From 269d44829205f2d75de5f9cf43226e2c6361c551 Mon Sep 17 00:00:00 2001
From: sichao <sichao_y@outlook.com>
Date: Mon, 28 Aug 2023 16:58:29 -0400
Subject: [PATCH 01/13] reformat pp external

---
 dynamo/preprocessing/external/__init__.py                | 2 +-
 dynamo/preprocessing/external/integration.py             | 4 +++-
 dynamo/preprocessing/external/pearson_residual_recipe.py | 2 +-
 dynamo/preprocessing/external/sctransform.py             | 1 +
 4 files changed, 6 insertions(+), 3 deletions(-)

diff --git a/dynamo/preprocessing/external/__init__.py b/dynamo/preprocessing/external/__init__.py
index d6551b301..bb73ed945 100644
--- a/dynamo/preprocessing/external/__init__.py
+++ b/dynamo/preprocessing/external/__init__.py
@@ -11,4 +11,4 @@
     "select_genes_by_pearson_residuals",
     "harmony_debatch",
     "integrate",
-]
\ No newline at end of file
+]
diff --git a/dynamo/preprocessing/external/integration.py b/dynamo/preprocessing/external/integration.py
index b7529b38a..e2b4da139 100644
--- a/dynamo/preprocessing/external/integration.py
+++ b/dynamo/preprocessing/external/integration.py
@@ -7,6 +7,7 @@
 # Convert sparse matrix to dense matrix.
 to_dense_matrix = lambda X: np.array(X.todense()) if isspmatrix(X) else np.asarray(X)
 
+
 def integrate(
     adatas: List[AnnData],
     batch_key: str = "slices",
@@ -78,6 +79,7 @@ def integrate(
 
     return integrated_adata
 
+
 def harmony_debatch(
     adata: AnnData,
     key: str,
@@ -125,4 +127,4 @@ def harmony_debatch(
 
     adata.obsm[adjusted_basis] = adjusted_matrix
 
-    return adata if copy else None
\ No newline at end of file
+    return adata if copy else None
diff --git a/dynamo/preprocessing/external/pearson_residual_recipe.py b/dynamo/preprocessing/external/pearson_residual_recipe.py
index 8ae353054..bc711fa51 100644
--- a/dynamo/preprocessing/external/pearson_residual_recipe.py
+++ b/dynamo/preprocessing/external/pearson_residual_recipe.py
@@ -28,6 +28,7 @@
 
 main_logger = LoggerManager.main_logger
 
+
 # TODO: Use compute_pearson_residuals function to calculate residuals
 def _highly_variable_pearson_residuals(
     adata: AnnData,
@@ -108,7 +109,6 @@ def _highly_variable_pearson_residuals(
     # Get pearson residuals for each batch separately
     residual_gene_vars_by_batch = []
     for batch in np.unique(batch_info):
-
         adata_subset = adata[batch_info == batch]
 
         # Filter out zero genes
diff --git a/dynamo/preprocessing/external/sctransform.py b/dynamo/preprocessing/external/sctransform.py
index b54c90dfd..3bbc12fae 100644
--- a/dynamo/preprocessing/external/sctransform.py
+++ b/dynamo/preprocessing/external/sctransform.py
@@ -218,6 +218,7 @@ def sctransform_core(
     """
     import multiprocessing
     import sys
+
     try:
         from KDEpy import FFTKDE
     except ImportError:

From f9411810570e9976c4ce3195b3a3aa839fa72b91 Mon Sep 17 00:00:00 2001
From: sichao <sichao_y@outlook.com>
Date: Mon, 28 Aug 2023 17:00:48 -0400
Subject: [PATCH 02/13] reformat Preprocessor

---
 dynamo/preprocessing/Preprocessor.py | 1 -
 1 file changed, 1 deletion(-)

diff --git a/dynamo/preprocessing/Preprocessor.py b/dynamo/preprocessing/Preprocessor.py
index d060ee3f6..666c94730 100644
--- a/dynamo/preprocessing/Preprocessor.py
+++ b/dynamo/preprocessing/Preprocessor.py
@@ -247,7 +247,6 @@ def standardize_adata(self, adata: AnnData, tkey: str, experiment_type: str) ->
         main_debug("applying convert_gene_name function...")
         self.convert_gene_name(adata)
 
