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mkdocs.yml
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mkdocs.yml
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# Project
site_name: Synapse Python/Command Line Client Documentation
site_author: Bryan Fauble
site_description: >-
A Python client for Sage Bionetworks' Synapse, a collaborative, open-source research
platform that allows teams to share data, track analyses, and collaborate. The Python
client can be used as a library for development of software that communicates with
Synapse or as a command-line utility.
site_dir: docs_site
# Repository
repo_url: https://github.com/Sage-Bionetworks/synapsePythonClient
repo_name: synapsePythonClient
# Navigation
nav:
- Home:
- Home: index.md
- Setup:
- Installation: tutorials/installation.md
- Authentication: tutorials/authentication.md
- Configuration: tutorials/configuration.md
# In each docs folder there is a README containing a guideline to follow when writing documentation.
- Tutorials:
- Home: tutorials/home.md
- Working with the Python client:
- Python client: tutorials/python_client.md
- Project: tutorials/python/project.md
- Folder: tutorials/python/folder.md
- File: tutorials/python/file.md
- Annotation: tutorials/python/annotation.md
# - Versions: tutorials/python/versions.md
# - Activity/Provenance: tutorials/python/activity.md
# - File View: tutorials/python/file_view.md
# - Table: tutorials/python/table.md
# - Using a Table: tutorials/python/table_crud.md
# - Dataset: tutorials/python/dataset.md
# - Sharing Settings: tutorials/python/sharing_settings.md
# - Wiki: tutorials/python/wiki.md
# - Team: tutorials/python/team.md
- Download data in bulk: tutorials/python/download_data_in_bulk.md
# - Upload data in bulk: tutorials/python/upload_data_in_bulk.md
# - Move Files and Folders: tutorials/python/move_files_and_folders.md
# - Migrate data to other storage locations: tutorials/python/migrate_data_to_other_storage_locations.md
- Working with the Command Line Client: tutorials/command_line_client.md
- Working with file versioning: tutorials/file_versioning.md
- Working with tables: tutorials/tables.md
- Synapseclient with R through reticulate: tutorials/reticulate.md
- How-To Guides:
- Home: guides/home.md
- Using Entity Views: guides/views.md
- Data Storage: guides/data_storage.md
- Access the REST API: guides/accessing_the_rest_api.md
- Expermental Features:
- Validating Annotations: guides/validate_annotations.md
- API Reference:
- Client: reference/client.md
- Synapse Utils: reference/synapse_utils.md
- Entity: reference/entity.md
- Project: reference/project.md
- Folder: reference/folder.md
- File: reference/file.md
- Annotations: reference/annotations.md
- Tables: reference/tables.md
- Table Schema: reference/table_schema.md
- Entity View Schema: reference/view_schema.md
- Activity/Provenance: reference/activity.md
- Teams: reference/teams.md
- Wiki: reference/wiki.md
- Evaluation: reference/evaluation.md
- Link: reference/link.md
- DockerRepository: reference/docker_repository.md
- JSON Schema: reference/json_schema.md
- Exceptions: reference/exceptions.md
- Permissions: reference/permissions.md
- Core: reference/core.md
- REST Apis: reference/rest_apis.md
- Experimental:
- Object-Orientated Models: reference/oop/models.md
- Async Object-Orientated Models: reference/oop/models_async.md
- Further Reading:
- Home: explanations/home.md
- Domain Models of Synapse: explanations/domain_models_of_synapse.md
- Access Control: explanations/access_control.md
- Properties vs Annotations: explanations/properties_vs_annotations.md
- Manifest TSV: explanations/manifest_tsv.md
- Benchmarking: explanations/benchmarking.md
- Structuring Your Project: explanations/structuring_your_project.md
- News:
- news.md
# Theme configuration
theme:
name: material
palette:
- media: "(prefers-color-scheme: light)"
scheme: default
primary: white
toggle:
icon: material/toggle-switch-off-outline
name: Switch to dark mode
- media: "(prefers-color-scheme: dark)"
scheme: slate
primary: black
toggle:
icon: material/toggle-switch
name: Switch to light mode
icon:
admonition:
note: octicons/tag-16
info: octicons/info-16
logo: assets/synapse_logo.png
favicon: assets/favicon.png
features:
- content.code.copy
- navigation.footer
- navigation.sections
- search.highlight
- search.share
- search.suggest
- toc.follow
- navigation.tabs
- navigation.tabs.sticky
extra_css:
- css/custom.css
plugins:
- search
- mkdocstrings:
default_handler: python
handlers:
python:
options:
members_order: source
show_if_no_docstring: False
show_root_heading: True
show_category_heading: True
docstring_style: google
docstring_section_style: spacy
filters:
- "!^_"
- autorefs
- termynal:
prompt_literal_start:
- "$"
- ">"
# Allows external links to open in a new tab
- open-in-new-tab
extra:
social:
- icon: fontawesome/brands/github
link: https://github.com/Sage-Bionetworks/synapsePythonClient
- icon: fontawesome/brands/docker
link: https://github.com/Sage-Bionetworks/synapsePythonClient/pkgs/container/synapsepythonclient
- icon: fontawesome/brands/python
link: https://pypi.org/project/synapseclient/
markdown_extensions:
- admonition
- pymdownx.details
- pymdownx.superfences:
custom_fences:
- name: mermaid
class: mermaid
format: !!python/name:pymdownx.superfences.fence_code_format
# Lets us include source code from any files
- markdown_include.include:
- toc:
permalink: true