From 1bf47ce7a93d7258a2165a97bed9fd9d8ad0ab4c Mon Sep 17 00:00:00 2001
From: Chris Granade <cgranade@cgranade.com>
Date: Wed, 12 Apr 2017 12:17:29 +1000
Subject: [PATCH 01/21] Added test:// URI schema.

---
 instruments/abstract_instruments/instrument.py | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/instruments/abstract_instruments/instrument.py b/instruments/abstract_instruments/instrument.py
index 2f19cc7bf..c97f4ca7f 100644
--- a/instruments/abstract_instruments/instrument.py
+++ b/instruments/abstract_instruments/instrument.py
@@ -286,7 +286,8 @@ def binblockread(self, data_width, fmt=None):
     # CLASS METHODS #
 
     URI_SCHEMES = ["serial", "tcpip", "gpib+usb",
-                   "gpib+serial", "visa", "file", "usbtmc", "vxi11"]
+                   "gpib+serial", "visa", "file", "usbtmc", "vxi11",
+                   "test"]
 
     @classmethod
     def open_from_uri(cls, uri):
@@ -306,6 +307,7 @@ def open_from_uri(cls, uri):
             gpib+serial:///dev/ttyACM0/15 # Currently non-functional.
             visa://USB::0x0699::0x0401::C0000001::0::INSTR
             usbtmc://USB::0x0699::0x0401::C0000001::0::INSTR
+            test://
 
         For the ``serial`` URI scheme, baud rates may be explicitly specified
         using the query parameter ``baud=``, as in the example
@@ -391,6 +393,8 @@ def open_from_uri(cls, uri):
             #   vxi11://192.168.1.104
             #   vxi11://TCPIP::192.168.1.105::gpib,5::INSTR
             return cls.open_vxi11(parsed_uri.netloc, **kwargs)
+        elif parsed_uri.scheme == "test":
+            return cls.open_test(**kwargs)
         else:
             raise NotImplementedError("Invalid scheme or not yet "
                                       "implemented.")

From 4eef89dc5a52d255bbe1b1f77f155cda041ee20f Mon Sep 17 00:00:00 2001
From: Chris Granade <cgranade@cgranade.com>
Date: Wed, 12 Apr 2017 12:17:53 +1000
Subject: [PATCH 02/21] Config: Py3 fix and support for setting attrs.

---
 instruments/config.py | 26 +++++++++++++++++++++-----
 1 file changed, 21 insertions(+), 5 deletions(-)

diff --git a/instruments/config.py b/instruments/config.py
index 74d09499b..f04f417cb 100644
--- a/instruments/config.py
+++ b/instruments/config.py
@@ -78,7 +78,7 @@ def load_instruments(conf_file_name, conf_path="/"):
     all other keys in the YAML file.
 
     :param str conf_file_name: Name of the configuration file to load
-        instruments from.
+        instruments from. Alternatively, a file-like object may be provided.
     :param str conf_path: ``"/"`` separated path to the section in the
         configuration file to load.
 
@@ -98,20 +98,36 @@ def load_instruments(conf_file_name, conf_path="/"):
         raise ImportError("Could not import PyYAML, which is required "
                           "for this function.")
 
-    with open(conf_file_name, 'r') as f:
-        conf_dict = yaml.load(f)
+    if isinstance(conf_file_name, (str, unicode)):
+        with open(conf_file_name, 'r') as f:
+            conf_dict = yaml.load(f)
+    else:
+        conf_dict = yaml.load(conf_file_name)
 
     conf_dict = walk_dict(conf_dict, conf_path)
 
     inst_dict = {}
-    for name, value in conf_dict.iteritems():
+    for name, value in conf_dict.items():
         try:
             inst_dict[name] = value["class"].open_from_uri(value["uri"])
+
+            if 'attrs' in value:
+                # We have some attrs we can set on the newly created instrument.
+                for attr_name, attr_value in value['attrs'].items():
+                    # Allow "." in attribute names so that we can set attributes
+                    # recursively.
+                    target = inst_dict[name]
+                    while '.' in attr_name:
+                        head, attr_name = attr_name.split('.', 1)
+                        target = getattr(target, head)
+                    setattr(target, attr_name, attr_value)
+
         except IOError as ex:
             # FIXME: need to subclass Warning so that repeated warnings
             #        aren't ignored.
-            warnings.warn("Exception occured loading device URI "
+            warnings.warn("Exception occured loading device with URI "
                           "{}:\n\t{}.".format(value["uri"], ex), RuntimeWarning)
             inst_dict[name] = None
 
+
     return inst_dict

From 6507fb3d63815460e6b6db5e0a90b7f807e0ef06 Mon Sep 17 00:00:00 2001
From: Chris Granade <cgranade@cgranade.com>
Date: Wed, 12 Apr 2017 12:50:42 +1000
Subject: [PATCH 03/21] Added sub/indexing to attrs config.

