Merge branch 'master' of github.com:smithlabcode/dnmtools

Author: andrewdavidsmith

.github/workflows/c-cpp.yml

@@ -0,0 +1,32 @@
+name: C/C++ CI
+
+on:
+  workflow_dispatch:
+  push:
+    branches: [ "master" ]
+  pull_request:
+    branches: [ "master" ]
+
+jobs:
+  build:
+
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v3
+      with:
+        submodules: recursive
+    - name: Install autotools
+      run: sudo apt-get install -y autoconf automake libtool
+    - name: Install dependencies
+      run: sudo apt-get install -y libhts-dev libgsl-dev
+    - name: Generate configure script
+      run: autoreconf -i src/abismal/src/smithlab_cpp src/abismal src/smithlab_cpp .
+    - name: configure
+      run: ./configure
+    - name: make
+      run: make
+    - name: make check
+      run: make check
+    - name: make distcheck
+      run: make distcheck

README.md

@@ -12,7 +12,7 @@ sequencing (RRBS). These tools focus on overcoming the computing
 challenges imposed by the scale of genome-wide DNA methylation data,
 which is usually the early parts of data analysis.
 
-## Installing release 1.2.1
+## Installing release 1.2.2
 
 The documentation for DNMTools can be found
 [here](https://dnmtools.readthedocs.io). But if you want to install
@@ -42,14 +42,14 @@ all the formatting.
 
 ### Configuration
 
-* Download [dnmtools-1.2.1.tar.gz](https://github.com/smithlabcode/dnmtools/releases/download/v1.2.1/dnmtools-1.2.1.tar.gz).
+* Download [dnmtools-1.2.2.tar.gz](https://github.com/smithlabcode/dnmtools/releases/download/v1.2.2/dnmtools-1.2.2.tar.gz).
 * Unpack the archive:
 ```console
-tar -zxvf dnmtools-1.2.1.tar.gz
+tar -zxvf dnmtools-1.2.2.tar.gz
 ```
 * Move into the dnmtools directory and create a build directory:
 ```console
-cd dnmtools-1.2.1 && mkdir build && cd build
+cd dnmtools-1.2.2 && mkdir build && cd build
 ```
 * Run the configuration script:
 ```console

configure.ac

@@ -1,6 +1,6 @@
 dnl This file is part of dnmtools
 dnl
-dnl Copyright (C) 2022: Andrew D. Smith
+dnl Copyright (C) 2022-2023: Andrew D. Smith
 dnl
 dnl Authors: Andrew D. Smith
 dnl
@@ -14,7 +14,7 @@ dnl but WITHOUT ANY WARRANTY; without even the implied warranty of
 dnl MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
 dnl General Public License for more details.
 
-AC_INIT([dnmtools], [1.2.1], [andrewds@usc.edu],
+AC_INIT([dnmtools], [1.2.2], [andrewds@usc.edu],
         [dnmtools], [https://github.com/smithlabcode/dnmtools])
 dnl the config.h is not currently #included in the source, and only
 dnl used to keep command lines short.

documentation/docs/quickstart.md

@@ -60,14 +60,14 @@ would need to be activated when you want to use dnmtools.
 
 ### Configuration
 
-* Download [dnmtools-1.2.1.tar.gz](https://github.com/smithlabcode/dnmtools/releases/download/v1.2.1/dnmtools-1.2.1.tar.gz).
+* Download [dnmtools-1.2.2.tar.gz](https://github.com/smithlabcode/dnmtools/releases/download/v1.2.2/dnmtools-1.2.2.tar.gz).
 * Unpack the archive:
 ```console
-$ tar -zxvf dnmtools-1.2.1.tar.gz
+$ tar -zxvf dnmtools-1.2.2.tar.gz
 ```
 * Move into the dnmtools directory and create a build directory:
 ```console
-$ cd dnmtools-1.2.1
+$ cd dnmtools-1.2.2
 $ mkdir build && cd build
 ```
 * Run the configuration script:

src/abismal

@@ -25,7 +25,7 @@ using std::cout;
 using std::endl;
 
 #define PROGRAM_NAME "dnmtools"
-#define PROGRAM_VERSION "1.2.1"
+#define PROGRAM_VERSION "1.2.2"
 
 int abismal(int argc, const char **argv);
 int abismalidx(int argc, const char **argv);