updates github org name

README.md

@@ -4,7 +4,7 @@ Material for presentation at Cold Spring Harbor vision course, 2024. See the web
 
 ## Binder
 
-The binder setup is the same as previous workshop tutorials I've put together but note that, when we had many users, the binder instance was freezing. I believe that was due to ffmpeg grabbing all the threads on the node and, since there were many users on the node ... that was bad. See [issue for discussion](https://github.com/LabForComputationalVision/plenoptic/issues/268), but I believe the solution is to add
+The binder setup is the same as previous workshop tutorials I've put together but note that, when we had many users, the binder instance was freezing. I believe that was due to ffmpeg grabbing all the threads on the node and, since there were many users on the node ... that was bad. See [issue for discussion](https://github.com/plenoptic-org/plenoptic/issues/268), but I believe the solution is to add
 
 ``` python
 plt.rcParams['animation.html'] = 'html5'

docs/source/conf.py

@@ -16,7 +16,7 @@
 extensions = [
     'myst_nb',
     'sphinx_copybutton',
-    'sphinx_togglebutton',
+    # 'sphinx_togglebutton',
 ]
 
 templates_path = ['_templates']
@@ -30,18 +30,18 @@
 nb_execution_timeout = -1
 # we have two versions of each notebook, one with explanatory text and one without
 # (which ends in `-stripped.md`). we don't need to run both of them
-nb_execution_excludepatterns = ['*stripped*']
+nb_execution_excludepatterns = ['*stripped*', 'intro*']
 nb_execution_raise_on_error = True
-html_theme = 'sphinx_book_theme'
+html_theme = 'pydata_sphinx_theme'
 html_static_path = ['_static']
 html_css_files = ['custom.css']
 html_favicon = '_static/plenoptic.ico'
 html_sourcelink_suffix = ""
 myst_enable_extensions = ["colon_fence"]
 html_theme_options = {
     "home_page_in_toc": True,
-    "github_url": "https://github.com/LabForComputationalVision/plenoptic-cshl-vision-2024",
-    "repository_url": "https://github.com/LabForComputationalVision/plenoptic-cshl-vision-2024",
+    "github_url": "https://github.com/plenoptic-org/plenoptic-cshl-vision-2024",
+    "repository_url": "https://github.com/plenoptic-org/plenoptic-cshl-vision-2024",
     "logo": {
         "alt_text": "Home",
         "image_light": "_static/plenoptic.svg",

docs/source/index.md

@@ -21,7 +21,7 @@ While we'll use the binder during this tutorial, if you'd like to run the notebo
 0. Make sure you have `git` installed. It is installed by default on most Mac and Linux machines, but you may need to install it if you are on Windows. [These instructions](https://github.com/git-guides/install-git) should help.
 1. Clone the github repo for this tutorial:
    ```shell
-   git clone https://github.com/LabForComputationalVision/plenoptic-cshl-vision-2024.git
+   git clone https://github.com/plenoptic-org/plenoptic-cshl-vision-2024.git
    ```
 2. Create a new python 3.11 virtual environment. If you do not have a preferred way of managing your python virtual environments, we recommend [miniconda](https://docs.anaconda.com/free/miniconda/). After installing it (if you have not done so already), run 
     ```shell

docs/source/introduction.md

@@ -555,6 +555,6 @@ We can thus see that the addition of gain control qualitatively changes the sens
 
 In this notebook, we saw the basics of using `plenoptic` to investigate the sensitivities and invariances of some simple convolutional models, and reasoned through how the model metamers and eigendistortions we saw enable us to understand how these models process images.
 
-`plenoptic` includes a variety of models and model components in the [plenoptic.simulate](https://plenoptic.readthedocs.io/en/latest/api/plenoptic.simulate.html) module, and you can (and should!) use the synthesis methods with your own models. Our documentation also has [examples](https://plenoptic.readthedocs.io/en/latest/tutorials/applications/Demo_Eigendistortion.html) showing how to use models from [torchvision](https://pytorch.org/vision/stable/index.html) (which contains a variety of pretrained neural network models) with plenoptic. In order to use your own models with plenoptic, check the [documentation](https://plenoptic.readthedocs.io/en/latest/models.html) for the specific requirements, and use the [`validate_model`](https://plenoptic.readthedocs.io/en/latest/api/plenoptic.tools.html#plenoptic.tools.validate.validate_model) function to check compatibility. If you have issues or want feedback, we're happy to help --- just post on the [Github discussions page](https://github.com/LabForComputationalVision/plenoptic/discussions)!
+`plenoptic` includes a variety of models and model components in the [plenoptic.simulate](https://plenoptic.readthedocs.io/en/latest/api/plenoptic.simulate.html) module, and you can (and should!) use the synthesis methods with your own models. Our documentation also has [examples](https://plenoptic.readthedocs.io/en/latest/tutorials/applications/Demo_Eigendistortion.html) showing how to use models from [torchvision](https://pytorch.org/vision/stable/index.html) (which contains a variety of pretrained neural network models) with plenoptic. In order to use your own models with plenoptic, check the [documentation](https://plenoptic.readthedocs.io/en/latest/models.html) for the specific requirements, and use the [`validate_model`](https://plenoptic.readthedocs.io/en/latest/api/plenoptic.tools.html#plenoptic.tools.validate.validate_model) function to check compatibility. If you have issues or want feedback, we're happy to help --- just post on the [Github discussions page](https://github.com/plenoptic-org/plenoptic/discussions)!
 
 </div>

requirements.txt

@@ -1,7 +1,7 @@
 sphinx
 myst-nb
 Pillow
-plenoptic @ git+https://github.com/LabForComputationalVision/plenoptic.git@frontend_params
+plenoptic @ git+https://github.com/plenoptic-org/plenoptic.git@frontend_params
 sphinx-book-theme
 myst-parser
 sphinx-copybutton