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superlint/dependencies/python/snakemake.txt

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Use Virtual Environment for Python Deps (#2294) * Build static python depenencies * Address linting * Fix copy path * cleaner * Stage virtual environments * Update Dockerfile to support virtual environments * Remove old python builds * Remove unnecessary RUN step * Fix merge conflicts * Remove test checking for PIP packages We use virtual environments and no longer install the packages via pip directly in the image. It should be enough that the version tests check for the existence already and that the version comes back correctly. * Remove binary installation of black * cleaner * Remove pip * pretty Co-authored-by: Admiral Awkbar <admiralawkbar@github.com>
2022-01-10 16:23:22 -05:00
appdirs==1.4.4
attrs==21.4.0
certifi==2021.10.8
Update deps
2022-02-14 13:03:43 -05:00
charset-normalizer==2.0.12
Use Virtual Environment for Python Deps (#2294) * Build static python depenencies * Address linting * Fix copy path * cleaner * Stage virtual environments * Update Dockerfile to support virtual environments * Remove old python builds * Remove unnecessary RUN step * Fix merge conflicts * Remove test checking for PIP packages We use virtual environments and no longer install the packages via pip directly in the image. It should be enough that the version tests check for the existence already and that the version comes back correctly. * Remove binary installation of black * cleaner * Remove pip * pretty Co-authored-by: Admiral Awkbar <admiralawkbar@github.com>
2022-01-10 16:23:22 -05:00
ConfigArgParse==1.5.3
connection-pool==0.0.3
datrie==0.8.2
Update Python dependencies
2022-02-27 12:03:20 -05:00
decorator==5.1.1
Use Virtual Environment for Python Deps (#2294) * Build static python depenencies * Address linting * Fix copy path * cleaner * Stage virtual environments * Update Dockerfile to support virtual environments * Remove old python builds * Remove unnecessary RUN step * Fix merge conflicts * Remove test checking for PIP packages We use virtual environments and no longer install the packages via pip directly in the image. It should be enough that the version tests check for the existence already and that the version comes back correctly. * Remove binary installation of black * cleaner * Remove pip * pretty Co-authored-by: Admiral Awkbar <admiralawkbar@github.com>
2022-01-10 16:23:22 -05:00
docutils==0.18.1
Update Python dependencies (#2546) Co-authored-by: Super-Linter Automation <noreply@github.com>
2022-02-22 12:21:32 -05:00
filelock==3.6.0
Use Virtual Environment for Python Deps (#2294) * Build static python depenencies * Address linting * Fix copy path * cleaner * Stage virtual environments * Update Dockerfile to support virtual environments * Remove old python builds * Remove unnecessary RUN step * Fix merge conflicts * Remove test checking for PIP packages We use virtual environments and no longer install the packages via pip directly in the image. It should be enough that the version tests check for the existence already and that the version comes back correctly. * Remove binary installation of black * cleaner * Remove pip * pretty Co-authored-by: Admiral Awkbar <admiralawkbar@github.com>
2022-01-10 16:23:22 -05:00
gitdb==4.0.9
Bump gitpython from 3.1.26 to 3.1.27 in /dependencies/python (#2532) Bumps [gitpython](https://github.com/gitpython-developers/GitPython) from 3.1.26 to 3.1.27. - [Release notes](https://github.com/gitpython-developers/GitPython/releases) - [Changelog](https://github.com/gitpython-developers/GitPython/blob/main/CHANGES) - [Commits](https://github.com/gitpython-developers/GitPython/compare/3.1.26...3.1.27) --- updated-dependencies: - dependency-name: gitpython dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
2022-02-22 09:57:48 -05:00
GitPython==3.1.27
Use Virtual Environment for Python Deps (#2294) * Build static python depenencies * Address linting * Fix copy path * cleaner * Stage virtual environments * Update Dockerfile to support virtual environments * Remove old python builds * Remove unnecessary RUN step * Fix merge conflicts * Remove test checking for PIP packages We use virtual environments and no longer install the packages via pip directly in the image. It should be enough that the version tests check for the existence already and that the version comes back correctly. * Remove binary installation of black * cleaner * Remove pip * pretty Co-authored-by: Admiral Awkbar <admiralawkbar@github.com>
2022-01-10 16:23:22 -05:00
idna==3.3
Update deps
2022-02-14 13:03:43 -05:00
importlib-resources==5.4.0
Use Virtual Environment for Python Deps (#2294) * Build static python depenencies * Address linting * Fix copy path * cleaner * Stage virtual environments * Update Dockerfile to support virtual environments * Remove old python builds * Remove unnecessary RUN step * Fix merge conflicts * Remove test checking for PIP packages We use virtual environments and no longer install the packages via pip directly in the image. It should be enough that the version tests check for the existence already and that the version comes back correctly. * Remove binary installation of black * cleaner * Remove pip * pretty Co-authored-by: Admiral Awkbar <admiralawkbar@github.com>
2022-01-10 16:23:22 -05:00
ipython-genutils==0.2.0
Update Python dependencies
2022-02-27 12:03:20 -05:00
Jinja2==3.0.3
Update deps
2022-02-14 13:03:43 -05:00
jsonschema==4.4.0
Bump jupyter-core from 4.9.1 to 4.9.2 in /dependencies/python (#2530) Bumps [jupyter-core](https://jupyter.org) from 4.9.1 to 4.9.2. --- updated-dependencies: - dependency-name: jupyter-core dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
2022-02-22 09:58:02 -05:00
jupyter-core==4.9.2
Update Python dependencies
2022-02-27 12:03:20 -05:00
