1.2.1. Prerequisites¶
Note
It is highly suggested to install UV-CDAT and other vacumm dependencies using conda.
1.2.1.1. List of packages¶
1.2.1.1.1. CDAT¶
CDAT is a meta-package containing:
- a version of python;
- standard and specialized python packages like numpy, scipy and matplotlib;
- python packages made by UV-CDAT providers, and specialized for manipulation and visualization of ocean/atmosphere data;
- numerous other libraries and tools.
The packages installed by CDAT and that are needed are the following:
- python
- numpy
- libgfortran
- cdms2
- cdutil
- genutil
- matplotlib
- basemap
- basemap-data-hires
- scipy
1.2.1.1.2. Other packages¶
Python
When you have installed CDAT or the , here is a list of necessary or useful packages that can be install using pip or easy_install:
| Package | Necessary? | Description |
|---|---|---|
| configobj (4.7.2) | Yes | Manipulate advanced configuration files |
| pytz | Only for time zone support | Work with time zones |
| paramiko | Only for remote |
Use SSH2 protocol. |
| seawater | Yes for advanced diags. | Sea water properties |
| xlwt | Only for xls_style(). |
Write excel files (better: xlutils) |
| cmocean | Only if you want cmocean colormaps | Make these colormaps available like cmocean_thermal |
| PIL (1.1.7) | Only sometimes for add_logo(). |
Manipulate images |
| sphinx_fortran (1.0) | Doc | Extension to sphinx: Documenting fortran codes |
| sphinxcontrib-cheeseshop (0.2) | Doc | Extension to sphinx: Linking to Cheese Shop (Python Package Index) packages |
| sphinxcontrib-programoutput (0.8) | Doc | Extension to sphinx: Include program output |
Documentation generation
These utilities are needed to fully compile the documentation.
- Graphviz
- Used to create hierarchical diagrams of class inheritance
during the generation of the documentation by the
sphinx extension
sphinx.ext.graphviz. See for instance modulecore_plot. The program dot may be also needed. You can install both with the pydot package. - dvipng
- Used to compile latex formula of the documentation.
- enumitem
- This package is needed to compile the PDF version of the documentation.
1.2.1.2. Install UV-CDAT¶
1.2.1.2.2. From sources¶
To install UV-CDAT, follow the official instructions. It can be installed on both linux and mac, by compiling sources or using availables binaries.
Note
If you compile it from sources, you need cmake and git, and it is highly suggested to have your own version of Qt4. Packets are generally availables on all plateforms.
If you use UV-CDAT in operational jobs, you should install a separate version. One way to manage several versions is to use environment modules (see Using environment modules).
1.2.1.3. Setup the environment¶
Once the installation is done, set environment variables (bash):
$ export PATH=/path/to/uvcdat/bin:$PATH
# For install from sources
$ export LD_LIBRARY_PATH=/path/to/uvcdat/Externals/lib:/path/to/uvcdat/lib:$LD_LIBRARY_PATH
$ export C_INCLUDE_PATH=/path/to/uvcdat/Externals/include:$C_INCLUDE_PATH
1.2.1.5. Install other packages¶
Using conda:
$ conda install -c conda-forge configobj PIL paramiko xlutils seawater pytz cmocean
Using pip:
$ pip install configobj PIL paramiko xlutils seawater pytz
$ pip install sphinxcontrib-cheeseshop sphinxcontrib-programoutput sphinx-fortran