---
 instruments/config.py   | 10 +++-------
 instruments/util_fns.py | 34 ++++++++++++++++++++++++++++++++--
 2 files changed, 35 insertions(+), 9 deletions(-)

diff --git a/instruments/config.py b/instruments/config.py
index f04f417cb..733595def 100644
--- a/instruments/config.py
+++ b/instruments/config.py
@@ -16,6 +16,8 @@
 except ImportError:
     yaml = None
 
+from instruments.util_fns import setattr_expression
+
 # FUNCTIONS ###################################################################
 
 
@@ -114,13 +116,7 @@ def load_instruments(conf_file_name, conf_path="/"):
             if 'attrs' in value:
                 # We have some attrs we can set on the newly created instrument.
                 for attr_name, attr_value in value['attrs'].items():
-                    # Allow "." in attribute names so that we can set attributes
-                    # recursively.
-                    target = inst_dict[name]
-                    while '.' in attr_name:
-                        head, attr_name = attr_name.split('.', 1)
-                        target = getattr(target, head)
-                    setattr(target, attr_name, attr_value)
+                    setattr_expression(inst_dict[name], attr_name, attr_value)
 
         except IOError as ex:
             # FIXME: need to subclass Warning so that repeated warnings
diff --git a/instruments/util_fns.py b/instruments/util_fns.py
index 316343fc9..977bfdcf3 100644
--- a/instruments/util_fns.py
+++ b/instruments/util_fns.py
@@ -14,11 +14,13 @@
 from enum import Enum, IntEnum
 import quantities as pq
 
-# FUNCTIONS ###################################################################
+# CONSTANTS ###################################################################
 
-# pylint: disable=too-many-arguments
+_IDX_REGEX = re.compile(r'([a-zA-Z_][a-zA-Z0-9_]*)\[(-?[0-9]*)\]')
 
+# FUNCTIONS ###################################################################
 
+# pylint: disable=too-many-arguments
 def assume_units(value, units):
     """
     If units are not provided for ``value`` (that is, if it is a raw
@@ -37,6 +39,34 @@ def assume_units(value, units):
         value = pq.Quantity(value, units)
     return value
 
+def setattr_expression(target, name_expr, value):
+    """
+    Recursively calls getattr/setattr for attribute
+    names that are miniature expressions with subscripting.
+    For instance, of the form ``a[0].b``.
+    """
+    # Allow "." in attribute names so that we can set attributes
+    # recursively.
+    if '.' in name_expr:
+        # Recursion: We have to strip off a level of getattr.
+        head, name_expr = name_expr.split('.', 1)
+        match = _IDX_REGEX.match(head)
+        if match:
+            head_name, head_idx = match.groups()
+            target = getattr(target, head_name)[int(head_idx)]
+        else:
+            target = getattr(target, head)
+
+        setattr_expression(target, name_expr, value)
+    else:
+        # Base case: We're in the last part of a dot-expression.
+        match = _IDX_REGEX.match(name_expr)
+        if match:
+            name, idx = match.groups()
+            getattr(target, name)[int(idx)] = value
+        else:
+            setattr(target, name_expr, value)
+
 
 def convert_temperature(temperature, base):
     """

From 8a48ace966aa470a3285a908a1a90fafb51927e3 Mon Sep 17 00:00:00 2001
From: Chris Granade <cgranade@cgranade.com>
Date: Wed, 12 Apr 2017 13:00:12 +1000
Subject: [PATCH 04/21] Added to docstring.

---
 instruments/config.py | 11 +++++++++++
 1 file changed, 11 insertions(+)

diff --git a/instruments/config.py b/instruments/config.py
index 733595def..e26601cab 100644
--- a/instruments/config.py
+++ b/instruments/config.py
@@ -65,6 +65,17 @@ def load_instruments(conf_file_name, conf_path="/"):
     the form
     ``{'ddg': instruments.srs.SRSDG645.open_from_uri('gpib+usb://COM7/15')}``.
 
+    Optionally, each the value of each instrument key can also contain a dictionary
+    of attributes to set on the newly-created instrument. For instance, the following
+    dictionary creates a ThorLabs APT motor controller instrument with a single motor
+    model configured::
+
+        rot_stage:
+            class: !!python/name:instruments.thorabsapt.APTMotorController
+            uri: serial:///dev/ttyUSB0?baud=115200
+            attrs:
+                channel[0].motor_model: PRM1-Z8
+
     By specifying a path within the configuration file, one can load only a part
     of the given file. For instance, consider the configuration::
 

From 90226878018298047b3b09ebd364de424a967a80 Mon Sep 17 00:00:00 2001
From: Chris Granade <cgranade@cgranade.com>
Date: Wed, 12 Apr 2017 13:15:56 +1000
Subject: [PATCH 05/21] Added support for physical quantities to config.

