add github actions (#15)

.github/workflows/R-CMD-check.yaml

@@ -0,0 +1,49 @@
+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+on:
+  push:
+    branches: [main, master]
+  pull_request:
+    branches: [main, master]
+
+name: R-CMD-check
+
+jobs:
+  R-CMD-check:
+    runs-on: ${{ matrix.config.os }}
+
+    name: ${{ matrix.config.os }} (${{ matrix.config.r }})
+
+    strategy:
+      fail-fast: false
+      matrix:
+        config:
+          - {os: macos-latest,   r: 'release'}
+          - {os: windows-latest, r: 'release'}
+          - {os: ubuntu-latest,   r: 'devel', http-user-agent: 'release'}
+          - {os: ubuntu-latest,   r: 'release'}
+            #          - {os: ubuntu-latest,   r: 'oldrel-1'}
+
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      R_KEEP_PKG_SOURCE: yes
+
+    steps:
+      - uses: actions/checkout@v3
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          r-version: ${{ matrix.config.r }}
+          http-user-agent: ${{ matrix.config.http-user-agent }}
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::rcmdcheck
+          needs: check
+
+      - uses: r-lib/actions/check-r-package@v2
+        with:
+          upload-snapshots: true

DESCRIPTION

@@ -32,7 +32,7 @@ Imports:
     pryr,
     htmlwidgets,
     htmltools,
-    shinyCyJS
+    shinyCyJS (>= 1.0.0)
 Suggests:
     testthat,
     knitr,

README.Rmd

@@ -2,21 +2,20 @@
 output: github_document
 ---
 
-[![Travis-CI Build Status](https://travis-ci.org/ctlab/gatom.svg?branch=master)](https://travis-ci.org/ctlab/gatom)
-[![codecov](https://codecov.io/gh/ctlab/gatom/branch/master/graph/badge.svg)](https://codecov.io/gh/ctlab/gatom)
+ [![R-CMD-check](https://github.com/ctlab/gatom/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/ctlab/gatom/actions/workflows/R-CMD-check.yaml)
+
 
 # gatom
 
 An R-package for finding active metabolic modules in atom transition network.
 
-Full vignette can be found [here](https://rawgit.com/ctlab/gatom/master/inst/Using_gatom_package.html).
+Full vignette can be found [here](https://rpubs.com/asergushichev/gatom-tutorial).
 
 
 ### Installation
 
 ```{r eval=FALSE}
 library(devtools)
-install_github("ctlab/mwcsr")
 install_github("ctlab/gatom")
 ```
 
@@ -88,7 +87,7 @@ head(V(m)$label)
 We can save the module to different formats (dot, xgmml, svg, pdf):
 
 ```{r results="hide", message=FALSE, warning=FALSE}
-saveModuleToPdf(m, file="M0.vs.M1.pdf", name="M0.vs.M1", n_iter=100, force=1e-5, seed=10)
+saveModuleToPdf(m, file="M0.vs.M1.pdf", name="M0.vs.M1", n_iter=100, force=1e-5)
 ```
 
 ![Module](https://rawgit.com/ctlab/gatom/master/inst/M0.vs.M1.png)