docs: auto-build docs on opening PR

.github/workflows/run_dev_tests.yml

@@ -38,7 +38,6 @@ jobs:
         python-version: ${{ matrix.python-version }}
     - name: Install dependencies
       run: |
-        sudo apt install graphviz libgraphviz-dev -y
         python -m pip install -e .[dev] -e .[docs] --no-cache-dir
     - name: Run tests and coverage
       run: coverage run -m unittest discover && coverage report

.github/workflows/run_main_tests.yml

@@ -40,7 +40,6 @@ jobs:
         python-version: ${{ matrix.python-version }}
     - name: Install dependencies
       run: |
-        sudo apt install graphviz libgraphviz-dev -y
         python -m pip install -e .[dev] -e .[docs] --no-cache-dir
     - name: Run tests and coverage
       run: coverage run -m unittest discover && coverage report

.github/workflows/update_dev_docs.yml

@@ -0,0 +1,34 @@
+name: Update docs for dev PR
+
+on:
+  pull_request:
+    branches:
+      - dev
+
+jobs:
+  update_docs:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+        with:
+          token: ${{ secrets.SERVICE_TOKEN }}
+          ref: ${{ github.head_ref }}
+      - name: Set up Python 3.10
+        uses: actions/setup-python@v3
+        with:
+          python-version: '3.10'
+      - name: Install dependencies
+        run: |
+          python -m pip install -e .[dev] -e .[docs] --no-cache-dir
+      - name: Generate docs
+        run: |
+          python src/aind_data_schema/utils/docs/model_generator.py
+          python src/aind_data_schema/utils/docs/registries_generator.py
+          python src/aind_data_schema/utils/docs/doc_generator.py
+          sphinx-build -b html docs/source/ docs/build/html
+      - name: Commit changes
+        uses: EndBug/add-and-commit@v9
+        with:
+          default_author: github_actions
+          message: "update docs [skip actions]"
+          add: '["docs"]'

.github/workflows/update_docs.yml

@@ -60,7 +60,6 @@ jobs:
           python-version: '3.10'
       - name: Install dependencies
         run: |
-          sudo apt install graphviz libgraphviz-dev -y
           python -m pip install -e .[dev] -e .[docs] --no-cache-dir
       - name: Commit changes
         uses: EndBug/add-and-commit@v9

CONTRIBUTING.md

@@ -39,7 +39,9 @@ Starting with the v2.0 release all changes must be accompanied by an [upgrader](
 
 ### Documentation
 
-**Note**: The core files (`docs/source/acquisition.md`, etc) are auto-generated from the base files in the folder `docs/base/core` with the model definitions appended. You must modify the **base** file or your changes will be overwritten when you run the documentation generators.
+Documentation is automatically built when you open a PR into the aind-data-schema repository. For **core files, please make sure that you modify the base file**, these are used to construct the source files: i.e. `docs/base/core/acquisition.md` will over-write any changes made to `docs/source/acquisition.md`. 
+
+#### Manually build documentation
 
 To generate the source files for the documentation and model class links, run:
 

docs/source/acquisition.md

@@ -78,7 +78,7 @@ while the StimulusEpoch represents all stimuli being presented.
 | Field | Type | Title (Description) |
 |-------|------|-------------|
 | `subject_id` | `str` | Subject ID (Unique identifier for the subject) |
-| `specimen_id` | `str or List[str] or NoneType` | Specimen ID (Specimen ID is required for in vitro imaging modalities) |
+| `specimen_id` | `str or List[str] or NoneType` | Specimen ID (Specimen ID(s) used in this acquisition. Required for in vitro imaging modalities.) |
 | `acquisition_start_time` | `datetime (timezone-aware)` | Acquisition start time (During validation, timezone information will be moved into the acquisition_start_tz field.) |
 | `acquisition_start_tz` | `int or pydantic_extra_types.timezone_name.TimeZoneName or NoneType` | Acquisition start timezone (Automatically populated by a validator based on acquisition_start_time. Will be a TimeZoneName (IANA name) when the datetime uses a ZoneInfo timezone, or an integer UTC offset in hours for fixed-offset timezones. Use ZoneInfo (from the zoneinfo standard library) to preserve the named timezone.) |
 | `acquisition_end_time` | `datetime (timezone-aware)` | Acquisition end time  |

