chore: update repository links after org migration (#1215)

MilesCranmer · MilesCranmerBot · commit e8f987925880 · 2026-06-28T00:41:28.000Z
diff --git a/.github/ISSUE_TEMPLATE/config.yml b/.github/ISSUE_TEMPLATE/config.yml
@@ -1,5 +1,5 @@
 blank_issues_enabled: true
 contact_links:
   - name: PySR Forums
-    url: https://github.com/MilesCranmer/PySR/discussions
+    url: https://github.com/astroautomata/PySR/discussions
     about: Please ask and answer questions about how to use PySR here.
diff --git a/.github/ISSUE_TEMPLATE/feature_request.yml b/.github/ISSUE_TEMPLATE/feature_request.yml
@@ -18,4 +18,4 @@ body:
   - type: markdown
     attributes:
       value: |
-        Be sure to check out the [PySR forums](https://github.com/MilesCranmer/PySR/discussions) to chat with other users about PySR use-cases!
+        Be sure to check out the [PySR forums](https://github.com/astroautomata/PySR/discussions) to chat with other users about PySR use-cases!
diff --git a/.github/workflows/CI.yml b/.github/workflows/CI.yml
@@ -86,7 +86,7 @@ jobs:
         uses: codecov/codecov-action@v5
         with:
           token: ${{ secrets.CODECOV_TOKEN }}
-          slug: MilesCranmer/PySR
+          slug: astroautomata/PySR
 
   dev_install:
     runs-on: ${{ matrix.os }}
diff --git a/.github/workflows/update_backend.yml b/.github/workflows/update_backend.yml
@@ -22,7 +22,7 @@ jobs:
         id: get-latest
         run: |
           cd $(mktemp -d)
-          git clone https://github.com/MilesCranmer/SymbolicRegression.jl
+          git clone https://github.com/astroautomata/SymbolicRegression.jl
           cd SymbolicRegression.jl
           echo "version=$(git describe --tags --match='v*' --abbrev=0 | sed 's/^v//')" >> $GITHUB_OUTPUT
 
@@ -44,7 +44,7 @@ jobs:
           body: |
             This PR was automatically generated by the GitHub Action `.github/workflows/update-backend.yml`
 
-            It updates the backend version to v${{ steps.get-latest.outputs.version }}. For a full description of the changes, see the backend changelog: [v${{ steps.get-latest.outputs.version }}](https://github.com/MilesCranmer/SymbolicRegression.jl/releases/tag/v${{ steps.get-latest.outputs.version }}).
+            It updates the backend version to v${{ steps.get-latest.outputs.version }}. For a full description of the changes, see the backend changelog: [v${{ steps.get-latest.outputs.version }}](https://github.com/astroautomata/SymbolicRegression.jl/releases/tag/v${{ steps.get-latest.outputs.version }}).
           delete-branch: true
           commit-message: "Update backend version to v${{ steps.get-latest.outputs.version }}"
           add-paths: |
diff --git a/CONTRIBUTORS.md b/CONTRIBUTORS.md
@@ -18,11 +18,11 @@ Here are some resources to help you get started with open source contributions i
 
 #### Create a new issue
 
-If you spot a problem with PySR, [search if an issue already exists](https://docs.github.com/en/github/searching-for-information-on-github/searching-on-github/searching-issues-and-pull-requests#search-by-the-title-body-or-comments). If a related issue doesn't exist, you can open a new issue using a relevant [issue form](https://github.com/MilesCranmer/PySR/issues/new/choose).
+If you spot a problem with PySR, [search if an issue already exists](https://docs.github.com/en/github/searching-for-information-on-github/searching-on-github/searching-issues-and-pull-requests#search-by-the-title-body-or-comments). If a related issue doesn't exist, you can open a new issue using a relevant [issue form](https://github.com/astroautomata/PySR/issues/new/choose).
 
 #### Solve an issue
 
-Scan through our [existing issues](https://github.com/MilesCranmer/PySR/issues) to find one that interests you (feel free to work on any!). You can narrow down the search using `labels` as filters. See [Labels](/contributing/how-to-use-labels.md) for more information. If you find an issue to work on, you are welcome to open a PR with a fix.
+Scan through our [existing issues](https://github.com/astroautomata/PySR/issues) to find one that interests you (feel free to work on any!). You can narrow down the search using `labels` as filters. See [Labels](/contributing/how-to-use-labels.md) for more information. If you find an issue to work on, you are welcome to open a PR with a fix.
 
 ### Make Changes
 
@@ -40,7 +40,7 @@ Scan through our [existing issues](https://github.com/MilesCranmer/PySR/issues)
 
 3. (Optional) If you would like to make changes to PySR itself, skip to step 4. However, if you are interested in making changes to the _symbolic regression code_ itself,
 check out the [guide](https://ai.damtp.cam.ac.uk/pysr/backend/) on modifying a custom SymbolicRegression.jl library.
-In this case, you might instead be interested in making suggestions to the [SymbolicRegression.jl](http://github.com/MilesCranmer/SymbolicRegression.jl) library.
+In this case, you might instead be interested in making suggestions to the [SymbolicRegression.jl](https://github.com/astroautomata/SymbolicRegression.jl) library.
 
 4. You can install your local version of PySR with `pip install -e '.[dev]'`, and run tests with `python -m pysr test main`.
 
diff --git a/README.md b/README.md
@@ -4,14 +4,14 @@
 
 PySR searches for symbolic expressions which optimize a particular objective.
 
-https://github.com/MilesCranmer/PySR/assets/7593028/c8511a49-b408-488f-8f18-b1749078268f
+https://github.com/astroautomata/PySR/assets/7593028/c8511a49-b408-488f-8f18-b1749078268f
 
 
 # PySR: High-Performance Symbolic Regression in Python and Julia
 
 | **Docs** | **Forums** | **Paper** | **colab demo** |
 |:---:|:---:|:---:|:---:|
-|[![Documentation](https://github.com/MilesCranmer/PySR/actions/workflows/docs.yml/badge.svg)](https://ai.damtp.cam.ac.uk/pysr/)|[![Discussions](https://img.shields.io/badge/discussions-github-informational)](https://github.com/MilesCranmer/PySR/discussions)|[![Paper](https://img.shields.io/badge/arXiv-2305.01582-b31b1b)](https://arxiv.org/abs/2305.01582)|[![Colab](https://img.shields.io/badge/colab-notebook-yellow)](https://colab.research.google.com/github/MilesCranmer/PySR/blob/master/examples/pysr_demo.ipynb)|
+|[![Documentation](https://github.com/astroautomata/PySR/actions/workflows/docs.yml/badge.svg)](https://ai.damtp.cam.ac.uk/pysr/)|[![Discussions](https://img.shields.io/badge/discussions-github-informational)](https://github.com/astroautomata/PySR/discussions)|[![Paper](https://img.shields.io/badge/arXiv-2305.01582-b31b1b)](https://arxiv.org/abs/2305.01582)|[![Colab](https://img.shields.io/badge/colab-notebook-yellow)](https://colab.research.google.com/github/astroautomata/PySR/blob/master/examples/pysr_demo.ipynb)|
 
 | **pip** | **conda** | **Stats** |
 | :---: | :---: | :---: |
@@ -36,9 +36,9 @@ If you've finished a project with PySR, please submit a PR to showcase your work
 
 | **Linux** | **Windows** | **macOS** |
 |---|---|---|
-|[![Linux](https://github.com/MilesCranmer/PySR/actions/workflows/CI.yml/badge.svg)](https://github.com/MilesCranmer/PySR/actions/workflows/CI.yml)|[![Windows](https://github.com/MilesCranmer/PySR/actions/workflows/CI_Windows.yml/badge.svg)](https://github.com/MilesCranmer/PySR/actions/workflows/CI_Windows.yml)|[![macOS](https://github.com/MilesCranmer/PySR/actions/workflows/CI_mac.yml/badge.svg)](https://github.com/MilesCranmer/PySR/actions/workflows/CI_mac.yml)|
+|[![Linux](https://github.com/astroautomata/PySR/actions/workflows/CI.yml/badge.svg)](https://github.com/astroautomata/PySR/actions/workflows/CI.yml)|[![Windows](https://github.com/astroautomata/PySR/actions/workflows/CI_Windows.yml/badge.svg)](https://github.com/astroautomata/PySR/actions/workflows/CI_Windows.yml)|[![macOS](https://github.com/astroautomata/PySR/actions/workflows/CI_mac.yml/badge.svg)](https://github.com/astroautomata/PySR/actions/workflows/CI_mac.yml)|
 | **Docker** | **Conda** | **Coverage** |
-|[![Docker](https://github.com/MilesCranmer/PySR/actions/workflows/CI_docker.yml/badge.svg)](https://github.com/MilesCranmer/PySR/actions/workflows/CI_docker.yml)|[![conda-forge](https://github.com/MilesCranmer/PySR/actions/workflows/CI_conda_forge.yml/badge.svg)](https://github.com/MilesCranmer/PySR/actions/workflows/CI_conda_forge.yml)|[![codecov](https://codecov.io/gh/MilesCranmer/PySR/branch/master/graph/badge.svg)](https://codecov.io/gh/MilesCranmer/PySR)|
+|[![Docker](https://github.com/astroautomata/PySR/actions/workflows/CI_docker.yml/badge.svg)](https://github.com/astroautomata/PySR/actions/workflows/CI_docker.yml)|[![conda-forge](https://github.com/astroautomata/PySR/actions/workflows/CI_conda_forge.yml/badge.svg)](https://github.com/astroautomata/PySR/actions/workflows/CI_conda_forge.yml)|[![codecov](https://codecov.io/gh/astroautomata/PySR/branch/master/graph/badge.svg)](https://codecov.io/gh/astroautomata/PySR)|
 
