khoca 0.4.dev7__tar.gz → 0.5__tar.gz

khoca-0.5/.gitignore

@@ -0,0 +1,11 @@
+bin/__pycache__/
+bin/pui.so
+src/krasner/krasner.o
+src/planar_algebra/coefficient_rings.o
+src/planar_algebra/planar_algebra.o
+src/planar_algebra/smith.o
+src/planar_algebra/sparsemat.o
+src/python_interface/pui.cpp
+src/python_interface/pui.o
+src/python_interface/pythonInterface.o
+src/shared.o

khoca-0.5/PKG-INFO

@@ -0,0 +1,210 @@
+Metadata-Version: 2.4
+Name: khoca
+Version: 0.5
+Summary: Khoca as pip installable package
+Project-URL: Homepage, https://github.com/soehms/khoca/
+Author-email: Sebastian Oehms <seb.oehms@gmail.com>
+License-Expression: GPL-2.0-or-later
+License-File: COPYING
+Keywords: Khovanov,Knot,homology,theory
+Classifier: Development Status :: 3 - Alpha
+Classifier: Intended Audience :: Science/Research
+Classifier: License :: OSI Approved :: GNU General Public License v2 or later (GPLv2+)
+Classifier: Operating System :: POSIX :: Linux
+Classifier: Programming Language :: C++
+Classifier: Programming Language :: Cython
+Classifier: Programming Language :: Python
+Classifier: Topic :: Scientific/Engineering :: Mathematics
+Description-Content-Type: text/markdown
+
+# README for Khoca, a knot homology calculator
+
+The same text as in this README file is available (with illustrations) at
+http://lewark.de/lukas/khoca.html
+
+Khoca is computer program to calculate sl(N)-homology of knots. The program has
+been written for joint projects with Andrew Lobb such as [3, 4]. The paper [3]
+also contains a description of the algorithm used by khoca. The main innovation
+is to use Krasner's calculation of the sl(N)-homology of the basic two-crossing
+tangle [2] for calculations of the homology of bipartite knots.
+
+Khoca calculates the following:
+
+* Khovanov sl(2)-homology of arbitrary links, given as a braid or in PD code.
+* Khovanov-Rozansky sl(N)-homology with N > 2 of bipartite knots, given by a
+  certain encoding of a matched diagram of the knot (see [3] and section
+  "Encoding of matched diagrams" below).
+* Homology over the integers, the rationals or a prime field.
+* Either equivariant homology, or homology with an arbitrary fixed potential.
+* All pages of the spectral sequence of filtered homology over a field.
+* Reduced and unreduced homology.
+* Homology of sums and mirror images of knots.
+
+You are encouraged to contact me with any kind of questions or comments
+regarding khoca. If you are using khoca for a project or publication, please
+cite this web page, or the paper [3].
+
+## Installation
+
+Binaries for Linux are available for download from 
+http://lewark.de/lukas/khoca.html
+They should run on any Linux installation that has python3.6. Binaries for
+Windows or Mac are not available at the moment.
+
+The source code, including instructions on how to compile it, is available at
+the GitHub repository khoca:
+https://github.com/LLewark/khoca
+
+To run Khoca in Docker type:
+
+```bash
+docker run -it soehms/khoca:latest
+```
+
+Its download size is 162 MB and it will need 516 MB of disk space on your
+device. To create a new (resp. locally own) Docker image cd to the khoca
+directory type
+
+```bash
+docker build -f Dockerfile --tag khoca:<your_tag> .
+```
+
+If your machine has an older CPU it can happen that you get *Illegal Instruction*
+errors. In that case you better should use the image `soehms/khoca:old_cpu`.
+
+
+## Usage
+
+To use the program, run khoca.py (a python3 script) from the command line.
+khoca.py takes three arguments:
+
+1. The coefficient ring; `0` for integers, `1` for rationals, a prime `p` for the
+corresponding finite field.
+
+2. A sequence of N integers `a_0, ..., a_{N-1}` separated by a non-digit
+character, defining the Frobenius algebra `F[X]/(X^N + a_{N-1}X^{N-1} + ... +
+a_0)`.  Alternatively, `e` followed by a number `N` for equivariant computation
+over `sl(N)`. For example, `-1.0.0` gives the Frobenius algebra `F[X]/(X3 - 1)`.
+
+3. A root of the polynomial given in 2. for the calculation of reduced homology
+(for the dependence of reduced homology on a root, see [3]).  For example, to
+get the standard graded reduced homology, use 0 as root. If you are not
+interested in reduced homology, it does not matter what root you chose (and
+khoca does not check that the number is actually a root).
+
+The option `-p` will show progress bars, `-v` will give more verbose
