bundle updates: add build step for conda R packages & mv competitors …

…to paper repo (https://github.com/szcf-weiya/paper_Monotone-Cubic-B-Splines) & rm unused functions

.github/workflows/ci.yml

@@ -30,10 +30,7 @@ jobs:
           options(repos=r)
           install.packages("fda")
           install.packages("lsei")
-          install.packages("Iso")
-          install.packages("cobs")
           install.packages("splines")
-          install.packages("monmlp")
         shell: sudo Rscript {0}
 
       - uses: julia-actions/setup-julia@latest

.gitignore

@@ -5,4 +5,5 @@ Manifest.toml
 *.sil
 *.png
 docs/build
-docs/src/examples
+docs/src/examples
+*.log

Project.toml

@@ -1,10 +1,11 @@
 name = "MonotoneSplines"
 uuid = "92812004-5f8d-4354-96af-0c8b7c0637d0"
 authors = ["szcf-weiya <[email protected]>"]
-version = "0.1.0"
+version = "0.1.1"
 
 [deps]
 BSON = "fbb218c0-5317-5bc6-957e-2ee96dd4b1f0"
+Conda = "8f4d0f93-b110-5947-807f-2305c1781a2d"
 ECOS = "e2685f51-7e38-5353-a97d-a921fd2c8199"
 Flux = "587475ba-b771-5e3f-ad9e-33799f191a9c"
 JuMP = "4076af6c-e467-56ae-b986-b466b2749572"
@@ -19,6 +20,7 @@ Zygote = "e88e6eb3-aa80-5325-afca-941959d7151f"
 
 [compat]
 BSON = "0.3"
+Conda = "1.4"
 ECOS = "1.1"
 Flux = "0.13"
 JuMP = "1.3"

README.md

@@ -8,16 +8,20 @@
 
 Check the following paper for more details.
 
-> Wang, L., Fan, X., Li, H., & Liu, J. S. (2023). Monotone Cubic B-Splines (arXiv:2307.01748). arXiv. https://doi.org/10.48550/arXiv.2307.01748
+> Wang, Lijun, Xiaodan Fan, Huabai Li, and Jun S. Liu. “Monotone Cubic B-Splines with a Neural-Network Generator.” arXiv, November 17, 2023. https://doi.org/10.48550/arXiv.2307.01748.
 
 ```
-@misc{wang2023monotone,
-      title={Monotone Cubic B-Splines}, 
-      author={Lijun Wang and Xiaodan Fan and Huabai Li and Jun S. Liu},
-      year={2023},
-      eprint={2307.01748},
-      archivePrefix={arXiv},
-      primaryClass={stat.ME}
+@online{wangMonotoneCubicBSplines2023c,
+  title = {Monotone {{Cubic B-Splines}} with a {{Neural-Network Generator}}},
+  author = {Wang, Lijun and Fan, Xiaodan and Li, Huabai and Liu, Jun S.},
+  date = {2023-11-17},
+  eprint = {2307.01748},
+  eprinttype = {arxiv},
+  eprintclass = {astro-ph, stat},
+  doi = {10.48550/arXiv.2307.01748},
+  url = {http://arxiv.org/abs/2307.01748},
+  urldate = {2023-11-20},
+  pubstate = {preprint}
 }
 ```
 
@@ -41,8 +45,6 @@ julia> ]
 (@v1.8) pkg> add MonotoneSplines
 ```
 
-
-
 By default, both `PyCall.jl` and `RCall.jl` would try to use the system Python and R, respectively (more details can be found in their repos). 
 
 ### :ladder: standalone R and Python via Conda.jl
@@ -56,6 +58,8 @@ julia> ]
 (@v1.8) pkg> add MonotoneSplines
 ```
 
+If you use the standalone R provided by Conda in Julia, the dependent R packages will be automatically installed during the building step.
+
 ## :books: Documentation
 
 The documentation <https://hohoweiya.xyz/MonotoneSplines.jl/stable/> elaborates on the usage of the package via various simulation examples and an interesting astrophysics application.

deps/build.jl

@@ -0,0 +1,27 @@
+Rhome = get(ENV, "R_HOME", "")
+if Rhome == "*"
+    try
+        import Conda
+        # If using Conda's R, install R package automatically.
+        Conda.add("r-fda")
+        Conda.add("r-splines")
+        Conda.add("r-lsei")
+        @info "R packages are installed successfully."
+    catch e
+        @warn """
+        Fail to automatically install dependent R packages in Conda due to $e. 
+        
+        Please fix the error message first and then reinstall via
+
+        ```julia
+        Conda.add("r-fda")
+        Conda.add("r-splines")
+        Conda.add("r-lsei")
+        ```
+        
+        Alternatively, you can consider using system R, and install the packages via the standard way `install.packages(..)`
+        """
+    end
+else
+    @info "You are not using Conda's R, please install R packages by yourself."
+end

src/MonotoneSplines.jl

@@ -28,16 +28,8 @@ _runtime_init() = @eval begin
     copy!(_py_boot, PyCall.pyimport("boot"))    
 end
 
-function __init__()
-    nothing
-end
-
-export check_CI,
-       check_acc,
-        cubic,
-        logit,
-        logit5,
-        sinhalfpi,
+export  check_CI,
+        check_acc,
         smooth_spline,
         mono_cs,
         mono_ss,

src/boot.jl

@@ -7,12 +7,6 @@ using BSON
 using Zygote
 using ProgressMeter
 
-## determine functions formally (NB: Be better not to change the name)
-cubic(x) = x^3
-logit(x) = 1/(1+exp(-x))
-logit5(x) = 1/(1+exp(-5x))
-sinhalfpi(x) = sin(pi/2 * x)
-
 """
     check_CI(; <keyword arguments>)
 

test/runtests.jl

@@ -101,13 +101,6 @@ end
     @test MonotoneSplines.conf_band_width([0 1; 0 3]) ≈ 2.0
 end
 
-@testset "example functions" begin
-    @test isa(cubic, Function)
-    @test isa(logit, Function)
-    @test isa(logit5, Function)
-    @test isa(sinhalfpi, Function)
-end
-
 R"""
 recover.Sigma <- function(Sigma) {
     n = length(Sigma)