At/eqm

.gitignore

@@ -157,3 +157,4 @@ tests/plotting/actual_figures/
 
 # huggingface
 hub/
+docs/notebooks/test.zarr

README.md

@@ -1,11 +1,11 @@
-<img src="docs/_static/images/cellflow_dark.png" width="500" alt="CellFlow">
+<img src="docs/_static/images/scaleflow_dark.png" width="500" alt="CellFlow">
 
-[![PyPI](https://img.shields.io/pypi/v/cellflow-tools.svg)](https://pypi.org/project/cellflow-tools/)
-[![Downloads](https://static.pepy.tech/badge/cellflow-tools)](https://pepy.tech/project/cellflow-tools)
-[![CI](https://img.shields.io/github/actions/workflow/status/theislab/cellflow/test.yaml?branch=main)](https://github.com/theislab/cellflow/actions)
+[![PyPI](https://img.shields.io/pypi/v/scaleflow-tools.svg)](https://pypi.org/project/scaleflow-tools/)
+[![Downloads](https://static.pepy.tech/badge/scaleflow-tools)](https://pepy.tech/project/scaleflow-tools)
+[![CI](https://img.shields.io/github/actions/workflow/status/theislab/scaleflow/test.yaml?branch=main)](https://github.com/theislab/scaleflow/actions)
 [![pre-commit.ci status](https://results.pre-commit.ci/badge/github/theislab/CellFlow/main.svg)](https://results.pre-commit.ci/latest/github/theislab/CellFlow/main)
-[![Codecov](https://codecov.io/gh/theislab/cellflow/branch/main/graph/badge.svg?token=Rgtm5Tsblo)](https://codecov.io/gh/theislab/cellflow)
-[![Docs](https://img.shields.io/readthedocs/cellflow)](https://cellflow.readthedocs.io/en/latest/)
+[![Codecov](https://codecov.io/gh/theislab/scaleflow/branch/main/graph/badge.svg?token=Rgtm5Tsblo)](https://codecov.io/gh/theislab/scaleflow)
+[![Docs](https://img.shields.io/readthedocs/scaleflow)](https://scaleflow.readthedocs.io/en/latest/)
 
 CellFlow - Modeling Complex Perturbations with Flow Matching 
 ============================================================
@@ -21,20 +21,20 @@ Check out the [preprint](https://www.biorxiv.org/content/10.1101/2025.04.11.6482
 - Modeling the development of perturbed organisms
 - Cell fate engineering
 - Optimizing protocols for growing organoids
-- ... and more; check out the [documentation](https://cellflow.readthedocs.io) for more information.
+- ... and more; check out the [documentation](https://scaleflow.readthedocs.io) for more information.
 
 
 Installation
 ------------
 Install **CellFlow** by running::
 
-    pip install cellflow-tools
+    pip install scaleflow-tools
 
 
 In order to install **CellFlow** in editable mode, run::
 
-    git clone https://github.com/theislab/cellflow
-    cd cellflow
+    git clone https://github.com/theislab/scaleflow
+    cd scaleflow
     pip install -e .
 
 For further instructions how to install jax, please refer to https://github.com/google/jax.

docs/conf.py

@@ -13,15 +13,15 @@
 # If extensions (or modules to document with autodoc) are in another directory,
 # add these directories to sys.path here. If the directory is relative to the
 # documentation root, use os.path.abspath to make it absolute, like shown here.
-import cellflow
+import scaleflow
 
 sys.path.insert(0, str(Path(__file__).parent / "extensions"))
 
 # -- Project information -----------------------------------------------------
 
-project = cellflow.__name__
-author = "CellFlow team"
-version = ilm.version("cellflow-tools")
+project = scaleflow.__name__
+author = "ScaleFlow team"
+version = ilm.version("scaleflow-tools")
 copyright = f"{datetime.now():%Y}, Theislab"
 
 # -- General configuration ---------------------------------------------------
@@ -67,9 +67,9 @@
 ]
 # TODO(michalk8): remove once typing has been cleaned-up
 nitpick_ignore_regex = [
-    (r"py:class", r"cellflow\..*(K|B|O)"),
-    (r"py:class", r"cellflow\._typing.*"),
-    (r"py:class", r"cellflow\..*Protocol.*"),
+    (r"py:class", r"scaleflow\..*(K|B|O)"),
+    (r"py:class", r"scaleflow\._typing.*"),
+    (r"py:class", r"scaleflow\..*Protocol.*"),
 ]
 
