From 8c8654c4560bef299f111b9a070c864fe93905bc Mon Sep 17 00:00:00 2001
From: Maria <maria.marchwicka@amu.edu.pl>
Date: Thu, 15 Jul 2021 13:48:37 +0200
Subject: [PATCH] fix problems with import_sage

---
 {cagosig => gaknot}/__init__.py               |   8 +-
 gaknot/__pycache__/__init__.cpython-38.pyc    | Bin 0 -> 1602 bytes
 .../cable_signature.cpython-38.pyc            | Bin 0 -> 22691 bytes
 gaknot/__pycache__/main.cpython-38.pyc        | Bin 0 -> 4240 bytes
 gaknot/__pycache__/signature.cpython-38.pyc   | Bin 0 -> 13178 bytes
 gaknot/__pycache__/utility.cpython-38.pyc     | Bin 0 -> 1571 bytes
 {cagosig => gaknot}/cable_signature.sage      |   5 +-
 gaknot/clean.sh                               |   5 +
 gaknot/main.py                                | 278 +++++++++++++
 {cagosig => gaknot}/main.sage                 |  18 +-
 gaknot/signature.py                           | 385 ++++++++++++++++++
 {cagosig => gaknot}/signature.sage            |  12 +-
 {cagosig => gaknot}/utility.py                |   0
 13 files changed, 696 insertions(+), 15 deletions(-)
 rename {cagosig => gaknot}/__init__.py (92%)
 create mode 100644 gaknot/__pycache__/__init__.cpython-38.pyc
 create mode 100644 gaknot/__pycache__/cable_signature.cpython-38.pyc
 create mode 100644 gaknot/__pycache__/main.cpython-38.pyc
 create mode 100644 gaknot/__pycache__/signature.cpython-38.pyc
 create mode 100644 gaknot/__pycache__/utility.cpython-38.pyc
 rename {cagosig => gaknot}/cable_signature.sage (99%)
 create mode 100755 gaknot/clean.sh
 create mode 100644 gaknot/main.py
 rename {cagosig => gaknot}/main.sage (96%)
 create mode 100644 gaknot/signature.py
 rename {cagosig => gaknot}/signature.sage (99%)
 rename {cagosig => gaknot}/utility.py (100%)

diff --git a/cagosig/__init__.py b/gaknot/__init__.py
similarity index 92%
rename from cagosig/__init__.py
rename to gaknot/__init__.py
index 91283f9..bf34a8a 100644
--- a/cagosig/__init__.py
+++ b/gaknot/__init__.py
@@ -45,9 +45,9 @@ So we can work in the following steps:
 from .utility import import_sage
 import os
 
-
-package = __name__.split('.')[0]
-path = os.path.dirname(__file__)
-import_sage('signature', package=package, path=path)
+#
+# package = __name__.split('.')[0]
+# path = os.path.dirname(__file__)
+# import_sage('signature', package=package, path=path)
 # import_sage('cable_signature', package=package, path=path)
 # import_sage('main', package=package, path=path)
diff --git a/gaknot/__pycache__/__init__.cpython-38.pyc b/gaknot/__pycache__/__init__.cpython-38.pyc
new file mode 100644
index 0000000000000000000000000000000000000000..14ef154247053baa3057a238b73da2bef7ff6e7b
GIT binary patch
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diff --git a/gaknot/__pycache__/cable_signature.cpython-38.pyc b/gaknot/__pycache__/cable_signature.cpython-38.pyc
new file mode 100644
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diff --git a/cagosig/cable_signature.sage b/gaknot/cable_signature.sage
similarity index 99%
rename from cagosig/cable_signature.sage
rename to gaknot/cable_signature.sage
index 9ff496e..efc0f04 100644
--- a/cagosig/cable_signature.sage
+++ b/gaknot/cable_signature.sage
@@ -8,9 +8,12 @@ from typing import Iterable
 from collections import Counter
 from sage.arith.functions import LCM_list
 import importlib
-from .utility import import_sage, mod_one
+
+
+from .utility import import_sage
 from . import signature as sig
 
+
 SIGMA = 0
 SIGNATURE = 1
 
diff --git a/gaknot/clean.sh b/gaknot/clean.sh
new file mode 100755
index 0000000..aeffd56
--- /dev/null
+++ b/gaknot/clean.sh
@@ -0,0 +1,5 @@
+#!/bin/bash
+
+rm cable_signature.py
+rm signature.py
+rm main.py
diff --git a/gaknot/main.py b/gaknot/main.py
new file mode 100644
index 0000000..17854af
--- /dev/null
+++ b/gaknot/main.py
@@ -0,0 +1,278 @@
+
+
+# This file was *autogenerated* from the file /home/maria/signature_function/gaknot/main.sage
+from sage.all_cmdline import *   # import sage library
+
+_sage_const_0 = Integer(0); _sage_const_1 = Integer(1); _sage_const_2 = Integer(2); _sage_const_3 = Integer(3); _sage_const_5 = Integer(5); _sage_const_7 = Integer(7); _sage_const_11 = Integer(11); _sage_const_13 = Integer(13); _sage_const_10 = Integer(10)#!/usr/bin/env sage -python
+
+# TBD: read about Factory Method, variable in docstring, sage documentation,
+# print calc. to output file
+# decide about printing option
+# make __main__?
