Overhaul SingleCellExperiment

README.md

@@ -25,6 +25,21 @@ import singlecellexperiment
 sce = singlecellexperiment.read_h5ad("tests/data/adata.h5ad")
 ```
 
+    ## output
+    class: SingleCellExperiment
+    dimensions: (20, 30)
+    assays(3): ['array', 'sparse', 'X']
+    row_data columns(5): ['var_cat', 'cat_ordered', 'int64', 'float64', 'uint8']
+    row_names(0):
+    column_data columns(5): ['obs_cat', 'cat_ordered', 'int64', 'float64', 'uint8']
+    column_names(0):
+    main_experiment_name:
+    reduced_dims(0): []
+    alternative_experiments(0): []
+    row_pairs(0): []
+    column_pairs(0): []
+    metadata(2): O_recarray nested
+
 ***OR construct one from scratch***
 
 ```python

docs/tutorial.md

@@ -22,12 +22,13 @@ Similarly `read_tenx_h5`, `read_tenx_mtx` and `from_anndata` methods are  availa
 ```python
 import pandas as pd
 import numpy as np
+from biocframe import BiocFrame
 from genomicranges import GenomicRanges
 
 nrows = 200
 ncols = 6
 counts = np.random.rand(nrows, ncols)
-df_gr = pd.DataFrame(
+row_data = BiocFrame(
     {
         "seqnames": [
             "chr1",
@@ -50,8 +51,6 @@ df_gr = pd.DataFrame(
     }
 )
 
-gr = GenomicRanges.from_pandas(df_gr)
-
 col_data = pd.DataFrame(
     {
         "celltype": ["cluster1", "cluster2"] * 3,
@@ -65,7 +64,7 @@ Finally construct the object,
 from singlecellexperiment import SingleCellExperiment
 
 tse = SingleCellExperiment(
-    assays={"counts": counts}, row_data=df_gr, col_data=col_data
+    assays={"counts": counts}, row_data=row_data, column_data=col_data
 )
 ```
 
@@ -76,11 +75,11 @@ Multiple methods are available to access various slots of a `SingleCellExperimen
 ```python
 tse.assays
 tse.row_data
-tse.col_data
+tse.column_data
 tse.reduced_dims
 tse.alternative_experiments
 tse.row_pairs
-tse.col_pairs
+tse.column_pairs
 ```
 
 ### Access specific sets

setup.cfg

@@ -41,15 +41,15 @@ package_dir =
     =src
 
 # Require a min/specific Python version (comma-separated conditions)
-# python_requires = >=3.8
+python_requires = >=3.8
 
 # Add here dependencies of your project (line-separated), e.g. requests>=2.2,<3.0.
 # Version specifiers like >=2.2,<3.0 avoid problems due to API changes in
 # new major versions. This works if the required packages follow Semantic Versioning.
 # For more information, check out https://semver.org/.
 install_requires =
     importlib-metadata; python_version<"3.8"
-    summarizedexperiment>=0.3.5
+    summarizedexperiment>=0.4.0,<0.5.0
 
 [options.packages.find]
 where = src