From 15e3eb0cafd88a28447b105d57ed68622aaf44f8 Mon Sep 17 00:00:00 2001
From: Chris Langfield <34426450+chris-langfield@users.noreply.github.com>
Date: Thu, 8 Feb 2024 12:29:08 -0500
Subject: [PATCH] Rename neurodsp (#23)

* initial drop-in replace

* bump version and update changelog

* you cant change history

* update tests

* catch and assert warning

* add dummy module to warn user

* flake

* update change log

* unused import

---------

Co-authored-by: chris-langfield <christopher.langfield@internationalbrainlab.org>
---
 README.md                                    |  2 +-
 release_notes.md                             |  5 +++
 setup.py                                     |  2 +-
 src/ibldsp/__init__.py                       |  0
 src/{neurodsp => ibldsp}/cadzow.py           |  0
 src/{neurodsp => ibldsp}/cuda_tools.py       |  0
 src/{neurodsp => ibldsp}/destripe_gpu.py     |  0
 src/{neurodsp => ibldsp}/filter_gpu.py       |  0
 src/{neurodsp => ibldsp}/fourier.py          |  0
 src/{neurodsp => ibldsp}/raw_metrics.py      |  4 +--
 src/{neurodsp => ibldsp}/smooth.py           |  2 +-
 src/{neurodsp => ibldsp}/sosfilt.cu          |  0
 src/{neurodsp => ibldsp}/spiketrains.py      |  0
 src/{neurodsp => ibldsp}/utils.py            |  0
 src/{neurodsp => ibldsp}/voltage.py          |  4 +--
 src/{neurodsp => ibldsp}/waveforms.py        |  1 +
 src/neurodsp/__init__.py                     |  8 +++++
 src/neuropixel.py                            |  2 +-
 src/neurowaveforms/model.py                  |  2 +-
 src/tests/integration/cpu/csd_experiments.py |  2 +-
 src/tests/integration/cpu/test_destripe.py   |  2 +-
 src/tests/unit/cpu/test_dsp.py               | 33 +++++++++++++++-----
 src/tests/unit/cpu/test_waveforms.py         |  2 +-
 src/tests/unit/gpu/test_filter_gpu.py        |  2 +-
 src/tests/unit/gpu/test_fourier.py           |  2 +-
 25 files changed, 54 insertions(+), 21 deletions(-)
 create mode 100644 src/ibldsp/__init__.py
 rename src/{neurodsp => ibldsp}/cadzow.py (100%)
 rename src/{neurodsp => ibldsp}/cuda_tools.py (100%)
 rename src/{neurodsp => ibldsp}/destripe_gpu.py (100%)
 rename src/{neurodsp => ibldsp}/filter_gpu.py (100%)
 rename src/{neurodsp => ibldsp}/fourier.py (100%)
 rename src/{neurodsp => ibldsp}/raw_metrics.py (97%)
 rename src/{neurodsp => ibldsp}/smooth.py (99%)
 rename src/{neurodsp => ibldsp}/sosfilt.cu (100%)
 rename src/{neurodsp => ibldsp}/spiketrains.py (100%)
 rename src/{neurodsp => ibldsp}/utils.py (100%)
 rename src/{neurodsp => ibldsp}/voltage.py (99%)
 rename src/{neurodsp => ibldsp}/waveforms.py (99%)

