MAINT: rename piqtree2 to piqtree

.github/actions/build-iqtree/action.yml

@@ -23,7 +23,7 @@ runs:
       id: cache
       with:
         key: libiqtree-${{ inputs.os }}-${{ steps.iqtree2-sha.outputs.iqtree2-sha }}
-        path: src/piqtree2/_libiqtree/libiqtree2.a
+        path: src/piqtree/_libiqtree/libiqtree2.a
         lookup-only: true
 
     - name: Build IQ-TREE

.github/actions/setup-piqtree/action.yml

@@ -17,5 +17,5 @@ runs:
     - uses: actions/cache/restore@v4
       with:
         key: ${{ inputs.cache-key }}
-        path: src/piqtree2/_libiqtree/libiqtree2.a
+        path: src/piqtree/_libiqtree/libiqtree2.a
         fail-on-cache-miss: true

.gitignore

@@ -10,8 +10,8 @@
 *.mldist
 *.treefile
 
-# piqtree2 specific ignores
-src/piqtree2/_libiqtree/**/*.a
+# piqtree specific ignores
+src/piqtree/_libiqtree/**/*.a
 
 # docs
 data

README.md

@@ -1,26 +1,26 @@
-# piqtree2
+# piqtree
 
-[![PyPI Version](https://img.shields.io/pypi/v/piqtree2)](https://pypi.org/project/piqtree2/)
-[![Python Version](https://img.shields.io/pypi/pyversions/piqtree2)](https://pypi.org/project/piqtree2/)
-[![License](https://img.shields.io/github/license/iqtree/piqtree2)](https://github.com/iqtree/piqtree2/blob/main/LICENSE)
+[![PyPI Version](https://img.shields.io/pypi/v/piqtree)](https://pypi.org/project/piqtree/)
+[![Python Version](https://img.shields.io/pypi/pyversions/piqtree)](https://pypi.org/project/piqtree/)
+[![License](https://img.shields.io/github/license/iqtree/piqtree)](https://github.com/iqtree/piqtree/blob/main/LICENSE)
 
-[![CI](https://github.com/iqtree/piqtree2/workflows/CI/badge.svg)](https://github.com/iqtree/piqtree2/actions/workflows/ci.yml)
-[![Coverage Status](https://coveralls.io/repos/github/iqtree/piqtree2/badge.svg?branch=main)](https://coveralls.io/github/iqtree/piqtree2?branch=main)
-[![Documentation Status](https://readthedocs.org/projects/piqtree2/badge/?version=latest)](https://piqtree2.readthedocs.io/en/latest/?badge=latest)
+[![CI](https://github.com/iqtree/piqtree/workflows/CI/badge.svg)](https://github.com/iqtree/piqtree/actions/workflows/ci.yml)
+[![Coverage Status](https://coveralls.io/repos/github/iqtree/piqtree/badge.svg?branch=main)](https://coveralls.io/github/iqtree/piqtree?branch=main)
+[![Documentation Status](https://readthedocs.org/projects/piqtree/badge/?version=latest)](https://piqtree.readthedocs.io/en/latest/?badge=latest)
 
-`piqtree2` is a library which allows you use IQ-TREE directly from Python! The interface with python is through [cogent3](https://cogent3.org) objects.
-For usage, please refer to the [documentation](https://piqtree2.readthedocs.io/) or the examples below.
+`piqtree` is a library which allows you use IQ-TREE directly from Python! The interface with python is through [cogent3](https://cogent3.org) objects.
+For usage, please refer to the [documentation](https://piqtree.readthedocs.io/) or the examples below.
 
-If you encounter any problems or have any feature requests feel free to raise an [issue](https://github.com/iqtree/piqtree2/issues)!
+If you encounter any problems or have any feature requests feel free to raise an [issue](https://github.com/iqtree/piqtree/issues)!
 
 ## Examples
 
 ### Phylogenetic Reconstruction
 
 ```python
-from piqtree2 import build_tree
-from piqtree2.model import Model
-from cogent3 import load_aligned_seqs # Included with piqtree2!
+from piqtree import build_tree
+from piqtree.model import Model
+from cogent3 import load_aligned_seqs # Included with piqtree!
 
 # Load Sequences
 aln = load_aligned_seqs("tests/data/example.fasta", moltype="dna")
@@ -40,9 +40,9 @@ print("Log-likelihood:", tree.params["lnL"])
 ### Fit Branch Lengths to Tree Topology
 
 ```python
-from piqtree2 import fit_tree
-from piqtree2.model import Model
-from cogent3 import load_aligned_seqs, make_tree # Included with piqtree2!
+from piqtree import fit_tree
+from piqtree.model import Model
+from cogent3 import load_aligned_seqs, make_tree # Included with piqtree!
 
