add ci

.Rbuildignore

@@ -6,3 +6,5 @@
 ^src/htslib-1.18/htscodecs/tests
 ^cran-comments\.md$
 ^CRAN-SUBMISSION$
+\.github
+.*\.tar\.gz$

.github/CONTRIBUTING.md

@@ -0,0 +1,9 @@
+
+### Contributing to vcfppR
+
+Please see the file [Contributing](https://github.com/Zilong-Li/vcfppR/blob/main/Contributing.md) for details on
+
+- how to report an issue: a [Minimally Complete (and) Verifiable Example (MCVE)](https://stackoverflow.com/questions/5963269/how-to-make-a-great-r-reproducible-example) helps a lot;
+- how to submit a pull request: post an issue first, get consensus about _what_ and _how_;
+- how to follow our (informal) coding style: simply do as other files do and do not invent a new style;
+- how to be nice and [NEWS.Rd](https://github.com/Zilong-Li/vcfppR/blob/main/NEWS.md)

.github/PULL_REQUEST_TEMPLATE.md

@@ -0,0 +1,11 @@
+
+### Pull Request Template for Rcpp
+
+Please explain the changes you want to apply to Rcpp, preferably in an issue ticket **before** you create a pull request. See the file [Contributing](https://github.com/RcppCore/Rcpp/blob/master/Contributing.md) and the other templates for details.
+
+#### Checklist
+
+- [ ] Code compiles correctly
+- [ ] `R CMD check` still passes all tests
+- [ ] Preferably, new tests were added which fail without the change
+- [ ] Document the changes by file in [ChangeLog](https://github.com/RcppCore/Rcpp/blob/master/ChangeLog)

.github/workflows/ci.yaml

@@ -0,0 +1,64 @@
+# Run CI for R using https://eddelbuettel.github.io/r-ci/
+# This file is a slight variant by running a matrix of containers
+
+name: ci
+
+on:
+  push:
+    branches:
+      - main
+      - dev
+  pull_request:
+
+env:
+  USE_BSPM: "true"
+  _R_CHECK_FORCE_SUGGESTS_: "false"
+
+jobs:
+  ci:
+
+    runs-on: ubuntu-latest
+
+    container:
+      image: ${{ matrix.cntr }}
+
+    strategy:
+      matrix:
+        include:
+          - name: release
+            cntr: vcfppR/ci
+            r: R
+          - name: r-4.2
+            cntr: vcfppR/ci-4.2
+            r: R
+          - name: r-4.1
+            cntr: vcfppR/ci-4.1
+            r: R
+          - name: r-4.0
+            cntr: vcfppR/ci-4.0
+            r: R
+          - name: r-3.6
+            cntr: vcfppR/ci-3.6
+            r: R
+          - name: dev
+            cntr: vcfppR/ci-dev
+            r: RD
+
+    steps:
+      - uses: actions/checkout@v3
+
+      #- name: Bootstrap
+      #  run: |
+      #    curl -OLs https://eddelbuettel.github.io/r-ci/run.sh
+      #    chmod 0755 run.sh
+      #    ./run.sh bootstrap
+
+      - name: SessionInfo
+        run: ${{ matrix.r }} -q -e 'sessionInfo()'
+
+      - name: Build
+        run: ${{matrix.r }} CMD build --no-build-vignettes --no-manual .
+
+      - name: Check
+        run: CI=true ${{ matrix.r }} CMD check --no-vignettes --no-manual vcfppR_*.tar.gz
+