-
         self.basic_stats(adata)
         self.add_experiment_info(adata, tkey, experiment_type)
         main_info_insert_adata("tkey=%s" % tkey, "uns['pp']", indent_level=2)

From fa6b7746e4f16b0766e7edd7f98f2f894f8e428c Mon Sep 17 00:00:00 2001
From: sichao <sichao_y@outlook.com>
Date: Mon, 28 Aug 2023 17:02:27 -0400
Subject: [PATCH 03/13] reformat gene_selection

---
 dynamo/preprocessing/gene_selection.py | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/dynamo/preprocessing/gene_selection.py b/dynamo/preprocessing/gene_selection.py
index 6314a5efe..58a621a4e 100644
--- a/dynamo/preprocessing/gene_selection.py
+++ b/dynamo/preprocessing/gene_selection.py
@@ -247,7 +247,11 @@ def calc_dispersion_by_svr(
         adata_ori.uns[key] = {"mean": mean, "cv": cv, "svr_gamma": svr_gamma}
 
         prefix = "" if layer == "X" else layer + "_"
-        (adata.var[prefix + "log_m"], adata.var[prefix + "log_cv"], adata.var[prefix + "score"],) = (
+        (
+            adata.var[prefix + "log_m"],
+            adata.var[prefix + "log_cv"],
+            adata.var[prefix + "score"],
+        ) = (
             np.nan,
             np.nan,
             -np.inf,

From 10b4c0adaa4ae9079cbdaab5b210cebbba6496e6 Mon Sep 17 00:00:00 2001
From: sichao <sichao_y@outlook.com>
Date: Mon, 28 Aug 2023 17:03:31 -0400
Subject: [PATCH 04/13] reformat pp deprecated

---
 dynamo/preprocessing/deprecated.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/dynamo/preprocessing/deprecated.py b/dynamo/preprocessing/deprecated.py
index 16488ee3c..b0b9fecb6 100644
--- a/dynamo/preprocessing/deprecated.py
+++ b/dynamo/preprocessing/deprecated.py
@@ -72,6 +72,7 @@ def wrapper(*args, **kwargs):
 
 # from __future__ import division, print_function
 
+
 # https://stats.stackexchange.com/questions/356053/the-identity-link-function-does-not-respect-the-domain-of-the-gamma-
 # family
 def _weight_matrix_legacy(fitted_model: sm.Poisson) -> np.ndarray:

From b85c14e3622275e49effb5b3bfa3860ae72dca0d Mon Sep 17 00:00:00 2001
From: sichao <sichao_y@outlook.com>
Date: Tue, 29 Aug 2023 10:43:52 -0400
Subject: [PATCH 05/13] reformat external

---
 dynamo/external/hodge.py | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/dynamo/external/hodge.py b/dynamo/external/hodge.py
index 5e8928833..472a15f3f 100644
--- a/dynamo/external/hodge.py
+++ b/dynamo/external/hodge.py
@@ -232,7 +232,11 @@ def func(x):
             W.dot(ddhodge_div),
             W.dot(potential_),
         )
-        (adata.obs[prefix + "ddhodge_sampled"], adata.obs[prefix + "ddhodge_div"], adata.obs[prefix + "potential"],) = (
+        (
+            adata.obs[prefix + "ddhodge_sampled"],
+            adata.obs[prefix + "ddhodge_div"],
+            adata.obs[prefix + "potential"],
+        ) = (
             False,
             0,
             0,

From 3147d0232751e3f2bd13af96412c283ef670476b Mon Sep 17 00:00:00 2001
From: sichao <sichao_y@outlook.com>
Date: Tue, 29 Aug 2023 10:46:04 -0400
Subject: [PATCH 06/13] reformat simulation

---
 dynamo/simulation/ODE.py              | 2 +-
 dynamo/simulation/simulate_anndata.py | 3 ---
 2 files changed, 1 insertion(+), 4 deletions(-)

diff --git a/dynamo/simulation/ODE.py b/dynamo/simulation/ODE.py
index 281e7fc57..c1599c674 100755
--- a/dynamo/simulation/ODE.py
+++ b/dynamo/simulation/ODE.py
@@ -105,7 +105,7 @@ def toggle(
     return res
 
