Summary

pysto are a few miscellaneous processing python functions.

The name is a play of words on "pisto", a Manchego dish made of tomatoes, onions, courgettes, green and red peppers and olive oil.

User instructions

Installing pysto as a user

1. Install the latest pysto PyPI package

    pip install pysto
   

Uninstalling pysto

1. Uninstall the package

    pip uninstall pysto
   

2. If you get the error pip error: Cannot locate installed-files.txt, remove pysto manually. For example, if you are in a conda environment

    rm -rf ${CONDA_PREFIX}/lib/python3.6/site-packages/pysto*
   

Developer instructions

We provide scripts install_pysto_environment.sh and build_SimpleElastix.sh to help install necessary software, and a Makefile to simplify testing and releasing.

Installing pysto as a developer

1. If you want to develop code for pysto, instead of installing the PyPI package, you want to clone the github repository

    git clone https://github.com/rcasero/pysto.git
   

2. Install the development dependencies (this creates local conda environments pysto_2.7 and pysto_3.6, for python 2.7 and 3.6, respectively and installs several Ubuntu and python packages). There are two options, depending on what SimpleITK you want:

   1. If you are happy with the official SimpleITK package, just run (this is very fast)

       cd pysto/tools
       ./install_pysto_environment.sh
      

   2. If you prefer SimpleElastix (an extension of SimpleITK with elastix registration software)

       cd pysto/tools
       ./install_pysto_environment.sh SimpleElastix
      

3. Install the pysto code to one or both of the local environments

    conda activate pysto_2.7
    pip install --upgrade .
    
    conda activate pysto_3.6
    pip install --upgrade .
   

4. You need to have a local file ~/.pypirc (replace <the password> by the password). This will be used by twine to release packages to PyPI

    [distutils]
    index-servers =
      pypi
      pypitest
    
    [pypi]
    username=rcasero
    password=<the password>
    
    [pypitest]
    repository = https://test.pypi.org/legacy/
    username=rcasero
    password=<the password>
   

5. Protect the file so that it can be read only by you

    chmod 600 ~/.pypirc
   

Uninstalling pysto as a developer

1. Delete the conda local environments (this will delete all the python packages inside the environments)

    source deactivate
    conda remove --name pysto_2.7 --all
    conda remove --name pysto_3.6 --all
   

Developing source code for pysto

1. Activate one of the pysto local environments

    cd ~/Software/pysto
    source activate pysto_3.6
   

2. Launch the development IDE, e.g.

    pycharm-community &
   

3. In your code, import the pysto modules/functions in the usual way, e.g.

    import pysto.imgproc as pym
    import pysto.imgprocITK as pymITK
    [...]
    imf = pym.imfuse(im1, im2)
    pymITK.imshow(im3)
   

4. While developing, you can run all tests (both for python 2.7 and 3.6) from the command line with

    make test
   

Making a new release (to GitHub and PyPI)

1. We assume that you have made some changes to the code, and commit/pushed them to the GitHub repository.

2. Update version and download_url in setup.py with new release number. If something else has changed in the project, update other relevant fields in setup.py.

    setup(
        ...
        version='1.0.0',
        download_url='https://github.com/rcasero/pysto/archive/1.0.0.tar.gz',
        ...
    )
   

3. Update ChangeLog.md with the main changes to this release, in markdown format.

4. Commit and push all changes to the repository.

5. Make a test package. (This will also tag the release in github, create the test package/wheel and upload to the test PyPI server), that you can see in https://test.pypi.org/project/pysto/

    make test-package
   

6. If everything has gone well, make the release package, that you can see in https://pypi.org/project/pysto/

    make package
   

7. Go to pysto GitHub release tags, click on "Edit release notes" and copy and paste the new entry from the ChangeLog.md