 # Load Sequences
 aln = load_aligned_seqs("tests/data/example.fasta", moltype="dna")
@@ -61,7 +61,7 @@ print("Log-likelihood:", tree.params["lnL"])
 ### Create a Collection of Random Trees
 
 ```python
-from piqtree2 import TreeGenMode, random_trees
+from piqtree import TreeGenMode, random_trees
 
 num_trees = 3 
 num_taxa = 5
@@ -78,8 +78,8 @@ print(trees) # A tuple of 3 trees with 5 taxa each.
 ### Pairwise Robinson-Foulds Distance between Trees
 
 ```python
-from piqtree2 import robinson_foulds
-from cogent3 import make_tree # Included with piqtree2!
+from piqtree import robinson_foulds
+from cogent3 import make_tree # Included with piqtree!
 
 # Construct trees
 tree1 = make_tree("(a,b,(c,(d,e)));")

build_tools/build_iqtree.sh

@@ -16,4 +16,4 @@ else
 fi
 
 cd ../..
-mv iqtree2/build/libiqtree2.a src/piqtree2/_libiqtree/
+mv iqtree2/build/libiqtree2.a src/piqtree/_libiqtree/

docs/api/genetic_distance/jc_distances.md

@@ -1,6 +1,6 @@
 # jc_distances
 
-::: piqtree2.jc_distances
+::: piqtree.jc_distances
 
 ## Usage
 

docs/api/model/FreqType.md

@@ -1,6 +1,6 @@
 # FreqType
 
-::: piqtree2.model.FreqType
+::: piqtree.model.FreqType
     options:
         show_if_no_docstring: true
 

docs/api/model/Model.md

@@ -1,6 +1,6 @@
 # Model
 
-::: piqtree2.Model
+::: piqtree.Model
 
 ## Usage
 

docs/api/model/RateModel.md

@@ -1,8 +1,8 @@
 # RateModel
 
-::: piqtree2.model.DiscreteGammaModel
+::: piqtree.model.DiscreteGammaModel
 
-::: piqtree2.model.FreeRateModel
+::: piqtree.model.FreeRateModel
 
 ## Usage
 

docs/api/model/SubstitutionModel.md

@@ -2,11 +2,11 @@
 
 Enums for available DNA and amino acid models. Strings may be used instead of the enums.
 
-::: piqtree2.model.DnaModel
+::: piqtree.model.DnaModel
     options:
         show_if_no_docstring: true
 
-::: piqtree2.model.AaModel
+::: piqtree.model.AaModel
     options:
         show_if_no_docstring: true
 

docs/api/model/model_finder.md

@@ -1,3 +1,3 @@
 # model_finder
 
-::: piqtree2.model_finder
+::: piqtree.model_finder

docs/api/tree/build_tree.md

@@ -1,6 +1,6 @@
 # build_tree
 
-::: piqtree2.build_tree
+::: piqtree.build_tree
 
 ## Usage
 

docs/api/tree/fit_tree.md

@@ -1,6 +1,6 @@
 # fit_tree
 
-::: piqtree2.fit_tree
+::: piqtree.fit_tree
 
 ## Usage
 

docs/api/tree/nj_tree.md

@@ -1,6 +1,6 @@
 # nj_tree
 
-::: piqtree2.nj_tree
+::: piqtree.nj_tree
 
 ## Usage
 

docs/api/tree/random_trees.md

@@ -1,8 +1,8 @@
 # random_trees
 
-::: piqtree2.random_trees
+::: piqtree.random_trees
 
-::: piqtree2.TreeGenMode
+::: piqtree.TreeGenMode
     options:
         show_if_no_docstring: true
 

