers_guide/index.rst index c22e833641..a1ecd0756f 100644 --- a/docs/iris/src/developers_guide/index.rst +++ b/docs/iris/src/developers_guide/index.rst @@ -38,4 +38,3 @@ tests.rst deprecations.rst release.rst - dask_interface.rst diff --git a/docs/iris/src/whatsnew/2.0.rst b/docs/iris/src/whatsnew/2.0.rst index 42a39057a7..c5c1af54c8 100644 --- a/docs/iris/src/whatsnew/2.0.rst +++ b/docs/iris/src/whatsnew/2.0.rst @@ -196,14 +196,15 @@ Incompatible Changes functionality is now delivered through :mod:`iris-grib`. * In Iris v1 it was possible to configure Iris to log at import time through - :attr:`iris.config.LOGGING`. This capability has been removed in iris v2. + `iris.config.LOGGING`. This capability has been removed in Iris v2. -* When coordinates have no well defined plot axis, iris.plot and iris.quickplot - routines now use the order of the cube's dimensions to determine the - coordinates to plot as the x and y axis of a plot. +* When coordinates have no well defined plot axis, :mod:`iris.plot` and + :mod:`iris.quickplot` routines now use the order of the cube's dimensions + to determine the coordinates to plot as the x and y axis of a plot. -* The cf_units dependency version has been updated to v1.2.0, which prints shorter - unit strings. +* The cf_units dependency version has been updated to v1.2.0, which prints + shorter unit strings. For example, the unit ``meter-second^-1`` is now + printed as ``m.s-1``. Deprecation removals diff --git a/requirements/core.txt b/requirements/core.txt index d2540da9f1..a078710396 100644 --- a/requirements/core.txt +++ b/requirements/core.txt @@ -7,6 +7,7 @@ cartopy matplotlib<1.9 netcdf4 numpy +scipy # pyke (not pip installable) #conda: pyke cf_units dask>=0.15.0 diff --git a/setup.py b/setup.py index 2b7787effc..347edef3b7 100644 --- a/setup.py +++ b/setup.py @@ -245,7 +245,7 @@ def extract_version(): zip_safe=False, setup_requires=pip_requirements('setup'), - install_requires=pip_requirements('core'), + install_requires=pip_requirements('setup') + pip_requirements('core'), tests_require=['{}[test]'.format(pypi_name)], extras_require = { 'test': pip_requirements('test'),