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Workflow for HDMF Dev compatibility (#77)
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|---|---|---|
| @@ -0,0 +1,28 @@ | ||
| name: Check HDMF Dev Compatibility | ||
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| on: [pull_request, workflow_dispatch] | ||
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| jobs: | ||
| check_compatibility: | ||
| runs-on: ubuntu-latest | ||
| steps: | ||
| - name: Cancel non-latest runs | ||
| uses: styfle/cancel-workflow-action@0.11.0 | ||
| with: | ||
| all_but_latest: true | ||
| access_token: ${{ github.token }} | ||
| - uses: actions/checkout@v4 | ||
| - name: Set up Python 3.11 | ||
| uses: actions/setup-python@v4 | ||
| with: | ||
| python-version: "3.11" | ||
| - name: Clone HDMF and Run HDMF tests | ||
| run: | | ||
| git clone https://github.com/hdmf-dev/hdmf.git --recurse-submodules | ||
| cd hdmf | ||
| python -m pip install -r requirements-dev.txt -r requirements.txt | ||
| python -m pip install -e . | ||
| cd src/hdmf/common/hdmf-common-schema | ||
| git checkout ${{ github.head_ref }} # checkout branch | ||
| cd ../../../.. | ||
| pytest tests/unit/common/ |
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| name: Validate schema | ||
|
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| on: [push, pull_request, workflow_dispatch] | ||
|
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| jobs: | ||
| validate: | ||
| # run pipeline on either a push event or a PR event on a fork | ||
| if: github.event_name != 'pull_request' || github.event.pull_request.head.repo.full_name != github.event.pull_request.base.repo.full_name | ||
| runs-on: ubuntu-latest | ||
| steps: | ||
| - uses: actions/checkout@v3 | ||
| - name: Set up Python 3.11 | ||
| uses: actions/setup-python@v4 | ||
| with: | ||
| python-version: "3.11" | ||
| - name: Install dev branch of HDMF | ||
| run: | | ||
| pip install git+https://github.com/hdmf-dev/hdmf.git | ||
| - name: Validate schema specification | ||
| run: | | ||
| validate_hdmf_spec common -m hdmf-common.schema.json |
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| { | ||
| "$schema": "http://json-schema.org/draft-07/schema#", | ||
| "$id": "hdmf-common.schema.json", | ||
| "title": "Schema for the HDMF Common specification", | ||
| "description": "A schema for validating HDMF Common YAML Files", | ||
| "version": "1.8.0", | ||
| "type": "object", | ||
| "additionalProperties": false, | ||
| "properties": { | ||
| "groups": {"$ref": "#/definitions/groups"}, | ||
| "attributes": {"$ref": "#/definitions/attributes"}, | ||
| "datasets": {"$ref": "#/definitions/datasets"}, | ||
| "links": {"$ref": "#/definitions/links"}, | ||
| "namespaces": { | ||
| "type": "array", | ||
| "items": { | ||
| "type": "object", | ||
| "additionalProperties": false, | ||
| "required": [ | ||
| "name", | ||
| "version", | ||
| "author", | ||
| "contact" | ||
| ], | ||
| "properties": { | ||
| "name": {"type": "string"}, | ||
| "version": {"type": "string", "pattern": "^(0|[1-9]\\d*)\\.(0|[1-9]\\d*)\\.(0|[1-9]\\d*)(?:-((?:0|[1-9]\\d*|\\d*[a-zA-Z-][0-9a-zA-Z-]*)(?:\\.(?:0|[1-9]\\d*|\\d*[a-zA-Z-][0-9a-zA-Z-]*))*))?(?:\\+([0-9a-zA-Z-]+(?:\\.[0-9a-zA-Z-]+)*))?$"}, | ||
| "doc": {"type": "string"}, | ||
| "author": {"type": "array", "items": {"type": "string"}}, | ||
| "contact": {"type": "array", "items": {"type": "string", "format": "email"}}, | ||
