From b73c58df2a68b019aa6cf03617e5d76b2102a18c Mon Sep 17 00:00:00 2001 From: alisandra Date: Sun, 16 Jul 2023 10:42:46 -0400 Subject: [PATCH] requirement and version update --- requirements.exact_pip_freeze.txt | 206 ++++++++++-------------------- setup.py | 2 +- 2 files changed, 69 insertions(+), 139 deletions(-) diff --git a/requirements.exact_pip_freeze.txt b/requirements.exact_pip_freeze.txt index 5f19eef..691632f 100644 --- a/requirements.exact_pip_freeze.txt +++ b/requirements.exact_pip_freeze.txt @@ -1,168 +1,98 @@ -absl-py==1.3.0 -anyio==3.6.2 +absl-py==1.4.0 appdirs==1.4.4 -argon2-cffi==21.3.0 -argon2-cffi-bindings==21.2.0 astor==0.8.1 -asttokens==2.1.0 astunparse==1.6.3 -attrs==22.1.0 -backcall==0.2.0 -beautifulsoup4==4.11.1 -bleach==5.0.1 -cachetools==5.2.0 -certifi==2022.9.24 -cffi==1.15.1 -charset-normalizer==2.1.1 -cloudpickle==2.2.0 -colorama==0.4.5 +cachetools==5.3.1 +certifi==2023.5.7 +charset-normalizer==3.2.0 +cloudpickle==2.2.1 +colorama==0.4.6 contextlib2==21.6.0 -contourpy==1.0.5 +contourpy==1.1.0 cycler==0.11.0 -debugpy==1.6.3 -decorator==5.1.1 -defusedxml==0.7.1 +Cython==0.29.36 dill==0.3.6 -dnspython==2.2.1 dustdas==0.1 entrypoints==0.4 -executing==1.2.0 -fastjsonschema==2.16.2 -filelock==3.8.0 -flatbuffers==22.9.24 -fonttools==4.38.0 -future==0.18.2 +exceptiongroup==1.1.2 +filelock==3.11.0 +flatbuffers==23.5.26 +fonttools==4.41.0 gast==0.4.0 --e git+git@github.com:weberlab-hhu/GeenuFF.git@c66c0ab9389cff60cbc4df74dce8c929a735175a#egg=geenuff -google-auth==2.13.0 -google-auth-oauthlib==0.4.6 +geenuff==0.3.0 +google-auth==2.22.0 +google-auth-oauthlib==1.0.0 google-pasta==0.2.0 -grpcio==1.50.0 -h5py==3.7.0 --e git+git@github.com:weberlab-hhu/Helixer.git@dd8b383cd4b8251498fded0279257cdc5f12aad5#egg=helixer -HTSeq==2.0.2 -hyperopt==0.1.2 +grpcio==1.56.0 +h5py==3.9.0 +-e git+https://github.com/weberlab-hhu/Helixer.git@fbd1a6737eb24e007db0e753e709306f60d66b68#egg=helixer +HTSeq==2.0.3 idna==3.4 -importlib-metadata==5.0.0 -importlib-resources==5.10.0 -iniconfig==1.1.1 +importlib-metadata==6.8.0 +importlib-resources==6.0.0 +iniconfig==2.0.0 intervaltree==3.1.0 -ipykernel==6.17.0 -ipython==8.6.0 -ipython-genutils==0.2.0 -ipywidgets==8.0.2 -jedi==0.18.1 -Jinja2==3.1.2 -joblib==1.2.0 -json-tricks==3.15.5 -jsonschema==4.17.0 -jupyter==1.0.0 -jupyter-client==7.4.4 -jupyter-console==6.4.4 -jupyter-core==4.11.2 -jupyter-server==1.21.0 -jupyterlab-pygments==0.2.2 -jupyterlab-widgets==3.0.3 -keras==2.10.0 +joblib==1.3.1 +json-tricks==3.17.1 +keras==2.13.1 keras-layer-normalization==0.16.0 -Keras-Preprocessing==1.1.2 kiwisolver==1.4.4 -libclang==14.0.6 -Markdown==3.4.1 -MarkupSafe==2.1.1 -matplotlib==3.6.0 -matplotlib-inline==0.1.6 -memory-profiler==0.60.0 -mistune==2.0.4 +libclang==16.0.6 +Markdown==3.4.3 +MarkupSafe==2.1.3 +matplotlib==3.7.2 multiprocess==0.70.14 -nbclassic==0.4.8 -nbclient==0.7.0 -nbconvert==7.2.3 -nbformat==5.7.0 -nest-asyncio==1.5.6 -networkx==2.8.7 -nni==2.9 -notebook==6.5.2 -notebook-shim==0.2.2 -numcodecs==0.10.2 -numpy==1.23.4 +nni==2.10.1 +numcodecs==0.11.0 +numpy==1.24.4 oauthlib==3.2.2 opt-einsum==3.3.0 -packaging==21.3 -pandas==1.5.1 -pandocfilters==1.5.0 -parso==0.8.3 -pexpect==4.8.0 -pickleshare==0.7.5 -Pillow==9.2.0 -pkgutil-resolve-name==1.3.10 -pluggy==1.0.0 -prettytable==3.4.1 -prometheus-client==0.15.0 -prompt-toolkit==3.0.32 -protobuf==3.19.6 -psutil==5.9.3 -ptyprocess==0.7.0 -pure-eval==0.2.2 -py==1.11.0 -pyasn1==0.4.8 -pyasn1-modules==0.2.8 -pycparser==2.21 -Pygments==2.13.0 -pymongo==4.3.2 +packaging==23.1 +pandas==2.0.3 +Pillow==10.0.0 +pluggy==1.2.0 +prettytable==3.8.0 +protobuf==4.23.4 +psutil==5.9.5 +pyasn1==0.5.0 +pyasn1-modules==0.3.0 pyparsing==3.0.9 -pyrsistent==0.19.2 -pysam==0.19.1 -pytest==7.1.3 +pysam==0.21.0 +pytest==7.4.0 python-dateutil==2.8.2 PythonWebHDFS==0.2.3 -pytz==2022.5 +pytz==2023.3 PyYAML==6.0 -pyzmq==24.0.1 -qtconsole==5.4.0 -QtPy==2.2.1 -requests==2.28.1 +requests==2.31.0 requests-oauthlib==1.3.1 -responses==0.22.0 +responses==0.23.1 rsa==4.9 schema==0.7.5 -scikit-learn==1.1.2 -scipy==1.9.3 -seaborn==0.12.1 -Send2Trash==1.8.0 -simplejson==3.17.6 +scikit-learn==1.3.0 +scipy==1.10.1 +seaborn==0.12.2 +simplejson==3.19.1 six==1.16.0 -sniffio==1.3.0 sortedcontainers==2.4.0 -soupsieve==2.3.2.post1 SQLAlchemy==1.3.22 -stack-data==0.6.0 -tensorboard==2.10.1 -tensorboard-data-server==0.6.1 -tensorboard-plugin-wit==1.8.1 -tensorflow==2.10.0 -tensorflow-addons==0.18.0 -tensorflow-estimator==2.10.0 -tensorflow-io-gcs-filesystem==0.27.0 -termcolor==2.0.1 -terminado==0.17.0 +tensorboard==2.13.0 +tensorboard-data-server==0.7.1 +tensorflow==2.13.0 +tensorflow-addons==0.21.0 +tensorflow-estimator==2.13.0 +tensorflow-io-gcs-filesystem==0.32.0 +termcolor==2.3.0 terminaltables==3.1.10 -threadpoolctl==3.1.0 -tinycss2==1.2.1 -toml==0.10.2 +threadpoolctl==3.2.0 tomli==2.0.1 -tornado==6.2 -tqdm==4.64.1 -traitlets==5.5.0 +tqdm==4.65.0 typeguard==2.13.3 -types-toml==0.10.8 -typing-extensions==4.4.0 -urllib3==1.26.12 -wcwidth==0.2.5 -webencodings==0.5.1 -websocket-client==1.4.2 -websockets==10.3 -Werkzeug==2.2.2 -widgetsnbextension==4.0.3 -wrapt==1.14.1 -zipp==3.10.0 +types-PyYAML==6.0.12.10 +typing-extensions==4.5.0 +tzdata==2023.3 +urllib3==2.0.3 +wcwidth==0.2.6 +websockets==11.0.3 +Werkzeug==2.3.6 +wrapt==1.15.0 +zipp==3.16.2 diff --git a/setup.py b/setup.py index 3169a22..d40a9cf 100644 --- a/setup.py +++ b/setup.py @@ -2,7 +2,7 @@ setup( name='helixer', - version='0.3.1', + version='0.3.2', description='Deep Learning fun on gene structure data', packages=['helixer', 'helixer.core', 'helixer.prediction', 'helixer.evaluation', 'helixer.tests', 'helixer.export'], package_data={'helixer': ['testdata/*.fa', 'testdata/*.gff']},