Rename phylotorch to torchtree

README.md

@@ -1,39 +1,39 @@
-# phylotorch
+# torchtree
 
-[![Python package](https://github.com/4ment/phylotorch/actions/workflows/python-package.yml/badge.svg)](https://github.com/4ment/phylotorch/actions/workflows/python-package.yml)
+[![Python package](https://github.com/4ment/torchtree/actions/workflows/python-package.yml/badge.svg)](https://github.com/4ment/torchtree/actions/workflows/python-package.yml)
 
 ## Installation
 
-### Get the phylotorch source
+### Get the torchtree source
 ```bash
-git clone https://github.com/4ment/phylotorch
-cd phylotorch
+git clone https://github.com/4ment/torchtree
+cd torchtree
 ```
 
 ### Install dependencies
 
 Installing dependencies using Anaconda
 ```bash
 conda env create -f environment.yml
-conda activate phylotorch
+conda activate torchtree
 ```
 
 or using pip
 ```bash
 pip install -r requirements.txt
 ```
 
-### Install phylotorch
+### Install torchtree
 ```bash
 python setup.py install
 ```
 
 ### Check install
 ```bash
-phylotorch --help
+torchtree --help
 ```
 
 ### Quick start
 ```bash
-phylotorch examples/advi/fluA.json
+torchtree examples/advi/fluA.json
 ```

benchmarks/benchmark.py

@@ -6,22 +6,22 @@
 
 import torch
 
-from phylotorch import Parameter
-from phylotorch.evolution.alignment import Alignment, Sequence
-from phylotorch.evolution.coalescent import ConstantCoalescent
-from phylotorch.evolution.datatype import NucleotideDataType
-from phylotorch.evolution.site_pattern import compress_alignment
-from phylotorch.evolution.substitution_model import JC69
-from phylotorch.evolution.taxa import Taxa, Taxon
-from phylotorch.evolution.tree_likelihood import (
+from torchtree import Parameter
+from torchtree.evolution.alignment import Alignment, Sequence
+from torchtree.evolution.coalescent import ConstantCoalescent
+from torchtree.evolution.datatype import NucleotideDataType
+from torchtree.evolution.site_pattern import compress_alignment
+from torchtree.evolution.substitution_model import JC69
+from torchtree.evolution.taxa import Taxa, Taxon
+from torchtree.evolution.tree_likelihood import (
     calculate_treelikelihood_discrete,
     calculate_treelikelihood_discrete_rescaled,
 )
-from phylotorch.evolution.tree_model import (
+from torchtree.evolution.tree_model import (
     ReparameterizedTimeTreeModel,
     heights_from_branch_lengths,
 )
-from phylotorch.io import read_tree, read_tree_and_alignment
+from torchtree.io import read_tree, read_tree_and_alignment
 
 
 def benchmark(f):

environment.yml

@@ -1,4 +1,4 @@
-name: phylotorch
+name: treetorch
 channels:
   - pytorch
 dependencies: