diff --git a/requirements/base.txt b/requirements/base.txt index 794a132..52342a6 100644 --- a/requirements/base.txt +++ b/requirements/base.txt @@ -1,23 +1,31 @@ -# SHA1:3bc19cfb3e64aa97db8dd905f46958134eeafdec +# SHA1:1fe4f34c934aec8444d3aa917925756f57eb7f74 # # This file is autogenerated by pip-compile-multi # To update, run: # # pip-compile-multi # -argcomplete==1.12.3 +argcomplete==2.0.0 # via # -r requirements/base.txt # cwltool -argon2-cffi==21.1.0 +argon2-cffi==21.3.0 # via # -r requirements/base.txt # notebook -arrow==1.2.1 +argon2-cffi-bindings==21.2.0 + # via + # -r requirements/base.txt + # argon2-cffi +arrow==1.2.2 # via # -r requirements/base.txt # jinja2-time -attrs==21.2.0 +asttokens==2.0.5 + # via + # -r requirements/base.txt + # stack-data +attrs==21.4.0 # via # -r requirements/base.txt # jsonschema @@ -37,6 +45,10 @@ bioconda2biocontainer==0.0.6 # via -r requirements/base.txt biopython==1.79 # via -r requirements/base.txt +black==22.1.0 + # via + # -r requirements/base.txt + # ipython bleach==4.1.0 # via # -r requirements/base.txt @@ -46,7 +58,7 @@ boltons==21.0.0 # via # -r requirements/base.txt # galaxy-util -cachecontrol==0.12.8 +cachecontrol==0.12.10 # via # -r requirements/base.txt # schema-salad @@ -57,18 +69,19 @@ certifi==2021.10.8 cffi==1.15.0 # via # -r requirements/base.txt - # argon2-cffi + # argon2-cffi-bindings chardet==4.0.0 # via # -r requirements/base.txt # binaryornot -charset-normalizer==2.0.7 +charset-normalizer==2.0.11 # via # -r requirements/base.txt # requests click==8.0.3 # via # -r requirements/base.txt + # black # cookiecutter coloredlogs==15.0.1 # via @@ -76,7 +89,7 @@ coloredlogs==15.0.1 # cwltool cookiecutter==1.7.3 # via -r requirements/base.txt -cwltool==3.1.20211020155521 +cwltool==3.1.20220202173120 # via -r requirements/base.txt cycler==0.11.0 # via @@ -86,7 +99,7 @@ debugpy==1.5.1 # via # -r requirements/base.txt # ipykernel -decorator==5.1.0 +decorator==5.1.1 # via # -r requirements/base.txt # ipython @@ -96,22 +109,30 @@ defusedxml==0.7.1 # nbconvert docker==5.0.3 # via -r requirements/base.txt -docutils==0.18 +docutils==0.18.1 # via # -r requirements/base.txt # galaxy-util -entrypoints==0.3 +entrypoints==0.4 # via # -r requirements/base.txt # jupyter-client # nbconvert -galaxy-containers==21.1.0 +executing==0.8.2 + # via + # -r requirements/base.txt + # stack-data +fonttools==4.29.1 + # via + # -r requirements/base.txt + # matplotlib +galaxy-containers==21.9.0 # via # -r requirements/base.txt # galaxy-tool-util -galaxy-tool-util==21.1.2 +galaxy-tool-util==21.9.2 # via -r requirements/base.txt -galaxy-util==21.1.0 +galaxy-util==21.9.0 # via # -r requirements/base.txt # galaxy-containers @@ -120,7 +141,7 @@ gitdb==4.0.9 # via # -r requirements/base.txt # gitpython -gitpython==3.1.24 +gitpython==3.1.26 # via -r requirements/base.txt goenrichment==1.0.3 # via -r requirements/base.txt @@ -132,7 +153,7 @@ idna==3.3 # via # -r requirements/base.txt # requests -ipykernel==6.4.2 +ipykernel==6.8.0 # via # -r requirements/base.txt # ipywidgets @@ -140,7 +161,7 @@ ipykernel==6.4.2 # jupyter-console # notebook # qtconsole -ipython==7.29.0 +ipython==8.0.1 # via # -r requirements/base.txt # ipykernel @@ -149,7 +170,6 @@ ipython==7.29.0 ipython-genutils==0.2.0 # via # -r requirements/base.txt - # ipykernel # ipywidgets # nbformat # notebook @@ -158,15 +178,15 @@ ipywidgets==7.6.5 # via # -r requirements/base.txt # jupyter -isodate==0.6.0 +isodate==0.6.1 # via # -r requirements/base.txt # rdflib -jedi==0.18.0 +jedi==0.18.1 # via # -r requirements/base.txt # ipython -jinja2==3.0.2 +jinja2==3.0.3 # via # -r requirements/base.txt # cookiecutter @@ -177,13 +197,13 @@ jinja2-time==0.2.0 # via # -r requirements/base.txt # cookiecutter -jsonschema==4.1.2 +jsonschema==4.4.0 # via # -r requirements/base.txt # nbformat jupyter==1.0.0 # via -r requirements/base.txt -jupyter-client==7.0.6 +jupyter-client==7.1.2 # via # -r requirements/base.txt # ipykernel @@ -219,7 +239,7 @@ lockfile==0.12.2 # via # -r requirements/base.txt # schema-salad -lxml==4.6.3 +lxml==4.7.1 # via # -r requirements/base.txt # galaxy-tool-util @@ -229,7 +249,7 @@ markupsafe==2.0.1 # -r requirements/base.txt # galaxy-util # jinja2 -matplotlib==3.4.3 +matplotlib==3.5.1 # via # -r requirements/base.txt # seaborn @@ -243,19 +263,20 @@ mistune==0.8.4 # -r requirements/base.txt # nbconvert # schema-salad -msgpack==1.0.2 +msgpack==1.0.3 # via # -r requirements/base.txt # cachecontrol mypy-extensions==0.4.3 # via # -r requirements/base.txt + # black # cwltool -nbclient==0.5.4 +nbclient==0.5.10 # via # -r requirements/base.txt # nbconvert -nbconvert==6.2.0 +nbconvert==6.4.1 # via # -r requirements/base.txt # jupyter @@ -267,22 +288,24 @@ nbformat==5.1.3 # nbclient # nbconvert # notebook -nest-asyncio==1.5.1 +nest-asyncio==1.5.4 # via # -r requirements/base.txt + # ipykernel # jupyter-client # nbclient + # notebook networkx==2.6.3 # via # -r requirements/base.txt # goenrichment # prov -notebook==6.4.5 +notebook==6.4.8 # via # -r requirements/base.txt # jupyter # widgetsnbextension -numpy==1.21.3 +numpy==1.22.2 # via # -r requirements/base.txt # biopython @@ -293,12 +316,14 @@ numpy==1.21.3 # scipy # seaborn # statsmodels -packaging==21.2 +packaging==21.3 # via # -r requirements/base.txt # bleach # galaxy-util -pandas==1.3.4 + # matplotlib + # qtpy +pandas==1.4.0 # via # -r requirements/base.txt # goenrichment @@ -308,10 +333,14 @@ pandocfilters==1.5.0 # via # -r requirements/base.txt # nbconvert -parso==0.8.2 +parso==0.8.3 # via # -r requirements/base.txt # jedi +pathspec==0.9.0 + # via + # -r requirements/base.txt + # black patsy==0.5.2 # via # -r requirements/base.txt @@ -326,20 +355,24 @@ pickleshare==0.7.5 # via # -r requirements/base.txt # ipython -pillow==8.4.0 +pillow==9.0.1 # via # -r requirements/base.txt # matplotlib # pdf2image +platformdirs==2.4.1 + # via + # -r requirements/base.txt + # black poyo==0.5.0 # via # -r requirements/base.txt # cookiecutter -prometheus-client==0.12.0 +prometheus-client==0.13.1 # via # -r requirements/base.txt # notebook -prompt-toolkit==3.0.21 +prompt-toolkit==3.0.26 # via # -r requirements/base.txt # ipython @@ -348,7 +381,7 @@ prov==1.5.1 # via # -r requirements/base.txt # cwltool -psutil==5.8.0 +psutil==5.9.0 # via # -r requirements/base.txt # cwltool @@ -357,15 +390,27 @@ ptyprocess==0.7.0 # -r requirements/base.txt # pexpect # terminado -pycparser==2.20 +pure-eval==0.2.2 + # via + # -r requirements/base.txt + # stack-data +pycparser==2.21 # via # -r requirements/base.txt # cffi +pycryptodome==3.14.0 + # via + # -r requirements/base.txt + # galaxy-util +pydantic==1.9.0 + # via + # -r requirements/base.txt + # galaxy-tool-util pydot==1.4.2 # via # -r requirements/base.txt # cwltool -pygments==2.10.0 +pygments==2.11.2 # via # -r requirements/base.txt # ipython @@ -373,14 +418,15 @@ pygments==2.10.0 # jupyterlab-pygments # nbconvert # qtconsole -pyparsing==2.4.7 +pyparsing==3.0.7 # via # -r requirements/base.txt + # cwltool # matplotlib # packaging # pydot # rdflib -pyrsistent==0.18.0 +pyrsistent==0.18.1 # via # -r requirements/base.txt # jsonschema @@ -411,25 +457,25 @@ pyzmq==22.3.0 # jupyter-client # notebook # qtconsole -qtconsole==5.1.1 +qtconsole==5.2.2 # via # -r requirements/base.txt # jupyter -qtpy==1.11.2 +qtpy==2.0.1 # via # -r requirements/base.txt # qtconsole -rdflib==6.0.2 +rdflib==6.1.1 # via # -r requirements/base.txt # cwltool # prov # schema-salad -repoze.lru==0.7 - # via - # -r requirements/base.txt - # routes -requests==2.26.0 +repoze-lru==0.7 + # via -r requirements/base.txt +repoze-lru==0.7 + # via routes +requests==2.27.1 # via # -r requirements/base.txt # bioconda2biocontainer @@ -444,20 +490,21 @@ routes==2.5.1 # via # -r requirements/base.txt # galaxy-util -ruamel.yaml==0.17.16 +ruamel-yaml==0.17.20 + # via -r requirements/base.txt +ruamel-yaml-clib==0.2.6 + # via -r requirements/base.txt +ruamel-yaml==0.17.20 # via - # -r requirements/base.txt # cwltool # schema-salad -ruamel.yaml.clib==0.2.6 - # via - # -r requirements/base.txt - # ruamel.yaml -schema-salad==8.2.20211029004247 +ruamel-yaml-clib==0.2.6 + # via ruamel-yaml +schema-salad==8.2.20220103095339 # via # -r requirements/base.txt # cwltool -scipy==1.7.1 +scipy==1.7.3 # via # -r requirements/base.txt # goenrichment @@ -476,6 +523,7 @@ shellescape==3.8.1 six==1.16.0 # via # -r requirements/base.txt + # asttokens # bleach # cookiecutter # galaxy-util @@ -488,11 +536,19 @@ smmap==5.0.0 # via # -r requirements/base.txt # gitdb -statsmodels==0.13.0 +sortedcontainers==2.4.0 + # via + # -r requirements/base.txt + # galaxy-tool-util +stack-data==0.1.4 + # via + # -r requirements/base.txt + # ipython +statsmodels==0.13.1 # via # -r requirements/base.txt # goenrichment -terminado==0.12.1 +terminado==0.13.1 # via # -r requirements/base.txt # notebook @@ -504,6 +560,10 @@ text-unidecode==1.3 # via # -r requirements/base.txt # python-slugify +tomli==2.0.0 + # via + # -r requirements/base.txt + # black tornado==6.1 # via # -r requirements/base.txt @@ -525,12 +585,14 @@ traitlets==5.1.1 # nbformat # notebook # qtconsole -typing-extensions==3.10.0.2 +typing-extensions==4.0.1 # via # -r requirements/base.txt + # black # cwltool - # gitpython -urllib3==1.26.7 + # galaxy-tool-util + # pydantic +urllib3==1.26.8 # via # -r requirements/base.txt # requests @@ -542,7 +604,7 @@ webencodings==0.5.1 # via # -r requirements/base.txt # bleach -websocket-client==1.2.1 +websocket-client==1.2.3 # via # -r requirements/base.txt # docker diff --git a/requirements/test.txt b/requirements/test.txt index 3e69473..6e1b695 100644 --- a/requirements/test.txt +++ b/requirements/test.txt @@ -6,24 +6,20 @@ # pip-compile-multi # -r base.txt -coverage[toml]==6.1.1 +coverage[toml]==6.3.1 # via pytest-cov iniconfig==1.1.1 # via pytest pluggy==1.0.0 # via pytest -py==1.10.0 +py==1.11.0 # via pytest -pytest==6.2.5 +pytest==7.0.0 # via # -r requirements/test.in # pytest-cov pytest-cov==3.0.0 # via -r requirements/test.in -toml==0.10.2 - # via pytest -tomli==1.2.2 - # via coverage # The following packages are considered to be unsafe in a requirements file: # setuptools