rename project and add license

.github/workflows/doc.yml

@@ -33,6 +33,6 @@ jobs:
       - run: |
           julia --project=docs -e '
             using Documenter: DocMeta, doctest
-            using CDGRN
-            DocMeta.setdocmeta!(CDGRN, :DocTestSetup, :(using CDGRN); recursive=true)
-            doctest(CDGRN)'
+            using CDGRNs
+            DocMeta.setdocmeta!(CDGRNs, :DocTestSetup, :(using CDGRNs); recursive=true)
+            doctest(CDGRNs)'

LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2022 Yueh-Hua Tu
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

Project.toml

@@ -1,4 +1,4 @@
-name = "CDGRN"
+name = "CDGRNs"
 uuid = "b97acbd9-7fbb-4cbc-bc29-58677f11bc5c"
 authors = ["Yueh-Hua Tu <a504082002@gmail.com>"]
 version = "0.0.1"

README.md

@@ -1,6 +1,6 @@
-# CDGRN.jl
+# CDGRNs.jl
 
-[![Stable](https://img.shields.io/badge/docs-stable-blue.svg)](https://yuehhua.github.io/CDGRN.jl/stable/)
-[![Dev](https://img.shields.io/badge/docs-dev-blue.svg)](https://yuehhua.github.io/CDGRN.jl/dev/)
-[![Build Status](https://github.com/yuehhua/CDGRN.jl/actions/workflows/CI.yml/badge.svg?branch=main)](https://github.com/yuehhua/CDGRN.jl/actions/workflows/CI.yml?query=branch%3Amain)
-[![Coverage](https://codecov.io/gh/yuehhua/CDGRN.jl/branch/main/graph/badge.svg)](https://codecov.io/gh/yuehhua/CDGRN.jl)
+[![Stable](https://img.shields.io/badge/docs-stable-blue.svg)](https://yuehhua.github.io/CDGRNs.jl/stable/)
+[![Dev](https://img.shields.io/badge/docs-dev-blue.svg)](https://yuehhua.github.io/CDGRNs.jl/dev/)
+[![Build Status](https://github.com/yuehhua/CDGRNs.jl/actions/workflows/test.yml/badge.svg?branch=main)](https://github.com/yuehhua/CDGRNs.jl/actions/workflows/test.yml?query=branch%3Amain)
+[![Coverage](https://codecov.io/gh/yuehhua/CDGRNs.jl/branch/main/graph/badge.svg)](https://codecov.io/gh/yuehhua/CDGRNs.jl)

docs/Project.toml

@@ -1,3 +1,3 @@
 [deps]
 Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
-CDGRN = "b97acbd9-7fbb-4cbc-bc29-58677f11bc5c"
+CDGRNs = "b97acbd9-7fbb-4cbc-bc29-58677f11bc5c"

docs/make.jl

@@ -1,16 +1,16 @@
-using CDGRN
+using CDGRNs
 using Documenter
 
-DocMeta.setdocmeta!(CDGRN, :DocTestSetup, :(using CDGRN); recursive=true)
+DocMeta.setdocmeta!(CDGRNs, :DocTestSetup, :(using CDGRNs); recursive=true)
 
 makedocs(;
-    modules=[CDGRN],
+    modules=[CDGRNs],
     authors="Yueh-Hua Tu",
-    repo="https://github.com/yuehhua/CDGRN.jl/blob/{commit}{path}#{line}",
-    sitename="CDGRN.jl",
+    repo="https://github.com/yuehhua/CDGRNs.jl/blob/{commit}{path}#{line}",
+    sitename="CDGRNs.jl",
     format=Documenter.HTML(;
         prettyurls=get(ENV, "CI", "false") == "true",
-        canonical="https://yuehhua.github.io/CDGRN.jl",
+        canonical="https://yuehhua.github.io/CDGRNs.jl",
         edit_link="main",
         assets=String[],
     ),
@@ -20,6 +20,6 @@ makedocs(;
 )
 
 deploydocs(;
-    repo="github.com/yuehhua/CDGRN.jl",
+    repo="github.com/yuehhua/CDGRNs.jl",
     devbranch="main",
 )

docs/src/index.md

@@ -1,14 +1,14 @@
 ```@meta
-CurrentModule = CDGRN
+CurrentModule = CDGRNs
 ```
 
-# CDGRN
+# CDGRNs
 
-Documentation for [CDGRN](https://github.com/yuehhua/CDGRN.jl).
+Documentation for [CDGRNs](https://github.com/yuehhua/CDGRNs.jl).
 
 ```@index
 ```
 
 ```@autodocs
-Modules = [CDGRN]
+Modules = [CDGRNs]
 ```

src/CDGRN.jl → src/CDGRNs.jl

@@ -1,4 +1,4 @@
-module CDGRN
+module CDGRNs
 
 using GaussianMixtures: GaussianMixture, size
 using LinearAlgebra

src/cdgrn.jl

@@ -2,7 +2,7 @@ function corr_table(pairs)
     # unit: component
     cor_pairs = map(x -> (tf=x[:tf_name], target=x[:gene_name], best_k=x[:best_k], corr=correlation(x[:model])), pairs)
     df = DataFrames.flatten(DataFrame(cor_pairs), :corr)
-    df.adjusted_corr = CDGRN.fisher_transform(df.corr)
+    df.adjusted_corr = CDGRNs.fisher_transform(df.corr)
     return df
 end
 

src/interface.jl

@@ -99,7 +99,7 @@ function test_cdf(ρ1, ρ2, condition1, condition2; step=0.1, plot_dir=nothing,
 end
 
 function save_cdgrn(filename, cdgrn, tfs, prof, cntx)
-    context_cor = CDGRN.cor(cdgrn, tfs, prof, cntx)
+    context_cor = CDGRNs.cor(cdgrn, tfs, prof, cntx)
     context_cor = context_cor[.!isnan.(context_cor.ρ), :]
     context_cor.reg_type = context_cor.ρ .> 0
     context_cor.reg_stng = abs.(context_cor.ρ)

test/mixture.jl

@@ -29,7 +29,7 @@ using GLM
     @test check_confint(model.models[2].β, stderror(model.models[2]), GLM.coef(model1_true)) | 
         check_confint(model.models[2].β, stderror(model.models[2]), GLM.coef(model2_true))
 
-    model = fit(MixtureRegression{2}, data.X, data.Y; max_iter=iter, init=()->CDGRN.random_init(k, 2n))
+    model = fit(MixtureRegression{2}, data.X, data.Y; max_iter=iter, init=()->CDGRNs.random_init(k, 2n))
     @test check_confint(model.models[1].β, stderror(model.models[1]), GLM.coef(model1_true)) | 
         check_confint(model.models[1].β, stderror(model.models[1]), GLM.coef(model2_true))
     @test check_confint(model.models[2].β, stderror(model.models[2]), GLM.coef(model1_true)) | 

test/runtests.jl

@@ -1,4 +1,4 @@
-using CDGRN
+using CDGRNs
 using DataFrames
 using CSV
 using SnowyOwl