Shift to workflow-session

.gitignore

@@ -1,119 +1,74 @@
-# vscode
-.vscode
-
-# User data
-.DS_Store
-
 # Byte-compiled / optimized / DLL files
 __pycache__/
 *.py[cod]
 *$py.class
 
-# C extensions
-*.so
-
-# Distribution / packaging
+# Distribution, packaging, PyInstaller
 .Python
 env/
 build/
-develop-eggs/
-dist/
+*egg*/
+*dist/
 downloads/
-eggs/
-.eggs/
-lib/
-lib64/
+lib*/
 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
+pip-*.txt
 
 # Unit test / coverage reports
 htmlcov/
 .tox/
-.coverage
-.coverage.*
+*.cov*
 .cache
 nosetests.xml
 coverage.xml
-*.cover
 .hypothesis/
+.pytest_cache/
+docker-compose.y*ml
 
-# Translations
+# C extension, Translations
+# editors: vscode, emacs, Mac
+*.so
 *.mo
 *.pot
+.vscode
+**/*~
+**/#*#
+**/.#*
+.DS_Store
 
-# Django stuff:
+# Django, Flask, Scrapy, Sphinx, mkdocs
+# PyBuilder, Jupyter, SageMath, celery beat
 *.log
 local_settings.py
-
-# Flask stuff:
 instance/
 .webassets-cache
-
-# Scrapy stuff:
 .scrapy
 scratchpaper.*
-
-# Sphinx documentation
 docs/_build/
-
-# PyBuilder
+/site
 target/
-
-# Jupyter Notebook
-.ipynb_checkpoints
-
-# pyenv
-.python-version
-
-# celery beat schedule file
+.*checkpoints
 celerybeat-schedule
-
-# SageMath parsed files
 *.sage.py
 
-# dotenv
-./.env
-
-# virtualenv
-.venv
+# dotenv, virtualenv, pyenv, mypy
+.*env
 venv/
 ENV/
-
-# Spyder project settings
-.spyderproject
-.spyproject
-
-# Rope project settings
-.ropeproject
-
-# mkdocs documentation
-/site
-
-# mypy
+.python-version
 .mypy_cache/
 
-# datajoint
-dj_local_conf.json
-dj_local_conf_old.json
+# Spyder/Rope project settings
+.spy*project
+.ropeproject
 
-# emacs
-**/*~
-**/#*#
-**/.#*
-docker-compose.yml
+# datajoint, notes, nwb export
+dj_local_c*.json
+temp*
+*nwb

CHANGELOG.md

@@ -0,0 +1,24 @@
+# Changelog
+
+Observes [Semantic Versioning](https://semver.org/spec/v2.0.0.html) standard and [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) convention.
+
+
+## 0.0.0b2
+### Added
++ Integration tests
+
+### Changed
++ Name `workflow-animal` -> `workflow-session`
+
+
+## [0.0.0b1] - 2021-03-24
+### Added
++ First beta release
+
+
+## [0.0.0a1] - 2021-03-18
+### Added
++ Added notebooks
+
+[0.0.0b1]: https://github.com/datajoint/workflow-session/tree/f6d6a3353aae83ca13ff9fcc536017eb34c18f90
+[0.0.0a1]: https://github.com/datajoint/workflow-session/tree/0d3d3c970056ff4c243d17cf4f738f48268d80ad

CONTRIBUTING.md

@@ -0,0 +1,3 @@
+# Contribution Guidelines
+
+This project follows the [DataJoint Contribution Guidelines](https://docs.datajoint.org/python/community/02-Contribute.html). Please reference the link for more full details.

Dockerfile.dev

@@ -0,0 +1,28 @@
+FROM datajoint/djlab:py3.8-debian
+
+USER anaconda:anaconda
+
+COPY ./workflow-session/apt_requirements.txt /tmp/
+RUN /entrypoint.sh echo "Installed dependencies."
+
+RUN mkdir /main/element-lab \
+          /main/element-animal \
+          /main/element-session \
+          /main/workflow-session
+
+# Copy user's local fork of elements and workflow
+COPY --chown=anaconda:anaconda ./element-lab /main/element-lab
+COPY --chown=anaconda:anaconda ./element-animal /main/element-animal
+COPY --chown=anaconda:anaconda ./element-session /main/element-session
+COPY --chown=anaconda:anaconda ./workflow-session /main/workflow-session
+
+# Install packages
+RUN pip install -e /main/element-lab
+RUN pip install -e /main/element-animal
+RUN pip install -e /main/element-session
+RUN pip install -e /main/workflow-session
+RUN pip install -r /main/workflow-session/requirements_test.txt
+
+WORKDIR /main/workflow-session
+
+ENTRYPOINT ["tail", "-f", "/dev/null"]

Dockerfile.test

@@ -0,0 +1,34 @@
+FROM datajoint/djlab:py3.8-debian
+
+USER anaconda:anaconda
+
+COPY ./workflow-session/apt_requirements.txt /tmp/
+RUN /entrypoint.sh echo "Installed dependencies."
+WORKDIR /main/workflow-session
+
+# Option 1 - Install DataJoint's remote fork of the workflow and elements
+# RUN git clone https://github.com/datajoint/workflow-session.git /main/
+
+# Option 2 - Install user's remote fork of element and workflow
+#            or an unreleased version of the element
+# RUN pip install git+https://github.com/<user>/element-lab.git
+# RUN pip install git+https://github.com/<user>/element-animal.git
+# RUN pip install git+https://github.com/<user>/element-session.git
+# RUN git clone https://github.com/<user>/workflow-session.git /main/
+
+# Option 3 - Install user's local fork of element and workflow
+RUN mkdir /main/element-lab
+COPY --chown=anaconda:anaconda ./element-lab /main/element-lab
+RUN pip install -e /main/element-lab
+RUN mkdir /main/element-animal
+COPY --chown=anaconda:anaconda ./element-animal /main/element-animal
+RUN pip install -e /main/element-animal
+RUN mkdir /main/element-session
+COPY --chown=anaconda:anaconda ./element-session /main/element-session
+RUN pip install -e /main/element-session
+COPY --chown=anaconda:anaconda ./workflow-session /main/workflow-session
+# RUN rm -f /main/workflow-session/dj_local_conf.json
+
+# Install the workflow
+RUN pip install -e /main/workflow-session
+RUN pip install -r /main/workflow-session/requirements_test.txt

LICENSE

@@ -1,6 +1,6 @@
 MIT License
 
-Copyright (c) 2020 DataJoint NEURO
+Copyright (c) 2022 DataJoint
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal