API: Rename apps

changelog.d/20250702_161144_robert.mcarthur_rename_apps.md

@@ -0,0 +1,48 @@
+<!--
+A new scriv changelog fragment.
+
+Uncomment the section that is right (remove the HTML comment wrapper).
+-->
+
+<!--
+### Contributors
+
+- A bullet item for the Contributors category.
+
+-->
+<!--
+### ENH
+
+- A bullet item for the ENH category.
+
+-->
+<!--
+### BUG
+
+- A bullet item for the BUG category.
+
+-->
+
+### API
+
+- All apps have been renamed to take the form `piq_<func_name>`.
+
+
+<!--
+### DOC
+
+- A bullet item for the DOC category.
+
+-->
+<!--
+### Deprecations
+
+- A bullet item for the Deprecations category.
+
+-->
+<!--
+### Discontinued
+
+- A bullet item for the Discontinued category.
+
+-->

docs/apps/app_pipeline.py

@@ -38,7 +38,7 @@
 divergent = get_app("dvs_nmost", n=10, k=6)
 just_nucs = get_app("omit_degenerates")  # has to go after the divergent selector
 min_length = get_app("min_length", length=600)
-best_model = get_app("piqtree_mfinder")
+best_model = get_app("piq_model_finder")
 app = loader + divergent + just_nucs + min_length + best_model
 model_counts = Counter(
     str(result.best_aic)

docs/apps/available_help.py

@@ -12,9 +12,9 @@
 # %%
 from cogent3 import app_help
 
-app_help("piqtree_phylo")
+app_help("piq_build_tree")
 
 # %%
 from cogent3 import app_help
 
-app_help("piqtree_fit")
+app_help("piq_fit_tree")

docs/apps/fit_tree.py

@@ -1,5 +1,5 @@
 # %% [markdown]
-# We evaluate a support for a specific phylogeny using `piqtree_fit`.
+# We evaluate a support for a specific phylogeny using `piq_fit_tree`.
 # For this simple case, we will assess the support for a specific phylogeny using the GTR model on one alignment.
 
 # %%
@@ -20,21 +20,21 @@
 tree.get_figure().show()
 
 # %% [markdown]
-# We now take a look at the help for the `piqtree_fit` app.
+# We now take a look at the help for the `piq_fit_tree` app.
 
 # %%
 
 from cogent3 import app_help
 
-app_help("piqtree_fit")
+app_help("piq_fit_tree")
 
 # %% [markdown]
 # We fit a GTR model and estimate the nucleotide frequencies by maximum likelihood.
 
 # %%
 from cogent3 import get_app
 
-fit_gtr = get_app("piqtree_fit", tree, model="GTR+FO")
+fit_gtr = get_app("piq_fit_tree", tree, model="GTR+FO")
 fit_gtr
 
 # %% [markdown]

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 ModelFinder tool.
+# We use the `piq_model_finder` 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
@@ -10,13 +10,13 @@
 aln = load_aligned_seqs(aln_path, moltype="dna", format="phylip")
 
 # %% [markdown]
-# Get help and then apply `piqtree_mfinder`.
+# Get help and then apply `piq_model_finder`.
 
 # %%
-app_help("piqtree_mfinder")
+app_help("piq_model_finder")
 
 # %%
-mfinder = get_app("piqtree_mfinder")
+mfinder = get_app("piq_model_finder")
 ranked = mfinder(aln)
 ranked
 
@@ -37,9 +37,9 @@
 # ## Using the best model
 # You can apply the selected model to a phylogenetic analysis.
 # > **Note**
-# > The process is the same for both the `piqtree_phylo` and the `piqtree_fit` apps.
+# > The process is the same for both the `piq_build_tree` and the `piq_fit_tree` apps.
 
 # %%
-fit = get_app("piqtree_phylo", selected)
+fit = get_app("piq_build_tree", selected)
 fitted = fit(aln)
 fitted

docs/apps/nj.py

@@ -1,5 +1,5 @@
 # %% [markdown]
-# 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.
+# The Neighbour-Joining method uses genetic distances to build a phylogenetic tree. `piqtree` provides only `piq_jc_distances` 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
@@ -18,16 +18,16 @@
 dists
 
 # %% [markdown]
-# Get help on the `piqtree_nj` app.
+# Get help on the `piq_nj_tree` app.
 
 # %%
-cogent3.app_help("piqtree_nj")
+cogent3.app_help("piq_nj_tree")
 
 # %% [markdown]
 # Make an app and apply it to the distance matrix.
 
 # %%
-nj = cogent3.get_app("piqtree_nj")
+nj = cogent3.get_app("piq_nj_tree")
 tree = nj(dists)
 
 # %% [markdown]
@@ -43,11 +43,11 @@
 
 # %% [markdown]
 # ## Combining the piqtree dist and nj apps
-# We can combine the `piqtree_jc_dists` and `piqtree_nj` apps to build a tree from an alignment in one step.
+# We can combine the `piq_jc_distances` and `piq_nj_tree` apps to build a tree from an alignment in one step.
 
 # %%
-jc = cogent3.get_app("piqtree_jc_dists")
-nj = cogent3.get_app("piqtree_nj")
+jc = cogent3.get_app("piq_jc_distances")
+nj = cogent3.get_app("piq_nj_tree")
 app = jc + nj
 tree = app(aln)
 tree.get_figure().show()

docs/apps/pairwise_dist.py

@@ -1,5 +1,5 @@
 # %% [markdown]
-# We estimate pairwise distances via the Jukes-Cantor model with the `piqtree_jc_dists` app.
+# We estimate pairwise distances via the Jukes-Cantor model with the `piq_jc_distances` app.
 
