bella-companion 0.0.35__tar.gz → 0.0.37__tar.gz

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.

Potentially problematic release.

This version of bella-companion might be problematic. Click here for more details.

Files changed (46) hide show
  1. {bella_companion-0.0.35 → bella_companion-0.0.37}/PKG-INFO +1 -1
  2. {bella_companion-0.0.35 → bella_companion-0.0.37}/bella_companion/platyrrhine/summarize_logs.py +11 -0
  3. {bella_companion-0.0.35 → bella_companion-0.0.37}/bella_companion.egg-info/PKG-INFO +1 -1
  4. {bella_companion-0.0.35 → bella_companion-0.0.37}/pyproject.toml +1 -1
  5. {bella_companion-0.0.35 → bella_companion-0.0.37}/README.md +0 -0
  6. {bella_companion-0.0.35 → bella_companion-0.0.37}/bella_companion/__init__.py +0 -0
  7. {bella_companion-0.0.35 → bella_companion-0.0.37}/bella_companion/cli.py +0 -0
  8. {bella_companion-0.0.35 → bella_companion-0.0.37}/bella_companion/eucovid/__init__.py +0 -0
  9. {bella_companion-0.0.35 → bella_companion-0.0.37}/bella_companion/eucovid/run_beast.py +0 -0
  10. {bella_companion-0.0.35 → bella_companion-0.0.37}/bella_companion/platyrrhine/__init__.py +0 -0
  11. {bella_companion-0.0.35 → bella_companion-0.0.37}/bella_companion/platyrrhine/results.py +0 -0
  12. {bella_companion-0.0.35 → bella_companion-0.0.37}/bella_companion/platyrrhine/run_beast.py +0 -0
  13. {bella_companion-0.0.35 → bella_companion-0.0.37}/bella_companion/simulations/__init__.py +0 -0
  14. {bella_companion-0.0.35 → bella_companion-0.0.37}/bella_companion/simulations/features.py +0 -0
  15. {bella_companion-0.0.35 → bella_companion-0.0.37}/bella_companion/simulations/figures/__init__.py +0 -0
  16. {bella_companion-0.0.35 → bella_companion-0.0.37}/bella_companion/simulations/figures/epi_multitype_results.py +0 -0
  17. {bella_companion-0.0.35 → bella_companion-0.0.37}/bella_companion/simulations/figures/epi_skyline_results.py +0 -0
  18. {bella_companion-0.0.35 → bella_companion-0.0.37}/bella_companion/simulations/figures/explain/__init__.py +0 -0
  19. {bella_companion-0.0.35 → bella_companion-0.0.37}/bella_companion/simulations/figures/explain/pdp.py +0 -0
  20. {bella_companion-0.0.35 → bella_companion-0.0.37}/bella_companion/simulations/figures/explain/shap.py +0 -0
  21. {bella_companion-0.0.35 → bella_companion-0.0.37}/bella_companion/simulations/figures/fbd_2traits_results.py +0 -0
  22. {bella_companion-0.0.35 → bella_companion-0.0.37}/bella_companion/simulations/figures/fbd_no_traits_results.py +0 -0
  23. {bella_companion-0.0.35 → bella_companion-0.0.37}/bella_companion/simulations/figures/scenarios.py +0 -0
  24. {bella_companion-0.0.35 → bella_companion-0.0.37}/bella_companion/simulations/figures/utils.py +0 -0
  25. {bella_companion-0.0.35 → bella_companion-0.0.37}/bella_companion/simulations/generate_data.py +0 -0
  26. {bella_companion-0.0.35 → bella_companion-0.0.37}/bella_companion/simulations/generate_figures.py +0 -0
  27. {bella_companion-0.0.35 → bella_companion-0.0.37}/bella_companion/simulations/metrics.py +0 -0
  28. {bella_companion-0.0.35 → bella_companion-0.0.37}/bella_companion/simulations/run_beast.py +0 -0
  29. {bella_companion-0.0.35 → bella_companion-0.0.37}/bella_companion/simulations/scenarios/__init__.py +0 -0
  30. {bella_companion-0.0.35 → bella_companion-0.0.37}/bella_companion/simulations/scenarios/common.py +0 -0
  31. {bella_companion-0.0.35 → bella_companion-0.0.37}/bella_companion/simulations/scenarios/epi_multitype.py +0 -0
  32. {bella_companion-0.0.35 → bella_companion-0.0.37}/bella_companion/simulations/scenarios/epi_skyline.py +0 -0
  33. {bella_companion-0.0.35 → bella_companion-0.0.37}/bella_companion/simulations/scenarios/fbd_2traits.py +1 -1
  34. {bella_companion-0.0.35 → bella_companion-0.0.37}/bella_companion/simulations/scenarios/fbd_no_traits.py +0 -0
  35. {bella_companion-0.0.35 → bella_companion-0.0.37}/bella_companion/simulations/scenarios/scenario.py +0 -0
  36. {bella_companion-0.0.35 → bella_companion-0.0.37}/bella_companion/simulations/summarize_logs.py +0 -0
  37. {bella_companion-0.0.35 → bella_companion-0.0.37}/bella_companion/utils/__init__.py +0 -0
  38. {bella_companion-0.0.35 → bella_companion-0.0.37}/bella_companion/utils/beast.py +0 -0
  39. {bella_companion-0.0.35 → bella_companion-0.0.37}/bella_companion/utils/explain.py +0 -0
  40. {bella_companion-0.0.35 → bella_companion-0.0.37}/bella_companion/utils/slurm.py +0 -0
  41. {bella_companion-0.0.35 → bella_companion-0.0.37}/bella_companion.egg-info/SOURCES.txt +0 -0
  42. {bella_companion-0.0.35 → bella_companion-0.0.37}/bella_companion.egg-info/dependency_links.txt +0 -0
  43. {bella_companion-0.0.35 → bella_companion-0.0.37}/bella_companion.egg-info/entry_points.txt +0 -0
  44. {bella_companion-0.0.35 → bella_companion-0.0.37}/bella_companion.egg-info/requires.txt +0 -0
  45. {bella_companion-0.0.35 → bella_companion-0.0.37}/bella_companion.egg-info/top_level.txt +0 -0
  46. {bella_companion-0.0.35 → bella_companion-0.0.37}/setup.cfg +0 -0
{bella_companion-0.0.35 → bella_companion-0.0.37}/PKG-INFO RENAMED
@@ -1,6 +1,6 @@
1
1
  Metadata-Version: 2.4
2
2
  Name: bella-companion
3
- Version: 0.0.35
3
+ Version: 0.0.37
4
4
  Summary: Add your description here
5
5
  Requires-Python: >=3.10
6
6
  Description-Content-Type: text/markdown
{bella_companion-0.0.35 → bella_companion-0.0.37}/bella_companion/platyrrhine/summarize_logs.py RENAMED
@@ -1,8 +1,12 @@
1
1
  import os
2
+ import shutil
3
+ from glob import glob
2
4
  from pathlib import Path
3
5
 