 
-def Ying_model(x: np.ndarray, t: Optional[float]=None):
+def Ying_model(x: np.ndarray, t: Optional[float] = None):
     """network used in the potential landscape paper from Ying, et. al:
     https://www.nature.com/articles/s41598-017-15889-2.
     This is also the mixture of Gaussian model.
diff --git a/dynamo/simulation/simulate_anndata.py b/dynamo/simulation/simulate_anndata.py
index 02c4472a1..aade2bdc4 100644
--- a/dynamo/simulation/simulate_anndata.py
+++ b/dynamo/simulation/simulate_anndata.py
@@ -82,7 +82,6 @@ def __init__(
         required_param_names: List = [],
         velocity_func: Optional[Callable] = None,
     ) -> None:
-
         # initialization of variables
         self.reactions = reactions
         self.C0s = np.atleast_2d(C0s)
@@ -193,7 +192,6 @@ def simulate(self, t_span, n_cells=None, **simulator_kwargs):
 
     def generate_anndata(self, remove_empty_cells: bool = False):
         if self.T is not None and self.C is not None:
-
             obs = pd.DataFrame(
                 {
                     "cell_name": np.arange(self.get_n_cells()),
@@ -391,7 +389,6 @@ def __init__(
         simulator: CellularModelSimulator,
         syn_rxn_tag: str = "synthesis",
     ) -> None:
-
         self.n_cells = simulator.C.shape[0]
         self.splicing = simulator.splicing
 

From 87fe93b646eddecfc17b8e682c34fc4410dce68d Mon Sep 17 00:00:00 2001
From: sichao <sichao_y@outlook.com>
Date: Tue, 29 Aug 2023 10:47:50 -0400
Subject: [PATCH 07/13] reformat prediction

---
 dynamo/prediction/fate.py              | 1 -
 dynamo/prediction/least_action_path.py | 2 +-
 dynamo/prediction/tscRNA_seq.py        | 1 -
 3 files changed, 1 insertion(+), 3 deletions(-)

diff --git a/dynamo/prediction/fate.py b/dynamo/prediction/fate.py
index acb5e7eda..786ba29c7 100755
--- a/dynamo/prediction/fate.py
+++ b/dynamo/prediction/fate.py
@@ -462,7 +462,6 @@ def fate_bias(
         while True:
             is_dist_larger_than_threshold = distances.flatten() < dist_threshold * median_dist
             if any(is_dist_larger_than_threshold):
-
                 # let us diffuse one step further to identify cells from terminal cell types in case
                 # cells with indices are all close to some random progenitor cells.
                 if hasattr(nbrs, "query"):
diff --git a/dynamo/prediction/least_action_path.py b/dynamo/prediction/least_action_path.py
index 5852d35a2..9336f0763 100644
--- a/dynamo/prediction/least_action_path.py
+++ b/dynamo/prediction/least_action_path.py
@@ -534,7 +534,7 @@ def least_action(
         A = []
 
     path_ind = 0
-    for (init_state, target_state) in LoggerManager.progress_logger(
+    for init_state, target_state in LoggerManager.progress_logger(
         pairs, progress_name=f"iterating through {len(pairs)} pairs"
     ):
         logger.info(
diff --git a/dynamo/prediction/tscRNA_seq.py b/dynamo/prediction/tscRNA_seq.py
index fb5797792..89eafd860 100644
--- a/dynamo/prediction/tscRNA_seq.py
+++ b/dynamo/prediction/tscRNA_seq.py
@@ -17,7 +17,6 @@ def get_pulse_r0(
     add_init_r0_key: str = "init_r0_pulse",
     copy: bool = False,
 ) -> Union[anndata.AnnData, None]:
-
     """Get the total RNA at the initial time point for a kinetic experiment with the formula:
            :math:`r_0 = \frac{(r - l)}{(1 - k)}`, where :math: `k = 1 - e^{- \gamma t}
 

From 2857cb885c8fcd4b1d590e5f494dfdf21e0a4af2 Mon Sep 17 00:00:00 2001
From: sichao <sichao_y@outlook.com>
Date: Thu, 31 Aug 2023 17:02:53 -0400
Subject: [PATCH 08/13] isort pp external

