Merge branch 'develop'

.travis.yml

@@ -14,6 +14,6 @@ install:
   - pip install -r requirements_dev.txt
   - python setup.py install
 script:
-  - python -m pytest --cov=diagnostics --cov-report term-missing
+  - python setup.py test -a "--verbose"
 after_success:
   - coveralls

diagnostics/classes.py

@@ -302,11 +302,9 @@ def __invert__(self):
     def empty(cls, t0, te, fs, name="", inclusive=False):
         if isinstance(t0, datetime.datetime):
             t0 = t0.timestamp()
-        t0 = round(t0, len(str(fs)) - 1)
         if isinstance(te, datetime.datetime):
             te = te.timestamp()
-        te = round(te, len(str(fs)) - 1)
-        k = int(((te - t0) * fs))
+        k = int(np.ceil((te - t0) * fs))
         if inclusive:
             k += 1
         data = np.zeros(k)
@@ -380,17 +378,27 @@ def to_channel(self, c):
             raise ValueError(
                 "can't modify channel to a different fs! please interpolate first"
             )
-        if c.t0 > self.t0:
+        t0_diff = self.t0 - c.t0
+        te_diff = c.te - self.te
+
+        if t0_diff < 0:
             raise DataLossError(
                 "channel data window does not fully overlap! (c.t0 > self.t0)"
             )
-        if c.te < self.te:
+        if te_diff < 0:
             raise DataLossError(
                 "channel data window does not fully overlap! (c.te < self.te)"
             )
-        # TODO: check that self.t0 and c_t0 can be exact t values for given fs
-        self.t0 - c.t0 * self.fs % 1
+
+        if (t0_diff * c.fs) % 1 > 0:
+            raise ValueError("Cant reach both t0 values using new fs")
+
         # TODO: modify data
+        pre_data = np.zeros(int(t0_diff * c.fs))
+        post_data = np.zeros(int(te_diff * c.fs))
+        self.data = np.append(pre_data, np.append(self.data, post_data))
+        self.t0 = c.t0
+
 
     @logged()
     def modify(self, method, inplace=False):
@@ -436,7 +444,6 @@ def to_bool(self, inplace=False):
     @logged()
     def to_events(self):
         return list(self.events())
-        # pass # TODO: create events (state changes) from data
 
     @logged()
     def events(self):
@@ -451,7 +458,6 @@ def events(self):
     def to_statechangearray(self):
         events = self.to_events()
         return StateChangeArray.from_events(events)
-        # pass # TODO: create statechangearray from data
 
     @logged()
     def from_events(self, events):

diagnostics/log.py

@@ -1,6 +1,5 @@
 import os
 import logging
-from logging.handlers import TimedRotatingFileHandler
 from functools import wraps
 
 MOD = "modification"
@@ -14,49 +13,13 @@
 
 formatter = logging.Formatter("%(message)s")
 
-file_handler = TimedRotatingFileHandler(
-    os.path.join(PWD, "modifications.log"),
-    when="W0",
-    interval=1,
-    backupCount=0,
-    encoding=None,
-    delay=False,
-    utc=False,
-)
-
-file_handler.setLevel(logging.DEBUG)
-file_handler.setFormatter(formatter)
-modification_logger.addHandler(file_handler)
-
-
-def logged(log=MOD):
+def logged():
     def wrap(function):
         @wraps(function)
-        def wrapper(
-            *args, **kwargs
-        ):  # TODO: shorten args/kwargs when too long (for instance, when containing data)
-            logger = logging.getLogger(log)
-            logger.debug(
-                "Calling function '{}' with args={} kwargs={}".format(
-                    function.__name__, args, kwargs
-                )
-            )
-            try:
-                response = function(*args, **kwargs)
-            except Exception as error:
-                logger.debug(
-                    "Function '{}' raised {} with error '{}'".format(
-                        function.__name__, error.__class__.__name__, str(error)
-                    )
-                )
-                raise error
-            logger.debug(
-                "Function '{}' returned {}".format(function.__name__, response)
-            )
+        def wrapper(*args, **kwargs):
+            response = function(*args, **kwargs)
             return response
-
         return wrapper
-
     return wrap
 