.github/workflows/docker.yaml

@@ -0,0 +1,90 @@
+name: docker
+
+on:
+  push:
+    branches:
+      - master
+  schedule:
+  - cron: "32 1 * * 6"
+
+jobs:
+  docker-ci:
+    runs-on: ubuntu-latest
+    name: ${{ matrix.tag }}
+
+    strategy:
+      fail-fast: false
+      matrix:
+        tag: [ci, ci-dev]
+
+    steps:
+    - name: Checkout
+      uses: actions/checkout@v3
+
+    - name: Set up Docker Buildx
+      uses: docker/setup-buildx-action@v2
+
+    - name: Login to DockerHub
+      uses: docker/login-action@v2
+      with:
+        username: ${{ secrets.DOCKER_USERNAME }}
+        password: ${{ secrets.DOCKER_PASSWORD }}
+
+    - name: Build and push
+      uses: docker/build-push-action@v3
+      with:
+        push: true
+        context: docker/${{ matrix.tag }}
+        tags: vcfppR/${{ matrix.tag }}
+
+
+  docker-run:
+    runs-on: ubuntu-latest
+    name: run
+    needs: docker-ci
+
+    steps:
+    - name: Checkout
+      uses: actions/checkout@v3
+
+    - name: Set up Docker Buildx
+      uses: docker/setup-buildx-action@v2
+
+    - name: Login to DockerHub
+      uses: docker/login-action@v2
+      with:
+        username: ${{ secrets.DOCKER_USERNAME }}
+        password: ${{ secrets.DOCKER_PASSWORD }}
+
+    - name: Build and push
+      uses: docker/build-push-action@v3
+      with:
+        push: true
+        context: docker/run
+        tags: vcfppR/run
+
+
+  docker-plus:
+    runs-on: ubuntu-latest
+    name: plus
+    needs: docker-run
+
+    steps:
+    - name: Checkout
+      uses: actions/checkout@v3
+
+    - name: Set up Docker Buildx
+      uses: docker/setup-buildx-action@v2
+
+    - name: Login to DockerHub
+      uses: docker/login-action@v2
+      with:
+        username: ${{ secrets.DOCKER_USERNAME }}
+        password: ${{ secrets.DOCKER_PASSWORD }}
+
+    - name: Build and push
+      uses: docker/build-push-action@v3
+      with:
+        push: true
+        context: docker/plus
+        tags: vcfppR/plus

.github/workflows/stale.yaml

@@ -0,0 +1,28 @@
+# Mark stale issues and pull requests
+# cf https://github.com/actions/stale
+
+name: stale
+
+on:
+  schedule:
+  - cron: "11 1 * * 6"
+
+jobs:
+  stale:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/stale@v8
+      with:
+        repo-token: ${{ secrets.GITHUB_TOKEN }}
+        stale-issue-label: 'no-issue-activity'
+        stale-pr-label: 'no-pr-activity'
+        days-before-stale: 365
+        days-before-close: 31
+        stale-issue-message: >
+          This issue is stale (365 days without activity) and will be closed
+          in 31 days unless new activity is seen. Please feel free to re-open
+          it is still a concern, possibly with additional data.
+        stale-pr-message: >
+          This pull request is is stale (365 days without activity) and will
+          be closed in 31 days unless new activity is seen. Please feel free
+          to open a new issue to discuss a fresh approach.

.gitignore

@@ -3,4 +3,15 @@
 .Rdata
 .httr-oauth
 .DS_Store
-src/htslib-1.18
+src/htslib-1.18
+*.tar.gz
+vignettes/*_cache
+
+## lsp
+.clangd
+.clang-format
+
+## R check
+src/symbols.rds
+*.Rcheck
+CRAN-SUBMISSION

DESCRIPTION

@@ -1,6 +1,8 @@
 Package: vcfppR
 Title: Rapid Manipulation of the VCF/BCF Format in R
 Version: 0.3.4
+Author: Zilong Li
+Maintainer: Zilong Li <zilong.dk@gmail.com>
 Authors@R: 
     person("Zilong", "Li", , "zilong.dk@gmail.com", role = c("aut", "cre", "cph"),
            comment = c(ORCID = "0000-0001-5859-2078"))

src/Makevars

@@ -1,4 +1,3 @@
-CXX_STD = CXX11
 HTSLIB_DIR=htslib-1.18
 PKG_CPPFLAGS = -I. -I${HTSLIB_DIR}
 PKG_LIBS = ${HTSLIB_DIR}/libhts.a -fPIC -lz -lm -lbz2 -llzma -lcurl

src/Makevars.win

@@ -1,4 +1,3 @@
-CXX_STD = CXX11
 HTSLIB_DIR=htslib-1.18
 PKG_CPPFLAGS = -I. -I${HTSLIB_DIR} -D_FILE_OFFSET_BITS=64
 PKG_LIBS+=${HTSLIB_DIR}/libhts.a -lz -lm -lbz2 -llzma -lcurl -lbcrypt -lidn2 -lunistring -liconv -lssl -lcrypto -lcrypt32 -lwsock32 -lwldap32 -lssh2 -lgcrypt -lgpg-error -lws2_32 -lzstd -lregex