---
 instruments/config.py | 19 +++++++++++++++++++
 1 file changed, 19 insertions(+)

diff --git a/instruments/config.py b/instruments/config.py
index e26601cab..8f625e65d 100644
--- a/instruments/config.py
+++ b/instruments/config.py
@@ -16,6 +16,8 @@
 except ImportError:
     yaml = None
 
+import quantities as pq
+
 from instruments.util_fns import setattr_expression
 
 # FUNCTIONS ###################################################################
@@ -48,6 +50,11 @@ def walk_dict(d, path):
         # Otherwise, resolve that segment and recurse.
         return walk_dict(d[path[0]], path[1:])
 
+def quantity_constructor(loader, node):
+    # Follows the example of http://stackoverflow.com/a/43081967/267841.
+    value = loader.construct_scalar(node)
+    magnitude, units = value.split(" ", 1)
+    return pq.Quantity(magnitude, units)
 
 def load_instruments(conf_file_name, conf_path="/"):
     """
@@ -76,6 +83,16 @@ def load_instruments(conf_file_name, conf_path="/"):
             attrs:
                 channel[0].motor_model: PRM1-Z8
 
+    Unitful attributes can be specified by using the ``!Q`` tag to quickly create
+    instances of `pq.Quantity`. In the example above, for instance, we can set a motion
+    timeout as a unitful quantity::
+
+        attrs:
+            motion_timeout: !Q 1 minute
+
+    When using the ``!Q`` tag, any text before a space is taken to be the magnitude
+    of the quantity, and text following is taken to be the unit specification.
+
     By specifying a path within the configuration file, one can load only a part
     of the given file. For instance, consider the configuration::
 
@@ -110,6 +127,8 @@ def load_instruments(conf_file_name, conf_path="/"):
     if yaml is None:
         raise ImportError("Could not import PyYAML, which is required "
                           "for this function.")
+    # Add support for the physical quantity tag.
+    yaml.add_constructor(u'!Q', quantity_constructor)
 
     if isinstance(conf_file_name, (str, unicode)):
         with open(conf_file_name, 'r') as f:

From b3ec1e25fa646cb75b1089fecf32067f0e7a7409 Mon Sep 17 00:00:00 2001
From: Chris Granade <cgranade@cgranade.com>
Date: Wed, 12 Apr 2017 17:09:11 +1000
Subject: [PATCH 06/21] pylint fixes

---
 instruments/config.py | 8 +++++++-
 1 file changed, 7 insertions(+), 1 deletion(-)

diff --git a/instruments/config.py b/instruments/config.py
index 8f625e65d..f4de35cd9 100644
--- a/instruments/config.py
+++ b/instruments/config.py
@@ -18,6 +18,8 @@
 
 import quantities as pq
 
+from future.builtins import str
+
 from instruments.util_fns import setattr_expression
 
 # FUNCTIONS ###################################################################
@@ -51,6 +53,10 @@ def walk_dict(d, path):
         return walk_dict(d[path[0]], path[1:])
 
 def quantity_constructor(loader, node):
+    """
+    Constructs a `pq.Quantity` instance from a PyYAML
+    node tagged as ``!Q``.
+    """
     # Follows the example of http://stackoverflow.com/a/43081967/267841.
     value = loader.construct_scalar(node)
     magnitude, units = value.split(" ", 1)
@@ -130,7 +136,7 @@ def load_instruments(conf_file_name, conf_path="/"):
     # Add support for the physical quantity tag.
     yaml.add_constructor(u'!Q', quantity_constructor)
 
-    if isinstance(conf_file_name, (str, unicode)):
+    if isinstance(conf_file_name, str):
         with open(conf_file_name, 'r') as f:
             conf_dict = yaml.load(f)
     else:

From 0ff31866b1421fb3521b65469409b5ecafae7e8a Mon Sep 17 00:00:00 2001
From: Chris Granade <cgranade@cgranade.com>
Date: Wed, 12 Apr 2017 17:23:40 +1000
Subject: [PATCH 07/21] Tests for new setattr_expression

---
 instruments/tests/test_util_fns.py | 46 +++++++++++++++++++++++++++++-
 1 file changed, 45 insertions(+), 1 deletion(-)

diff --git a/instruments/tests/test_util_fns.py b/instruments/tests/test_util_fns.py
index 914372404..7144f1bc7 100644
--- a/instruments/tests/test_util_fns.py
+++ b/instruments/tests/test_util_fns.py
@@ -16,7 +16,8 @@
 
 from instruments.util_fns import (
     ProxyList,
-    assume_units, convert_temperature
+    assume_units, convert_temperature,
+    setattr_expression
 )
 
