Merge pull request #824 from jenshnielsen/mypy_exp

Run mypy type checking on the codebase with Travis

.travis.yml

@@ -35,7 +35,10 @@ script:
     - py.test --cov=qcodes --cov-report xml --cov-config=.coveragerc
     # build docs with warnings as errors
     - |
-      cd ../docs
+      cd ..
+      mypy qcodes --ignore-missing-imports
+    - |
+      cd docs
       make SPHINXOPTS="-W" html-api
     - cd ..
 

qcodes/__init__.py

@@ -10,7 +10,7 @@
 # we dont want spyder to reload qcodes as this will overwrite the default station
 # instrument list and running monitor
 add_to_spyder_UMR_excludelist('qcodes')
-config = Config()
+config = Config() # type: Config
 
 from qcodes.version import __version__
 
@@ -88,7 +88,7 @@
 del _c
 
 try:
-    get_ipython() # Check if we are in iPython
+    get_ipython() # type: ignore # Check if we are in iPython
     from qcodes.utils.magic import register_magic_class
     _register_magic = config.core.get('register_magic', False)
     if _register_magic is not False:

qcodes/config/config.py

@@ -9,6 +9,7 @@
 from pathlib import Path
 
 import jsonschema
+from typing import Dict
 
 logger = logging.getLogger(__name__)
 
@@ -87,8 +88,8 @@ class Config():
     defaults = None
     defaults_schema = None
 
-    _diff_config = {}
-    _diff_schema = {}
+    _diff_config: Dict[str, dict] = {}
+    _diff_schema: Dict[str, dict] = {}
 
     def __init__(self):
         self.defaults, self.defaults_schema = self.load_default()

qcodes/data/data_set.py

@@ -5,6 +5,7 @@
 from traceback import format_exc
 from copy import deepcopy
 from collections import OrderedDict
+from typing import Dict, Callable
 
 from .gnuplot_format import GNUPlotFormat
 from .io import DiskIO
@@ -168,7 +169,7 @@ class DataSet(DelegateAttributes):
     default_formatter = GNUPlotFormat()
     location_provider = FormatLocation()
 
-    background_functions = OrderedDict()
+    background_functions: Dict[str, Callable] = OrderedDict()
 
     def __init__(self, location=None, arrays=None, formatter=None, io=None,
                  write_period=5):

qcodes/data/location.py

@@ -3,7 +3,7 @@
 import re
 import string
 
-from qcodes import config
+import qcodes.config
 
 class SafeFormatter(string.Formatter):
 
@@ -83,7 +83,7 @@ class FormatLocation:
         as '{date:%Y-%m-%d}' or '{counter:03}'
     """
 
-    default_fmt = config['core']['default_fmt']
+    default_fmt = qcodes.config['core']['default_fmt']
 
     def __init__(self, fmt=None, fmt_date=None, fmt_time=None,
                  fmt_counter=None, record=None):

qcodes/dataset/data_set.py

@@ -179,8 +179,8 @@ def _new(self, name, exp_id, specs: SPECS = None, values=None,
         Actually perform all the side effects needed for
         the creation of a new dataset.
         """
-        _, run_id, _ = create_run(self.conn, exp_id, name,
-                                  specs, values, metadata)
+        _, run_id, __ = create_run(self.conn, exp_id, name,
+                                   specs, values, metadata)
 
         # this is really the UUID (an ever increasing count in the db)
         self.run_id = run_id
@@ -440,7 +440,7 @@ def modify_results(self, start_index: int,
                                flattened_keys,
                                flattened_values)
 
-    def add_parameter_values(self, spec: ParamSpec, values: List[VALUES]):
+    def add_parameter_values(self, spec: ParamSpec, values: VALUES):
         """
         Add a parameter to the DataSet and associates result values with the
         new parameter.

