Closes #24

beat/cmdline/scripts/beat.py

@@ -30,7 +30,7 @@
 
 Usage:
   %(prog)s [--verbose ...] [--prefix=<path>] [--cache=<path>] [--user=<user>]
-           [--platform=<url>] [--token=<token>] [--color=<theme>]
+           [--platform=<url>] [--token=<token>]
            [--test-mode] <command> [<args>...]
   %(prog)s (--help | -h)
   %(prog)s (--version | -V)
@@ -40,14 +40,20 @@ Options:
   -h, --help            Show this screen
   -v, --verbose         Increases the verbosity (may appear multiple times)
   -V, --version         Show version
-  -p, --prefix=<path>   Prefix of your local data [default: .]
-  -c, --cache=<path>    Cache prefix, otherwise defaults to `<prefix>/cache'
-  -o, --color=<theme>   The color theme to use for colored messages (choose
-                        between `dark', for dark backgrounds or `light', for
-                        lighther ones - the default is `none')
-  -t, --token=<token>   User token for server operations
-  -u, --user=<user>     The user name on the remote platform
+  -p, --prefix=<path>   Overrides the prefix of your local data. If not set use
+                        the value from your RC file
+                        [default: %(prefix)s]
+  -c, --cache=<path>    Overrides the cache prefix. If not set, use the value
+                        from your RC file, otherwise defaults to
+                        `<prefix>/%(cache)s'
+  -t, --token=<token>   Overrides the user token for server operations. If not
+                        set, use the value from your RC file. There are no
+                        defaults for this option.
+  -u, --user=<user>     Overrides the user name on the remote platform. If not
+                        set, use the value from your RC file.
+                        [default: %(user)s]
   -m, --platform=<url>  The URL of the BEAT platform to access
+                        [default: %(platform)s]
   -T, --test-mode       Assume test mode and doesn't setup the logging module
 
 
@@ -65,6 +71,7 @@ Commands:
 
 See 'beat <command> --help' for more information on a specific command.
 
+N.B.: The values of options "prefix", "cache" "user", "token", "platform" and
 """
 
 import os
@@ -76,7 +83,6 @@ from ..config import Configuration
 import difflib
 
 import logging
-import colorlog
 
 
 # defines our own logging level for extra information to be printed
@@ -98,17 +104,21 @@ def main(user_input=None):
     else:
         arguments = sys.argv[1:]
 
+    from ..config import DEFAULTS
+
     prog = os.path.basename(sys.argv[0])
     completions = dict(
         prog=prog,
         version=__version__,
-    )
+        **DEFAULTS,
+        )
+
     args = docopt(
         __doc__ % completions,
         argv=arguments,
         options_first=True,
         version='BEAT command-line swiss army knife v%s' % __version__,
-    )
+        )
 
     try:
 
@@ -150,23 +160,12 @@ def main(user_input=None):
       console_handler = logging.StreamHandler()
       console_handler.setLevel(logging.INFO) # default level
 
-      format_str = "%(log_color)s%(message)s"
+      format_str = "%(message)s"
       if args['--verbose'] >= 2:
-        format_str = "%(log_color)s[%(asctime)s - %(name)s]%(reset)s %(levelname)s: %(message)s"
-
-      # Some coloring
-      formatter = colorlog.ColoredFormatter(format_str,
-                                            log_colors={
-                                                'DEBUG': config.color_debug,
-                                                'EXTRA': config.color_info,
-                                                'INFO': config.color_info,
-                                                'WARNING': config.color_warn,
-                                                'ERROR': config.color_error,
-                                                'CRITICAL': config.color_critical,
-                                            },
-                                            style='%',
-                                            datefmt="%d/%b/%Y %H:%M:%S"
-      )
+        format_str = "[%(asctime)s - %(name)s]%(reset)s %(levelname)s: %(message)s"
+
+      formatter = logging.Formatter(format_str, style='%',
+          datefmt="%d/%b/%Y %H:%M:%S")
       console_handler.setFormatter(formatter)
       logger.addHandler(console_handler)
 

beat/cmdline/test/__init__.py

@@ -33,6 +33,7 @@ import tempfile
 import shutil
 import subprocess
 import pkg_resources
+import contextlib
 
 import six.moves.urllib as urllib
 
@@ -95,3 +96,14 @@ def setup_package():
 
 def teardown_package():
     shutil.rmtree(prefix_folder)
+
+
+@contextlib.contextmanager
+def temp_cwd():
+    tempdir = tempfile.mkdtemp(prefix=__name__, suffix='.cwd')
+    curdir = os.getcwd()
+    os.chdir(tempdir)
+    try: yield tempdir
+    finally:
+      os.chdir(curdir)
+      shutil.rmtree(tempdir)

beat/cmdline/test/test_algorithms.py

@@ -33,7 +33,7 @@ import os
 import shutil
 import json
 
-from . import platform, disconnected, prefix, tmp_prefix, user, token
+from . import platform, disconnected, prefix, tmp_prefix, user, token, temp_cwd
 from ..common import Selector
 from ..scripts.beat import main
 from beat.core.test.utils import slow, cleanup, skipif
@@ -47,15 +47,16 @@ def call(*args, **kwargs):
   use_platform = kwargs.get('platform', platform)
   use_cache = kwargs.get('cache', 'cache')
 