4
6
  import joblib
5
7
  import polars as pl
8
+ from phylogenie import Tree, load_nexus
9
+ from tqdm import tqdm
6
10
 
7
11
  from bella_companion.utils import read_weights_dir, summarize_logs_dir
8
12
 
@@ -28,3 +32,10 @@ def summarize_logs():
28
32
  os.makedirs(summaries_dir, exist_ok=True)
29
33
  summaries.write_csv(summaries_dir / "MLP.csv")
30
34
  joblib.dump(weights, summaries_dir / "MLP.weights.pkl")
35
+
36
+ trees: list[Tree] = []
37
+ for tree_file in tqdm(glob(str(logs_dir / "*.trees")), "Summarizing trees"):
38
+ trees.extend(list(load_nexus(tree_file).values())[:-10])
39
+ joblib.dump(trees, summaries_dir / "trees.pkl")
40
+
41
+ shutil.copy(logs_dir / "0.trees", summaries_dir / "0.trees")
{bella_companion-0.0.35 → bella_companion-0.0.37}/bella_companion.egg-info/PKG-INFO RENAMED
@@ -1,6 +1,6 @@
1
1
  Metadata-Version: 2.4
2
2
  Name: bella-companion
3
- Version: 0.0.35
3
+ Version: 0.0.37
4
4
  Summary: Add your description here
5
5
  Requires-Python: >=3.10
6
6
  Description-Content-Type: text/markdown
{bella_companion-0.0.35 → bella_companion-0.0.37}/pyproject.toml RENAMED
@@ -1,6 +1,6 @@
1
1
  [project]
2
2
  name = "bella-companion"
3
- version = "0.0.35"
3
+ version = "0.0.37"
4
4
  description = "Add your description here"
5
5
  readme = "README.md"
6
6
  requires-python = ">=3.10"
{bella_companion-0.0.35 → bella_companion-0.0.37}/bella_companion/simulations/scenarios/fbd_2traits.py RENAMED
@@ -89,9 +89,9 @@ SCENARIO = Scenario(
89
89
  features={
90
90
  f"{rate}Rate": {
91
91
  "timePredictor": Feature(is_binary=False, is_relevant=True),
92
+ "randomPredictor": Feature(is_binary=False, is_relevant=False),
92
93
  "trait1Predictor": Feature(is_binary=True, is_relevant=True),
93
94
  "trait2Predictor": Feature(is_binary=True, is_relevant=False),
94
- "randomPredictor": Feature(is_binary=False, is_relevant=False),
95
95
  }
96
96
  for rate in RATES
97
97
  },