geneontology / pipeline

Declarative pipeline for the Gene Ontology.
https://build.geneontology.org/job/geneontology/job/pipeline/
BSD 3-Clause "New" or "Revised" License
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Realign various python versions and libraries (and any other free-floating software requirements) #272

Open kltm opened 2 years ago

kltm commented 2 years ago

As the older versions of python and libraries slowly clock out for good, we're increasingly running into problems like #250 #262 #271.

Closing this ticket would be that, as much as possible, all requirements are locked in to a reproducible version. For example, all (python) software would be required to:

kltm commented 2 years ago

As a note, for now the scripts running outside of images are more-or-less chugging along with:

python3 --version
Python 3.5.2
python3 ./mypyenv/bin/pip3 list
awscli (1.22.52)
bagit (1.8.1)
bagit-profile (1.3.1)
bdbag (1.6.3)
boto3 (1.18.52)
botocore (1.21.52)
certifi (2021.10.8)
chardet (4.0.0)
charset-normalizer (2.0.11)
click (7.1.2)
colorama (0.4.3)
docutils (0.15.2)
filechunkio (1.8)
idna (2.10)
jmespath (0.10.0)
pip (8.1.1)
pkg-resources (0.0.0)
pyasn1 (0.4.8)
pycurl (7.44.1)
pypandoc (1.7.2)
pystache (0.5.4)
python-dateutil (2.8.2)
pytz (2021.3)
PyYAML (5.4.1)
requests (2.25.1)
requests-toolbelt (0.9.1)
rsa (4.7.2)
s3transfer (0.5.0)
setuptools (20.7.0)
setuptools-scm (5.0.2)
six (1.16.0)
tzlocal (2.1)
urllib3 (1.26.8)
yamldown (0.1.8)