Update links from murthylab to talmolab (#724)

* Update links from murthylab to talmolab

* Add conda channel for pip install in no cuda yml

* Add try/except for release checker

* Update rest API link

.github/PULL_REQUEST_TEMPLATE.md

@@ -15,8 +15,8 @@
 
 ### Outside contributors checklist
 
-- [ ] Review the [guidelines for contributing](https://github.com/murthylab/sleap/wiki/Developer-Guide) to this repository
-- [ ] Read and sign the [CLA](https://github.com/murthylab/sleap/blob/develop/sleap-cla.pdf) and add yourself to the [authors list](https://github.com/murthylab/sleap/blob/develop/AUTHORS)
+- [ ] Review the [guidelines for contributing](https://github.com/talmolab/sleap/wiki/Developer-Guide) to this repository
+- [ ] Read and sign the [CLA](https://github.com/talmolab/sleap/blob/develop/sleap-cla.pdf) and add yourself to the [authors list](https://github.com/talmolab/sleap/blob/develop/AUTHORS)
 - [ ] Make sure you are making a pull request against the **develop** branch (not *main*). Also you should start *your branch* off *develop*
 - [ ] Add tests that prove your fix is effective or that your feature works
 - [ ] Add necessary documentation (if appropriate)

README.rst

@@ -1,17 +1,17 @@
 |CI| |Coverage| |Documentation| |Downloads| |Stable version| |Latest version|
 
 .. |CI| image:: 
-   https://github.com/murthylab/sleap/workflows/CI/badge.svg?event=push&branch=develop
-   :target: https://github.com/murthylab/sleap/actions?query=workflow:CI
+   https://github.com/talmolab/sleap/workflows/CI/badge.svg?event=push&branch=develop
+   :target: https://github.com/talmolab/sleap/actions?query=workflow:CI
    :alt: Continuous integration status
 
 .. |Coverage| image::
-   https://codecov.io/gh/murthylab/sleap/branch/develop/graph/badge.svg?token=YWQYBN6820
-   :target: https://codecov.io/gh/murthylab/sleap
+   https://codecov.io/gh/talmolab/sleap/branch/develop/graph/badge.svg?token=YWQYBN6820
+   :target: https://codecov.io/gh/talmolab/sleap
    :alt: Coverage
 
 .. |Documentation| image:: 
-   https://img.shields.io/github/workflow/status/murthylab/sleap/Build%20website?label=Documentation
+   https://img.shields.io/github/workflow/status/talmolab/sleap/Build%20website?label=Documentation
    :target: https://sleap.ai
    :alt: Documentation
 
@@ -20,12 +20,12 @@
    :target: https://pepy.tech/project/sleap
    :alt: Downloads
 
-.. |Stable version| image:: https://img.shields.io/github/v/release/murthylab/sleap?label=stable
-   :target: https://github.com/murthylab/sleap/releases/
+.. |Stable version| image:: https://img.shields.io/github/v/release/talmolab/sleap?label=stable
+   :target: https://github.com/talmolab/sleap/releases/
    :alt: Stable version
 
-.. |Latest version| image:: https://img.shields.io/github/v/release/murthylab/sleap?include_prereleases&label=latest
-   :target: https://github.com/murthylab/sleap/releases/
+.. |Latest version| image:: https://img.shields.io/github/v/release/talmolab/sleap?include_prereleases&label=latest
+   :target: https://github.com/talmolab/sleap/releases/
    :alt: Latest version
 
 
@@ -57,7 +57,7 @@ Get some SLEAP
 --------------
 SLEAP is installed as a Python package. We strongly recommend using `Miniconda <https://https://docs.conda.io/en/latest/miniconda.html>`_ to install SLEAP in its own environment.
 
-You can find the latest version of SLEAP in the `Releases <https://github.com/murthylab/sleap/releases>`_ page.
+You can find the latest version of SLEAP in the `Releases <https://github.com/talmolab/sleap/releases>`_ page.
 
 Quick install
 ^^^^^^^^^^^^^
@@ -138,7 +138,7 @@ Follow `@talmop <https://twitter.com/talmop>`_ on Twitter for news and updates!
 **Technical issue with the software?**
 
 1. Check the `Help page <https://sleap.ai/help.html>`_.
-2. Search the `issues on GitHub <https://github.com/murthylab/sleap/issues>`_ or open a new one.
+2. Search the `issues on GitHub <https://github.com/talmolab/sleap/issues>`_ or open a new one.
 
