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[CIVIS-1555] python patch update #83

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[CIVIS-1555] python patch update #83

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141737e
script to upgrade minor package versions
mattyb Nov 6, 2021
1fa576e
try 3.7.11 which was getting installed by apt-get
mattyb Nov 7, 2021
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4 changes: 2 additions & 2 deletions Dockerfile
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Original file line number Diff line number Diff line change
Expand Up @@ -30,8 +30,8 @@ ENV LANG=en_US.UTF-8 \
BASH_ENV=/etc/profile \
PATH=/opt/conda/bin:$PATH \
CIVIS_MINICONDA_VERSION=4.5.12 \
CIVIS_CONDA_VERSION=4.8.1 \
CIVIS_PYTHON_VERSION=3.7.6
CIVIS_CONDA_VERSION=4.8.5 \
CIVIS_PYTHON_VERSION=3.7.11

# Conda install.
#
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40 changes: 20 additions & 20 deletions environment.yml
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Original file line number Diff line number Diff line change
@@ -1,23 +1,22 @@
name: datascience
channels:
- defaults
- conda-forge
dependencies:
- awscli=1.17.15
- awscli=1.17.17
- beautifulsoup4=4.8.2
- botocore=1.14.15
- botocore=1.14.17
- boto=2.49.0
- boto3=1.11.15
- bqplot=0.12.3
- boto3=1.11.17
- bqplot=0.12.31
- click=6.7
- cloudpickle=1.2.2
- cython=0.29.15
- cython=0.29.24
- dask=2.10.1
- feather-format=0.4.0
- feather-format=0.4.1
- glmnet=2.1.1
- ipython=7.12.0
- ipywidgets=7.5.1
- jinja2=2.11.1
- jinja2=2.11.3
- joblib=0.14.1
- jsonschema=3.2.0
- jupyter=1.0.0
Expand All @@ -29,33 +28,34 @@ dependencies:
- nomkl=3.0
- notebook=6.0.3
- nose=1.3.7
- numexpr=2.7.1
- numpy=1.17.3
- numexpr=2.7.3
- numpy=1.17.5
- openblas=0.3.6
- pandas=0.25.3
- patsy=0.5.1
- patsy=0.5.2
- pip=20.0.2
- psycopg2=2.8.4
- psycopg2=2.8.6
- pyarrow=0.16.0
- pycrypto=2.6.1
- pytest=5.3.5
- python=3.7.6
- python=3.7.11
- pyyaml=5.2
- requests=2.22.0
- s3fs=0.4.0
- seaborn=0.10.0
- s3fs=0.4.2
- seaborn=0.10.1
- scipy=1.4.1
- scikit-learn=0.22.1
- statsmodels=0.11.0
- urllib3=1.25.7
- scikit-learn=0.22.2.post1
- statsmodels=0.11.1
- urllib3=1.25.11
- xgboost=0.81
- pip:
- civis==1.15.1
- civisml-extensions==0.2.1
- dropbox==9.4.0
- ftputil==3.4
- muffnn==2.3.1
- muffnn==2.3.2
- pubnub==4.3.0
- pysftp==0.2.9
- requests-toolbelt==0.9.1
- tensorflow==1.15.4
- tensorflow==1.15.5
name: datascience
46 changes: 46 additions & 0 deletions upgrade_env.py
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Original file line number Diff line number Diff line change
@@ -0,0 +1,46 @@
import json
import yaml
from urllib.request import urlopen
from urllib.error import HTTPError
import packaging.version

def newest_patch_version(package_name, version):
version = packaging.version.parse(version)
url = "https://pypi.org/pypi/%s/json" % (package_name,)
try:
data = json.load(urlopen(url))
versions = [packaging.version.parse(r) for r in data["releases"].keys()]
versions.sort(reverse=True)
return [v for v in versions
if not isinstance(v, packaging.version.LegacyVersion) and
version.major == v.major and
version.minor == v.minor][0]
except (HTTPError, IndexError) as e:
print(f"Error: {e}")
return version

env = yaml.safe_load(open('environment.yml', 'r'))
new_dependencies = []
for package in env['dependencies']:
if isinstance(package, dict):
new_pip = []
for pkg in package['pip']:
name, version = pkg.split('==')
print(name)
print(version)
new_version = newest_patch_version(name, version)
print(new_version)
new_pip.append(f'{name}=={new_version}')
new_dependencies.append({'pip': new_pip})
continue
print(package)
name, version = package.split('=')
print(name)
print(version)
new_version = newest_patch_version(name, version)
print(new_version)
new_dependencies.append(f'{name}={new_version}')

env['dependencies'] = new_dependencies
with open('environment.yml', 'w') as f:
yaml.dump(env, f)