+non-mathematical information, and `-h` will print a short help text. Each
+argument after the first three arguments, can be one of the following.
+
+1. `BraidX` calculates homology of a link given as closure of the braid `X`,
+formatted as in knotscape (`a` = first Artin generator, `A` = its inverse, `b` =
+second Artin generator, etc.). This works only for `sl(2)` homology, otherwise
+output is nonsensical.
+
+2. `PdX` calculates homology of a link given in PD notation (as e.g. given on
+KnotInfo). Again, this works only for `sl(2)` homology, otherwise output is
+nonsensical.
+
+3. `GaussX` calculates homology of a bipartite knot given as a matched diagram,
+following the convention explained in the section below. This works for `sl(N)`
+homology for all `N`.
+
+4. `MirrorX` takes the dual of the result at spot `X`.
+
+5. `SumXY` computes the homology of the connected sum of the results saved at
+spots `X` and `Y` (numbers separated by a non-digit character).
+
+6. `CalcX` outputs the result saved at spot `X`. If you forget this command, the
+program will have no output.
+
+The program keeps a stack of computed homologies, enumerated 0,1,2... . Each of
+the commands 1 - 5 puts a new homology on that stack, whereas the command 6.
+prints the homology at a certain spot. This is mainly useful to compute
+homology of sums of knots.
+
+Here are some examples:
+
+```bash
+./khoca.py 0 0.0 0 braidaBaB calc0
+```
+
+calculates the classical `sl(2)` Khovanov homology (both reduced and unreduced)
+of the closure of the braid `aBaB` (knotscape notation), i.e. the figure-eight
+knot.
+
+
+```bash
+./khoca.py 0 e2 0 pd[[4,2,5,1],[8,6,1,5],[6,3,7,4],[2,7,3,8]] calc0
+```
+
+calculates integral equivariant `sl(2)` homology of the figure-eight knot.
+
+
+```bash
+./khoca.py 7 0.-1 0 braidabcdefabcdefabcdefabcdefabcdefabcdefabcdefabcdef
+calc0 -p
+```
+
+calculates Khovanov homology of the `(7,8)`-torus knot over `F7` with perturbed
+potential, displaying progress bars. This calculation takes roughly two
+minutes, and shows that the spectral sequence does not collapse on the second
+page, refuting the knight-move conjecture over finite fields (cf. [1]).
+
+
+```bash
+./converters/montesinos.py [1/5,1/3,-1/2]
+```
+
+outputs `[12,4,16,10,15,9,14,13]`, the code for a matched diagram of the
+`(5,3,-2)`-pretzel knot, aka the `(3,5)`-torus knot, aka `10_{124}`. So
+
+```bash
+./khoca.py 1 1.0.0.0.0 0 gauss[12,4,16,10,15,9,14,13] calc0 calculates
+```
+
+rational `sl(5)` homology and the corresponding Rasmussen invariant of the `(3,5)`
+torus knot.
+
+
+```bash
+./khoca.py 1 1.0 0 braidaaa dual0 sum0+1 braidaBaB sum2+3 calc4
+```
+
+calculates `sl(2)` homology of the sum of the trefoil, its mirror image and a figure-8-knot.
+
+
+# Encoding of matched diagrams
+
+This section describes how to encode a matched knot diagram, i.e. a diagram
+that consists of `n` copies of the basic 2-crossing tangle. Resolving each basic
+tangle into two intervals and a chord results in a single circle with n
+non-intersecting (red) chords, which may be on either side of the circle.
+Enumerate the `2n` chord endpoints by walking around the circle. If a chord
+connects the points `i` and `j`, let `f(i) = j`. Write down the list `f(1), f(2), ...,
+f(2n)` omitting `f(i)` if `f(i) < i`. Moreover, make the list entries signed, and
+let the sign reflect the sign of the two crossings of the corresponding
+2-crossing tangle. This list of `n` non-zero integers uniquely determines the
+matched diagram. As an example, the standard diagram of `6_1` is matched and
+encoded as `[-4,6,5]`.
+
+"Half" of Montesinos knots are bipartite [3]. You may use the python3 script
+`./converters/montesinos.py` to obtain the encoding of a matched diagram of
+Montesinos knots.
+
+# References
+
+[1] Bar-Natan: Fast Khovanov Homology Computations, Journal of Knot Theory and
+its Ramifications 16 (2007), no.3, pp. 243-255, arXiv:math/0606318, MR2320156.
+
+[2] Daniel Krasner: A computation in Khovanov-Rozansky Homology, Fundamenta
+Mathematicae 203 (2009), pp. 75-95, arXiv:0801.4018, MR2491784.
+
+[3] Lukas Lewark and Andrew Lobb: New Quantum Obstructions to Sliceness,
+Proceedings of the London Mathematical Society 112 (2016), no. 1, pp. 81-114,
+arXiv:1501.07138, MR3458146.
+
+[4] Lukas Lewark and Andrew Lobb: Upsilon-like concordance invariants from
+sl(n) knot cohomology, arXiv:1707.00891.
+
+
+Lukas Lewark, 2018

