Merge pull request #98 from CurricularAnalytics/development

Version 1.0.3

.travis.yml

@@ -13,11 +13,14 @@ julia:
   - 1.1
   - 1.2
   - 1.3
+  - 1.4
+  - 1.5
+
 
 jobs: 
   include:
     - stage: "Documentation"
-      julia: 1.1
+      julia: 1.0.5
       os: linux
       script:
         - julia --project=docs/ -e 'using Pkg; Pkg.instantiate(); Pkg.develop(PackageSpec(path=pwd()))'

Manifest.toml

@@ -10,22 +10,22 @@ version = "0.0.4"
 uuid = "2a0f44e3-6c83-55bd-87e4-b1978d98bd5f"
 
 [[CSV]]
-deps = ["CategoricalArrays", "DataFrames", "Dates", "FilePathsBase", "Mmap", "Parsers", "PooledArrays", "Tables", "Unicode", "WeakRefStrings"]
-git-tree-sha1 = "c5ef3e34d21aa4b0e88521f1dc8031515d389148"
+deps = ["CategoricalArrays", "DataFrames", "Dates", "Mmap", "Parsers", "PooledArrays", "SentinelArrays", "Tables", "Unicode"]
+git-tree-sha1 = "a390152e6850405a48ca51bd7ca33d11a21d6230"
 uuid = "336ed68f-0bac-5ca0-87d4-7b16caf5d00b"
-version = "0.5.26"
+version = "0.7.7"
 
 [[CategoricalArrays]]
-deps = ["Compat", "DataAPI", "Future", "JSON", "Missings", "Printf", "Reexport", "Statistics", "Unicode"]
-git-tree-sha1 = "23d7324164c89638c18f6d7f90d972fa9c4fa9fb"
+deps = ["DataAPI", "Future", "JSON", "Missings", "Printf", "Statistics", "Unicode"]
+git-tree-sha1 = "a6c17353ee38ddab30e73dcfaa1107752de724ec"
 uuid = "324d7699-5711-5eae-9e2f-1d82baa6b597"
-version = "0.7.7"
+version = "0.8.1"
 
 [[Compat]]
 deps = ["Base64", "Dates", "DelimitedFiles", "Distributed", "InteractiveUtils", "LibGit2", "Libdl", "LinearAlgebra", "Markdown", "Mmap", "Pkg", "Printf", "REPL", "Random", "SHA", "Serialization", "SharedArrays", "Sockets", "SparseArrays", "Statistics", "Test", "UUIDs", "Unicode"]
-git-tree-sha1 = "48c20c43e157c6eab6cf88326504ec042b05e456"
+git-tree-sha1 = "a6a8197ae253f2c1a22b2ae17c2dfaf5812c03aa"
 uuid = "34da2185-b29b-5c13-b0c7-acf172513d20"
-version = "3.10.0"
+version = "3.13.0"
 
 [[DataAPI]]
 git-tree-sha1 = "176e23402d80e7743fc26c19c681bfb11246af32"
@@ -34,15 +34,15 @@ version = "1.3.0"
 
 [[DataFrames]]
 deps = ["CategoricalArrays", "Compat", "DataAPI", "Future", "InvertedIndices", "IteratorInterfaceExtensions", "Missings", "PooledArrays", "Printf", "REPL", "Reexport", "SortingAlgorithms", "Statistics", "TableTraits", "Tables", "Unicode"]
-git-tree-sha1 = "7d5bf815cc0b30253e3486e8ce2b93bf9d0faff6"
+git-tree-sha1 = "4fe99dbfb5201c5766d20d32a65209434347fd58"
 uuid = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0"
-version = "0.20.2"
+version = "0.21.6"
 
 [[DataStructures]]
 deps = ["InteractiveUtils", "OrderedCollections"]
-git-tree-sha1 = "af6d9c86e191c917c2276fbede1137e8ea20157f"
+git-tree-sha1 = "88d48e133e6d3dd68183309877eac74393daa7eb"
 uuid = "864edb3b-99cc-5e75-8d2d-829cb0a9cfe8"
-version = "0.17.17"
+version = "0.17.20"
 
 [[DataValueInterfaces]]
 git-tree-sha1 = "bfc1187b79289637fa0ef6d4436ebdfe6905cbd6"
@@ -63,22 +63,16 @@ uuid = "8ba89e20-285c-5b6f-9357-94700520ee1b"
 
