Update doc to remote remote path mapping features vatlab/sos#1535

src/user_guide/cli.ipynb

@@ -51,7 +51,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 1,
+   "execution_count": 2,
    "metadata": {
     "kernel": "SoS",
     "tags": []
@@ -62,25 +62,25 @@
      "output_type": "stream",
      "text": [
       "usage: sos [-h] [--version]\n",
-      "           {install,run,dryrun,status,push,pull,execute,kill,purge,config,convert,remove}\n",
+      "           {install,run,dryrun,status,execute,kill,purge,config,convert,remove}\n",
       "           ...\n",
       "\n",
       "A workflow system for the execution of commands and scripts in different\n",
       "languages.\n",
       "\n",
-      "optional arguments:\n",
+      "options:\n",
       "  -h, --help            show this help message and exit\n",
       "  --version             show program's version number and exit\n",
       "\n",
       "subcommands:\n",
-      "  {install,run,dryrun,status,push,pull,execute,kill,purge,config,convert,remove}\n",
+      "  {install,run,dryrun,status,execute,kill,purge,config,convert,remove}\n",
       "    run                 Execute default or specified workflow in script\n",
       "    dryrun              Execute workflow in dryrun mode\n",
       "    status              Check the status of specified tasks\n",
       "    remote              Listing and testing remote configurations\n",
       "    execute             Execute a packages task\n",
       "    kill                Stop the execution of running task\n",
-      "    purge               Remove local or remote tasks\n",
+      "    purge               Remove local or remote tasks or workflows\n",
       "    config              Read and write sos configuration files\n",
       "    convert             Convert between .sos, .ipynb and other formats\n",
       "    remove              Remove specified files and/or their signatures\n",

src/user_guide/remote_execution.ipynb

@@ -35,7 +35,8 @@
     "* **Time need to lean**: 30 minutes or less\n",
     "* **Key points**:\n",
     "  * Option `-r host` executes workflow on `host`, optionally through a `workflow_template` specified through host configuration.\n",
-    "  * The remote host could be a regular server, or a cluster system, in which case the workflow could be executed using multiple computing nodes."
+    "  * The remote host could be a regular server, or a cluster system, in which case the workflow could be executed using multiple computing nodes.\n",
+    "  * Local and remote hosts should share directories (e.g. via NFS mount) for input and output files."
    ]
   },
   {
@@ -489,7 +490,9 @@
   },
   {
    "cell_type": "markdown",
-   "metadata": {},
+   "metadata": {
+    "kernel": "SoS"
+   },
    "source": [
     "Note that local configrations, including the ones specified with option `-c` will be transferred and used on the remote host, with only the `localhost` definition switched to be the remote host. It is therefore safe to use local configurations with option `-r`."
    ]
@@ -513,7 +516,9 @@
   },
   {
    "cell_type": "markdown",
-   "metadata": {},
+   "metadata": {
+    "kernel": "SoS"
+   },
    "source": [
     "If the remote host specified by option `-r host` is a cluster system, the workflow will be submitted to the cluster as a regular cluster job. The `workflow_template` of `host` will be used, using options specified from command line (`-r host KEY=VALUE KEY=VALUE`.\n",
     "\n",
@@ -525,7 +530,9 @@
   {
    "cell_type": "code",
    "execution_count": 2,
-   "metadata": {},
+   "metadata": {
+    "kernel": "SoS"
+   },
    "outputs": [],
    "source": [
     "## Executing entire workflows on remote cluster systems with job submission"

src/user_guide/sos_remote.ipynb

@@ -28,7 +28,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 1,
+   "execution_count": 2,
    "metadata": {
     "kernel": "SoS",
     "tags": []
@@ -38,15 +38,14 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "usage: sos remote [-h] [-c CONFIG] [-p PASSWORD] [--files [FILES [FILES ...]]]\n",
+      "usage: sos remote [-h] [-c CONFIG] [-p PASSWORD] [--files [FILES ...]]\n",
       "                  [--cmd ...] [-v {0,1,2,3,4}]\n",
-      "                  {list,status,setup,test,login,push,pull,run}\n",
-      "                  [hosts [hosts ...]]\n",
+      "                  {list,status,setup,test,login,run} [hosts ...]\n",
       "\n",
       "Listing and testing remote configurations\n",
       "\n",
       "positional arguments:\n",
-      "  {list,status,setup,test,login,push,pull,run}\n",
+      "  {list,status,setup,test,login,run}\n",
       "                        List (list), check status of tasks (status), setup\n",
       "                        public-key authentication (setup), test configuration\n",
       "                        (test), login (login), push files to one or more\n",
@@ -59,7 +58,7 @@
       "                        acceptable even if it is defined in configuration\n",
       "                        file.\n",
       "\n",
-      "optional arguments:\n",
+      "options:\n",
       "  -h, --help            show this help message and exit\n",
       "  -c CONFIG, --config CONFIG\n",
       "                        A configuration file with host definitions, in case\n",
@@ -72,8 +71,7 @@
       "                        password will be used for all specified hosts so you\n",
       "                        will need to use separate setup commands for hosts\n",
       "                        with different passwords.\n",
-      "  --files [FILES [FILES ...]]\n",
-      "                        files or directories to be push or pulled for action\n",
+      "  --files [FILES ...]   files or directories to be push or pulled for action\n",
       "                        \"push\" or \"pull\"\n",
       "  --cmd ...             commands to be executed by action \"run\" or tested by\n",
       "                        action \"test\". This option takes all remaining options\n",

src/user_guide/sos_targets.ipynb

@@ -560,7 +560,6 @@
     "| `q`     |quote    | `quoted()` | `file 1.txt` | `'file 1.txt'`|\n",
     "| `r`     | repr | `repr()` | `file.txt` | `'file.txt'` |\n",
     "| `s`    | str | `str()` | `file.txt` | `file.txt` |\n",
-    "| `R`   | resolve remote and other targets | `.resolve()`| `remote('a.txt')` | `a.txt`|\n",
     "| `U`   | undo expanduser | `replace(expanduser('~'), '~')` | `/home/user/test.sos` | `~/test.sos` |\n",
     "| `x`      | file extension   | `splitext()[1]` | `~/SoS/test.sos` | `.sos` |\n",
     "| `,`   | join with comma      | `','.join()` | `['a.txt', 'b.txt']` | `a.txt,b.txt`|\n"