MarkupSafe==2.1.0
Use Virtual Environment for Python Deps (#2294) * Build static python depenencies * Address linting * Fix copy path * cleaner * Stage virtual environments * Update Dockerfile to support virtual environments * Remove old python builds * Remove unnecessary RUN step * Fix merge conflicts * Remove test checking for PIP packages We use virtual environments and no longer install the packages via pip directly in the image. It should be enough that the version tests check for the existence already and that the version comes back correctly. * Remove binary installation of black * cleaner * Remove pip * pretty Co-authored-by: Admiral Awkbar <admiralawkbar@github.com>
2022-01-10 16:23:22 -05:00
nbformat==5.1.3
Update Python dependencies
2022-02-27 12:03:20 -05:00
plac==1.3.4
Use Virtual Environment for Python Deps (#2294) * Build static python depenencies * Address linting * Fix copy path * cleaner * Stage virtual environments * Update Dockerfile to support virtual environments * Remove old python builds * Remove unnecessary RUN step * Fix merge conflicts * Remove test checking for PIP packages We use virtual environments and no longer install the packages via pip directly in the image. It should be enough that the version tests check for the existence already and that the version comes back correctly. * Remove binary installation of black * cleaner * Remove pip * pretty Co-authored-by: Admiral Awkbar <admiralawkbar@github.com>
2022-01-10 16:23:22 -05:00
psutil==5.9.0
PuLP==2.6.0
Update Python dependencies
2022-02-27 12:03:20 -05:00
py==1.11.0
Bump pyrsistent from 0.18.0 to 0.18.1 in /dependencies/python Bumps [pyrsistent](https://github.com/tobgu/pyrsistent) from 0.18.0 to 0.18.1. - [Release notes](https://github.com/tobgu/pyrsistent/releases) - [Changelog](https://github.com/tobgu/pyrsistent/blob/master/CHANGES.txt) - [Commits](https://github.com/tobgu/pyrsistent/compare/v0.18.0...v0.18.1) --- updated-dependencies: - dependency-name: pyrsistent dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] <support@github.com>
2022-01-18 13:29:39 -05:00
pyrsistent==0.18.1
Use Virtual Environment for Python Deps (#2294) * Build static python depenencies * Address linting * Fix copy path * cleaner * Stage virtual environments * Update Dockerfile to support virtual environments * Remove old python builds * Remove unnecessary RUN step * Fix merge conflicts * Remove test checking for PIP packages We use virtual environments and no longer install the packages via pip directly in the image. It should be enough that the version tests check for the existence already and that the version comes back correctly. * Remove binary installation of black * cleaner * Remove pip * pretty Co-authored-by: Admiral Awkbar <admiralawkbar@github.com>
2022-01-10 16:23:22 -05:00
PyYAML==6.0
ratelimiter==1.2.0.post0
requests==2.27.1
Update Python dependencies
2022-02-27 12:03:20 -05:00
retry==0.9.2
Use Virtual Environment for Python Deps (#2294) * Build static python depenencies * Address linting * Fix copy path * cleaner * Stage virtual environments * Update Dockerfile to support virtual environments * Remove old python builds * Remove unnecessary RUN step * Fix merge conflicts * Remove test checking for PIP packages We use virtual environments and no longer install the packages via pip directly in the image. It should be enough that the version tests check for the existence already and that the version comes back correctly. * Remove binary installation of black * cleaner * Remove pip * pretty Co-authored-by: Admiral Awkbar <admiralawkbar@github.com>
2022-01-10 16:23:22 -05:00
smart-open==5.2.1
smmap==5.0.0
Update Python dependencies
2022-02-27 12:03:20 -05:00
snakemake==7.0.1
Use Virtual Environment for Python Deps (#2294) * Build static python depenencies * Address linting * Fix copy path * cleaner * Stage virtual environments * Update Dockerfile to support virtual environments * Remove old python builds * Remove unnecessary RUN step * Fix merge conflicts * Remove test checking for PIP packages We use virtual environments and no longer install the packages via pip directly in the image. It should be enough that the version tests check for the existence already and that the version comes back correctly. * Remove binary installation of black * cleaner * Remove pip * pretty Co-authored-by: Admiral Awkbar <admiralawkbar@github.com>
2022-01-10 16:23:22 -05:00
stopit==1.1.2
tabulate==0.8.9
toposort==1.7
traitlets==5.1.1
Bump urllib3 from 1.26.7 to 1.26.8 in /dependencies/python (#2334) Bumps [urllib3](https://github.com/urllib3/urllib3) from 1.26.7 to 1.26.8. - [Release notes](https://github.com/urllib3/urllib3/releases) - [Changelog](https://github.com/urllib3/urllib3/blob/1.26.8/CHANGES.rst) - [Commits](https://github.com/urllib3/urllib3/compare/1.26.7...1.26.8) --- updated-dependencies: - dependency-name: urllib3 dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
2022-01-11 13:01:58 -05:00
urllib3==1.26.8
Use Virtual Environment for Python Deps (#2294) * Build static python depenencies * Address linting * Fix copy path * cleaner * Stage virtual environments * Update Dockerfile to support virtual environments * Remove old python builds * Remove unnecessary RUN step * Fix merge conflicts * Remove test checking for PIP packages We use virtual environments and no longer install the packages via pip directly in the image. It should be enough that the version tests check for the existence already and that the version comes back correctly. * Remove binary installation of black * cleaner * Remove pip * pretty Co-authored-by: Admiral Awkbar <admiralawkbar@github.com>
2022-01-10 16:23:22 -05:00
wrapt==1.13.3
Update Python dependencies
2022-02-28 10:31:00 -05:00
yte==1.2.0
Update deps
2022-02-14 13:03:43 -05:00
zipp==3.7.0
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