def test_tqdm_style_loops():
for i in main_tqdm(range(1, 11), desc="using TQDM style logging"):
time.sleep(0.1)
for i in LoggerManager.progress_logger(
range(1,
11), progress_name="using LoggerManager's progress_logger"):
time.sleep(0.1)
def test_logger_simple_progress_logger(test_logger):
total = 10
test_logger.log_time()
for _ in LoggerManager.progress_logger(
range(total),
test_logger,
progress_name=
"progress logger test looooooooooooooooooooooooooooooong"):
time.sleep(0.1)
def test_logger():
return LoggerManager.get_main_logger()
dyn.pp.top_pca_genes(adata)
top_pca_genes = adata.var.index[adata.var.top_pca_genes]
dyn.vf.jacobian(adata, regulators=top_pca_genes, effectors=top_pca_genes)
dyn.pd.state_graph(adata, group="Cell_type", basis="pca", method="vf")
def test_cell_cycle_score_logger_pancreatic_endocrinogenesis():
adata = dyn.sample_data.pancreatic_endocrinogenesis()
adata = adata[:1000]
dyn.pp.recipe_monocle(
adata,
n_top_genes=1000,
fg_kwargs={"shared_count": 20},
# genes_to_append=['Xkr4', 'Gm28672', 'Gm20837'],
genes_to_exclude=["Sbspon", "Adgrb3", "Eif2s3y"],
)
dyn.pp.cell_cycle_scores(adata)
if __name__ == "__main__":
test_tqdm_style_loops()
test_logger_simple_output_1(LoggerManager.get_main_logger())
test_logger_simple_progress_naive(LoggerManager.get_main_logger())
test_logger_simple_progress_logger(LoggerManager.get_main_logger())
test_logger_simple_progress_logger(LoggerManager.get_temp_timer_logger())
test_vectorField_logger()
test_zebrafish_topography_tutorial_logger()
test_cell_cycle_score_logger_pancreatic_endocrinogenesis()
from dynamo import LoggerManager
import dynamo.tools
import dynamo as dyn
import pytest
import time
import numpy as np
import os
from test_utils import *
logger = LoggerManager.get_main_logger()
@pytest.fixture
def adata():
return gen_or_read_zebrafish_data()
def test_simple_cluster_community_adata(adata):
dyn.tl.louvain(adata)
dyn.tl.leiden(adata)
dyn.tl.infomap(adata)
try:
dyn.tl.louvain(adata, directed=True)
except ValueError as e:
print("################################################")
print("PASSED: Value error captured as EXPECTED, Exception info:")
print(e)
print("################################################")
dyn.tl.leiden(adata, directed=True)
dyn.vf.acceleration(adata, basis="pca")
dyn.vf.rank_acceleration_genes(adata, groups="Cell_type")
dyn.pp.top_pca_genes(adata)
top_pca_genes = adata.var.index[adata.var.top_pca_genes]
dyn.vf.jacobian(adata, regulators=top_pca_genes, effectors=top_pca_genes)
def test_zebrafish_topography_tutorial_logger():
adata = dyn.sample_data.zebrafish()
dyn.pp.recipe_monocle(adata, num_dim=20, exprs_frac_max=0.005)
dyn.tl.dynamics(adata, model="stochastic", cores=8)
dyn.tl.reduceDimension(adata, n_pca_components=5, enforce=True)
dyn.tl.cell_velocities(adata, basis="pca")
dyn.vf.VectorField(adata, basis="pca", M=100)
dyn.vf.curvature(adata, basis="pca")
dyn.vf.acceleration(adata, basis="pca")
dyn.vf.rank_acceleration_genes(adata, groups="Cell_type")
dyn.pp.top_pca_genes(adata)
top_pca_genes = adata.var.index[adata.var.top_pca_genes]
dyn.vf.jacobian(adata, regulators=top_pca_genes, effectors=top_pca_genes)
dyn.pd.state_graph(adata, group="Cell_type", basis="pca", method="vf")
if __name__ == "__main__":
# test_logger_simple_output_1(LoggerManager.get_main_logger())
# test_logger_simple_progress_naive(LoggerManager.get_main_logger())
# test_logger_simple_progress_logger(LoggerManager.get_main_logger())
test_logger_simple_progress_logger(LoggerManager.get_temp_timer_logger())
# test_vectorField_logger()
# test_zebrafish_topography_tutorial_logger()