From 52a1975fd1ab0d844b3d1c96f8c1f48fd885a235 Mon Sep 17 00:00:00 2001
From: Zilong-Li <zimusen94@gmail.com>
Date: Mon, 28 Aug 2023 11:33:24 +0200
Subject: [PATCH] add auto release in workflow

---
 .github/workflows/release.yaml | 46 ++++++++++++++++++++++++++++++++++
 doc/paper.org                  | 41 +++++++++++++++++-------------
 2 files changed, 70 insertions(+), 17 deletions(-)
 create mode 100644 .github/workflows/release.yaml

diff --git a/.github/workflows/release.yaml b/.github/workflows/release.yaml
new file mode 100644
index 0000000..210433e
--- /dev/null
+++ b/.github/workflows/release.yaml
@@ -0,0 +1,46 @@
+---
+name: 'tagged-release'
+
+on:
+  push:
+    tags:
+      - 'v*'
+
+jobs:
+  tagged-release:
+    name: 'tagged-release'
+    runs-on: 'ubuntu-latest'
+    env:
+      JEST_VERBOSE: ${{ secrets.JEST_VERBOSE }}
+
+    steps:
+      - name: 'Checkout source code'
+        uses: 'actions/checkout@v3'
+        with:
+          submodules: recursive
+
+      - name: 'install dependency'
+        run: |
+          sudo apt update
+          sudo apt-get update
+          sudo apt-get -qy install build-essential zlib1g zlib1g-dev curl libcurl4-openssl-dev lzma-dev liblzma-dev libeigen3-dev
+          git clone --recursive https://github.com/samtools/htslib.git
+          cd htslib && autoreconf -i && ./configure --enable-libcurl
+          sudo make -j 4 install
+          sudo ldconfig
+          cd -
+
+      - name: 'run tests'
+        run: |
+          cd test
+          make
+          make test
+
+      - uses: 'marvinpinto/action-automatic-releases@latest'
+        with:
+          repo_token: '${{ secrets.GITHUB_TOKEN }}'
+          prerelease: false
+          files: |
+            vcfpp.h
+        id: 'automatic_releases'
+
diff --git a/doc/paper.org b/doc/paper.org
index 8183802..a259b51 100644
--- a/doc/paper.org
+++ b/doc/paper.org
@@ -30,25 +30,18 @@ Email: zilong.dk@gamil.com.}}
 
 * Introduction
 
-The VCF format [cite:@danecek2011] is the standard for
-representing genetic variation observed in DNA sequencing
-studies. The strength of the VCF format is its ability to represent
-the location of a variant, the genotype of the sequenced
-individual at each locus, as well as extensive variant
-metadata. Furthermore, the VCF format provided a substantial advance
-for the research community, as it follows a rigorous format
-specification that enables direct comparison of results from
-multiple studies and facilitates reproducible research. However, the
-consequence of this flexibility and the rather complicated
-specification of the VCF format, is that researchers require
-powerful software libraries to access, query and manipulate variants
-from VCF files.
+The VCF format [cite:@danecek2011] is the standard for representing
+genetic variation observed in DNA sequencing studies. The strength
+of the VCF format is its ability to represent the location of a
+variant, the genotype of the sequenced individual at each locus, as
+well as extensive variant metadata. However, the consequence of this
+flexibility and the rather complicated specification of the VCF
+format, is that researchers require powerful software libraries to
+access, query and manipulate variants from VCF files. Many efforts from computaional biologists 
 
 \newpage
 
-* Results
-
-** Features
+* Features 
 
 vcfpp is implemented as a single header file for being easily
 intergrated and compiled. There are four core classes for
@@ -65,6 +58,13 @@ manipulating VCF/BCF as showed in [[tb:class]].
 | VCF/BCF header and operations   | BcfHeader |
 |---------------------------------+-----------|
 
+* Usage
+
+In an effort to demonstrate the power and performance of vcfpp, the
+following sections highlight typical VCF analyses and illustrate
+commonly used features in cyvcf2. Other examples and further details
+of the vcfpp can be found at https://github.com/Zilong-Li/vcfpp.
+
 ** Python-like API
 
 In this example, we count the number of heterozygous sites for
@@ -122,7 +122,7 @@ sourceCpp("vcfpp-r.cpp")
 gts <- genotypes("vcf.gz")
 #+end_src
 
-** Benchmarking
+* Benchmarking
 
 vcfR [cite:@brian2017] is an R package that provides function to parse vcf into data tables in R.
 
@@ -147,6 +147,13 @@ vcfR [cite:@brian2017] is an R package that provides function to parse vcf into
 |-------------------+----------+-------+----------|
 
 
+* Discussion
+
+We have developed vcfpp, a fast and flexible C++ API for scripting
+high-perfomance genetic variant analyses. Its easy-to-use can be
+very useful for both package developers and writing of daily used
+scripts.
+
 #+print_bibliography:
 
 * Local setup :noexport: