Merge pull request #1 from ttngu207/main

`element-session` design and packaging (to be used in the workflows)

Author: shenshan

.gitignore

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+# Byte-compiled / optimized / DLL 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
+.idea/
+
+# 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
+scratchpaper.*
+
+# 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
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+
+# datajoint
+dj_local_conf.json
+dj_local_conf_old.json
+
+# emacs
+**/*~
+**/#*#
+**/.#*

Background.md

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+# Session Element
+
+## Description of modality, user population 
+
+Session information is part of most data modalities. 
+This is a minimal schema with a few number of tables describing the experiment session (date and time, experimenter, subject reference, experiment rig, aims, and notes), 
+the project in which the sessions may belong to (project description, DOI, keywords, etc.), data directory for each session. 
+
+## Precursor projects and interviews
+
+All DataJoint pipelines have some form of a session schema or tables. 
+The session table is typically in the upstream part of the pipeline, referencing the subject and serves as a common node for other modalities to connect to and expand downstream (e.g. ephys, imaging, video tracking, behavioral events, optogenetic perturbation, etc.). 
+
+## Development
+We developed the Session Element under https://github.com/datajoint/element-session. This schema is validated as part of complete workflows in the specific modalities.

CONTRIBUTING.md

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+# Contribution Guidelines
+
+This project follows the [DataJoint Contribution Guidelines](https://docs.datajoint.io/python/community/02-Contribute.html). Please reference the link for more full details.

LICENSE

@@ -1,6 +1,6 @@
 MIT License
 
-Copyright (c) 2021 DataJoint
+Copyright (c) 2021 DataJoint NEURO
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

README.md

@@ -1,2 +1,20 @@
-# element-session
-DataJoint Element for Session - NIH U24
+# DataJoint Element - Session
+
+DataJoint element for session management - U24 effort
+
++ `element-session` features a DataJoint pipeline design for session management. 
+
++ `element-session` is not a complete workflow by itself, but rather a modular design of tables and dependencies. 
+
++ `element-session` can be flexibly attached to any DataJoint workflow.
+
+See [Background](Background.md) for the background information and development timeline.
+
+## Element usage
+
++ See the [workflow-calcium-imaging](https://github.com/datajoint/workflow-calcium-imaging)
+ and [workflow-array-ephys](https://github.com/datajoint/workflow-array-ephys) repositories for example usages of `element-session`.
+
++ See the [datajoint-elements](https://github.com/datajoint/datajoint-elements) repository for a detailed description of the DataJoint elements and workflows.
+
+

element_session/__init__.py

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+import datajoint as dj
+import importlib
+import inspect
+
+schema = dj.schema()
+
+
+def activate(schema_name, create_schema=True, create_tables=True, linking_module=None):
+    """
+    activate(schema_name, create_schema=True, create_tables=True, linking_module=None)
+        :param schema_name: schema name on the database server to activate the `session` element
+        :param create_schema: when True (default), create schema in the database if it does not yet exist.
+        :param create_tables: when True (default), create tables in the database if they do not yet exist.
+        :param linking_module: a module name or a module containing the
+         required dependencies to activate the `session` element:
+             Upstream tables:
+                + Subject: the subject for which a particular experimental session is associated with
+                + Project: the project for which experimental sessions are associated with
+    """
+    if isinstance(linking_module, str):
+        linking_module = importlib.import_module(linking_module)
+    assert inspect.ismodule(linking_module),\
+        "The argument 'dependency' must be a module's name or a module"
+
+    schema.activate(schema_name, create_schema=create_schema,
+                    create_tables=create_tables, add_objects=linking_module.__dict__)
+
+
+@schema
+class Session(dj.Manual):
+    definition = """
+    -> Subject
+    session_datetime: datetime(3)
+    """
+
+
+@schema
+class SessionDirectory(dj.Manual):
+    definition = """
+    -> Session
+    ---
+    session_dir: varchar(256)       # Path to the data directory for a particular session
+    """
+
+
+@schema
+class ProjectSession(dj.Manual):
+    definition = """
+    -> Project
+    -> Session
+    """

element_session/session.py

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+datajoint>=0.13.dev7

requirements.txt

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+from setuptools import setup, find_packages
+from os import path
+
+here = path.abspath(path.dirname(__file__))
+
+long_description = """"
+DataJoint Element for Session Management
+"""
+
+with open(path.join(here, 'requirements.txt')) as f:
+    requirements = f.read().splitlines()
+
+setup(
+    name='element-session',
+    version='0.0.1',
+    description="DataJoint Element for Session Management",
+    long_description=long_description,
+    author='DataJoint NEURO',
+    author_email='[email protected]',
+    license='MIT',
+    url='https://github.com/datajoint/element-session',
+    keywords='neuroscience session-management datajoint',
+    packages=find_packages(exclude=['contrib', 'docs', 'tests*']),
+    install_requires=requirements,
+)