docs/source/aind_data_schema_models/devices.md

@@ -95,6 +95,7 @@ Detector type name
 |------|-------|
 | `CAMERA` | `Camera` |
 | `PMT` | `Photomultiplier Tube` |
+| `SiPM` | `Silicon Photomultiplier` |
 | `OTHER` | `Other` |
 
 

docs/source/aind_data_schema_models/organizations.md

@@ -9,97 +9,98 @@ Organization
 | Name | abbreviation | name | registry | registry_identifier |
 |------|------|------|------|------|
 | `AA_OPTO_ELECTRONIC` | `None` | `AA Opto Electronic` | `None` | `None` |
-| `ABCAM` | `None` | `Abcam` | `Registry.ROR` | `02e1wjw63` |
-| `ADDGENE` | `None` | `Addgene` | `Registry.ROR` | `01nn1pw54` |
-| `AI` | `AI` | `Allen Institute` | `Registry.ROR` | `03cpe7c52` |
-| `AIBS` | `AIBS` | `Allen Institute for Brain Science` | `Registry.ROR` | `00dcv1019` |
+| `ABCAM` | `None` | `Abcam` | `Research Organization Registry (ROR)` | `02e1wjw63` |
+| `ADDGENE` | `None` | `Addgene` | `Research Organization Registry (ROR)` | `01nn1pw54` |
+| `AI` | `AI` | `Allen Institute` | `Research Organization Registry (ROR)` | `03cpe7c52` |
+| `AIBS` | `AIBS` | `Allen Institute for Brain Science` | `Research Organization Registry (ROR)` | `00dcv1019` |
 | `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` |
+| `AIND` | `AIND` | `Allen Institute for Neural Dynamics` | `Research Organization Registry (ROR)` | `04szwah67` |
+| `AMS_OSRAM` | `None` | `ams OSRAM` | `Research Organization 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` |
+| `ASUS` | `None` | `ASUS` | `Research Organization Registry (ROR)` | `00bxkz165` |
 | `BASLER` | `None` | `Basler` | `None` | `None` |
-| `BCM` | `BCM` | `Baylor College of Medicine` | `Registry.ROR` | `02pttbw34` |
-| `BU` | `BU` | `Boston University` | `Registry.ROR` | `05qwgg493` |
-| `CAJAL` | `Cajal` | `Cajal Neuroscience` | `Registry.ROR` | `05pdc0q70` |
+| `BCM` | `BCM` | `Baylor College of Medicine` | `Research Organization Registry (ROR)` | `02pttbw34` |
+| `BRUKER` | `None` | `Bruker` | `Research Organization Registry (ROR)` | `04r739x86` |
+| `BU` | `BU` | `Boston University` | `Research Organization Registry (ROR)` | `05qwgg493` |
+| `CAJAL` | `Cajal` | `Cajal Neuroscience` | `Research Organization Registry (ROR)` | `05pdc0q70` |
 | `CAMBRIDGE_TECHNOLOGY` | `None` | `Cambridge Technology` | `None` | `None` |
-| `CARL_ZEISS` | `None` | `Carl Zeiss` | `Registry.ROR` | `01xk5xs43` |
+| `CARL_ZEISS` | `None` | `Carl Zeiss` | `Research Organization Registry (ROR)` | `01xk5xs43` |
 | `CATHETER_IMPLANT_INSTITUTIONS` | `N/A` | `N/A` | `N/A` | `N/A` |
-| `CHAMPALIMAUD` | `Champalimaud` | `Champalimaud Foundation` | `Registry.ROR` | `03g001n57` |
+| `CHAMPALIMAUD` | `Champalimaud` | `Champalimaud Foundation` | `Research Organization Registry (ROR)` | `03g001n57` |
 | `CHROMA` | `None` | `Chroma` | `None` | `None` |
