use python 3.10 again

.github/workflows/build.yml

@@ -23,10 +23,10 @@ jobs:
           fetch-depth: 0
           ref: main
 
-      # - name: Set up Python
-      #   uses: actions/setup-python@v4
-      #   with:
-      #     python-version: "3.10"
+      - name: Set up Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: "3.9"
 
       - name: Upgrading pip
         run: pip install --upgrade pip
@@ -37,6 +37,9 @@ jobs:
       - name: Installing package
         run: pip install -e .
 
+      - name: Installing packages again (this prevents a weird error)
+        run: pip install -r requirements.txt
+
       - name: Installing build dependencies
         run: |
           pip install markupsafe==2.0.1

data/contributors.csv

@@ -5,16 +5,20 @@ Ahad Bawany,,Allen Institute,[email protected],https://github.com/A
 Corbett Bennett,0009-0001-2847-7754,Allen Institute,[email protected],https://github.com/corbennett,,"Processing"
 Benjamin Dichter,0000-0001-5725-6910,CatalystNeuro,[email protected],https://github.com/bendichter,,"Conceptualization"
 Yaroslav Halchenko,,Dartmouth College,,https://github.com/yarikoptic,,"Processing"
+Daniel Hulsey,0000-0003-3243-6282,University of Oregon,[email protected],https://github.com/dhulsey,,"Processing"
+Santiago Jaramillo,0000-0002-6595-8450,University of Oregon,[email protected],https://github.com/sjara,,"Processing"
 Satrajit Ghosh,0000-0002-5312-6729,Massachusetts Institute of Technology,[email protected],https://github.com/satra,NIH R24MH117295,"Conceptualization"
-Colleen J. Gillon,0000-0002-2253-7816,Imperial College London,colleen.gillon@mail.utoronto.ca,https://github.com/colleenjg,,"Processing"
+Colleen J. Gillon,0000-0002-2253-7816,Imperial College London,c.gillon@imperial.ac.uk,https://github.com/colleenjg,,"Processing"
 Yeerim Kim,0009-0001-1217-3801,Seoul National University,[email protected],https://github.com/yrk24,,"Processing"
 Carly Kiselycznyk,,Allen Institute,[email protected],,,"Management"
 Jerome Lecoq,0000-0002-0131-0938,Allen Institute,[email protected],https://github.com/jeromelecoq,,"Conceptualization, Management"
 Mackenzie Mathis,0000-0001-7368-4456,Swiss Federal Institute of Technology in Lausanne,[email protected],https://github.com/MMathisLab,,"Review"
 NIH U24 NS113646,,,,,,"Funding"
-R. Carter Peene,0009-0000-6660-2264,Allen Institute,[email protected],rcpeene,,"Conceptualization, Processing"
+R. Carter Peene,0009-0000-6660-2264,Allen Institute,[email protected],https://github.com/rcpeene,,"Conceptualization, Processing"
+Stephanie Prince,0000-0002-3083-6955,Lawrence Berkeley National Laboratory,[email protected],https://github.com/stephprince,,"Review"
 Jason Pina,0000-0003-1385-8762,York University,[email protected],https://github.com/jayepi,,"Conceptualization"
 Hyeyoung Shin,,Seoul National University,[email protected],https://github.com/hs13,,"Conceptualization"
 Josh Siegle,,Allen Institute,[email protected],https://github.com/jsiegle,NIH U24,"Processing"
+Shih-Yi Tseng,0000-0002-5029-433X,"University of California, San Francisco",[email protected],https://github.com/sytseng,,"Processing"
 Jacob Westerberg,0000-0001-5331-8707,Netherlands Institute for Neuroscience,[email protected],https://github.com/jakewesterberg,,"Conceptualization"
 Alex Williams,0000-0001-5853-103X,New York University,[email protected],https://github.com/ahwillia,,"Review"

