bella-companion 0.0.16__py3-none-any.whl → 0.0.18__py3-none-any.whl

bella_companion/{fbd_empirical → platyrrhine}/results.py

@@ -10,7 +10,7 @@ from phylogenie import get_node_depths, load_newick
 
 def _plot_predictions(output_dir: Path):
     log_summaries_dir = Path(os.environ["BELLA_LOG_SUMMARIES_DIR"])
-    log_summary = pl.read_csv(log_summaries_dir / "fbd-empirical" / "MLP.csv")
+    log_summary = pl.read_csv(log_summaries_dir / "platyrrhine" / "MLP.csv")
 
     data_dir = Path(__file__).parent / "data"
     change_times = (
@@ -46,27 +46,8 @@ def _plot_predictions(output_dir: Path):
                         for i in range(len(change_times) + 1)
                     ]
                 ).to_numpy()
-
             median = np.median(estimates, axis=0)
-            lower = np.percentile(estimates, 2.5, axis=0)
-            upper = np.percentile(estimates, 97.5, axis=0)
-
             color = colors[rate][type]
-
-            plt.fill_between(  # pyright: ignore
-                time_bins,
-                [lower[0], *lower],
-                [upper[0], *upper],
-                step="pre",
-                alpha=0.25,
-                color=color,
-            )
-
-            for estimate in estimates:
-                plt.step(  # pyright: ignore
-                    time_bins, [estimate[0], *estimate], color=color, alpha=0.15
-                )
-
             plt.step(  # pyright: ignore
                 time_bins, [median[0], *median], color=color, label=type
             )
@@ -82,7 +63,7 @@ def _plot_predictions(output_dir: Path):
         plt.close()
 
 
-def plot_fbd_empirical_results():
-    output_dir = Path(os.environ["BELLA_FIGURES_DIR"]) / "fbd-empirical"
+def plot_platyrrhine_results():
+    output_dir = Path(os.environ["BELLA_FIGURES_DIR"]) / "platyrrhine"
     os.makedirs(output_dir, exist_ok=True)
     _plot_predictions(output_dir)

bella_companion/{fbd_empirical → platyrrhine}/run_beast.py

@@ -12,7 +12,7 @@ from bella_companion.utils import submit_job
 
 def run_beast():
     base_output_dir = Path(os.environ["BELLA_BEAST_OUTPUT_DIR"])
-    output_dir = base_output_dir / "fbd-empirical"
+    output_dir = base_output_dir / "platyrrhine"
     os.makedirs(output_dir, exist_ok=True)
 
     data_dir = Path(__file__).parent / "data"
@@ -64,9 +64,9 @@ def run_beast():
         )
         job_ids[i] = submit_job(
             command,
-            Path(os.environ["BELLA_SBATCH_LOG_DIR"]) / "fbd-empirical" / str(i),
+            Path(os.environ["BELLA_SBATCH_LOG_DIR"]) / "platyrrhine" / str(i),
             mem_per_cpu="12000",
         )
 
-    with open(base_output_dir / "fbd_empirical_job_ids.json", "w") as f:
+    with open(base_output_dir / "platyrrhine_job_ids.json", "w") as f:
         json.dump(job_ids, f)

bella_companion/{fbd_empirical → platyrrhine}/summarize_logs.py

@@ -12,7 +12,7 @@ def summarize_logs():
     change_times = pl.read_csv(data_dir / "change_times.csv", has_header=False)
     n_time_bins = len(change_times) + 1
 
-    logs_dir = Path(os.environ["BELLA_BEAST_OUTPUT_DIR"]) / "fbd-empirical"
+    logs_dir = Path(os.environ["BELLA_BEAST_OUTPUT_DIR"]) / "platyrrhine"
     summaries = summarize_logs_dir(
         logs_dir=logs_dir,
         target_columns=[
@@ -24,7 +24,7 @@ def summarize_logs():
     )
     weights = read_weights_dir(logs_dir)
 