khoca-0.5/pyproject.toml

@@ -0,0 +1,46 @@
+[build-system]
+requires = ["hatchling",
+"hatch-vcs"]
+build-backend = "hatchling.build"
+
+[project]
+name = "khoca"
+dynamic = ["version"]
+description = "Khoca as pip installable package"
+readme = "README.md"
+license = "GPL-2.0-or-later"
+authors = [
+    { name = "Sebastian Oehms", email = "seb.oehms@gmail.com" },
+]
+keywords = [
+    "Khovanov",
+    "Knot",
+    "homology",
+    "theory",
+]
+classifiers = [
+    "Development Status :: 3 - Alpha",
+    "Intended Audience :: Science/Research",
+    "License :: OSI Approved :: GNU General Public License v2 or later (GPLv2+)",
+    "Operating System :: POSIX :: Linux",
+    "Programming Language :: C++",
+    "Programming Language :: Cython",
+    "Programming Language :: Python",
+    "Topic :: Scientific/Engineering :: Mathematics",
+]
+dependencies = []
+
+[project.urls]
+Homepage = "https://github.com/soehms/khoca/"
+
+[tool.hatch.version]
+source = "vcs"
+
+#[tool.hatch.build.hooks.vcs]
+#version-file = "khoca/_version.py"
+
+[tool.hatch.build.targets.sdist]
+include = [
+    "/khoca",
+]
+

khoca-0.4.dev7/.github/workflows/push_docker.yml

@@ -1,20 +0,0 @@
-name: Publish Docker
-
-on:
-  create:
-    tag:
-      - '*'
-  workflow_dispatch:
-
-jobs:
-  build:
-    runs-on: ubuntu-latest
-    steps:
-    - uses: actions/checkout@master
-    - name: Publish to Registry
-      uses: elgohr/Publish-Docker-Github-Action@master
-      with:
-        name: soehms/khoca
-        username: ${{ secrets.DOCKER_USER }}
-        password: ${{ secrets.DOCKER_API_TOKEN }}
-        tag_names: true

