timelined_array 0.1.0__tar.gz → 0.1.2__tar.gz

{timelined_array-0.1.0 → timelined_array-0.1.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: timelined_array
-Version: 0.1.0
+Version: 0.1.2
 Summary: Manage easily 1 or multidimensionnal samples numpy arrays that are time related. Extends numpy without removing any of it's abilities on such arrays.
 Author-Email: Timothe Jost <44769559+JostTim@users.noreply.github.com>
 License: MIT
@@ -12,11 +12,12 @@ Description-Content-Type: text/markdown
 
 # timelined_array
 
-![Python](https://img.shields.io/badge/python-3.11-blue.svg)
-[![PyPI version](https://badge.fury.io/py/timelined_array.svg)](https://badge.fury.io/py/timelined_array)
-![Publish Status](https://github.com/JostTim/timelined_array/actions/workflows/publish.yml/badge.svg)
-![Test Status](https://github.com/JostTim/timelined_array/actions/workflows/test.yml/badge.svg)
-[![codecov](https://codecov.io/gh/JostTim/timelined_array/branch/main/graph/badge.svg)](https://codecov.io/gh/JostTim/timelined_array)
+![Python Version from PEP 621 TOML](https://img.shields.io/python/required-version-toml?tomlFilePath=https%3A%2F%2Fraw.githubusercontent.com%2FJostTim%2Ftimelined_array%2Frefs%2Fheads%2Fmain%2Fpyproject.toml)
+![PyPI - Version](https://img.shields.io/pypi/v/timelined_array)
+![GitHub Actions Workflow Status](https://img.shields.io/github/actions/workflow/status/JostTim/timelined_array/publish.yml?label=Publishing)
+![GitHub Actions Workflow Status](https://img.shields.io/github/actions/workflow/status/JostTim/timelined_array/test.yml?label=Testing)
+[![Codecov](https://img.shields.io/codecov/c/github/JostTim/timelined_array)](https://codecov.io/gh/JostTim/timelined_array)
+
 
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{timelined_array-0.1.0 → timelined_array-0.1.2}/README.md

@@ -1,10 +1,11 @@
 # timelined_array
 
-![Python](https://img.shields.io/badge/python-3.11-blue.svg)
-[![PyPI version](https://badge.fury.io/py/timelined_array.svg)](https://badge.fury.io/py/timelined_array)
-![Publish Status](https://github.com/JostTim/timelined_array/actions/workflows/publish.yml/badge.svg)
-![Test Status](https://github.com/JostTim/timelined_array/actions/workflows/test.yml/badge.svg)
-[![codecov](https://codecov.io/gh/JostTim/timelined_array/branch/main/graph/badge.svg)](https://codecov.io/gh/JostTim/timelined_array)
+![Python Version from PEP 621 TOML](https://img.shields.io/python/required-version-toml?tomlFilePath=https%3A%2F%2Fraw.githubusercontent.com%2FJostTim%2Ftimelined_array%2Frefs%2Fheads%2Fmain%2Fpyproject.toml)
+![PyPI - Version](https://img.shields.io/pypi/v/timelined_array)
+![GitHub Actions Workflow Status](https://img.shields.io/github/actions/workflow/status/JostTim/timelined_array/publish.yml?label=Publishing)
+![GitHub Actions Workflow Status](https://img.shields.io/github/actions/workflow/status/JostTim/timelined_array/test.yml?label=Testing)
+[![Codecov](https://img.shields.io/codecov/c/github/JostTim/timelined_array)](https://codecov.io/gh/JostTim/timelined_array)
+
 
 <!-- eventually, add ?cache-bust=1 to badges url above, and update the value of cache-bust randomly at git commits (or based on the commit name) so that we always see the latest badge produced, and not the cached badge in the browser.-->
 

{timelined_array-0.1.0 → timelined_array-0.1.2}/pyproject.toml

@@ -10,7 +10,7 @@ dependencies = [
 requires-python = ">=3.11"
 readme = "README.md"
 dynamic = []
-version = "0.1.0"
+version = "0.1.2"
 
 [project.license]
 text = "MIT"
@@ -39,11 +39,17 @@ dev = [
 ]
 
