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loli
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medpy
Medical image processing in Python
http://loli.github.io/medpy/
GNU General Public License v3.0
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Release 0.5.0
#122
Closed
loli
closed
3 months ago
loli
commented
6 months ago
Pre:
[X] Write a pre-release checklist for future releases and add to repo as documentation
TODO
[X] Bump-up library version
[X] Supported formats
python3 tests/support.py > myformats.log
fails due to random package in scipy
[X] Depreciation and error fixes
scipy. => numpy.*
list(slice) => tuple(slice)
[X] Run tests and fix errors:
switch from nose to pytest
add test requirements.txt: pytest-7.4.3 & hypothesis-6.92.0
fix errors
[x] Error in saving an image that is of type bool, at least for .nii format: fix
[x] Run all notebooks, to test the code
fix all error that occurr
[x] Check Readme.md
check consistency and update
[x] Update setup.py
[x] Check & improve documentation
[x] check
https://loli.github.io/medpy/
#
[x] generate and improve
[x] Add graphcut help for
https://github.com/loli/medpy/issues/103
CentOs
Add note that, under Debian / Ubuntu, lib can be found under /usr/lib/x86_64-linux-gnu/libboost_python* if linker error
Generally, write better error handling for GraphCut installation and link in open issues on the topic for people to find (keep open)
e.g. add install -v for more info to
http://loli.github.io/medpy/installation/graphcutsupport.html
[x]- Issue of broken links and notebooks:
https://github.com/loli/medpy/issues/97
[x] Check badges in README.md
[x] Bioconda / conda
Now in conda-forge:
https://anaconda.org/conda-forge/medpy
[x] Add badge from here to Readme
test install and update docu (e.g.
https://loli.github.io/medpy/installation/conda.html
) accordingly
edit recipes to ppoint to 0.5.0?
maybe this:
https://github.com/conda-forge/medpy-feedstock
?
seem like it, version is here:
https://github.com/conda-forge/medpy-feedstock/blob/main/recipe/meta.yaml
[x] fork & PR for file
https://github.com/conda-forge/medpy-feedstock/blob/main/recipe/meta.yaml
plus see Readme of that repo
[x] Remove travis build
move to github builds, if possible
[x] Check config files:
.bettercodehub
.gitmodules
[x] Try installation on different systems
with different library versions to figure out minimal
with graph cut support and without
use
pip install -v -e .
to see installation logs for graphcut
[x] check why they exists and remove/ edit requirements-dev.* files in root folder
[x] Dockerfiles: won't do anymore
remove linked repo
remove from documentation
[x] Others:
Maybe write a short docu / docstring comment on this:
https://github.com/loli/medpy/issues/76
[x] Auto-build and auto-tests: Introduce appropriate gituhub actions
[x] test for pre-commit hook usage on commit
[x] run install and test
[x] linux
[x] MacOs
[x] Windows (won't do)
[x] run graphcut install and test
ubuntu22.10 with p3.10 & ubuntu20.04 with p3.8
[x] trigger build & upload to test.pypi on release
[x] manually trigger release to pypi [needs: build]
[x] manually trigger doc release [needs: build]
new minimal dependency versions
[x] old dtypes depreciates from numpy >= 1.24
[x] inspect.getfullargspec recommended since python >= 3.4
[x] dump minima dependencies in setup.py
Optional (rather for v0.6)
[ ] Introduce new build system (e.g. poetry)
interesting, but would be quite some effort to get the c++ compiled extension running
maybe for the next release?
https://towardsdatascience.com/setuptools-python-571e7d5500f2
https://packaging.python.org/en/latest/guides/writing-pyproject-toml/
[ ] Adapt GitHib actions to also build wheels
https://github.com/pypa/manylinux
for MacOs
for windows
[ ] Harmonize imports, aka "import numpy" > "import numpy as np"
[ ] Switch to more modern documentation builder
Release TODO
[x] Generate docs and place to upload
[x] Update setup.py
[x] Update CHANGES.txt
[x] Update github-pages
[x] create package and upload to pypi
Post-Release to do
[ ] Update conda-forge recipe
Pre:
TODO
python3 tests/support.py > myformats.log
fails due to random package in scipypip install -v -e .
to see installation logs for graphcutnew minimal dependency versions
Optional (rather for v0.6)
Release TODO
Post-Release to do