PyNCBI Package Reference
========================

Every public symbol is documented once, under the top-level ``PyNCBI`` package. The module
sections below carry each module's overview so you can see where a piece lives.

Top-Level Package (`PyNCBI`)
----------------------------

.. automodule:: PyNCBI
   :members:
   :undoc-members:
   :show-inheritance:
   :exclude-members: HttpClient, HttpClientConfig, CompressedPickleCache

Core Subpackage (`PyNCBI.core`)
-------------------------------

.. automodule:: PyNCBI.core
   :no-index:

Domains Subpackage (`PyNCBI.domains`)
-------------------------------------

.. automodule:: PyNCBI.domains
   :no-index:

GEO Objects Subpackage (`PyNCBI.geo`)
-------------------------------------

.. automodule:: PyNCBI.geo
   :no-index:

I/O Subpackage (`PyNCBI.io`)
----------------------------

.. automodule:: PyNCBI.io
   :no-index:

.. automodule:: PyNCBI.io.urls
   :no-index:

.. automodule:: PyNCBI.io.responses
   :no-index:

.. automodule:: PyNCBI.io.telemetry
   :no-index:

Metadata Subpackage (`PyNCBI.metadata`)
---------------------------------------

.. automodule:: PyNCBI.metadata
   :no-index:

.. automodule:: PyNCBI.metadata.vocabulary
   :members:
   :no-index:

Parsing Subpackage (`PyNCBI.parsing`)
-------------------------------------

.. automodule:: PyNCBI.parsing
   :no-index:

Domain Modules
--------------

.. automodule:: PyNCBI.domains.geo
   :no-index:

.. automodule:: PyNCBI.domains.geo.urls
   :no-index:

.. automodule:: PyNCBI.domains.geo.transfer
   :no-index:

.. automodule:: PyNCBI.domains.geo.resolve
   :no-index:

.. automodule:: PyNCBI.domains.geo.planning
   :no-index:

.. automodule:: PyNCBI.domains.geo.samples
   :no-index:

.. automodule:: PyNCBI.domains.geo.inspection
   :no-index:

.. automodule:: PyNCBI.domains.geo.tables
   :no-index:

.. automodule:: PyNCBI.domains.geo.downloads
   :no-index:

.. automodule:: PyNCBI.domains.geo.preview
   :no-index:

.. automodule:: PyNCBI.domains.annotation
   :no-index:

.. automodule:: PyNCBI.domains.entrez
   :no-index:

.. automodule:: PyNCBI.domains.literature
   :no-index:

.. automodule:: PyNCBI.domains.sequencing
   :no-index:

.. automodule:: PyNCBI.domains.genomes
   :no-index:

.. automodule:: PyNCBI.domains.variants
   :no-index:

.. automodule:: PyNCBI.domains.bundle
   :no-index:

.. automodule:: PyNCBI.domains.citations
   :no-index:

Sessions (`PyNCBI.session`)
---------------------------

.. automodule:: PyNCBI.session
   :no-index:

MCP Server Modules (`PyNCBI.mcp`)
---------------------------------

.. automodule:: PyNCBI.mcp.server
   :no-index:

.. automodule:: PyNCBI.mcp.tools
   :no-index:

.. automodule:: PyNCBI.mcp.handlers
   :no-index:

.. automodule:: PyNCBI.mcp.resources
   :no-index:

.. automodule:: PyNCBI.mcp.prompts
   :no-index:

.. automodule:: PyNCBI.mcp.protocol
   :no-index:

.. automodule:: PyNCBI.mcp.transport
   :no-index:

.. automodule:: PyNCBI.mcp.validation
   :no-index:

CLI Modules (`PyNCBI.cli`)
--------------------------

.. automodule:: PyNCBI.cli.main
   :no-index:

.. automodule:: PyNCBI.cli.parser
   :no-index:

.. automodule:: PyNCBI.cli.console
   :no-index:

.. automodule:: PyNCBI.cli.cmd_geo
   :no-index:

.. automodule:: PyNCBI.cli.cmd_search
   :no-index:

.. automodule:: PyNCBI.cli.cmd_sequence
   :no-index:

.. automodule:: PyNCBI.cli.cmd_study
   :no-index:

.. automodule:: PyNCBI.cli.cmd_admin
   :no-index: