Merge branch 'master' into backed-sparse

.gitignore

@@ -1,116 +1,23 @@
-*~
-
-# tests
-*.pytest_cache/*
-
-# anndata
-docs/_build
-docs/anndata.*
-
-# Mac
+# Temp files
 .DS_Store
+*~
 
-# Byte-compiled / optimized / DLL files
+# Compiled files
 __pycache__/
-*.py[cod]
-*$py.class
-
-# C extensions
-*.so
 
 # Distribution / packaging
-.Python
-env/
-build/
-develop-eggs/
-dist/
-downloads/
-eggs/
-.eggs/
-lib/
-lib64/
-parts/
-sdist/
-var/
-wheels/
-*.egg-info/
-.installed.cfg
-*.egg
-
-# PyInstaller
-#  Usually these files are written by a python script from a template
-#  before PyInstaller builds the exe, so as to inject date/other infos into it.
-*.manifest
-*.spec
-
-# Installer logs
-pip-log.txt
-pip-delete-this-directory.txt
-
-# Unit test / coverage reports
-htmlcov/
-.tox/
-.coverage
-.coverage.*
-.cache
-nosetests.xml
-coverage.xml
-*.cover
-.hypothesis/
-
-# Translations
-*.mo
-*.pot
-
-# Django stuff:
-*.log
-local_settings.py
-
-# Flask stuff:
-instance/
-.webassets-cache
-
-# Scrapy stuff:
-.scrapy
-
-# Sphinx documentation
-docs/_build/
-
-# PyBuilder
-target/
-
-# Jupyter Notebook
-.ipynb_checkpoints
-
-# pyenv
-.python-version
-
-# celery beat schedule file
-celerybeat-schedule
-
-# SageMath parsed files
-*.sage.py
-
-# dotenv
-.env
-
-# virtualenv
-.venv
-venv/
-ENV/
-
-# Spyder project settings
-.spyderproject
-.spyproject
+/build/
+/dist/
+/*.egg-info/
 
-# Rope project settings
-.ropeproject
+# Tests and coverage
+/.pytest_cache/
+/.cache/
 
-# PyCharm project settings
-.idea/
+# docs
+/docs/anndata.*
+/docs/_build/
 
-# mkdocs documentation
-/site
+# IDEs
+/.idea/
 
-# mypy
-.mypy_cache/

anndata/core/anndata.py

@@ -1,6 +1,5 @@
 """Main class and helper functions.
 """
-import os
 from enum import Enum
 from collections import OrderedDict
 from collections.abc import MutableMapping
@@ -1152,7 +1151,7 @@ def filename(self, filename: Optional[PathLike]):
                     # write the content of self to the old file
                     # and close the file
                     self.write()
-                    os.rename(self.filename, filename)
+                    self.filename.rename(filename)
                 else:
                     # do nothing
                     return

anndata/tests/test_h5py.py

@@ -1,22 +1,20 @@
 # Had to rename the test module to h5py_ so that it wouldn't conflict with the
 # h5py import upon testing.
 
-import os
-from tempfile import mkstemp
-
 import numpy as np
 import scipy.sparse as ss
 
 from anndata import h5py
 
 
-def test_create_and_read_dataset():
-    h5_path = mkstemp(suffix=".h5")[1]
-    sparse_matrix = ss.csr_matrix([[0, 1, 0],
-                                   [0, 0, 1],
-                                   [0, 0, 0],
-                                   [1, 1, 0]],
-                                  dtype=np.float64)
+def test_create_and_read_dataset(tmp_path):
+    h5_path = tmp_path / 'test.h5'
+    sparse_matrix = ss.csr_matrix([
+        [0, 1, 0],
+        [0, 0, 1],
+        [0, 0, 0],
+        [1, 1, 0],
+    ], dtype=np.float64)
     with h5py.File(h5_path) as h5f:
         h5f.create_dataset('sparse/matrix', data=sparse_matrix)
     with h5py.File(h5_path) as h5f:
@@ -27,43 +25,39 @@ def test_create_and_read_dataset():
         assert (h5f['sparse']['matrix'][:-2] != sparse_matrix[:-2]).size == 0
         assert (h5f['sparse']['matrix'].value != sparse_matrix).size == 0
 
-    os.remove(h5_path)
-
 
-def test_create_dataset_from_dataset():
-    from_h5_path = mkstemp(suffix=".h5")[1]
-    to_h5_path = mkstemp(suffix=".h5")[1]
-    sparse_matrix = ss.csr_matrix([[0, 1, 0],
-                                   [0, 0, 1],
-                                   [0, 0, 0],
-                                   [1, 1, 0]],
-                                  dtype=np.float64)
+def test_create_dataset_from_dataset(tmp_path):
+    from_h5_path = tmp_path / 'from.h5'
+    to_h5_path = tmp_path / 'to.h5'
+    sparse_matrix = ss.csr_matrix([
+        [0, 1, 0],
+        [0, 0, 1],
+        [0, 0, 0],
+        [1, 1, 0],
+    ], dtype=np.float64)
     with h5py.File(from_h5_path) as from_h5f:
         from_dset = from_h5f.create_dataset('sparse/matrix', data=sparse_matrix)
 
         with h5py.File(to_h5_path) as to_h5f:
             to_h5f.create_dataset('sparse/matrix', data=from_dset)
             assert (to_h5f['sparse/matrix'].value != sparse_matrix).size == 0
 
-    os.remove(from_h5_path)
-    os.remove(to_h5_path)
 
-
-def test_dataset_append():
-    h5_path = mkstemp(suffix=".h5")[1]
-    sparse_matrix = ss.csr_matrix([[0, 1, 0],
-                                   [0, 0, 1],
-                                   [0, 0, 0],
-                                   [1, 1, 0]],
-                                  dtype=np.float64)
-    to_append = ss.csr_matrix([[0, 1, 1],
-                               [1, 0, 0]],
-                              dtype=np.float64)
+def test_dataset_append(tmp_path):
+    h5_path = tmp_path / 'test.h5'
+    sparse_matrix = ss.csr_matrix([
+        [0, 1, 0],
+        [0, 0, 1],
+        [0, 0, 0],
+        [1, 1, 0],
+    ], dtype=np.float64)
+    to_append = ss.csr_matrix([
+        [0, 1, 1],
+        [1, 0, 0],
+    ], dtype=np.float64)
     appended_matrix = ss.vstack((sparse_matrix, to_append))
 
     with h5py.File(h5_path) as h5f:
         h5f.create_dataset('matrix', data=sparse_matrix, chunks=(100000,))
         h5f['matrix'].append(to_append)
         assert (h5f['matrix'].value != appended_matrix).size == 0
-
-    os.remove(h5_path)