From 1a7ba58c7cb53a2a17b0718555ff3f4c394313a2 Mon Sep 17 00:00:00 2001
From: Cody Baker <51133164+CodyCBakerPhD@users.noreply.github.com>
Date: Tue, 28 Nov 2023 10:45:40 -0500
Subject: [PATCH] Fix api docs for YAML (#666)

* fix api docs for YAML

* Update tools.rst

* Create tools.data_transfers

* Rename tools.data_transfers to tools.data_transfers.rst

* add __all__

* Update tools.yaml_to_nwb_conversion.rst

* add __all__ to data transfer

* add __all__ to nwb_helpers

* Update tools.rst

* Create tools.nwb_helpers.rst

* Update tools.data_transfers.rst

* Update __init__.py
---
 docs/api/tools.data_transfers.rst                  |  3 +++
 docs/api/tools.nwb_helpers.rst                     |  3 +++
 docs/api/tools.rst                                 |  2 ++
 docs/api/tools.yaml_to_nwb_conversion.rst          |  2 +-
 src/neuroconv/tools/data_transfers/__init__.py     |  8 ++++++++
 src/neuroconv/tools/nwb_helpers/__init__.py        | 14 ++++++++++++++
 .../yaml_conversion_specification/__init__.py      |  2 ++
 7 files changed, 33 insertions(+), 1 deletion(-)
 create mode 100644 docs/api/tools.data_transfers.rst
 create mode 100644 docs/api/tools.nwb_helpers.rst

diff --git a/docs/api/tools.data_transfers.rst b/docs/api/tools.data_transfers.rst
new file mode 100644
index 000000000..b5d16a136
--- /dev/null
+++ b/docs/api/tools.data_transfers.rst
@@ -0,0 +1,3 @@
+Data Transfers
+--------------
+.. automodule:: neuroconv.tools.data_transfers
diff --git a/docs/api/tools.nwb_helpers.rst b/docs/api/tools.nwb_helpers.rst
new file mode 100644
index 000000000..68cbda03e
--- /dev/null
+++ b/docs/api/tools.nwb_helpers.rst
@@ -0,0 +1,3 @@
+NWB Helpers
+-----------
+.. automodule:: neuroconv.tools.nwb_helpers
diff --git a/docs/api/tools.rst b/docs/api/tools.rst
index 4dbb93c86..41515facd 100644
--- a/docs/api/tools.rst
+++ b/docs/api/tools.rst
@@ -11,3 +11,5 @@ Tools
     tools.testing
     tools.path_expansion
     tools.signal_processing
+    tools.data_transfers
+    tools.nwb_helpers
diff --git a/docs/api/tools.yaml_to_nwb_conversion.rst b/docs/api/tools.yaml_to_nwb_conversion.rst
index 5e4a1f67d..367a4105b 100644
--- a/docs/api/tools.yaml_to_nwb_conversion.rst
+++ b/docs/api/tools.yaml_to_nwb_conversion.rst
@@ -1,3 +1,3 @@
 YAML conversion specification
 -----------------------------
-.. automodule:: neuroconv.tools.yaml_conversion_specification.yaml_conversion_specification
+.. automodule:: neuroconv.tools.yaml_conversion_specification
diff --git a/src/neuroconv/tools/data_transfers/__init__.py b/src/neuroconv/tools/data_transfers/__init__.py
index 03c2dc980..ce3312c7e 100644
--- a/src/neuroconv/tools/data_transfers/__init__.py
+++ b/src/neuroconv/tools/data_transfers/__init__.py
@@ -3,3 +3,11 @@
 from ._dandi import automatic_dandi_upload
 from ._globus import get_globus_dataset_content_sizes, transfer_globus_content
 from ._helpers import estimate_total_conversion_runtime
+
+__all__ = [
+    "estimate_s3_conversion_cost",
+    "automatic_dandi_upload",
+    "get_globus_dataset_content_sizes",
+    "transfer_globus_content",
+    "estimate_total_conversion_runtime",
+]
diff --git a/src/neuroconv/tools/nwb_helpers/__init__.py b/src/neuroconv/tools/nwb_helpers/__init__.py
index cb78a67a5..1b321cf42 100644
--- a/src/neuroconv/tools/nwb_helpers/__init__.py
+++ b/src/neuroconv/tools/nwb_helpers/__init__.py
@@ -20,3 +20,17 @@
 
 BACKEND_CONFIGURATIONS = dict(hdf5=HDF5BackendConfiguration, zarr=ZarrBackendConfiguration)
 DATASET_IO_CONFIGURATIONS = dict(hdf5=HDF5DatasetIOConfiguration, zarr=ZarrDatasetIOConfiguration)
+
+__all__ = [
+    "get_default_dataset_io_configurations",
+    "add_device_from_metadata",
+    "get_default_nwbfile_metadata",
+    "get_module",
+    "make_nwbfile_from_metadata",
+    "make_or_load_nwbfile",
+    "DatasetInfo",
+    "HDF5BackendConfiguration",
+    "HDF5DatasetIOConfiguration",
+    "ZarrBackendConfiguration",
+    "ZarrDatasetIOConfiguration",
+]
diff --git a/src/neuroconv/tools/yaml_conversion_specification/__init__.py b/src/neuroconv/tools/yaml_conversion_specification/__init__.py
index cd63559dc..f2adb6948 100644
--- a/src/neuroconv/tools/yaml_conversion_specification/__init__.py
+++ b/src/neuroconv/tools/yaml_conversion_specification/__init__.py
@@ -1 +1,3 @@
 from ._yaml_conversion_specification import run_conversion_from_yaml
+
+__all__ = ["run_conversion_from_yaml"]