Closed creisle closed 2 years ago
For the functions that are in the setup.py
To help debugging the pysam dependency issues, I collected the frozen list of dependencies from the last mavis production install on our end (v2.2.9). This should give us an idea of what might have changed if we compare it to what we get now
Package Version
----------------------------- --------
alabaster 0.7.12
Babel 2.7.0
biopython 1.73
bleach 3.1.0
braceexpand 0.1.2
certifi 2019.3.9
chardet 3.0.4
colour 0.1.5
decorator 4.4.0
Distance 0.1.3
docutils 0.14
idna 2.8
imagesize 1.1.0
Jinja2 2.10.1
m2r 0.2.1
MarkupSafe 1.1.1
mavis 2.2.6
mistune 0.8.4
networkx 1.11
numpy 1.16.4
packaging 19.0
pip 21.3.1
pkginfo 1.5.0.1
Pygments 2.4.2
pyparsing 2.4.0
pysam 0.15.2
pytz 2019.1
PyVCF 0.6.8
readme-renderer 24.0
requests 2.22.0
requests-toolbelt 0.9.1
setuptools 59.6.0
Shapely 1.7a1
shortuuid 0.5.0
six 1.12.0
snowballstemmer 1.2.1
Sphinx 2.1.0
sphinx-rtd-theme 0.4.3
sphinxcontrib-applehelp 1.0.1
sphinxcontrib-devhelp 1.0.1
sphinxcontrib-htmlhelp 1.0.2
sphinxcontrib-jsmath 1.0.1
sphinxcontrib-qthelp 1.0.2
sphinxcontrib-serializinghtml 1.1.3
svgwrite 1.3b2
tqdm 4.32.1
twine 1.13.0
urllib3 1.25.3
webencodings 0.5.1
wheel 0.37.0
zc.buildout 3.0.0b5
Closing issue, will be integrated into v3.
In order to keep up to date with PEP-517, update the setup.cfg and add a pyproject.toml to work with the new version of setuptools and prep for new versions of package installs with python
See example from other gsc repo: https://github.com/bcgsc/pori_ipr_python/pull/55
see the setuptools docs for how to structure the setup.cfg: https://setuptools.pypa.io/en/latest/build_meta.html