 [[DocStringExtensions]]
 deps = ["LibGit2", "Markdown", "Pkg", "Test"]
-git-tree-sha1 = "88bb0edb352b16608036faadcc071adda068582a"
+git-tree-sha1 = "c5714d9bcdba66389612dc4c47ed827c64112997"
 uuid = "ffbed154-4ef7-542d-bbb7-c09d3a79fcae"
-version = "0.8.1"
+version = "0.8.2"
 
 [[Documenter]]
 deps = ["Base64", "Dates", "DocStringExtensions", "InteractiveUtils", "JSON", "LibGit2", "Logging", "Markdown", "REPL", "Test", "Unicode"]
 git-tree-sha1 = "395fa1554c69735802bba37d9e7d9586fd44326c"
 uuid = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
 version = "0.24.11"
 
-[[FilePathsBase]]
-deps = ["Dates", "LinearAlgebra", "Printf", "Test", "UUIDs"]
-git-tree-sha1 = "2cd6e2e7965934f72cb80251f760228e2264bab3"
-uuid = "48062228-2e41-5def-b9a4-89aafe57970f"
-version = "0.7.0"
-
 [[Future]]
 deps = ["Random"]
 uuid = "9fa8497b-333b-5362-9e8d-4d0656e87820"
@@ -149,15 +143,15 @@ version = "0.4.3"
 uuid = "a63ad114-7e13-5084-954f-fe012c677804"
 
 [[OrderedCollections]]
-git-tree-sha1 = "12ce190210d278e12644bcadf5b21cbdcf225cd3"
+git-tree-sha1 = "293b70ac1780f9584c89268a6e2a560d938a7065"
 uuid = "bac558e1-5e72-5ebc-8fee-abe8a469f55d"
-version = "1.2.0"
+version = "1.3.0"
 
 [[Parsers]]
 deps = ["Dates", "Test"]
-git-tree-sha1 = "0c16b3179190d3046c073440d94172cfc3bb0553"
+git-tree-sha1 = "10134f2ee0b1978ae7752c41306e131a684e1f06"
 uuid = "69de0a69-1ddd-5017-9359-2bf0b02dc9f0"
-version = "0.3.12"
+version = "1.0.7"
 
 [[Pkg]]
 deps = ["Dates", "LibGit2", "Libdl", "Logging", "Markdown", "Printf", "REPL", "Random", "SHA", "UUIDs"]
@@ -190,6 +184,12 @@ version = "0.2.0"
 [[SHA]]
 uuid = "ea8e919c-243c-51af-8825-aaa63cd721ce"
 
+[[SentinelArrays]]
+deps = ["Dates", "Random"]
+git-tree-sha1 = "7871163033b83a0d08bb601af56488c6f642a113"
+uuid = "91c51154-3ec4-41a3-a24f-3f23e20d615c"
+version = "1.2.10"
+
 [[Serialization]]
 uuid = "9e88b42a-f829-5b0c-bbe9-9e923198166b"
 
@@ -218,9 +218,9 @@ uuid = "2f01184e-e22b-5df5-ae63-d93ebab69eaf"
 
 [[StaticArrays]]
 deps = ["LinearAlgebra", "Random", "Statistics"]
-git-tree-sha1 = "5c06c0aeb81bef54aed4b3f446847905eb6cbda0"
+git-tree-sha1 = "016d1e1a00fabc556473b07161da3d39726ded35"
 uuid = "90137ffa-7385-5640-81b9-e52037218182"
-version = "0.12.3"
+version = "0.12.4"
 
 [[Statistics]]
 deps = ["LinearAlgebra", "SparseArrays"]
@@ -234,9 +234,9 @@ version = "1.0.0"
 
 [[Tables]]
 deps = ["DataAPI", "DataValueInterfaces", "IteratorInterfaceExtensions", "LinearAlgebra", "TableTraits", "Test"]
-git-tree-sha1 = "c45dcc27331febabc20d86cb3974ef095257dcf3"
+git-tree-sha1 = "b7f762e9820b7fab47544c36f26f54ac59cf8abf"
 uuid = "bd369af6-aec1-5ad0-b16a-f7cc5008161c"
-version = "1.0.4"
+version = "1.0.5"
 
