remove commented content

aristoteleo · Jul 6, 2023 · 8a6bf80 · 8a6bf80
1 parent 23e0ab0
commit 8a6bf80
Showing 1 changed file with 0 additions and 52 deletions.
diff --git a/tests/conftest.py b/tests/conftest.py
@@ -40,46 +40,6 @@ def mkdirs_wrapper(path: Union[str, Path], abort=True):
             os.makedirs(path)
             return True
 
-    # def gen_zebrafish_test_data(basis="pca"):
-    #     adata = dyn.sample_data.zebrafish()
-    #     # adata = adata[:3000]
-    #     dyn.pp.recipe_monocle(adata, num_dim=20, exprs_frac_for_gene_exclusion=0.005)
-    #     dyn.tl.dynamics(adata, model="stochastic", cores=12)
-    #     dyn.tl.reduceDimension(adata, basis="umap", n_pca_components=30, enforce=True)
-    #     dyn.tl.cell_velocities(adata, basis="umap")
-    #     dyn.vf.VectorField(adata, basis="umap", M=100)
-    #     dyn.tl.reduceDimension(adata, basis=basis, n_pca_components=30, enforce=True)
-    #     dyn.tl.cell_velocities(adata, basis=basis)
-    #     dyn.vf.VectorField(adata, basis=basis, M=100)
-    #     dyn.vf.curvature(adata, basis=basis)
-    #     dyn.vf.acceleration(adata, basis=basis)
-    #
-    #     dyn.vf.rank_acceleration_genes(adata, groups="Cell_type", akey="acceleration", prefix_store="rank")
-    #     dyn.vf.rank_curvature_genes(adata, groups="Cell_type", ckey="curvature", prefix_store="rank")
-    #     dyn.vf.rank_velocity_genes(adata, groups="Cell_type", vkey="velocity_S", prefix_store="rank")
-    #
-    #     dyn.pp.top_pca_genes(adata, n_top_genes=100)
-    #     top_pca_genes = adata.var.index[adata.var.top_pca_genes]
-    #     dyn.vf.jacobian(adata, regulators=top_pca_genes, effectors=top_pca_genes)
-    #     dyn.cleanup(adata)
-    #     adata.uns.pop("cell_phase_genes")
-    #     adata.var = adata.var.drop(columns=['beta', 'gamma', 'half_life', 'alpha_b', 'alpha_r2', 'gamma_b', 'gamma_r2',
-    #                                         'gamma_logLL', 'delta_b', 'delta_r2', 'bs', 'bf', 'uu0', 'ul0', 'su0',
-    #                                         'sl0', 'U0', 'S0', 'total0'], axis=1)
-    #     TestUtils.mkdirs_wrapper(test_data_dir, abort=False)
-    #     adata.write_h5ad(test_zebrafish_data_path)
-    #
-    # def gen_or_read_zebrafish_data():
-    #     # generate data if needed
-    #     if not os.path.exists(test_zebrafish_data_path):
-    #         print("generating test data...")
-    #         TestUtils.gen_zebrafish_test_data()
-    #
-    #     print("reading test data...")
-    #     # TODO use a fixture in future
-    #     adata = dyn.read_h5ad(test_zebrafish_data_path)
-    #     return adata
-
     def read_test_spatial_genomics_data():
         return dyn.read_h5ad(test_spatial_genomics_path)
 
@@ -89,18 +49,6 @@ def utils():
     return TestUtils
 
 
-ZEBRAFISH_ADATA = None
-
-
-# @pytest.fixture
-# def adata(utils):
-#     global ZEBRAFISH_ADATA
-#     if ZEBRAFISH_ADATA:
-#         return ZEBRAFISH_ADATA
-#     ZEBRAFISH_ADATA = utils.gen_or_read_zebrafish_data()
-#     return ZEBRAFISH_ADATA
-
-
 @pytest.fixture(scope="session")
 def processed_zebra_adata():
     raw_adata = dyn.sample_data.zebrafish()