 # TEST CASES #################################################################
@@ -169,3 +170,46 @@ def test_temperater_conversion_failure():
 @raises(ValueError)
 def test_assume_units_failures():
     assume_units(1, 'm').rescale('s')
+
+def test_setattr_expression_simple():
+    class A(object):
+        x = 'x'
+        y = 'y'
+        z = 'z'
+
+    a = A()
+    setattr_expression(a, 'x', 'foo')
+    assert a.x == 'foo'
+
+def test_setattr_expression_index():
+    class A(object):
+        x = ['x', 'y', 'z']
+
+    a = A()
+    setattr_expression(a, 'x[1]', 'foo')
+    assert a.x[1] == 'foo'
+
+def test_setattr_expression_nested():
+    class B(object):
+        x = 'x'
+    class A(object):
+        b = None
+        def __init__(self):
+            self.b = B()
+
+    a = A()
+    setattr_expression(a, 'b.x', 'foo')
+    assert a.b.x == 'foo'
+
+def test_setattr_expression_both():
+    class B(object):
+        x = 'x'
+    class A(object):
+        b = None
+        def __init__(self):
+            self.b = [B()]
+
+    a = A()
+    setattr_expression(a, 'b[0].x', 'foo')
+    assert a.b[0].x == 'foo'
+

From bf8bcc1a9b324b9f2db337ebd7d8de15fec2407f Mon Sep 17 00:00:00 2001
From: Chris Granade <cgranade@cgranade.com>
Date: Wed, 12 Apr 2017 17:41:36 +1000
Subject: [PATCH 08/21] Added tests for new config, YAML.

---
 instruments/config.py            | 15 ++++---
 instruments/tests/test_config.py | 75 ++++++++++++++++++++++++++++++++
 2 files changed, 84 insertions(+), 6 deletions(-)
 create mode 100644 instruments/tests/test_config.py

diff --git a/instruments/config.py b/instruments/config.py
index f4de35cd9..57afa9be3 100644
--- a/instruments/config.py
+++ b/instruments/config.py
@@ -20,7 +20,7 @@
 
 from future.builtins import str
 
-from instruments.util_fns import setattr_expression
+from instruments.util_fns import setattr_expression, split_unit_str
 
 # FUNCTIONS ###################################################################
 
@@ -43,8 +43,9 @@ def walk_dict(d, path):
     # Treat as a base case that the path is empty.
     if not path:
         return d
-    if isinstance(path, str):
+    if not isinstance(path, list):
         path = path.split("/")
+
     if not path[0]:
         # If the first part of the path is empty, do nothing.
         return walk_dict(d, path[1:])
@@ -59,8 +60,12 @@ def quantity_constructor(loader, node):
     """
     # Follows the example of http://stackoverflow.com/a/43081967/267841.
     value = loader.construct_scalar(node)
-    magnitude, units = value.split(" ", 1)
-    return pq.Quantity(magnitude, units)
+    return pq.Quantity(*split_unit_str(value))
+
+# We avoid having to register !Q every time by doing as soon as the
+# relevant constructor is defined.
+if yaml:
+    yaml.add_constructor(u'!Q', quantity_constructor)
 
 def load_instruments(conf_file_name, conf_path="/"):
     """
@@ -133,8 +138,6 @@ def load_instruments(conf_file_name, conf_path="/"):
     if yaml is None:
         raise ImportError("Could not import PyYAML, which is required "
                           "for this function.")
-    # Add support for the physical quantity tag.
-    yaml.add_constructor(u'!Q', quantity_constructor)
 
     if isinstance(conf_file_name, str):
         with open(conf_file_name, 'r') as f:
diff --git a/instruments/tests/test_config.py b/instruments/tests/test_config.py
new file mode 100644
index 000000000..8c7c5ae64
--- /dev/null
+++ b/instruments/tests/test_config.py
@@ -0,0 +1,75 @@
+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+"""
+Module containing tests for util_fns.py
+"""
+
+# IMPORTS ####################################################################
+
+from __future__ import absolute_import, unicode_literals
+
+from io import StringIO
+
+import quantities as pq
+
+from unittest import skipIf
+
+try:
+    import yaml
+except ImportError:
+    yaml = None
+
+from instruments import Instrument
+from instruments.config import (
+    load_instruments
+)
+
+# TEST CASES #################################################################
+
+# pylint: disable=protected-access,missing-docstring
+
+@skipIf(yaml is None, "PyYAML is not installed.")
+def test_load_test_instrument():
+    config_data = StringIO(u"""
+test:
+    class: !!python/name:instruments.Instrument
+    uri: test://
+""")
+    insts = load_instruments(config_data)
+    assert isinstance(insts['test'], Instrument)
+
+@skipIf(yaml is None, "PyYAML is not installed.")
+def test_load_test_instrument_subtree():
+    config_data = StringIO(u"""
+instruments:
+    test:
+        class: !!python/name:instruments.Instrument
+        uri: test://
+""")
+    insts = load_instruments(config_data, conf_path="/instruments")
+    assert isinstance(insts['test'], Instrument)
+
+@skipIf(yaml is None, "PyYAML is not installed.")
+def test_yaml_quantity_tag():
+    yaml_data = StringIO(u"""
+a:
+    b: !Q 37 tesla
+    c: !Q 41.2 inches
+    d: !Q 98
+""")
+    data = yaml.load(yaml_data)
+    assert data['a']['b'] == pq.Quantity(37, 'tesla')
+    assert data['a']['c'] == pq.Quantity(41.2, 'inches')
+    assert data['a']['d'] == 98
+
+@skipIf(yaml is None, "PyYAML is not installed.")
+def test_load_test_instrument_setattr():
+    config_data = StringIO(u"""
+test:
+    class: !!python/name:instruments.Instrument
+    uri: test://
+    attrs:
+        foo: !Q 111 GHz
+""")
+    insts = load_instruments(config_data)
+    assert insts['test'].foo == pq.Quantity(111, 'GHz')

From f4d23bf84c4b704bbb834c7c9ca4c86b47c6a94f Mon Sep 17 00:00:00 2001
From: Chris Granade <cgranade@cgranade.com>
Date: Wed, 12 Apr 2017 17:45:12 +1000
Subject: [PATCH 09/21] pylint fix for new tests

---
 instruments/tests/test_config.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/instruments/tests/test_config.py b/instruments/tests/test_config.py
index 8c7c5ae64..eaec4d6ab 100644
--- a/instruments/tests/test_config.py
+++ b/instruments/tests/test_config.py
@@ -10,10 +10,10 @@
 
 from io import StringIO
 
-import quantities as pq
-
 from unittest import skipIf
 
+import quantities as pq
+
 try:
     import yaml
 except ImportError:

From 5f4ac278ea7e68d1589d0881d6a50b9e79c2633b Mon Sep 17 00:00:00 2001
From: Chris Granade <cgranade@cgranade.com>
Date: Wed, 12 Apr 2017 18:33:02 +1000
Subject: [PATCH 10/21] Very minor pylint fix

---
 instruments/tests/test_util_fns.py | 1 -
 1 file changed, 1 deletion(-)

diff --git a/instruments/tests/test_util_fns.py b/instruments/tests/test_util_fns.py
index 7144f1bc7..ecf8e6ec5 100644
--- a/instruments/tests/test_util_fns.py
+++ b/instruments/tests/test_util_fns.py
@@ -212,4 +212,3 @@ def __init__(self):
     a = A()
     setattr_expression(a, 'b[0].x', 'foo')
     assert a.b[0].x == 'foo'
-

From 86ca2e6cb600655b03e64bedf8cf6c073c69baea Mon Sep 17 00:00:00 2001
From: Chris Granade <cgranade@cgranade.com>
Date: Thu, 13 Apr 2017 14:06:53 +1000
Subject: [PATCH 11/21] Added ruamel.yaml as testing dep.

---
 dev-requirements.txt             |  1 +
 instruments/config.py            |  7 +++++--
 instruments/tests/test_config.py | 13 +------------
 3 files changed, 7 insertions(+), 14 deletions(-)

diff --git a/dev-requirements.txt b/dev-requirements.txt
index 7418bc754..3f8a28360 100644
--- a/dev-requirements.txt
+++ b/dev-requirements.txt
@@ -1,3 +1,4 @@
 mock
 nose
 pylint
+ruamel.yaml
diff --git a/instruments/config.py b/instruments/config.py
index 57afa9be3..05f5dc509 100644
--- a/instruments/config.py
+++ b/instruments/config.py
@@ -12,9 +12,12 @@
 import warnings
 
 try:
-    import yaml
+    import ruamel_yaml as yaml
 except ImportError:
-    yaml = None
+    try:
+        import yaml
+    except ImportError:
+        yaml = None
 
 import quantities as pq
 
diff --git a/instruments/tests/test_config.py b/instruments/tests/test_config.py
index eaec4d6ab..00a0a635d 100644
--- a/instruments/tests/test_config.py
+++ b/instruments/tests/test_config.py
@@ -10,25 +10,17 @@
 
 from io import StringIO
 
-from unittest import skipIf
-
 import quantities as pq
 
-try:
-    import yaml
-except ImportError:
-    yaml = None
-
 from instruments import Instrument
 from instruments.config import (
-    load_instruments
+    load_instruments, yaml
 )
 