-| `COHERENT_SCIENTIFIC` | `None` | `Coherent Scientific` | `Registry.ROR` | `031tysd23` |
-| `COLUMBIA` | `Columbia` | `Columbia University` | `Registry.ROR` | `00hj8s172` |
+| `COHERENT_SCIENTIFIC` | `None` | `Coherent Scientific` | `Research Organization Registry (ROR)` | `031tysd23` |
+| `COLUMBIA` | `Columbia` | `Columbia University` | `Research Organization Registry (ROR)` | `00hj8s172` |
 | `COMPUTAR` | `None` | `Computar` | `None` | `None` |
 | `CONOPTICS` | `None` | `Conoptics` | `None` | `None` |
 | `CRESTOPTICS` | `None` | `CrestOptics` | `None` | `None` |
-| `CRL` | `CRL` | `Charles River Laboratories` | `Registry.ROR` | `03ndmsg87` |
+| `CRL` | `CRL` | `Charles River Laboratories` | `Research Organization Registry (ROR)` | `03ndmsg87` |
 | `CUSTOM` | `None` | `Custom` | `None` | `None` |
-| `CZI` | `CZI` | `Chan Zuckerberg Initiative` | `Registry.ROR` | `02qenvm24` |
+| `CZI` | `CZI` | `Chan Zuckerberg Initiative` | `Research Organization Registry (ROR)` | `02qenvm24` |
 | `DAQ_DEVICE_MANUFACTURERS` | `N/A` | `N/A` | `N/A` | `N/A` |
 | `DETECTOR_MANUFACTURERS` | `N/A` | `N/A` | `N/A` | `N/A` |
 | `DIGIKEY` | `None` | `DigiKey` | `None` | `None` |
 | `DODOTRONIC` | `None` | `Dodotronic` | `None` | `None` |
-| `DORIC` | `None` | `Doric` | `Registry.ROR` | `059n53q30` |
+| `DORIC` | `None` | `Doric` | `Research Organization Registry (ROR)` | `059n53q30` |
 | `EALING` | `None` | `Ealing` | `None` | `None` |
-| `EDMUND_OPTICS` | `None` | `Edmund Optics` | `Registry.ROR` | `01j1gwp17` |
-| `EMORY` | `Emory` | `Emory University` | `Registry.ROR` | `03czfpz43` |
+| `EDMUND_OPTICS` | `None` | `Edmund Optics` | `Research Organization Registry (ROR)` | `01j1gwp17` |
+| `EMORY` | `Emory` | `Emory University` | `Research Organization Registry (ROR)` | `03czfpz43` |
 | `EURESYS` | `None` | `Euresys` | `None` | `None` |
 | `FILTER_MANUFACTURERS` | `N/A` | `N/A` | `N/A` | `N/A` |
-| `FLIR` | `FLIR` | `Teledyne FLIR` | `Registry.ROR` | `01j1gwp17` |
+| `FLIR` | `FLIR` | `Teledyne FLIR` | `Research Organization Registry (ROR)` | `01j1gwp17` |
 | `FUJINON` | `None` | `Fujinon` | `None` | `None` |
 | `FUNDERS` | `N/A` | `N/A` | `N/A` | `N/A` |
-| `HAMAMATSU` | `None` | `Hamamatsu` | `Registry.ROR` | `03natb733` |
+| `HAMAMATSU` | `None` | `Hamamatsu` | `Research Organization Registry (ROR)` | `03natb733` |
 | `HAMILTON` | `None` | `Hamilton` | `None` | `None` |
-| `HUST` | `HUST` | `Huazhong University of Science and Technology` | `Registry.ROR` | `00p991c53` |
-| `IDT` | `IDT` | `Integrated DNA Technologies` | `Registry.ROR` | `009jvpf03` |
-| `IMEC` | `IMEC` | `Interuniversity Microelectronics Center` | `Registry.ROR` | `02kcbn207` |
+| `HUST` | `HUST` | `Huazhong University of Science and Technology` | `Research Organization Registry (ROR)` | `00p991c53` |
