SingleCellExperiment 0.4.1__tar.gz → 0.4.3__tar.gz

{SingleCellExperiment-0.4.1 → SingleCellExperiment-0.4.3}/.pre-commit-config.yaml

@@ -33,7 +33,7 @@ repos:
 
 - repo: https://github.com/astral-sh/ruff-pre-commit
   # Ruff version.
-  rev: v0.1.9
+  rev: v0.1.14
   hooks:
     - id: ruff
       args: [--fix, --exit-non-zero-on-fix]

{SingleCellExperiment-0.4.1 → SingleCellExperiment-0.4.3}/CHANGELOG.md

@@ -1,6 +1,15 @@
 # Changelog
 
-## Version 0.3.0 (development)
+## Version 0.4.0 to 0.4.1
+
+This is a complete rewrite of the package, following the functional paradigm from our [developer notes](https://github.com/BiocPy/developer_guide#use-functional-discipline).
+
+- Migrates package to the newly udpated SE/RSE classes.
+- Implement combine generics on SCE.
+- Reduce dependency on a number of external packages.
+- Update docstrings, tests
+
+## Version 0.3.0
 
 This release migrates the package to a more palatable Google's Python style guide. A major modification to the package is with casing, all `camelCase` properties, methods, functions and parameters are now `snake_case`.
 

{SingleCellExperiment-0.4.1 → SingleCellExperiment-0.4.3}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: SingleCellExperiment
-Version: 0.4.1
+Version: 0.4.3
 Summary: Container class for single-cell experiments
 Home-page: https://github.com/BiocPy/SingleCellExperiment
 Author: jkanche

{SingleCellExperiment-0.4.1 → SingleCellExperiment-0.4.3}/docs/changelog.md

@@ -1,6 +1,15 @@
 # Changelog
 
-## Version 0.3.0 (development)
+## Version 0.4.0 to 0.4.1
+
+This is a complete rewrite of the package, following the functional paradigm from our [developer notes](https://github.com/BiocPy/developer_guide#use-functional-discipline).
+
+- Migrates package to the newly udpated SE/RSE classes.
+- Implement combine generics on SCE.
+- Reduce dependency on a number of external packages.
+- Update docstrings, tests
+
+## Version 0.3.0
 
 This release migrates the package to a more palatable Google's Python style guide. A major modification to the package is with casing, all `camelCase` properties, methods, functions and parameters are now `snake_case`.
 

{SingleCellExperiment-0.4.1 → SingleCellExperiment-0.4.3}/src/SingleCellExperiment.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: SingleCellExperiment
-Version: 0.4.1
+Version: 0.4.3
 Summary: Container class for single-cell experiments
 Home-page: https://github.com/BiocPy/SingleCellExperiment
 Author: jkanche

{SingleCellExperiment-0.4.1 → SingleCellExperiment-0.4.3}/src/singlecellexperiment/SingleCellExperiment.py

@@ -490,7 +490,7 @@ class SingleCellExperiment(RangedSummarizedExperiment):
             if dimension < 0:
                 raise IndexError("Index cannot be negative.")
 
-            if dimension > len(self.assay_names):
+            if dimension > len(self.reduced_dim_names):
                 raise IndexError("Index greater than the number of reduced dimensions.")
 
             return self._reduced_dims[self.reduced_dim_names[dimension]]
@@ -680,15 +680,19 @@ class SingleCellExperiment(RangedSummarizedExperiment):
             if name < 0:
                 raise IndexError("Index cannot be negative.")
 
-            if name > len(self.assay_names):
-                raise IndexError("Index greater than the number of reduced dimensions.")
+            if name > len(self.alternative_experiment_names):
+                raise IndexError(
+                    "Index greater than the number of alternative experiments."
+                )
 
-            return self.alternative_experiments[self.alternative_experiment_names[name]]
+            return self._alternative_experiments[
+                self.alternative_experiment_names[name]
+            ]
         elif isinstance(name, str):
-            if name not in self.reduced_dim:
-                raise AttributeError(f"Reduced dimension: {name} does not exist.")
+            if name not in self._alternative_experiments:
+                raise AttributeError(f"Alternative experiment: {name} does not exist.")
 
-            return self.alternative_experiments[name]
+            return self._alternative_experiments[name]
 
         raise TypeError(f"'name' must be a string or integer, provided '{type(name)}'.")
 
@@ -917,22 +921,19 @@ class SingleCellExperiment(RangedSummarizedExperiment):
 
         new_row_ranges = None
         if slicer.row_indices != slice(None):
-            new_row_ranges = self.row_ranges[slicer.row_indices]
+            new_row_ranges = self._row_ranges[slicer.row_indices]
 
         new_reduced_dims = {}
         for rdim, rmat in self._reduced_dims.items():
-            if slicer.row_indices != slice(None):
-                rmat = rmat[slicer.row_indices, :]
-
             if slicer.col_indices != slice(None):
-                rmat = rmat[:, slicer.col_indices]
+                rmat = rmat[slicer.col_indices, :]
 
             new_reduced_dims[rdim] = rmat
 
         new_alt_expts = {}
         for altname, altexpt in self._alternative_experiments.items():
             if slicer.row_indices != slice(None):
-                altexpt = altexpt[rows, :]
+                altexpt = altexpt[slicer.row_indices, :]
 
             if slicer.col_indices != slice(None):
                 altexpt = altexpt[:, slicer.col_indices]
@@ -944,16 +945,10 @@ class SingleCellExperiment(RangedSummarizedExperiment):
             if slicer.row_indices != slice(None):
                 rpair = rpair[slicer.row_indices, :]
 
-            if slicer.col_indices != slice(None):
-                rpair = rpair[:, slicer.col_indices]
-
             new_row_pairs[rname] = rpair
 
         new_col_pairs = {}
         for cname, cpair in self._column_pairs.items():
-            if slicer.row_indices != slice(None):
-                cpair = cpair[slicer.row_indices, :]
-
             if slicer.col_indices != slice(None):
                 cpair = cpair[:, slicer.col_indices]
 

{SingleCellExperiment-0.4.1 → SingleCellExperiment-0.4.3}/tests/test_sce_slice.py

@@ -51,7 +51,10 @@ col_data = pd.DataFrame(
 
 def test_SCE_slice():
     tse = SingleCellExperiment(
-        assays={"counts": counts}, row_data=row_data, column_data=col_data
+        assays={"counts": counts},
+        row_data=row_data,
+        column_data=col_data,
+        reduced_dims={"random_embeds": np.random.rand(ncols, 5)},
     )
 
     tse_slice = tse[0:10, 0:3]