docs/_toc.yml

@@ -42,7 +42,6 @@ parts:
   - file: projects/glo.ipynb
   - file: projects/illusion.ipynb
   - file: projects/dendritic_coupling.ipynb
-  - file: projects/vippo.ipynb
 - caption: Embargoed Datasets
   chapters:
   - file: embargoed/modality_alignment.ipynb

docs/basics/read_nwb.ipynb

@@ -1756,7 +1756,7 @@
    "metadata": {},
    "source": [
     "### OpenScope's File Schemas\n",
-    "OpenScope works with two main types of brain data files for different experiments. There's Extracellular Electrophysiology, *Ecephys*, which uses **Neuropixel** probes to gather electrical data, and Optical Physiology, *Ophys*, which uses **2-Photon** Calcium imaging to gather fluorescence data. Since the NWB Standard is very flexible, and these files are used for different needs, there are several differences between these data types. These table schemas were made as comprehensive descriptions of what goes in our NWB files. Below, **Pandas** is used to display a general outline for each file type where every field within the NWB file is described. Note that NWB files or files from other institutions could vary from these significantly. These tables are just meant to be used as a reference, don't be overwhelmed trying to understand all the fields!"
+    "OpenScope works with two main types of brain data files for different experiments. There's Extracellular Electrophysiology, *Ecephys*, which uses **Neuropixels** probes to gather electrical data, and Optical Physiology, *Ophys*, which uses **2-Photon** Calcium imaging to gather fluorescence data. Since the NWB Standard is very flexible, and these files are used for different needs, there are several differences between these data types. These table schemas were made as comprehensive descriptions of what goes in our NWB files. Below, **Pandas** is used to display a general outline for each file type where every field within the NWB file is described. Note that NWB files or files from other institutions could vary from these significantly. These tables are just meant to be used as a reference, don't be overwhelmed trying to understand all the fields!"
    ]
   },
   {

docs/projects/glo.ipynb

@@ -489,7 +489,7 @@
    "metadata": {},
    "source": [
     "### Showing Probe Tracks\n",
-    "The images below were rendered using the [Visualizing Neuropixel Probe Locations](../visualization/visualize_neuropixel_probes.ipynb) notebook. The probes are using the [Common Coordinate Framework](https://community.brain-map.org/t/allen-mouse-ccf-accessing-and-using-related-data-and-tools/359) (CCF). The experiment uses six probes labeled A-F to target various regions."
+    "The images below were rendered using the [Visualizing Neuropixels Probe Locations](../visualization/visualize_neuropixels_probes.ipynb) notebook. The probes are using the [Common Coordinate Framework](https://community.brain-map.org/t/allen-mouse-ccf-accessing-and-using-related-data-and-tools/359) (CCF). The experiment uses six probes labeled A-F to target various regions."
    ]
   },
   {

docs/projects/illusion.ipynb

@@ -543,7 +543,7 @@
    "metadata": {},
    "source": [
     "### Showing Probe Tracks\n",
-    "The images below were rendered using the [Visualizing Neuropixels Probe Locations](../visualization/visualize_neuropixel_probes.ipynb) notebook. The probes are using the [Common Coordinate Framework](https://community.brain-map.org/t/allen-mouse-ccf-accessing-and-using-related-data-and-tools/359) (CCF). The experiment uses six probes labeled A-F to target various regions. It can be seen that the probe tracks look bent. This is due to the fact that each mouse brain varies slightly, so the coordinate space is slightly warped when mapping the CCF coordinates to each mouse's brain."
+    "The images below were rendered using the [Visualizing Neuropixels Probe Locations](../visualization/visualize_neuropixels_probes.ipynb) notebook. The probes are using the [Common Coordinate Framework](https://community.brain-map.org/t/allen-mouse-ccf-accessing-and-using-related-data-and-tools/359) (CCF). The experiment uses six probes labeled A-F to target various regions. It can be seen that the probe tracks look bent. This is due to the fact that each mouse brain varies slightly, so the coordinate space is slightly warped when mapping the CCF coordinates to each mouse's brain."
    ]
   },
   {