Merge branch 'shapefile_masking' of https://github.com/acchamber/iris …

…into shapefile_masking

* 'shapefile_masking' of https://github.com/acchamber/iris:
  fixed spacing (SciTools#5572)
  DOCS: Removed broken git links. (SciTools#5569)

docs/src/conf.py

@@ -390,7 +390,6 @@ def _dotv(version):
     "https://docs.github.com",
     "https://github.com",
     "http://www.personal.psu.edu/cab38/ColorBrewer/ColorBrewer_updates.html",
-    "http://schacon.github.com/git",
     "http://scitools.github.com/cartopy",
     "http://www.wmo.int/pages/prog/www/DPFS/documents/485_Vol_I_en_colour.pdf",
     "https://software.ac.uk/how-cite-software",

docs/src/developers_guide/gitwash/development_workflow.rst

@@ -74,7 +74,7 @@ what the changes in the branch are for.  For example ``add-ability-to-fly``, or
     git checkout my-new-feature
 
 Generally, you will want to keep your feature branches on your public github_
-fork of `iris`_.  To do this, you `git push`_ this new branch up to your
+fork of `iris`_.  To do this, you ``git push`` this new branch up to your
 github repo.  Generally (if you followed the instructions in these pages, and by
 default), git will have a link to your github repo, called ``origin``.  You push
 up to your own repo on github with::
@@ -108,7 +108,7 @@ In More Detail
 --------------
 
 #. Make some changes
-#. See which files have changed with ``git status`` (see `git status`_).
+#. See which files have changed with ``git status``.
    You'll see a listing like this one::
 
      # On branch ny-new-feature
@@ -124,16 +124,15 @@ In More Detail
      #	INSTALL
      no changes added to commit (use "git add" and/or "git commit -a")
 
-#. Check what the actual changes are with ``git diff`` (`git diff`_).
-#. Add any new files to version control ``git add new_file_name`` (see
-   `git add`_).
+#. Check what the actual changes are with ``git diff``.
+#. Add any new files to version control ``git add new_file_name``.
 #. To commit all modified files into the local copy of your repo, do
    ``git commit -am 'A commit message'``.  Note the ``-am`` options to
    ``commit``. The ``m`` flag just signals that you're going to type a
    message on the command line.  The ``a`` flag will automatically stage
    all files that have been modified and deleted.
 #. To push the changes up to your forked repo on github, do a ``git
-   push`` (see `git push`_).
+   push``.
 
 
 Testing Your Changes

docs/src/developers_guide/gitwash/git_links.inc

@@ -13,20 +13,6 @@
 .. _github help: https://help.github.com
 .. _git documentation: https://git-scm.com/docs
 
-.. _git clone: http://schacon.github.com/git/git-clone.html
-.. _git checkout: http://schacon.github.com/git/git-checkout.html
-.. _git commit: http://schacon.github.com/git/git-commit.html
-.. _git push: http://schacon.github.com/git/git-push.html
-.. _git pull: http://schacon.github.com/git/git-pull.html
-.. _git add: http://schacon.github.com/git/git-add.html
-.. _git status: http://schacon.github.com/git/git-status.html
-.. _git diff: http://schacon.github.com/git/git-diff.html
-.. _git log: http://schacon.github.com/git/git-log.html
-.. _git branch: http://schacon.github.com/git/git-branch.html
-.. _git remote: http://schacon.github.com/git/git-remote.html
-.. _git rebase: http://schacon.github.com/git/git-rebase.html
-.. _git config: http://schacon.github.com/git/git-config.html
-
 .. _linux git workflow: http://www.mail-archive.com/[email protected]/msg39091.html
 
 .. |emdash| unicode:: U+02014

docs/src/further_topics/dask_best_practices/index.rst

@@ -144,8 +144,8 @@ Iris provides a basic chunking shape to Dask, attempting to set the shape for
 best performance. The chunking that is used can depend on the file format that
 is being loaded. See below for how chunking is performed for:
 
-  * :ref:`chunking_netcdf`
-  * :ref:`chunking_pp_ff`
+* :ref:`chunking_netcdf`
+* :ref:`chunking_pp_ff`
 
 It can in some cases be beneficial to re-chunk the arrays in Iris cubes.
 For information on how to do this, see :ref:`dask_rechunking`.
@@ -208,9 +208,9 @@ If you feel you have an example of a Dask best practice that you think may be he
 please share them with us by raising a new `discussion on the Iris repository <https://github.com/SciTools/iris
 /discussions/>`_.
 
