Merge branch 'integration'

Project.toml

@@ -1,7 +1,7 @@
 name = "XPORTA"
 uuid = "8c143463-af6f-456f-8aed-72447cb569d2"
 authors = ["Brian Doolittle"]
-version = "0.1.0"
+version = "0.1.1"
 
 [deps]
 PORTA_jll = "c3fa2e09-48e0-5371-872a-ed3ac32dd1fc"

README.md

@@ -4,13 +4,13 @@
 
 | Documentation | Test Coverage | Linux/Mac | Windows | FreeBSD |
 |:-------------:|:-------------:|:---------:|:-------:|:-------:|
-|[![Dev](https://img.shields.io/badge/docs-dev-blue.svg)](https://JuliaPolyhedra.github.io/XPORTA.jl/dev) | [![Coverage Status](https://coveralls.io/repos/github/JuliaPolyhedra/XPORTA.jl/badge.svg?branch=master)](https://coveralls.io/github/JuliaPolyhedra/XPORTA.jl?branch=master)[![codecov](https://codecov.io/gh/JuliaPolyhedra/XPORTA.jl/branch/master/graph/badge.svg)](https://codecov.io/gh/JuliaPolyhedra/XPORTA.jl) | [![Linux/Mac Build Status](https://travis-ci.org/JuliaPolyhedra/XPORTA.jl.svg?branch=master)](https://travis-ci.org/github/JuliaPolyhedra/XPORTA.jl) | [![Windows Build status](https://ci.appveyor.com/api/projects/status/2kjsbavtulwhsamu?svg=true)](https://ci.appveyor.com/project/bdoolittle/xporta-jl) | [![FreeBSD Build Status](https://api.cirrus-ci.com/github/JuliaPolyhedra/XPORTA.jl.svg)](https://cirrus-ci.com/github/JuliaPolyhedra/XPORTA.jl) |
+|[![Stable](https://img.shields.io/badge/docs-stable-blue.svg)](https://JuliaPolyhedra.github.io/XPORTA.jl/stable) [![Dev](https://img.shields.io/badge/docs-dev-blue.svg)](https://JuliaPolyhedra.github.io/XPORTA.jl/dev) | [![Coverage Status](https://coveralls.io/repos/github/JuliaPolyhedra/XPORTA.jl/badge.svg?branch=master)](https://coveralls.io/github/JuliaPolyhedra/XPORTA.jl?branch=master)[![codecov](https://codecov.io/gh/JuliaPolyhedra/XPORTA.jl/branch/master/graph/badge.svg)](https://codecov.io/gh/JuliaPolyhedra/XPORTA.jl) | [![Linux/Mac Build Status](https://travis-ci.org/JuliaPolyhedra/XPORTA.jl.svg?branch=master)](https://travis-ci.org/github/JuliaPolyhedra/XPORTA.jl) | [![Windows Build status](https://ci.appveyor.com/api/projects/status/2kjsbavtulwhsamu?svg=true)](https://ci.appveyor.com/project/bdoolittle/xporta-jl) | [![FreeBSD Build Status](https://api.cirrus-ci.com/github/JuliaPolyhedra/XPORTA.jl.svg)](https://cirrus-ci.com/github/JuliaPolyhedra/XPORTA.jl) |
 
 ## Documentation
 
-* XPORTA.jl documentation is published at [JuliaPolyhedra.github.io/XPORTA.jl/dev/](https://JuliaPolyhedra.github.io/XPORTA.jl/dev/).
-* PORTA documentation is easily accessible at [github.com/bdoolittle/julia-porta](https://github.com/bdoolittle/julia-porta).
-* PORTA source code may be downloaded from [http://porta.zib.de](http://porta.zib.de/).
+* XPORTA.jl documentation: [JuliaPolyhedra.github.io/XPORTA.jl/dev/](https://JuliaPolyhedra.github.io/XPORTA.jl/stable/).
+* PORTA documentation: [github.com/bdoolittle/julia-porta](https://github.com/bdoolittle/julia-porta).
+* Official PORTA software: [http://porta.zib.de](http://porta.zib.de/).
 
 ## Licensing
 

docs/src/Internals/binaries.md

@@ -15,5 +15,7 @@ run_xporta
 
 ## valid
 
-!!! danger "Not Implemented"
-    Please reach out if you are interested in the `valid` subroutines.
+```@docs
+run_valid
+iespo
+```

docs/src/exports.md

@@ -17,6 +17,18 @@ IEQ
 
 ## Methods
 
+!!! note "Temp Files"
+    By default, files created by the PORTA binaries are deleted. When performing
+    longer computations with PORTA, it may be desirable to keep intermediate files.
+    The argument, `cleanup = false`, causes XPORTA.jl methods to write files to
+    the directory specified by the `dir` argument.
+
 ```@docs
 traf
+dim
+fmel
+vint
+portsort
+posie
+fctp
 ```

docs/src/index.md

@@ -34,7 +34,7 @@ PORTA and XPORTA.jl are licensed under the GNU General Public License (GPL) v2.0
 
 ## Acknowledgments
 
-Development of Porta.jl was made possible by the advisory
+Development of XPORTA.jl was made possible by the advisory
 of Dr. Eric Chitambar and general support from the Physics Department at the
 University of Illinois Urbana-Champaign. Funding was provided by NSF Award 1914440.
 

src/XPORTA.jl

@@ -5,9 +5,18 @@ historical names from the PORTA software.
 