khoca-0.4.dev7/.github/workflows/run_tests.yml

@@ -1,37 +0,0 @@
-# This workflow runs tests to build Khoca on verois systems
-
-name: Run Tests
-
-# Triggers the workflow on push or pull request events and manually
-on: [push, pull_request, workflow_dispatch]
-
-jobs:
-  # This workflow contains one job called build
-  build:
-    name: Build Khoca
-    runs-on: ubuntu-latest
-
-    steps:
-      # Checks-out the repository under $GITHUB_WORKSPACE, so our job can access it
-      - name: Checkout code
-        id: checkout_code
-        uses: actions/checkout@v2
-
-      # Installs dependencies
-      - name: Install Dependencies
-        id: dependencies
-        run: |
-            sudo apt-get update -y
-            sudo apt-get install -y make g++ python3 python3-pip libgmp-dev pari-gp2c
-            pip3 install cython
-
-      # Building Khoca
-      - name: Make
-        id: make
-        run: make
-
-      # Run a Test (should result to 1)
-      - name: Run Test
-        id: run_test
-        run: |
-          ./khoca.py 0 0.0 0 braidaBaB calc0 | grep -c "t^-2q^4 + t^-1q^2 + t^0q^0 + t^1q^-2 + t^2q^-4"

khoca-0.4.dev7/.github/workflows/upload_pypi.yml

@@ -1,15 +0,0 @@
-name: PyPI Deployer
-on:
-  push:
-    tags:
-      - "*" # Push events of new tags
-jobs:
-  Linux-build:
-    runs-on: ubuntu-latest
-    env:
-      TWINE_USERNAME: ${{ secrets.PYPI_USER }}
-      TWINE_PASSWORD: ${{ secrets.PYPI_API_TOKEN }}
-    steps:
-      - uses: actions/checkout@v2
-      - name: build and upload manylinux wheels
-        uses: Niraj-Kamdar/manylinux-wheel-builder@master

khoca-0.4.dev7/Dockerfile

@@ -1,27 +0,0 @@
-################################################################################
-# HOWTO use this file for local builds                                         #
-################################################################################
-# To build Khoca, run this command from your khoca/ directory:                 #
-# $ docker build -f Dockerfile --tag khoca:<your_tag> .                        #
-# To run Khoca:                                                                #
-# $ docker run -it khoca:<your_tag>                                            #
-################################################################################
-FROM ubuntu:latest
-LABEL maintainer="Sebastian Oehms <seb.oehms@gmail.com>"
-# Set sane defaults for common environment variables.
-ENV LC_ALL C.UTF-8
-ENV LANG C.UTF-8
-ENV SHELL /bin/bash
-# install prerequisites
-RUN apt-get -qq update \
-    && apt-get -qq install -y --no-install-recommends git g++ make libgmp-dev pari-gp2c python3 python3-dev python3-pip \
-    && apt-get -qq clean \
-    && rm -r /var/lib/apt/lists/* \
-    && pip install cython \
-    && git clone https://github.com/soehms/khoca.git \
-    && cd khoca/ \
-    && make
-WORKDIR "/khoca/"
-COPY ./docker/entrypoint.sh /usr/local/bin/khoca-entrypoint
-ENTRYPOINT ["/usr/local/bin/khoca-entrypoint"]
-CMD ["bash"]