diff --git a/README.md b/README.md
index f2ed5b7..d81eb1b 100644
--- a/README.md
+++ b/README.md
@@ -13,7 +13,7 @@ This relies on a fast fourier transform external library: `pip install pyfftw`.
 Minimal working example to destripe a neuropixel binary file. 
 ```python
 from pathlib import Path
-from neurodsp.voltage import decompress_destripe_cbin
+from ibldsp.voltage import decompress_destripe_cbin
 sr_file = Path('/datadisk/Data/spike_sorting/pykilosort_tests/imec_385_100s.ap.bin')
 out_file = Path('/datadisk/scratch/imec_385_100s.ap.bin')
 
diff --git a/release_notes.md b/release_notes.md
index 5c7f134..e4af704 100644
--- a/release_notes.md
+++ b/release_notes.md
@@ -1,3 +1,8 @@
+# 0.9.1
+## 0.9.1 
+-   `neurodsp` is now `ibldsp`. Drop-in replacement of the package name is all that is required to update. The `neurodsp` name will disappear on
+01-Sep-2024; until then both names will work.
+
 # 0.9.0
 ## 0.9.0 2024-01-17
 -   `neurodsp.utils.sync_timestamps`: uses FFT based correlation to speed up large arrays alignments
diff --git a/setup.py b/setup.py
index 689b73f..2c311ab 100644
--- a/setup.py
+++ b/setup.py
@@ -8,7 +8,7 @@
 
 setuptools.setup(
     name="ibl-neuropixel",
-    version="0.9.0",
+    version="0.9.1",
     author="The International Brain Laboratory",
     description="Collection of tools for Neuropixel 1.0 and 2.0 probes data",
     long_description=long_description,
diff --git a/src/ibldsp/__init__.py b/src/ibldsp/__init__.py
new file mode 100644
index 0000000..e69de29
diff --git a/src/neurodsp/cadzow.py b/src/ibldsp/cadzow.py
similarity index 100%
rename from src/neurodsp/cadzow.py
rename to src/ibldsp/cadzow.py
diff --git a/src/neurodsp/cuda_tools.py b/src/ibldsp/cuda_tools.py
similarity index 100%
rename from src/neurodsp/cuda_tools.py
rename to src/ibldsp/cuda_tools.py
diff --git a/src/neurodsp/destripe_gpu.py b/src/ibldsp/destripe_gpu.py
similarity index 100%
rename from src/neurodsp/destripe_gpu.py
rename to src/ibldsp/destripe_gpu.py
diff --git a/src/neurodsp/filter_gpu.py b/src/ibldsp/filter_gpu.py
similarity index 100%
rename from src/neurodsp/filter_gpu.py
rename to src/ibldsp/filter_gpu.py
diff --git a/src/neurodsp/fourier.py b/src/ibldsp/fourier.py
similarity index 100%
rename from src/neurodsp/fourier.py
rename to src/ibldsp/fourier.py
diff --git a/src/neurodsp/raw_metrics.py b/src/ibldsp/raw_metrics.py
similarity index 97%
rename from src/neurodsp/raw_metrics.py
rename to src/ibldsp/raw_metrics.py
index 0026526..d382752 100644
--- a/src/neurodsp/raw_metrics.py
+++ b/src/ibldsp/raw_metrics.py
@@ -1,5 +1,5 @@
-from neurodsp.voltage import destripe, destripe_lfp, detect_bad_channels
-from neurodsp.utils import rms
+from ibldsp.voltage import destripe, destripe_lfp, detect_bad_channels
+from ibldsp.utils import rms
 import spikeglx
 import pandas as pd
 import scipy
diff --git a/src/neurodsp/smooth.py b/src/ibldsp/smooth.py
similarity index 99%
rename from src/neurodsp/smooth.py
rename to src/ibldsp/smooth.py
index 34ecd74..494d40f 100644
--- a/src/neurodsp/smooth.py
+++ b/src/ibldsp/smooth.py
@@ -1,7 +1,7 @@
 import numpy as np
 from scipy.interpolate import interp1d
 
-import neurodsp.fourier as ft
+import ibldsp.fourier as ft
 
 
 def lp(ts, fac, pad=0.2):