---
 dynamo/preprocessing/external/__init__.py             |  6 ++----
 .../preprocessing/external/pearson_residual_recipe.py | 11 ++++-------
 dynamo/preprocessing/external/sctransform.py          |  3 ++-
 3 files changed, 8 insertions(+), 12 deletions(-)

diff --git a/dynamo/preprocessing/external/__init__.py b/dynamo/preprocessing/external/__init__.py
index bb73ed945..0d21bd4aa 100644
--- a/dynamo/preprocessing/external/__init__.py
+++ b/dynamo/preprocessing/external/__init__.py
@@ -1,8 +1,6 @@
 from .integration import harmony_debatch, integrate
-from .pearson_residual_recipe import (
-    normalize_layers_pearson_residuals,
-    select_genes_by_pearson_residuals,
-)
+from .pearson_residual_recipe import (normalize_layers_pearson_residuals,
+                                      select_genes_by_pearson_residuals)
 from .sctransform import sctransform
 
 __all__ = [
diff --git a/dynamo/preprocessing/external/pearson_residual_recipe.py b/dynamo/preprocessing/external/pearson_residual_recipe.py
index bc711fa51..8dac00483 100644
--- a/dynamo/preprocessing/external/pearson_residual_recipe.py
+++ b/dynamo/preprocessing/external/pearson_residual_recipe.py
@@ -17,13 +17,10 @@
 from scipy.sparse import issparse
 
 from ...configuration import DKM
-from ...dynamo_logger import (
-    LoggerManager,
-    main_info,
-    main_info_insert_adata_layer,
-    main_warning,
-)
-from ...preprocessing.utils import is_nonnegative_integer_arr, seurat_get_mean_var
+from ...dynamo_logger import (LoggerManager, main_info,
+                              main_info_insert_adata_layer, main_warning)
+from ...preprocessing.utils import (is_nonnegative_integer_arr,
+                                    seurat_get_mean_var)
 from ..QC import filter_genes_by_outliers
 
 main_logger = LoggerManager.main_logger
diff --git a/dynamo/preprocessing/external/sctransform.py b/dynamo/preprocessing/external/sctransform.py
index 3bbc12fae..b43cc1e70 100644
--- a/dynamo/preprocessing/external/sctransform.py
+++ b/dynamo/preprocessing/external/sctransform.py
@@ -20,7 +20,8 @@
 from scipy import stats
 
 from ...configuration import DKM
-from ...dynamo_logger import main_info, main_info_insert_adata_layer, main_warning
+from ...dynamo_logger import (main_info, main_info_insert_adata_layer,
+                              main_warning)
 from ..utils import get_gene_selection_filter
 
 _EPS = np.finfo(float).eps

From a06dd952f1dc2d0eade427657ec2ee44a109fffb Mon Sep 17 00:00:00 2001
From: sichao <sichao_y@outlook.com>
Date: Thu, 31 Aug 2023 17:11:12 -0400
Subject: [PATCH 09/13] isort preprocessor

---
 dynamo/preprocessing/Preprocessor.py | 28 +++++++---------------------
 1 file changed, 7 insertions(+), 21 deletions(-)

diff --git a/dynamo/preprocessing/Preprocessor.py b/dynamo/preprocessing/Preprocessor.py
index 666c94730..e275e6249 100644
--- a/dynamo/preprocessing/Preprocessor.py
+++ b/dynamo/preprocessing/Preprocessor.py
@@ -9,21 +9,13 @@
 from anndata import AnnData
 
 from ..configuration import DKM
-from ..dynamo_logger import (
-    LoggerManager,
-    main_debug,
-    main_info,
-    main_info_insert_adata,
-    main_warning,
-)
+from ..dynamo_logger import (LoggerManager, main_debug, main_info,
+                             main_info_insert_adata, main_warning)
 from ..tools.connectivity import neighbors as default_neighbors
 from ..tools.utils import update_dict
 from .cell_cycle import cell_cycle_scores
-from .external import (
-    normalize_layers_pearson_residuals,
-    sctransform,
-    select_genes_by_pearson_residuals,
-)
+from .external import (normalize_layers_pearson_residuals, sctransform,
+                       select_genes_by_pearson_residuals)
 from .gene_selection import select_genes_by_seurat_recipe, select_genes_monocle
 from .normalization import calc_sz_factor, normalize
 from .pca import pca
@@ -32,15 +24,9 @@
 from .QC import filter_genes_by_outliers as monocle_filter_genes_by_outliers
 from .QC import regress_out_parallel
 from .transform import Freeman_Tukey, log, log1p, log2
-from .utils import (
-    _infer_labeling_experiment_type,
-    calc_new_to_total_ratio,
-    collapse_species_adata,
-    convert2symbol,
-    convert_layers2csr,
-    detect_experiment_datatype,
-    unique_var_obs_adata,
-)
+from .utils import (_infer_labeling_experiment_type, calc_new_to_total_ratio,
+                    collapse_species_adata, convert2symbol, convert_layers2csr,
+                    detect_experiment_datatype, unique_var_obs_adata)
 
 
 class Preprocessor:

