rename to CICOBase

insysbio · Feb 12, 2025 · 839236a · 839236a
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diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -64,8 +64,8 @@ jobs:
       - run: |
           julia --project=docs -e '
             using Documenter: doctest
-            using CICOCore
-            doctest(CICOCore)' # change MYPACKAGE to the name of your package
+            using CICOBase
+            doctest(CICOBase)' # change MYPACKAGE to the name of your package
       - run: julia --project=docs docs/make.jl
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
diff --git a/Project.toml b/Project.toml
@@ -1,10 +1,10 @@
-name = "CICOCore"
+name = "CICOBase"
 uuid = "33444335-3134-4342-4659-594331344435"
 keywords = ["package", "identifiability", "modeling"]
 license = "MIT"
 desc = "practical identifiability analysis and confidence intervals evaluation"
 authors = ["borisov <[email protected]>", "metelkin <[email protected]>"]
-repo-url = "https://github.com/insysbio/CICOCore.jl"
+repo-url = "https://github.com/insysbio/CICOBase.jl"
 version = "0.5.2"
 
 [deps]

diff --git a/README.md b/README.md
@@ -1,15 +1,15 @@
 # CICO - Confidence Intervals by Constrained Optimization
 
-[![Documentation](https://img.shields.io/badge/docs-latest-blue.svg)](https://insysbio.github.io/CICOCore.jl/latest)
-[![Build status](https://github.com/insysbio/CICOCore.jl/workflows/CI/badge.svg)](https://github.com/insysbio/CICOCore.jl/actions?query=workflow%3ACI)
-[![Coverage Status](https://coveralls.io/repos/github/insysbio/CICOCore.jl/badge.svg?branch=master)](https://coveralls.io/github/insysbio/CICOCore.jl?branch=master)
-[![version](https://juliahub.com/docs/General/CICOCore/stable/version.svg)](https://juliahub.com/ui/Packages/General/CICOCore)
-[![GitHub license](https://img.shields.io/github/license/insysbio/CICOCore.jl.svg)](https://github.com/insysbio/CICOCore.jl/blob/master/LICENSE)
+[![Documentation](https://img.shields.io/badge/docs-latest-blue.svg)](https://insysbio.github.io/CICOBase.jl/latest)
+[![Build status](https://github.com/insysbio/CICOBase.jl/workflows/CI/badge.svg)](https://github.com/insysbio/CICOBase.jl/actions?query=workflow%3ACI)
+[![Coverage Status](https://coveralls.io/repos/github/insysbio/CICOBase.jl/badge.svg?branch=master)](https://coveralls.io/github/insysbio/CICOBase.jl?branch=master)
+[![version](https://juliahub.com/docs/General/CICOBase/stable/version.svg)](https://juliahub.com/ui/Packages/General/CICOBase)
+[![GitHub license](https://img.shields.io/github/license/insysbio/CICOBase.jl.svg)](https://github.com/insysbio/CICOBase.jl/blob/master/LICENSE)
 [![DOI:10.1371/journal.pcbi.1008495](https://zenodo.org/badge/DOI/10.1371/journal.pcbi.1008495.svg)](https://doi.org/10.1371/journal.pcbi.1008495)
 
-**CICOCore** is a [Julia language](https://julialang.org/downloads/) package for [identifiability analysis](https://en.wikipedia.org/wiki/Identifiability_analysis) and confidence intervals estimation.
+**CICOBase** is a [Julia language](https://julialang.org/downloads/) package for [identifiability analysis](https://en.wikipedia.org/wiki/Identifiability_analysis) and confidence intervals estimation.
 
-See [documentation](https://insysbio.github.io/CICOCore.jl/latest/).
+See [documentation](https://insysbio.github.io/CICOBase.jl/latest/).
 
 ## Use cases
 Notebooks with use cases can be found in a separate repository: <https://github.com/insysbio/likelihoodprofiler-cases>
@@ -29,13 +29,13 @@ Notebooks with use cases can be found in a separate repository: <https://github.
 ```julia
 julia> ]
 
-(v1.9) pkg> add CICOCore
+(v1.9) pkg> add CICOBase
 ```
 
 ## Quick start
 
 ```julia
-using CICOCore
+using CICOBase
 
 # testing profile function
 f(x) = 5.0 + (x[1]-3.0)^2 + (x[1]-x[2]-1.0)^2 + 0*x[3]^2

diff --git a/docs/make.jl b/docs/make.jl
@@ -1,10 +1,10 @@
 
-using CICOCore
+using CICOBase
 using Documenter
 
 makedocs(
-    modules = [CICOCore],
-    sitename = "CICOCore Documentation",
+    modules = [CICOBase],
+    sitename = "CICOBase Documentation",
     pages = [
         "Home" => "index.md",
         "Methods" => "methods.md",
@@ -16,7 +16,7 @@ makedocs(
 
 
 deploydocs(
-    repo   = "github.com/insysbio/CICOCore.jl.git",
+    repo   = "github.com/insysbio/CICOBase.jl.git",
     devbranch="master",
     devurl = "latest",
 )
diff --git a/docs/mkdocs.yml b/docs/mkdocs.yml
@@ -1,5 +1,5 @@
-site_name:        CICOCore.jl
-repo_url:         https://github.com/insysbio/CICOCore.jl
+site_name:        CICOBase.jl
+repo_url:         https://github.com/insysbio/CICOBase.jl
 site_description: A Julia package for identifiability analysis and confidence intervals estimation.
 site_author:      InSysBio
 

diff --git a/docs/src/api.md b/docs/src/api.md
@@ -3,6 +3,6 @@
 The package exports the following functions for **parameters identifiability analysis**, **confidence intervals evaluation** and **results visualization**.
 