 
 **General inquiries?**
@@ -170,7 +170,7 @@ This work was made possible through our funding sources, including:
 
 License
 -------
-SLEAP is released under a `Clear BSD License <https://raw.githubusercontent.com/murthylab/sleap/main/LICENSE>`_ and is intended for research/academic use only. For commercial use, please contact: Laurie Tzodikov (Assistant Director, Office of Technology Licensing), Princeton University, 609-258-7256.
+SLEAP is released under a `Clear BSD License <https://raw.githubusercontent.com/talmolab/sleap/main/LICENSE>`_ and is intended for research/academic use only. For commercial use, please contact: Laurie Tzodikov (Assistant Director, Office of Technology Licensing), Princeton University, 609-258-7256.
 
 
 .. end-inclusion-marker-do-not-remove

docs/conf.py

@@ -100,7 +100,7 @@ def linkcode_resolve(domain, info):
         filename = docs.utils.resolve(info["module"], info["fullname"])
         if filename is None:
             return None
-        return f"https://github.com/murthylab/sleap/blob/{release}/{filename}"
+        return f"https://github.com/talmolab/sleap/blob/{release}/{filename}"
     except:
         print(info)
         raise
@@ -132,7 +132,7 @@ def linkcode_resolve(domain, info):
     # "light_logo": "logo.png",
     # "dark_logo": "logo.png",
     # https://sphinx-book-theme.readthedocs.io/en/stable/customize/index.html#theme-options
-    "repository_url": "https://github.com/murthylab/sleap",
+    "repository_url": "https://github.com/talmolab/sleap",
     "use_download_button": False,
     "use_fullscreen_button": False,
     "use_repository_button": True,

docs/guides/cli.rst

@@ -296,7 +296,7 @@ Debugging
 ``sleap-diagnostic``
 ++++++++++++++++++++
 
-There's also a script to output diagnostic information which may help us if you need to contact us about problems installing or running SLEAP. If you were able to install the SLEAP Python package, you can run this script with :code:`sleap-diagnostic`. Otherwise, you can download `diagnostic.py <https://raw.githubusercontent.com/murthylab/sleap/main/sleap/diagnostic.py>`_ and run :code:`python diagnostic.py`.
+There's also a script to output diagnostic information which may help us if you need to contact us about problems installing or running SLEAP. If you were able to install the SLEAP Python package, you can run this script with :code:`sleap-diagnostic`. Otherwise, you can download `diagnostic.py <https://raw.githubusercontent.com/talmolab/sleap/main/sleap/diagnostic.py>`_ and run :code:`python diagnostic.py`.
 
 
 .. code-block:: none

docs/guides/custom-training.md

@@ -8,7 +8,7 @@ Hyperparameters include the model architecture, learning rate, and data augmenta
 
 This guide will explain how to create a custom training profile but doesn't cover how to decide what the hyperpameters should be. For more information about the hyperparameters, see our guide to {ref}`choosing-models`.
 
-Training profiles are JSON files. The JSON format is fairly easy to read (and edit) with a text-editor and you can use the default "baseline" profiles as a starting point for creating your own training profiles. For example, take a look at the [baseline bottom-up profile](https://github.com/murthylab/sleap/blob/main/sleap/training_profiles/baseline_medium_rf.bottomup.json) or our [other baseline profiles](https://github.com/murthylab/sleap/blob/main/sleap/training_profiles).
+Training profiles are JSON files. The JSON format is fairly easy to read (and edit) with a text-editor and you can use the default "baseline" profiles as a starting point for creating your own training profiles. For example, take a look at the [baseline bottom-up profile](https://github.com/talmolab/sleap/blob/main/sleap/training_profiles/baseline_medium_rf.bottomup.json) or our [other baseline profiles](https://github.com/talmolab/sleap/blob/main/sleap/training_profiles).
 
 But if this sounds intimidating, you don't have to edit the JSON file by hand! You can use the same GUI that's used for training on a local machine to export custom training profiles.
 