From 11a6b9672095a7db091cf2915e6db0943c559286 Mon Sep 17 00:00:00 2001
From: sichao <sichao_y@outlook.com>
Date: Thu, 31 Aug 2023 17:11:56 -0400
Subject: [PATCH 10/13] isort pp steps

---
 dynamo/preprocessing/QC.py             | 14 +++-----
 dynamo/preprocessing/__init__.py       | 44 ++++++++------------------
 dynamo/preprocessing/deprecated.py     | 34 +++++++-------------
 dynamo/preprocessing/gene_selection.py | 23 ++++----------
 dynamo/preprocessing/normalization.py  | 12 ++-----
 dynamo/preprocessing/pca.py            |  3 +-
 6 files changed, 39 insertions(+), 91 deletions(-)

diff --git a/dynamo/preprocessing/QC.py b/dynamo/preprocessing/QC.py
index f972de43e..7102b6963 100644
--- a/dynamo/preprocessing/QC.py
+++ b/dynamo/preprocessing/QC.py
@@ -13,16 +13,10 @@
 from scipy.sparse import issparse, spmatrix
 
 from ..configuration import DKM
-from ..dynamo_logger import (
-    LoggerManager,
-    main_debug,
-    main_exception,
-    main_finish_progress,
-    main_info,
-    main_info_insert_adata_obs,
-    main_log_time,
-    main_warning,
-)
+from ..dynamo_logger import (LoggerManager, main_debug, main_exception,
+                             main_finish_progress, main_info,
+                             main_info_insert_adata_obs, main_log_time,
+                             main_warning)
 from .utils import get_inrange_shared_counts_mask
 
 
diff --git a/dynamo/preprocessing/__init__.py b/dynamo/preprocessing/__init__.py
index 22d95a23e..dc94fc821 100755
--- a/dynamo/preprocessing/__init__.py
+++ b/dynamo/preprocessing/__init__.py
@@ -2,40 +2,21 @@
 """
 
 from .cell_cycle import cell_cycle_scores
+from .deprecated import (calc_sz_factor_legacy, cook_dist, filter_cells_legacy,
+                         normalize_cell_expr_by_size_factors, recipe_monocle,
+                         recipe_velocyto)
 from .dynast import lambda_correction
-from .external import (
-    harmony_debatch,
-    integrate,
-    normalize_layers_pearson_residuals,
-    sctransform,
-    select_genes_by_pearson_residuals,
-)
+from .external import (harmony_debatch, integrate,
+                       normalize_layers_pearson_residuals, sctransform,
+                       select_genes_by_pearson_residuals)
 from .normalization import calc_sz_factor, normalize
-from .QC import (
-    basic_stats,
-    filter_genes_by_clusters,
-    filter_cells_by_outliers,
-    filter_genes_by_outliers,
-    filter_genes_by_pattern,
-)
 from .pca import pca, top_pca_genes
+from .QC import (basic_stats, filter_cells_by_outliers,
+                 filter_genes_by_clusters, filter_genes_by_outliers,
+                 filter_genes_by_pattern)
 from .transform import log1p, log1p_adata_layer
-from .utils import (
-    compute_gene_exp_fraction,
-    convert2symbol,
-    decode,
-    get_svr_filter,
-    relative2abs,
-    scale,
-)
-from .deprecated import (
-    cook_dist,
-    calc_sz_factor_legacy,
-    normalize_cell_expr_by_size_factors,
-    filter_cells_legacy,
-    recipe_monocle,
-    recipe_velocyto,
-)
+from .utils import (compute_gene_exp_fraction, convert2symbol, decode,
+                    get_svr_filter, relative2abs, scale)
 
 filter_cells = filter_cells_by_outliers
 filter_genes = filter_genes_by_outliers
@@ -43,7 +24,8 @@
 normalize_cells = normalize
 
 from .CnmfPreprocessor import CnmfPreprocessor
-from .gene_selection import calc_Gini, calc_dispersion_by_svr, highest_frac_genes, select_genes_monocle
+from .gene_selection import (calc_dispersion_by_svr, calc_Gini,
+                             highest_frac_genes, select_genes_monocle)
 from .Preprocessor import Preprocessor
 
