add algo docs

Makefile

@@ -32,7 +32,6 @@ build_frontend:
 docs:
  rm -rf docs/_build/
  poetry install --with doc --no-root
- # sphinx-apidoc -f -o ./docs/_build/modules ./studio
  sphinx-autobuild -b html docs docs/_build --port 8001
 
 .PHONY: dockerhub

docs/algorithms/caiman.rst

@@ -0,0 +1,23 @@
+CaImAn
+======
+
+caiman\_cnmf
+------------
+
+.. automodule:: studio.app.optinist.wrappers.caiman.cnmf
+ :members:
+ :undoc-members:
+
+caiman\_cnmfe
+-------------
+
+.. automodule:: studio.app.optinist.wrappers.caiman.cnmfe
+ :members:
+ :undoc-members:
+
+caiman\_motion\_correction
+--------------------------
+
+.. automodule:: studio.app.optinist.wrappers.caiman.motion_correction
+ :members:
+ :undoc-members:

docs/algorithms/index.rst

@@ -0,0 +1,15 @@
+**********
+ALGORITHMS
+**********
+
+.. toctree::
+ :maxdepth: 2
+
+ caiman
+ suite2p
+ lccd
+
+.. toctree::
+ :maxdepth: 3
+
+ optinist/index

docs/algorithms/lccd.rst

@@ -0,0 +1,9 @@
+Lccd
+====
+
+lccd\_detection
+---------------
+
+.. automodule:: studio.app.optinist.wrappers.lccd.lccd_detection
+ :members:
+ :undoc-members:

docs/algorithms/optinist/basic_neural_analysis.rst

@@ -0,0 +1,16 @@
+Basic Neural Analysis
+=====================
+
+cell\_grouping
+--------------
+
+.. automodule:: studio.app.optinist.wrappers.optinist.basic_neural_analysis.cell_grouping
+ :members:
+ :undoc-members:
+
+eta
+---
+
+.. automodule:: studio.app.optinist.wrappers.optinist.basic_neural_analysis.eta
+ :members:
+ :undoc-members:

docs/algorithms/optinist/dimension_reduction.rst

@@ -0,0 +1,30 @@
+Dimension Reduction
+==================
+
+cca
+---
+
+.. automodule:: studio.app.optinist.wrappers.optinist.dimension_reduction.cca
+ :members:
+ :undoc-members:
+
+dpca\_fit
+---------
+
+.. automodule:: studio.app.optinist.wrappers.optinist.dimension_reduction.dpca_fit
+ :members:
+ :undoc-members:
+
+pca
+---
+
+.. automodule:: studio.app.optinist.wrappers.optinist.dimension_reduction.pca
+ :members:
+ :undoc-members:
+
+tsne
+----
+
+.. automodule:: studio.app.optinist.wrappers.optinist.dimension_reduction.tsne
+ :members:
+ :undoc-members:

docs/algorithms/optinist/index.rst

@@ -0,0 +1,11 @@
+**********
+OptiNiSt
+**********
+
+.. toctree::
+ :maxdepth: 2
+
+ basic_neural_analysis
+ dimension_reduction
+ neural_decoding
+ neural_population_analysis

docs/algorithms/optinist/neural_decoding.rst

@@ -0,0 +1,23 @@
+Neural Decoding
+===============
+
+glm
+---
+
+.. automodule:: studio.app.optinist.wrappers.optinist.neural_decoding.glm
+ :members:
+ :undoc-members:
+
+lda
+---
+
+.. automodule:: studio.app.optinist.wrappers.optinist.neural_decoding.lda
+ :members:
+ :undoc-members:
+
+svm
+---
+
+.. automodule:: studio.app.optinist.wrappers.optinist.neural_decoding.svm
+ :members:
+ :undoc-members:

docs/algorithms/optinist/neural_population_analysis.rst

@@ -0,0 +1,23 @@
+Neural Population Analysis
+==========================
+
+correlation
+-----------
+
+.. automodule:: studio.app.optinist.wrappers.optinist.neural_population_analysis.correlation
+ :members:
+ :undoc-members:
+
+cross\_correlation
+------------------
+
+.. automodule:: studio.app.optinist.wrappers.optinist.neural_population_analysis.cross_correlation
+ :members:
+ :undoc-members:
+
+granger
+-------
+
+.. automodule:: studio.app.optinist.wrappers.optinist.neural_population_analysis.granger
+ :members:
+ :undoc-members:

