Merge branch 'lhqing:master' into zarr_parallel

Author: theAeon

.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 1.1.0
+current_version = 1.1.1
 tag = True
 commit = True
 

.pre-commit-config.yaml

@@ -2,24 +2,24 @@ fail_fast: false
 default_language_version:
     python: python3
 default_stages:
-    - commit
-    - push
+    - pre-commit
+    - pre-push
 minimum_pre_commit_version: 2.16.0
 repos:
     - repo: https://github.com/psf/black
-      rev: 24.4.2
+      rev: 25.1.0
       hooks:
           - id: black
     - repo: https://github.com/pre-commit/mirrors-prettier
       rev: v4.0.0-alpha.8
       hooks:
           - id: prettier
     - repo: https://github.com/asottile/blacken-docs
-      rev: 1.18.0
+      rev: 1.19.1
       hooks:
           - id: blacken-docs
     - repo: https://github.com/PyCQA/isort
-      rev: 5.13.2
+      rev: 6.0.0
       hooks:
           - id: isort
     - repo: https://github.com/asottile/yesqa
@@ -34,7 +34,7 @@ repos:
                 - flake8-bugbear
                 - flake8-blind-except
     - repo: https://github.com/pre-commit/pre-commit-hooks
-      rev: v4.6.0
+      rev: v5.0.0
       hooks:
           - id: detect-private-key
           - id: check-ast
@@ -53,7 +53,7 @@ repos:
                 - --remove-unused-variable
                 - --ignore-init-module-imports
     - repo: https://github.com/PyCQA/flake8
-      rev: 7.1.0
+      rev: 7.1.2
       hooks:
           - id: flake8
             additional_dependencies:
@@ -64,7 +64,7 @@ repos:
                 - flake8-bugbear
                 - flake8-blind-except
     - repo: https://github.com/asottile/pyupgrade
-      rev: v3.16.0
+      rev: v3.19.1
       hooks:
           - id: pyupgrade
             args: [--py3-plus, --py38-plus, --keep-runtime-typing]

ALLCools/__main__.py

@@ -322,7 +322,7 @@ def merge_allc_register_subparser(subparser):
         "--output_path",
         type=str,
         required=True,
-        help="Path to the output merged ALLC file.",
+        help="Path to the output merged ALLC file (specify tsv.gz extension)",
     )
 
     parser_req.add_argument("--chrom_size_path", type=str, required=True, help=chrom_size_path_doc)

ALLCools/_merge_allc.py

@@ -40,7 +40,7 @@ def __init__(self, path, region):
             self.f_region = TabixIterator()
 
     def readline(self):
-        return self.f_region.next()
+        return self.f_region.__next__()
 
     def close(self):
         self.f.close()

ALLCools/count_matrix/dataset.py

@@ -98,7 +98,7 @@ def _determine_datasets(regions, quantifiers, chrom_size_path):
                     "do not have index in its fourth column, adding it automatically. "
                     "If this is not desired, add a fourth column containing UNIQUE IDs to the BED file.",
                 )
-                region_bed_df[name] = (f"{name}_{i}" for i in range(region_bed_df.shape[0]))
+                region_bed_df[name] = [f"{name}_{i}" for i in range(region_bed_df.shape[0])]
             # check if name is unique()
             if region_bed_df.iloc[:, 3].duplicated().sum() > 0:
                 raise ValueError(f"Region IDs in {region_path} (fourth column) are not unique.")

ALLCools/mcds/mcds.py

@@ -1026,7 +1026,7 @@ def get_score_adata(
         if quant_type.lower().startswith("hypo"):
             quant_type = "hypo-score"
         elif quant_type.lower().startswith("hyper"):
-            quant_type = "hyper_score"
+            quant_type = "hyper-score"
         else:
             pass
         if quant_type not in QUANT_TYPES:

ALLCools/mcds/utilities.py

@@ -260,7 +260,7 @@ def highly_variable_methylation_feature(
 
     # Select n_top_feature
     if n_top_feature is not None:
-        feature_subset = df.index.isin(df.sort_values("dispersion_norm", ascending=False).index[:5000])
+        feature_subset = df.index.isin(df.sort_values("dispersion_norm", ascending=False).index[:n_top_feature])
     else:
         max_disp = np.inf if max_disp is None else max_disp
         dispersion_norm[np.isnan(dispersion_norm)] = 0  # similar to Seurat

ALLCools/utilities.py

@@ -76,6 +76,8 @@ def parse_mc_pattern(pattern: str) -> set:
         except KeyError:
             raise KeyError(f"Base {base} is not in IUPAC table.")
     context_set = {"".join(i) for i in itertools.product(*all_pos_list)}
+    if pattern == "CH":
+        context_set.add("CH")
     return context_set
 
 

pyproject.toml

@@ -10,7 +10,7 @@ maintainers = [
 urls.Documentation = "https://lhqing.github.io/ALLCools/intro.html"
 urls.Source = "https://github.com/lhqing/ALLCools"
 urls.Home-page = "https://github.com/lhqing/ALLCools"
-version = "1.1.0"
+version = "1.1.1"
 requires-python = ">=3.7"
 license = { file = "LICENSE" }
 readme = "README.md"