 [[Test]]
 deps = ["Distributed", "InteractiveUtils", "Logging", "Random"]
@@ -248,9 +248,3 @@ uuid = "cf7118a7-6976-5b1a-9a39-7adc72f591a4"
 
 [[Unicode]]
 uuid = "4ec0a83e-493e-50e2-b9ac-8f72acf5a8f5"
-
-[[WeakRefStrings]]
-deps = ["DataAPI", "Random", "Test"]
-git-tree-sha1 = "28807f85197eaad3cbd2330386fac1dcb9e7e11d"
-uuid = "ea10d353-3f73-51f8-a26c-33c1cb351aa5"
-version = "0.6.2"

Project.toml

@@ -1,7 +1,7 @@
 name = "CurricularAnalytics"
 uuid = "593ffa3d-269e-5d81-88bc-c3b6809c35a6"
 authors = ["Greg Heileman <gregheileman@gmail.com>", "Hayden Free <hayden.free@uky.edu>", "Orhan Abar <orhan.abar@uky.edu>", "Will Thompson <wgthompson@uky.edu>"]
-version = "1.0.2"
+version = "1.0.3"
 
 [deps]
 CSV = "336ed68f-0bac-5ca0-87d4-7b16caf5d00b"
@@ -15,9 +15,9 @@ Printf = "de0858da-6303-5e67-8744-51eddeeeb8d7"
 Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
 
 [compat]
-CSV = "0.5.9"
-DataFrames = "0.20.0"
+CSV = "0.7"
+DataFrames = "0.21.0"
 DataStructures = "0.17.0"
 Documenter = "0.24.0"
-LightGraphs = "1.2.0"
-julia = "1.0.5, 1.1, 1.2, 1.3, 1.4"
+LightGraphs = "1.3.0"
+julia = "1.0.5, 1.1, 1.2, 1.3, 1.4, 1.5"

src/CSVUtilities.jl

@@ -100,8 +100,8 @@ function csv_line_reader(line::AbstractString, delimeter::Char=',')
 end
 
 function find_cell(row, header)
-    if !(header in names(row)) #I assume this means if header is not in names 
-        return ""
+    if !(string(header) in names(row)) #I assume this means if header is not in names 
+        error("$(header) column is missing")
     elseif typeof(row[header]) == Missing
         return ""
     else

src/CurricularAnalytics.jl

@@ -23,11 +23,12 @@ include("DegreePlanCreation.jl")
 
 export AA, AAS, AS, BA, BS, Course, CourseCatalog, Curriculum, Degree, DegreePlan, EdgeClass, LearningOutcome, Requisite, System, Term, add_course!, 
         add_lo_requisite!, add_requisite!, all_paths, basic_metrics, basic_statistics, bin_filling, blocking_factor, centrality, co, compare_curricula, 
-        complexity, course, course_from_id, course_from_vertex, course_id, courses_from_vertices, create_degree_plan, dead_ends, delay_factor, delete_requisite!, 
-        dfs, extraneous_requisites, find_term, gad, homology, is_duplicate, isvalid_curriculum, isvalid_degree_plan, longest_path, longest_paths, merge_curricula, 
-        pre, print_plan, quarter, reach, reach_subgraph, reachable_from, reachable_from_subgraph, reachable_to, reachable_to_subgraph, read_csv, requisite_distance, 
-        requisite_type, semester, similarity, strict_co, topological_sort, total_credits, write_csv, Grade, grade, AbstractRequirement, CourseSet, RequirementSet, 
-        CourseRecord, StudentRecord, TransferArticulation, add_transfer_catalog, add_transfer_course, transfer_equiv
+        complexity, convert_ids, course, course_from_id, course_from_vertex, course_id, courses_from_vertices, create_degree_plan, dead_ends, delay_factor, 
+        delete_requisite!, dfs, extraneous_requisites, find_term, gad, homology, is_duplicate, isvalid_curriculum, isvalid_degree_plan, longest_path, 
+        longest_paths, merge_curricula, pre, print_plan, quarter, reach, reach_subgraph, reachable_from, reachable_from_subgraph, reachable_to, 
+        reachable_to_subgraph, read_csv, requisite_distance, requisite_type, semester, similarity, strict_co, topological_sort, total_credits, write_csv, 
+        Grade, grade, AbstractRequirement, CourseSet, RequirementSet, CourseRecord, StudentRecord, TransferArticulation, add_transfer_catalog, 
+        add_transfer_course, transfer_equiv
 