-    summaries_dir = Path(os.environ["BELLA_LOG_SUMMARIES_DIR"], "fbd-empirical")
+    summaries_dir = Path(os.environ["BELLA_LOG_SUMMARIES_DIR"], "platyrrhine")
     os.makedirs(summaries_dir, exist_ok=True)
     summaries.write_csv(summaries_dir / "MLP.csv")
     joblib.dump(weights, summaries_dir / "MLP.weights.pkl")

{bella_companion-0.0.16.dist-info → bella_companion-0.0.18.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: bella-companion
-Version: 0.0.16
+Version: 0.0.18
 Summary: 
 Author: gabriele-marino
 Author-email: gabmarino.8601@gmail.com
@@ -12,5 +12,5 @@ Classifier: Programming Language :: Python :: 3.12
 Requires-Dist: arviz (>=0.22.0,<0.23.0)
 Requires-Dist: bella-lumiere (>=0.0.14,<0.0.15)
 Requires-Dist: dotenv (>=0.9.9,<0.10.0)
-Requires-Dist: phylogenie (>=3.1.1,<4.0.0)
+Requires-Dist: phylogenie (>=3.1.2,<4.0.0)
 Requires-Dist: seaborn (>=0.13.2,<0.14.0)

{bella_companion-0.0.16.dist-info → bella_companion-0.0.18.dist-info}/RECORD

@@ -1,13 +1,34 @@
 bella_companion/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-bella_companion/cli.py,sha256=D-kQuj0I-g5Vm5-mXdOZoio68mhOBpJ3jVG8B2Kwvn4,2190
-bella_companion/fbd_empirical/__init__.py,sha256=FgzjaEpwZImvBsJs17ghF0ltZvhFmgmkTGGF3HgdsGo,284
-bella_companion/fbd_empirical/beast_config.xml,sha256=McImvRgzYflbfCLQdo6sqTgvJcSDc8CQiRjDhgUWkFI,7075
-bella_companion/fbd_empirical/data/change_times.csv,sha256=tedobHbaY7-6M3V6F6HSqGAU9dpeeajR5mu1XGJfp6w,68
-bella_companion/fbd_empirical/data/traits.csv,sha256=N_mCnaM9Gy0Qot7-l_mK0vMvr7e_5BZ4bgUHpcoG9UM,3949
-bella_companion/fbd_empirical/data/trees.nwk,sha256=Y5ro7vQ8vz2Cp3kpNtOTRBfOdQAT-eJUwkb75x79bHE,539477
-bella_companion/fbd_empirical/results.py,sha256=skf7PsdWZuOVkMeGgKsSCKDfho6tVWT7bUVFWTthxag,3114
-bella_companion/fbd_empirical/run_beast.py,sha256=60t8tbqlgdv86JwBk_DvUQ8i7TpThz0EmwEv-OkBAQM,2560
-bella_companion/fbd_empirical/summarize_logs.py,sha256=f3NgdyrCmbD5eHDHYwiA8ggh4b3rZ63SrlfDt0FAZmc,955
+bella_companion/cli.py,sha256=0SwDxkDPqvsp36kGnrBMLPIhAQM8PIpNXrztZayqmDc,2409
+bella_companion/eucovid/__init__.py,sha256=09Ld_G7fZvCDCgEWsmaOyLVQ8pFc9QHAGnXKJ9Zm2AM,81
+bella_companion/eucovid/beast_configs/GLM.xml,sha256=Qn3AP1NvMDXnCQp_qZvVOjoDQujuurQop4IqgJs6lKQ,11670
+bella_companion/eucovid/beast_configs/MLP.xml,sha256=4niHx3FmSsmKyDv9eNS1g9cZ6ShHbWjzXIbfg8pQa-k,11347