docs/api/tree_distance/robinson_foulds.md

@@ -1,6 +1,6 @@
 # robinson_foulds
 
-::: piqtree2.robinson_foulds
+::: piqtree.robinson_foulds
 
 ## Usage
 

docs/apps/app_pipeline.py

@@ -1,15 +1,15 @@
 # %% [markdown]
-# ## Building workflows using `piqtree2` apps
+# ## Building workflows using `piqtree` apps
 # > **WARNING**
 # > This page is under construction!
 #
-# We can combine `piqtree2` apps with other cogent3 apps to develop a pipeline. There are multiple concepts involved here, particularly data stores, composed apps, parallel execution, log files etc... See the cogent3 [app documentation](https://cogent3.org/doc/app/index.html) for more details.
+# We can combine `piqtree` apps with other cogent3 apps to develop a pipeline. There are multiple concepts involved here, particularly data stores, composed apps, parallel execution, log files etc... See the cogent3 [app documentation](https://cogent3.org/doc/app/index.html) for more details.
 #
 # To develop a pipeline efficiently we only need a subset of the sequences in an alignment. We will use the [diverse-seq](https://pypi.org/project/diverse-seq/) plugin for that purpose. This allows selecting a specified subset of sequences that capture the diversity in an alignment.
 #
 # But first, we need the data.
 # %%
-from piqtree2 import download_dataset
+from piqtree import download_dataset
 
 alns_path = download_dataset("mammal-orths.zip", dest_dir="data", inflate_zip=False)
 

docs/apps/available_help.py

@@ -1,5 +1,5 @@
 # %% [markdown]
-# To see the apps that `piqtree2` makes available, use the cogent3 function `available_apps()` as follows.
+# To see the apps that `piqtree` makes available, use the cogent3 function `available_apps()` as follows.
 
 # %%
 from cogent3 import available_apps

docs/apps/fit_tree.py

@@ -5,7 +5,7 @@
 # %%
 import cogent3
 
-from piqtree2 import download_dataset
+from piqtree import download_dataset
 
 aln_path = download_dataset("example.phy.gz", dest_dir="data")
 aln = cogent3.load_aligned_seqs(aln_path, moltype="dna", format="phylip")

docs/apps/model_finder.py

@@ -4,7 +4,7 @@
 # %%
 from cogent3 import app_help, get_app, load_aligned_seqs
 
-from piqtree2 import download_dataset
+from piqtree import download_dataset
 
 aln_path = download_dataset("example.phy.gz", dest_dir="data")
 # format argument not required after cogent3 2024.11 release

docs/apps/nj.py

@@ -1,10 +1,10 @@
 # %% [markdown]
-# The Neighbour-Joining method uses genetic distances to build a phylogenetic tree. `piqtree2` provides only `piqtree_jc_dists` for this. `cogent3` includes many more methods. The  results of either can be used to build a tree. For divergent sequences we will use Lake's paralinear measure as it accomodates divergent sequence compositions.
+# The Neighbour-Joining method uses genetic distances to build a phylogenetic tree. `piqtree` provides only `piqtree_jc_dists` for this. `cogent3` includes many more methods. The  results of either can be used to build a tree. For divergent sequences we will use Lake's paralinear measure as it accomodates divergent sequence compositions.
 
 # %%
 import cogent3
 
-from piqtree2 import download_dataset
+from piqtree import download_dataset
 
 aln_path = download_dataset("example.phy.gz", dest_dir="data")
 aln = cogent3.load_aligned_seqs(aln_path, moltype="dna", format="phylip")
@@ -32,7 +32,7 @@
 
 # %% [markdown]
 # > **Warning**
-# > Branch lengths can be negative in the piqtree2 NJ tree. This manifests as branches going backwards!
+# > Branch lengths can be negative in the piqtree NJ tree. This manifests as branches going backwards!
 
 # %%
 tree.get_figure().show()

docs/apps/options.py

@@ -3,7 +3,7 @@
 
 
 # %%
-from piqtree2 import available_rate_type
+from piqtree import available_rate_type
 
 available_rate_type()
 
@@ -12,7 +12,7 @@
 
 # %% tags=hide_code
 
-from piqtree2 import available_freq_type
+from piqtree import available_freq_type
 
 available_freq_type()
 
@@ -25,6 +25,6 @@
 
 
 # %%
-from piqtree2 import available_models
+from piqtree import available_models
 
 available_models()

docs/apps/pairwise_dist.py

@@ -4,7 +4,7 @@
 # %%
 import cogent3
 
-from piqtree2 import download_dataset
+from piqtree import download_dataset
 
 aln_path = download_dataset("example.phy.gz", dest_dir="data")
 aln = cogent3.load_aligned_seqs(aln_path, moltype="dna", format="phylip")

docs/apps/phylo.py

@@ -6,7 +6,7 @@
 # %%
 import cogent3
 
-from piqtree2 import download_dataset
+from piqtree import download_dataset
 
 aln_path = download_dataset("example.phy.gz", dest_dir="data")
 aln = cogent3.load_aligned_seqs(aln_path, moltype="dna", format="phylip")

docs/citation.md

@@ -1,6 +1,6 @@
 # Citation
 
-Please cite piqtree2 as follows:
+Please cite piqtree as follows:
 
