Browse Source

Removed unneeded dependencies

pull/150/head
Micah Halter 3 years ago
parent
commit
f727db9b2e
  1. 1
      .gitignore
  2. 2
      Project.toml
  3. 19
      REQUIRE
  4. 15
      examples/odegraft.jl
  5. 27
      test/Project.toml

1
.gitignore vendored

@ -1,3 +1,4 @@ @@ -1,3 +1,4 @@
Manifest.toml
*.jl.cov
*.jl.*.cov
*.jl.mem

2
Project.toml

@ -9,8 +9,6 @@ Cassette = "7057c7e9-c182-5462-911a-8362d720325c" @@ -9,8 +9,6 @@ Cassette = "7057c7e9-c182-5462-911a-8362d720325c"
Colors = "5ae59095-9a9b-59fe-a467-6f913c188581"
DataFrames = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0"
DataFramesMeta = "1313f7d8-7da2-5740-9ea0-a2ca25f37964"
DiffEqBase = "2b5f629d-d688-5b77-993f-72d75c75574e"
DifferentialEquations = "0c46a032-eb83-5123-abaf-570d42b7fbaa"
Distributions = "31c24e10-a181-5473-b8eb-7969acd0382f"
Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
GLM = "38e38edf-8417-5370-95a0-9cbb8c7f171a"

19
REQUIRE

@ -1,10 +1,19 @@ @@ -1,10 +1,19 @@
Test
Unitful
DiffEqBase
DifferentialEquations
CSV
Cassette
Colors
DataFrames
DataFramesMeta
Distributions
Documenter
GLM
GraphDataFrameBridge
JSON
Latexify
LightGraphs
LinearAlgebra
Logging
MetaGraphs
MetaGraphDataFrameBridge
Plots
Random
Test
Unitful

15
examples/odegraft.jl

@ -6,15 +6,22 @@ @@ -6,15 +6,22 @@
#
# This notebook is an example based on the SEIR model and the ScalingModel examples in the epirecipes cookbook.
# using DifferentialEquations
using Pkg
try
using DifferentialEquations
catch
Pkg.add("DifferentialEquations")
end
using DifferentialEquations
using SemanticModels.Parsers
using SemanticModels.ModelTools
using SemanticModels.ModelTools.ExpODEModels
# ## Loading the original model
# We use parsefile to load the model into an expression. The original model is an SEIR model which has 4 states suceptible, exposed, infected, and recovered. It has parameters $\beta, \gamma, \mu, \sigma$.
expr1 = parsefile("../examples/epicookbook/src/SEIRmodel.jl")
model1 = model(ExpODEProblem, expr1)
model1 = model(ExpODEModel, expr1)
module1 = eval(model1.expr)
@ -34,8 +41,8 @@ expr2 = parsefile("../examples/epicookbook/src/ScalingModel.jl") @@ -34,8 +41,8 @@ expr2 = parsefile("../examples/epicookbook/src/ScalingModel.jl")
# Once the ASTs are processed into a structured representation we can manipulate with regular julia code, we are able to write manipulations of the models that operate on a higher level than textual changes to the code.
model2 = model(ExpODEProblem, expr2)
fluxes(x::ExpODEProblem) = x.variables[1].flux
model2 = model(ExpODEModel, expr2)
fluxes(x::ExpODEModel) = x.variables[1].flux
# Find the expression we want to graft
# vital dynamics S rate expression

27
test/Project.toml

@ -0,0 +1,27 @@ @@ -0,0 +1,27 @@
name = "SemanticModels"
uuid = "88974b6f-63f0-5f7a-882c-b779d2960b8e"
authors = ["James Fairbanks <james.fairbanks@gtri.gatech.edu>"]
version = "0.1.1"
[deps]
CSV = "336ed68f-0bac-5ca0-87d4-7b16caf5d00b"
Cassette = "7057c7e9-c182-5462-911a-8362d720325c"
Colors = "5ae59095-9a9b-59fe-a467-6f913c188581"
DataFrames = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0"
DataFramesMeta = "1313f7d8-7da2-5740-9ea0-a2ca25f37964"
DiffEqBase = "2b5f629d-d688-5b77-993f-72d75c75574e"
DifferentialEquations = "0c46a032-eb83-5123-abaf-570d42b7fbaa"
Distributions = "31c24e10-a181-5473-b8eb-7969acd0382f"
Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
GLM = "38e38edf-8417-5370-95a0-9cbb8c7f171a"
GraphDataFrameBridge = "3c71623a-a715-5176-9801-629b201a4880"
JSON = "682c06a0-de6a-54ab-a142-c8b1cf79cde6"
Latexify = "23fbe1c1-3f47-55db-b15f-69d7ec21a316"
LightGraphs = "093fc24a-ae57-5d10-9952-331d41423f4d"
LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
Logging = "56ddb016-857b-54e1-b83d-db4d58db5568"
MetaGraphs = "626554b9-1ddb-594c-aa3c-2596fe9399a5"
Plots = "91a5bcdd-55d7-5caf-9e0b-520d859cae80"
Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
Unitful = "1986cc42-f94f-5a68-af5c-568840ba703d"
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