+
+import os
+import sys
+
+import itertools as it
+import re
+import numpy as np
+import importlib
+from .utility import import_sage
+# from . import signature as sig
+# from . import cable_signature as cs
+
+package = __name__.split('.')[_sage_const_0 ]
+path = os.path.dirname(__file__)
+print(path)
+
+sg = import_sage('signature', package='gaknot', path=path)
+cs = import_sage('cable_signature', package='gaknot', path=path)
+
+
+
+
+# class Config:
+#     def __init__(self):
+#         self.f_results = os.path.join(os.getcwd(), "results.out")
+
+class Schemas:
+
+
+    # knot_formula = "[[k[0],  k[1],  k[2]],\
+    #                 [        k[3],  k[4]],\
+    #                 [-k[0], -k[3], -k[4]],\
+    #                 [       -k[1], -k[2]]]"
+    #
+    # knot_formula = "[[k[0],   k[1],  k[2]],\
+    #                  [               k[3]],\
+    #                  [-k[0], -k[1], -k[3]],\
+    #                  [              -k[2]]]"
+
+
+    short_3_layers_a = "[[         k[5],  k[3]], " + \
+                        "[        -k[1], -k[3]], " + \
+                        "[                k[3]], " + \
+                        "[ -k[4], -k[6], -k[3]]]"
+
+    short_3_layers_b = "[[k[4],   k[1],  k[7]], " + \
+                        "[               -k[7]], " + \
+                        "[         k[6],  k[7]], " + \
+                        "[         -k[5], -k[7]]]"
+
+    schema_short1 = "[ [k[5],  k[3]], " + \
+                    "[ -k[1], -k[3]], " + \
+                    "[         k[3]], " + \
+                    "[ -k[6], -k[3]]]"
+
+    schema_short2 = "[[ k[1],  k[7]], " + \
+                    "[        -k[7]], " + \
+                    "[  k[6],  k[7]], " + \
+                    "[ -k[5], -k[7]]]"
+
+    schema_short = "[[ k[5],  k[3]], " + \
+                   "[ -k[1], -k[3]], " + \
+                   "[         k[3]], " + \
+                   "[ -k[6], -k[3]], " + \
+                   "[  k[1],  k[7]], " + \
+                   "[        -k[7]], " + \
+                   "[  k[6],  k[7]], " + \
+                   "[ -k[5], -k[7]]]"
+
+    # two_summands_schema = "[ [k[0], k[1], k[4]], [-k[1], -k[3]],\
+    #                        [k[2], k[3]], [-k[0], -k[2], -k[4]] ]"
+    # two_small_summands_schema = "[[k[3]], [-k[3]],\
+    #                             [k[3]], [-k[3]] ]"
+    #
+    # four_summands_schema = "[[k[3],  k[2],  k[0]],\
+    #                         [       -k[2], -k[0]],\
+    #                         [        k[1],  k[0]],\
+    #                         [-k[3], -k[1], -k[0]]]"
+    #
+    four_summands_schema = "[[ k[0],  k[1],  k[3]]," + \
+                           "[        -k[1], -k[3]]," + \
+                           "[         k[2],  k[3]]," + \
+                           "[ -k[0], -k[2], -k[3]]]"
+
+    # formula_1 = "[[ k[0],  k[5],  k[3]], " + \
+    #             "[        -k[1], -k[3]], " + \
+    #             "[         k[2],  k[3]], " + \
+    #             "[ -k[0], -k[2], -k[3]]]"
+    #
+    # formula_2 = "[[ k[4],  k[1],  k[7]], " + \
+    #             "[        -k[5], -k[7]], " + \
+    #             "[         k[6],  k[7]], " + \
+    #             "[ -k[4], -k[6], -k[7]]]"
+    #
+    # formula_1 = "[[ k[0], k[5],  k[3]], " + \
+    #             "[       -k[5], -k[3]], " + \
+    #             "[        k[2],  k[3]], " + \
+    #             "[-k[4], -k[2], -k[3]]]"
+    #
+    # formula_2 = "[[ k[4], k[1],  k[7]], " + \
+    #             "[       -k[1], -k[7]], " + \
+    #             "[        k[6],  k[7]], " + \
+    #             "[-k[0], -k[6], -k[7]]]"
+
+
+def main(arg=None):
+    try:
+        limit = int(arg[_sage_const_1 ])
+    except (IndexError, TypeError):
+        limit = None
+    conf = Config()
+    cable_loop_with_details(conf)
+
+
+def print_sigma_for_cable(verbose=True, Schemas=None):
+
+    schema_short1 = Schemas.schema_short1
+    schema_short2 = Schemas.schema_short2
+    schema_short = Schemas.schema_short
+    schema_four = Schemas.four_summands_schema
+
+    cable_template = cs.CableTemplate(knot_formula=schema_short)
+    cable_template.fill_q_vector()
+    q_v = cable_template.q_vector
+    print(q_v)
+    print(cable_template.cable.knot_description)
+    cable1 = cs.CableTemplate(knot_formula=schema_short1,
+                              verbose=verbose,
+                              q_vector=q_v
+                             ).cable
+    cable2 = cs.CableTemplate(knot_formula=schema_short2,
+                              verbose=verbose,
+                              q_vector=q_v
+                             ).cable
+    cable = cs.CableTemplate(knot_formula=schema_short1,
+                              verbose=verbose,
+                              q_vector=q_v
+                             ).cable
+
+    cable.plot_sigma_for_summands()
+    # cable1.plot_sigma_for_summands()
+    # cable2.plot_sigma_for_summands()
+
+
+def cable_loop_with_details(verbose=True):
+    # verbose = False
+    schema_short1 = Schemas.schema_short1
+    schema_short2 = Schemas.schema_short2
+    schema_short = Schemas.schema_short
+    cable_template = cs.CableTemplate(knot_formula=schema_short)
+
+    list_of_q_vectors = []
+    # for el in [2, 3, 5, 7, 11, 13]:
+    for el in [_sage_const_2 ]:
+        cable_template.fill_q_vector(lowest_number=el)
+        q_v = cable_template.q_vector
+        print(q_v)
+        print(cable_template.cable.knot_description)
+        cable1 = cs.CableTemplate(knot_formula=schema_short1,
+                                  verbose=verbose,
+                                  q_vector=q_v
+                                 ).cable
+        cable2 = cs.CableTemplate(knot_formula=schema_short2,
+                                  verbose=verbose,
+                                  q_vector=q_v
+                                 ).cable
+    #     print("\n")
+    #     print(cable1.knot_description)
+        is_1 = cable1.is_function_big_for_all_metabolizers(invariant=cs.SIGMA)
+        is_2 = cable2.is_function_big_for_all_metabolizers(invariant=cs.SIGMA)
+        if is_1 and is_2:
+            print("sigma is big for all metabolizers")
+        else:
+            print("sigma is not big for all metabolizers")
+        print("\n" * _sage_const_3 )
+
+
+def few_cable_without_calc(verbose=False):
+
+    schema_short1 = Schemas.schema_short1
+    schema_short2 = Schemas.schema_short2
+    schema_short = Schemas.schema_short
+
+    cable_template = cs.CableTemplate(knot_formula=schema_short)
+
+    list_of_q_vectors = []
+    for el in [_sage_const_2 , _sage_const_3 , _sage_const_5 , _sage_const_7 , _sage_const_11 , _sage_const_13 ]:
+        cable_template.fill_q_vector(lowest_number=el)
+        q_v = cable_template.q_vector
+        print(q_v)
+        print(cable_template.cable.knot_description)
+        cable1 = cs.CableTemplate(knot_formula=schema_short1,
+                              verbose=verbose,
+                              q_vector=q_v
+                             ).cable
+        cable2 = cs.CableTemplate(knot_formula=schema_short2,
+                                  verbose=verbose,
+                                  q_vector=q_v
+                                 ).cable
+        is_1 = cable1.is_function_big_for_all_metabolizers(invariant=sigma)
+        is_2 = cable2.is_function_big_for_all_metabolizers(invariant=sigma)
+        if is_1 and is_2:
+            print("sigma is big for all metabolizers")
+        else:
+            print("sigma is not big for all metabolizers")
+        print("\n" * _sage_const_3 )
+
+
+def smallest_cable(verbose=True):
+
+    schema_short1 = Schemas.schema_short1
+    schema_short2 = Schemas.schema_short2
+    schema_short = Schemas.schema_short
+
+
+    cable_template = cs.CableTemplate(knot_formula=schema_short)
+    q_v = cable_template.q_vector
+    print(q_v)
+    cable1 = cs.CableTemplate(knot_formula=schema_short1,
+                              verbose=verbose,
+                              q_vector=q_v).cable
+    cable2 = cs.CableTemplate(knot_formula=schema_short2,
+                              verbose=verbose,
+                              q_vector=q_v).cable
+    cable1.is_function_big_for_all_metabolizers(invariant=sigma)
+    cable2.is_function_big_for_all_metabolizers(invariant=sigma)
+
+
+def plot_many_untwisted_signature_functions(range_tuple=(_sage_const_1 , _sage_const_10 )):
+    P = Primes()
+    for i in range(*range_tuple):
+        q = P.unrank(i)
+        a = cs.CableSummand.get_untwisted_signature_function(q=q)
+        a.plot()
+
+
+if __name__ == '__main__':
+    if '__file__' in globals():
+        # skiped in interactive mode as __file__ is not defined
+        main(sys.argv)
+    else:
+        pass
+        # main()
+
+
+# formula_long = "[[k[0], k[5], k[3]], " + \
+#                   "[-k[5], -k[3]], " + \
+#                    "[k[2], k[3]], " + \
+#             "[-k[4], -k[2], -k[3]]" + \
+#             "[k[4], k[1], k[7]], " + \
+#                   "[-k[1], -k[7]], " + \
+#                    "[k[6], k[7]], " + \
+#             "[-k[0], -k[6], -k[7]]]"
+#
+#
+# formula_1 = "[[k[0], k[5], k[3]], " + \
+#                   "[-k[1], -k[3]], " + \
+#                          "[ k[3]], " + \
+#             "[-k[4], -k[6], -k[3]]]"
+#
+# formula_2 = "[[k[4], k[1], k[7]], " + \
+#                        "[ -k[7]], " + \
+#                    "[k[6], k[7]], " + \
+#             "[-k[0], -k[5], -k[7]]]"
+#
+#
+
diff --git a/cagosig/main.sage b/gaknot/main.sage
similarity index 96%
rename from cagosig/main.sage
rename to gaknot/main.sage
index 377b31b..30ccec6 100644
--- a/cagosig/main.sage
+++ b/gaknot/main.sage
@@ -12,12 +12,20 @@ import itertools as it
 import re
 import numpy as np
 import importlib
-from .utility import import_sage
-from . import signature as sig
-from . import cable_signature as cs
 
-package = __name__.split('.')[0]
-path = os.path.dirname(__file__)
+
+if __name__ == '__main__':
+    from utility import import_sage
+    package = None
+    path = ''
+
+else:
+    from .utility import import_sage
+    package = os.path.join( __name__.split('.')[0])
+    path = '../'
+sg = import_sage('signature', package=package, path=path)
+cs = import_sage('cable_signature', package=package, path=path)
+
 
 
 
diff --git a/gaknot/signature.py b/gaknot/signature.py
new file mode 100644
index 0000000..a6292da
--- /dev/null
+++ b/gaknot/signature.py
@@ -0,0 +1,385 @@
+
+
+# This file was *autogenerated* from the file /home/maria/signature_function/gaknot/signature.sage
+from sage.all_cmdline import *   # import sage library
+
+_sage_const_0 = Integer(0); _sage_const_1 = Integer(1); _sage_const_2 = Integer(2); _sage_const_36 = Integer(36); _sage_const_10 = Integer(10); _sage_const_5 = Integer(5); _sage_const_0p3 = RealNumber('0.3'); _sage_const_0p7 = RealNumber('0.7'); _sage_const_0p05 = RealNumber('0.05'); _sage_const_4 = Integer(4); _sage_const_3 = Integer(3)#!/usr/bin/env sage -python
+
+from collections import Counter
+import matplotlib.pyplot as plt
+import inspect
+from PIL import Image
+from pathlib import Path
+import warnings
+from .utility import mod_one
+
+# 9.11 (9.8)
+# 9.15 (9.9)
+import sys
+import os
+
+
+JUPYTER = 'ipykernel'
+IPy_TERMINAL = 'IPython'
+
+def get_ipython_info():
+    if JUPYTER in sys.modules:
+        return JUPYTER
+    elif IPy_TERMINAL in sys.modules:
+        return IPy_TERMINAL
+    return False
+
+global ipython_info
+ipython_info = get_ipython_info()
+
+
+class SignatureFunction:
+
+    def __init__(self, values=None, counter=None, plot_title=''):
+
+        # counter of signature jumps
+        if counter is None:
+            counter = Counter()
+            values = values or []
+            for k, v in values:
+                counter[k] += v
+
+        counter = Counter({k : v for k, v in counter.items() if v != _sage_const_0 })
+        if any(k >= _sage_const_1  for k in counter.keys()):
+                msg = "Signature function is defined on the interval [0, 1)."
+                raise ValueError(msg)
+
+        counter[_sage_const_0 ] += _sage_const_0 
+        counter[_sage_const_1 ] += _sage_const_0 
+        self.jumps_counter = counter
+        self.plot_title = plot_title
+
+    def __rshift__(self, shift):
+        # A shift of the signature functions corresponds to the rotation.
+        counter = Counter({mod_one(k + shift) : v \
+                          for k, v in self.jumps_counter.items()})
+        return SignatureFunction(counter=counter)
+
+    def __lshift__(self, shift):
+        return self.__rshift__(-shift)
+
+    def __neg__(self):
+        counter = Counter()
+        counter.subtract(self.jumps_counter)
+        return SignatureFunction(counter=counter)
+
+    def __add__(self, other):
+        counter = copy(self.jumps_counter)
+        counter.update(other.jumps_counter)
+        if self.plot_title and other.plot_title:
+            title = self.plot_title + " + " + other.plot_title
+        else:
+            title = self.plot_title or other.plot_title
+        return SignatureFunction(counter=counter, plot_title=title)
+
+    def __sub__(self, other):
+        counter = copy(self.jumps_counter)
+        counter.subtract(other.jumps_counter)
+        return SignatureFunction(counter=counter)
+
+    def __mul__(self, number):
+        # scalar multiplication
+        counter = Counter({k : number * v \
+                          for k, v in self.jumps_counter.items()})
+        return SignatureFunction(counter=counter)
+
+    def __rmul__(self, number):
+        return(self.__mul__(number))
+
+    def __eq__(self, other):
+        return self.jumps_counter == other.jumps_counter
+
+    def __str__(self):
+        result = ''.join([str(jump_arg) + ": " + str(jump) + "\n"
+                for jump_arg, jump in sorted(self.jumps_counter.items())])
+        return result
+
+    def __repr__(self):
+        result = ''.join([str(jump_arg) + ": " + str(jump) + ", "
+                for jump_arg, jump in sorted(self.jumps_counter.items())])
+        return result[:-_sage_const_2 ] + "."