@@ -46,4 +46,4 @@ for each model you want to train (where `path/to/custom/profile.json` should be
 
 ```{note}
 If you exported the training package as a ZIP file, it contains both the `.pkg.slp` and `.json` files necessary to train with the configuration you selected in the GUI. Before running the [`sleap-train`](sleap-train) command, make sure to unzip this file.
-```
+```

docs/guides/remote.md

@@ -28,7 +28,7 @@ But in most cases it's best to create a training job package and just use that f
 
 **Training profile**:
 
-SLEAP comes with "default" training profiles for training confidence maps, part affinity fields, centroids, or top-down confidence maps (which allow multi-instance inference without using part affinity fields). Any file in the [training_profiles](https://github.com/murthylab/sleap/tree/main/sleap/training_profiles) directory of the SLEAP package can be used by specifying its filename (e.g., {code}`baseline_medium_rf.bottomup.json`) as the training profile—the full path isn't required to use these built-in profiles.
+SLEAP comes with "default" training profiles for training confidence maps, part affinity fields, centroids, or top-down confidence maps (which allow multi-instance inference without using part affinity fields). Any file in the [training_profiles](https://github.com/talmolab/sleap/tree/main/sleap/training_profiles) directory of the SLEAP package can be used by specifying its filename (e.g., {code}`baseline_medium_rf.bottomup.json`) as the training profile—the full path isn't required to use these built-in profiles.
 
 Our guide to [custom-training] explains how to use the GUI to export custom training profiles. You can also use the {code}`initial_config.json` file saved from previous training run as a template for a new training config. You can copy the {code}`json` file and edit it in any text editor.
 

docs/guides/troubleshooting-workflows.md

@@ -25,6 +25,6 @@ performance by tuning hyperparameters that don't perform as well with little dat
 ![Stage 3 troubleshooting workflow](../_static/troubleshooting_stage3.png)
 
 If you still aren't getting good results, feel free to reach out by emailing us at
-`[email protected]` or opening a [Github Issue](https://github.com/murthylab/sleap/issues) 
+`[email protected]` or opening a [Github Issue](https://github.com/talmolab/sleap/issues) 
 and tell us a bit about your data (preferably with sample screenshots/clips) and what
-kinds of problems you're facing.
+kinds of problems you're facing.

docs/help.md

@@ -9,7 +9,7 @@ Stuck? Can't get SLEAP to run? Crashing? Try the recommended tips below.
 
 Have you tried all of the steps in the [installation instructions](installation)?
 
-If so, please feel free to [open an issue](https://github.com/murthylab/sleap/issues) and tell us how you're trying to install it, what error messages you're getting and which operating system you're on.
+If so, please feel free to [open an issue](https://github.com/talmolab/sleap/issues) and tell us how you're trying to install it, what error messages you're getting and which operating system you're on.
 
 ### Can I install it on a computer without a GPU?
 
@@ -73,10 +73,10 @@ Check out the [Analysis examples](notebooks/Analysis_examples) notebooks.
 
 ### I've found a bug or have another problem!
 
-Feel free to [open an issue](https://github.com/murthylab/sleap/issues) and we'll get back to you as soon as we can!
+Feel free to [open an issue](https://github.com/talmolab/sleap/issues) and we'll get back to you as soon as we can!
 
 ### Can I just talk to someone?
 
 SLEAP is a complex machine learning system intended for general use, so it's possible that we failed to consider the specifics of the situation in which you may be interested in using it with.
 
-Feel free to reach out to us at `[email protected]` if you have a question that isn't covered here.
+Feel free to reach out to us at `[email protected]` if you have a question that isn't covered here.

docs/index.rst

@@ -17,6 +17,6 @@ SLEAP Documentation
     notebooks/index
     Developer API <api>
     datasets
-    GitHub <https://github.com/murthylab/sleap>
-    Releases <https://github.com/murthylab/sleap/releases>
+    GitHub <https://github.com/talmolab/sleap>
+    Releases <https://github.com/talmolab/sleap/releases>
     help

docs/installation.md

@@ -4,7 +4,7 @@ SLEAP can be installed as a Python package on Windows, Linux and Mac OS X. We cu
 
 SLEAP requires many complex dependencies, so we **strongly** recommend using [Miniconda](https://docs.conda.io/en/latest/miniconda.html) to install it in its own isolated environment. See {ref}`Installing Miniconda<miniconda>` below for more instructions.
 
-The newest version of SLEAP can always be found in the [Releases page](https://github.com/murthylab/sleap/releases).
+The newest version of SLEAP can always be found in the [Releases page](https://github.com/talmolab/sleap/releases).
 
 ```{contents} Contents
 ---
@@ -68,7 +68,7 @@ conda create -y -n sleap -c sleap -c nvidia -c conda-forge sleap=1.2.2
 ### `conda` from source
 1. First, clone the repository:
    ```bash
-   git clone https://github.com/murthylab/sleap && cd sleap
+   git clone https://github.com/talmolab/sleap && cd sleap
    ```
 
 2. Then, install from the environment file:
@@ -125,7 +125,7 @@ SLEAP can be installed on newer M1 Macs by following these instructions:
 
 5. **Download the SLEAP M1 branch**:
    ```bash
-   cd ~ && git clone -b talmo/m1 --single-branch https://github.com/murthylab/sleap.git sleap_m1 && cd sleap_m1
+   cd ~ && git clone -b talmo/m1 --single-branch https://github.com/talmolab/sleap.git sleap_m1 && cd sleap_m1
    ```
    *Note:* This installs SLEAP in development mode, so changes to the source code are immediately applied in case you wanted to mess around with it. You can also just do a `git pull` to update it (no need to re-do any of the previous steps).
 
@@ -140,7 +140,7 @@ SLEAP can be installed on newer M1 Macs by following these instructions:
    conda activate sleap_m1 && sleap-label
    ```
 
-See [this Issue](https://github.com/murthylab/sleap/issues/579#issuecomment-1028602327) for more information on M1 support.
+See [this Issue](https://github.com/talmolab/sleap/issues/579#issuecomment-1028602327) for more information on M1 support.
 
 
 ## Testing that things are working
@@ -242,7 +242,7 @@ Once the environment has been removed, you are free to install SLEAP using any o
 
 
 ## Getting help
-If you run into any problems, check out the [GitHub Issues](https://github.com/murthylab/sleap/issues) to see if others have had the same problem.
+If you run into any problems, check out the [GitHub Issues](https://github.com/talmolab/sleap/issues) to see if others have had the same problem.
 
 If you get any errors or the GUI fails to launch, try running the diagnostics to see what SLEAP is able to detect on your system:
 ```bash
@@ -254,4 +254,4 @@ If you were not able to get SLEAP installed, activate the conda environment it i
 conda list
 ```
 
-Then, [open a new Issue](https://github.com/murthylab/sleap/issues) providing the versions from either command above, as well as any errors you saw in the console during the installation.
+Then, [open a new Issue](https://github.com/talmolab/sleap/issues) providing the versions from either command above, as well as any errors you saw in the console during the installation.