qcodes/dataset/experiment_container.py

@@ -236,8 +236,8 @@ def load_experiment_by_name(name: str,
         for row in rows:
             s = f"exp_id:{row['exp_id']} ({row['name']}-{row['sample_name']}) started at({row['start_time']})"
             _repr.append(s)
-        _repr = "\n".join(_repr)
-        raise ValueError(f"Many experiments matching your request found {_repr}")
+        _repr_str = "\n".join(_repr)
+        raise ValueError(f"Many experiments matching your request found {_repr_str}")
     else:
         e.exp_id = rows[0]['exp_id']
     return e

qcodes/dataset/measurements.py

@@ -11,7 +11,7 @@
 
 import qcodes as qc
 from qcodes import Station
-from qcodes.instrument.parameter import ArrayParameter, _BaseParameter
+from qcodes.instrument.parameter import ArrayParameter, _BaseParameter, Parameter
 from qcodes.dataset.experiment_container import Experiment
 from qcodes.dataset.param_spec import ParamSpec
 from qcodes.dataset.data_set import DataSet
@@ -29,7 +29,7 @@ class DataSaver:
     datasaving to the database
     """
 
-    default_callback = None
+    default_callback: Optional[dict] = None
 
     def __init__(self, dataset: DataSet, write_period: float,
                  parameters: Dict[str, ParamSpec]) -> None:
@@ -45,7 +45,7 @@ def __init__(self, dataset: DataSet, write_period: float,
         self._known_parameters = list(parameters.keys())
         self._results: List[dict] = []  # will be filled by addResult
         self._last_save_time = monotonic()
-        self._known_dependencies: Dict[str, str] = {}
+        self._known_dependencies: Dict[str, List[str]] = {}
         for param, parspec in parameters.items():
             if parspec.depends_on != '':
                 self._known_dependencies.update({str(param):
@@ -152,6 +152,7 @@ def add_result(self,
                 # For compatibility with the old Loop, setpoints are
                 # tuples of numbers (usually tuple(np.linspace(...))
                 if hasattr(value, '__len__') and not(isinstance(value, str)):
+                    value = cast(Union[Sequence,np.ndarray], value)
                     res_dict.update({param: value[index]})
                 else:
                     res_dict.update({param: value})
@@ -398,6 +399,7 @@ def register_parameter(
         name = str(parameter)
 
         if isinstance(parameter, ArrayParameter):
+            parameter = cast(ArrayParameter, parameter)
             if parameter.setpoint_names:
                 spname = (f'{parameter._instrument.name}_'
                           f'{parameter.setpoint_names[0]}')
@@ -416,8 +418,10 @@ def register_parameter(
                            label=splabel, unit=spunit)
 
             self.parameters[spname] = sp
-            setpoints = setpoints if setpoints else ()
-            setpoints += (spname,)
+            my_setpoints: Tuple[Union[_BaseParameter, str], ...] = setpoints if setpoints else ()
+            my_setpoints += (spname,)
+        else:
+            my_setpoints = setpoints
 
         # We currently treat ALL parameters as 'numeric' and fail to add them
         # to the dataset if they can not be unraveled to fit that description
@@ -426,12 +430,13 @@ def register_parameter(
         # requirement later and start saving binary blobs with the datasaver,
         # but for now binary blob saving is referred to using the DataSet
         # API directly
+        parameter = cast(Union[Parameter, ArrayParameter], parameter)
         paramtype = 'numeric'
         label = parameter.label
         unit = parameter.unit
 
-        if setpoints:
-            sp_strings = [str(sp) for sp in setpoints]
+        if my_setpoints:
+            sp_strings = [str(sp) for sp in my_setpoints]
         else:
             sp_strings = []
         if basis:

qcodes/dataset/plotting.py

@@ -13,11 +13,10 @@
 log = logging.getLogger(__name__)
 DB = qc.config["core"]["db_location"]
 
