search

AlexsLemonade / refinebio

Refine.bio harmonizes petabytes of publicly available biological data into ready-to-use datasets for cancer researchers and AI/ML scientists.
https://www.refine.bio/
Other
128 stars 19 forks source link

Fix failing test_smasher tests #3205

Closed arkid15r closed 1 year ago

arkid15r commented 1 year ago

Context

In order to restore staging/prod deploy process CI/CD tests need to be fixed.

Problem or idea

#13 26.44 ERROR: Ignored the following versions that require a different python version: 2023.2.0 Requires-Python >=3.9
#13 26.44 ERROR: Could not find a version that satisfies the requirement xarray==2023.2.0 (from versions: 0.7.0, 0.7.1, 0.7.2, 0.8.0rc1, 0.8.0, 0.8.1, 0.8.2, 0.9.0rc1, 0.9.0, 0.9.1, 0.9.2, 0.9.3, 0.9.4, 0.9.5, 0.9.6, 0.10.0rc1, 0.10.0rc2, 0.10.0, 0.10.1, 0.10.2, 0.10.3, 0.10.4, 0.10.5, 0.10.6, 0.10.7, 0.10.8, 0.10.9, 0.11.0, 0.11.1, 0.11.2, 0.11.3, 0.12.0, 0.12.1, 0.12.2, 0.12.3, 0.13.0, 0.14.0, 0.14.1, 0.15.0, 0.15.1, 0.16.0, 0.16.1, 0.16.2, 0.17.0, 0.18.0, 0.18.1, 0.18.2, 0.19.0, 0.20.0, 0.20.1, 0.20.2, 0.21.0, 0.21.1, 2022.3.0, 2022.6.0rc0, 2022.6.0, 2022.9.0, 2022.10.0, 2022.11.0, 2022.12.0, 2023.1.0)
#13 26.44 ERROR: No matching distribution found for xarray==2023.2.0
#13 ERROR: executor failed running [/bin/bash -o pipefail -c pip3 install --ignore-installed --no-cache-dir --upgrade pip &&     pip3 install --ignore-installed --no-cache-dir nose numpy rpy2==3.4.5 &&     pip3 install --ignore-installed --no-cache-dir -r requirements.txt]: exit code: 1
------
 > importing cache manifest from ghrc.io/alexslemonade/refinebio/dr_smasher:
------
------
 > [ 7/13] RUN pip3 install --ignore-installed --no-cache-dir --upgrade pip &&     pip3 install --ignore-installed --no-cache-dir nose numpy rpy2==3.4.5 &&     pip3 install --ignore-installed --no-cache-dir -r requirements.txt:
#13 26.16   Downloading vcrpy-4.2.1-py2.py3-none-any.whl (40 kB)
#13 26.16      ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 40.8/40.8 kB 206.3 MB/s eta 0:00:00
#13 26.18 Collecting webencodings==0.5.1
#13 26.19   Downloading webencodings-0.5.1-py2.py3-none-any.whl (11 kB)
#13 26.32 Collecting wrapt==1.14.1
#13 26.33   Downloading wrapt-1.14.1-cp38-cp38-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl (81 kB)
#13 26.33      ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 81.0/81.0 kB 254.7 MB/s eta 0:00:00
#13 26.44 ERROR: Ignored the following versions that require a different python version: 2023.2.0 Requires-Python >=3.9
#13 26.44 ERROR: Could not find a version that satisfies the requirement xarray==2023.2.0 (from versions: 0.7.0, 0.7.1, 0.7.2, 0.8.0rc1, 0.8.0, 0.8.1, 0.8.2, 0.9.0rc1, 0.9.0, 0.9.1, 0.9.2, 0.9.3, 0.9.4, 0.9.5, 0.9.6, 0.10.0rc1, 0.10.0rc2, 0.10.0, 0.10.1, 0.10.2, 0.10.3, 0.10.4, 0.10.5, 0.10.6, 0.10.7, 0.10.8, 0.10.9, 0.11.0, 0.11.1, 0.11.2, 0.11.3, 0.12.0, 0.12.1, 0.12.2, 0.12.3, 0.13.0, 0.14.0, 0.14.1, 0.15.0, 0.15.1, 0.16.0, 0.16.1, 0.16.2, 0.17.0, 0.18.0, 0.18.1, 0.18.2, 0.19.0, 0.20.0, 0.20.1, 0.20.2, 0.21.0, 0.21.1, 2022.3.0, 2022.6.0rc0, 2022.6.0, 2022.9.0, 2022.10.0, 2022.11.0, 2022.12.0, 2023.1.0)
#13 26.44 ERROR: No matching distribution found for xarray==2023.2.0

Solution or next step

Resolve dependency problem.

arkid15r commented 1 year ago

Fixed in https://github.com/AlexsLemonade/refinebio/pull/3233