diff --git a/.github/workflows/run_dev_tests.yml b/.github/workflows/run_dev_tests.yml index 5a18bcb92..8b3382ec8 100644 --- a/.github/workflows/run_dev_tests.yml +++ b/.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 diff --git a/.github/workflows/run_main_tests.yml b/.github/workflows/run_main_tests.yml index 51883eb25..0a483b39d 100644 --- a/.github/workflows/run_main_tests.yml +++ b/.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 diff --git a/.github/workflows/update_dev_docs.yml b/.github/workflows/update_dev_docs.yml new file mode 100644 index 000000000..d5dfb3238 --- /dev/null +++ b/.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"]' diff --git a/.github/workflows/update_docs.yml b/.github/workflows/update_docs.yml index d063ed7e1..a04e681ea 100644 --- a/.github/workflows/update_docs.yml +++ b/.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 diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md index 7ec795e40..99aa66523 100644 --- a/CONTRIBUTING.md +++ b/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: diff --git a/docs/source/acquisition.md b/docs/source/acquisition.md index 5e81efc8c..b365aa8bd 100644 --- a/docs/source/acquisition.md +++ b/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 | diff --git a/docs/source/aind_data_schema_models/devices.md b/docs/source/aind_data_schema_models/devices.md index 2a1d135f9..e93c4e762 100644 --- a/docs/source/aind_data_schema_models/devices.md +++ b/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` | diff --git a/docs/source/aind_data_schema_models/organizations.md b/docs/source/aind_data_schema_models/organizations.md index 75e1c9bdc..d88b119ec 100644 --- a/docs/source/aind_data_schema_models/organizations.md +++ b/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` | diff --git a/docs/source/aind_data_schema_models/species.md b/docs/source/aind_data_schema_models/species.md index 43cf74ae0..b2de0504a 100644 --- a/docs/source/aind_data_schema_models/species.md +++ b/docs/source/aind_data_schema_models/species.md @@ -8,18 +8,18 @@ Species | Name | name | common_name | registry | registry_identifier | |------|------|------|------|------| -| `ALPACA` | `Vicuna pacos` | `Alpaca` | `Registry.NCBI` | `NCBI:txid30538` | -| `CHICKEN` | `Gallus gallus` | `Chicken` | `Registry.NCBI` | `NCBI:txid9031` | -| `COMMON_MARMOSET` | `Callithrix jacchus` | `Common marmoset` | `Registry.NCBI` | `NCBI:txid9483` | -| `DONKEY` | `Equus asinus` | `Donkey` | `Registry.NCBI` | `NCBI:txid9793` | -| `EUROPEAN_RABBIT` | `Oryctolagus cuniculus` | `European rabbit` | `Registry.NCBI` | `NCBI:txid9986` | -| `GOAT` | `Carpa hircus` | `Goat` | `Registry.NCBI` | `NCBI:txid9925` | -| `GUINEA_PIG` | `Cavia porcellus` | `Guinea pig` | `Registry.NCBI` | `NCBI:txid10141` | -| `HOUSE_MOUSE` | `Mus musculus` | `House mouse` | `Registry.NCBI` | `NCBI:txid10090` | -| `HUMAN` | `Homo sapiens` | `Human` | `Registry.NCBI` | `NCBI:txid9606` | -| `LLAMA` | `Lama glama` | `Llama` | `Registry.NCBI` | `NCBI:txid9844` | -| `NORWAY_RAT` | `Rattus norvegicus` | `Norway rat` | `Registry.NCBI` | `NCBI:txid10116` | -| `RHESUS_MACAQUE` | `Macaca mulatta` | `Rhesus macaque` | `Registry.NCBI` | `NCBI:txid9544` | +| `ALPACA` | `Vicuna pacos` | `Alpaca` | `National Center for Biotechnology Information (NCBI)` | `NCBI:txid30538` | +| `CHICKEN` | `Gallus gallus` | `Chicken` | `National Center for Biotechnology Information (NCBI)` | `NCBI:txid9031` | +| `COMMON_MARMOSET` | `Callithrix jacchus` | `Common marmoset` | `National Center for Biotechnology Information (NCBI)` | `NCBI:txid9483` | +| `DONKEY` | `Equus asinus` | `Donkey` | `National Center for Biotechnology Information (NCBI)` | `NCBI:txid9793` | +| `EUROPEAN_RABBIT` | `Oryctolagus cuniculus` | `European rabbit` | `National Center for Biotechnology Information (NCBI)` | `NCBI:txid9986` | +| `GOAT` | `Carpa hircus` | `Goat` | `National Center for Biotechnology Information (NCBI)` | `NCBI:txid9925` | +| `GUINEA_PIG` | `Cavia porcellus` | `Guinea pig` | `National Center for Biotechnology Information (NCBI)` | `NCBI:txid10141` | +| `HOUSE_MOUSE` | `Mus musculus` | `House mouse` | `National Center for Biotechnology Information (NCBI)` | `NCBI:txid10090` | +| `HUMAN` | `Homo sapiens` | `Human` | `National Center for Biotechnology Information (NCBI)` | `NCBI:txid9606` | +| `LLAMA` | `Lama glama` | `Llama` | `National Center for Biotechnology Information (NCBI)` | `NCBI:txid9844` | +| `NORWAY_RAT` | `Rattus norvegicus` | `Norway rat` | `National Center for Biotechnology Information (NCBI)` | `NCBI:txid10116` | +| `RHESUS_MACAQUE` | `Macaca mulatta` | `Rhesus macaque` | `National Center for Biotechnology Information (NCBI)` | `NCBI:txid9544` | ### Strain @@ -28,8 +28,8 @@ Strain | Name | name | species | registry | registry_identifier | |------|------|------|------|------| -| `BALB_C` | `BALB/c` | `Mus musculus` | `Registry.MGI` | `MGI:2159737` | -| `C57BL_6J` | `C57BL/6J` | `Mus musculus` | `Registry.MGI` | `MGI:3028467` | +| `BALB_C` | `BALB/c` | `Mus musculus` | `Mouse Genome Informatics (MGI)` | `MGI:2159737` | +| `C57BL_6J` | `C57BL/6J` | `Mus musculus` | `Mouse Genome Informatics (MGI)` | `MGI:3028467` | | `UNKNOWN` | `Unknown` | `Mus musculus` | `None` | `None` | diff --git a/docs/source/components/devices.md b/docs/source/components/devices.md index dbdc150f4..2c42105f4 100644 --- a/docs/source/components/devices.md +++ b/docs/source/components/devices.md @@ -777,7 +777,7 @@ Multichannel electrophysiology DAQ | Field | Type | Title (Description) | |-------|------|-------------| | `ports` | List[[ProbePort](#probeport)] | Acquisition board ports | -| `data_interface` | `"DataInterface.USB"` | | +| `data_interface` | `"USB"` | | | `manufacturer` | [Organization](../aind_data_schema_models/organizations.md#organization) | | | `channels` | List[[DAQChannel](#daqchannel)] | DAQ channels | | `firmware_version` | `Optional[str]` | Firmware version | diff --git a/docs/source/components/identifiers.md b/docs/source/components/identifiers.md index adf09c542..b20bf0b68 100644 --- a/docs/source/components/identifiers.md +++ b/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._local.Path]` | Run script (Path to run script) | +| `run_script` | `Optional[pathlib.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) |