 __all__ = [
diff --git a/dynamo/preprocessing/deprecated.py b/dynamo/preprocessing/deprecated.py
index b0b9fecb6..6f4da4a21 100644
--- a/dynamo/preprocessing/deprecated.py
+++ b/dynamo/preprocessing/deprecated.py
@@ -19,36 +19,24 @@
 from sklearn.decomposition import FastICA
 
 from ..configuration import DKM, DynamoAdataConfig, DynamoAdataKeyManager
-from ..dynamo_logger import (
-    LoggerManager,
-    main_debug,
-    main_info,
-    main_info_insert_adata_obsm,
-    main_warning,
-)
+from ..dynamo_logger import (LoggerManager, main_debug, main_info,
+                             main_info_insert_adata_obsm, main_warning)
 from ..tools.utils import update_dict
 from ..utils import copy_adata
 from .cell_cycle import cell_cycle_scores
 from .gene_selection import calc_dispersion_by_svr
-from .normalization import calc_sz_factor, get_sz_exprs, normalize_mat_monocle, sz_util
+from .normalization import (calc_sz_factor, get_sz_exprs,
+                            normalize_mat_monocle, sz_util)
 from .pca import pca
 from .QC import basic_stats, filter_genes_by_clusters, filter_genes_by_outliers
 from .transform import _Freeman_Tukey
-from .utils import (
-    _infer_labeling_experiment_type,
-    add_noise_to_duplicates,
-    calc_new_to_total_ratio,
-    collapse_species_adata,
-    compute_gene_exp_fraction,
-    convert2symbol,
-    convert_layers2csr,
-    detect_experiment_datatype,
-    get_inrange_shared_counts_mask,
-    get_nan_or_inf_data_bool_mask,
-    get_svr_filter,
-    merge_adata_attrs,
-    unique_var_obs_adata,
-)
+from .utils import (_infer_labeling_experiment_type, add_noise_to_duplicates,
+                    calc_new_to_total_ratio, collapse_species_adata,
+                    compute_gene_exp_fraction, convert2symbol,
+                    convert_layers2csr, detect_experiment_datatype,
+                    get_inrange_shared_counts_mask,
+                    get_nan_or_inf_data_bool_mask, get_svr_filter,
+                    merge_adata_attrs, unique_var_obs_adata)
 
 
 def deprecated(func):
diff --git a/dynamo/preprocessing/gene_selection.py b/dynamo/preprocessing/gene_selection.py
index 58a621a4e..b1771a1c7 100644
--- a/dynamo/preprocessing/gene_selection.py
+++ b/dynamo/preprocessing/gene_selection.py
@@ -16,24 +16,13 @@
 from scipy.sparse import csr_matrix, issparse
 
 from ..configuration import DKM
-from ..dynamo_logger import (
-    LoggerManager,
-    main_critical,
-    main_debug,
-    main_info,
-    main_info_insert_adata_uns,
-    main_info_insert_adata_var,
-    main_warning,
-)
+from ..dynamo_logger import (LoggerManager, main_critical, main_debug,
+                             main_info, main_info_insert_adata_uns,
+                             main_info_insert_adata_var, main_warning)
 from .pca import pca
-from .utils import (
-    compute_gene_exp_fraction,
-    get_gene_selection_filter,
-    get_nan_or_inf_data_bool_mask,
-    get_svr_filter,
-    merge_adata_attrs,
-    seurat_get_mean_var,
-)
+from .utils import (compute_gene_exp_fraction, get_gene_selection_filter,
+                    get_nan_or_inf_data_bool_mask, get_svr_filter,
+                    merge_adata_attrs, seurat_get_mean_var)
 