docs/notebooks/Analysis_examples.ipynb

@@ -7,7 +7,7 @@
     "id": "view-in-github"
    },
    "source": [
-    "<a href=\"https://colab.research.google.com/github/murthylab/sleap/blob/main/docs/notebooks/Analysis_examples.ipynb\" target=\"_parent\"><img src=\"https://colab.research.google.com/assets/colab-badge.svg\" alt=\"Open In Colab\"/></a>"
+    "<a href=\"https://colab.research.google.com/github/talmolab/sleap/blob/main/docs/notebooks/Analysis_examples.ipynb\" target=\"_parent\"><img src=\"https://colab.research.google.com/assets/colab-badge.svg\" alt=\"Open In Colab\"/></a>"
    ]
   },
   {
@@ -38,7 +38,7 @@
    "source": [
     "## Example analysis data\n",
     "\n",
-    "Let's start by download a sample HDF5. These predictions were created with models trained on our [sample Drosophila melanogaster courtship dataset](https://github.com/murthylab/sleap-datasets). Using these models we can inference on a video clip with 3000 frames. The video clip, resulting predictions, and exported HDF5 are all available [here](https://github.com/murthylab/sleap/tree/main/docs/notebooks/analysis_example).\n",
+    "Let's start by download a sample HDF5. These predictions were created with models trained on our [sample Drosophila melanogaster courtship dataset](https://github.com/talmolab/sleap-datasets). Using these models we can inference on a video clip with 3000 frames. The video clip, resulting predictions, and exported HDF5 are all available [here](https://github.com/talmolab/sleap/tree/main/docs/notebooks/analysis_example).\n",
     "\n",
     "We'll just download the `predictions.analysis.h5` file:"
    ]
@@ -58,12 +58,12 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "--2021-01-04 03:24:05--  https://github.com/murthylab/sleap/raw/main/docs/notebooks/analysis_example/predictions.analysis.h5\n",
+      "--2021-01-04 03:24:05--  https://github.com/talmolab/sleap/raw/main/docs/notebooks/analysis_example/predictions.analysis.h5\n",
       "Resolving github.com (github.com)... 140.82.113.4\n",
       "Connecting to github.com (github.com)|140.82.113.4|:443... connected.\n",
       "HTTP request sent, awaiting response... 302 Found\n",
-      "Location: https://raw.githubusercontent.com/murthylab/sleap/main/docs/notebooks/analysis_example/predictions.analysis.h5 [following]\n",
-      "--2021-01-04 03:24:05--  https://raw.githubusercontent.com/murthylab/sleap/tree/main/docs/notebooks/analysis_example/predictions.analysis.h5\n",
+      "Location: https://raw.githubusercontent.com/talmolab/sleap/main/docs/notebooks/analysis_example/predictions.analysis.h5 [following]\n",
+      "--2021-01-04 03:24:05--  https://raw.githubusercontent.com/talmolab/sleap/tree/main/docs/notebooks/analysis_example/predictions.analysis.h5\n",
       "Resolving raw.githubusercontent.com (raw.githubusercontent.com)... 151.101.0.133, 151.101.64.133, 151.101.128.133, ...\n",
       "Connecting to raw.githubusercontent.com (raw.githubusercontent.com)|151.101.0.133|:443... connected.\n",
       "HTTP request sent, awaiting response... 200 OK\n",
@@ -78,7 +78,7 @@
     }
    ],
    "source": [
-    "!wget -O predictions.analysis.h5 https://github.com/murthylab/sleap/raw/main/docs/notebooks/analysis_example/predictions.analysis.h5"
+    "!wget -O predictions.analysis.h5 https://github.com/talmolab/sleap/raw/main/docs/notebooks/analysis_example/predictions.analysis.h5"
    ]
   },
   {

docs/notebooks/Data_structures.ipynb

@@ -24,7 +24,7 @@
         "id": "view-in-github"
       },
       "source": [
-        "<a href=\"https://colab.research.google.com/github/murthylab/sleap/blob/main/docs/notebooks/Data_structures.ipynb\" target=\"_parent\"><img src=\"https://colab.research.google.com/assets/colab-badge.svg\" alt=\"Open In Colab\"/></a>"
+        "<a href=\"https://colab.research.google.com/github/talmolab/sleap/blob/main/docs/notebooks/Data_structures.ipynb\" target=\"_parent\"><img src=\"https://colab.research.google.com/assets/colab-badge.svg\" alt=\"Open In Colab\"/></a>"
       ]
     },
     {
@@ -951,4 +951,4 @@
       ]
     }
   ]
-}
+}

docs/notebooks/Interactive_and_realtime_inference.ipynb

@@ -21,7 +21,7 @@
         "id": "view-in-github"
       },
       "source": [
-        "<a href=\"https://colab.research.google.com/github/murthylab/sleap/blob/main/docs/notebooks/Interactive_and_realtime_inference.ipynb\" target=\"_parent\"><img src=\"https://colab.research.google.com/assets/colab-badge.svg\" alt=\"Open In Colab\"/></a>"
+        "<a href=\"https://colab.research.google.com/github/talmolab/sleap/blob/main/docs/notebooks/Interactive_and_realtime_inference.ipynb\" target=\"_parent\"><img src=\"https://colab.research.google.com/assets/colab-badge.svg\" alt=\"Open In Colab\"/></a>"
       ]
     },
     {
@@ -1569,4 +1569,4 @@
       ]
     }
   ]
-}
+}