 
@@ -152,8 +152,8 @@
 html_show_sourcelink = False
 html_theme_options = {
     "sidebar_hide_name": True,
-    "light_logo": "images/cellflow_dark.png",
-    "dark_logo": "images/cellflow_dark.png",
+    "light_logo": "images/scaleflow_dark.png",
+    "dark_logo": "images/scaleflow_dark.png",
     "light_css_variables": {
         "color-brand-primary": "#003262",
         "color-brand-content": "#003262",
@@ -164,7 +164,7 @@
     "footer_icons": [
         {
             "name": "GitHub",
-            "url": "https://github.com/theislab/cellflow",
+            "url": "https://github.com/theislab/scaleflow",
             "html": "",
             "class": "fab fa-github",
         },

docs/developer.rst

@@ -4,8 +4,8 @@ Developer API
 CellFlow model
 ~~~~~~~~~~~~~~
 
-.. module:: cellflow.data
-.. currentmodule:: cellflow.data
+.. module:: scaleflow.data
+.. currentmodule:: scaleflow.data
 .. autosummary::
     :toctree: genapi
 

docs/index.rst

@@ -1,11 +1,11 @@
 
 CellFlow
 =====================
-.. module:: cellflow
+.. module:: scaleflow
 
-:mod:`cellflow` is a framework for modeling single-cell perturbation screens. CellFlow is very flexible and enables researchers to systematically explore how cells respond to a wide range of experimental interventions, including drug treatments, genetic modifications, cytokine stimulation, morphogen pathway modulation or even entire organoid protocols.
+:mod:`scaleflow` is a framework for modeling single-cell perturbation screens. CellFlow is very flexible and enables researchers to systematically explore how cells respond to a wide range of experimental interventions, including drug treatments, genetic modifications, cytokine stimulation, morphogen pathway modulation or even entire organoid protocols.
 
-:note: This is a work in progress. We are actively working on extending the documentation of :mod:`cellflow` with more tutorials to cover a wide range of use cases. If you have any questions or suggestions, please feel free to reach out to us.
+:note: This is a work in progress. We are actively working on extending the documentation of :mod:`scaleflow` with more tutorials to cover a wide range of use cases. If you have any questions or suggestions, please feel free to reach out to us.
 
 
 .. grid:: 3
@@ -15,13 +15,13 @@ CellFlow
         :link: installation
         :link-type: doc
 
-        Learn how to install :mod:`cellflow`.
+        Learn how to install :mod:`scaleflow`.
 
     .. grid-item-card:: User API
         :link: user/index
         :link-type: doc
 
-        The API reference with all the details on how to use :mod:`cellflow` functions.
+        The API reference with all the details on how to use :mod:`scaleflow` functions.
 
 
     .. grid-item-card:: Manuscript

docs/installation.rst

@@ -1,22 +1,22 @@
 Installation
 ============
-:mod:`cellflow` requires Python version >= 3.11 to run.
+:mod:`scaleflow` requires Python version >= 3.11 to run.
 
 PyPI
 ----
-Install :mod:`cellflow` by running::
+Install :mod:`scaleflow` by running::
 
-    pip install cellflow-tools
+    pip install scaleflow-tools
 
 Installing `rapids-singlecell` and `cuml`:
 
-While it's not necessary to install :mod:`cellflow` with `rapids-singlecell` and `cuml`, 
+While it's not necessary to install :mod:`scaleflow` with `rapids-singlecell` and `cuml`, 
 it is recommended to do so for faster preprocessing or downstream functions. 
-To install :mod:`cellflow` with `rapids-singlecell` and `cuml`, please refer to 
+To install :mod:`scaleflow` with `rapids-singlecell` and `cuml`, please refer to 
 `instructions how to install rapids <https://rapids-singlecell.readthedocs.io/en/latest/Installation.html>`_.
 
 Development version
 -------------------
-To install :mod:`cellflow` from `GitHub <https://github.com/theislab/CellFlow>`_, run::
+To install :mod:`scaleflow` from `GitHub <https://github.com/theislab/CellFlow>`_, run::
 
     pip install git+https://github.com/theislab/CellFlow.git@main