docs/algorithms/suite2p.rst

@@ -0,0 +1,30 @@
+Suite2p
+=======
+
+suite2p\_file\_convert
+----------------------
+
+.. automodule:: studio.app.optinist.wrappers.suite2p.file_convert
+ :members:
+ :undoc-members:
+
+suite2p\_registration
+---------------------
+
+.. automodule:: studio.app.optinist.wrappers.suite2p.registration
+ :members:
+ :undoc-members:
+
+suite2p\_roi
+------------
+
+.. automodule:: studio.app.optinist.wrappers.suite2p.roi
+ :members:
+ :undoc-members:
+
+suite2p\_spike\_deconv
+----------------------
+
+.. automodule:: studio.app.optinist.wrappers.suite2p.spike_deconv
+ :members:
+ :undoc-members:

docs/conf.py

@@ -5,6 +5,7 @@
 # https://www.sphinx-doc.org/en/master/usage/configuration.html
 
 import os
+import sys
 from datetime import datetime
 
 # -- Path setup --------------------------------------------------------------
@@ -13,7 +14,7 @@
 # add these directories to sys.path here. If the directory is relative to the
 # documentation root, use os.path.abspath to make it absolute, like shown here.
 #
-
+sys.path.insert(0, os.path.abspath("../studio"))
 
 # -- Project information -----------------------------------------------------
 project = "OptiNiSt"
@@ -44,11 +45,16 @@
  "sphinx.ext.extlinks",
  "sphinx.ext.autodoc.typehints",
  "sphinx_copybutton",
+ "sphinxcontrib.autodoc_pydantic",
 ]
 
+# autodoc_pydantic config
+autodoc_pydantic_model_show_field_summary = False
+autodoc_pydantic_settings_show_json_error_strategy = "coerce"
+autodoc_pydantic_model_show_json = False
+
 # Tell myst-parser to assign header anchors for h1-h3.
 myst_heading_anchors = 4
-
 suppress_warnings = ["myst.header"]
 
 # Add any paths that contain templates here, relative to this directory.
@@ -79,6 +85,7 @@
 html_show_sourcelink = False
 
 autosummary_generate = True
+napoleon_custom_sections = [("Returns", "params_style")]
 
 html_theme_options = {
  "canonical_url": "",

docs/index.rst

@@ -34,6 +34,7 @@ Main Features
  installation/index
  tutorials
  gui/index
+ algorithms/index
  host_for_multiuser/index
  utils/index
  for_developers/index

frontend/src/App.tsx

@@ -33,9 +33,7 @@ const App: FC = () => {
  dispatch(getModeStandalone())
  .unwrap()
  .catch(() => {
- new Promise((resolve) =>
- setTimeout(resolve, RETRY_WAIT),
- ).then(() => {
+ new Promise((resolve) => setTimeout(resolve, RETRY_WAIT)).then(() => {
  getMode()
  })
  })

frontend/src/api/nwb/NWB.ts

@@ -1,8 +1,8 @@
 import { BASE_URL } from "const/API"
 import axios from "utils/axios"
-import { ParamDTO } from "utils/param/ParamType"
+import { ParamMap } from "utils/param/ParamType"
 
-export async function getNWBParamsApi(): Promise<ParamDTO> {
+export async function getNWBParamsApi(): Promise<ParamMap> {
  const response = await axios.get(`${BASE_URL}/nwb`)
  return response.data
 }

frontend/src/api/params/Params.ts

@@ -1,8 +1,8 @@
 import { BASE_URL } from "const/API"
 import axios from "utils/axios"
-import { ParamDTO } from "utils/param/ParamType"
+import { ParamMap } from "utils/param/ParamType"
 
-export async function getAlgoParamsApi(algoName: string): Promise<ParamDTO> {
+export async function getAlgoParamsApi(algoName: string): Promise<ParamMap> {
  const response = await axios.get(`${BASE_URL}/params/${algoName}`)
  return response.data
 }

frontend/src/api/run/Run.ts

@@ -7,14 +7,14 @@ import type {
 } from "store/slice/FlowElement/FlowElementType"
 import type { FILE_TYPE } from "store/slice/InputNode/InputNodeType"
 import axios from "utils/axios"
-import type { ParamMap } from "utils/param/ParamType"
+import type { ParamMapWithoutMeta } from "utils/param/ParamType"
 
 export type RunPostData = {
  name: string
  nodeDict: NodeDict
  edgeDict: EdgeDict
- nwbParam: ParamMap
- snakemakeParam: ParamMap
+ nwbParam: ParamMapWithoutMeta
+ snakemakeParam: ParamMapWithoutMeta
  forceRunList: { nodeId: string; name: string }[]
 }
 