 ```@autodocs
-Modules = [CICOCore]
+Modules = [CICOBase]
 Order   = [:function, :type, :module]
 ```
diff --git a/docs/src/index.md b/docs/src/index.md
@@ -1,6 +1,6 @@
 # Overview
 
-**CICOCore** is a [Julia](https://julialang.org/downloads/) package for **identifiability analysis** and **confidence intervals** estimation.
+**CICOBase** is a [Julia](https://julialang.org/downloads/) package for **identifiability analysis** and **confidence intervals** estimation.
 
 ## Use cases
 Notebooks with use cases can be found in a separate repository: <https://github.com/insysbio/likelihoodprofiler-cases>
@@ -19,13 +19,13 @@ Notebooks with use cases can be found in a separate repository: <https://github.
 ```julia
 julia> ]
 
-(v1.9) pkg> add CICOCore
+(v1.9) pkg> add CICOBase
 ```
 
 ## Quick start
 
 ```julia
-using CICOCore
+using CICOBase
 
 # testing profile function
 f(x) = 5.0 + (x[1]-3.0)^2 + (x[1]-x[2]-1.0)^2 + 0*x[3]^2
@@ -46,11 +46,11 @@ plotly()
 plot(res_1)
 ```
 
-![plot_lin](https://github.com/insysbio/CICOCore.jl/blob/master/img/plot_lin.png?raw=true)
+![plot_lin](https://github.com/insysbio/CICOBase.jl/blob/master/img/plot_lin.png?raw=true)
 
 ## Intro
 
-The reliability and predictability of a **kinetic systems biology (SB) and systems pharmacology (SP) model** depends on the calibration of model parameters. Experimental data can be insufficient to determine all the parameters unambiguously. This results in "non-identifiable" parameters and parameters identifiable within confidence intervals (CIs). The algorithms included in **CICOCore** implement Profile Likelihood (PL) [2] method for parameters identification and can be applied to complex SB models. The results of the algorithms can be used to qualify and calibrate parameters or to reduce the model.
+The reliability and predictability of a **kinetic systems biology (SB) and systems pharmacology (SP) model** depends on the calibration of model parameters. Experimental data can be insufficient to determine all the parameters unambiguously. This results in "non-identifiable" parameters and parameters identifiable within confidence intervals (CIs). The algorithms included in **CICOBase** implement Profile Likelihood (PL) [2] method for parameters identification and can be applied to complex SB models. The results of the algorithms can be used to qualify and calibrate parameters or to reduce the model.
 
 ## Objective
 

diff --git a/docs/src/methods.md b/docs/src/methods.md
@@ -1,6 +1,6 @@
 # Methods
 
- Three methods implemented in **CICOCore** package: `:CICO_ONE_PASS`,
+ Three methods implemented in **CICOBase** package: `:CICO_ONE_PASS`,
  `:LIN_EXTRAPOL`,
  `:QUADR_EXTRAPOL`.
 

diff --git a/docs/src/optimizers.md b/docs/src/optimizers.md
@@ -1,8 +1,8 @@
 # Note on optimizers
 
-Currently **CICOCore** relies on [`NLopt`](https://nlopt.readthedocs.io/en/latest/). 
+Currently **CICOBase** relies on [`NLopt`](https://nlopt.readthedocs.io/en/latest/). 
 
-Internally **CICOCore** utilizes `:LN_AUGLAG` algorithm from **NLopt** to construct an augmented objective function with a set of bound constrains. Then the augmented objective function is passed to an optimization algorithm, which is defined by the keyword argument `local_alg` (see [`CICOCore.get_interval`](@ref)).
+Internally **CICOBase** utilizes `:LN_AUGLAG` algorithm from **NLopt** to construct an augmented objective function with a set of bound constrains. Then the augmented objective function is passed to an optimization algorithm, which is defined by the keyword argument `local_alg` (see [`CICOBase.get_interval`](@ref)).
 
 Default `local_alg` = `:LN_NELDERMEAD`, which is the most reliable for the current problem among the derivative-free algorithms. 
 Any [`NLopt`](https://nlopt.readthedocs.io/en/latest/NLopt_Algorithms/) algorithm could be potentially used as `local_alg`.

diff --git a/docs/src/visualization.md b/docs/src/visualization.md
@@ -1,15 +1,15 @@
 # Visualization
 
-[`CICOCore.get_interval`](@ref) function returns estimated
+[`CICOBase.get_interval`](@ref) function returns estimated
 confidence interval along with other data as
-[`CICOCore.ParamInterval`](@ref) structure.
+[`CICOBase.ParamInterval`](@ref) structure.
 
-**CICOCore** provides a `@recipe` for **Plots.jl** to visualize
+**CICOBase** provides a `@recipe` for **Plots.jl** to visualize
 confidence interval estimation and plot parameter's profile based on
-[`CICOCore.ParamInterval`](@ref).
+[`CICOBase.ParamInterval`](@ref).
 