 # %%
 import cogent3
@@ -13,12 +13,12 @@
 # We get help on the `piqtree_jc_dist` app.
 
 # %%
-cogent3.app_help("piqtree_jc_dists")
+cogent3.app_help("piq_jc_distances")
 
 # %% [markdown]
 # Make an app and apply it to the alignment.
 
 # %%
-jc_dists = cogent3.get_app("piqtree_jc_dists")
+jc_dists = cogent3.get_app("piq_jc_distances")
 dists = jc_dists(aln)
 dists

docs/apps/phylo.py

@@ -1,5 +1,5 @@
 # %% [markdown]
-# We use the `piqtree_phylo` app to build phylogenies.
+# We use the `piq_build_tree` app to build phylogenies.
 # For this simple case, we will build a single phylogeny using the GTR model on one alignment.
 # We have a utility script for this documentation that provides the local path to that data. We will then load that data and, as it contains quite a few sequences, we will use a subset of it. We use methods on the `cogent3` object to do that.
 
@@ -14,21 +14,21 @@
 
 
 # %% [markdown]
-# We now take a look at the help for the `piqtree_phylo` app.
+# We now take a look at the help for the `piq_build_tree` app.
 
 # %%
 
 from cogent3 import app_help
 
-app_help("piqtree_phylo")
+app_help("piq_build_tree")
 
 # %% [markdown]
 # We build an app for estimating phylogenies with a GTR model
 
 # %%
 from cogent3 import get_app
 
-phylo_gtr = get_app("piqtree_phylo", model="GTR", bootstrap_reps=1000)
+phylo_gtr = get_app("piq_build_tree", model="GTR", bootstrap_reps=1000)
 phylo_gtr
 
 # %% [markdown]

pyproject.toml

@@ -76,16 +76,16 @@ doc = [
 ]
 
 [project.entry-points."cogent3.app"]
-piqtree_phylo = "piqtree._app:piqtree_phylo"
-piqtree_fit = "piqtree._app:piqtree_fit"
-piqtree_random_tree = "piqtree._app:piqtree_random_tree"
-piqtree_jc_dists = "piqtree._app:piqtree_jc_dists"
-piqtree_nj = "piqtree._app:piqtree_nj"
-piqtree_mfinder = "piqtree._app:piqtree_mfinder"
-piqtree_consensus = "piqtree._app:piqtree_consensus"
+piq_build_tree = "piqtree._app:piq_build_tree"
+piq_fit_tree = "piqtree._app:piq_fit_tree"
+piq_random_tree = "piqtree._app:piq_random_tree"
+piq_jc_distances = "piqtree._app:piq_jc_distances"
+piq_nj_tree = "piqtree._app:piq_nj_tree"
+piq_model_finder = "piqtree._app:piq_model_finder"
+piq_consensus_tree = "piqtree._app:piq_consensus_tree"
 
 [project.entry-points."cogent3.hook"]
-quick_tree = "piqtree._app:piqtree_nj"
+quick_tree = "piqtree._app:piq_nj_tree"
 
 [tool.setuptools.dynamic]
 version = { attr = "piqtree.__version__" }

src/piqtree/_app/__init__.py

@@ -22,7 +22,7 @@
 
 
 @composable.define_app
-class piqtree_phylo:
+class piq_build_tree:
     @extend_docstring_from(build_tree)
     def __init__(
         self,
@@ -53,7 +53,7 @@ def main(
 
 
 @composable.define_app
-class piqtree_fit:
+class piq_fit_tree:
     @extend_docstring_from(fit_tree)
     def __init__(
         self,
@@ -82,7 +82,7 @@ def main(
 
 @composable.define_app
 @extend_docstring_from(random_tree)
-def piqtree_random_tree(
+def piq_random_tree(
     num_taxa: int,
     tree_mode: TreeGenMode,
     rand_seed: int | None = None,
@@ -91,7 +91,7 @@ def piqtree_random_tree(
 
 
 @composable.define_app
-class piqtree_jc_dists:
+class piq_jc_distances:
     @extend_docstring_from(jc_distances)
     def __init__(
         self,
@@ -113,7 +113,7 @@ def main(
 
 @composable.define_app
 @extend_docstring_from(nj_tree)
-def piqtree_nj(
+def piq_nj_tree(
     dists: c3_types.PairwiseDistanceType,
     *,
     allow_negative: bool = False,
@@ -126,15 +126,15 @@ def piqtree_nj(
 
 @composable.define_app
 @extend_docstring_from(model_finder)
-def piqtree_mfinder(
+def piq_model_finder(
     aln: c3_types.AlignedSeqsType,
 ) -> ModelFinderResult | c3_types.SerialisableType:
     return model_finder(aln)
 
 
 @composable.define_app
 @extend_docstring_from(consensus_tree)
-def piqtree_consensus(
+def piq_consensus_tree(
     trees: Iterable[cogent3.PhyloNode],
     *,
     min_support: float = 0.5,
@@ -143,11 +143,11 @@ def piqtree_consensus(
 
 
 _ALL_APP_NAMES = [
-    "piqtree_phylo",
-    "piqtree_fit",
-    "piqtree_random_tree",
-    "piqtree_jc_dists",
-    "piqtree_nj",
-    "piqtree_mfinder",
-    "piqtree_consensus",
+    "piq_build_tree",
+    "piq_fit_tree",
+    "piq_random_tree",
+    "piq_jc_distances",
+    "piq_nj_tree",
+    "piq_model_finder",
+    "piq_consensus_tree",
 ]