зеркало из https://github.com/Azure/covid19model.git
fix organisation
This commit is contained in:
harrisonzhu508
Коммит
bab7656208
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@ -2,7 +2,7 @@
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"cells": [
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{
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"cell_type": "code",
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"execution_count": 4,
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"execution_count": 1,
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"metadata": {},
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"outputs": [],
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"source": [
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@ -12,18 +12,9 @@
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},
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{
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"cell_type": "code",
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"execution_count": 5,
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"execution_count": 2,
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"metadata": {},
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"outputs": [
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{
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"name": "stdout",
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"output_type": "stream",
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"text": [
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"The autoreload extension is already loaded. To reload it, use:\n",
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" %reload_ext autoreload\n"
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]
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}
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],
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"outputs": [],
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"source": [
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"%load_ext autoreload\n",
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"%autoreload 2"
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@ -31,29 +22,29 @@
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},
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{
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"cell_type": "code",
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"execution_count": 6,
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"execution_count": 3,
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"metadata": {},
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"outputs": [],
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"source": [
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"from Python.dataset import HierarchicalDataset\n",
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"from src.dataset import HierarchicalDataset\n",
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"import pandas as pd"
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]
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},
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{
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"cell_type": "code",
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"execution_count": 40,
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"execution_count": 4,
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"metadata": {},
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"outputs": [
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{
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"name": "stderr",
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"output_type": "stream",
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"text": [
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"../Python/dataset.py:73: SettingWithCopyWarning: \n",
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"../src/dataset.py:73: SettingWithCopyWarning: \n",
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"A value is trying to be set on a copy of a slice from a DataFrame\n",
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"\n",
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"See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy\n",
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" ifr[\"country\"][ifr[\"country\"] == \"United Kingdom\"] = \"United_Kingdom\"\n",
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"../Python/dataset.py:90: SettingWithCopyWarning: \n",
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"../src/dataset.py:90: SettingWithCopyWarning: \n",
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"A value is trying to be set on a copy of a slice from a DataFrame\n",
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"\n",
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"See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy\n",
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@ -62,11 +53,11 @@
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}
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],
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"source": [
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"dataset = HierarchicalDataset(config_dir=\"../config/catalog.yml\", \n",
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" cases_dir=\"../data/COVID-19-up-to-date.csv\", \n",
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" ifr_dir=\"../data/weighted_fatality.csv\", \n",
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" serial_interval_dir=\"../data/serial_interval.csv\", \n",
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" interventions_dir=\"../data/interventions.csv\", num_covariates=7)"
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"dataset = HierarchicalDataset(config_dir=\"../../config/catalog.yml\", \n",
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" cases_dir=\"../../data/COVID-19-up-to-date.csv\", \n",
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" ifr_dir=\"../../data/weighted_fatality.csv\", \n",
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" serial_interval_dir=\"../../data/serial_interval.csv\", \n",
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" interventions_dir=\"../../data/interventions.csv\", num_covariates=7)"
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]
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},
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{
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@ -0,0 +1,5 @@
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PyYAML
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pandas numpy
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scipy
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statsmodels
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datetime
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@ -1,7 +1,7 @@
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import yaml
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import pandas as pd
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import numpy as np
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from Python.util import poly, dt_to_dec
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from src.util import poly, dt_to_dec
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from scipy.stats import gamma as gamma_scipy
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from numpy.random import gamma as gamma_np
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from statsmodels.distributions.empirical_distribution import ECDF
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@ -37,11 +37,11 @@ class HierarchicalDataset:
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def __init__(
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self,
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config_dir="data/catalog.yml",
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cases_dir="data/COVID-19-up-to-date.csv",
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ifr_dir="data/weighted_fatality.csv",
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serial_interval_dir="data/serial_interval.csv",
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interventions_dir="data/interventions.csv",
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config_dir="../data/catalog.yml",
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cases_dir="../data/COVID-19-up-to-date.csv",
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ifr_dir="../data/weighted_fatality.csv",
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serial_interval_dir="../data/serial_interval.csv",
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interventions_dir="../data/interventions.csv",
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num_countries=11,
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num_covariates=6,
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N2=75,
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210
requirements.txt
210
requirements.txt
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@ -1,210 +0,0 @@
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alabaster==0.7.12
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anaconda-client==1.7.2
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anaconda-navigator==1.9.7
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anaconda-project==0.8.3
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asn1crypto==0.24.0
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astroid==2.2.5
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astropy==3.2.1
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atomicwrites==1.3.0
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attrs==19.1.0
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Babel==2.7.0
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backcall==0.1.0
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backports.functools-lru-cache==1.5
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backports.os==0.1.1
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backports.shutil-get-terminal-size==1.0.0
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backports.tempfile==1.0
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backports.weakref==1.0.post1
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beautifulsoup4==4.7.1
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bitarray==0.9.3
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bkcharts==0.2
