unnest docs, make titles match module names in api docs

Aharoni-Lab · Jun 22, 2024 · 5291343 · 5291343
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diff --git a/README.md b/README.md
@@ -1,6 +1,6 @@
 # miniscope-io
 
-![PyPI - Version](https://img.shields.io/pypi/v/miniscope-io)
+[![PyPI - Version](https://img.shields.io/pypi/v/miniscope-io)](https://pypi.org/project/miniscope_io/)
 [![Documentation Status](https://readthedocs.org/projects/miniscope-io/badge/?version=latest)](https://miniscope-io.readthedocs.io/en/latest/?badge=latest)
 ![PyPI - Python Version](https://img.shields.io/pypi/pyversions/miniscope-io)
 ![PyPI - Status](https://img.shields.io/pypi/status/miniscope-io)

diff --git a/docs/api/data.md b/docs/api/data.md
@@ -1,4 +1,4 @@
-# Data
+# data
 
 ```{eval-rst}
 .. automodule:: miniscope_io.data

diff --git a/docs/api/devices.md b/docs/api/devices.md
@@ -1,4 +1,4 @@
-# Devices
+# devices
 
 Interfaces to external devices like miniscopes and DAQs
 

diff --git a/docs/api/formats/index.md b/docs/api/formats/index.md
@@ -1,4 +1,4 @@
-# Formats
+# formats
 
 ```{eval-rst}
 .. automodule:: miniscope_io.formats

diff --git a/docs/api/formats/sdcard.md b/docs/api/formats/sdcard.md
@@ -1,4 +1,4 @@
-# SDCard
+# sdcard
 
 ```{eval-rst}
 .. automodule:: miniscope_io.formats.sdcard

diff --git a/docs/api/formats/stream.md b/docs/api/formats/stream.md
@@ -1,4 +1,4 @@
-# Stream
+# stream
 
 ```{eval-rst}
 .. automodule:: miniscope_io.formats.stream

diff --git a/docs/api/index.md b/docs/api/index.md
diff --git a/docs/api/logging.md b/docs/api/logging.md
@@ -1,4 +1,4 @@
-# Logging
+# logging
 
 ```{eval-rst}
 .. automodule:: miniscope_io.logging

diff --git a/docs/api/models/buffer.md b/docs/api/models/buffer.md
@@ -1,4 +1,4 @@
-# Buffer
+# buffer
 
 ```{eval-rst}
 .. automodule:: miniscope_io.models.buffer

diff --git a/docs/api/models/config.md b/docs/api/models/config.md
@@ -1,4 +1,4 @@
-# Config
+# config
 
 ```{eval-rst}
 .. automodule:: miniscope_io.models.config

diff --git a/docs/api/models/index.md b/docs/api/models/index.md
@@ -1,4 +1,4 @@
-# Models
+# models
 
 Pydantic models used throughout `miniscope_io`.
 

diff --git a/docs/api/models/mixins.md b/docs/api/models/mixins.md
@@ -1,4 +1,4 @@
-# Mixins
+# mixins
 
 ```{eval-rst}
 .. automodule:: miniscope_io.models.mixins

diff --git a/docs/api/models/models.md b/docs/api/models/models.md
@@ -1,4 +1,4 @@
-# Models
+# models
 
 ```{eval-rst}
 .. automodule:: miniscope_io.models.models

diff --git a/docs/api/models/sdcard.md b/docs/api/models/sdcard.md
@@ -1,4 +1,4 @@
-# SDCard
+# sdCard
 
 ```{eval-rst}
 .. automodule:: miniscope_io.models.sdcard

diff --git a/docs/api/models/stream.md b/docs/api/models/stream.md
@@ -1,4 +1,4 @@
-# Stream
+# stream
 
 ```{eval-rst}
 .. automodule:: miniscope_io.models.stream

diff --git a/docs/api/plots/headers.md b/docs/api/plots/headers.md
@@ -1,4 +1,4 @@
-# Headers
+# headers
 
 ```{eval-rst}
 .. automodule:: miniscope_io.plots.headers

diff --git a/docs/api/plots/index.md b/docs/api/plots/index.md
@@ -1,4 +1,4 @@
-# Plots
+# plots
 
 ```{toctree}
 :caption: Plots

diff --git a/docs/api/stream_daq.md b/docs/api/stream_daq.md
@@ -1,4 +1,4 @@
-# Stream DAQ
+# stream_daq
 This module is a data acquisition module that captures video streams from Miniscopes based on the `Miniscope-SAMD-Framework` firmware. The firmware repository will be published in future updates but is currently under development and private.
 
 ## Command

diff --git a/docs/api/utils.md b/docs/api/utils.md
@@ -1,4 +1,4 @@
-# Utils
+# utils
 
 ```{eval-rst}
 .. automodule:: miniscope_io.utils

diff --git a/docs/api/vendor/index.md b/docs/api/vendor/index.md
@@ -1,4 +1,4 @@
-# Vendor
+# vendor
 
 Modules that incorporate some proprietary/nonfree component and are vendored in
 

diff --git a/docs/api/vendor/opalkelly.md b/docs/api/vendor/opalkelly.md
@@ -1,4 +1,4 @@
-# OpalKelly FrontPanel
+# opalkelly
 
 (your docs on what this is for and how it works here!!!)
 
diff --git a/docs/guide/index.md b/docs/guide/index.md
diff --git a/docs/guide/usage.md b/docs/guide/usage.md
@@ -1,2 +1,5 @@
-```{include} ../api/stream_daq.md
-```
+# Usage
+
+## Stream Daq
+
+(see [stream_daq](../api/stream_daq.md))
diff --git a/docs/index.md b/docs/index.md
@@ -1,27 +1,36 @@
-.. miniscope-io documentation master file, created by
-   sphinx-quickstart on Tue Jun 27 10:52:50 2023.
-   You can adapt this file completely to your liking, but it should at least
-   contain the root `toctree` directive.
-
 # miniscope-io
 
 ```{toctree}
 :caption: Guide:
+:maxdepth: 2
 
-guide/index
+guide/installation
+guide/usage
 ```
 
 ```{toctree}
 :maxdepth: 2
-:caption: Contents:
-
-api/index
+:caption: API:
+
+api/data
+api/devices
+api/formats/index
+api/io
+api/logging
+api/models/index
+api/exceptions
+api/plots/index
+api/utils
+api/stream_daq
+api/vendor/index
 ```
 
 ```{toctree}
 :caption: Meta:
 
-meta/index
+meta/changelog
+meta/contributing
+meta/todo
 ```
 
 

diff --git a/docs/meta/index.md b/docs/meta/index.md