The MiriTE package contains software developed by the MIRI 
European Consortium software team. The software contained here is 
designed to support the creation and management of the MIRI
calibration data products, support the development of MIRI
simulators and pipeline algorithms and support the development of
STScI JWST pipeline software (while not being part of that
pipeline software).

The software depends on MIRICLE, the MIRI software installation system,
which includes the JWST infrastructure libraries and STScI ASDF package.
See INSTALLATION for more information on MIRICLE. JWST documentation can
be found in "JDox" articles at

https://jwst-docs.stsci.edu/display/HOM/JWST+User+Documentation+Home


CONTENTS
--------

MiriTools
~~~~~~~~~
Tools and utilities which are used by many MIRI applications.

miri.tools - A collection of general purpose tools and utilities.
See https://wiki.miricle.org/pub/Public/MIRISim_Public/miri_tools.pdf

miri.datamodels
           - MIRI data models, including two collections:
   .cdp    - Data models supporting MIRI Calibration Data Products
   .sim    - Data models supporting MIRI simulators
See https://wiki.miricle.org/pub/Public/MIRISim_Public/miri_datamodels.pdf

miri.apt_parser
             - A tool to read APT XML files.
    .mirisim - Process them via the MIRI simulator

See also the following Jupyter notebooks:

https://github.com/JWST-MIRI/MiriTE/blob/master/notebooks/How_to_use_the_data_models_to_obtain_calibration_reference_files.ipynb
https://github.com/JWST-MIRI/MiriTE/blob/master/notebooks/Using_the_data_models_to_create_a_new_reference_file.ipynb

MiriSimulators
~~~~~~~~~~~~~~
A collection of MIRI data simulators.

miri.simulators
             - One MIRI simulator is installed as part of the MiriTE package:
   .scasim   - The MIRI Sensor Chip Assembly simulator (SCASim)

More general documentation on the MIRI simulators may be found here
https://wiki.miricle.org/Public/MIRISim_Public

The top-level MiriTE directory contains the following top level tools,
utilities and documents:

README       - Read this file first.
LICENCE      - Terms and conditions of use.
setup.py     - Python setup file used to build the MIRI packages
setup.cfg    - Configuration file for commonly used utilities.
miri_installation_check.py
             - Script which checks all packages are installed correctly.
__init__.py  - Initialisation script for a Python source code
               directory. Also contains a package description and version
               control information.


STANDARD DIRECTORY NAMES
------------------------
Software is stored within this repository in a standard directory tree 
consisting of these directories:

data     - Data used by the package
doc      - Documentation for the package
doc/source  - Source directory containing release notes etc...
doc/source/reference  - Contains additional documents referenced from source
scripts  - Scripts and application programs for the package
tests    - Unit tests for the package


INSTALLATION
------------
The recommended way to install the MiriTE package is with the "MIRICLE"
installer, which manages all the package dependencies automatically.
See http://miri.ster.kuleuven.be/bin/view/Public/MirisimInstallation.

The software can also be extracted directly from the

   https://github.com/JWST-MIRI

repository and built and installed manually with the command

   python setup.py install

but in this case the user is responsible for ensuring all other dependent
packages are installed. A formal list of the packages managed by MIRICLE
may be found at

https://github.com/JWST-MIRI/MIRICLE2/blob/conda-devel/miricle-linux-py36.0.txt

The top-level script miri_installation_check.py can be run to verify the
MiriTE package has been installed successfully.

TROUBLESHOOTING
---------------
Installation and build problems are commonly caused by having incompatible or
old versions of the software installed in an anaconda environment. Make sure
you use the "source activate" command to enable the correct anaconda
environment before building the software. If you have a problem, try the
following commands (where "<>" means insert the text appropriate to your own
circumstance):

1) Remove any MIRI software accidentally installed into your root environment

   \rm -rf <...>/anaconda/lib/python3.5/site-packages/miri-*

2) Remove old versions of the MIRI software from the current anaconda
   environment before building a new version

   conda activate <environment>
   \rm -rf ${CONDA_PREFIX}/lib/python3.5/site-packages/miri-*
   python setup.py install

TESTING
-------
The unit tests included with the MIRI software can be run from the
top-level directory using nosetests or pytest by running either of
the commands

   nosetests
   pytest
  
from the top-level installation directory. If nosetests complains about
the --with-xcoverage parameter not being recognised, try the command 
 
   conda install nosexcover 

Individual tests can also be run from within the "tests" directory.
For example:

   cd MiriTE/datamodels/tests
   python test_measured_model.py


See the LICENCE file for terms and conditions of use.