+bella_companion/eucovid/beast_configs/Nonparametric.xml,sha256=S9B7mzbPWAQ2ngjpaaswUBF8Cigfha1StkFJtSVz2fo,11620
+bella_companion/eucovid/data/case_data.tsv,sha256=XaSzZh5NcEMVt9d_XlQ19T8UuEkHGrjpSFXhe9IycNg,12412
+bella_companion/eucovid/data/change_dates.tsv,sha256=_pmVFYiL4X9Pd79uYVgyz3sKeRap7xVcXk0OjqVhuVQ,227
+bella_companion/eucovid/data/msa.fasta,sha256=sWaVSINSJDDLjmwlpl31JWM5VnKF7yViSpERI69glQc,4839354
+bella_companion/eucovid/data/osi.tsv,sha256=iTDWL_-PnVQPg_-hWROXWKNFakDq_S1fEig1A_MqMVI,9228
+bella_companion/eucovid/data/predictors/all/closedborders_7e_nt.tsv,sha256=5gP-cEzgKSCvlK0_PlkrimYGEwOaLPO0GiiM4PIKU-M,280
+bella_companion/eucovid/data/predictors/all/dist_7e_ls.tsv,sha256=rr71QPiJu35CYbySMJyH_GDX51D2iTIncZImwAXIvlo,1890
+bella_companion/eucovid/data/predictors/all/flight_7e_ls.tsv,sha256=5WztZpQrjK7puERA1oxsCn5t2G1w9NGTGKjr85gMQ54,1873
+bella_companion/eucovid/data/predictors/all/flight_pop_x_7e_ls.tsv,sha256=qfRTXyZItzEm8pxurhFYO-DvpJXD-J4lMH5eyZKF0aE,1862
+bella_companion/eucovid/data/predictors/all/osi_x_7e_ls.tsv,sha256=kke2eHlVuc84qMj1WBllhBG2BQt7JHUWDZeiVoAP8Lw,1900
+bella_companion/eucovid/data/predictors/all/osi_y_7e_ls.tsv,sha256=5YDXe4GstyyRKP15213cAAEm5lVFW_bC98R8ipc1XoE,1900
+bella_companion/eucovid/data/predictors/all/pop_x_7e_ls.tsv,sha256=3fVYRQ1ylwsa7YptMU8f_xELwwqIF3Ux8akL9UaXKis,1904
+bella_companion/eucovid/data/predictors/all/pop_y_7e_ls.tsv,sha256=Ku39Ts0HW9r5lThAZ01V7HJDi0aoRYs0aQs5EXlZCkQ,1904
+bella_companion/eucovid/data/predictors/all/sharedborders_7e_nt.tsv,sha256=pPVT5DIaZuc3B0mSs-B3kw3G2zja1LfmL_xLwlNtLDo,280
+bella_companion/eucovid/data/predictors/changetimes_all_7e.tsv,sha256=hH0xXD2lr_8RPQRqvENv6clPHauAXH22SGQHb3hlfzs,120
+bella_companion/eucovid/data/predictors/changetimes_flights_4e.tsv,sha256=XEepIXKRwcKknJq4-ovKlorvCypGi67B8znuQ5f1LTg,60
+bella_companion/eucovid/data/predictors/flight_pop_x_4e_ls.tsv,sha256=tMR9-tuGtC3rVABXUtNdV9irUX-9aCCVb_fwksHTn8U,1068
+bella_companion/eucovid/run_beast.py,sha256=BTttqmFNaUslDfpXTwF8qcIbiyLg3cvsPmdQkuqGvG4,3654
+bella_companion/platyrrhine/__init__.py,sha256=dIx6exNz-vuKiG5FZumvq74QUWcIEFd3L6ErqnOa83c,274
+bella_companion/platyrrhine/beast_config.xml,sha256=8A6E5iPu9FqDL3UdlsqDbabLFlC6Qhfa4Ta47niRkVA,7090