 [tool.pytest.ini_options]
-addopts = "--pdbcls=IPython.terminal.debugger:TerminalPdb --cov-report xml --cov --junitxml=pytest_results.xml"
+addopts = "--pdbcls=IPython.terminal.debugger:TerminalPdb --cov-report xml --cov=timelined_array --junitxml=pytest_results.xml --cov-config=pyproject.toml"
 testpaths = [
     "tests",
 ]
 
+[tool.coverage.run]
+omit = [
+    ".vscode/*",
+    ".tests/*",
+]
+
 [tool.black]
 preview = true
 line-length = 120

{timelined_array-0.1.0 → timelined_array-0.1.2}/src/timelined_array/__init__.py

@@ -1,3 +1,3 @@
-__version__ = "0.1.0"
+__version__ = "0.1.2"
 
 from .time import TimelinedArray, MaskedTimelinedArray, Timeline

{timelined_array-0.1.0 → timelined_array-0.1.2}/src/timelined_array/time.py

@@ -7,7 +7,9 @@ import operator
 
 from numpy.typing import NDArray
 from types import MethodType
-from typing import Tuple, List, Protocol, Type, Callable, Any, Optional
+from typing import Tuple, List, Protocol, Type, Callable, Any, Optional, TypeVar, Sequence
+
+Tp = TypeVar("Tp", bound="TimelinedArray")
 
 OperatorType = Callable[[Any, Any], bool]
 
@@ -635,8 +637,10 @@ class BaseTimeArray(TimeMixin, np.ndarray):
         Returns:
             TimelinedArray: The synchronized and cut arrray.
         """
+        # this slice is to select the number of elements, on the time_dimension
+        slices = tuple(slice(None) if i != self.time_dimension else slice(None, element_nb) for i in range(self.ndim))
 
-        return self.itime[start:][:element_nb]  # type: ignore
+        return self.itime[start:][slices]  # type: ignore
 
     def shift_values(
         self,
@@ -829,7 +833,7 @@ class BaseTimeArray(TimeMixin, np.ndarray):
     def all_axes(self):
         return tuple([i for i in range(self.ndim)])
 
-    def mean(self, axis: int | Tuple[int, ...] | None = None, dtype=None, out=None, keepdims=False):
+    def mean(self: Tp, axis: int | Tuple[int, ...] | None = None, dtype=None, out=None, keepdims=False) -> Tp:
         """Calculates the mean along the specified axis.
 
         Args:
@@ -1238,7 +1242,7 @@ class TimelinedArray(BaseTimeArray):
         return type(self).__name__ + np.asarray(self).__str__()
 
     @staticmethod
-    def align_from_iterable(iterable) -> "TimelinedArray":
+    def align_from_iterable(iterable: "Sequence[TimelinedArray]") -> "TimelinedArray":
         """Aligns arrays from an iterable based on their timelines.
 
         Args:

{timelined_array-0.1.0 → timelined_array-0.1.2}/tests/test_timelined_array.py

@@ -25,6 +25,13 @@ def timelined_array_3D():
     return TimelinedArray(np.random.rand(25, 50, 75), timeline=np.arange(50), time_dimension=1)
 
 
+@pytest.fixture
+def masked_timelined_array_1D():
+    data = np.random.rand(50)
+    mask = data > 0.5
+    return MaskedTimelinedArray(data, mask=mask, timeline=np.arange(50), time_dimension=0)
+
+
 @pytest.fixture
 def pickle_path():
     file_path = Path("serialized_test_3D_ta_array.pickle")
@@ -33,6 +40,38 @@ def pickle_path():
         file_path.unlink(missing_ok=True)
 
 
+def test_timelined_array_1D_properties(timelined_array_1D):
+    assert timelined_array_1D.time_dimension == 0
+    assert timelined_array_1D.timeline.shape == (50,)
+
+
+def test_timelined_array_3D_properties(timelined_array_3D):
+    assert timelined_array_3D.time_dimension == 1
+    assert timelined_array_3D.timeline.shape == (50,)
+
+
+def test_masked_timelined_array_1D_properties(masked_timelined_array_1D):
+    assert masked_timelined_array_1D.time_dimension == 0
+    assert np.all(masked_timelined_array_1D.mask == (masked_timelined_array_1D.data > 0.5))
+    assert masked_timelined_array_1D.timeline.shape == (50,)
+
+
+def test_timelined_array_indexing(timelined_array_1D):
+    sub_array = timelined_array_1D[10:20]
+    assert isinstance(sub_array, TimelinedArray)
+    assert sub_array.shape == (10,)
+    assert np.array_equal(sub_array.timeline, np.arange(10, 20))
+    assert timelined_array_1D[[1]] == timelined_array_1D[1]
+
+
+def test_masked_timelined_array_indexing(masked_timelined_array_1D):
+    sub_array = masked_timelined_array_1D[10:20]
+    assert isinstance(sub_array, MaskedTimelinedArray)
+    assert sub_array.shape == (10,)
+    assert np.array_equal(sub_array.timeline, np.arange(10, 20))
+    assert np.all(sub_array.mask == (sub_array.data > 0.5))
+
+
 def get_axis_parameters_3D():
     # affected_axis, time_dimension, shape
     # if None, we expect an AttributeError
@@ -54,12 +93,23 @@ def test_timeline_creation():
     assert isinstance(timeline, Timeline)
     assert timeline.max() == 9
     assert timeline.min() == 0
+    assert 5 in timeline
+    assert timeline.step == 1
 
