argile 0.0.1__tar.gz

argile-0.0.1/.gitignore

@@ -0,0 +1,22 @@
+.DS_Store
+.ipynb_checkpoints/
+datasets/
+meeting_figures/
+scripts_to_remove/
+__pycache__/
+terracotta/to_delete.py
+devlog/overview.md
+devlog/threads.md
+slim/
+papers/
+.vscode/
+devlog/20250501/assets/hexagonal_world_map/world_elevation.tif
+devlog/20250501/assets/hexagonal_world_map/ETOPO2v2c_f4.nc
+devlog/20250630/assets/maize_from_regina/
+devlog/20250801/assets/chimps
+devlog/20250801/assets/gis_tooling/gis/elevation
+devlog/20250801/assets/redoing_evolution_example/dataset/starting_files/elevation
+devlog/20250929/assets/low_coverage/dataset/arg.trees
+old/
+dist/
+argile.egg-info/

argile-0.0.1/CHANGELOG.rst

@@ -0,0 +1,5 @@
+--------------------
+[0.0.1] - 2026-10-22
+--------------------
+
+First release!

argile-0.0.1/LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2026 James Kitchens
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

argile-0.0.1/PKG-INFO

@@ -0,0 +1,67 @@
+Metadata-Version: 2.4
+Name: argile
+Version: 0.0.1
+Summary: Estimating migration surfaces and the locations of genetic ancestors from gene trees
+Author-email: James Kitchens <kitchensjn@gmail.com>
+License-Expression: MIT
+Project-URL: Homepage, https://github.com/kitchensjn/argile
+Project-URL: Changelog, https://github.com/kitchensjn/argile/blob/main/CHANGELOG.rst
+Project-URL: Bug Tracker, https://github.com/kitchensjn/argile/issues
+Keywords: population genetics,tree sequence,ancestral recombination graph,gene tree,spatial analysis,migration,location
+Classifier: Programming Language :: Python
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.7
+Classifier: Programming Language :: Python :: 3.8
+Classifier: Programming Language :: Python :: 3.9
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3 :: Only
+Classifier: Development Status :: 3 - Alpha
+Classifier: Environment :: Other Environment
+Classifier: Intended Audience :: Science/Research
+Classifier: Operating System :: POSIX
+Classifier: Operating System :: MacOS :: MacOS X
+Classifier: Operating System :: Microsoft :: Windows
+Classifier: Topic :: Scientific/Engineering
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Requires-Python: >=3.7
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: numpy
+Requires-Dist: numba
+Requires-Dist: scipy
+Requires-Dist: pandas
+Requires-Dist: tskit
+Dynamic: license-file
+
+# `argile`
+
+`argile` (formerly `terracotta`) is a Python package for estimating migration surfaces and the locations of genetic ancestors from gene trees. The latest release is available either here on GitHub or through [PyPI](https://pypi.org/project/argile/). See [example_dataset/](https://github.com/kitchensjn/argile/tree/main/example_dataset) for details about file formats.
+
+#### Estimate the most likely migration surface
+
+```
+import argile
+
+result, loglikelihood = argile.run(
+    demes_path="example_dataset/demes.tsv",
+    connections_path="example_dataset/connections.tsv",
+    samples_path="example_dataset/samples.tsv",
+    trees_dir_path="example_dataset/trees",
+    output_file="output.tsv"
+)
+```
+
+`argile.run()` estimates the most likely migration surface using the `L-BFGS-B` algorithm. It estimates values for the `coefficient` (the default migration rate) and any migration rate modifier variables (here `r0`, `r1`, and `r2`). These variables will be automatically included in this search if present in `connections.tsv`. This fucntion takes the paths to the files as input rather than loading the world map prior.
+
+
+#### Loading the world map
+
+```
+import pandas as pd
+import argile
+
+demes = pd.read_csv("example_dataset/demes.tsv", sep="\t")
+connections = pd.read_csv("example_dataset/connections.tsv", sep="\t")
+samples = pd.read_csv("example_dataset/samples.tsv", sep="\t")
+world_map = argile.WorldMap(demes, connections, samples)
+```

argile-0.0.1/README.md

@@ -0,0 +1,32 @@
+# `argile`
+
+`argile` (formerly `terracotta`) is a Python package for estimating migration surfaces and the locations of genetic ancestors from gene trees. The latest release is available either here on GitHub or through [PyPI](https://pypi.org/project/argile/). See [example_dataset/](https://github.com/kitchensjn/argile/tree/main/example_dataset) for details about file formats.
+
+#### Estimate the most likely migration surface
+
+```
+import argile
+
+result, loglikelihood = argile.run(
+    demes_path="example_dataset/demes.tsv",
+    connections_path="example_dataset/connections.tsv",
+    samples_path="example_dataset/samples.tsv",
+    trees_dir_path="example_dataset/trees",
+    output_file="output.tsv"
+)
+```
+
+`argile.run()` estimates the most likely migration surface using the `L-BFGS-B` algorithm. It estimates values for the `coefficient` (the default migration rate) and any migration rate modifier variables (here `r0`, `r1`, and `r2`). These variables will be automatically included in this search if present in `connections.tsv`. This fucntion takes the paths to the files as input rather than loading the world map prior.
+
+
+#### Loading the world map
+
+```
+import pandas as pd
+import argile
+
+demes = pd.read_csv("example_dataset/demes.tsv", sep="\t")
+connections = pd.read_csv("example_dataset/connections.tsv", sep="\t")
+samples = pd.read_csv("example_dataset/samples.tsv", sep="\t")
+world_map = argile.WorldMap(demes, connections, samples)
+```

argile-0.0.1/argile/__init__.py

@@ -0,0 +1,4 @@
+from argile.main import *
+from argile.world_map import *
+from argile.likelihood import *
+from argile.locate import *