-  * :doc:`dask_pp_to_netcdf`
-  * :doc:`dask_parallel_loop`
-  * :doc:`dask_bags_and_greed`
+* :doc:`dask_pp_to_netcdf`
+* :doc:`dask_parallel_loop`
+* :doc:`dask_bags_and_greed`
 
 .. toctree::
    :hidden:

docs/src/further_topics/ugrid/data_model.rst

@@ -484,20 +484,20 @@ How UGRID information is stored
   | Described in detail in `MeshCoords`_.
   | Stores the following information:
 
-    * | :attr:`~iris.experimental.ugrid.MeshCoord.mesh`
-      | The :class:`~iris.experimental.ugrid.Mesh` associated with this
-        :class:`~iris.experimental.ugrid.MeshCoord`. This determines the
-        :attr:`~iris.cube.Cube.mesh` attribute of any :class:`~iris.cube.Cube`
-        this :class:`~iris.experimental.ugrid.MeshCoord` is attached to (see
-        `The Basics`_)
-
-    * | :attr:`~iris.experimental.ugrid.MeshCoord.location`
-      | ``node``/``edge``/``face`` - the element detailed by this
-        :class:`~iris.experimental.ugrid.MeshCoord`. This determines the
-        :attr:`~iris.cube.Cube.location` attribute of any
-        :class:`~iris.cube.Cube` this
-        :class:`~iris.experimental.ugrid.MeshCoord` is attached to (see
-        `The Basics`_).
+  * | :attr:`~iris.experimental.ugrid.MeshCoord.mesh`
+    | The :class:`~iris.experimental.ugrid.Mesh` associated with this
+      :class:`~iris.experimental.ugrid.MeshCoord`. This determines the
+      :attr:`~iris.cube.Cube.mesh` attribute of any :class:`~iris.cube.Cube`
+      this :class:`~iris.experimental.ugrid.MeshCoord` is attached to (see
+      `The Basics`_)
+
+  * | :attr:`~iris.experimental.ugrid.MeshCoord.location`
+    | ``node``/``edge``/``face`` - the element detailed by this
+      :class:`~iris.experimental.ugrid.MeshCoord`. This determines the
+      :attr:`~iris.cube.Cube.location` attribute of any
+      :class:`~iris.cube.Cube` this
+      :class:`~iris.experimental.ugrid.MeshCoord` is attached to (see
+      `The Basics`_).
 
 .. _ugrid MeshCoords:
 

docs/src/techpapers/um_files_loading.rst

@@ -125,21 +125,21 @@ with latitude and longitude axes are also supported).
 For an ordinary latitude-longitude grid, the cubes have coordinates called
 'longitude' and 'latitude':
 
- *  These are mapped to the appropriate data dimensions.
- *  They have units of 'degrees'.
- *  They have a coordinate system of type :class:`iris.coord_systems.GeogCS`.
- *  The coordinate points are normally set to the regular sequence
-    ``ZDX/Y + BDX/Y * (1 .. LBNPT/LBROW)`` (*except*, if BDX/BDY is zero, the
-    values are taken from the extra data vector X/Y, if present).
- *  If X/Y_LOWER_BOUNDS extra data is available, this appears as bounds values
-    of the horizontal coordinates.
+*  These are mapped to the appropriate data dimensions.
+*  They have units of 'degrees'.
+*  They have a coordinate system of type :class:`iris.coord_systems.GeogCS`.
+*  The coordinate points are normally set to the regular sequence
+   ``ZDX/Y + BDX/Y * (1 .. LBNPT/LBROW)`` (*except*, if BDX/BDY is zero, the
+   values are taken from the extra data vector X/Y, if present).
+*  If X/Y_LOWER_BOUNDS extra data is available, this appears as bounds values
+   of the horizontal coordinates.
 
 For **rotated** latitude-longitude coordinates (as for LBCODE=101), the
 horizontal coordinates differ only slightly --
 
- *  The names are 'grid_latitude' and 'grid_longitude'.
- *  The coord_system is a :class:`iris.coord_systems.RotatedGeogCS`, created
-    with a pole defined by BPLAT, BPLON.
+*  The names are 'grid_latitude' and 'grid_longitude'.
+*  The coord_system is a :class:`iris.coord_systems.RotatedGeogCS`, created
+   with a pole defined by BPLAT, BPLON.
 
 For example:
     >>> # Load a PP field.
@@ -304,10 +304,9 @@ For hybrid height levels (LBVC=65):
     multidimensional or non-monotonic.
 
 See an example printout of a hybrid height cube,
-:ref:`here <hybrid_cube_printout>`:
-
-    Notice that this contains all of the above coordinates --
-    'model_level_number', 'sigma', 'level_height' and the derived 'altitude'.
+:ref:`here <hybrid_cube_printout>`.  Notice that this contains all of the 
+above coordinates -- ``model_level_number``, ``sigma``, ``level_height`` and
+the derived ``altitude``.
 
