Update docs for v2.4.0 (#1681)

* docs: update contributing to be more clear about squash requirements

* docs: fix issue with GenericModel wrapping

Author: dbirman

CONTRIBUTING.md

@@ -179,6 +179,6 @@ When you are ready to open a pull request, please link any relevant issues and r
 - Manually increment the major/minor/patch versions of the core files as needed
 - Push the branch and open a PR into main
 - After this push, any last minute changes to the release-vX.Y.Z will have to done to via a PR
-- After review, use a merge commit to merge into main
-- Open a PR from main back into dev so they're synced again
+- After review, use a **merge commit** to merge into main, DO NOT SQUASH INTO MAIN
+- Open a PR from main back into dev so they're synced again, bypass the rules to use a **merge commit**, DO NOT SQUASH MAIN INTO DEV
 - Create a Github release with the corresponding tag, modify the auto-generated release notes to focus on the major changes that occurred

docs/source/acquisition.md

@@ -149,7 +149,7 @@ Summary of a StimulusEpoch
 
 | Field | Type | Title (Description) |
 |-------|------|-------------|
-| `output_parameters` | `dict` | Additional metrics  |
+| `output_parameters` | `Optional[dict]` | Additional metrics  |
 | `reward_consumed_during_epoch` | `Optional[decimal.Decimal]` | Reward consumed during training (uL)  |
 | `reward_consumed_unit` | Optional[[VolumeUnit](aind_data_schema_models/units.md#volumeunit)] | Reward consumed unit  |
 | `trials_total` | `Optional[int]` | Total trials  |

docs/source/aind_data_schema_models/coordinates.md

@@ -64,13 +64,14 @@ Origin positions for coordinate systems
 | `ORIGIN` | `Origin` |
 | `BREGMA` | `Bregma` |
 | `LAMBDA` | `Lambda` |
-| `C1` | `C1` |
-| `C2` | `C2` |
-| `C3` | `C3` |
-| `C4` | `C4` |
-| `C5` | `C5` |
-| `C6` | `C6` |
-| `C7` | `C7` |
+| `BETWEEN_C1_C2` | `Between_C1-C2` |
+| `BETWEEN_C2_C3` | `Between_C2-C3` |
+| `BETWEEN_C3_C4` | `Between_C3-C4` |
+| `BETWEEN_C4_C5` | `Between_C4-C5` |
+| `BETWEEN_C6_C7` | `Between_C6-C7` |
+| `BETWEEN_C7_C8` | `Between_C7-C8` |
+| `BETWEEN_C8_T1` | `Between_C8-T1` |
+| `BETWEEN_T1_T2` | `Between_T1-T2` |
 | `TIP` | `Tip` |
 | `FRONT_CENTER` | `Front_center` |
 | `ARENA_CENTER` | `Arena_center` |

docs/source/aind_data_schema_models/modalities.md

@@ -8,19 +8,25 @@ Modalities
 
 | Name | name | abbreviation |
 |------|------|------|
+| `BARSEQ` | `Barcoded anatomy resolved by sequencing` | `BARseq` |
 | `BEHAVIOR` | `Behavior` | `behavior` |
 | `BEHAVIOR_VIDEOS` | `Behavior videos` | `behavior-videos` |
+| `BRIGHTFIELD` | `Brightfield microscopy` | `brightfield` |
 | `CONFOCAL` | `Confocal microscopy` | `confocal` |
 | `ECEPHYS` | `Extracellular electrophysiology` | `ecephys` |
+| `EM` | `Electron microscopy` | `EM` |
 | `EMG` | `Electromyography` | `EMG` |
 | `FIB` | `Fiber photometry` | `fib` |
 | `FMOST` | `Fluorescence micro-optical sectioning tomography` | `fMOST` |
 | `ICEPHYS` | `Intracellular electrophysiology` | `icephys` |
 | `ISI` | `Intrinsic signal imaging` | `ISI` |
+| `MAPSEQ` | `Multiplexed analysis of projections by sequencing` | `MAPseq` |
 | `MERFISH` | `Multiplexed error-robust fluorescence in situ hybridization` | `merfish` |
 | `MRI` | `Magnetic resonance imaging` | `MRI` |
 | `POPHYS` | `Planar optical physiology` | `pophys` |
-| `SLAP` | `Scanned line projection imaging` | `slap` |
+| `SCRNASEQ` | `Single cell RNA sequencing` | `scRNAseq` |
+| `SLAP2` | `Random access projection microscopy` | `slap2` |
 | `SPIM` | `Selective plane illumination microscopy` | `SPIM` |
+| `STPT` | `Serial two-photon tomogrophy` | `STPT` |
 
