MAINT: Remove references to IQ-TREE 2 in favour of simply IQ-TREE

Author: rmcar17

docs/apps/model_finder.py

@@ -1,5 +1,5 @@
 # %% [markdown]
-# We use the `piqtree_mfinder` app to rank models. This is the python binding to the IQ-TREE 2 ModelFinder tool.
+# We use the `piqtree_mfinder` app to rank models. This is the python binding to the IQ-TREE ModelFinder tool.
 
 # %%
 from cogent3 import app_help, get_app, load_aligned_seqs

docs/index.md

@@ -2,18 +2,18 @@
 
 ## Overview
 
-`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.
+`piqtree` is a Python package that exposes selected [IQ-TREE](http://www.iqtree.org) capabilities within Python, using the [cogent3](https://cogent3.org) library as the interface.
 
 `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.
+- making the individual high-performance components of IQ-TREE 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 piqtree apps should be easy to understand.
 
 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**
-> `piqtree` does not implement all of the capabilities of IQ-TREE 2!
+> `piqtree` does not implement all of the capabilities of IQ-TREE!
 
 ## Installation
 

src/piqtree/_libiqtree/_piqtree.cpp

@@ -171,7 +171,7 @@ int mine() {
 }
 
 PYBIND11_MODULE(_piqtree, m) {
-  m.doc() = "piqtree - Unlock the Power of IQ-TREE 2 with Python!";
+  m.doc() = "_piqtree - Linking IQ-TREE to Python!";
 
   m.attr("__iqtree_version__") = version();
 

src/piqtree/_libiqtree/_piqtree.h

@@ -130,4 +130,4 @@ extern "C" StringResult build_njtree(StringArray& names,
  */
 extern "C" StringResult version();
 
-#endif /* LIBIQTREE2_FUN */
+#endif /* _PIQTREE_H */

src/piqtree/iqtree/_jc_distance.py

@@ -47,7 +47,7 @@ def jc_distances(
     aln : c3_types.AlignedSeqsType
         alignment to compute pairwise JC distances for.
     num_threads: int | None, optional
-        Number of threads for IQ-TREE 2 to use, by default None (all available threads).
+        Number of threads for IQ-TREE to use, by default None (all available threads).
 
     Returns
     -------

src/piqtree/iqtree/_model_finder.py

@@ -140,7 +140,7 @@ def model_finder(
     rand_seed : int | None, optional
         The random seed - 0 or None means no seed, by default None.
     num_threads: int | None, optional
-        Number of threads for IQ-TREE 2 to use, by default None (single-threaded).
+        Number of threads for IQ-TREE to use, by default None (single-threaded).
         If 0 is specified, IQ-TREE attempts to find the optimal number of threads.
 
     Returns

src/piqtree/iqtree/_tree.py

@@ -218,7 +218,7 @@ def build_tree(
         If 0 is provided, then no bootstrapping is performed.
         At least 1000 is required to perform bootstrapping.
     num_threads: int | None, optional
-        Number of threads for IQ-TREE 2 to use, by default None (single-threaded).
+        Number of threads for IQ-TREE to use, by default None (single-threaded).
         If 0 is specified, IQ-TREE attempts to find the optimal number of threads.
 
     Returns
@@ -284,7 +284,7 @@ def fit_tree(
     rand_seed : int | None, optional
         The random seed - 0 or None means no seed, by default None.
     num_threads: int | None, optional
-        Number of threads for IQ-TREE 2 to use, by default None (single-threaded).
+        Number of threads for IQ-TREE to use, by default None (single-threaded).
         If 0 is specified, IQ-TREE attempts to find the optimal number of threads.
 
     Returns