Merge pull request #110 from briney/development

Development

.readthedocs.yaml

@@ -0,0 +1,30 @@
+# .readthedocs.yaml
+# Read the Docs configuration file
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+# Required
+version: 2
+
+# Set the version of Python and other tools you might need
+build:
+  os: ubuntu-20.04
+  tools:
+    python: "3.9"
+    # You can also specify other tool versions:
+    # nodejs: "16"
+    # rust: "1.55"
+    # golang: "1.17"
+
+# Build documentation in the docs/ directory with Sphinx
+sphinx:
+   configuration: docs/source/conf.py
+
+# If using Sphinx, optionally build your docs in additional formats such as PDF
+# formats:
+#    - pdf
+
+# Optionally declare the Python requirements required to build your docs
+python:
+   install:
+   - requirements: docs/doc_requirements.txt
+   - requirements: requirements.txt

abstar/version.py

@@ -2,4 +2,4 @@
 # 1) we don't load dependencies by storing it in __init__.py
 # 2) we can import it in setup.py for the same reason
 # 3) we can import it into your module module
-__version__ = '0.5.8'
+__version__ = '0.5.9'

docs/source/conf.py

@@ -26,10 +26,10 @@
 
 
 if os.environ.get('READTHEDOCS', None) == 'True':
-    class Mock(MagicMock):
-        @classmethod
-        def __getattr__(cls, name):
-                return Mock()
+    # class Mock(MagicMock):
+    #     @classmethod
+    #     def __getattr__(cls, name):
+    #             return Mock()
 
     MOCK_MODULES = ['pygtk', 'gtk', 'gobject', 'argparse', 'numpy', 'nwalign', 'pandas', 'abutils', 'dask', 'dask.dataframe',
                     'abutils.utils', 'abutils.core', 'abutils.core.sequence', 'abutils.utils.log', 'abutils.utils.alignment',
@@ -38,12 +38,12 @@ def __getattr__(cls, name):
                     'BaseSpacePy.model', 'BaseSpacePy.api.BaseSpaceAPI', 'BaseSpacePy.model.QueryParameters',
                     'Bio', 'Bio.Align', 'Bio.Alphabet', 'Bio.SeqIO', 'Bio.Seq', 'Bio.SeqRecord',
                     'Bio.Blast', 'Bio.Blast.Applications']
-    sys.modules.update((mod_name, Mock()) for mod_name in MOCK_MODULES)
+    sys.modules.update((mod_name, MagicMock()) for mod_name in MOCK_MODULES)
 
 # If extensions (or modules to document with autodoc) are in another directory,
 # add these directories to sys.path here. If the directory is relative to the
 # documentation root, use os.path.abspath to make it absolute, like shown here.
-#sys.path.insert(0, os.path.abspath('.'))
+# sys.path.insert(0, os.path.abspath('.'))
 
 # -- General configuration ------------------------------------------------
 

requirements.txt

@@ -1,11 +1,11 @@
-abutils>=0.2.9
-biopython==1.78
+abutils >= 0.2.9
+biopython == 1.78
 celery
 dask[complete]
-numpy>=1.16.5
+numpy >= 1.16.5
 nwalign3
 pandas
 pyarrow
 pymongo
 pytest
-scikit-bio==0.5.6
+scikit-bio == 0.5.6