+
+    def __call__(self, arg):
+        # return the value of the signature function at the point arg, i.e.
+        # sum of all signature jumps that occur before arg
+        items = self.jumps_counter.items()
+        result = [jump for jump_arg, jump in items if jump_arg < mod_one(arg)]
+        return _sage_const_2  * sum(result) + self.jumps_counter[arg]
+
+    def double_cover(self):
+        # to read values for t^2
+        items = self.jumps_counter.items()
+        counter = Counter({(_sage_const_1  + k) / _sage_const_2  : v for k, v in items})
+        counter.update(Counter({k / _sage_const_2  : v for k, v in items}))
+        return SignatureFunction(counter=counter)
+
+    def square_root(self):
+        # to read values for t^(1/2)
+        counter = Counter()
+        for jump_arg, jump in self.jumps_counter.items():
+            if jump_arg < _sage_const_1 /_sage_const_2 :
+                counter[_sage_const_2  * jump_arg] = jump
+        return SignatureFunction(counter=counter)
+
+    def minus_square_root(self):
+        # to read values for t^(1/2)
+        items = self.jumps_counter.items()
+        counter = Counter({mod_one(_sage_const_2  * k) : v for k, v in items if k >= _sage_const_1 /_sage_const_2 })
+        return SignatureFunction(counter=counter)
+
+    def is_zero_everywhere(self):
+        return not any(self.jumps_counter.values())
+
+    def extremum(self, limit=math.inf):
+        max_point = (_sage_const_0 , _sage_const_0 )
+        current = _sage_const_0 
+        items = sorted(self.jumps_counter.items())
+        for arg, jump in items:
+            current += _sage_const_2  * jump
+            assert current == self(arg) + jump
+            if abs(current) > abs(max_point[_sage_const_1 ]):
+                max_point  = (arg, current)
+                if abs(current) > limit:
+                    break
+        return max_point
+
+    def total_sign_jump(self):
+        # Total signature jump is the sum of all jumps.
+        return sum([j[_sage_const_1 ] for j in sorted(self.jumps_counter.items())])
+
+    def plot(self, *args, **kargs):
+        SignaturePloter.plot(self, *args, **kargs)
+
+
+class SignaturePloter:
+
+    @classmethod
+    def plot_many(cls, *sf_list, save_path=None, title='', cols=None):
+
+        axes_num = len(sf_list)
+        if axes_num > _sage_const_36 :
+            sf_list = sf_list[_sage_const_36 ]
+            axes_num = _sage_const_36 
+            msg = "To many functions for the plot were given. "
+            msg += "Only 36 can be plotted "
+            warnings.warn(msg)
+
+            # print war, set val in conf
+        cols = cols or ceil(sqrt(axes_num))
+        rows = ceil(axes_num/cols)
+        fig, axes_matrix = plt.subplots(rows, cols,
+                                        sharex='col', sharey='row',
+                                        gridspec_kw={'hspace': _sage_const_0 , 'wspace': _sage_const_0 },
+                                        # sharey=True,
+                                        # sharex=True,
+                                        )
+        for i, sf in enumerate(sf_list):
+            col = i % cols
+            row = (i - col)/cols
+            sf.plot(subplot=True,
+                     ax=axes_matrix[row][col],
+                     title=sf.plot_title)
+
+        fig.suptitle(title)
+        plt.tight_layout()
+
+        cls.show_and_save(save_path)
+
+    @classmethod
+    def plot_sum_of_two(cls, sf1, sf2, save_path=None, title=''):
+
+        sf = sf1 + sf2
+        fig, axes_matrix = plt.subplots(_sage_const_2 , _sage_const_2 , sharey=True, figsize=(_sage_const_10 ,_sage_const_5 ))
+
+        sf1.plot(subplot=True,
+                 ax=axes_matrix[_sage_const_0 ][_sage_const_1 ])
+
+        sf2.plot(subplot=True,
