Merge pull request #1 from mrc-ide/develop

added github actions

.Rbuildignore

@@ -2,3 +2,4 @@
 ^\.Rproj\.user$
 ^ignore$
 ^R_ignore$
+^\.github$

.github/.gitignore

@@ -0,0 +1 @@
+*.html

.github/workflows/checks_develop.yaml

@@ -0,0 +1,37 @@
+# Workflow derived from https://github.com/r-lib/actions/tree/master/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+on:
+  push:
+    branches:
+      - develop
+  pull_request:
+    branches:
+      - develop
+
+name: checks_develop
+
+jobs:
+  R-CMD-check:
+    runs-on: ${{ matrix.config.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        config:
+          - {os: windows-latest, r: 'release'}
+          - {os: macOS-latest, r: 'release'}
+          - {os: ubuntu-20.04, r: 'release'}
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      R_KEEP_PKG_SOURCE: yes
+    steps:
+      - uses: actions/checkout@v2
+
+      - uses: r-lib/actions/setup-r@v1
+        with:
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v1
+        with:
+          extra-packages: rcmdcheck
+
+      - uses: r-lib/actions/check-r-package@v1

.github/workflows/checks_master.yaml

@@ -0,0 +1,37 @@
+# Workflow derived from https://github.com/r-lib/actions/tree/master/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+on:
+  push:
+    branches:
+      - master
+  pull_request:
+    branches:
+      - master
+
+name: checks_master
+
+jobs:
+  R-CMD-check:
+    runs-on: ${{ matrix.config.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        config:
+          - {os: windows-latest, r: 'release'}
+          - {os: macOS-latest, r: 'release'}
+          - {os: ubuntu-20.04, r: 'release'}
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      R_KEEP_PKG_SOURCE: yes
+    steps:
+      - uses: actions/checkout@v2
+
+      - uses: r-lib/actions/setup-r@v1
+        with:
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v1
+        with:
+          extra-packages: rcmdcheck
+
+      - uses: r-lib/actions/check-r-package@v1

DESCRIPTION

@@ -14,7 +14,7 @@ Description: Malaria infections often contain multiple genotypes. When
     assume a model of allele frequencies rather than a reference panel. We also
     implement parallel tempered MCMC to ensure good mixing, and produce a
     different set of outputs.
-License: GPL-3
+License: MIT + file LICENSE
 Encoding: UTF-8
 LazyData: true
 RoxygenNote: 7.1.1

README.md

@@ -1 +1,14 @@
-# Tapestry
+ <!-- badges: start -->
+  [![checks_develop](https://github.com/mrc-ide/Tapestry/workflows/checks_develop/badge.svg)](https://github.com/mrc-ide/Tapestry/actions)
+  [![checks_master](https://github.com/mrc-ide/Tapestry/workflows/checks_master/badge.svg)](https://github.com/mrc-ide/Tapestry/actions)
+  <!-- badges: end -->
+
+# Tapestry
+
+Malaria infections often contain multiple genotypes. When sequenced together,
+these produce a complex signal that is a mixture of the individual genotypes.
+Like earlier programs like DEploid, Tapestry attempts to pull these individual
+genotypes apart by exploiting allele frequency imbalances within a sample. The
+difference in Tapestry is that we assume a model of allele frequencies rather
+than a reference panel. We also implement parallel tempered MCMC to ensure good
+mixing, and produce a different set of outputs.