-  return main((
-      '--platform=%s' % use_platform,
-      '--user=%s' % user,
-      '--token=%s' % token,
-      '--prefix=%s' % use_prefix,
-      '--cache=%s' % use_cache,
-      '--test-mode',
-      'algorithm',
-  ) + args)
+  with temp_cwd():
+    return main((
+        '--platform=%s' % use_platform,
+        '--user=%s' % user,
+        '--token=%s' % token,
+        '--prefix=%s' % use_prefix,
+        '--cache=%s' % use_cache,
+        '--test-mode',
+        'algorithm',
+    ) + args)
 
 
 @slow

beat/cmdline/test/test_cache.py

@@ -32,7 +32,7 @@ import os
 
 import nose.tools
 
-from . import prefix, tmp_prefix
+from . import prefix, tmp_prefix, temp_cwd
 from .utils import index_experiment_dbs
 
 from ..scripts.beat import main
@@ -45,11 +45,12 @@ def call(*args, **kwargs):
 
   use_prefix = kwargs.get('prefix', prefix)
 
-  return main((
-      '--prefix=%s' % use_prefix,
-      '--cache=%s' % tmp_prefix,
-      '--test-mode',
-  ) + args)
+  with temp_cwd():
+    return main((
+        '--prefix=%s' % use_prefix,
+        '--cache=%s' % tmp_prefix,
+        '--test-mode',
+    ) + args)
 
 
 def setup_module():

beat/cmdline/test/test_config.py

@@ -34,7 +34,7 @@ import nose.tools
 from nose.tools import assert_raises
 import simplejson
 
-from . import tmp_prefix
+from . import tmp_prefix, temp_cwd
 from ..scripts.beat import main
 from beat.core.test.utils import cleanup
 from .. import config
@@ -52,11 +52,12 @@ def call(*args, **kwargs):
 
 
 def test_config_list():
-  nose.tools.eq_(call('config', 'list'), 0)
+  nose.tools.eq_(call('config', 'show'), 0)
 
 
 def test_config_cache():
   cache_dir = 'cache'
+
   c = config.Configuration({'--cache': cache_dir})
   nose.tools.eq_(c.cache, os.path.join(c.path, cache_dir))
 
@@ -66,48 +67,42 @@ def test_config_cache():
 
 
 @nose.tools.with_setup(teardown=cleanup)
-def test_config_save():
-  nose.tools.eq_(call('config', 'save'), 0)
-  config = os.path.join(tmp_prefix, '.beat', 'config.json')
-  assert os.path.exists(config)
-  with open(config, 'rt') as f: contents = simplejson.load(f)
-  assert contents
-
-
-@nose.tools.with_setup(teardown=cleanup)
-def test_set_token():
+def test_set_local_token():
   token_value = '123456abcdef'
-  nose.tools.eq_(call('config', 'set', 'token', token_value), 0)
-  config = os.path.join(tmp_prefix, '.beat', 'config.json')
-  assert os.path.exists(config)
-  with open(config, 'rt') as f: contents = simplejson.load(f)
-  assert contents['token'] == token_value
+  with temp_cwd() as d:
+    nose.tools.eq_(call('config', 'set', '--local', 'token', token_value), 0)
+    config = os.path.join(d, '.beatrc')
+    assert os.path.exists(config)
+    with open(config, 'rt') as f: contents = simplejson.load(f)
+    assert contents['token'] == token_value
 
 
 @nose.tools.with_setup(teardown=cleanup)
-def test_set_atnt_db():
+def test_set_local_atnt_db():
   db_config = 'database/atnt'
   db_path = './atnt_db'
-  nose.tools.eq_(call('config', 'set', db_config, db_path), 0)
-  config = os.path.join(tmp_prefix, '.beat', 'config.json')
-  assert os.path.exists(config)
-  with open(config, 'rt') as f: contents = simplejson.load(f)
-  assert contents[db_config] == db_path
+  with temp_cwd() as d:
+    nose.tools.eq_(call('config', 'set', '--local', db_config, db_path), 0)
+    config = os.path.join(d, '.beatrc')
+    assert os.path.exists(config)
+    with open(config, 'rt') as f: contents = simplejson.load(f)
+    assert contents[db_config] == db_path
 
 
 @nose.tools.with_setup(teardown=cleanup)
-def test_set_get_atnt_db():
+def test_set_get_local_atnt_db():
   db_config = 'database/atnt'
   db_path = './atnt_db'
-  nose.tools.eq_(call('config', 'set', db_config, db_path), 0)
-  nose.tools.eq_(call('config', 'get', db_config), 0)
+  with temp_cwd() as d:
+    nose.tools.eq_(call('config', 'set', '--local', db_config, db_path), 0)
+    nose.tools.eq_(call('config', 'get', db_config), 0)
 