+                ax=axes_matrix[_sage_const_1 ][_sage_const_0 ],
+                color='red',
+                linestyle='dotted')
+
+        sf.plot(subplot=True,
+                ax=axes_matrix[_sage_const_0 ][_sage_const_0 ],
+                color='black')
+
+        sf1.plot(subplot=True,
+                ax=axes_matrix[_sage_const_1 ][_sage_const_1 ],
+                alpha=_sage_const_0p3 )
+
+        sf2.plot(subplot=True,
+                ax=axes_matrix[_sage_const_1 ][_sage_const_1 ],
+                color='red', alpha=_sage_const_0p3 ,
+                linestyle='dotted')
+
+        sf.plot(subplot=True,
+                ax=axes_matrix[_sage_const_1 ][_sage_const_1 ],
+                color='black',
+                alpha=_sage_const_0p7 ,)
+
+        fig.suptitle(title)
+        plt.tight_layout()
+
+        cls.show_and_save(save_path)
+
+    @classmethod
+    def plot(cls, sf, subplot=False, ax=None,
+             save_path=None,
+             title='',
+             alpha=_sage_const_1 ,
+             color='blue',
+             linestyle='solid',
+             special_point=None,
+             special_label='',
+             extraticks=None,
+             ylabel=''):
+
+        if ax is None:
+            fig, ax = plt.subplots(_sage_const_1 , _sage_const_1 )
+
+        keys = sorted(sf.jumps_counter.keys())
+        y = [(sf(k) + sf.jumps_counter[k]) for k in keys[:-_sage_const_1 ]]
+        xmax = keys[_sage_const_1 :]
+        xmin = keys[:-_sage_const_1 ]
+
+        ax.set(ylabel=ylabel)
+        ax.set(title=title)
+        ax.hlines(y, xmin, xmax, color=color, linestyle=linestyle, alpha=alpha)
+        if special_point is not None:
+            arg, val = special_point
+            extraticks = extraticks or []
+            plt.xticks(list(plt.xticks()[_sage_const_0 ]) + extraticks)
+            ext = sf.extremum()[_sage_const_1 ]
+            ytext = ext/_sage_const_2  + _sage_const_1 /_sage_const_2 
+            xtext = arg + _sage_const_1 /_sage_const_5 
+
+            ax.annotate(special_label, xy=(arg, val), xytext=(xtext, ytext),
+                        arrowprops=dict(facecolor='black', shrink=_sage_const_0p05 ,
+                                        alpha=_sage_const_0p7 , width=_sage_const_2 ),)
+        if subplot:
+            return ax
+
+        cls.show_and_save(save_path)
+
+    @staticmethod
+    def show_and_save(save_path):
+
+        if save_path is not None:
+            save_path = Path(save_path)
+            save_path = save_path.with_suffix('.png')
+            plt.savefig(save_path)
+
+        if ipython_info == JUPYTER:
+            plt.show()
+
+        elif True:  # save_path is None:
+            plt.savefig('tmp.png')
+            plt.close()
+            image = Image.open('tmp.png')
+            image.show()
+            # msg = "For interactive shell set save_path."
+            # warnings.warn(msg)
+
+    @staticmethod
+    def step_function_data(sf):
+        # Transform the signature jump data to a format understandable
+        # by the plot function.
+        result = [(k, sf.sf(k) + sf.jumps_counter[k])
+                 for k in sorted(sf.jumps_counter.keys())]
+        return result
+
+    @staticmethod
+    def tikz_plot(sf, save_as):
+        plt_sin = plot(sin(x), (x, _sage_const_0 , _sage_const_2 *pi))
+        # plt_sin.show()
+        plt_sin.save("MyPic.pdf")
+
+        return
+        # Draw the graph of the signature and transform it into TiKz.
+        # header of the LaTeX file
+        head = inspect.cleandoc(
+            r"""
+            \documentclass{standalone}
+            \usepackage{tikz}
+            \usetikzlibrary{calc}
+            \begin{document}
+            \begin{tikzpicture}
+            """)
+
+        body = \
+            r"""
+            %A piecewise linear function is drawn over the interval.