 
 def calc_Gini(adata: AnnData, layers: Union[Literal["all"], List[str]] = "all") -> AnnData:
diff --git a/dynamo/preprocessing/normalization.py b/dynamo/preprocessing/normalization.py
index 991f599cf..003d28608 100644
--- a/dynamo/preprocessing/normalization.py
+++ b/dynamo/preprocessing/normalization.py
@@ -14,15 +14,9 @@
 from scipy.sparse.base import issparse
 
 from ..configuration import DKM
-from ..dynamo_logger import (
-    main_debug,
-    main_info_insert_adata_layer,
-    main_info_insert_adata_obsm,
-    main_warning,
-)
-from .utils import (
-    merge_adata_attrs,
-)
+from ..dynamo_logger import (main_debug, main_info_insert_adata_layer,
+                             main_info_insert_adata_obsm, main_warning)
+from .utils import merge_adata_attrs
 
 
 def calc_sz_factor(
diff --git a/dynamo/preprocessing/pca.py b/dynamo/preprocessing/pca.py
index c3437d784..245b46240 100644
--- a/dynamo/preprocessing/pca.py
+++ b/dynamo/preprocessing/pca.py
@@ -16,7 +16,8 @@
 from sklearn.utils.sparsefuncs import mean_variance_axis
 
 from ..configuration import DKM
-from ..dynamo_logger import main_info_insert_adata_obsm, main_info_insert_adata_var
+from ..dynamo_logger import (main_info_insert_adata_obsm,
+                             main_info_insert_adata_var)
 
 
 def _truncatedSVD_with_center(

From 112ab9698a265707d4d9d16b55cd532b08b8f490 Mon Sep 17 00:00:00 2001
From: sichao <sichao_y@outlook.com>
Date: Fri, 1 Sep 2023 11:47:20 -0400
Subject: [PATCH 11/13] isort external

---
 dynamo/external/hodge.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/dynamo/external/hodge.py b/dynamo/external/hodge.py
index 472a15f3f..d2d31e49e 100644
--- a/dynamo/external/hodge.py
+++ b/dynamo/external/hodge.py
@@ -10,7 +10,6 @@
 from scipy.sparse import csr_matrix, issparse
 
 from ..dynamo_logger import main_finish_progress, main_info, main_log_time
-
 # from ..vectorfield.scVectorField import graphize_vecfld
 from ..tools.graph_calculus import divergence, graphize_velocity, potential
 from ..tools.sampling import sample_by_velocity, trn
@@ -21,7 +20,8 @@
     div,
     potential,
 )"""
-from ..tools.connectivity import _gen_neighbor_keys, check_and_recompute_neighbors
+from ..tools.connectivity import (_gen_neighbor_keys,
+                                  check_and_recompute_neighbors)
 
 
 def ddhodge(

From 4499ae9d33c13068630987d51f4406df6c8b7222 Mon Sep 17 00:00:00 2001
From: sichao <sichao_y@outlook.com>
Date: Fri, 1 Sep 2023 11:48:49 -0400
Subject: [PATCH 12/13] isort simulation

---
 dynamo/simulation/__init__.py         | 30 +++++++--------------------
 dynamo/simulation/simulate_anndata.py | 20 ++++--------------
 dynamo/simulation/utils.py            | 10 ++-------
 3 files changed, 14 insertions(+), 46 deletions(-)

diff --git a/dynamo/simulation/__init__.py b/dynamo/simulation/__init__.py
index 23e1f1ff2..2175d2f10 100755
--- a/dynamo/simulation/__init__.py
+++ b/dynamo/simulation/__init__.py
@@ -1,25 +1,11 @@
 from .evaluation import evaluate
 from .Gillespie import Gillespie
-from .ODE import (
-    Simulator,
-    Ying_model,
-    jacobian_bifur2genes,
-    neurongenesis,
-    ode_bifur2genes,
-    state_space_sampler,
-    toggle,
-)
-from .simulate_anndata import (
-    AnnDataSimulator,
-    BifurcationTwoGenes,
-    CellularModelSimulator,
-    KinLabelingSimulator,
-    Neurongenesis,
-    OscillationTwoGenes,
-    bifur2genes_params,
-    bifur2genes_splicing_params,
-    neurongenesis_params,
-    osc2genes_params,
-    osc2genes_splicing_params,
-)
+from .ODE import (Simulator, Ying_model, jacobian_bifur2genes, neurongenesis,
+                  ode_bifur2genes, state_space_sampler, toggle)
+from .simulate_anndata import (AnnDataSimulator, BifurcationTwoGenes,
+                               CellularModelSimulator, KinLabelingSimulator,
+                               Neurongenesis, OscillationTwoGenes,
+                               bifur2genes_params, bifur2genes_splicing_params,
+                               neurongenesis_params, osc2genes_params,
+                               osc2genes_splicing_params)
 from .utils import CellularSpecies, directMethod
diff --git a/dynamo/simulation/simulate_anndata.py b/dynamo/simulation/simulate_anndata.py
index aade2bdc4..5d2493a56 100644
--- a/dynamo/simulation/simulate_anndata.py
+++ b/dynamo/simulation/simulate_anndata.py
@@ -5,24 +5,12 @@
 import pandas as pd
 