 # TEST CASES #################################################################
 
 # pylint: disable=protected-access,missing-docstring
 
-@skipIf(yaml is None, "PyYAML is not installed.")
 def test_load_test_instrument():
     config_data = StringIO(u"""
 test:
@@ -38,7 +30,6 @@ def test_load_test_instrument():
     insts = load_instruments(config_data)
     assert isinstance(insts['test'], Instrument)
 
-@skipIf(yaml is None, "PyYAML is not installed.")
 def test_load_test_instrument_subtree():
     config_data = StringIO(u"""
 instruments:
@@ -49,7 +40,6 @@ def test_load_test_instrument_subtree():
     insts = load_instruments(config_data, conf_path="/instruments")
     assert isinstance(insts['test'], Instrument)
 
-@skipIf(yaml is None, "PyYAML is not installed.")
 def test_yaml_quantity_tag():
     yaml_data = StringIO(u"""
 a:
@@ -62,7 +52,6 @@ def test_yaml_quantity_tag():
     assert data['a']['c'] == pq.Quantity(41.2, 'inches')
     assert data['a']['d'] == 98
 
-@skipIf(yaml is None, "PyYAML is not installed.")
 def test_load_test_instrument_setattr():
     config_data = StringIO(u"""
 test:

From fa0a518e839b38998b074f91a14c0d611aa8fb92 Mon Sep 17 00:00:00 2001
From: Chris Granade <cgranade@cgranade.com>
Date: Thu, 13 Apr 2017 14:10:30 +1000
Subject: [PATCH 12/21] Reworked awkward sentence.

---
 instruments/config.py | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/instruments/config.py b/instruments/config.py
index 05f5dc509..dfe144be8 100644
--- a/instruments/config.py
+++ b/instruments/config.py
@@ -86,8 +86,9 @@ def load_instruments(conf_file_name, conf_path="/"):
     the form
     ``{'ddg': instruments.srs.SRSDG645.open_from_uri('gpib+usb://COM7/15')}``.
 
-    Optionally, each the value of each instrument key can also contain a dictionary
-    of attributes to set on the newly-created instrument. For instance, the following
+    Each instrument configuration section can also specify one or more attributes
+    to set. These attributes are specified using a ``attrs`` section as well as the
+    required ``class`` and ``uri`` sections. For instance, the following
     dictionary creates a ThorLabs APT motor controller instrument with a single motor
     model configured::
 

From a0aff098ff7398b80a95290a78f78f3575077a1c Mon Sep 17 00:00:00 2001
From: Chris Granade <cgranade@cgranade.com>
Date: Thu, 13 Apr 2017 14:12:10 +1000
Subject: [PATCH 13/21] Updated docs for ruamel.yaml dep.

---
 doc/source/intro.rst | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/doc/source/intro.rst b/doc/source/intro.rst
index c1943320e..072c1e582 100644
--- a/doc/source/intro.rst
+++ b/doc/source/intro.rst
@@ -36,7 +36,7 @@ $ pip install -r requirements.txt
 Optional Dependencies
 ~~~~~~~~~~~~~~~~~~~~~
 
-- `PyYAML`_ (required for configuration file support)
+- `ruamel.yaml`_ (required for configuration file support)
 - `PyUSB`_ (version 1.0a or higher, required for raw USB support)
 - `PyVISA`_ (required for accessing instruments via VISA library)
 
@@ -44,7 +44,7 @@ Optional Dependencies
 .. _quantities: http://pythonhosted.org/quantities/
 .. _enum34: https://pypi.python.org/pypi/enum34
 .. _future: https://pypi.python.org/pypi/future
-.. _PyYAML: https://bitbucket.org/xi/pyyaml
+.. _ruamel.yaml: http://yaml.readthedocs.io
 .. _PyUSB: http://sourceforge.net/apps/trac/pyusb/
 .. _PyVISA: http://pyvisa.sourceforge.net/
 

From 29ffc572cf2ac27e20ddeee017ff514284c44a09 Mon Sep 17 00:00:00 2001
From: Steven Casagrande <scasagrande@galvant.ca>
Date: Wed, 19 Apr 2017 17:13:33 -0400
Subject: [PATCH 14/21] Remove pyyaml, only use ruamel.yaml

---
 dev-requirements.txt  |  1 -
 doc/source/intro.rst  |  6 ++----
 instruments/config.py | 12 ++----------
 requirements.txt      |  2 +-
 setup.py              |  2 +-
 5 files changed, 6 insertions(+), 17 deletions(-)

diff --git a/dev-requirements.txt b/dev-requirements.txt
index bddd7459e..c42f8689e 100644
--- a/dev-requirements.txt
+++ b/dev-requirements.txt
@@ -1,4 +1,3 @@
 mock
 nose
 pylint==1.6.5
-ruamel.yaml
diff --git a/doc/source/intro.rst b/doc/source/intro.rst
index c62902376..733a33c44 100644
--- a/doc/source/intro.rst
+++ b/doc/source/intro.rst
@@ -33,15 +33,13 @@ $ pip install -r requirements.txt
 - `enum34`_
 - `future`_
 - `python-vxi11`_
-- `PyUSB`_
+- `PyUSB`_ (version 1.0a or higher, required for raw USB support)
 - `python-usbtmc`_
-- `PyYAML`_
+- `ruamel.yaml`_ (required for configuration file support)
 
 Optional Dependencies
 ~~~~~~~~~~~~~~~~~~~~~
 