     with pytest.raises(NotImplementedError):
         timeline = Timeline(np.random.rand(10), uniform_space=True)
     # assert np.unique(np.diff(timeline)).size == 1
 
 
+def test_timelined_array_creation(timelined_array_1D):
+
+    with pytest.raises(ValueError):
+        array = TimelinedArray(np.array(timelined_array_1D))
+
+    with pytest.raises(ValueError):
+        array = TimelinedArray(np.array(timelined_array_1D), time_dimension=5.5)
+
+
 def test_pickle_unpickle(timelined_array_3D, pickle_path):
     # Pickle the numpy array
     with open(pickle_path, "wb") as f:
@@ -76,13 +126,13 @@ def test_pickle_unpickle(timelined_array_3D, pickle_path):
 
 
 def test_start_boundary():
-    assert StartBoundary.inclusive.value(5, 5)
-    assert not StartBoundary.exclusive.value(5, 5)
+    assert StartBoundary.inclusive.value(5, 5)  # 5 is => than 5
+    assert not StartBoundary.exclusive.value(5, 5)  # 5 is not > than 5
 
 
 def test_stop_boundary():
-    assert StoptBoundary.inclusive.value(5, 5)
-    assert not StoptBoundary.exclusive.value(5, 5)
+    assert StoptBoundary.inclusive.value(5, 5)  # 5 is =< than 5
+    assert not StoptBoundary.exclusive.value(5, 5)  # 5 is not < than 5
 
 
 def test_edge_policy():
@@ -106,6 +156,10 @@ def test_ta_transpose(timelined_array_3D):
     assert transposed.shape == (75, 25, 50)
     assert transposed.time_dimension == 2
 
+    transposed = timelined_array_3D.T
+    assert transposed.shape == (75, 50, 25)
+    assert transposed.time_dimension == 1
+
 
 def test_ta_swapaxes(timelined_array_3D):
     swapped = timelined_array_3D.swapaxes(1, 2)
@@ -171,3 +225,43 @@ def test_masked_ta_creation():
 def test_seconds_to_index():
     sec = Seconds(10)
     assert sec.to_index(2) == 20
+
+
+def test_timelined_array_from_iterable(timelined_array_3D):
+    array = TimelinedArray.align_from_iterable(timelined_array_3D)
+    assert np.all(array == timelined_array_3D)
+
+
+def test_rebase_timelined_array(timelined_array_1D):
+
+    array = timelined_array_1D.rebase_timeline(at=16)
+    assert array.timeline[16] == 0
+
+
+def test_offset_timeline(timelined_array_1D):
+    array = timelined_array_1D.offset_timeline(offset=84)
+    assert array.timeline[22] == (22 + 84)
+
+
+def test_shift_period(timelined_array_1D):
+
+    with pytest.raises(NotImplementedError):
+        array = timelined_array_1D.shift_values(period=slice(8, 10))
+
+
+def test_moveaxis(timelined_array_3D):
+
+    array = timelined_array_3D.moveaxis(1, 2)
+    assert array.time_dimension == 2
+    assert array.shape[2] == 50
+
+    array = timelined_array_3D.moveaxis(0, 2)
+    assert array.time_dimension == 0
+    assert array.shape[1] == 75
+
+
+def test_pack(timelined_array_1D):
+
+    timeline, array = timelined_array_1D.pack
+    assert timeline is timelined_array_1D.timeline
+    assert np.all(array == timelined_array_1D)