| "full_name": {"type": "string"}, | ||
| "date": {"type": "string", "format": "date"}, | ||
| "schema": { | ||
| "type": "array", | ||
| "items": { | ||
| "type": "object", | ||
| "oneOf": [ | ||
| {"required": ["namespace"]}, | ||
| {"required": ["source"]} | ||
| ], | ||
| "properties": { | ||
| "namespace": {"type": "string"}, | ||
| "doc": {"type": "string"}, | ||
| "source": {"type": "string"}, | ||
| "title": {"type": "string"}, | ||
| "data_types": { | ||
| "type": "array", | ||
| "items": { | ||
| "type": "string" | ||
| } | ||
| } | ||
| } | ||
| } | ||
| } | ||
| } | ||
| } | ||
| } | ||
| }, | ||
| "definitions": { | ||
| "protectedString": { | ||
| "type": "string", | ||
| "pattern": "^[A-Za-z_][A-Za-z0-9_]*$" | ||
| }, | ||
| "quantity": { | ||
| "description": "Quantity marker", | ||
| "anyOf": [ | ||
| { | ||
| "type": "integer", | ||
| "minimum": 1 | ||
| }, | ||
| { | ||
| "type": "string", | ||
| "enum": [ | ||
| "*", | ||
| "?", | ||
| "+", | ||
| "zero_or_many", | ||
| "one_or_many", | ||
| "zero_or_one" | ||
| ] | ||
| } | ||
| ] | ||
| }, | ||
| "flat_dtype": { | ||
| "description": "Required string describing the data type of the attribute", | ||
| "anyOf": [ | ||
| { | ||
| "type": "string", | ||
| "enum": [ | ||
| "float", | ||
| "float32", | ||
| "double", | ||
| "float64", | ||
| "long", | ||
| "int64", | ||
| "int", | ||
| "int32", | ||
| "int16", | ||
| "int8", | ||
| "uint", | ||
| "uint32", | ||
| "uint16", | ||
| "uint8", | ||
| "uint64", | ||
| "numeric", | ||
| "text", | ||
| "utf", | ||
| "utf8", | ||
| "utf-8", | ||
| "ascii", | ||
| "bool", | ||
| "isodatetime" | ||
| ] | ||
| }, | ||
| {"$ref": "#/definitions/ref_dtype"} | ||
| ] | ||
| }, | ||
| "dtype": { | ||
| "anyOf": [ | ||
| {"$ref": "#/definitions/flat_dtype"}, | ||
| {"$ref": "#/definitions/compound_dtype"} | ||
| ] | ||
| }, | ||
| "dims": { | ||
| "description": "Optional list describing the names of the dimensions of the data array stored by the attribute (default=None)", | ||
| "type": "array", | ||
| "items": { | ||
| "anyOf": [ | ||
| {"type": "string"}, | ||
| { | ||
| "type": "array", | ||
| "items": {"type": "string"} | ||
| } | ||
| ] | ||
| } | ||
| }, | ||
| "shape": { | ||
| "description": "Optional list describing the allowed shape(s) of the data array stored by the attribute (default=None)", | ||
| "anyOf": [ | ||
| {"$ref": "#/definitions/shape_spec"}, | ||
| { | ||
| "type": "array", | ||
| "items": {"$ref": "#/definitions/shape_spec"} | ||
| } | ||
| ] | ||
| }, | ||
| "shape_spec": { | ||
| "type": "array", | ||
| "items": { | ||
| "anyOf": [ | ||
| { | ||
| "type": "integer", | ||
| "minimum": 1 | ||
| }, | ||
| { | ||
| "value": null | ||
| } | ||
| ] | ||
| } | ||
| }, | ||
| "ref_dtype": { | ||
| "type": "object", | ||
| "required": ["target_type", "reftype"], | ||
| "properties": { | ||
| "target_type": { | ||
| "description": "Describes the data_type of the target that the reference points to", | ||
| "type": "string" | ||
| }, | ||
| "reftype": { | ||
| "description": "describes the kind of reference", | ||
| "type": "string", | ||
| "enum": ["ref", "reference", "object", "region"] | ||
| } | ||
| } | ||
| }, | ||
| "compound_dtype": { | ||
| "type": "array", | ||
| "items": { | ||
| "type": "object", | ||
| "required": ["name", "doc", "dtype"], | ||
| "properties": { | ||