-- `ruamel.yaml`_ (required for configuration file support)
-- `PyUSB`_ (version 1.0a or higher, required for raw USB support)
 - `PyVISA`_ (required for accessing instruments via VISA library)
 
 .. _PySerial: http://pyserial.sourceforge.net/
diff --git a/instruments/config.py b/instruments/config.py
index dfe144be8..022010ea2 100644
--- a/instruments/config.py
+++ b/instruments/config.py
@@ -11,14 +11,7 @@
 
 import warnings
 
-try:
-    import ruamel_yaml as yaml
-except ImportError:
-    try:
-        import yaml
-    except ImportError:
-        yaml = None
-
+import ruamel.yaml as yaml
 import quantities as pq
 
 from future.builtins import str
@@ -67,8 +60,7 @@ def quantity_constructor(loader, node):
 
 # We avoid having to register !Q every time by doing as soon as the
 # relevant constructor is defined.
-if yaml:
-    yaml.add_constructor(u'!Q', quantity_constructor)
+yaml.add_constructor(u'!Q', quantity_constructor)
 
 def load_instruments(conf_file_name, conf_path="/"):
     """
diff --git a/requirements.txt b/requirements.txt
index 113c7a6a3..622bb14d0 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -6,4 +6,4 @@ enum34
 python-vxi11>=0.8
 pyusb
 python-usbtmc
-pyyaml
+ruamel.yaml
diff --git a/setup.py b/setup.py
index c928c9608..b422efd4b 100644
--- a/setup.py
+++ b/setup.py
@@ -43,7 +43,7 @@
     "python-vxi11",
     "python-usbtmc",
     "pyusb",
-    "pyyaml"
+    "ruamel.yaml"
 ]
 EXTRAS_REQUIRE = {
     'VISA': ["pyvisa"]

From ccda2a1d2f20056e7f13fdf77d158026ec9d93af Mon Sep 17 00:00:00 2001
From: Chris Granade <cgranade@cgranade.com>
Date: Thu, 20 Apr 2017 11:17:12 +1000
Subject: [PATCH 15/21] Disabled info category messages from mylint.

---
 .travis.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.travis.yml b/.travis.yml
index 7cbb7d02b..f2f27b526 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -12,8 +12,8 @@ install:
   - pip install coverage
 script:
   - nosetests --with-coverage -w instruments
-  - pylint --py3k instruments/
-  - pylint instruments/
+  - pylint --py3k instruments
+  - pylint --disable=I instruments
 after_success:
   - coveralls
 deploy:

From 8711b96e32e2d89ffc8e13a0ad1b13c0f984c956 Mon Sep 17 00:00:00 2001
From: Chris Granade <cgranade@cgranade.com>
Date: Thu, 20 Apr 2017 11:25:14 +1000
Subject: [PATCH 16/21] Added version dump to travis config.

---
 .travis.yml | 11 +++++++++++
 1 file changed, 11 insertions(+)

diff --git a/.travis.yml b/.travis.yml
index f2f27b526..ed6d2479f 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -10,6 +10,17 @@ install:
   - "pip install -r dev-requirements.txt"
   - pip install python-coveralls
   - pip install coverage
+before_script:
+  # We use before_script to report version and path information in a way
+  # that can be easily hidden by Travis' log folding. Moreover, a nonzero
+  # exit code from this block kills the entire job, meaning that if we can't
+  # even sensibly get version information, we correctly abort.
+  - which python
+  - python --version
+  - which nosetests
+  - nosetests --version
+  - which pylint
+  - pylint --version
 script:
   - nosetests --with-coverage -w instruments
   - pylint --py3k instruments

From f73a2439116ba89b867893dbcfe00f1982e03694 Mon Sep 17 00:00:00 2001
From: Chris Granade <cgranade@cgranade.com>
Date: Thu, 20 Apr 2017 11:42:02 +1000
Subject: [PATCH 17/21] Trying ot use python -m to work around venv issues.

