V0.65 Update development workflow, method code packaging, and general…

… housekeeping

.gitignore

@@ -1,17 +1,111 @@
-# IntelliJ IDEA editor files
-.idea
-*.iml
+.idea/
+.vscode/
+.env/
+test-output/
+LOGTOX
 
-# Environments
-/venv/
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
 
-# Unit tests / reports
-.tox/
-rcsb/db/tests/test-output/*
+# C extensions
+*.so
 
 # Distribution / packaging
-*.egg-info/
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
 .eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# 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/
+.pytest_cache/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+
+# 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
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+.vscode/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
 
-# Byte-compiled
-*.pyc
+# mypy
+.mypy_cache/

.isort.cfg

@@ -0,0 +1,8 @@
+[settings]
+multi_line_output=3
+include_trailing_comma=True
+force_grid_wrap=0
+line_length=180
+force_single_line=true
+project=rcsb.utils.io
+

HISTORY.txt

@@ -149,4 +149,5 @@
                     and removed _rcsb_entry_info.nonpolymer_ligand_entity_count
  20-May-2019  V0.63 Category rcsb_prot_sec_struct_info added to core_entity_instance and prune primary secondary structure
                     categories from this collection.
- 21-May-2019  V0.64 Handle odd ordering of records in struct_ref_seq_dif
+ 21-May-2019  V0.64 Handle odd ordering of records in struct_ref_seq_dif
+ 29-Jun-2019  V0.65 Update development workflow, method code packaging,  and general housekeeping