+bella_companion/platyrrhine/data/change_times.csv,sha256=tedobHbaY7-6M3V6F6HSqGAU9dpeeajR5mu1XGJfp6w,68
+bella_companion/platyrrhine/data/traits.csv,sha256=N_mCnaM9Gy0Qot7-l_mK0vMvr7e_5BZ4bgUHpcoG9UM,3949
+bella_companion/platyrrhine/data/trees.nwk,sha256=lpSiGUG5s3zE--IKPOyWrJ5vpJb_xAPnfxychs3YNIs,488232
+bella_companion/platyrrhine/results.py,sha256=qosxqstTy7uadHARRt1WqmxZzxnQ3hiTjtw6V-YWKGA,2556
+bella_companion/platyrrhine/run_beast.py,sha256=caUmebyZMzOukI8RdOlECsT3DStShi0NZNzEJ72qAaw,2554
+bella_companion/platyrrhine/summarize_logs.py,sha256=82N7rcmLthCyQqmP4Yub4KUsIjNzQl9vEuFLMvIv03o,951
 bella_companion/simulations/__init__.py,sha256=ShYRdp1iSjnS_SzcsH-8jbqXz6P1nyRQZqAtPZJCMVE,454
 bella_companion/simulations/beast_configs/epi-multitype/GLM.xml,sha256=VymAYsaZVuB3EPE0DCQSXpKepVq8pPjKaB5yhEpaVkE,4334
 bella_companion/simulations/beast_configs/epi-multitype/MLP.xml,sha256=J-OVblMRmk4XRhz9DHhLpMwaIzqSqYZ7Yq7dTMvQW1s,4094
@@ -48,7 +69,7 @@ bella_companion/utils/__init__.py,sha256=UtMwPK9dWf9NAl0ic8CSsgdW7aSm-5J49OqgvD7
 bella_companion/utils/beast.py,sha256=TBa0cLklX1_tXqoQE4LRYvds7mLg_9fS2-6U6OHENHo,2184
 bella_companion/utils/explain.py,sha256=uP7HPyn2YiykAI69BQV3RooDpC6qKoCLXfp3Uibp4zk,1475
 bella_companion/utils/slurm.py,sha256=v5DaG7YHVyK8KRFptgGDC6I8jxEhyJuMVK9N08pZSAI,1812
-bella_companion-0.0.16.dist-info/METADATA,sha256=Kd_M6fOFsQ9v3Ph7_saJZp3_GGZHfGC88-0Uk3UPJS8,576
-bella_companion-0.0.16.dist-info/WHEEL,sha256=sP946D7jFCHeNz5Iq4fL4Lu-PrWrFsgfLXbbkciIZwg,88
-bella_companion-0.0.16.dist-info/entry_points.txt,sha256=rSeKoAhmjnQqAYFcXBv0gAM2ViJfJe0D8_dD-fWrXeg,50
-bella_companion-0.0.16.dist-info/RECORD,,
+bella_companion-0.0.18.dist-info/METADATA,sha256=Mha1XlV0JnOlM3ru7d0vSBc0uPwvX66v_ggOFcgJDKw,576
+bella_companion-0.0.18.dist-info/WHEEL,sha256=sP946D7jFCHeNz5Iq4fL4Lu-PrWrFsgfLXbbkciIZwg,88
+bella_companion-0.0.18.dist-info/entry_points.txt,sha256=rSeKoAhmjnQqAYFcXBv0gAM2ViJfJe0D8_dD-fWrXeg,50
+bella_companion-0.0.18.dist-info/RECORD,,

bella_companion/fbd_empirical/__init__.py

@@ -1,5 +0,0 @@
-from bella_companion.fbd_empirical.results import plot_fbd_empirical_results
-from bella_companion.fbd_empirical.run_beast import run_beast
-from bella_companion.fbd_empirical.summarize_logs import summarize_logs
-
-__all__ = ["plot_fbd_empirical_results", "run_beast", "summarize_logs"]