---
 .travis.yml | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/.travis.yml b/.travis.yml
index ed6d2479f..816f0f3d6 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -23,8 +23,10 @@ before_script:
   - pylint --version
 script:
   - nosetests --with-coverage -w instruments
-  - pylint --py3k instruments
-  - pylint --disable=I instruments
+  # We invoke pylint using -m to ensure that we get the exact same
+  # version as in the virtualenv that Travis creates for 3.5.
+  - python -m pylint --py3k instruments
+  - python -m pylint --disable=I instruments
 after_success:
   - coveralls
 deploy:

From 8d969813abed3d102a72e09aefdb0c711e6f2a39 Mon Sep 17 00:00:00 2001
From: Chris Granade <cgranade@cgranade.com>
Date: Thu, 20 Apr 2017 12:06:39 +1000
Subject: [PATCH 18/21] Revert "Trying ot use python -m to work around venv
 issues."

This reverts commit f73a2439116ba89b867893dbcfe00f1982e03694.
---
 .travis.yml | 6 ++----
 1 file changed, 2 insertions(+), 4 deletions(-)

diff --git a/.travis.yml b/.travis.yml
index 816f0f3d6..ed6d2479f 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -23,10 +23,8 @@ before_script:
   - pylint --version
 script:
   - nosetests --with-coverage -w instruments
-  # We invoke pylint using -m to ensure that we get the exact same
-  # version as in the virtualenv that Travis creates for 3.5.
-  - python -m pylint --py3k instruments
-  - python -m pylint --disable=I instruments
+  - pylint --py3k instruments
+  - pylint --disable=I instruments
 after_success:
   - coveralls
 deploy:

From 5b148b6f9c2d438b1222306b0ed11646f644eaa6 Mon Sep 17 00:00:00 2001
From: Chris Granade <cgranade@cgranade.com>
Date: Thu, 20 Apr 2017 14:19:26 +1000
Subject: [PATCH 19/21] ruamel.yaml vs ruamel_yaml and fixing pylint false +ve.

---
 instruments/config.py | 13 ++++++++++++-
 1 file changed, 12 insertions(+), 1 deletion(-)

diff --git a/instruments/config.py b/instruments/config.py
index 022010ea2..20f2b8f17 100644
--- a/instruments/config.py
+++ b/instruments/config.py
@@ -11,7 +11,18 @@
 
 import warnings
 
-import ruamel.yaml as yaml
+try:
+    import ruamel.yaml as yaml
+except ImportError:
+    # Some versions of ruamel.yaml are named ruamel_yaml, so try that
+    # too.
+    #
+    # In either case, we've observed issues with pylint where it will raise
+    # a false positive from its import-error checker, so we locally disable
+    # it here. Once the cause for the false positive has been identified,
+    # the import-error check should be re-enabled.
+    import ruamel_yaml as yaml # pylint: disable=import-error
+
 import quantities as pq
 
 from future.builtins import str

From 3099d079e7f93d82c4e791307b4b27090d646d82 Mon Sep 17 00:00:00 2001
From: Chris Granade <cgranade@cgranade.com>
Date: Thu, 20 Apr 2017 14:26:21 +1000
Subject: [PATCH 20/21] Explicitly use unsafe loader as suggested by
 ruamel.yaml warnings.

---
 instruments/config.py | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/instruments/config.py b/instruments/config.py
index 20f2b8f17..107daa157 100644
--- a/instruments/config.py
+++ b/instruments/config.py
@@ -143,14 +143,14 @@ def load_instruments(conf_file_name, conf_path="/"):
     """
 
     if yaml is None:
-        raise ImportError("Could not import PyYAML, which is required "
+        raise ImportError("Could not import ruamel.yaml, which is required "
                           "for this function.")
 
     if isinstance(conf_file_name, str):
         with open(conf_file_name, 'r') as f:
-            conf_dict = yaml.load(f)
+            conf_dict = yaml.load(f, Loader=yaml.Loader)
     else:
-        conf_dict = yaml.load(conf_file_name)
+        conf_dict = yaml.load(conf_file_name, Loader=yaml.Loader)
 
     conf_dict = walk_dict(conf_dict, conf_path)
 

From afca981707f592c7c1d19e9f30287db6ec7b642a Mon Sep 17 00:00:00 2001
From: Chris Granade <cgranade@cgranade.com>
Date: Thu, 20 Apr 2017 14:34:33 +1000
Subject: [PATCH 21/21] Marked test as explicitly unsafe as well.

---
 instruments/tests/test_config.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/instruments/tests/test_config.py b/instruments/tests/test_config.py
index 00a0a635d..6a2119fa5 100644
--- a/instruments/tests/test_config.py
+++ b/instruments/tests/test_config.py
@@ -47,7 +47,7 @@ def test_yaml_quantity_tag():
     c: !Q 41.2 inches
     d: !Q 98
 """)
-    data = yaml.load(yaml_data)
+    data = yaml.load(yaml_data, Loader=yaml.Loader)
     assert data['a']['b'] == pq.Quantity(37, 'tesla')
     assert data['a']['c'] == pq.Quantity(41.2, 'inches')
     assert data['a']['d'] == 98