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.
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Install the latest pysto PyPI package
pip install pysto
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Uninstall the package
pip uninstall pysto -
If you get the error
pip error: Cannot locate installed-files.txt, remove pysto manually. For example, if you are in a conda environmentrm -rf ${CONDA_PREFIX}/lib/python3.6/site-packages/pysto*
We provide scripts install_pysto_environment.sh and build_SimpleElastix.sh to help install necessary software, and a Makefile to simplify testing and releasing.
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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 -
Install the development dependencies (this creates local conda environments
pysto_2.7andpysto_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:-
If you are happy with the official SimpleITK package, just run (this is very fast)
cd pysto/tools ./install_pysto_environment.sh -
If you prefer SimpleElastix (an extension of SimpleITK with elastix registration software)
cd pysto/tools ./install_pysto_environment.sh SimpleElastix
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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 . -
You need to have a local file
~/.pypirc(replace<the password>by the password). This will be used bytwineto 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> -
Protect the file so that it can be read only by you
chmod 600 ~/.pypirc
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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
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Activate one of the pysto local environments
cd ~/Software/pysto source activate pysto_3.6 -
Launch the development IDE, e.g.
pycharm-community & -
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) -
While developing, you can run all tests (both for python 2.7 and 3.6) from the command line with
make test
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We assume that you have made some changes to the code, and commit/pushed them to the GitHub repository.
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Update
versionanddownload_urlinsetup.pywith new release number. If something else has changed in the project, update other relevant fields insetup.py.setup( ... version='1.0.0', download_url='https://github.com/rcasero/pysto/archive/1.0.0.tar.gz', ... ) -
Update
ChangeLog.mdwith the main changes to this release, in markdown format. -
Commit and push all changes to the repository.
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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 -
If everything has gone well, make the release package, that you can see in https://pypi.org/project/pysto/
make package -
Go to pysto GitHub release tags, click on "Edit release notes" and copy and paste the new entry from the
ChangeLog.md