 

setup.cfg

@@ -0,0 +1,5 @@
+[aliases]
+test=pytest
+
+[tool:pytest]
+addopts = --cov-report html --cov=diagnostics

setup.py

@@ -1,5 +1,26 @@
 import os
+import sys
+
 from setuptools import setup, find_packages
+from setuptools.command.test import test as TestCommand
+
+
+class PyTest(TestCommand):
+    user_options = [("pytest-args=", "a", "Arguments to pass to pytest")]
+
+    def initialize_options(self):
+        TestCommand.initialize_options(self)
+        self.pytest_args = ""
+
+    def run_tests(self):
+        import shlex
+
+        # import here, cause outside the eggs aren't loaded
+        import pytest
+
+        errno = pytest.main(shlex.split(self.pytest_args))
+        sys.exit(errno)
+
 
 with open("README.md", "r") as readme_file:
     readme = readme_file.read()
@@ -9,6 +30,7 @@
 # upload to pypi:
 #   python setup.py sdist bdist_wheel
 #   python -m twine upload
+
 setup(
     name="bonkie-diagnostics",
     version="0.2.1",
@@ -20,6 +42,8 @@
     url="https://github.com/tim00w/diagnostics/",
     packages=find_packages(),
     install_requires=requirements,
+    tests_require=["pytest", "pytest-cov", "pytest-mpl"],
+    cmdclass={"pytest": PyTest},
     classifiers=[
         "Programming Language :: Python :: 3.7",
     ],

tests/test_classes.py

@@ -9,6 +9,7 @@
     Report,
     Event,
 )
+from diagnostics.errors import DataLossError
 import datetime as dt
 import pytz
 
@@ -377,7 +378,7 @@ def test_timeserie_empty():
     a = TimeSerie.empty(1, 10, fs=10, name="a")
     assert len(a) == 90
     assert a.te == 9.9
-    b = TimeSerie.empty(2, 5, 4, name="b", inclusive=True)
+    b = TimeSerie.empty(2, 5, fs=4, name="b", inclusive=True)
     assert len(b) == 13
     assert b.te == 5.0
     c = TimeSerie.empty(
@@ -388,6 +389,9 @@ def test_timeserie_empty():
         inclusive=True,
     )
     assert c.te - c.t0 == 3600.0
+    d = TimeSerie.empty(1.2, 4.8, fs=100, name='d')
+    assert d.t0 == 1.2
+    assert d.te == 4.79
     return True
 
 
@@ -401,6 +405,40 @@ def test_timeserie_plot():
     return True
 
 
+def test_timeserie_tochannel():
+    a = TimeSerie([-2, -1, 0, 1, 2, 3, 4, 5], name="a", fs=1, t0=3)
+    b = TimeSerie.empty(0, 20, fs=1)
+    a.to_channel(b)
+    assert len(a) == 20
+    assert a.t0 == 0
+    assert a.te == 19
+    assert a.at(3) == -2
+    assert a.at(4) == -1
+    assert a.at(5) == 0
+    assert a.at(6) == 1
+    assert a.at(7) == 2
+    assert a.at(8) == 3
+    assert a.at(9) == 4
+    assert a.at(10) == 5
+    c = TimeSerie([-2, -1, 0, 1, 2, 3, 4, 5], name="a", fs=1, t0=3)
+    d = TimeSerie.empty(0,20, fs=2)
+    with pytest.raises(ValueError):
+        c.to_channel(d)
+    e = TimeSerie([-2, -1, 0, 1, 2, 3, 4, 5], name="a", fs=1, t0=3)
+    f = TimeSerie.empty(4,20, fs=1)
+    with pytest.raises(DataLossError):
+        e.to_channel(f)
+    g = TimeSerie([-2, -1, 0, 1, 2, 3, 4, 5], name="a", fs=1, t0=3)
+    h = TimeSerie.empty(0,8, fs=1)
+    with pytest.raises(DataLossError):
+        g.to_channel(h)
+    i = TimeSerie([-2, -1, 0, 1, 2, 3, 4, 5], name="a", fs=1, t0=3)
+    j = TimeSerie.empty(0.5,20.5, fs=1)
+    with pytest.raises(ValueError):
+        i.to_channel(j)
+    return True
+
+
 def test_timserie_mod():
     a = TimeSerie([-2, -1, 0, 1, 2, 3, 4, 5], name="a", fs=1, t0=1)
     b = a.modify("default", inplace=False)