Merge pull request #287 from josephrich98/low_memory_h5ad

h5ad lower RAM

Author: Yenaled

.github/workflows/release.yml

@@ -14,7 +14,7 @@ jobs:
       - name: Setup python
         uses: actions/setup-python@v1
         with:
-          python-version: '3.8'
+          python-version: '3.9'
           architecture: x64
       - name: Install dependencies
         run: pip install -r dev-requirements.txt

README.md

@@ -1,6 +1,6 @@
 # kb-python
-![github version](https://img.shields.io/badge/Version-0.29.1-informational)
-[![pypi version](https://img.shields.io/pypi/v/kb-python)](https://pypi.org/project/kb-python/0.29.1/)
+![github version](https://img.shields.io/badge/Version-0.29.2-informational)
+[![pypi version](https://img.shields.io/pypi/v/kb-python)](https://pypi.org/project/kb-python/0.29.2/)
 ![python versions](https://img.shields.io/pypi/pyversions/kb_python)
 ![status](https://github.com/pachterlab/kb_python/workflows/CI/badge.svg)
 [![codecov](https://codecov.io/gh/pachterlab/kb_python/branch/master/graph/badge.svg)](https://codecov.io/gh/pachterlab/kb_python)
@@ -98,7 +98,7 @@ The `kb info` command prints out package information including the version of `k
 
 ```bash
 $ kb info
-kb_python 0.29.1 ...
+kb_python 0.29.2 ...
 kallisto: 0.51.1 ...
 bustools: 0.44.1 ...
 ...

docs/conf.py

@@ -24,7 +24,7 @@
 author = 'Kyung Hoi (Joseph) Min'
 
 # The full version, including alpha/beta/rc tags
-release = '0.29.1'
+release = '0.29.2'
 master_doc = 'index'
 
 # -- General configuration ---------------------------------------------------

docs/index.rst

@@ -6,7 +6,7 @@
 Welcome to kb-python's documentation!
 =====================================
 
-This page contains **DEVELOPER** documentation for ``kb-python`` version ``0.29.1``.
+This page contains **DEVELOPER** documentation for ``kb-python`` version ``0.29.2``.
 For user documentation and tutorials, please go to `kallisto | bustools <https://www.kallistobus.tools/>`_.
 
 Development Prerequisites

kb_python/__init__.py

@@ -1 +1 @@
-__version__ = '0.29.1'
+__version__ = '0.29.2'

kb_python/utils.py

@@ -664,11 +664,13 @@ def import_matrix_as_anndata(
         )
         df_barcodes.index = df_batch_barcodes.index + df_barcodes.index
     df_genes = pd.read_csv(
-        genes_path, header=None, index_col=0, names=[name_column], sep='\t'
+        genes_path,
+        header=None,
+        index_col=0,
+        names=[name_column],
+        sep='\t',
+        dtype={0: str}
     )
-    df_genes.index = df_genes.index.astype(
-        str
-    )  # To prevent logging from anndata
     mtx = scipy.io.mmread(matrix_path)
     adata = collapse_anndata(
         anndata.AnnData(X=mtx.tocsr(), obs=df_barcodes, var=df_genes)

setup.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 0.29.1
+current_version = 0.29.2
 commit = True
 tag = True
 

setup.py

@@ -10,7 +10,7 @@ def read(path):
 
 setup(
     name='kb_python',
-    version='0.29.1',
+    version='0.29.2',
     url='https://github.com/pachterlab/kb_python',
     author='Kyung Hoi (Joseph) Min',
     author_email='[email protected]',