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Add all Python packages (versioned!) to Dockerfile (AlexsLemonade#1008)
* Add requirements.txt for reference * consolidate python and add version numbers for everything * Add back setuptools at start * Add Cython to starting set * Add back EPN subtyping back to CI * print python package list for debugging * No really, use the right packages * Test a python check script * Test making the python package test fail * Revert "Test making the python package test fail" This reverts commit 8a221e6. * Make the python package test better * Add one more error check * Fix filename second time * Use tmp and clean up * One more failure check * Revert test & add docs * One more doc comment
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,84 @@ | ||
| appdirs==1.4.4 | ||
| attrs==20.3.0 | ||
| backcall==0.2.0 | ||
| bleach==3.3.0 | ||
| bx-python==0.8.8 | ||
| certifi==2020.12.5 | ||
| chardet==4.0.0 | ||
| ConfigArgParse==1.4 | ||
| CrossMap==0.3.9 | ||
| cycler==0.10.0 | ||
| Cython==0.29.15 | ||
| datrie==0.8.2 | ||
| decorator==4.4.2 | ||
| defusedxml==0.7.1 | ||
| docutils==0.16 | ||
| entrypoints==0.3 | ||
| gitdb==4.0.7 | ||
| GitPython==3.1.14 | ||
| idna==2.10 | ||
| importlib-metadata==2.1.1 | ||
| ipykernel==4.8.1 | ||
| ipython==7.9.0 | ||
| ipython-genutils==0.2.0 | ||
| jedi==0.17.2 | ||
| Jinja2==2.11.3 | ||
| jsonschema==3.2.0 | ||
| jupyter-client==6.1.12 | ||
| jupyter-core==4.6.3 | ||
| kiwisolver==1.1.0 | ||
| MarkupSafe==1.1.1 | ||
| matplotlib==3.0.3 | ||
| mistune==0.8.4 | ||
| mizani==0.5.4 | ||
| nbconvert==5.6.1 | ||
| nbformat==5.1.2 | ||
| notebook==6.0.0 | ||
| numpy==1.17.3 | ||
| packaging==20.9 | ||
| palettable==3.3.0 | ||
| pandas==0.25.3 | ||
| pandocfilters==1.4.3 | ||
| parso==0.7.1 | ||
| patsy==0.5.1 | ||
| pexpect==4.8.0 | ||
| pickleshare==0.7.5 | ||
| plotnine==0.3.0 | ||
| prometheus-client==0.9.0 | ||
| prompt-toolkit==2.0.10 | ||
| psutil==5.8.0 | ||
| ptyprocess==0.7.0 | ||
| pyarrow==0.16.0 | ||
| pybedtools==0.8.1 | ||
| pyBigWig==0.3.17 | ||
| Pygments==2.8.1 | ||
| pyparsing==2.4.5 | ||
| pyreadr==0.2.1 | ||
| pyrsistent==0.17.3 | ||
| pysam==0.15.4 | ||
| python-dateutil==2.8.1 | ||
| pytz==2019.3 | ||
| PyYAML==5.3.1 | ||
| pyzmq==20.0.0 | ||
| ratelimiter==1.2.0.post0 | ||
| requests==2.25.1 | ||
| rpy2==2.9.3 | ||
| scikit-learn==0.19.1 | ||
| scipy==1.3.2 | ||
| seaborn==0.8.1 | ||
| Send2Trash==1.5.0 | ||
| six==1.14.0 | ||
| smmap==4.0.0 | ||
| snakemake==5.8.1 | ||
| statsmodels==0.10.2 | ||
| terminado==0.8.3 | ||
| testpath==0.4.4 | ||
| tornado==6.1 | ||
| traitlets==4.3.3 | ||
| tzlocal==2.0.0 | ||
| urllib3==1.26.4 | ||
| wcwidth==0.2.5 | ||
| webencodings==0.5.1 | ||
| widgetsnbextension==2.0.0 | ||
| wrapt==1.12.1 | ||
| zipp==1.2.0 |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,33 @@ | ||
| #!/bin/bash | ||
|
|
||
| set -e | ||
| set -o pipefail | ||
|
|
||
| # This script checks that all python files in the docker image match | ||
| # requirements.txt | ||
|
|
||
| # run from this file location but move up to root | ||
| cd "$(dirname "${BASH_SOURCE[0]}")" | ||
| cd .. | ||
|
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| req_diff=/tmp/package_diffs.txt | ||
|
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| ## diff will exit code 1 with differences, so we need to pass true | ||
| pip3 freeze | diff requirements.txt - > $req_diff || true | ||
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| # check if there are any differences in the file | ||
| if [ -s $req_diff ] | ||
| then | ||
| cat $req_diff && rm $req_diff | ||
| echo "Python packages do not match requirements.txt, please check." | ||
| exit 1 | ||
| fi | ||
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| # if the diffs file was not produced for some reason, we should be sure to fail the same way | ||
| if [ ! -e $req_diff ] | ||
| then | ||
| pip3 freeze | diff requirements.txt - | ||
| fi | ||
|
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||
| # clean up | ||
| rm $req_diff |