 
 @nose.tools.with_setup(teardown=cleanup)
 def test_set_bad_config_key():
   db_config = 'fail'
-  with assert_raises(SystemExit) as c:
-    call('config', 'set', db_config, db_config)
+  with assert_raises(SystemExit) as c, temp_cwd() as d:
+    call('config', 'set', '--local', db_config, db_config)
 
   assert c.exception.code == 1
 
@@ -122,13 +117,3 @@ def test_get_bad_config_key():
 @nose.tools.with_setup(teardown=cleanup)
 def test_get_token():
   nose.tools.eq_(call('config', 'get', 'token'), 0)
-
-
-@nose.tools.with_setup(teardown=cleanup)
-def test_color_list():
-  nose.tools.eq_(call('config', 'color', '--list'), 0)
-
-
-@nose.tools.with_setup(teardown=cleanup)
-def test_color_set():
-  nose.tools.eq_(call('config', 'color', 'dark'), 0)

beat/cmdline/test/test_databases.py

@@ -30,7 +30,7 @@
 
 import nose.tools
 
-from . import platform, disconnected, prefix, tmp_prefix, user, token
+from . import platform, disconnected, prefix, tmp_prefix, user, token, temp_cwd
 
 from ..scripts.beat import main
 from beat.core.test.utils import slow, cleanup, skipif
@@ -47,14 +47,15 @@ def call(*args, **kwargs):
   use_prefix = kwargs.get('prefix', prefix)
   use_platform = kwargs.get('platform', platform)
 
-  return main((
-      '--platform=%s' % use_platform,
-      '--user=%s' % user,
-      '--token=%s' % token,
-      '--prefix=%s' % use_prefix,
-      '--test-mode',
-      'database',
-  ) + args)
+  with temp_cwd():
+    return main((
+        '--platform=%s' % use_platform,
+        '--user=%s' % user,
+        '--token=%s' % token,
+        '--prefix=%s' % use_prefix,
+        '--test-mode',
+        'database',
+    ) + args)
 
 
 @slow

beat/cmdline/test/test_experiments.py

@@ -32,7 +32,7 @@ import os
 import sys
 import nose.tools
 
-from . import platform, disconnected, prefix, tmp_prefix, user, token
+from . import platform, disconnected, prefix, tmp_prefix, user, token, temp_cwd
 from .utils import index_experiment_dbs
 from ..common import Selector
 from ..scripts.beat import main
@@ -52,15 +52,16 @@ def call(*args, **kwargs):
   use_platform = kwargs.get('platform', platform)
   use_cache = kwargs.get('cache', 'cache')
 
-  return main((
-      '--platform=%s' % use_platform,
-      '--user=%s' % user,
-      '--token=%s' % token,
-      '--prefix=%s' % use_prefix,
-      '--cache=%s' % use_cache,
-      '--test-mode',
-      'experiment',
-  ) + args)
+  with temp_cwd():
+    return main((
+        '--platform=%s' % use_platform,
+        '--user=%s' % user,
+        '--token=%s' % token,
+        '--prefix=%s' % use_prefix,
+        '--cache=%s' % use_cache,
+        '--test-mode',
+        'experiment',
+    ) + args)
 
 
 @slow

beat/cmdline/test/test_toolchains.py

@@ -31,7 +31,7 @@
 import os
 import nose.tools
 
-from . import platform, disconnected, prefix, tmp_prefix, user, token
+from . import platform, disconnected, prefix, tmp_prefix, user, token, temp_cwd
 from ..common import Selector, dot_diagram
 from ..scripts.beat import main
 from beat.core.test.utils import slow, cleanup, skipif
@@ -44,14 +44,15 @@ def call(*args, **kwargs):
   use_prefix = kwargs.get('prefix', prefix)
   use_platform = kwargs.get('platform', platform)
 
-  return main((
-      '--platform=%s' % use_platform,
-      '--user=%s' % user,
-      '--token=%s' % token,
-      '--prefix=%s' % use_prefix,
-      '--test-mode',
-      'toolchain',
-  ) + args)
+  with temp_cwd():
+    return main((
+        '--platform=%s' % use_platform,
+        '--user=%s' % user,
+        '--token=%s' % token,
+        '--prefix=%s' % use_prefix,
+        '--test-mode',
+        'toolchain',
+    ) + args)
 
 
 @slow

conda/meta.yaml

@@ -28,14 +28,14 @@ requirements:
     - beat.backend.python
     - beat.core
     - termcolor
-    - colorlog
     - oset
+    - bob.extension
+    - docopt
 
 test:
   requires:
     - bob-devel {{ bob_devel }}.*
     - beat-devel {{ beat_devel }}.*
-    - bob.extension
     - nose
     - coverage
     - sphinx

requirements.txt

 setuptools
 beat.core
 beat.backend.python
-colorlog
 oset
 termcolor
+bob.extension
+docopt