 </div>
 
@@ -50,7 +50,7 @@ task where the goal is to find an interpretable symbolic expression that optimiz
 Over a period of several years, PySR has been engineered from the ground up
 to be (1) as high-performance as possible,
 (2) as configurable as possible, and (3) easy to use.
-PySR is developed alongside the Julia library [SymbolicRegression.jl](https://github.com/MilesCranmer/SymbolicRegression.jl),
+PySR is developed alongside the Julia library [SymbolicRegression.jl](https://github.com/astroautomata/SymbolicRegression.jl),
 which forms the powerful search engine of PySR.
 The details of these algorithms are described in the [PySR paper](https://arxiv.org/abs/2305.01582).
 
@@ -155,7 +155,7 @@ to your `.bashrc` or `.zshrc` file.
 
 ## Quickstart
 
-You might wish to try the interactive tutorial [here](https://colab.research.google.com/github/MilesCranmer/PySR/blob/master/examples/pysr_demo.ipynb), which uses the notebook in `examples/pysr_demo.ipynb`.
+You might wish to try the interactive tutorial [here](https://colab.research.google.com/github/astroautomata/PySR/blob/master/examples/pysr_demo.ipynb), which uses the notebook in `examples/pysr_demo.ipynb`.
 
 In practice, I highly recommend using IPython rather than Jupyter, as the printing is much nicer.
 Below is a quick demo here which you can paste into a Python runtime.
@@ -370,8 +370,8 @@ before the `build` and `run` commands.
 
 </div>
 
-We are eager to welcome new contributors! Check out our contributors [guide](https://github.com/MilesCranmer/PySR/blob/master/CONTRIBUTORS.md) for tips 🚀.
-If you have an idea for a new feature, don't hesitate to share it on the [issues](https://github.com/MilesCranmer/PySR/issues) or [discussions](https://github.com/MilesCranmer/PySR/discussions) page.
+We are eager to welcome new contributors! Check out our contributors [guide](https://github.com/astroautomata/PySR/blob/master/CONTRIBUTORS.md) for tips 🚀.
+If you have an idea for a new feature, don't hesitate to share it on the [issues](https://github.com/astroautomata/PySR/issues) or [discussions](https://github.com/astroautomata/PySR/discussions) page.
 
 <!-- ALL-CONTRIBUTORS-LIST:START - Do not remove or modify this section -->
 <!-- prettier-ignore-start -->
diff --git a/docs/all_contributors/.all-contributorsrc b/docs/all_contributors/.all-contributorsrc
@@ -1,6 +1,6 @@
 {
   "projectName": "PySR",
-  "projectOwner": "MilesCranmer",
+  "projectOwner": "astroautomata",
   "repoType": "github",
   "repoHost": "https://github.com",
   "files": [
diff --git a/docs/all_contributors/package.json b/docs/all_contributors/package.json
@@ -2,7 +2,7 @@
   "name": "PySR",
   "version": "1.0.0",
   "main": "index.js",
-  "repository": "git@github.com:MilesCranmer/PySR.git",
+  "repository": "git@github.com:astroautomata/PySR.git",
   "author": "MilesCranmer <miles.cranmer@gmail.com>",
   "license": "Apache-2.0",
   "devDependencies": {
diff --git a/docs/backend.md b/docs/backend.md
@@ -1,7 +1,7 @@
 # Customization
 
 If you have explored the [options](options.md) and [PySRRegressor reference](api.md), and still haven't figured out how to specify a constraint or objective required for your problem, you might consider editing the backend.
-The backend of PySR is written as a pure Julia package under the name [SymbolicRegression.jl](https://github.com/MilesCranmer/SymbolicRegression.jl).
+The backend of PySR is written as a pure Julia package under the name [SymbolicRegression.jl](https://github.com/astroautomata/SymbolicRegression.jl).
 This package is accessed with [`juliacall`](https://github.com/JuliaPy/PythonCall.jl), which allows us to transfer objects back and forth between the Python and Julia runtimes.
 