 # Exports
 
-- [`POI`](@ref) - *Type*, The vertex representation of a polyhedra.
-- [`IEQ`](@ref) - *Type*, The intersecting halfspace representation of a polyhedra.
-- [`traf`](@ref) - *Method*, Converts a `POI` -> `IEQ` or `IEQ` -> `POI`.
+*Types*
+- [`POI`](@ref) - The vertex representation of a polyhedra.
+- [`IEQ`](@ref) - The intersecting halfspace representation of a polyhedra.
+
+*Methods*
+- [`traf`](@ref) - Converts a `POI` -> `IEQ` or `IEQ` -> `POI`.
+- [`dim`](@ref) - Given a `POI` computes the dimension and constraining equalities of the `POI` convex hull.
+- [`fmel`](@ref) - Projects the linear system of `IEQ` onto a subspace using fourier-motzkin elimination.
+- [`vint`](@ref) - Enumerates the integral points which satisfy the linear system specified by an `IEQ`.
+- [`portsort`](@ref) - Sorts the elements of `POI` and `IEQ` structs.
+- [`posie`](@ref) - Enumerates the points and rays of a `POI` which satisfy the linear system of an `IEQ`.
+- [`fctp`](@ref) - Determines if inequalities are tight or violated by elements of a `POI`.
 
 The compiled PORTA binaries are accessed through [PORTA_jll.jl](https://github.com/JuliaBinaryWrappers/PORTA_jll.jl)
 
@@ -31,12 +40,14 @@ using PORTA_jll
 using Suppressor
 
 export POI, IEQ # types
-export traf     # xporta methods
+export traf, portsort, dim, fmel # xporta methods
+export fctp, posie, vint         # valid methods
 
 # including local files
 include("./types.jl")
 include("./filesystem.jl") # utilities for create and removing directories
 include("./file_io.jl")    # read/write functionality
-include("./xporta_subroutines.jl")  # wrapper for the xporta binaries.
+include("./xporta_subroutines.jl") # wrapper for the xporta binaries.
+include("./valid_subroutines.jl") # wrapper for the valid binaries
 
 end # module

src/file_io.jl

@@ -137,12 +137,13 @@ function read_ieq(filepath::String)::IEQ{Rational{Int}}
                     end
 
                     # match in/equality sign and rhs value
-                    rhs_match = match(r"(<=|=<|>=|=>|==|=)\s*([-+]?)\s*(\d+)", line)
+                    rhs_match = match(r"(<=|=<|>=|=>|==|=)\s*([-+]?)\s*(\d+)(?:/(\d+))?", line)
 
                     rel_sign = rhs_match.captures[1]
-                    int_sign = (rhs_match.captures[2] === nothing) ? "+" : rhs_match.captures[2]
-                    rhs_int = parse(Int, int_sign*rhs_match.captures[3])
-                    data_vector[end] = rhs_int
+                    rhs_sign = (rhs_match.captures[2] === nothing) ? "+" : rhs_match.captures[2]
+                    rhs_num = parse(Int, rhs_sign*rhs_match.captures[3])
+                    rhs_den = (rhs_match.captures[4] === nothing) ? 1 : parse(Int, rhs_match.captures[4])
+                    data_vector[end] = Rational(rhs_num, rhs_den)
 
                     if (rel_sign == "<=") || (rel_sign == "=<")
                         push!(inequality_rows, data_vector)

src/types.jl

@@ -27,7 +27,8 @@ converted to type `Rational{Int}`.
 Fields:
 * `conv_section` - each matrix row is a vertex.
 * `cone_section` - each matrix row is a ray.
-* `valid` -  a feasible point for the vertex representation.
+* `valid` -  a feasible point for the vertex representation. In the context of a `POI`,
+        this field has no known use.
 * `dim` - the dimension of vertices and rays. This field is auto-populated on construction.
 
 A `DomainError` is thrown if the column dimension of rays and vertices is not equal.
@@ -113,8 +114,8 @@ both have the following form.
 `IEQ` Fields:
 * `inequalities`: each matrix row is a linear inequality, the first M elements indexed `1:(end-1)` are α and the last element indexed `end` is β.
 * `equalities`: each matrix row is linear equality, the first M elements indexed `1:(end-1)` are α and the last element indexed `end` is β.
-* `lower_bounds`: each matrix row is a lower bound for enumerating integral points with `vint`.
-* `upper_bounds`: each matrix row is an upper bound for enumerating integral points with `vint`.
+* `lower_bounds`: a row vector which specifies the lower bound on each individual parameter. Used for enumerating integral points with `vint`.
+* `upper_bounds`: a row vector which specifies the upper bound on each individual parameter. Used for enumerating integral points with `vint`.
 * `valid`: a feasible point for the linear system.
 * `dim`: the dimension of in/equalities, upper/lower bounds, etc. This field is auto-populated on construction.