diff --git a/.github/workflows/CompatHelper.yml b/.github/workflows/CompatHelper.yml index 7784f241..3dfba52e 100644 --- a/.github/workflows/CompatHelper.yml +++ b/.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 }} \ No newline at end of file diff --git a/.github/workflows/TagBot.yml b/.github/workflows/TagBot.yml index f49313b6..f3896111 100644 --- a/.github/workflows/TagBot.yml +++ b/.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' diff --git a/Project.toml b/Project.toml index 8d32363e..1b84759b 100644 --- a/Project.toml +++ b/Project.toml @@ -21,12 +21,12 @@ ToeplitzMatrices = "c751599d-da0a-543b-9d20-d0a503d91d24" [compat] BenchmarkTools = "1" -Convex = "0.14" +Convex = "0.14, 0.15" DataFrames = "1" Distributions = "0.25" FFTW = "1" GLM = "1" -Ipopt = "0.8" +Ipopt = "0.8, 1" LoopVectorization = "0.12" MathProgBase = "0.7" RDatasets = "0.7" diff --git a/README.md b/README.md index ff99c6e1..03a5ee7c 100644 --- a/README.md +++ b/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*