+| `IDT` | `IDT` | `Integrated DNA Technologies` | `Research Organization Registry (ROR)` | `009jvpf03` |
+| `IMEC` | `IMEC` | `Interuniversity Microelectronics Center` | `Research Organization Registry (ROR)` | `02kcbn207` |
 | `INFINITY_PHOTO_OPTICAL` | `None` | `Infinity Photo-Optical` | `None` | `None` |
-| `INVITROGEN` | `None` | `Invitrogen` | `Registry.ROR` | `03x1ewr52` |
+| `INVITROGEN` | `None` | `Invitrogen` | `Research Organization Registry (ROR)` | `03x1ewr52` |
 | `IR_ROBOT_CO` | `None` | `IR Robot Co` | `None` | `None` |
 | `ISL` | `ISL` | `ISL Products International` | `None` | `None` |
 | `ITEM` | `None` | `Item` | `None` | `None` |
-| `JANELIA` | `Janelia` | `Janelia Research Campus` | `Registry.ROR` | `013sk6x84` |
-| `JAX` | `JAX` | `Jackson Laboratory` | `Registry.ROR` | `021sy4w91` |
-| `JENOPTIK` | `None` | `Jenoptik` | `Registry.ROR` | `05g7t5c49` |
-| `JHU` | `JHU` | `Johns Hopkins University` | `Registry.ROR` | `00za53h95` |
+| `JANELIA` | `Janelia` | `Janelia Research Campus` | `Research Organization Registry (ROR)` | `013sk6x84` |
+| `JAX` | `JAX` | `Jackson Laboratory` | `Research Organization Registry (ROR)` | `021sy4w91` |
+| `JENOPTIK` | `None` | `Jenoptik` | `Research Organization Registry (ROR)` | `05g7t5c49` |
+| `JHU` | `JHU` | `Johns Hopkins University` | `Research Organization Registry (ROR)` | `00za53h95` |
 | `JULABO` | `None` | `Julabo` | `None` | `None` |
-| `KOWA` | `None` | `Kowa` | `Registry.ROR` | `03zbwg482` |
+| `KOWA` | `None` | `Kowa` | `Research Organization Registry (ROR)` | `03zbwg482` |
 | `LASER_MANUFACTURERS` | `N/A` | `N/A` | `N/A` | `N/A` |
 | `LASOS` | `LASOS` | `LASOS Lasertechnik` | `None` | `None` |
 | `LED_MANUFACTURERS` | `N/A` | `N/A` | `N/A` | `N/A` |
 | `LEICA` | `None` | `Leica` | `None` | `None` |
 | `LENS_MANUFACTURERS` | `N/A` | `N/A` | `N/A` | `N/A` |
-| `LG` | `None` | `LG` | `Registry.ROR` | `02b948n83` |
+| `LG` | `None` | `LG` | `Research Organization Registry (ROR)` | `02b948n83` |
 | `LIFECANVAS` | `None` | `LifeCanvas` | `None` | `None` |
 | `LUMENCOR` | `None` | `Lumencor` | `None` | `None` |
 | `LUMEN_DYNAMICS` | `None` | `Lumen Dynamics` | `None` | `None` |
 | `MANIPULATOR_MANUFACTURERS` | `N/A` | `N/A` | `N/A` | `N/A` |
-| `MBF` | `MBF` | `MBF Bioscience` | `Registry.ROR` | `02zynam48` |
-| `MEADOWLARK_OPTICS` | `None` | `Meadowlark Optics` | `Registry.ROR` | `00n8qbq54` |
-| `MIBR` | `MIBR` | `McGovern Institute for Brain Research` | `Registry.ROR` | `05ymca674` |
+| `MBF` | `MBF` | `MBF Bioscience` | `Research Organization Registry (ROR)` | `02zynam48` |
+| `MEADOWLARK_OPTICS` | `None` | `Meadowlark Optics` | `Research Organization Registry (ROR)` | `00n8qbq54` |
+| `MIBR` | `MIBR` | `McGovern Institute for Brain Research` | `Research Organization Registry (ROR)` | `05ymca674` |