| "name": {"$ref": "#/definitions/protectedString"}, | ||
| "doc": {"type": "string"}, | ||
| "dtype": {"$ref": "#/definitions/flat_dtype"} | ||
| } | ||
| } | ||
| }, | ||
| "groups": { | ||
| "description": "list of groups", | ||
| "type": "array", | ||
| "items": { | ||
| "title": "group", | ||
| "type": "object", | ||
| "required": ["doc"], | ||
| "additionalProperties": false, | ||
| "anyOf":[ | ||
| {"required": ["data_type_def"]}, | ||
| {"required": ["data_type_inc"]}, | ||
| {"required": ["name"]} | ||
| ], | ||
| "properties": { | ||
| "name": {"$ref": "#/definitions/protectedString"}, | ||
| "default_name": {"$ref": "#/definitions/protectedString"}, | ||
| "doc": {"type": "string"}, | ||
| "data_type_def": {"$ref": "#/definitions/protectedString"}, | ||
| "data_type_inc": {"$ref": "#/definitions/protectedString"}, | ||
| "quantity": {"$ref": "#/definitions/quantity"}, | ||
| "linkable": {"type": "boolean"}, | ||
| "datasets": {"$ref": "#/definitions/datasets"}, | ||
| "links": {"$ref": "#/definitions/links"}, | ||
| "groups": {"$ref": "#/definitions/groups"}, | ||
| "attributes": {"$ref": "#/definitions/attributes"} | ||
| } | ||
| } | ||
| }, | ||
| "attributes": { | ||
| "type": "array", | ||
| "items": { | ||
| "title": "attribute", | ||
| "type": "object", | ||
| "required": ["doc"], | ||
| "additionalProperties": false, | ||
| "properties": { | ||
| "dtype": {"$ref": "#/definitions/dtype"}, | ||
| "dims": {"$ref": "#/definitions/dims"}, | ||
| "shape": {"$ref": "#/definitions/shape"}, | ||
| "name": {"type": "string"}, | ||
| "doc": {"type": "string"}, | ||
| "required": {"type": "boolean"}, | ||
| "value": {"description": "Optional constant, fixed value for the attribute."}, | ||
| "default_value": {"description": "Optional default value for variable-valued attributes."} | ||
| } | ||
| } | ||
| }, | ||
| "links": { | ||
| "type": "array", | ||
| "items": { | ||
| "title": "link", | ||
| "type": "object", | ||
| "required": ["target_type", "doc"], | ||
| "additionalProperties": false, | ||
| "properties": { | ||
| "name": {"type": "string"}, | ||
| "doc": {"type": "string"}, | ||
| "target_type": {"type": "string"}, | ||
| "quantity": {"$ref": "#/definitions/quantity"} | ||
| } | ||
| } | ||
| }, | ||
| "datasets": { | ||
| "type": "array", | ||
| "items": { | ||
| "title": "dataset", | ||
| "type": "object", | ||
| "required": ["doc"], | ||
| "additionalProperties": false, | ||
| "anyOf":[ | ||
| {"required": ["data_type_def"]}, | ||
| {"required": ["data_type_inc"]}, | ||
| {"required": ["name"]} | ||
| ], | ||
| "properties": { | ||
| "name": {"$ref": "#/definitions/protectedString"}, | ||
| "default_name": {"$ref": "#/definitions/protectedString"}, | ||
| "doc": {"type": "string"}, | ||
| "dtype": {"$ref": "#/definitions/dtype"}, | ||
| "dims": {"$ref": "#/definitions/dims"}, | ||
| "shape": {"$ref": "#/definitions/shape"}, | ||
| "data_type_def": {"$ref": "#/definitions/protectedString"}, | ||
| "data_type_inc": {"$ref": "#/definitions/protectedString"}, | ||
| "quantity": {"$ref": "#/definitions/quantity"}, | ||
| "linkable": {"type": "boolean"}, | ||
| "attributes": {"$ref": "#/definitions/attributes"}, | ||
| "value": {"description": "Optional constant, fixed value for the attribute."}, | ||
| "default_value": {"description": "Optional default value for variable-valued attributes."} | ||
| } | ||
| } | ||
| } | ||
| } | ||
| } |