 # Check if a curriculum graph has requisite cycles.
 """

src/DataTypes/Course.jl

@@ -1,3 +1,7 @@
+# Course-related data DataTypes
+
+abstract type AbstractCourse end
+
 ##############################################################
 # Course data type
 """
@@ -21,7 +25,7 @@ Keyword:
 julia> Course("Calculus with Applications", 4, prefix="MA", num="112", canonical_name="Calculus I")
 ```
 """
-mutable struct Course
+mutable struct Course <: AbstractCourse
     id::Int                             # Unique course id
     vertex_id::Dict{Int, Int}           # The vertex id of the course w/in a curriculum graph, stored as 
                                         # (curriculum_id, vertex_id)
@@ -70,6 +74,46 @@ mutable struct Course
     end
 end
 
+mutable struct CourseCollection <: AbstractCourse
+    id::Int                             # Unique course id
+    vertex_id::Dict{Int, Int}           # The vertex id of the course w/in a curriculum graph, stored as 
+                                        # (curriculum_id, vertex_id)
+    courses::Array{Course}              # Courses associated with the collection                                   
+    name::AbstractString                # Name of the course, e.g., Introduction to Psychology
+    credit_hours::Real                  # Number of credit hours associated with a "typcial" course in the collection
+    institution::AbstractString         # Institution offering the course
+    college::AbstractString             # College or school (within the institution) offering the course
+    department::AbstractString          # Department (within the school or college) offering the course
+    canonical_name::AbstractString      # Standard name used to denote the course collection, e.g., math genearl education 
+    requisites::Dict{Int, Requisite}    # List of requisites, in (requisite_course id, requisite_type) format
+    metrics::Dict{String, Any}          # Course-related metrics
+    metadata::Dict{String, Any}         # Course-related metadata
+
+    # Constructor
+    function CourseCollection(name::AbstractString, credit_hours::Real, courses::Array{Course,1}; institution::AbstractString="", 
+         college::AbstractString="", department::AbstractString="", canonical_name::AbstractString="", id::Int=0)
+        this = new()
+        this.name = name
+        this.credit_hours = credit_hours
+        this.courses = courses
+        this.institution = institution
+        if id == 0
+            this.id = mod(hash(this.name * this.institution * string(length(courses))), UInt32)
+        else 
+            this.id = id
+        end
+        this.college = college
+        this.department = department
+        this.canonical_name = canonical_name
+        this.requisites = Dict{Int, Requisite}()
+        #this.requisite_formula
+        this.metrics = Dict{String, Any}()
+        this.metadata = Dict{String, Any}()
+        this.vertex_id = Dict{Int, Int}()       # curriculum id -> vertex id
+        return this
+    end
+end
+
 function course_id(prefix::AbstractString, num::AbstractString, name::AbstractString, institution::AbstractString)
     convert(Int, mod(hash(name * prefix * num * institution), UInt32))
 end
@@ -85,7 +129,7 @@ One of the following requisite types must be specified for `rc`:
 - `co`  : a co-requisite course that may be taken before or at the same time as `tc`.
 - `strict_co` : a strict co-requisite course that must be taken at the same time as `tc`.
 """
-function add_requisite!(requisite_course::Course, course::Course, requisite_type::Requisite)
+function add_requisite!(requisite_course::AbstractCourse, course::AbstractCourse, requisite_type::Requisite)
     course.requisites[requisite_course.id] = requisite_type
 end
 
@@ -100,7 +144,7 @@ The following requisite types may be specified for `rc`:
 - `co`  : a co-requisite course that may be taken before or at the same time as `tc`.
 - `strict_co` : a strict co-requisite course that must be taken at the same time as `tc`.
 """
-function add_requisite!(requisite_courses::Array{Course}, course::Course, requisite_types::Array{Requisite})
+function add_requisite!(requisite_courses::Array{AbstractCourse}, course::AbstractCourse, requisite_types::Array{Requisite})
     @assert length(requisite_courses) == length(requisite_types)
     for i = 1:length(requisite_courses)
         course.requisites[requisite_courses[i].id] = requisite_types[i]