khoca-0.4.dev7/INSTALL

@@ -1,36 +0,0 @@
-If you downloaded binaries, the only slightly exotic library that needs to be
-present on your system is libpython3.6m.so.1.0.
-
-This file gives some instructions on how to compile khoca from source. You are
-welcome to email me at <lukas@lewark.de> for help.
-You will need:
-* a version of gcc that supports c++11.
-* cython.
-* mpir, compiled with c++ support.
-* gp/pari.
-* python3
-
-If your python version is not 3.6, change the variable PYTHONVERSION in the
-make file accordingly.  If you installed the above-mentioned libraries to a
-non-standard location, you might need to add an -I parameter to GENERALCFLAGS,
-or an -L parameter to STATIC_DIRECTIVE. Then, run make. This should produce the
-file bin/pui.so. Compilation may take quite a while. If you encounter problems,
-you may wish to uncomment the two lines after "Fast compile" in the Makefile,
-and comment out the two lines after "Not Debugging". Also, you can delete lines
-81 - 93 in src/shared.h. These measures will lead to faster compilation.
-
-Now you are set! Run
-
-./khoca.py 0 0.0 0 braidaaa calc0
-
-to test. The output should be:
-
-Frobenius algebra: Z[X] / (1*X^2).
-Result:
-Reduced Homology:
-Non-equivariant homology:
-t^-3q^8 + t^-2q^6 + t^0q^2
-Unreduced Homology:
-Non-equivariant homology:
-t^-3q^9 + t^-2q^5 + t^0q^1 + t^0q^3 + t^-2q^7[2]
-