 | `MIDOPT` | `MidOpt` | `Midwest Optical Systems, Inc.` | `None` | `None` |
-| `MIT` | `MIT` | `Massachusetts Institute of Technology` | `Registry.ROR` | `042nb2s44` |
+| `MIT` | `MIT` | `Massachusetts Institute of Technology` | `Research Organization Registry (ROR)` | `042nb2s44` |
 | `MITUTUYO` | `None` | `Mitutuyo` | `None` | `None` |
 | `MIT_BCS` | `MIT-BCS` | `MIT Department of Brain and Cognitive Sciences` | `None` | `None` |
-| `MJFF` | `MJFF` | `Michael J. Fox Foundation for Parkinson's Research` | `Registry.ROR` | `03arq3225` |
-| `MKS_NEWPORT` | `None` | `MKS Newport` | `Registry.ROR` | `00k17f049` |
+| `MJFF` | `MJFF` | `Michael J. Fox Foundation for Parkinson's Research` | `Research Organization Registry (ROR)` | `03arq3225` |
+| `MKS_NEWPORT` | `None` | `MKS Newport` | `Research Organization Registry (ROR)` | `00k17f049` |
 | `MONITOR_MANUFACTURERS` | `N/A` | `N/A` | `N/A` | `N/A` |
 | `MPI` | `MPI` | `MPI` | `None` | `None` |
-| `NATIONAL_INSTRUMENTS` | `None` | `National Instruments` | `Registry.ROR` | `026exqw73` |
+| `NATIONAL_INSTRUMENTS` | `None` | `National Instruments` | `Research Organization Registry (ROR)` | `026exqw73` |
 | `NAVITAR` | `None` | `Navitar` | `None` | `None` |
-| `NCCIH` | `NCCIH` | `National Center for Complementary and Integrative Health` | `Registry.ROR` | `00190t495` |
+| `NCCIH` | `NCCIH` | `National Center for Complementary and Integrative Health` | `Research Organization Registry (ROR)` | `00190t495` |
 | `NEURALYNX` | `None` | `NeuraLynx` | `None` | `None` |
 | `NEUROPHOTOMETRICS` | `None` | `Neurophotometrics` | `None` | `None` |
 | `NEW_SCALE_TECHNOLOGIES` | `None` | `New Scale Technologies` | `None` | `None` |
-| `NIKON` | `None` | `Nikon` | `Registry.ROR` | `0280y9h11` |
-| `NIMH` | `NIMH` | `National Institute of Mental Health` | `Registry.ROR` | `04xeg9z08` |
-| `NINDS` | `NINDS` | `National Institute of Neurological Disorders and Stroke` | `Registry.ROR` | `01s5ya894` |
+| `NIKON` | `None` | `Nikon` | `Research Organization Registry (ROR)` | `0280y9h11` |
+| `NIMH` | `NIMH` | `National Institute of Mental Health` | `Research Organization Registry (ROR)` | `04xeg9z08` |
+| `NINDS` | `NINDS` | `National Institute of Neurological Disorders and Stroke` | `Research Organization Registry (ROR)` | `01s5ya894` |
 | `NRESEARCH_INC` | `None` | `NResearch Inc` | `None` | `None` |
-| `NYU` | `NYU` | `New York University` | `Registry.ROR` | `0190ak572` |
-| `OEPS` | `OEPS` | `Open Ephys Production Site` | `Registry.ROR` | `007rkz355` |
-| `OLYMPUS` | `None` | `Olympus` | `Registry.ROR` | `02vcdte90` |
+| `NYU` | `NYU` | `New York University` | `Research Organization Registry (ROR)` | `0190ak572` |
+| `OEPS` | `OEPS` | `Open Ephys Production Site` | `Research Organization Registry (ROR)` | `007rkz355` |
+| `OLYMPUS` | `None` | `Olympus` | `Research Organization Registry (ROR)` | `02vcdte90` |
