Merge branch 'master' of https://github.com/OpenMendel/VarianceComponentModels.jl

Author: kose-y

.github/workflows/CI.yml

@@ -18,6 +18,7 @@ jobs:
       fail-fast: false
       matrix:
         version:
+          - "1"
           - "1.6"
         os:
           - ubuntu-latest

.github/workflows/JuliaNightly.yml

@@ -0,0 +1,42 @@
+
+#source: https://github.com/invenia/PkgTemplates.jl/blob/master/.github/workflows/JuliaNightly.yml
+name: JuliaNightly
+# Nightly Scheduled Julia Nightly Run
+on:
+  schedule:
+    - cron: '0 2 * * *'  # Daily at 2 AM UTC (8 PM CST)
+jobs:
+  test:
+    name: Julia Nightly - Ubuntu - x64
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        os:
+          - ubuntu-latest
+          - macOS-latest
+          - windows-latest
+        arch:
+          - x64
+    steps:
+      - uses: actions/checkout@v2
+      - uses: julia-actions/setup-julia@v1
+        with:
+          version: nightly
+      - uses: actions/cache@v2
+        env:
+          cache-name: julia-nightly-cache-artifacts
+        with:
+          path: ~/.julia/artifacts
+          key: ${{ env.cache-name }}-${{ hashFiles('**/Project.toml') }}
+          restore-keys: |
+            ${{ env.cache-name }}-
+      - uses: julia-actions/julia-buildpkg@latest
+      - run: |
+          git config --global user.name Tester
+          git config --global user.email te@st.er
+      - uses: julia-actions/julia-runtest@latest
+      - uses: julia-actions/julia-processcoverage@v1
+      - uses: codecov/codecov-action@v1
+        with:
+          file: lcov.info

.github/workflows/TagBot.yml

@@ -0,0 +1,15 @@
+name: TagBot
+on:
+  issue_comment:
+    types:
+      - created
+  workflow_dispatch:
+jobs:
+  TagBot:
+    if: github.event_name == 'workflow_dispatch' || github.actor == 'JuliaTagBot'
+    runs-on: ubuntu-latest
+    steps:
+      - uses: JuliaRegistries/TagBot@v1
+        with:
+          token: ${{ secrets.GITHUB_TOKEN }}
+          ssh: ${{ secrets.DOCUMENTER_KEY }}

Project.toml

@@ -2,7 +2,7 @@ name = "VarianceComponentModels"
 uuid = "813005db-34b4-5f71-be9e-1bbf0a1d8f1c"
 keywords = ["variance components model", "GWAS"]
 author = ["Hua Zhou <huazhou@ucla.edu>", "OpenMendel Team"]
-version = "0.1.1"
+version = "0.1.3"
 
 [deps]
 Ipopt = "b6b21f68-93f8-5de0-b562-5493be1d77c9"
@@ -13,8 +13,9 @@ SparseArrays = "2f01184e-e22b-5df5-ae63-d93ebab69eaf"
 Statistics = "10745b16-79ce-11e8-11f9-7d13ad32a3b2"
 
 [compat]
-Ipopt = "0.6.5 - 0.7"
+Ipopt = "0.6.5 - 0.7, 0.8"
 MathProgBase = "0.7"
+julia = "1.6"
 
 [extras]
 Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"

README.md

@@ -12,22 +12,19 @@ This package requires Julia v0.7.0 or later, which can be obtained from
 https://julialang.org/downloads/ or by building Julia from the sources in the
 https://github.com/JuliaLang/julia repository.
 
-The package has not yet been registered and must be installed using the repository location.
-Start julia and use the `]` key to switch to the package manager REPL
+
+This package is registered in the default Julia package registry, and can be installed through standard package installation procedure: e.g., running the following code in Julia REPL.
 ```julia
-(v1.2) pkg> add https://github.com/OpenMendel/VarianceComponentModels.jl
+using Pkg
+pkg"add VarianceComponentModels"
 ```
-Use the backspace key to return to the Julia REPL.
 
 ## Citation
 
 If you use [OpenMendel](https://openmendel.github.io) analysis packages in your research, please cite the following reference in the resulting publications:
 
-*Zhou, H., Sinsheimer, J., German, C., Ji, S., Bates, D., Chu, B. B., Keys, K., Kim, J., Ko, S., Mosher, G., Papp, J., Sobel, E., Zhai, J., Zhou, J., and Lange, K. (2020). OPENMENDEL: a cooperative programming project for statistical genetics, Human Genetics, 139(1):61-71.*
-
-<!--- ## Contributing
-We welcome contributions to this Open Source project. To contribute, follow this procedure ... --->
+*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 is supported by the National Institutes of Health under NIGMS awards R01GM053275 and R25GM103774 and NHGRI award R01HG006139.
+This project has been supported by the National Institutes of Health under awards R01GM053275, R01HG006139, R25GM103774, and 1R25HG011845.