Skip to content

Extended the installation description #3958

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
trexfeathers merged 7 commits into from
Jan 27, 2021
Merged

Extended the installation description #3958

Show file tree
Hide file tree
Changes from 5 commits
Commits
Show all changes
7 commits
Select commit Hold shift + click to select a range
34e06c9
Extended the installation description
MHBalsmeier Jan 26, 2021
daa6490
Renamed a label.
MHBalsmeier Jan 26, 2021
9672f48
Formatting of code improved.
MHBalsmeier Jan 26, 2021
dee1f3c
update links (#3942)
rcomer Dec 30, 2020
d82f4e4
Reset.
MHBalsmeier Jan 26, 2021
3b85f06
Simplified installation and modified latest.rst.
MHBalsmeier Jan 27, 2021
96911c1
Included missing link in latest.rst.
MHBalsmeier Jan 27, 2021
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
38 changes: 36 additions & 2 deletions docs/iris/src/installing.rst
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -41,11 +41,45 @@ need the Iris sample data. This can also be installed using conda::
Further documentation on using conda and the features it provides can be found
at https://conda.io/en/latest/index.html.

.. _installing_from_source_without_conda:

Installing from source without conda on Debian-based Linux distros (devs)
-------------------------------------------------------------------------

Iris can also be installed without a conda environment. The instructions in
this section are valid for Debian-based Linux distributions (Debian, Ubuntu,
Kubuntu, etc.).

Iris and its dependencies need some shared libraries in order to work properly.
These can be installed
with apt::

sudo apt-get install python3-pip python3-tk libudunits2-dev libproj-dev proj-bin libgeos-dev libcunit1-dev

Consider executing::

sudo apt-get update

before and after installation of Debian packages.

The rest can be done with pip. Begin with numpy::

pip3 install numpy

Finally, Iris and its Python dependencies can be installed with the following
command::

pip3 install astropy tqdm oktopus bs4 setuptools nc_time_axis cython cfunits cf-units cf-python pandas stratify pyugrid scitools-pyke black imagehash nose asv scitools-iris
Copy link
Member

@bjlittle bjlittle Jan 26, 2021

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

@MHBalsmeier You seem to have quite a few extra dependencies and optional dependencies mixed in here... would it be possible to strip this example back to it's essential bare minimum?

I'm guessing that this is the package dependency requirements for your specific area of research/work.

The following appear to extra dependencies for your particular needs:

  • astropy
  • tqdm
  • oktopus
  • bs4
  • cython
  • cf-python
  • asv

The following appear to be optional dependencies of iris, but not strictly necessary:

  • nc_time_axis
  • pandas
  • stratify
  • pyugrid
  • black
  • imagehash
  • nose

I'm also assuming that cfunits isn't a necessary dependency for cf-units? (cfunits is a similar package as our SciTools cf-units, which is maintained by David Hassell from Reading University)

So, I guess my question is, could this actually boil down to simply:

> pip3 install setuptools cf-units scitools-pyke scitools-iris

Although, I'm guessing (off the top of my head) that cython is necessary for cf-units? If that's the case then we have:

> pip3 install setuptools cython cf-units scitools-pyke scitools-iris

Is it possible for you to confirm this?


This procedure was tested on a Ubuntu 20.04 system on the
26th of January, 2021.
Be aware that through updates of the involved Debian and/or Python packages,
dependency conflicts might arise or the procedure might have to modified.

.. _installing_from_source:

Installing from source (devs)
-----------------------------
Installing from source with conda (devs)
----------------------------------------

The latest Iris source release is available from
https://github.com/SciTools/iris.
Expand Down
2 changes: 1 addition & 1 deletion docs/iris/src/userguide/citation.rst
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -48,7 +48,7 @@ For example::

Iris. Met Office. [email protected]:SciTools/iris.git 06-03-2013

.. _How to cite and describe software: http://software.ac.uk/so-exactly-what-software-did-you-use
.. _How to cite and describe software: https://software.ac.uk/how-cite-software


Reference: [Jackson]_.
Expand Down
2 changes: 1 addition & 1 deletion docs/iris/src/userguide/cube_maths.rst
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -243,7 +243,7 @@ unit (if ``a`` had units ``'m2'`` then ``a ** 0.5`` would result in a cube
with units ``'m'``).

Iris inherits units from `cf_units <https://scitools.org.uk/cf-units/docs/latest/>`_
which in turn inherits from `UDUNITS <https://www.unidata.ucar.edu/software/udunits/udunits-current/doc/udunits/udunits2.html>`_.
which in turn inherits from `UDUNITS <https://www.unidata.ucar.edu/software/udunits/udunits-current/udunits2.html>`_.
As well as the units UDUNITS provides, cf units also provides the units
``'no-unit'`` and ``'unknown'``. A unit of ``'no-unit'`` means that the
associated data is not suitable for describing with a unit, cf units
Expand Down