Merge branch 'master' into add_annotations_to_intan

Author: h-mayorquin

.github/workflows/core-test.yml

@@ -26,17 +26,32 @@ jobs:
       matrix:
         os: ["ubuntu-latest", "windows-latest"]
         # "macos-latest",
-        python-version: ['3.8', '3.9', '3.10', '3.11']
-        numpy-version: ['1.20.3', '1.21.6', '1.22.4', '1.23.5', '1.24.1', '1.25.1']
+        python-version: ['3.8', '3.9', '3.10', '3.11', '3.12']
+        numpy-version: ['1.20.3', '1.21.6', '1.22.4', '1.23.5', '1.24.1', '1.25.1', '1.26.4']
         exclude:
            - python-version: '3.8'
              numpy-version: '1.25.1'
+           - python-version: '3.8'
+             numpy-version: '1.26.4'
            - python-version: '3.10'
              numpy-version: '1.20.3'
            - python-version: '3.11'
              numpy-version: '1.20.3'
            - python-version: '3.11'
              numpy-version: '1.21.6'
+           - python-version: '3.12'
+             numpy-version: '1.20.3'
+           # python 3.12 only works on latest numpy
+           - python-version: '3.12'
+             numpy-version: '1.21.6'
+           - python-version: '3.12'
+             numpy-version: '1.22.4'
+           - python-version: '3.12'
+             numpy-version: '1.23.5'
+           - python-version: '3.12'
+             numpy-version: '1.24.1'
+           - python-version: '3.12'
+             numpy-version: '1.25.1'
     steps:
         - name: Set up Python ${{ matrix.python-version }}
           uses: actions/setup-python@v4

.github/workflows/io-test.yml

@@ -13,12 +13,12 @@ concurrency:  # Cancel previous workflows on the same pull request
 
 jobs:
   build-and-test:
-    name: Test on (${{ inputs.os }})
+    name: Test on (${{ inputs.os }}) (${{ matrix.python-version}})
     runs-on: ${{ inputs.os }}
     strategy:
       fail-fast: true
       matrix:
-        python-version: ['3.9', ]
+        python-version: ['3.9', '3.11']
     defaults:
       # by default run in bash mode (required for conda usage)
       run:
@@ -75,6 +75,7 @@ jobs:
         if: steps.cache-conda-env.outputs.cache-hit != 'true'
         run: |
           conda env update --name neo-test-env --file environment_testing.yml --prune
+          conda install python=${{ matrix.python-version }}
 
       - name: Configure git
         run: |

environment_testing.yml

@@ -2,6 +2,5 @@ name: neo-test-env
 channels:
   - conda-forge
 dependencies:
-  - python=3.9
   - datalad
   - pip

neo/rawio/intanrawio.py

@@ -20,8 +20,6 @@
 """
 
 from pathlib import Path
-import os
-from collections import OrderedDict
 from packaging.version import Version
 import warnings
 
@@ -44,8 +42,12 @@ class IntanRawIO(BaseRawIO):
     Parameters
     ----------
     filename: str, default: ''
-        name of the 'rhd' or 'rhs' data/header file
-
+         name of the 'rhd' or 'rhs' data/header file
+    ignore_integrity_checks: bool, default: False
+        If True, data that violates integrity assumptions will be loaded. At the moment the only integrity
+        check we perform is that timestamps are continuous. Setting this to True will ignore this check and set
+        the attribute `discontinuous_timestamps` to True if the timestamps are not continous. This attribute can be checked 
+        after parsing the header to see if the timestamps are continuous or not.
     Notes
     -----
     * The Intan reader can handle two file formats 'rhd' and 'rhs'. It will automatically
@@ -99,10 +101,13 @@ class IntanRawIO(BaseRawIO):
     extensions = ["rhd", "rhs", "dat"]
     rawmode = "one-file"
 
-    def __init__(self, filename=""):
+    def __init__(self, filename="", ignore_integrity_checks=False):
 
         BaseRawIO.__init__(self)
         self.filename = filename
+        self.ignore_integrity_checks = ignore_integrity_checks
+        self.discontinuous_timestamps = False
+
 
     def _source_name(self):
         return self.filename
@@ -202,11 +207,18 @@ def _parse_header(self):
         elif self.file_format == "one-file-per-channel":
             time_stream_index = max(self._raw_data.keys())
             timestamp = self._raw_data[time_stream_index][0]
-
-        if not np.all(np.diff(timestamp) == 1):
-            raise NeoReadWriteError(
-                f"Timestamp have gaps, this could be due to a corrupted file or an inappropriate file merge"
-            )
+        
+        discontinuous_timestamps = np.diff(timestamp) != 1
+        timestamps_are_not_contiguous = np.any(discontinuous_timestamps)
+        if timestamps_are_not_contiguous:
+            self.discontinuous_timestamps = True
+            if not self.ignore_integrity_checks:
+                error_msg = (
+                    "Timestamps are not continuous, this could be due to a corrupted file or an inappropriate file merge. "
+                    "Initialize the reader with `ignore_integrity_checks=True` to ignore this error and open the file. \n"
+                    f"Timestamps around discontinuities: {timestamp[discontinuous_timestamps]}"
+                )
+                raise NeoReadWriteError(error_msg)
 
         # signals
         signal_channels = []