CompatHelper: bump compat for Convex to 0.15, (keep existing compat)

.github/workflows/CompatHelper.yml

@@ -3,16 +3,35 @@ on:
   schedule:
     - cron: 0 0 * * *
   workflow_dispatch:
+permissions:
+  contents: write
+  pull-requests: write
 jobs:
   CompatHelper:
     runs-on: ubuntu-latest
     steps:
+      - name: Check if Julia is already available in the PATH
+        id: julia_in_path
+        run: which julia
+        continue-on-error: true
+      - name: Install Julia, but only if it is not already available in the PATH
+        uses: julia-actions/setup-julia@v1
+        with:
+          version: '1'
+          arch: ${{ runner.arch }}
+        if: steps.julia_in_path.outcome != 'success'
+      - name: "Add the General registry via Git"
+        run: |
+          import Pkg
+          ENV["JULIA_PKG_SERVER"] = ""
+          Pkg.Registry.add("General")
+        shell: julia --color=yes {0}
       - name: "Install CompatHelper"
         run: |
           import Pkg
           name = "CompatHelper"
           uuid = "aa819f21-2bde-4658-8897-bab36330d9b7"
-          version = "2"
+          version = "3"
           Pkg.add(; name, uuid, version)
         shell: julia --color=yes {0}
       - name: "Run CompatHelper"
@@ -23,4 +42,4 @@ jobs:
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
           COMPATHELPER_PRIV: ${{ secrets.DOCUMENTER_KEY }}
-          # COMPATHELPER_PRIV: ${{ secrets.COMPATHELPER_PRIV }}
+          # COMPATHELPER_PRIV: ${{ secrets.COMPATHELPER_PRIV }}

.github/workflows/TagBot.yml

@@ -4,6 +4,11 @@ on:
     types:
       - created
   workflow_dispatch:
+    inputs:
+      lookback:
+        default: 3
+permissions:
+  contents: write
 jobs:
   TagBot:
     if: github.event_name == 'workflow_dispatch' || github.actor == 'JuliaTagBot'

Project.toml

@@ -21,7 +21,7 @@ ToeplitzMatrices = "c751599d-da0a-543b-9d20-d0a503d91d24"
 
 [compat]
 BenchmarkTools = "1"
-Convex = "0.14"
+Convex = "0.14, 0.15"
 DataFrames = "1"
 Distributions = "0.25"
 FFTW = "1"
@@ -32,7 +32,7 @@ MathProgBase = "0.7"
 RDatasets = "0.7"
 Reexport = "1.2"
 SpecialFunctions = "2.1"
-StatsFuns = "0.9"
+StatsFuns = "0.9, 1"
 ToeplitzMatrices = "0.7"
 julia = "1.6"
 

README.md

@@ -15,7 +15,15 @@ pkg"add QuasiCopula"
 ```
 
 ## Citation
+The manuscript for `QuasiCopula.jl` is available on [arXiv](https://arxiv.org/abs/2205.03505).
 
-If you use [OpenMendel](https://openmendel.github.io) analysis packages in your research, please cite the following reference in the resulting publications:
+*A Flexible Quasi-Copula Distribution for Statistical Modeling. Ji SS, Chu BB, Sinsheimer JS, Zhou H, Lange K. arXiv preprint arXiv:2205.03505. 2022 May 6.*
+
+If you use other [OpenMendel](https://openmendel.github.io) analysis packages in your research, please cite the following reference in the resulting publications:
+
+*Zhou H, Sinsheimer JS, Bates DM, Chu BB, German CA, Ji SS, Keys KL, Kim J, Ko S, Mosher GD, Papp JC, Sobel EM, Zhai J, Zhou JJ, Lange K. OPENMENDEL: a cooperative programming project for statistical genetics. Hum Genet. 2020 Jan;139(1):61-71. doi: 10.1007/s00439-019-02001-z. Epub 2019 Mar 26. PMID: 30915546; PMCID: [PMC6763373](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6763373/).*
+
+### Acknowledgments
+
+This project has been supported by the National Institutes of Health under awards R01GM053275, R01HG006139, R25GM103774, and 1R25HG011845.
 
-*OPENMENDEL: a cooperative programming project for statistical genetics. Zhou H, Sinsheimer JS, Bates DM, Chu BB, German CA, Ji SS, Keys KL, Kim J, Ko S, Mosher GD, Papp JC, Sobel EM, Zhai J, Zhou JJ, Lange K. Hum Genet. 139, 61–71 (2020). [doi:10.1007/s00439-019-02001-z](10.1007/s00439-019-02001-z). PMID: 30915546*