diff --git a/.github/workflows/pages.yml b/.github/workflows/pages.yml index 66d71c3..687df6f 100644 --- a/.github/workflows/pages.yml +++ b/.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 diff --git a/.gitignore b/.gitignore index 470a291..096a086 100644 --- a/.gitignore +++ b/.gitignore @@ -1,3 +1,14 @@ .DS_Store .ipynb_checkpoints -napari-workshops/_build/ \ No newline at end of file +tutorial/_build/ + +# data files +*.zip +*.tif +*.csv +*_track.txt + +# ultrack files +metadata.toml +*.lock +data.db diff --git a/README.md b/README.md index a801837..67b10b4 100644 --- a/README.md +++ b/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://.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. \ No newline at end of file diff --git a/environment.yml b/environment.yml index 0a7029c..7aea7ed 100644 --- a/environment.yml +++ b/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 \ No newline at end of file + - py-ctcmetrics + - napari + - ultrack diff --git a/requirements.txt b/requirements.txt index 77489eb..8dd405d 100644 --- a/requirements.txt +++ b/requirements.txt @@ -4,4 +4,6 @@ jupytext napari[all] napari-animation matplotlib - +py-ctcmetrics +cellpose +ultrack