-mplaxes = matplotlib.axes.Axes
 
 def plot_by_id(run_id: int,
-               axes: Optional[Union[mplaxes,
-                                  Sequence[mplaxes]]]=None) -> List[mplaxes]:
+               axes: Optional[Union[matplotlib.axes.Axes,
+                                    Sequence[matplotlib.axes.Axes]]]=None) -> List[matplotlib.axes.Axes]:
     def set_axis_labels(ax, data):
         if data[0]['label'] == '':
             lbl = data[0]['name']
@@ -50,7 +49,7 @@ def set_axis_labels(ax, data):
     """
     alldata = get_data_by_id(run_id)
     nplots = len(alldata)
-    if isinstance(axes, mplaxes):
+    if isinstance(axes, matplotlib.axes.Axes):
         axes = [axes]
 
     if axes is None:
@@ -115,7 +114,7 @@ def set_axis_labels(ax, data):
 
 def plot_on_a_plain_grid(x: np.ndarray, y: np.ndarray,
                          z: np.ndarray,
-                         ax: mplaxes) -> mplaxes:
+                         ax: matplotlib.axes.Axes) -> matplotlib.axes.Axes:
     """
     Plot a heatmap of z using x and y as axes. Assumes that the data
     are rectangular, i.e. that x and y together describe a rectangular

qcodes/dataset/sqlite_base.py

@@ -107,7 +107,7 @@ def _convert_array(text: bytes) -> ndarray:
     return np.load(out)
 
 
-def one(curr: sqlite3.Cursor, column: str) -> Any:
+def one(curr: sqlite3.Cursor, column: Union[int, str]) -> Any:
     """Get the value of one column from one row
     Args:
         curr: cursor to operate on
@@ -408,11 +408,11 @@ def insert_many_values(conn: sqlite3.Connection,
     # According to the SQLite changelog, the version number
     # to check against below
     # ought to be 3.7.11, but that fails on Travis
-    if LooseVersion(version) <= LooseVersion('3.8.2'):
+    if LooseVersion(str(version)) <= LooseVersion('3.8.2'):
         max_var = qc.SQLiteSettings.limits['MAX_COMPOUND_SELECT']
     else:
         max_var = qc.SQLiteSettings.limits['MAX_VARIABLE_NUMBER']
-    rows_per_transaction = int(max_var/no_of_columns)
+    rows_per_transaction = int(int(max_var)/no_of_columns)
 
     _columns = ",".join(columns)
     _values = "(" + ",".join(["?"] * len(values[0])) + ")"

qcodes/dataset/sqlite_settings.py

@@ -2,7 +2,7 @@
 from typing import Tuple, Dict, Union
 
 
-def _read_settings() -> Tuple[Dict[str, str],
+def _read_settings() -> Tuple[Dict[str, Union[str,int]],
                               Dict[str, Union[bool, int, str]]]:
     """
     Function to read the local SQLite settings at import time.
@@ -19,6 +19,7 @@ def _read_settings() -> Tuple[Dict[str, str],
     """
     # For the limits, there are known default values
     # (known from https://www.sqlite.org/limits.html)
+    DEFAULT_LIMITS: Dict[str, Union[str, int]]
     DEFAULT_LIMITS = {'MAX_ATTACHED': 10,
                       'MAX_COLUMN': 2000,
                       'MAX_COMPOUND_SELECT': 500,
@@ -35,6 +36,7 @@ def _read_settings() -> Tuple[Dict[str, str],
     opt_num = 0
     resp = ''
 
+    limits: Dict[str, Union[str,int]]
     limits = DEFAULT_LIMITS.copy()
     settings = {}
 