diff --git a/src/neurodsp/sosfilt.cu b/src/ibldsp/sosfilt.cu
similarity index 100%
rename from src/neurodsp/sosfilt.cu
rename to src/ibldsp/sosfilt.cu
diff --git a/src/neurodsp/spiketrains.py b/src/ibldsp/spiketrains.py
similarity index 100%
rename from src/neurodsp/spiketrains.py
rename to src/ibldsp/spiketrains.py
diff --git a/src/neurodsp/utils.py b/src/ibldsp/utils.py
similarity index 100%
rename from src/neurodsp/utils.py
rename to src/ibldsp/utils.py
diff --git a/src/neurodsp/voltage.py b/src/ibldsp/voltage.py
similarity index 99%
rename from src/neurodsp/voltage.py
rename to src/ibldsp/voltage.py
index 8798e54..882ad0a 100644
--- a/src/neurodsp/voltage.py
+++ b/src/ibldsp/voltage.py
@@ -13,8 +13,8 @@
 import spikeglx
 import neuropixel
 
-import neurodsp.fourier as fourier
-import neurodsp.utils as utils
+import ibldsp.fourier as fourier
+import ibldsp.utils as utils
 
 
 def agc(x, wl=.5, si=.002, epsilon=1e-8, gpu=False):
diff --git a/src/neurodsp/waveforms.py b/src/ibldsp/waveforms.py
similarity index 99%
rename from src/neurodsp/waveforms.py
rename to src/ibldsp/waveforms.py
index da6056c..4eae3c1 100644
--- a/src/neurodsp/waveforms.py
+++ b/src/ibldsp/waveforms.py
@@ -284,6 +284,7 @@ def plot_peaktiptrough(df, arr, ax, nth_wav=0, plot_grey=True, fs=30000):
     ax.set_ylabel('(Volt)')
     ax.set_xlabel('Time (ms)')
 
+
 def half_peak_point(arr_peak, df):
     '''
     Compute the two intersection points at halp-maximum peak
diff --git a/src/neurodsp/__init__.py b/src/neurodsp/__init__.py
index e69de29..f9a6d74 100644
--- a/src/neurodsp/__init__.py
+++ b/src/neurodsp/__init__.py
@@ -0,0 +1,8 @@
+import ibldsp, sys
+from warnings import warn
+
+sys.modules["neurodsp"] = ibldsp
+warn(
+    "neurodsp has been renamed to ibldsp and the old name will be deprecated on 01-Sep-2024.",
+    FutureWarning,
+)
diff --git a/src/neuropixel.py b/src/neuropixel.py
index ab9fc5e..0d42436 100644
--- a/src/neuropixel.py
+++ b/src/neuropixel.py
@@ -9,7 +9,7 @@
 import numpy as np
 
 import spikeglx
-from neurodsp.utils import WindowGenerator
+from ibldsp.utils import WindowGenerator
 
 _logger = logging.getLogger('ibllib')
 
diff --git a/src/neurowaveforms/model.py b/src/neurowaveforms/model.py
index 44178fa..c35ded2 100644
--- a/src/neurowaveforms/model.py
+++ b/src/neurowaveforms/model.py
@@ -1,5 +1,5 @@
 import numpy as np
-from neurodsp.fourier import fshift
+from ibldsp.fourier import fshift
 
 
 def generate_waveform(spike=None, sxy=None, wxy=None, fs=30000, vertical_velocity_mps=3):
diff --git a/src/tests/integration/cpu/csd_experiments.py b/src/tests/integration/cpu/csd_experiments.py
index eae99f2..744649e 100644
--- a/src/tests/integration/cpu/csd_experiments.py
+++ b/src/tests/integration/cpu/csd_experiments.py
@@ -9,7 +9,7 @@
 from ibllib.atlas import BrainRegions
 from viewephys.gui import viewephys
 
-from neurodsp import voltage, fourier
+from ibldsp import voltage, fourier
 from neuropixel import trace_header
 
 
diff --git a/src/tests/integration/cpu/test_destripe.py b/src/tests/integration/cpu/test_destripe.py
index b7e574d..281a427 100644
--- a/src/tests/integration/cpu/test_destripe.py
+++ b/src/tests/integration/cpu/test_destripe.py
@@ -7,7 +7,7 @@
 
 from neuropixel import trace_header
 import spikeglx
-from neurodsp import voltage, utils