+            \draw (5,0) -- (6,-4);
+            %The axes are drawn.
+            \draw[latex-latex] ($(0,{-4*(2/5)}) +(0pt,-12.5pt)$) --
+            ($(0,{4*(2/5)}) +(0pt,12.5pt)$) node[above right]{$y$};
+            \draw[latex-latex] ($({-4*(2/5)},0) +(-12.5pt,0pt)$) --
+            ($({12*(2/5)},0) +(12.5pt,0pt)$) node[below right]{$x$};
+            """
+        tail = \
+            r"""
+            \end{tikzpicture}
+            \end{document}
+            """
+        tikzpicture = re.sub(r' +', ' ', ''.join([head, body, tail]))
+        tikzpicture = re.sub(r'\n ', '\n', tikzpicture)
+
+        with open("tmp.tex", "w") as f:
+            f.write(tikzpicture)
+
+        data = self.step_function_data()
+        with open(save_as, "w") as f:
+            head = \
+                r"""
+                \documentclass[tikz]{{standalone}}
+                %\usepackage{{tikz}}
+                \usetikzlibrary{{datavisualization}}
+                \usetikzlibrary{{datavisualization.formats.functions}}
+                %\usetikzlibrary{{calc}}
+                \begin{{document}}
+                \begin{{tikzpicture}}
+                \datavisualization[scientific axes, visualize as smooth line,
+                x axis={{ticks={{none,major={{at={{, {arg0} " as \\( {val0} \\
+                %]
+                """.format(arg0=str(N(data[_sage_const_0 ][_sage_const_0 ] ,digits=_sage_const_4 )), val0=str(data[_sage_const_0 ][_sage_const_0 ]))
+            f.write(head)
+
+
+            # f.write(", " + str(N(data[0][0],digits=4)) + " as \\(" + \
+            #                          str(data[0][0]) + "\\)")
+            for jump_arg, jump  in data[_sage_const_1 :_sage_const_3 ]:
+                f.write(", " + str(N(jump_arg,digits=_sage_const_4 )) +
+                        " as \\(" + str(jump_arg) + "\\)")
+            f.write("}}}}\n")
+            f.write("  ]\n")
+            f.write("data [format=function]{\n")
+            f.write("var x : interval [0:1];\n")
+            f.write("func y = \\value x;\n")
+            f.write("};\n")
+                # close LaTeX enviroments
+            tail = \
+                r"""
+                %};
+                \end{tikzpicture}
+                \end{document}
+                """
+            f.write(tail)
+
+
+SignatureFunction.__doc__ = \
+    """
+    This simple class encodes twisted and untwisted signature functions
+    of knots. Since the signature function is entirely encoded by its signature
+    jump, the class stores only information about signature jumps
+    in a dictionary self.jumps_counter.
+    The dictionary stores data of the signature jump as a key/values pair,
+    where the key is the argument at which the functions jumps
+    and value encodes the value of the jump. Remember that we treat
+    signature functions as defined on the interval [0,1).
+    """
+
diff --git a/cagosig/signature.sage b/gaknot/signature.sage
similarity index 99%
rename from cagosig/signature.sage
rename to gaknot/signature.sage
index 531d505..f5af7c9 100644
--- a/cagosig/signature.sage
+++ b/gaknot/signature.sage
@@ -1,5 +1,8 @@
 #!/usr/bin/env sage -python
 
+import sys
+import os
+
 from collections import Counter
 import matplotlib.pyplot as plt
 import inspect
@@ -8,11 +11,6 @@ from pathlib import Path
 import warnings
 from .utility import mod_one
 
-# 9.11 (9.8)
-# 9.15 (9.9)
-import sys
-import os
-
 
 JUPYTER = 'ipykernel'
 IPy_TERMINAL = 'IPython'
@@ -27,6 +25,10 @@ def get_ipython_info():
 global ipython_info
 ipython_info = get_ipython_info()
 
+# 9.11 (9.8)
+# 9.15 (9.9)
+
+
 
 class SignatureFunction:
 
diff --git a/cagosig/utility.py b/gaknot/utility.py
similarity index 100%
rename from cagosig/utility.py
rename to gaknot/utility.py