updated environment and builds

.github/workflows/pages.yml

@@ -4,7 +4,7 @@ name: Deploy static content to Pages
 on:
   # Runs on pushes targeting the default branch
   push:
-    branches: ["main"]
+    branches: ["main", "ultrack"]
 
   # Allows you to run this workflow manually from the Actions tab
   workflow_dispatch:
@@ -33,7 +33,7 @@ jobs:
       - name: Setup Python
         uses: actions/setup-python@v5
         with:
-          python-version: '3.11'
+          python-version: '3.12'
       - name: qt libs
         uses: tlambert03/setup-qt-libs@v1
       - name: Setup Pages
@@ -43,11 +43,11 @@ jobs:
         with:
           run: |
             pip install -r requirements.txt
-            jupyter book build napari-workshops
+            jupyter book build tutorial
       - name: Upload artifact
         uses: actions/upload-pages-artifact@v3
         with:
-          path: 'napari-workshops/_build/html'
+          path: 'tutorial/_build/html'
       - name: Deploy to GitHub Pages
         id: deployment
         uses: actions/deploy-pages@v4

.gitignore

@@ -1,3 +1,14 @@
 .DS_Store
 .ipynb_checkpoints
-napari-workshops/_build/
+tutorial/_build/
+
+# data files
+*.zip
+*.tif
+*.csv
+*_track.txt
+
+# ultrack files
+metadata.toml
+*.lock
+data.db

README.md

@@ -1,28 +1,7 @@
-# napari-workshop-template
+# Ultrack I2K 2024 Workshop
 
-A JupyterBook template for napari workshops.
+## Acknowledgements
 
-**To see the built website, go to
-https://<your_github_username>.github.io/napari-workshop-template**. For
-example, see this template [here](https://napari.org/napari-workshop-template/home.html).
+This workshop is based on [napari/napari-workshop-template](https://github.com/napari/napari-workshop-template).
 
-**To see a live version where you can execute the notebooks on your browser, use [![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/napari/napari-workshop-template/main)** (make sure this link points to your own repository!)
-
-## What is this repository?
-
-This repository is meant to be [forked](https://docs.github.com/en/get-started/quickstart/fork-a-repo) and edited so that you have a starting point when creating your own napari workshop. All instructions below are meant to be executed _on your own fork_, so that you have a copy of the template that you can adjust to your needs.
-
-You can also click the `Use this template` button in the GitHub web interface for this repository:
-
-![Use this template button on GitHub interface](napari-workshops/docs/images/00-template.png)
-
-> [!TIP]
-> Once you have created your workshop, if you would like the event to be listed [in the workshops page in napari.org](https://napari.org/stable/further-resources/napari-workshops.html), feel free to [submit a pull request to the napari/docs repository](https://github.com/napari/docs/blob/main/docs/further-resources/napari-workshops.md).
-
-## Documentation
-
-To learn more about how to build, publish, share and cite your workshop materials, check the [Build your own workshop section](https://napari.github.io/napari-workshop-template/docs/build_your_workshop.html).
-
-## Contributing to this repository
-
-If you find typos, incomplete or misleading instructions, or have suggestions for improvements to this template, open an issue at the napari/napari-workshop-template repo.
+We make use of [napari-convpaint](https://github.com/guiwitz/napari-convpaint) for segmentation.

environment.yml

@@ -1,12 +1,26 @@
-name: workshop
+name: ultrack-i2k2024
 channels:
+  - gurobi
+  - pytorch
   - conda-forge
+  - defaults
 dependencies:
+  - python=3.12
+  - pytorch
   - jupyterlab
   - jupytext
-  - matplotlib
-  - napari
+  - jupyterlab-myst
+  - jupyter-book
+  - notebook
+  - cellpose
+  - coin-or-cbc
+  - gurobi
+  - jupyter
+  - nodejs
   - pip
+  - pyqt
+  - higra
   - pip:
-    - jupyter-book
-    - napari-animation
+    - py-ctcmetrics
+    - napari
+    - ultrack

requirements.txt

@@ -4,4 +4,6 @@ jupytext
 napari[all]
 napari-animation
 matplotlib
-
+py-ctcmetrics
+cellpose
+ultrack