 ```
-using CICOCore
+using CICOBase
 
 # Likelihood function
 f(x) = 5.0 + (x[1]-3.0)^2 + (x[1]-x[2]-1.0)^2 + 0*x[3]^2
@@ -30,14 +30,14 @@ plotly()
 plot(res[2])
 ```
 
-![](https://github.com/insysbio/CICOCore.jl/blob/master/img/plot_cico.png?raw=true)
+![](https://github.com/insysbio/CICOBase.jl/blob/master/img/plot_cico.png?raw=true)
 
-To make a smooth plot one can compute more profile points with [`CICOCore.update_profile_points!`](@ref) which internally uses [`PlotUtils.adapted_grid`](https://github.com/JuliaPlots/PlotUtils.jl/blob/master/src/adapted_grid.jl)
+To make a smooth plot one can compute more profile points with [`CICOBase.update_profile_points!`](@ref) which internally uses [`PlotUtils.adapted_grid`](https://github.com/JuliaPlots/PlotUtils.jl/blob/master/src/adapted_grid.jl)
 
 ```
 update_profile_points!(res[2])
 
 plot(res[2])
 ```
 
-![](https://github.com/insysbio/CICOCore.jl/blob/master/img/plot_cico_smooth.png?raw=true)
+![](https://github.com/insysbio/CICOBase.jl/blob/master/img/plot_cico_smooth.png?raw=true)
diff --git a/src/CICOCore.jl → src/CICOBase.jl b/src/CICOCore.jl → src/CICOBase.jl
@@ -1,6 +1,6 @@
 #__precompile__(false)
 """
-Main module for `CICOCore.jl`.
+Main module for `CICOBase.jl`.
 
 Four functions are exported from this module for public use:
 
@@ -10,7 +10,7 @@ Four functions are exported from this module for public use:
 - [`update_profile_points!`](@ref). Updates confidence interval with likelihood profile points.
 
 """
-module CICOCore
+module CICOBase
 
 using NLopt, ForwardDiff
 using Calculus

diff --git a/test/runtests.jl b/test/runtests.jl
@@ -2,7 +2,7 @@
 # Pkg.add("NLopt")
 # Pkg.add("RecipesBase")
 
-using CICOCore, Test
+using CICOBase, Test
 using NLopt
 
 NLopt.srand(12345)

diff --git a/test/test_deriv_free_algs.jl b/test/test_deriv_free_algs.jl
@@ -1,6 +1,6 @@
 ### Derivative free optimization tests
 
-using CICOCore
+using CICOBase
 
 # The following NLopt derivative-free algorithms are compared
 dfo_algorithms = [

diff --git a/test/test_get_optimal.jl b/test/test_get_optimal.jl
@@ -1,6 +1,6 @@
 # tests for `get_optimal` method
 # testing only the case f_2p
-# using CICOCore
+# using CICOBase
 
 @testset "testing get_optimal() for :LN_PRAXIS and f_2p, identifiable" begin
     res0 = get_optimal(

diff --git a/test/test_loss_error.jl b/test/test_loss_error.jl
@@ -28,7 +28,7 @@ end
 
 @testset "test profile error" begin
     err_func = err_fun_generate()
-    prof = CICOCore._profile(
+    prof = CICOBase._profile(
         [3., 4.],
         1,
         err_func

diff --git a/test/test_noderiv.jl b/test/test_noderiv.jl
@@ -1,4 +1,4 @@
-using CICOCore, Plots
+using CICOBase, Plots
 
 # functions with zero derivative at one of the endpoints
 f1(x) = 3x[1]^4 - 6x[1]^3 + 5

diff --git a/test/test_plots.jl b/test/test_plots.jl
@@ -14,7 +14,7 @@ using Plots
         silent = true
     ) for i in 1:3]
     update_profile_points!(res0[1]; max_recursions=1)
-    a_grid_1 = CICOCore.get_grid(res0[1])
+    a_grid_1 = CICOBase.get_grid(res0[1])
     @test length(a_grid_1[2]) > 0
     p = plot(res0[1])
     @test p isa Plots.Plot

diff --git a/test/test_profile.jl b/test/test_profile.jl
@@ -1,5 +1,5 @@
 @testset "profile" begin
-    prof = CICOCore._profile(
+    prof = CICOBase._profile(
         [3., 2., 2.1],
         1,
         f_3p_1im_dep;