Merge pull request #1 from LorenFrankLab/main

keep jmunroe version up to date with lorenfrank version

.github/workflows/sync-notebooks.yml

@@ -0,0 +1,40 @@
+name: Sync Notebooks Folder
+
+on:
+  schedule:
+    - cron: '0 0 * * 0'  # Runs at 00:00 every Sunday
+  workflow_dispatch:
+
+jobs:
+  sync-notebooks:
+    runs-on: ubuntu-latest
+    steps:
+    - name: Checkout destination repository
+      uses: actions/checkout@v2
+      with:
+        token: ${{ secrets.GITHUB_TOKEN }}
+        fetch-depth: 0  # Fetch all history for all branches and tags
+
+    - name: Install rsync
+      run: sudo apt-get install rsync
+
+    - name: Rsync notebooks
+      run: |
+        git clone https://github.com/LorenFrankLab/spyglass.git tmp --depth=1
+        rsync -av --exclude='.git/' tmp/notebooks/ ./notebooks/
+
+    - name: Configure git
+      run: |
+        git config user.name "GitHub Actions"
+        git config user.email "[email protected]"
+
+    - name: Commit changes
+      run: |
+        git add notebooks/
+        git diff --staged --quiet || git commit -m "Sync notebooks"
+
+    - name: Pull with rebase
+      run: git pull --rebase
+
+    - name: Push changes
+      run: git push origin HEAD:main

.gitignore

@@ -0,0 +1 @@
+*.DS_Store

README.md

@@ -1,19 +1,18 @@
 [Magic Link](
-https://spyglass.hhmi.2i2c.cloud/hub/user-redirect/git-pull?repo=https%3A%2F%2Fgithub.com%2Fjmunroe%2Fspyglass-notebooks&urlpath=lab%2Ftree%2Fspyglass-notebooks%2Fnotebooks%2F01_Insert_Data.ipynb&branch=main)
+https://spyglass.hhmi.2i2c.cloud/hub/user-redirect/git-pull?repo=https%3A%2F%2Fgithub.com%2FLorenFrankLab%2Fspyglass-demo&urlpath=lab%2Ftree%2Fspyglass-demo%2Fnotebooks%2F01_Insert_Data.ipynb&branch=main)
 
 This repository is meant to support the paper:
+> Lee, K.H.\*, Denovellis, E.L.\*, Ly, R., Magland, J., Soules, J., Comrie, A.E., Gramling, D.P., Guidera, J.A., Nevers, R., Adenekan, P., Brozdowski, C., Bray, S., Monroe, E., Bak, J.H., Coulter, M.E., Sun, X., Broyles, E., Shin, D., Chiang, S., Holobetz, C., Tritt, A., Rübel, O., Nguyen, T., Yatsenko, D., Chu, J., Kemere, C., Garcia, S., Buccino, A., Frank, L.M., 2024. Spyglass: a data analysis framework for reproducible and shareable neuroscience research. bioRxiv. [10.1101/2024.01.25.577295](https://doi.org/10.1101/2024.01.25.577295).
 
-Spyglass: a data analysis framework for reproducible and shareable neuroscience research
+*\* Equal contribution*
 
-Kyu Hyun Lee,  View ORCID ProfileEric Denovellis, Ryan Ly, Jeremy Magland, Jeff Soules, Alison E. Comrie, Daniel P. Gramling, Jennifer A. Guidera, Rhino Nevers, Philip Adenekan, Chris Brozdowski, Sam Bray, Emily Monroe, Ji Hyun Bak, Michael Coulter, Xulu Sun, Andrew Tritt, Oliver Rübel, Thinh Nguyen, Dimitri Yatsenko, Joshua Chu, Caleb Kemere, Samuel Garcia, Alessio Buccino, Loren M. Frank
+# spyglass-demo
 
-doi: https://doi.org/10.1101/2024.01.25.577295
+The Jupyter notebooks have been copied from <https://github.com/LorenFrankLab/spyglass> and a local DataJoint configuration created so that the notebooks work 'out-of-the-box' when used in conjuction with ephemeral the JupyterHub <https://spyglass.hhmi.cloud> managed by [2i2c](https://2i2c.org)
 
-# spyglass-notebooks
+The image used to run the JupyterHub is located at: <https://quay.io/repository/lorenlab/hhmi-spyglass-image> and the source code for the image is located at <https://github.com/LorenFrankLab/hhmi-spyglass-image>.
 
-The Jupyter notebooks have been copied from https://github.com/LorenFrankLab/spyglass and a local DataJoint configuration created so that the notebooks work 'out-of-the-box' when used in conjuction with ephemeral the JupyterHub https://spyglass.hhmi.cloud managed by [2i2c](https://2i2c.org)
-
-The [magic link](https://spyglass.hhmi.2i2c.cloud/hub/user-redirect/git-pull?repo=https%3A%2F%2Fgithub.com%2Fjmunroe%2Fspyglass-notebooks&urlpath=lab%2Ftree%2Fspyglass-notebooks%2Fnotebooks%2F01_Insert_Data.ipynb&branch=main)
+The [magic link](https://spyglass.hhmi.2i2c.cloud/hub/user-redirect/git-pull?repo=https%3A%2F%2Fgithub.com%2FLorenFrankLab%2Fspyglass-demo&urlpath=lab%2Ftree%2Fspyglass-demo%2Fnotebooks%2F01_Insert_Data.ipynb&branch=main)
 is a application of the [nbgitpuller](https://nbgitpuller.readthedocs.io/) project.  Please use this [nbgitpuller link generator](https://nbgitpuller.readthedocs.io/en/latest/link.html) to create a new link if this repository is moved or forked.
 
-nbgitpuller is compatiable with URL shorteners if that is desired. 
+nbgitpuller is compatiable with URL shorteners if that is desired.

dj_local_conf.json

@@ -18,22 +18,22 @@
     "stores": {
         "raw": {
             "protocol": "file",
-            "location": "/home/jovyan/spyglass-notebooks/data/nwb/raw",
-            "stage": "/home/jovyan/spyglass-notebooks/data/nwb/raw"
+            "location": "/home/jovyan/spyglass-demo/data/nwb/raw",
+            "stage": "/home/jovyan/spyglass-demo/data/nwb/raw"
         },
         "analysis": {
             "protocol": "file",
-            "location": "/home/jovyan/spyglass-notebooks/data/nwb/analysis",
-            "stage": "/home/jovyan/spyglass-notebooks/data/nwb/analysis"
+            "location": "/home/jovyan/spyglass-demo/data/nwb/analysis",
+            "stage": "/home/jovyan/spyglass-demo/data/nwb/analysis"
         }
     },
     "custom": {
         "spyglass_dirs": {
-            "base": "/home/jovyan/spyglass-notebooks/data/nwb"
+            "base": "/home/jovyan/spyglass-demo/data/nwb"
         },
         "kachery_dirs": {
-            "cloud": "/home/jovyan/spyglass-notebooks/data/.kachery_cloud"
+            "cloud": "/home/jovyan/spyglass-demo/data/.kachery_cloud"
         },
         "kachery_zone": "franklab.collaborators"
     }
-}
+}