khoca-0.4.dev7/MANIFEST.in

@@ -1 +0,0 @@
-include data/

khoca-0.4.dev7/Makefile

@@ -1,83 +0,0 @@
-CC=g++
-PYTHONVERSION=3.8
-GENERALCFLAGS=-c -std=c++11 -I/usr/include/python$(PYTHONVERSION) -D__STDC_LIMIT_MACROS -Wall -Wextra -march=native
-
-STATIC_DIRECTIVE=-lpython$(PYTHONVERSION) -lgmpxx -lgmp -L/usr/local/lib -lpari
-# To compile a version of the library that contains static copies of mpir and pari, set variable STATIC to 1.
-ifeq ($(STATIC),1)
-  STATIC_DIRECTIVE=-Wl,--no-as-needed -ldl -lutil -static-libgcc -lpython$(PYTHONVERSION) -L/usr/local/lib /usr/local/lib/libmpirxx.a /usr/local/lib/libmpir.a /usr/local/lib/libpari.a
-endif
-
-CFLAGSPYXO=-Wno-write-strings -Wimplicit-fallthrough=0 -fno-strict-aliasing -fwrapv -pthread
-SHAREDCFLAGS=-shared -fPIC
-
-# HOW TO DEBUG:
-# Turn on Debugging here in Makefile; change the switches in shared.h (and maybe compile only with one bitsize for speed); and turn on debugging-bool-constant in khoroho.py.
-# If multithreading is not disabled, there will be plenty of errors, because sanity checks are done while other threads are active.
-
-# FAST COMPILE
-# CFLAGS=$(GENERALCFLAGS) $(SHAREDCFLAGS) -O0 -ggdb -g3 -fopenmp
-# COMPILERFLAGSINFO=\"Fast compilation\"
-
-# DEBUGGING
-# CFLAGS=$(GENERALCFLAGS) $(SHAREDCFLAGS) -Og -ggdb -g3 -fopenmp
-# COMPILERFLAGSINFO=\"Debug\"
-
-# FAST, BUT DEBUG INFO
-# CFLAGS=$(GENERALCFLAGS) $(SHAREDCFLAGS) -O3 -g3 -fopenmp
-# COMPILERFLAGSINFO=\"Fast program, but including debug info\"
-
-# NOT DEBUGGING
-CFLAGS=$(GENERALCFLAGS) $(SHAREDCFLAGS) -O3 -fopenmp
-COMPILERFLAGSINFO=\"Release\"
-
-CMPIRFLAGS=-I/usr/local/include
-LDFLAGS=$(STATIC_DIRECTIVE) $(SHAREDCFLAGS) -z defs -lpthread -lstdc++ -Wl,-t
-
-PYX=src/python_interface/pui.pyx
-PYXCPP=src/python_interface/pui.cpp
-PYXO=src/python_interface/pui.o
-PYI=src/python_interface/pythonInterface.cpp
-PYIO=src/python_interface/pythonInterface.o
-SOURCES=src/planar_algebra/planar_algebra.cpp src/shared.cpp src/krasner/krasner.cpp src/planar_algebra/sparsemat.cpp src/planar_algebra/coefficient_rings.cpp src/planar_algebra/smith.cpp src/planar_algebra/coefficient_rings_explicitTemplates.cpp
-OBJECTS=src/planar_algebra/planar_algebra.o src/shared.o src/krasner/krasner.o src/planar_algebra/sparsemat.o src/planar_algebra/coefficient_rings.o src/planar_algebra/smith.o
-EXECUTABLE=bin/pui.so
-
-
-.PHONY : clean
-
-all:	$(EXECUTABLE)
-
-$(EXECUTABLE): $(SOURCES) $(OBJECTS) $(PYX) $(PYXCPP) $(PYXO) $(PYI) $(PYIO) Makefile
-	$(CC) $(OBJECTS) $(PYIO) $(PYXO) -o $@ $(LDFLAGS)
-
-$(PYXCPP): $(PYX) Makefile
-	cython -3 --cplus $(PYX)
-
-$(PYXO): $(PYXCPP) src/python_interface/pythonInterface.h src/shared.h Makefile
-	$(CC) $(CFLAGS) $(CFLAGSPYXO) $< -o $@
-
-src/python_interface/pythonInterface.o: src/python_interface/pythonInterface.cpp src/planar_algebra/planar_algebra.h src/krasner/krasner.h src/shared.h src/planar_algebra/sparsemat.h src/planar_algebra/coefficient_rings.h Makefile
-	echo "#define COMPILERFLAGSINFO $(COMPILERFLAGSINFO)" > src/compilerFlagsInfo.cpp
-	$(CC) $(CMPIRFLAGS) $(CFLAGS) $< -o $@
-
-src/planar_algebra/planar_algebra.o: src/planar_algebra/planar_algebra.cpp src/planar_algebra/planar_algebra.h src/shared.h src/planar_algebra/explicitTemplates.cpp src/planar_algebra/sparsemat.h src/planar_algebra/coefficient_rings.h src/krasner/krasner.h Makefile
-	$(CC) $(CMPIRFLAGS) $(CFLAGS) $< -o $@
-
-src/shared.o: src/shared.cpp src/shared.h Makefile
-	$(CC) $(CFLAGS) $< -o $@
-
-src/krasner/krasner.o: src/krasner/krasner.cpp src/krasner/krasner.h src/krasner/krasnerExplicitTemplates.cpp src/planar_algebra/planar_algebra.h src/shared.h src/planar_algebra/sparsemat.h src/planar_algebra/coefficient_rings.h Makefile
-	$(CC) $(CMPIRFLAGS) $(CFLAGS) $< -o $@
-
-src/planar_algebra/sparsemat.o: src/planar_algebra/sparsemat.cpp src/planar_algebra/planar_algebra.h src/krasner/krasner.h src/shared.h src/planar_algebra/sparsemat.h src/planar_algebra/sparsematExplicitTemplates.cpp src/planar_algebra/coefficient_rings.h Makefile
-	$(CC) $(CMPIRFLAGS) $(CFLAGS) $< -o $@
-	
-src/planar_algebra/coefficient_rings.o: src/planar_algebra/coefficient_rings.cpp src/planar_algebra/coefficient_rings.h src/shared.h src/planar_algebra/coefficient_rings_explicitTemplates.cpp Makefile
-	$(CC) $(CMPIRFLAGS) $(CFLAGS) $< -o $@
-
-src/planar_algebra/smith.o:  src/planar_algebra/smith.cpp src/planar_algebra/planar_algebra.h src/shared.h src/planar_algebra/explicitTemplates.cpp src/planar_algebra/sparsemat.h src/planar_algebra/coefficient_rings.h Makefile
-	$(CC) $(CMPIRFLAGS) $(CFLAGS) $< -o $@
-
-clean:
-	rm -f $(OBJECTS) $(PYIO) $(PYXO) $(TESTER) $(EXECUTABLE) $(PYXCPP)