Merge branch 'main' into multisession-tutorial

docs/tutorials/dataset.rst

@@ -17,7 +17,7 @@ Navigate to the **Settings** page using the main sidebar. Then press the **Gener
 
   Press the Generate button on the Settings page to create the dataset.
 
-The generated data will populate in the `~/NWB_GUIDE/test_data` directory and include a `data` folder with the original data as well as a `dataset` folder that duplicates this `data` across multiple subjects and sessions.
+The generated data will populate in the ``~/NWB_GUIDE/test_data`` directory and include a ``data`` folder with the original data as well as a ``dataset`` folder that duplicates this ``data`` across multiple subjects and sessions.
 
 .. code-block:: bash
 

docs/tutorials/next_steps.rst

@@ -1,3 +1,13 @@
 What's Next?
 =======================================
-Coming soon...
+
+Considerations when Using Your Own Data
+---------------------------------------
+When using your own data, there are a few things to consider:
+
+Choosing an Output Location
+^^^^^^^^^^^^^^^^^^^^^^^^^^^
+   Choosing a good output location is important for two reasons, namely **conversion speed** and **disk space**.
+
+   1. SSDs will be much faster than HDDs. We’d recommend moving the output location to an SSD if available.
+   2. If you don’t have much disk space available on your main drive, we recommend changing the output location to a drive that has ample space.

docs/tutorials/single_session.rst

@@ -3,7 +3,7 @@ Converting a Single Session
 
 As a researcher, you’ve just completed an experimental session and you’d like to convert your data to NWB right away.
 
-Upon launching the GUIDE, you'll begin on the Conversions page. If you’re opening the application for the first time, there should be no pipelines listed on this page.
+Upon launching the GUIDE, you'll begin on the Convert page. If you’re opening the application for the first time, there should be no pipelines listed on this page.
 
 .. figure:: ../assets/tutorials/home-page.png
   :align: center
@@ -19,13 +19,6 @@ Project Setup
 
 The Project Setup page will have you define two pieces of information about your pipeline: the **name** and, optionally, the **output location** for your NWB files.
 
-.. note::
-   Choosing a good output location is important for two reasons, namely **conversion speed** and **disk space**.
-
-   1. SSDs will be much faster than HDDs. We’d recommend moving the output location to an SSD if available.
-   2. If you don’t have much disk space available on your main drive, we recommend changing the output location to a drive that has ample space.
-
-
 You’ll notice that the name property has a red asterisk next to it, which identifies it as a required property.
 
 .. figure:: ../assets/tutorials/single/info-page.png
@@ -59,7 +52,7 @@ Next, you’ll specify the data formats you’re working with on the Data Format
   :align: center
   :alt: Date Formats page
 
-The tutorial we're working with uses the SpikeGLX and Phy formats, a common output for NeuroPixel recordings and subsequent spike sorting. To specify that your pipeline will handle these files, you’ll press the “Add Format” button.
+The tutorial we're working with uses the SpikeGLX and Phy formats, a common output for Neuropixels recordings and subsequent spike sorting. To specify that your pipeline will handle these files, you’ll press the “Add Format” button.
 
 .. figure:: ../assets/tutorials/single/format-options.png
   :align: center
@@ -92,7 +85,7 @@ Source Data Information
 ^^^^^^^^^^^^^^^^^^^^^^^
 On this page, specify the relevant **.bin** (Spikeglx) file and **phy** folder so that the GUIDE can find this source data to complete the conversion.
 
-As discussed in the :doc:`Dataset Generation </tutorials/dataset>` tutorial, these can be found in the `~/NWB_GUIDE/test-data/data` directory.
+As discussed in the :doc:`Dataset Generation </tutorials/dataset>` tutorial, these can be found in the ``~/NWB_GUIDE/test-data/data`` directory.
 
 You can either click the file selector to navigate to the file or drag-and-drop into the GUIDE from your file navigator.
 

environments/environment-Windows.yml

@@ -22,4 +22,3 @@ dependencies:
       - pytest == 7.2.2
       - pytest-cov == 4.1.0
       - scikit-learn == 1.4.0
-      - scipy == 1.12.0

nwb-guide.spec

@@ -12,7 +12,12 @@ from PyInstaller.utils.hooks import collect_all
 
 datas = [('./paths.config.json', '.'), ('./package.json', '.')]
 binaries = []
-hiddenimports = [ 'email_validator', *collect_submodules('scipy.special.cython_special'), *os.path.join(os.path.dirname(scipy.__file__), '.libs')]
+hiddenimports = [
+    'email_validator',
+    *collect_submodules('scipy.special.cython_special'),
+    *collect_submodules('scipy.special._cdflib'),
+    *os.path.join(os.path.dirname(scipy.__file__), '.libs')
+]
 
 datas += collect_data_files('jsonschema_specifications')
 tmp_ret = collect_all('dandi')

pyflask/manageNeuroconv/manage_neuroconv.py

@@ -1063,7 +1063,7 @@ def generate_test_data(output_path: str):
     spikeglx_output_folder = base_path / "spikeglx"
     phy_output_folder = base_path / "phy"
 
-    # Define NeuroPixel-like values for sampling rates and conversion factors
+    # Define Neuropixels-like values for sampling rates and conversion factors
     duration_in_s = 3.0
     number_of_units = 50
     number_of_channels = 385  # Have to include 'sync' channel to be proper SpikeGLX. TODO: artificiate sync pulses