 PySR gives you access to everything in SymbolicRegression.jl, but there are some specific use-cases which require modifications to the backend itself.
@@ -12,8 +12,8 @@ Generally you can do this as follows:
 Clone a copy of the backend as well as PySR:
 
 ```bash
-git clone https://github.com/MilesCranmer/SymbolicRegression.jl
-git clone https://github.com/MilesCranmer/PySR
+git clone https://github.com/astroautomata/SymbolicRegression.jl
+git clone https://github.com/astroautomata/PySR
 ```
 
 You may wish to check out the specific versions, which you can do with:
@@ -36,11 +36,11 @@ Here are some tips:
 -  The documentation for the backend is given [here](https://ai.damtp.cam.ac.uk/symbolicregression/dev/).
 - Throughout the package, you will often see template functions which typically use a symbol `T` (such as in the string `where {T<:Real}`). Here, `T` is simply the datatype of the input data and stored constants, such as `Float32` or `Float64`. Writing functions in this way lets us write functions generic to types, while still having access to the specific type specified at compilation time.
 - Expressions are stored as binary trees, using the `Node{T}` type, described [here](https://ai.damtp.cam.ac.uk/symbolicregression/dev/types/#SymbolicRegression.CoreModule.EquationModule.Node).
-- For reference, the main loop itself is found in the `equation_search` function inside [`src/SymbolicRegression.jl`](https://github.com/MilesCranmer/SymbolicRegression.jl/blob/master/src/SymbolicRegression.jl).
+- For reference, the main loop itself is found in the `equation_search` function inside [`src/SymbolicRegression.jl`](https://github.com/astroautomata/SymbolicRegression.jl/blob/master/src/SymbolicRegression.jl).
 - Parts of the code which are typically edited by users include:
-    - [`src/CheckConstraints.jl`](https://github.com/MilesCranmer/SymbolicRegression.jl/blob/master/src/CheckConstraints.jl), particularly the function `check_constraints`. This function checks whether a given expression satisfies constraints, such as having a complexity lower than `maxsize`, and whether it contains any forbidden nestings of functions.
+    - [`src/CheckConstraints.jl`](https://github.com/astroautomata/SymbolicRegression.jl/blob/master/src/CheckConstraints.jl), particularly the function `check_constraints`. This function checks whether a given expression satisfies constraints, such as having a complexity lower than `maxsize`, and whether it contains any forbidden nestings of functions.
         - Note that all expressions, *even intermediate expressions*, must comply with constraints. Therefore, make sure that evolution can still reach your desired expression (with one mutation at a time), before setting a hard constraint. In other cases you might want to instead put in the loss function.
-    - [`src/Options.jl`](https://github.com/MilesCranmer/SymbolicRegression.jl/blob/master/src/Options.jl), as well as the struct definition in [`src/OptionsStruct.jl`](https://github.com/MilesCranmer/SymbolicRegression.jl/blob/master/src/OptionsStruct.jl). This file specifies all the options used in the search: an instance of `Options` is typically available throughout every function in `SymbolicRegression.jl`. If you add new functionality to the backend, and wish to make it parameterizable (including from PySR), you should specify it in the options.
+    - [`src/Options.jl`](https://github.com/astroautomata/SymbolicRegression.jl/blob/master/src/Options.jl), as well as the struct definition in [`src/OptionsStruct.jl`](https://github.com/astroautomata/SymbolicRegression.jl/blob/master/src/OptionsStruct.jl). This file specifies all the options used in the search: an instance of `Options` is typically available throughout every function in `SymbolicRegression.jl`. If you add new functionality to the backend, and wish to make it parameterizable (including from PySR), you should specify it in the options.
 
 ## 3. Let PySR use the modified backend
 
diff --git a/docs/examples.md b/docs/examples.md
@@ -175,7 +175,7 @@ If all goes well, you should find that it predicts the correct input equation, w
 
 ## 7. Julia packages and types
 
-PySR uses [SymbolicRegression.jl](https://github.com/MilesCranmer/SymbolicRegression.jl)
+PySR uses [SymbolicRegression.jl](https://github.com/astroautomata/SymbolicRegression.jl)
 as its search backend. This is a pure Julia package, and so can interface easily with any other
 Julia package.
 For some tasks, it may be necessary to load such a package.
diff --git a/docs/stylesheets/papers_header.txt b/docs/stylesheets/papers_header.txt
@@ -5,4 +5,4 @@ These are sorted by the date of release, with most recent papers at the top.
 
 
 If you have used PySR in your research,
-please submit a pull request to add your paper to [this file](https://github.com/MilesCranmer/PySR/blob/master/docs/papers.yml).
+please submit a pull request to add your paper to [this file](https://github.com/astroautomata/PySR/blob/master/docs/papers.yml).
diff --git a/docs/tuning.md b/docs/tuning.md
@@ -10,7 +10,7 @@ I run from IPython (Jupyter Notebooks don't work as well[^1]) on the head node o
 
 I use the [tensorboard feature](https://ai.damtp.cam.ac.uk/pysr/examples/#12-using-tensorboard-for-logging) for experiment tracking.
 
-[^1]: Jupyter Notebooks are supported by PySR, but miss out on some useful features available in IPython and Python: the progress bar, and early stopping with "q". In Jupyter you cannot interrupt a search once it has started; you have to restart the kernel. See [this issue](https://github.com/MilesCranmer/PySR/issues/260) for updates.
+[^1]: Jupyter Notebooks are supported by PySR, but miss out on some useful features available in IPython and Python: the progress bar, and early stopping with "q". In Jupyter you cannot interrupt a search once it has started; you have to restart the kernel. See [this issue](https://github.com/astroautomata/PySR/issues/260) for updates.
 
 1. I start by using the default parameters.
 2. I use only the operators I think it needs and no more.
@@ -47,5 +47,5 @@ Once a run is finished, I use the `PySRRegressor.from_file` function to load the
 
 ## More Tips
 
-You might also wish to explore the [discussions](https://github.com/MilesCranmer/PySR/discussions/) page for more tips, and to see if anyone else has had similar questions.
+You might also wish to explore the [discussions](https://github.com/astroautomata/PySR/discussions/) page for more tips, and to see if anyone else has had similar questions.
 Be sure to also read through the [reference](api.md).
diff --git a/examples/pysr_demo.ipynb b/examples/pysr_demo.ipynb
@@ -731,7 +731,7 @@
     "id": "tOdNHheUG-KN"
    },
    "source": [
-    "PySR uses [SymbolicRegression.jl](https://github.com/MilesCranmer/SymbolicRegression.jl)\n",
+    "PySR uses [SymbolicRegression.jl](https://github.com/astroautomata/SymbolicRegression.jl)\n",
     "as its search backend. This is a pure Julia package, and so can interface easily with any other\n",
     "Julia package.\n",
     "For some tasks, it may be necessary to load such a package.\n",
diff --git a/pysr/sr.py b/pysr/sr.py
@@ -1999,7 +1999,7 @@ def _run(
         self.logger_ = logger
 
         # Call to Julia backend.
-        # See https://github.com/MilesCranmer/SymbolicRegression.jl/blob/master/src/OptionsStruct.jl
+        # See https://github.com/astroautomata/SymbolicRegression.jl/blob/master/src/OptionsStruct.jl
         options = SymbolicRegression.Options(
             binary_operators=jl_array(jl_binary_operators, dtype=jl.Function),
             unary_operators=jl_array(jl_unary_operators, dtype=jl.Function),
diff --git a/pysr/test/test_dev_pysr.dockerfile b/pysr/test/test_dev_pysr.dockerfile
@@ -38,7 +38,7 @@ RUN python3 -c 'import json; print(json.load(open("/pysr/pysr/juliapkg.json", "r
 RUN cat /pysr/sr_version | sed 's/[\^=~]//g' > /pysr/sr_version_processed
 
 # Now, we check out the version of SymbolicRegression.jl that PySR is using:
-RUN git clone -b "v$(cat /pysr/sr_version_processed)" --single-branch https://github.com/MilesCranmer/SymbolicRegression.jl /srjl
+RUN git clone -b "v$(cat /pysr/sr_version_processed)" --single-branch https://github.com/astroautomata/SymbolicRegression.jl /srjl
 
 # Edit SymbolicRegression.jl to create a new function.
 # We want to put this function immediately after `module SymbolicRegression`:

Original file line number	Diff line number	Diff line change
`@@ -1,6 +1,6 @@`
`1`	`1`	`{`
`2`	`2`	`"projectName": "PySR",`
`3`		`- "projectOwner": "MilesCranmer",`
	`3`	`+ "projectOwner": "astroautomata",`
`4`	`4`	`"repoType": "github",`
`5`	`5`	`"repoHost": "https://github.com",`
`6`	`6`	`"files": [`