Fix bug in args & less-aggressive update

Without args.prog, AliasCommand fail. Alias is better documented
in the readme and initial config files.

Update will now only trigger with version bumps. And the plugins
section is not updated. Removes the --upgrade flag.

pubs/config/spec.py

@@ -71,6 +71,14 @@ pages     = string(default='')
 # comma-separated list of the plugins to load
 active = list(default=list())
 
+[[alias]]
+# new subcommands can be defined, e.g.:
+# print = open --with lp
+# evince = open --with evince
+
+# shell commands can also be defined, by prefixing them with a bang `!`, e.g:
+# count = !pubs list -k | wc -l
+
 [internal]
 # The version of this configuration file. Do not edit.
 version = string(min=5, default='{}')

pubs/pubs_cmd.py

@@ -33,15 +33,15 @@ CORE_CMDS = collections.OrderedDict([
 
 def execute(raw_args=sys.argv):
 
-    conf_parser = argparse.ArgumentParser(add_help=False)
+    conf_parser = argparse.ArgumentParser(prog="pubs", add_help=False)
     conf_parser.add_argument("-c", "--config", help="path to config file",
                              type=str, metavar="FILE")
-    conf_parser.add_argument("-u", "--update", help="update config if needed",
-                             default=False, action='store_true')
-    args, remaining_args = conf_parser.parse_known_args(raw_args[1:])
+    #conf_parser.add_argument("-u", "--update", help="update config if needed",
+    #                         default=False, action='store_true')
+    top_args, remaining_args = conf_parser.parse_known_args(raw_args[1:])
 
-    if args.config:
-        conf_path = args.config
+    if top_args.config:
+        conf_path = top_args.config
     else:
         conf_path = config.get_confpath(verify=False)  # will be checked on load
 
@@ -49,7 +49,7 @@ def execute(raw_args=sys.argv):
     if len(remaining_args) > 0 and remaining_args[0] != 'init':
         try:
             conf = config.load_conf(path=conf_path, check=False)
-            if args.update and update.update_check(conf, path=conf.filename):
+            if update.update_check(conf, path=conf.filename):
                 # an update happened, reload conf.
                 conf = config.load_conf(path=conf_path, check=False)
             config.check_conf(conf)
@@ -81,4 +81,5 @@ def execute(raw_args=sys.argv):
 
     # Parse and run appropriate command
     args = parser.parse_args(remaining_args)
+    args.prog = "pubs" # FIXME?
     args.func(conf, args)

pubs/update.py

@@ -69,7 +69,7 @@ def update(conf, code_version, repo_version, path=None):
         return True
 
     # continuous update while configuration is stabilizing
-    if repo_version == code_version == ['0', '6', '0']:
+    if repo_version == ['0', '6', '0'] and repo_version < code_version:
         default_conf = config.load_default_conf()
         for section_name, section in conf.items():
             for key, value in section.items():
@@ -78,6 +78,10 @@ def update(conf, code_version, repo_version, path=None):
                     default_conf[section_name][key] = value
                 except KeyError:
                     pass
+        # we don't update plugins
+        for section_name, section in conf['plugins'].items():
+            default_conf[section_name]['plugins'][section_name] = section
+
 
         # comparing potential changes
         with open(path, 'r') as f:
@@ -85,7 +89,6 @@ def update(conf, code_version, repo_version, path=None):
         new_conf_text = io.BytesIO()
         default_conf.write(outfile=new_conf_text)
 
-
         if new_conf_text.getvalue() != old_conf_text:
 
             backup_path = path + '.old'

readme.md

@@ -52,16 +52,16 @@ This ensure that your reference file is always up-to-date; you can cite a paper
 
 and then add `\cite{Loeb_2012}` in your manuscript. After running the bash script, the citation will correctly appear in your compiled pdf.
 
-Customization
--------------
-Pubs is designed to interact well with your command line tool chain. You can add custom commands to pubs by defining aliases in your config file. Here are a few examples.
+## Customization
 
-    [alias]
-    print = open -w lp
-    count = !pubs list -k | wc -l
+Pubs is designed to interact well with your command line tool chain. You can add custom commands to pubs by defining aliases in your config file.
 
-For more advanced functionalities, pubs also support plugins. Actually *alias* is itself a plugin!
+    [[alias]]
+    evince = open --with evince
+    count = !pubs list -k | wc -l
 
+The first command defines a new subcommand: `pubs open -w lp` will be executed when `pubs print` is typed.
+The second starts with a bang: `!`, and is treated as a shell command.
 
 ## Requirements