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bleach==3.1.4
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bokeh==1.2.0
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boto==2.49.0
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Bottleneck==1.2.1
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certifi==2019.6.16
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cffi==1.12.3
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chardet==3.0.4
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Click==7.0
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cloudpickle==1.2.1
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clyent==1.2.2
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colorama==0.4.1
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conda==4.7.10
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conda-build==3.18.8
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conda-package-handling==1.3.11
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conda-verify==3.4.2
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contextlib2==0.5.5
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cryptography==2.7
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cycler==0.10.0
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Cython==0.29.12
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cytoolz==0.10.0
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dask==2.1.0
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decorator==4.4.0
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defusedxml==0.6.0
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distributed==2.1.0
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docutils==0.14
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entrypoints==0.3
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et-xmlfile==1.0.1
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fastcache==1.1.0
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filelock==3.0.12
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Flask==1.1.1
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future==0.17.1
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gevent==1.4.0
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glob2==0.7
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gmpy2==2.0.8
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greenlet==0.4.15
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h5py==2.9.0
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heapdict==1.0.0
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html5lib==1.0.1
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idna==2.8
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imageio==2.5.0
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imagesize==1.1.0
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importlib-metadata==0.17
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ipykernel==5.1.1
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ipython==7.6.1
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ipython-genutils==0.2.0
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ipywidgets==7.5.0
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isort==4.3.21
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itsdangerous==1.1.0
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jdcal==1.4.1
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jedi==0.13.3
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jeepney==0.4
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Jinja2==2.10.1
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joblib==0.13.2
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json5==0.8.4
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jsonschema==3.0.1
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jupyter==1.0.0
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jupyter-client==5.3.1
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jupyter-console==6.0.0
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jupyter-core==4.5.0
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jupyterlab==1.0.2
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jupyterlab-server==1.0.0
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keyring==18.0.0
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kiwisolver==1.1.0
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lazy-object-proxy==1.4.1
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libarchive-c==2.8
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lief==0.9.0
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llvmlite==0.29.0
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locket==0.2.0
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lxml==4.3.4
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MarkupSafe==1.1.1
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matplotlib==3.1.0
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mccabe==0.6.1
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mistune==0.8.4
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mkl-fft==1.0.12
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mkl-random==1.0.2
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mkl-service==2.0.2
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mock==3.0.5
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more-itertools==7.0.0
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mpmath==1.1.0
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msgpack==0.6.1
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multipledispatch==0.6.0
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navigator-updater==0.2.1
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nbconvert==5.5.0
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nbformat==4.4.0
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networkx==2.3
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nltk==3.4.5
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nose==1.3.7
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notebook==6.0.0
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numba==0.44.1
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numexpr==2.6.9
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numpy==1.16.4
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numpydoc==0.9.1
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olefile==0.46
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openpyxl==2.6.2
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packaging==19.0
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pandas==0.24.2
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pandocfilters==1.4.2
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parso==0.5.0
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partd==1.0.0
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path.py==12.0.1
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pathlib2==2.3.4
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patsy==0.5.1
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pep8==1.7.1
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pexpect==4.7.0
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pickleshare==0.7.5
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Pillow==6.1.0
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pkginfo==1.5.0.1
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pluggy==0.12.0
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ply==3.11
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prometheus-client==0.7.1
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prompt-toolkit==2.0.9
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psutil==5.6.6
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ptyprocess==0.6.0
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py==1.8.0
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pycodestyle==2.5.0
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pycosat==0.6.3
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pycparser==2.19
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pycrypto==2.6.1
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pycurl==7.43.0.3
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pyflakes==2.1.1
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Pygments==2.4.2
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pylint==2.3.1
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pyodbc==4.0.26
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pyOpenSSL==19.0.0
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pyparsing==2.4.0
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pyrsistent==0.14.11
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||||
PySocks==1.7.0
|
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pytest==5.0.1
|
||||
pytest-arraydiff==0.3
|
||||
pytest-astropy==0.5.0
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||||
pytest-doctestplus==0.3.0
|
||||
pytest-openfiles==0.3.2
|
||||
pytest-remotedata==0.3.1
|
||||
python-dateutil==2.8.0
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||||
pytz==2019.1
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||||
PyWavelets==1.0.3
|
||||
PyYAML==5.1.1
|
||||
pyzmq==18.0.0
|
||||
QtAwesome==0.5.7
|
||||
qtconsole==4.5.1
|
||||
QtPy==1.8.0
|
||||
requests==2.22.0
|
||||
rope==0.14.0
|
||||
ruamel-yaml==0.15.46
|
||||
scikit-image==0.15.0
|
||||
scikit-learn==0.21.2
|
||||
scipy==1.3.0
|
||||
seaborn==0.9.0
|
||||
SecretStorage==3.1.1
|
||||
Send2Trash==1.5.0
|
||||
simplegeneric==0.8.1
|
||||
singledispatch==3.4.0.3
|
||||
six==1.12.0
|
||||
snowballstemmer==1.9.0
|
||||
sortedcollections==1.1.2
|
||||
sortedcontainers==2.1.0
|
||||
soupsieve==1.8
|
||||
Sphinx==2.1.2
|
||||
sphinxcontrib-applehelp==1.0.1
|
||||
sphinxcontrib-devhelp==1.0.1
|
||||
sphinxcontrib-htmlhelp==1.0.2
|
||||
sphinxcontrib-jsmath==1.0.1
|
||||
sphinxcontrib-qthelp==1.0.2
|
||||
sphinxcontrib-serializinghtml==1.1.3
|
||||
sphinxcontrib-websupport==1.1.2
|
||||
spyder==3.3.6
|
||||
spyder-kernels==0.5.1
|
||||
SQLAlchemy==1.3.5
|
||||
statsmodels==0.10.0
|
||||
sympy==1.4
|
||||
tables==3.5.2
|
||||
tblib==1.4.0
|
||||
terminado==0.8.2
|
||||
testpath==0.4.2
|
||||
toolz==0.10.0
|
||||
tornado==6.0.3
|
||||
tqdm==4.32.1
|
||||
traitlets==4.3.2
|
||||
unicodecsv==0.14.1
|
||||
urllib3==1.24.2
|
||||
wcwidth==0.1.7
|
||||
webencodings==0.5.1
|
||||
Werkzeug==0.15.4
|
||||
widgetsnbextension==3.5.0
|
||||
wrapt==1.11.2
|
||||
wurlitzer==1.0.2
|
||||
xlrd==1.2.0
|
||||
XlsxWriter==1.1.8
|
||||
xlwt==1.3.0
|
||||
zict==1.0.0
|
||||
zipp==0.5.1
|
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