fix_correlate_shift_coord_length (#485)

* fix_correlate_shift_coord_length

* remove_commented_breakpoint

* try drop uv

* lint

* add test deps

* handle the units

---------

Co-authored-by: Derrick Chambers <chambers.ja.derrick@gmail.com>

.github/workflows/run_min_dep_tests.yml

@@ -42,15 +42,16 @@ jobs:
           install-package: false
           environment-file: './.github/min_deps_environment.yml'
 
-      # Then switch over to uv. We can use this exclusively once we drop pytables.
-      - name: Install uv
-        uses: astral-sh/setup-uv@v3
+      - name: Install dascore (min deps)
+        shell: bash -l {0}
+        run: pip install -e .[test]
 
+      # Runs test suite and calculates coverage
       - name: run test suite
-        shell: bash -l {0}
-        run: uv run --extra test --python ${{ matrix.python-version }} pytest -s --cov dascore --cov-append --cov-report=xml
+        shell: bash -el {0}
+        run: ./.github/test_code.sh
 
       # Runs examples in docstrings
       - name: test docstrings
-        shell: bash -l {0}
-        run: uv run --extra test --python ${{ matrix.python-version }} pytest dascore --doctest-modules
+        shell: bash -el {0}
+        run: ./.github/test_code.sh doctest

dascore/proc/correlate.py

@@ -73,7 +73,13 @@ def correlate_shift(patch, dim, undo_weighting=True):
     step = coord.step
     new_start = -np.ceil((len(coord) - 1) / 2) * step
     new_end = np.ceil((len(coord) - 1) / 2) * step
-    new_coord = dc.get_coord(start=new_start, stop=new_end, step=step)
+    # if len(coord) % 2 != 0:  # Odd coord length
+    #     new_end += step
+    _new_coord = dc.get_coord(
+        start=new_start, stop=new_end, step=step, units=coord.units
+    )
+    new_coord = _new_coord.change_length(len(coord))
+    # new_coord = dc.get_coord(start=new_start, stop=new_end, step=step)
     assert len(new_coord) == len(coord)
     cm = patch.coords
     new_cm = cm.update(**{dim: new_coord}).rename_coord(**{dim: f"lag_{dim}"})

dascore/proc/filter.py

@@ -271,11 +271,10 @@ def notch_filter(patch: PatchType, q, **kwargs) -> PatchType:
         Used to specify the dimension(s) and associated frequency and/or wavelength
         (or equivalent values) for the filter.
 
-    Notes
-    -----
-    See [scipy.signal.iirnotch]
-        (https://docs.scipy.org/doc/scipy/reference/generated/scipy.signal.iirnotch.html)
-        for more information.
+    See Also
+    --------
+    [scipy.signal.iirnotch](https://docs.scipy.org/doc/scipy/reference
+    /generated/scipy.signal.iirnotch.html).
 
     Examples
     --------
@@ -286,10 +285,10 @@ def notch_filter(patch: PatchType, q, **kwargs) -> PatchType:
     >>> filtered = pa.notch_filter(time=60, q=30)
 
     >>>  # Apply a notch filter along distance axis to remove 5 m wavelength
-    >>> filtered = pa.notch_filter(distance=0.2, q=10)
+    >>> filtered = pa.notch_filter(distance=0.2, q=30)
 
     >>>  # Apply a notch filter along both time and distance axes
-    >>> filtered = pa.notch_filter(time=60, distance=0.2, q=40)
+    >>> filtered = pa.notch_filter(time=60, distance=0.2, q=30)
 
     >>> # Optionally, units can be specified for a more expressive API.
     >>> from dascore.units import m, ft, s, Hz

docs/recipes/how_to_contribute.qmd

@@ -29,7 +29,6 @@ pip install -e ".[dev]"
 ```
 
 ```bash
-cd dascore
 pytest
 ```
 

tests/test_proc/test_correlate.py

@@ -12,6 +12,18 @@
 class TestCorrelateShift:
     """Tests for the correlation shift function."""
 
+    @pytest.fixture(scope="class")
+    def random_patch_odd(self):
+        """Create a random patch with odd number of time samples."""
+        patch = dc.get_example_patch("random_das", shape=(2, 11))
+        return patch
+
+    @pytest.fixture(scope="class")
+    def random_patch_even(self):
+        """Create a random patch with even number of time samples."""
+        patch = dc.get_example_patch("random_das", shape=(2, 10))
+        return patch
+
     def test_auto_correlation(self, random_dft_patch):
         """Perform auto correlation and undo shifting."""
         dft_conj = random_dft_patch.conj()
@@ -26,6 +38,22 @@ def test_auto_correlation(self, random_dft_patch):
         argmax = np.argmax(random_dft_patch.data, axis=time_ax)
         assert np.all(coord_array[argmax] == dc.to_timedelta64(0))
 
+    def test_auto_correlation_odd_coord(self, random_patch_odd):
+        """Ensure correlate_shift works when dim's coord length is odd."""
+        dft = random_patch_odd.dft(dim="time")
+        dft_conj = dft.conj()
+        dft_sq = dft * dft_conj
+        idft = dft_sq.idft()
+        assert isinstance(idft.correlate_shift(dim="time"), dc.Patch)
+
+    def test_auto_correlation_even_coord(self, random_patch_even):
+        """Ensure correlate_shift works when dim's coord length is even."""
+        dft = random_patch_even.dft(dim="time")
+        dft_conj = dft.conj()
+        dft_sq = dft * dft_conj
+        idft = dft_sq.idft()
+        assert isinstance(idft.correlate_shift(dim="time"), dc.Patch)
+
 
 class TestCorrelateInternal:
     """Tests case of intra-patch correlation function."""