@@ -119,7 +163,7 @@ The following requisite types may be specified for `rc`:
 - `co`  : a co-requisite course that may be taken before or at the same time as `tc`.
 - `strict_co` : a strict co-requisite course that must be taken at the same time as `tc`.
 """
-function delete_requisite!(requisite_course::Course, course::Course)
+function delete_requisite!(requisite_course::AbstractCourse, course::AbstractCourse)
     #if !haskey(course.requisites, requisite_course.id)  
     #    error("The requisite you are trying to delete does not exist")
     #end

src/DataTypes/Curriculum.jl

@@ -33,7 +33,7 @@ mutable struct Curriculum
     degree_type::Degree                 # Type of degree_type
     system_type::System                 # Semester or quarter system
     CIP::AbstractString                 # CIP code associated with the curriculum
-    courses::Array{Course}              # Array of required courses in curriculum
+    courses::Array{AbstractCourse}              # Array of required courses in curriculum
     num_courses::Int                    # Number of required courses in curriculum
     credit_hours::Real                  # Total number of credit hours in required curriculum
     graph::SimpleDiGraph{Int}           # Directed graph representation of pre-/co-requisite structure
@@ -43,7 +43,7 @@ mutable struct Curriculum
     metadata::Dict{String, Any}         # Curriculum-related metadata
 
     # Constructor
-    function Curriculum(name::AbstractString, courses::Array{Course}; learning_outcomes::Array{LearningOutcome}=Array{LearningOutcome,1}(),
+    function Curriculum(name::AbstractString, courses::Array{AbstractCourse}; learning_outcomes::Array{LearningOutcome}=Array{LearningOutcome,1}(),
                         degree_type::Degree=BS, system_type::System=semester, institution::AbstractString="", CIP::AbstractString="", 
                         id::Int=0, sortby_ID::Bool=true)
         this = new()
@@ -76,13 +76,37 @@ mutable struct Curriculum
         end
         return this
     end
+
+    function Curriculum(name::AbstractString, courses::Array{Course}; learning_outcomes::Array{LearningOutcome}=Array{LearningOutcome,1}(),
+        degree_type::Degree=BS, system_type::System=semester, institution::AbstractString="", CIP::AbstractString="", 
+        id::Int=0, sortby_ID::Bool=true)
+        Curriculum(name, convert(Array{AbstractCourse},courses), learning_outcomes=learning_outcomes, degree_type=degree_type, 
+              system_type=system_type, institution=institution, CIP=CIP, id=id, sortby_ID=sortby_ID)
+    end
 end
 
 # TODO: update a curriculum graph if requisites have been added/removed or courses have been added/removed
 #function update_curriculum(curriculum::Curriculum, courses::Array{Course}=())
 #    # if courses array is empty, no new courses were added
 #end
 
+# Converts course ids, from those used in CSV file format, to the standard hashed id used by the data structures in the toolbox
+function convert_ids(curriculum::Curriculum)
+    for c1 in curriculum.courses
+        old_id = c1.id
+        c1.id = mod(hash(c1.name * c1.prefix * c1.num * c1.institution), UInt32)
+        if old_id != c1.id 
+            for c2 in curriculum.courses
+                if old_id in keys(c2.requisites)
+                    add_requisite!(c1, c2, c2.requisites[old_id])
+                    delete!(c2.requisites, old_id)
+                end
+            end
+        end
+    end
+    return curriculum
+end
+
 # Map course IDs to vertex IDs in an underlying curriculum graph.
 function map_vertex_ids(curriculum::Curriculum)
     mapped_ids = Dict{Int, Int}()
@@ -92,6 +116,16 @@ function map_vertex_ids(curriculum::Curriculum)
     return mapped_ids
 end
 
+# Compute the hash value used to create the id for a course, and return the course if it exists in the curriculum supplied as input
+function course(curric::Curriculum, prefix::AbstractString, num::AbstractString, name::AbstractString, institution::AbstractString)
+    hash_val = mod(hash(name * prefix * num * institution), UInt32)
+    if hash_val in collect(c.id for c in curric.courses)
+        return curric.courses[findfirst(x->x.id==hash_val, curric.courses)]
+    else
+        error("Course: $prefix $num: $name at $institution does not exist in curriculum: $(curric.name)")
+    end
+end
+
 # Return the course associated with a course id in a curriculum
 function course_from_id(curriculum::Curriculum, id::Int)
     for c in curriculum.courses