+from ibldsp import voltage, utils
 
 _logger = logging.getLogger(__name__)
 
diff --git a/src/tests/unit/cpu/test_dsp.py b/src/tests/unit/cpu/test_dsp.py
index fa826ff..fe59fab 100644
--- a/src/tests/unit/cpu/test_dsp.py
+++ b/src/tests/unit/cpu/test_dsp.py
@@ -4,13 +4,13 @@
 import scipy.fft
 import spikeglx
 
-import neurodsp.fourier as fourier
-import neurodsp.utils as utils
-import neurodsp.voltage as voltage
-import neurodsp.cadzow as cadzow
-import neurodsp.smooth as smooth
-import neurodsp.spiketrains as spiketrains
-import neurodsp.raw_metrics as raw_metrics
+import ibldsp.fourier as fourier
+import ibldsp.utils as utils
+import ibldsp.voltage as voltage
+import ibldsp.cadzow as cadzow
+import ibldsp.smooth as smooth
+import ibldsp.spiketrains as spiketrains
+import ibldsp.raw_metrics as raw_metrics
 
 from pathlib import Path
 import tempfile
@@ -604,3 +604,22 @@ def test_compute_features(self):
         self.assertEqual(multi_index, list(df.index))
         self.assertEqual(["snippet_id", "channel_id"], list(df.index.names))
         self.assertEqual(num_snippets * (self.nc - 1), len(df))
+
+
+class TestNameDeprecationDate(unittest.TestCase):
+    def test_neurodsp_import(self):
+        # Check that the old import still works and gives the same package.
+        # (ibldsp.voltage is imported at the top of this file.)
+        with self.assertWarnsRegex(FutureWarning, "01-Sep-2024"):
+            import neurodsp
+        self.assertEqual(neurodsp.voltage, voltage)
+
+    def test_deprecation_countdown(self):
+        # Fail on 01-Sep-2024, when `neurodsp` will be retired.
+        # When this test fails, remove the entire dummy
+        # `neurodsp` package at the top level of the ibl-neuropixel
+        # repository
+        import datetime
+        if datetime.datetime.now() > datetime.datetime(2024, 9, 1):
+            raise NotImplementedError("neurodsp will not longer be supported. "
+                                      "Change all references to ibldsp.")
diff --git a/src/tests/unit/cpu/test_waveforms.py b/src/tests/unit/cpu/test_waveforms.py
index 61ccd0e..ded4996 100644
--- a/src/tests/unit/cpu/test_waveforms.py
+++ b/src/tests/unit/cpu/test_waveforms.py
@@ -3,7 +3,7 @@
 import numpy as np
 import pandas as pd
 
-import neurodsp.waveforms as waveforms
+import ibldsp.waveforms as waveforms
 from neurowaveforms.model import generate_waveform
 
 
diff --git a/src/tests/unit/gpu/test_filter_gpu.py b/src/tests/unit/gpu/test_filter_gpu.py
index cdcdd9d..366097c 100644
--- a/src/tests/unit/gpu/test_filter_gpu.py
+++ b/src/tests/unit/gpu/test_filter_gpu.py
@@ -3,7 +3,7 @@
 from scipy.signal import butter, sosfiltfilt
 import unittest
 
-from neurodsp.filter_gpu import sosfiltfilt_gpu
+from ibldsp.filter_gpu import sosfiltfilt_gpu
 
 
 class TestFilterGpuCpuParity(unittest.TestCase):
diff --git a/src/tests/unit/gpu/test_fourier.py b/src/tests/unit/gpu/test_fourier.py
index 5f9b24b..278cbc6 100644
--- a/src/tests/unit/gpu/test_fourier.py
+++ b/src/tests/unit/gpu/test_fourier.py
@@ -2,7 +2,7 @@
 import cupy as cp
 import unittest
 
-from neurodsp.fourier import fshift, channel_shift
+from ibldsp.fourier import fshift, channel_shift
 
 
 class TestFourierAlignmentGpuCpuParity(unittest.TestCase):