Add aeon_api

.gitmodules

@@ -1,7 +1,11 @@
 [submodule "aeon_mecha"]
 	path = aeon_mecha
 	url = https://github.com/SainsburyWellcomeCentre/aeon_mecha
-	branch = data-preview
+	branch = sfn2024
+[submodule "aeon_api"]
+	path = aeon_api
+	url = https://github.com/SainsburyWellcomeCentre/aeon_api.git
+	branch = main
 [submodule "aeon_experiments"]
 	path = aeon_experiments
 	url = https://github.com/SainsburyWellcomeCentre/aeon_experiments

Makefile

@@ -14,7 +14,7 @@ help:
 
 $(SOURCEDIR)/reference/api.rst:
 	@echo "Generating API documentation..."
-	@python make_mecha_doctree.py
+	@python make_api_doctree.py
 	@python make_acquisition_doctree.py
 
 copy-examples:

make.bat

@@ -14,7 +14,7 @@ if "%1" == "" goto help
 
 if not "%1" == "clean" (
 	@echo Building API docs...
-	python make_mecha_doctree.py
+	python make_api_doctree.py
 	python make_acquisition_doctree.py
 
 	@echo Copying example notebooks into 'src'...

make_mecha_doctree.py → make_api_doctree.py

@@ -1,20 +1,16 @@
 import os
 from pathlib import Path
 
-
 # modules to ignore in the api doc
-ignore_modules = [
-    "aeon.dj_pipeline",
-    "aeon.qc.video",
-]
+ignore_modules = []
 
 
-def make_mecha_doctree():
+def make_api_doctree():
     """
     Create a doctree of all modules in aeon_mecha/aeon.
     """
     doctree = ""
-    api_path = Path("aeon_mecha") / "aeon"
+    api_path = Path("aeon_api") / "swc" / "aeon"
     for path in sorted(api_path.rglob("*.py")):
         if path.name.startswith("_"):
             continue
@@ -36,4 +32,4 @@ def make_mecha_doctree():
 
 
 if __name__ == "__main__":
-    make_mecha_doctree()
+    make_api_doctree()

readme.md

@@ -28,12 +28,20 @@ Below are the required sets of credentials for Aeon members:
 To be granted these credentials, please send a single email to [all contact parties](mailto:[email protected],[email protected],[email protected],[email protected],[email protected]?subject=Request%20for%20Aeon%20credentials) requesting this access.
 
 ## Repositories
+
+### [aeon_api](https://github.com/SainsburyWellcomeCentre/aeon_api)
+
+![aeon_api_env_build_and_tests](https://github.com/SainsburyWellcomeCentre/aeon_api/actions/workflows/build_env_run_tests.yml/badge.svg?branch=main)
+[![aeon_api_tests_code_coverage](https://codecov.io/gh/SainsburyWellcomeCentre/aeon_api/branch/main/graph/badge.svg?token=973EC1CG03)](https://codecov.io/gh/SainsburyWellcomeCentre/aeon_api)
+
+Aeon's low-level library for interfacing with acquired data. Contains Python modules for raw data file io, data querying, and data processing.
+
 ### [aeon_mecha](https://github.com/SainsburyWellcomeCentre/aeon_mecha)
 
 ![aeon_mecha_env_build_and_tests](https://github.com/SainsburyWellcomeCentre/aeon_mecha/actions/workflows/build_env_run_tests.yml/badge.svg?branch=main)
 [![aeon_mecha_tests_code_coverage](https://codecov.io/gh/SainsburyWellcomeCentre/aeon_mecha/branch/main/graph/badge.svg?token=973EC1CG03)](https://codecov.io/gh/SainsburyWellcomeCentre/aeon_mecha)
 
-Aeon's main library for interfacing with acquired data. Contains Python modules for raw data file io, data querying, data processing, data qc, database ingestion, and building computational data pipelines. This is the main user repository.
+Aeon's library for the Aeon DataJoint pipeline. Contains Python modules for Aeon experiment schema definitions, data quality control, data processing, and data ingestion into a DataJoint MySQL database.
 
 ### [aeon_experiments](https://github.com/SainsburyWellcomeCentre/aeon_experiments)
 

src/_templates/api_mecha_head.rst

@@ -1,15 +1,15 @@
 ..
   This file is auto-generated.
 
-.. _target-mecha-reference:
+.. _target-aeon-api-reference:
 
-``aeon_mecha``
+``aeon_api``
 ==============
 
 .. toctree::
-   :caption: aeon_mecha API
+   :caption: aeon API
    :maxdepth: 1
 
 .. autosummary::
-   :toctree: mecha
+   :toctree: api
 

src/conf.py

@@ -19,6 +19,7 @@
     [
         os.path.abspath("."),
         os.path.abspath("../aeon_mecha/"),
+        os.path.abspath("../aeon_api/"),
         os.path.abspath("../aeon_acquisition"),
         os.path.abspath("../aeon_experiments"),
     ]
@@ -68,7 +69,7 @@ def get_current_release_tag():
     "myst_nb",
     "sphinx_design",
     "sphinx_copybutton",
-    "convertworkflow"
+    "convertworkflow",
 ]
 
 # Configure the myst parser to enable cool markdown features
@@ -146,7 +147,7 @@ def get_current_release_tag():
     "css/custom.css",
 ]
 html_js_files = [
-    'js/workflow.js', # javascript for embedded workflows
+    "js/workflow.js",  # javascript for embedded workflows
 ]
 
 # linkcheck will skip checking these URLs entirely
@@ -175,6 +176,7 @@ def get_current_release_tag():
     "aeon-experiments-github": "https://github.com/SainsburyWellcomeCentre/aeon_experiments/{{path}}",
     "aeon-lineardrive-github": "https://github.com/SainsburyWellcomeCentre/aeon_lineardrive/{{path}}",
     "aeon-feeder-github": "https://github.com/SainsburyWellcomeCentre/aeon_feeder/{{path}}",
+    "aeon-api-github": "https://github.com/SainsburyWellcomeCentre/aeon_api/{{path}}",
     "myst-parser": "https://myst-parser.readthedocs.io/en/latest/{{path}}#{{fragment}}",
     "semver": "https://semver.org/",
     "harp-tech": "https://harp-tech.org/{{path}}#{{fragment}}",

src/getting_started/index.md

@@ -41,8 +41,8 @@ As each of these different components is built using different languages, spanni
 ::::{grid} 1 2 2 2
 :gutter: 3 
 
-:::{grid-item-card} {fas}`database;sd-text-primary` aeon_mecha
-:link: https://github.com/SainsburyWellcomeCentre/aeon_mecha
+:::{grid-item-card} {fas}`database;sd-text-primary` aeon_api
+:link: https://github.com/SainsburyWellcomeCentre/aeon_api
 :link-type: url
 Aeon's main library for interfacing with acquired data
 :::
@@ -76,7 +76,7 @@ Source code for pellet delivery via feeders used in Aeon experiments
 :::{note}
 All experiment data is acquired and/or triggered and/or synced by 
 [Harp devices](https://www.cf-hw.org/harp). 
-Code in the `aeon_acquisition` and `aeon_mecha` repositories makes use of 
+Code in the `aeon_acquisition` and `aeon_api` repositories makes use of 
 the [Harp protocol](harp-tech:articles/about) during data acquisition, 
 raw data file writing, and raw data file reading. 
 See also the documentation on 

src/getting_started/installation.md

@@ -1,11 +1,11 @@
 # Installation
 
-This guide will walk you through the installation of the `aeon_mecha` package, the main package for interacting with raw Aeon data. It also includes instructions for setting up data access to the Aeon data hosted on SWC's Ceph storage (currently only applicable to SWC members).
+This guide will walk you through the installation of the `aeon_api` package, the main package for interacting with raw Aeon data. It also includes instructions for setting up data access to the Aeon data hosted on SWC's Ceph storage (currently only applicable to SWC members).
 
-## `aeon_mecha`
+## `aeon_api`
 
 :::{note}
-We always recommend installing `aeon_mecha` inside a 
+We always recommend installing `aeon_api` inside a 
 [conda](https://docs.conda.io/en/latest/)
 or [mamba](https://mamba.readthedocs.io/en/latest/) environment, 
 to avoid dependency conflicts with other packages.
@@ -40,12 +40,12 @@ export PATH=$PATH:/ceph/aeon/aeon/code/dotnet
 ```
 :::
 
-Clone the `aeon_mecha` repository into the `~/ProjectAeon/aeon_mecha` directory. 
+Clone the `aeon_api` repository into the `~/ProjectAeon/aeon_api` directory. 
 ```sh
 mkdir ~/ProjectAeon 
 cd ~/ProjectAeon
-git clone https://github.com/SainsburyWellcomeCentre/aeon_mecha
-cd aeon_mecha
+git clone https://github.com/SainsburyWellcomeCentre/aeon_api
+cd aeon_api
 ```
 
 Create the `aeon` conda environment and activate it.
@@ -54,7 +54,7 @@ conda create -n aeon -c conda-forge python>=3.11
 conda activate aeon
 ```
 
-Install the `aeon_mecha` package in editable mode.
+Install the `aeon_api` package in editable mode.
 ::::{tab-set}
 :::{tab-item} Users
 ```sh
@@ -108,4 +108,4 @@ The next step is to configure your IDE to connect to the `swc-gateway` node via
 ::::
 :::::
 
-Within the `aeon` conda environment, Aeon data can be accessed directly from Ceph or the DataJoint database using the [`aeon_mecha` API](target-mecha-reference). Examples for retrieving and visualizing the data can be found in the [User Guide](target-user-guide).
+Within the `aeon` conda environment, Aeon data can be accessed directly from Ceph or the DataJoint database using the [`aeon_api` API](target-aeon-api-reference). Examples for retrieving and visualizing the data can be found in the [User Guide](target-user-guide).

src/reference/api.md

@@ -5,13 +5,13 @@
 :gutter: 3 
 
 :::{grid-item-card} Data API Reference
-:link: target-mecha-reference
+:link: target-aeon-api-reference
 :link-type: ref
 :img-bottom: ../images/api-python-logo.png
 :class-img-bottom: sd-px-2
 :class-card: sd-height-25
 
-This reference guide contains a detailed description of the `aeon_mecha` low-level API.
+This reference guide contains a detailed description of `aeon_api`, Aeon's low-level API.
 :::
 
 :::{grid-item-card} Acquisition API Reference