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Merge branch 'u/soehms/knotinfo' of trac.sagemath.org:sage into knotinfo_30352
2 parents 8453ffb + 5844cae commit 1721a44

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‎build/pkgs/database_knotinfo/SPKG.rst

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database_knotinfo: Tables of Knots and Links from the KnotInfo Databases
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========================================================================
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Description
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-----------
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Database for named knots and links provided at
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https://knotinfo.math.indiana.edu/
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and
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https://linkinfo.sitehost.iu.edu'
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Dependencies
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------------
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- Sage library
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Upstream Contact
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----------------
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- Charles Livingston <[email protected]>
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- Allison H. Moore <[email protected]>
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Update Instructions
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-------------------
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- See the Python script ``create_knotinfo_tarball.py`` in the current directory.
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Changelog
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---------
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- 20200713 (Sebastian Oehms, 13 Juli 2020, :trac:`30352`, initial version)
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The tarball has been created from the both download files at the
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given date:
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``knotinfo_data_complete.xls``
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``linkinfo_data_complete.xlsx``
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exporting them to CSV via LibreOffice.
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The second file has been changed manually deleting one character:
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a trailing "}" occuring in the homfly_polynomial column of the last
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link ``L11n459{1,1,1}``.
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- 20210201 (Sebastian Oehms, 1 February 2021, :trac:`30352`, upgrade)
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Three new columns have been added to ``knotinfo_data_complete.xls``
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(``montesinos_notation``, ``boundary_slopes`` and ``pretzel_notation``).
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``linkinfo_data_complete.xlsx`` remains unchanged.
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The tarball has been created using ``create_knotinfo_tarball.py``.
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The fix concerning the misplaced character for ``L11n459{1,1,1}``
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is performed in :meth:`KnotInfoBase.homfly_polynomial`, now.

‎build/pkgs/database_knotinfo/checksums.ini

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tarball=knotinfo-20210201.tar.bz2
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sha1=a8a69dacd1f61f19a921d8e5b90d6cfdea85d859
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md5=5f53bd7e3a672648d41460c4d22d52b3
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cksum=1608275975
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upstream_url=https://github.com/soehms/sagemath_knotinfo/blob/main/knotinfo-20210201.tar.bz2?raw=true

‎build/pkgs/database_knotinfo/create_knotinfo_tarball.py

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#!/usr/bin/python
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r"""
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Python script to create a tarball for the sage-package ``database_knotinfo``
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in the given path. This utility should be used in case of a switch to a
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new version of the data files (that is if the original files on the
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KnotInfo LinkInfo web-page have changed). In that case an invocation of
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``sage -package update database_knotinfo <new version>`` and
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``sage -package fix-checksum database_knotinfo`` will be necessary.
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..NOTE::
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This function demands the Python package ``pandas``, ``xlrd`` and
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``xlsx2csv`` to be installed. If not you have to run::
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pip install pandas
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pip install xlrd
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pip install xlsx2csv
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before using this function.
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INPUT:
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- ``version`` -- string, name of the new version to be created
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(by default date of the day of creation)
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- ``path`` -- string of the path where the tarball should be stored
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(by default ``pwd``)
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EXAMPLES::
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~/sage $ build/pkgs/database_knotinfo/create_knotinfo_tarball.py 20210201 upstream
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src/
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src/knotinfo_data_complete.csv
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src/linkinfo_data_complete.csv
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"""
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import sys, os
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from xlsx2csv import Xlsx2csv
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from pandas import read_excel
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##############################################################################
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# Copyright (C) 2021 Sebastian Oehms <[email protected]>
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#
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# This program is free software: you can redistribute it and/or modify
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# it under the terms of the GNU General Public License as published by
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# the Free Software Foundation, either version 2 of the License, or
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# (at your option) any later version.
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# http://www.gnu.org/licenses/
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##############################################################################
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cmdline_args = sys.argv[1:]
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version = None
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path = None
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if len(cmdline_args) > 1:
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path = cmdline_args[1]
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if len(cmdline_args) > 0:
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version = cmdline_args[0]
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if not version:
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from datetime import datetime
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version = str(datetime.today().date()).replace('-','')
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if not path:
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path = os.environ['PWD']
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path_temp = os.path.join(path, 'special_knotinfo_spkg_temp_dir')
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path_src = os.path.join(path_temp, 'src')
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os.makedirs(path_temp)
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os.makedirs(path_src)
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def convert(path_src, url, filen, reader):
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if reader == Xlsx2csv:
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excel = filen + '.xlsx'
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else:
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excel = filen + '.xls'
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csv = filen + '.csv'
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inp = os.path.join(url, excel)
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out = os.path.join(path_src, csv)
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if reader == Xlsx2csv:
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from six.moves.urllib.request import urlopen
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f = urlopen(inp)
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url_data = f.read()
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temp_file = os.path.join(path_temp, 'temp.xlsx')
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f = open(temp_file, 'wt')
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f.write(url_data)
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f.close()
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data = reader(temp_file, delimiter='|', skip_empty_lines=True)
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data.convert(out)
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else:
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data = reader(inp)
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data.to_csv(out, sep='|', index=False)
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# first KnotInfo (using pandas and xlrd)
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convert(path_src, 'https://knotinfo.math.indiana.edu/', 'knotinfo_data_complete', read_excel)
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# now LinkInfo (using xlsx2csv)
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convert(path_src, 'https://linkinfo.sitehost.iu.edu/', 'linkinfo_data_complete', Xlsx2csv)
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tar_file = 'knotinfo-%s.tar.bz2' %version
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path_tar = os.path.join(path_temp, tar_file)
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os.system('cd %s; tar -cvjSf %s src' %(path_temp, tar_file))
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os.system('mv %s %s; rm -rf %s' %(path_tar, path, path_temp))

‎build/pkgs/database_knotinfo/dependencies

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| $(SAGERUNTIME)
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----------
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All lines of this file are ignored except the first.
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It is copied by SAGE_ROOT/build/make/install into SAGE_ROOT/build/make/Makefile.

‎build/pkgs/database_knotinfo/package-version.txt

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20210201

‎build/pkgs/database_knotinfo/spkg-check.in

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cd $SAGE_ROOT/src/sage/
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echo "Testing databases/knotinfo_db.py"
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sage -t --long --optional="sage,database_knotinfo" databases/knotinfo_db.py || sdh_die "Error testing KnotInfo databases"
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echo "Testing knots/knotinfo.py"
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sage -t --optional="sage,database_knotinfo" knots/knotinfo.py || sdh_die "Error testing KnotInfo funcionality"
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echo "Testing knots/link.py"
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sage -t --optional="sage,database_knotinfo" knots/link.py || sdh_die "Error testing KnotInfo funcionality"

‎build/pkgs/database_knotinfo/spkg-install.in

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INSTALL="yes"
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TARGET="${SAGE_SHARE}/knotinfo"
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VERSION=`cat package-version.txt`
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if [ -d $TARGET ]
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then
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diff package-version.txt $TARGET > /dev/null 2>&1
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if [ $? -eq 0 ]
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then
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INSTALL="no"
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echo "Version $VERSION of knotinfo already installed"
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else
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OLD_VERSION=`cat $TARGET/package-version.txt`
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echo "Removing former version $OLD_VERSION of knotinfo"
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rm -rf $TARGET
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fi
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fi
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if [ "$INSTALL" = "yes" ]
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then
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exec sage-python23 spkg-install.py
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fi

‎build/pkgs/database_knotinfo/spkg-install.py

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import os
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from sage.env import SAGE_SHARE
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from sage.misc.misc import sage_makedirs
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install_root = os.path.join(SAGE_SHARE, 'knotinfo')
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if __name__ == '__main__':
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sage_makedirs(install_root)
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print("Creating the KnotInfo database.")
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from sage.databases.knotinfo_db import KnotInfoDataBase
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KnotInfoDataBase(install=True)
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os.system('cp package-version.txt %s' %install_root)

‎build/pkgs/database_knotinfo/type

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optional

‎src/doc/en/reference/databases/index.rst

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sage/databases/cunningham_tables
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sage/databases/db_class_polynomials
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sage/databases/db_modular_polynomials
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sage/databases/knotinfo_db
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.. include:: ../footer.txt

‎src/doc/en/reference/knots/index.rst

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sage/knots/knot
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sage/knots/link
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sage/knots/knotinfo
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.. include:: ../footer.txt

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