Merge pull request #21 from KrishnaswamyLab/dev

scprep v0.9.0

Author: scottgigante

.travis.yml

@@ -1,20 +1,41 @@
   language: python
   python:
-    - "2.7"
     - "3.5"
     - "3.6"
+    - "3.7-dev"
 
   sudo: required
 
-  cache: packages
+  dist: xenial
+
+  addons:
+    apt:
+      packages:
+        - libhdf5-dev
+        - ffmpeg
+
+  cache: 
+    - pip
+    - apt
 
   install:
     - cd python; python setup.py install; cd ..
 
   script:
     - cd python; pip install -U .[test,doc]
-    - python setup.py test
+    - travis_wait 30 python setup.py test
     - cd doc; make html; cd ../..
 
+  deploy:
+    provider: pypi
+    user: scottgigante
+    password: ${PYPI_PASSWORD}
+    distributions: sdist bdist_wheel
+    skip_existing: true
+    skip_cleanup: true
+    on:
+      tags: true
+      branch: master
+
   after_success:
     - cd python; coveralls; cd ..

python/doc/source/conf.py

@@ -52,16 +52,16 @@
 # General information about the project.
 project = 'scprep'
 copyright = '2018 Krishnaswamy Lab, Yale University'
-author = 'Jay Stanley and Scott Gigante, Krishnaswamy Lab, Yale University'
+author = 'Scott Gigante, Jay Stanley, Daniel Burkhardt'
 
 # The version info for the project you're documenting, acts as replacement for
 # |version| and |release|, also used in various other places throughout the
 # built documents.
 #
 # The short X.Y version.
-version = '0.1.0'
+version = '0.7.2'
 # The full version, including alpha/beta/rc tags.
-release = '0.1.0'
+release = '0.7.2'
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.
@@ -132,7 +132,7 @@
 #  author, documentclass [howto, manual, or own class]).
 latex_documents = [
     (master_doc, 'scprep.tex', 'scprep Documentation',
-     'Jay Stanley and Scott Gigante, Krishnaswamy Lab, Yale University', 'manual'),
+     'Scott Gigante, Jay Stanley, Daniel Burkhardt', 'manual'),
 ]
 
 

python/requirements.txt

@@ -1,5 +1,5 @@
 numpy>=1.10.0
-scipy>=0.18.0
+scipy>=0.18.0,!=1.2.0.*
 scikit-learn>=0.19.1
 future
 pandas>=0.19.0

python/scprep/hdf5.py

@@ -154,7 +154,7 @@ def get_values(dataset):
         Data read from HDF5 dataset
     """
     if _is_h5py(dataset, allow_file=False, allow_group=False):
-        return dataset.value
+        return dataset[()]
     elif _is_tables(dataset, allow_file=False, allow_group=False):
         return dataset.read()
     else: