Commit bbdd584d authored by Loic Huder's avatar Loic Huder
Browse files

Rewrote install.rst to account for pygeodyn_data submodule

parent a833d6d2
......@@ -18,33 +18,40 @@ The installation of pygeodyn requires Python 3 (tested under 3.5) to be installe
* *setuptools* (tested against 40.4.3): to be able to run ``setup.py``.
* *numpy* (at least 1.7): to be able to wrap Fortran files with *f2py*.
The other dependencies will be automatically installed by the next step but are listed here for the sake of completeness:
The other dependencies will be automatically installed by the next step.
* *numpy* (at least 1.10)
* *scipy* (at least 0.17)
* *h5py*
* *mpi4py*
* *sklearn*
* *hypothesis* (only for the tests)
Get pygeodyn
============
Sources and data
----------------
The pygeodyn package is versioned on a git repository (https://gricad-gitlab.univ-grenoble-alpes.fr/Geodynamo/pygeodyn) where the source code can be fetched by running:
.. code-block:: bash
Get the pygeodyn sources
========================
git clone --recursive https://gricad-gitlab.univ-grenoble-alpes.fr/Geodynamo/pygeodyn.git
The pygeodyn package is versioned on a git repository (https://gricad-gitlab.univ-grenoble-alpes.fr/Geodynamo/pygeodyn) where the source code can be fetched:
This will clone the `pygeodyn`_ repository containing the sources and the `pygeodyn_data`_ repository containing several datasets (~1.5 GB) to run the algorithms.
* Release sources can be downloaded on the `Releases page <https://gricad-gitlab.univ-grenoble-alpes.fr/Geodynamo/pygeodyn/releases>`_.
* Or clone the full repository with ``git``:
Only sources
------------
The `pygeodyn_data`_ repository containing the datasets is handled as a git submodule of `pygeodyn`_. Therefore, it is possible to get **only the sources** of pygeodyn and not the data by running
.. code-block:: bash
git clone https://gricad-gitlab.univ-grenoble-alpes.fr/Geodynamo/pygeodyn.git
instead. The absence of the ``--recursive`` option will prevent the cloning of the `pygeodyn_data`_ submodule.
Note however that you will not be able to run the `run_algo <https://geodynamo.gricad-pages.univ-grenoble-alpes.fr/pygeodyn/usage_run_algo.html>`_ script unless you supply your own dataset (procedure described at https://geodynamo.gricad-pages.univ-grenoble-alpes.fr/pygeodyn/usage_new_types.html).
.. _pygeodyn: https://gricad-gitlab.univ-grenoble-alpes.fr/Geodynamo/pygeodyn
.. _pygeodyn_data: https://gricad-gitlab.univ-grenoble-alpes.fr/Geodynamo/pygeodyn_data
Install the pygeodyn package from sources
=========================================
Regular installation
--------------------
Once the sources are downloaded as described above, pygeodyn can be installed by navigating to the sources directory and running
Once the sources are downloaded as described above (with or without data), pygeodyn can be installed by navigating to the package directory and running
.. code-block:: bash
......@@ -58,6 +65,8 @@ If the installation succeeded, you should be able to import pygeodyn with Python
This should print the current version of pygeodyn.
Note however that with this installation, any change to the source code will not be taken into account unless the package is reinstalled (see `Reinstallation`_ section).
Develop installation
--------------------
If you intend to change the source code of pygeodyn (by defining new types), it is easier to install it with ``develop``:
......@@ -80,7 +89,7 @@ If you are installing in a virtual environment (see the Python venv_ page), you
Testing
=======
Tests on the package can be run in the pygeodyn directory using
If the repository was cloned with the data, tests on the package can be run in the pygeodyn directory using
.. code-block:: bash
......@@ -93,6 +102,8 @@ Detailed information on the coverage of the tests can be found `here <https://ge
Reinstallation
==============
To reinstall the package, run the following commands in the package folder:
.. code-block:: bash
python3 setup.py clean --all
......
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