 # dynamo logger related
-from ..dynamo_logger import (
-    LoggerManager,
-    main_critical,
-    main_exception,
-    main_info,
-    main_tqdm,
-    main_warning,
-)
+from ..dynamo_logger import (LoggerManager, main_critical, main_exception,
+                             main_info, main_tqdm, main_warning)
 from ..tools.sampling import sample
 from ..tools.utils import flatten, isarray
-from .ODE import (
-    hill_act_func,
-    hill_inh_func,
-    neurongenesis,
-    ode_bifur2genes,
-    ode_neurongenesis,
-    ode_osc2genes,
-)
+from .ODE import (hill_act_func, hill_inh_func, neurongenesis, ode_bifur2genes,
+                  ode_neurongenesis, ode_osc2genes)
 from .utils import CellularSpecies, GillespieReactions, Reaction
 
 bifur2genes_params = {
diff --git a/dynamo/simulation/utils.py b/dynamo/simulation/utils.py
index d5e7e9653..9c71e3502 100644
--- a/dynamo/simulation/utils.py
+++ b/dynamo/simulation/utils.py
@@ -3,14 +3,8 @@
 import numpy as np
 
 # dynamo logger related
-from ..dynamo_logger import (
-    LoggerManager,
-    main_critical,
-    main_exception,
-    main_info,
-    main_tqdm,
-    main_warning,
-)
+from ..dynamo_logger import (LoggerManager, main_critical, main_exception,
+                             main_info, main_tqdm, main_warning)
 
 
 def directMethod(

From 6126b634cc9517d0ae1fadbc36b9827ff4144e5b Mon Sep 17 00:00:00 2001
From: sichao <sichao_y@outlook.com>
Date: Fri, 3 Nov 2023 15:53:11 -0400
Subject: [PATCH 13/13] update code quality check in workflow

---
 .github/workflows/python-plain-run-test.yml | 26 +++++++++++++--------
 1 file changed, 16 insertions(+), 10 deletions(-)

diff --git a/.github/workflows/python-plain-run-test.yml b/.github/workflows/python-plain-run-test.yml
index 0fe8e62ab..e92eeedea 100644
--- a/.github/workflows/python-plain-run-test.yml
+++ b/.github/workflows/python-plain-run-test.yml
@@ -9,6 +9,21 @@ on:
     branches: [ master ]
 
 jobs:
+  check-code:
+    name: Check code quality
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout branch
+        uses: actions/checkout@v2
+      - name: Setup python
+        uses: actions/setup-python@v2
+        with:
+          python-version: '3.9'
+          architecture: x64
+      - name: Install dependencies
+        run: pip install isort black
+      - name: Check code quality
+        run: isort --profile black --check dynamo tests && black --check dynamo tests && echo OK
   build:
     runs-on: ubuntu-latest
     strategy:
@@ -25,20 +40,11 @@ jobs:
       run: |
         python -m pip install --upgrade pip
         pip install git+https://github.com/pypa/pip.git@611e9253ff74ca5b8ce438c2423373ab0d44c961
-        pip install flake8 pytest
+        pip install pytest
         if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
     - name: Install package
       run: |
         pip install -e .[test]
-    - name: Lint with flake8
-      run: |
-        # stop the build if there are Python syntax errors or undefined names
-        flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
-        # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
-        flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
-#    - name: Test with pytest
-#      run: |
-#        pytest
     - name: Run tests and collect coverage
       run: |
         pip install pytest-cov