 Bui Quang Minh, Heiko A Schmidt, Olga Chernomor, Dominik Schrempf, Michael D Woodhams, Arndt von Haeseler, Robert Lanfear, IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era, Molecular Biology and Evolution, Volume 37, Issue 5, May 2020, Pages 1530–1534, [10.1093/molbev/msaa015](https://doi.org/10.1093/molbev/msaa015)
 
@@ -30,4 +30,4 @@ Huttley, G. (2021). cogent3: comparative genomics toolkit (2020.12.21). [10.5281
 }
 ```
 
-<!-- ::: piqtree2 -->
+<!-- ::: piqtree -->

docs/index.md

@@ -1,34 +1,34 @@
-# piqtree2 documentation
+# piqtree documentation
 
 ## Overview
 
-`piqtree2` is a Python package that exposes selected [IQ-TREE 2](http://www.iqtree.org) capabilities within Python, using the [cogent3](https://cogent3.org) library as the interface.
+`piqtree` is a Python package that exposes selected [IQ-TREE 2](http://www.iqtree.org) capabilities within Python, using the [cogent3](https://cogent3.org) library as the interface.
 
-`piqtree2` is implemented with the goals of:
+`piqtree` is implemented with the goals of:
 
 - making the individual high-performance components of IQ-TREE 2 available within Python, enabling the community to take advantage of these routines.
 - facilitating exploratory analyses by leveraging cogent3's capabilities to provide a rich user experience in interactive Jupyter notebooks, e.g. trivial parallelisation across collections of alignments.
-- code using piqtree2 apps should be easy to understand.
+- code using piqtree apps should be easy to understand.
 
-In addition to the functions provided, `piqtree2` provides mini-applications in the form of [cogent3 apps](https://cogent3.org/doc/app/index.html). These can interplay with other such apps, e.g. the [cogent3-ete3](https://pypi.org/project/cogent3-ete3/) tree conversion plugin, the [diverse-seqs](https://pypi.org/project/diverse-seq/) sequence subsampling plugin.
+In addition to the functions provided, `piqtree` provides mini-applications in the form of [cogent3 apps](https://cogent3.org/doc/app/index.html). These can interplay with other such apps, e.g. the [cogent3-ete3](https://pypi.org/project/cogent3-ete3/) tree conversion plugin, the [diverse-seqs](https://pypi.org/project/diverse-seq/) sequence subsampling plugin.
 
 > **Note**
-> `piqtree2` does not implement all of the capabilities of IQ-TREE 2!
+> `piqtree` does not implement all of the capabilities of IQ-TREE 2!
 
 ## Installation
 
-You get the vanilla version of `piqtree2` by running the following command.
+You get the vanilla version of `piqtree` by running the following command.
 
 ```bash
-pip install piqtree2
+pip install piqtree
 ```
 
 To get visualisation support with plotly, use the `[extra]` option.
 
 ```bash
-pip install "piqtree2[extra]"
+pip install "piqtree[extra]"
 ```
 
 ## Supported platforms
 
-At present we do not provide native binaries for Windows. Windows users can run `piqtree2` using the Windows Subsystem for Linux (WSL) which can installed via the Windows Store.
+At present we do not provide native binaries for Windows. Windows users can run `piqtree` using the Windows Subsystem for Linux (WSL) which can installed via the Windows Store.

docs/quickstart/calculate_jc_distances.md

@@ -11,7 +11,7 @@ Construct a `cogent3` alignment object, then calculate the pairwise JC distance
 
 ```python
 from cogent3 import load_aligned_seqs
-from piqtree2 import jc_distances
+from piqtree import jc_distances
 
 aln = load_aligned_seqs("my_alignment.fasta", moltype="dna")
 
@@ -28,7 +28,7 @@ The number of threads to be used may be specified. By default, or if 0 is specif
 
 ```python
 from cogent3 import load_aligned_seqs
-from piqtree2 import jc_distances
+from piqtree import jc_distances
 
 aln = load_aligned_seqs("my_alignment.fasta", moltype="dna")