 .. note::
 
@@ -364,7 +363,7 @@ Data at a single measurement timepoint (LBTIM.IB=0):
     defined according to LBTIM.IC.
 
 Values forecast from T2, valid at T1 (LBTIM.IB=1):
-    Coordinates ``time` and ``forecast_reference_time`` are created from the T1
+    Coordinates ``time`` and ``forecast_reference_time`` are created from the T1
     and T2 values, respectively.  These have no bounds, and units of
     'hours since 1970-01-01 00:00:00', with the appropriate calendar.
     A ``forecast_period`` coordinate is also created, with values T1-T2, no
@@ -383,12 +382,11 @@ these may become dimensions of the resulting data cube.  This will depend on
 the values actually present in the source fields for each of the elements.
 
 See an example printout of a forecast data cube,
-:ref:`here <cube-statistics_forecast_printout>` :
-
-    Notice that this example contains all of the above coordinates -- 'time',
-    'forecast_period' and 'forecast_reference_time'.  In this case the data are
-    forecasts, so 'time' is a dimension, 'forecast_period' varies with time and
-    'forecast_reference_time' is a constant.
+:ref:`here <cube-statistics_forecast_printout>`.  Notice that this example
+contains all of the above coordinates -- ``time``, ``forecast_period`` and
+``forecast_reference_time``.  In this case the data are forecasts, so ``time``
+is a dimension, ``forecast_period``` varies with time and 
+``forecast_reference_time`` is a constant.
 
 
 Statistical Measures

docs/src/userguide/navigating_a_cube.rst

@@ -191,10 +191,10 @@ Adding and Removing Metadata to the Cube at Load Time
 Sometimes when loading a cube problems occur when the amount of metadata is more or less than expected.
 This is often caused by one of the following:
 
- * The file does not contain enough metadata, and therefore the cube cannot know everything about the file.
- * Some of the metadata of the file is contained in the filename, but is not part of the actual file.
- * There is not enough metadata loaded from the original file as Iris has not handled the format fully. *(in which case, 
-   please let us know about it)*
+* The file does not contain enough metadata, and therefore the cube cannot know everything about the file.
+* Some of the metadata of the file is contained in the filename, but is not part of the actual file.
+* There is not enough metadata loaded from the original file as Iris has not handled the format fully. *(in which case, 
+  please let us know about it)*
 
 To solve this, all of :func:`iris.load`, :func:`iris.load_cube`, and :func:`iris.load_cubes` support a callback keyword. 
 

docs/src/userguide/real_and_lazy_data.rst

@@ -247,20 +247,21 @@ output file, to be performed by  `Dask <https://docs.dask.org/en/stable/>`_  lat
 thus enabling parallel save operations.
 
 This works in the following way :
-    1. an :func:`iris.save` call is made, with a NetCDF file output and the additional
-       keyword ``compute=False``.
-       This is currently *only* available when saving to NetCDF, so it is documented in
-       the Iris NetCDF file format API.  See: :func:`iris.fileformats.netcdf.save`.
 
-    2. the call creates the output file, but does not fill in variables' data, where
-       the data is a lazy array in the Iris object.  Instead, these variables are
-       initially created "empty".
+1. an :func:`iris.save` call is made, with a NetCDF file output and the additional
+   keyword ``compute=False``.
+   This is currently *only* available when saving to NetCDF, so it is documented in
+   the Iris NetCDF file format API.  See: :func:`iris.fileformats.netcdf.save`.
 
-    3. the :meth:`~iris.save` call returns a ``result`` which is a
-       :class:`~dask.delayed.Delayed` object.
+2. the call creates the output file, but does not fill in variables' data, where
+   the data is a lazy array in the Iris object.  Instead, these variables are
+   initially created "empty".
 
-    4. the save can be completed later by calling ``result.compute()``, or by passing it
-       to the :func:`dask.compute` call.
+3. the :meth:`~iris.save` call returns a ``result`` which is a
+   :class:`~dask.delayed.Delayed` object.
+
+4. the save can be completed later by calling ``result.compute()``, or by passing it
+   to the :func:`dask.compute` call.
 
 The benefit of this, is that costly data transfer operations can be performed in
 parallel with writes to other data files.  Also, where array contents are calculated

docs/src/whatsnew/latest.rst

@@ -91,6 +91,8 @@ This document explains the changes made to Iris for this release
    links shown.  Also improved how the warning banner is implemented.
    (:pull:`5505` and :pull:`5508`)
 
+#. `@tkknight`_  removed broken git links. (:pull:`5569`)
+
 
 💼 Internal
 ===========