@@ -39,7 +39,7 @@ export interface InputNodePostData extends InputNodeData {
 
 export interface AlgorithmNodePostData extends AlgorithmNodeData {
  path: string
- param: ParamMap
+ param: ParamMapWithoutMeta
 }
 
 export async function runApi(

frontend/src/api/snakemake/Snakemake.ts

@@ -1,8 +1,8 @@
 import { BASE_URL } from "const/API"
 import axios from "utils/axios"
-import { ParamDTO } from "utils/param/ParamType"
+import { ParamMap } from "utils/param/ParamType"
 
-export async function getSnakemakeParamsApi(): Promise<ParamDTO> {
+export async function getSnakemakeParamsApi(): Promise<ParamMap> {
  const response = await axios.get(`${BASE_URL}/snakemake`)
  return response.data
 }

frontend/src/store/slice/AlgorithmNode/AlgorithmNodeActions.ts

@@ -2,10 +2,10 @@ import { createAsyncThunk } from "@reduxjs/toolkit"
 
 import { getAlgoParamsApi } from "api/params/Params"
 import { ALGORITHM_NODE_SLICE_NAME } from "store/slice/AlgorithmNode/AlgorithmNodeType"
-import { ParamDTO } from "utils/param/ParamType"
+import { ParamMap } from "utils/param/ParamType"
 
 export const getAlgoParams = createAsyncThunk<
- ParamDTO,
+ ParamMap,
  { nodeId: string; algoName: string }
 >(
  `${ALGORITHM_NODE_SLICE_NAME}/getAlgoParams`,

frontend/src/store/slice/AlgorithmNode/AlgorithmNodeSlice.ts

@@ -19,7 +19,7 @@ import {
  importWorkflowConfig,
  fetchWorkflow,
 } from "store/slice/Workflow/WorkflowActions"
-import { convertToParamMap, getChildParam } from "utils/param/ParamUtils"
+import { getChildParam } from "utils/param/ParamUtils"
 
 const initialState: AlgorithmNode = {}
 
@@ -50,7 +50,7 @@ export const algorithmNodeSlice = createSlice({
  builder
  .addCase(getAlgoParams.fulfilled, (state, action) => {
  const { nodeId } = action.meta.arg
- state[nodeId].params = convertToParamMap(action.payload)
+ state[nodeId].params = action.payload
  })
  .addCase(addAlgorithmNode.fulfilled, (state, action) => {
  const { node, functionPath, name, runAlready } = action.meta.arg
@@ -59,7 +59,7 @@ export const algorithmNodeSlice = createSlice({
  state[node.id] = {
  functionPath,
  name,
- params: convertToParamMap(params),
+ params: params,
  isUpdated: runAlready ?? false,
  }
  }

frontend/src/store/slice/FlowElement/FlowElementActions.ts

@@ -8,13 +8,13 @@ import {
  NodeData,
 } from "store/slice/FlowElement/FlowElementType"
 import { FILE_TYPE } from "store/slice/InputNode/InputNodeType"
-import { ParamDTO } from "utils/param/ParamType"
+import { ParamMap } from "utils/param/ParamType"
 
 export type AddingNodeData = Omit<Node<NodeData>, "position"> &
  Partial<Pick<Node<NodeData>, "position">>
 
 export const addAlgorithmNode = createAsyncThunk<
- ParamDTO,
+ ParamMap,
  {
  node: AddingNodeData
  functionPath: string

frontend/src/store/slice/NWB/NWBAction.ts

@@ -2,9 +2,9 @@ import { createAsyncThunk } from "@reduxjs/toolkit"
 
 import { getNWBParamsApi } from "api/nwb/NWB"
 import { NWB_SLICE_NAME } from "store/slice/NWB/NWBType"
-import { ParamDTO } from "utils/param/ParamType"
+import { ParamMap } from "utils/param/ParamType"
 
-export const getNWBParams = createAsyncThunk<ParamDTO, void>(
+export const getNWBParams = createAsyncThunk<ParamMap, void>(
  `${NWB_SLICE_NAME}/getNWBParams`,
  async (_, thunkAPI) => {
  const { rejectWithValue } = thunkAPI