fix circleci test

.circleci/config.yml

@@ -9,7 +9,7 @@ jobs:
       # specify the version you desire here
       - image: bioinstaller/ngsjs:latest
 
-    working_directory: ~/repo
+    working_directory: /tmp/ngsjs
 
     steps:
       - checkout
@@ -21,12 +21,10 @@ jobs:
           # fallback to using the latest cache if no exact match is found
           - v1-dependencies-
 
-      - run: source /etc/profile && yarn install
-
       - save_cache:
           paths:
             - node_modules
           key: v1-dependencies-{{ checksum "package.json" }}
 
       # run tests!
-      - run: source /etc/profile && yarn test
+      - run: source /etc/profile && yarn global add /tmp/ngsjs && yarn test

README.Rmd

@@ -23,7 +23,8 @@ knitr::opts_chunk$set(
 </p>
 
 <p align="center">
-   <a href="https://circleci.com/gh/ngsjs/ngsjs/tree/master"><img src="https://img.shields.io/circleci/project/github/ngsjs/ngsjs/master.svg" alt="Build Status"></a>
+  <a href="https://www.npmjs.com/package/ngsjs"><img src="https://img.shields.io/badge/lifecycle-experimental-orange.svg" alt="Life cycle: experimental">
+  <a href="https://circleci.com/gh/ngsjs/ngsjs/tree/master"><img src="https://img.shields.io/circleci/project/github/ngsjs/ngsjs/master.svg" alt="Build Status"></a>
   <a href="https://npmcharts.com/compare/ngsjs?minimal=true"><img src="https://img.shields.io/npm/dm/ngsjs.svg" alt="Downloads"></a>
   <a href="https://www.npmjs.com/package/ngsjs"><img src="https://img.shields.io/npm/v/ngsjs.svg" alt="Version"></a>
   <a href="https://www.npmjs.com/package/ngsjs"><img src="https://img.shields.io/npm/l/ngsjs.svg" alt="License"></a>

README.md

@@ -12,7 +12,8 @@
 </p>
 
 <p align="center">
-   <a href="https://circleci.com/gh/ngsjs/ngsjs/tree/master"><img src="https://img.shields.io/circleci/project/github/ngsjs/ngsjs/master.svg" alt="Build Status"></a>
+  <a href="https://www.npmjs.com/package/ngsjs"><img src="https://img.shields.io/badge/lifecycle-experimental-orange.svg" alt="Life cycle: experimental">
+  <a href="https://circleci.com/gh/ngsjs/ngsjs/tree/master"><img src="https://img.shields.io/circleci/project/github/ngsjs/ngsjs/master.svg" alt="Build Status"></a>
   <a href="https://npmcharts.com/compare/ngsjs?minimal=true"><img src="https://img.shields.io/npm/dm/ngsjs.svg" alt="Downloads"></a>
   <a href="https://www.npmjs.com/package/ngsjs"><img src="https://img.shields.io/npm/v/ngsjs.svg" alt="Version"></a>
   <a href="https://www.npmjs.com/package/ngsjs"><img src="https://img.shields.io/npm/l/ngsjs.svg" alt="License"></a>

bin/ngsjs

@@ -9,14 +9,14 @@ suppressMessages(if(!require('pacman')) install.packages('pacman'))
 pkgs <- c("optparse")
 suppressMessages(pacman::p_load(pkgs, character.only = TRUE))
 option_list <- list(
-  make_option(c("--list-all-subcmds"), action = "store_true", default = FALSE, help = "Print all supported subcmds of ngsjs.")
+  make_option(c("-l", "--list-all-subcmds"), action = "store_true", default = FALSE, help = "Print all supported subcmds of ngsjs.")
 )
 
-subcmds <- "rbashful, rconfig, rdeps, rinstall, rsession, rclrs, rmv, rtime_stamp, ranystr, rdownload"
+subcmds <- "rbashful rconfig rdeps rinstall rsession rclrs rmv rtime_stamp ranystr rdownload"
 description <- sprintf("Description:\n%s %s\n%s", 
                        "Main interface of ngsjs package tools.",
                        sprintf("Now, total %s subcmds are supported: %s.",
-                       length(strsplit(subcmds, ", ")[[1]]), subcmds),
+                       length(strsplit(subcmds, " ")[[1]]), subcmds),
                        "View the ngsjs homepage https://github.com/ngsjs/ngsjs for more detail."
                       )
 usage <- paste(sprintf("%%prog [subcmds: %s]", subcmds),
@@ -29,7 +29,7 @@ opt <- opt$option
 if (length(opt_args) == 0 && !opt[['list-all-subcmds']]) {
   print_help(opt_parser_obj)
 } else if (length(opt_args) == 0 && opt[['list-all-subcmds']]) {
-  cat(sprintf("Availabe: %s", subcmds), sep = "\n")
+  cat(sprintf("%s", subcmds), sep = "\n")
 } else {
   if (opt$help) system(sprintf("%s -h", paste(opt_args, collapse = " ")))
   else system(paste(opt_args, collapse = " "))

doc/changelogs/CHANGELOG_V0.1.5.md

@@ -17,6 +17,11 @@
 - './bin/rtime_stamp' support to generate time stamp
 - `./bin/ranstr` support to generate random strings
 - `./bin/rdownload` support to parallel download urls
+- `ngsjs --list-all-subcmds` return all sub-commands split by space
+
+**Test related:
+
+- add `./scripts/test/start_cli_test` to test the command line tools default output
 
 **Minor bug fix:
 

package.json

@@ -42,7 +42,7 @@
   ],
   "scripts": {
     "gadd": "yarn global add `pwd`",
-    "test": "./bin/rdeps && ./bin/ngsjs && ./bin/rbashful && ./bin/rconfig && ./bin/rinstall && ./bin/rsession && ./bin/rclrs && ./bin/rmv && "
+    "test": "./scripts/test/start_cli_test"
   },
   "bin": {
     "ngsjs": "./bin/ngsjs",

scripts/test/start_cli_test

@@ -0,0 +1,6 @@
+#!/usr/bin/env Rscript
+subcmds <- system("ngsjs --list-all-subcmds", intern = TRUE)
+subcmds <- strsplit(subcmds, " ")[[1]]
+status <- sapply(subcmds, system)
+if (!all(status == 0))
+  stop("Test error.")

src/ngsjs/DESCRIPTION

@@ -14,6 +14,8 @@ Encoding: UTF-8
 LazyData: true
 Imports:
   configr (>= 0.3.4.1),
+  BioInstaller (>= 0.3.6.3001),
+  ngstk (>= 0.2.2.2)
 Remotes:
   Miachol/configr,
   JhuangLab/BioInstaller,