 

docs/source/aind_data_schema_models/organizations.md

@@ -16,6 +16,7 @@ Organization
 | `AILIPU` | `Ailipu` | `Ailipu Technology Co` | `None` | `None` |
 | `AIND` | `AIND` | `Allen Institute for Neural Dynamics` | `Registry.ROR` | `04szwah67` |
 | `AMS_OSRAM` | `None` | `ams OSRAM` | `Registry.ROR` | `045d0h266` |
+| `ARDUINO` | `None` | `Arduino` | `None` | `None` |
 | `ARECONT_VISION_COSTAR` | `None` | `Arecont Vision Costar` | `None` | `None` |
 | `ASI` | `ASI` | `Applied Scientific Instrumentation` | `None` | `None` |
 | `ASUS` | `None` | `ASUS` | `Registry.ROR` | `00bxkz165` |
@@ -126,6 +127,7 @@ Organization
 | `TWCF` | `TWCF` | `Templeton World Charity Foundation` | `Registry.ROR` | `00x0z1472` |
 | `TYMPHANY` | `None` | `Tymphany` | `None` | `None` |
 | `UCSD` | `UCSD` | `University of California, San Diego` | `Registry.ROR` | `0168r3w48` |
+| `UNKNOWN` | `UNKNOWN` | `Unknown` | `None` | `None` |
 | `UPENN` | `UPENN` | `University of Pennsylvania` | `Registry.ROR` | `00b30xv10` |
 | `VIEWORKS` | `None` | `Vieworks` | `None` | `None` |
 | `VORTRAN` | `None` | `Vortran` | `None` | `None` |

docs/source/aind_data_schema_models/process_names.md

@@ -37,6 +37,7 @@ Process names
 | `IMAGE_TILE_PROJECTION` | `Image tile projection` |
 | `MODEL_EVALUATION` | `Model evaluation` |
 | `MODEL_TRAINING` | `Model training` |
+| `NEURON_SKELETON_PROCESSING` | `Neuron skeleton processing` |
 | `NEUROPIL_SUBTRACTION` | `Neuropil subtraction` |
 | `OTHER` | `Other` |
 | `PIPELINE` | `Pipeline` |

docs/source/aind_data_schema_models/registries.md

@@ -9,8 +9,10 @@ Registries
 | Name | Value |
 |------|-------|
 | `ADDGENE` | `Addgene (ADDGENE)` |
+| `DOI` | `Digital Object Identifier (DOI)` |
 | `EMAPA` | `Edinburgh Mouse Atlas Project (EMAPA)` |
 | `MGI` | `Mouse Genome Informatics (MGI)` |
+| `GENBANK` | `NCBI GenBank (GENBANK)` |
 | `NCBI` | `National Center for Biotechnology Information (NCBI)` |
 | `ORCID` | `Open Researcher and Contributor ID (ORCID)` |
 | `ROR` | `Research Organization Registry (ROR)` |

docs/source/components/configs.md

@@ -261,7 +261,7 @@ Configuration of a 3D scan
 | `subject_position` | [SubjectPosition](#subjectposition) | Subject position  |
 | `resolution` | Optional[[Scale](coordinates.md#scale)] | Voxel resolution  |
 | `resolution_unit` | Optional[[SizeUnit](../aind_data_schema_models/units.md#sizeunit)] | Voxel resolution unit  |
-| `additional_scan_parameters` | `dict` | Parameters  |
+| `additional_scan_parameters` | `Optional[dict]` | Parameters  |
 | `notes` | `Optional[str]` | Notes  |
 | `device_name` | `str` | Device name (Must match a device defined in the instrument.json) |
 

docs/source/components/devices.md

@@ -622,9 +622,9 @@ Description of visual display for visual stimuli
 | `viewing_distance` | `decimal.Decimal` | Viewing distance (cm)  |
 | `viewing_distance_unit` | [SizeUnit](../aind_data_schema_models/units.md#sizeunit) | Viewing distance unit  |
 | `contrast` | `Optional[int]` | Contrast (Monitor's contrast setting) |
-| `contrast_unit` | `Optional[UnitlessUnit]` | Contrast unit |
+| `contrast_unit` | Optional[[UnitlessUnit](../aind_data_schema_models/units.md#unitlessunit)] | Contrast unit  |
 | `brightness` | `Optional[int]` | Brightness (Monitor's brightness setting) |
-| `brightness_unit` | `Optional[UnitlessUnit]` | Brightness unit |
+| `brightness_unit` | Optional[[UnitlessUnit](../aind_data_schema_models/units.md#unitlessunit)] | Brightness unit  |
 | `name` | `str` | Device name  |
 | `serial_number` | `Optional[str]` | Serial number  |
 | `model` | `Optional[str]` | Model  |

docs/source/components/identifiers.md

@@ -12,7 +12,7 @@ Code or script identifier
 | `name` | `Optional[str]` | Name  |
 | `version` | `Optional[str]` | Code version  |
 | `container` | Optional[[Container](#container)] | Container  |
-| `run_script` | `Optional[pathlib.Path]` | Run script (Path to run script) |
+| `run_script` | `Optional[pathlib._local.Path]` | Run script (Path to run script) |
 | `language` | `Optional[str]` | Programming language (Programming language used) |
 | `language_version` | `Optional[str]` | Programming language version  |
 | `input_data` | Optional[List[[DataAsset](#dataasset) or [CombinedData](#combineddata)]] | Input data (Input data used in the code or script) |