diff --git a/README.md b/README.md index 0aa3b80..fb9c86e 100644 --- a/README.md +++ b/README.md @@ -1,4 +1,4 @@ -[![Tests](https://github.com/afloresep/TMAP/actions/workflows/tests.yml/badge.svg)](https://github.com/afloresep/TMAP/actions/workflows/tests.yml) +[![Tests](https://github.com/afloresep/tmap2/actions/workflows/tests.yml/badge.svg)](https://github.com/afloresep/tmap2/actions/workflows/tests.yml) [![PyPI](https://img.shields.io/pypi/v/tmap2)](https://pypi.org/project/tmap2/) [![Python 3.11+](https://img.shields.io/badge/python-3.11+-blue.svg)](https://www.python.org/downloads/) @@ -26,9 +26,9 @@ For example, in a TMAP of pet breed images, following the branch from terriers t Because the layout is a tree, you get operations that point clouds can't support: ```python -path = model.path(idx_a, idx_b) # nodes along the tree path -d = model.distance(idx_a, idx_b) # sum of edge weights along the path -pseudotime = model.distances_from(idx) # tree distance from one point to all others +path = model.path(idx_a, idx_b) # nodes along the tree path +d = model.distance(idx_a, idx_b # sum of edge weights along the path +pseudotime = model.distances_from(idx) # tree distance from one point to all others ``` ## Installation @@ -40,7 +40,7 @@ pip install tmap2 Optional extras: ```bash -pip install rdkit # chemistry helpers (fingerprints_from_smiles, molecular_properties) +pip install rdkit # chemistry helpers (fingerprints_from_smiles, molecular_properties) pip install jupyter-scatter # notebook interactive widgets ``` @@ -81,9 +81,9 @@ model.plot(color_by="label", data=df, tooltip_properties=["name", "score"]) ## Visualization -**Interactive HTML** — lasso selection, light/dark theme, filter and search panels, pinned metadata cards, binary mode for large datasets. +**Interactive HTML**: lasso selection, light/dark theme, filter and search panels, pinned metadata cards, binary mode for large datasets. -**Notebook widgets** — color switching, categorical filtering, and lasso selection with pandas-backed metadata: +**Notebook widgets**: color switching, categorical filtering, and lasso selection with pandas-backed metadata: ```python viz = model.to_tmapviz() @@ -145,8 +145,8 @@ Your Data ## Development ```bash -git clone https://github.com/afloresep/TMAP.git -cd TMAP +git clone https://github.com/afloresep/tmap2.git +cd tmap2 pip install ".[dev]" pytest -v ``` diff --git a/pyproject.toml b/pyproject.toml index 795a4f5..24ecdf0 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -50,9 +50,9 @@ dev = [ ] [project.urls] -Homepage = "https://github.com/afloresep/TMAP" -Documentation = "https://github.com/afloresep/TMAP#readme" -Repository = "https://github.com/afloresep/TMAP" +Homepage = "https://github.com/afloresep/tmap2" +Documentation = "https://github.com/afloresep/tmap2#readme" +Repository = "https://github.com/afloresep/tmap2" [tool.scikit-build] wheel.packages = ["src/tmap"]