@@ -47,6 +49,7 @@ def _read_settings() -> Tuple[Dict[str, str],
         opt_num += 1
         lst = resp.split('=')
         if len(lst) == 2:
+            val: Union[str,int]
             (param, val) = lst
             if val.isnumeric():
                 val = int(val)

qcodes/instrument/base.py

@@ -3,14 +3,15 @@
 import time
 import warnings
 import weakref
-from typing import Sequence, Optional, Dict, Union, Callable, Any, List
+from typing import Sequence, Optional, Dict, Union, Callable, Any, List, TYPE_CHECKING, cast
 
 import numpy as np
-
+if TYPE_CHECKING:
+    from qcodes.instrumet.channel import ChannelList
 from qcodes.utils.helpers import DelegateAttributes, strip_attrs, full_class
 from qcodes.utils.metadata import Metadatable
 from qcodes.utils.validators import Anything
-from .parameter import Parameter
+from .parameter import Parameter, _BaseParameter
 from .function import Function
 
 log = logging.getLogger(__name__)
@@ -45,9 +46,9 @@ def __init__(self, name: str,
                  metadata: Optional[Dict]=None, **kwargs) -> None:
         self.name = str(name)
 
-        self.parameters = {}
-        self.functions = {}
-        self.submodules = {}
+        self.parameters = {} # type: Dict[str, _BaseParameter]
+        self.functions = {} # type: Dict[str, Function]
+        self.submodules = {} # type: Dict[str, Union['InstrumentBase', 'ChannelList']]
         super().__init__(**kwargs)
 
     def add_parameter(self, name: str,
@@ -109,7 +110,7 @@ def add_function(self, name: str, **kwargs) -> None:
         func = Function(name=name, instrument=self, **kwargs)
         self.functions[name] = func
 
-    def add_submodule(self, name: str, submodule: Metadatable) -> None:
+    def add_submodule(self, name: str, submodule:  Union['InstrumentBase', 'ChannelList']) -> None:
         """
         Bind one submodule to this instrument.
 
@@ -360,7 +361,9 @@ class Instrument(InstrumentBase):
 
     shared_kwargs = ()
 
-    _all_instruments = {}
+    _all_instruments = {} # type: Dict[str, weakref.ref[Instrument]]
+    _type = None
+    _instances = [] # type: List[weakref.ref]
 
     def __init__(self, name: str,
                  metadata: Optional[Dict]=None, **kwargs) -> None:
@@ -377,7 +380,7 @@ def __init__(self, name: str,
 
         self.record_instance(self)
 
-    def get_idn(self) -> Dict:
+    def get_idn(self) -> Dict[str, Optional[str]]:
         """
         Parse a standard VISA '\*IDN?' response into an ID dict.
 
@@ -399,6 +402,7 @@ def get_idn(self) -> Dict:
             idstr = self.ask('*IDN?')
             # form is supposed to be comma-separated, but we've seen
             # other separators occasionally
+            idparts = [] # type: List[Optional[str]]
             for separator in ',;:':
                 # split into no more than 4 parts, so we don't lose info
                 idparts = [p.strip() for p in idstr.split(separator, 3)]
@@ -580,14 +584,14 @@ def find_instrument(cls, name: str,
         if ins is None:
             del cls._all_instruments[name]
             raise KeyError('Instrument {} has been removed'.format(name))
-
+        inst = cast('Instrument', ins)
         if instrument_class is not None:
-            if not isinstance(ins, instrument_class):
+            if not isinstance(inst, instrument_class):
                 raise TypeError(
                     'Instrument {} is {} but {} was requested'.format(
-                        name, type(ins), instrument_class))
+                        name, type(inst), instrument_class))
 
-        return ins
+        return inst
 
     # `write_raw` and `ask_raw` are the interface to hardware                #
     # `write` and `ask` are standard wrappers to help with error reporting   #
@@ -658,7 +662,7 @@ def ask(self, cmd: str) -> str:
             e.args = e.args + ('asking ' + repr(cmd) + ' to ' + inst,)
             raise e
 
-    def ask_raw(self, cmd: str) -> None:
+    def ask_raw(self, cmd: str) -> str:
         """
         Low level method to write to the hardware and return a response.