 | `OPTOTUNE` | `None` | `Optotune` | `None` | `None` |
 | `OTHER` | `None` | `Other` | `None` | `None` |
 | `OXXIUS` | `None` | `Oxxius` | `None` | `None` |
@@ -114,25 +115,25 @@ Organization
 | `SEMROCK` | `None` | `Semrock` | `None` | `None` |
 | `SICGEN` | `None` | `SICGEN` | `None` | `None` |
 | `SIGMA_ALDRICH` | `None` | `Sigma-Aldrich` | `None` | `None` |
-| `SIMONS_FOUNDATION` | `None` | `Simons Foundation` | `Registry.ROR` | `01cmst727` |
+| `SIMONS_FOUNDATION` | `None` | `Simons Foundation` | `Research Organization Registry (ROR)` | `01cmst727` |
 | `SPEAKER_MANUFACTURERS` | `N/A` | `N/A` | `N/A` | `N/A` |
-| `SPECTRA_PHYSICS` | `None` | `Spectra-Physics` | `Registry.ROR` | `02ad9kp97` |
+| `SPECTRA_PHYSICS` | `None` | `Spectra-Physics` | `Research Organization Registry (ROR)` | `02ad9kp97` |
 | `SPINNAKER` | `None` | `Spinnaker` | `None` | `None` |
 | `SUBJECT_SOURCES` | `N/A` | `N/A` | `N/A` | `N/A` |
 | `TAMRON` | `None` | `Tamron` | `None` | `None` |
 | `TELEDYNE_VISION_SOLUTIONS` | `None` | `Teledyne Vision Solutions` | `None` | `None` |
-| `TE_CONNECTIVITY` | `None` | `TE Connectivity` | `Registry.ROR` | `034frgp20` |
-| `THERMO_FISHER_SCIENTIFIC` | `None` | `Thermo Fisher Scientific` | `Registry.ROR` | `03x1ewr52` |
+| `TE_CONNECTIVITY` | `None` | `TE Connectivity` | `Research Organization Registry (ROR)` | `034frgp20` |
+| `THERMO_FISHER_SCIENTIFIC` | `None` | `Thermo Fisher Scientific` | `Research Organization Registry (ROR)` | `03x1ewr52` |
 | `THE_IMAGING_SOURCE` | `None` | `The Imaging Source` | `None` | `None` |
 | `THE_LEE_COMPANY` | `None` | `The Lee Company` | `None` | `None` |
-| `THORLABS` | `None` | `Thorlabs` | `Registry.ROR` | `04gsnvb07` |
+| `THORLABS` | `None` | `Thorlabs` | `Research Organization Registry (ROR)` | `04gsnvb07` |
 | `TMC` | `TMC` | `Technical Manufacturing Corporation` | `None` | `None` |
 | `TRANSDUCER_TECHNIQUES` | `None` | `Transducer Techniques` | `None` | `None` |
-| `TWCF` | `TWCF` | `Templeton World Charity Foundation` | `Registry.ROR` | `00x0z1472` |
+| `TWCF` | `TWCF` | `Templeton World Charity Foundation` | `Research Organization Registry (ROR)` | `00x0z1472` |
 | `TYMPHANY` | `None` | `Tymphany` | `None` | `None` |
-| `UCSD` | `UCSD` | `University of California, San Diego` | `Registry.ROR` | `0168r3w48` |
+| `UCSD` | `UCSD` | `University of California, San Diego` | `Research Organization Registry (ROR)` | `0168r3w48` |
 | `UNKNOWN` | `UNKNOWN` | `Unknown` | `None` | `None` |
-| `UPENN` | `UPENN` | `University of Pennsylvania` | `Registry.ROR` | `00b30xv10` |
+| `UPENN` | `UPENN` | `University of Pennsylvania` | `Research Organization Registry (ROR)` | `00b30xv10` |
 | `VIEWORKS` | `None` | `Vieworks` | `None` | `None` |
 | `VORTRAN` | `None` | `Vortran` | `None` | `None` |