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Workflow for HDMF Dev compatibility (#77)
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@mavaylon1
mavaylon1 committed Sep 12, 2023
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28 changes: 28 additions & 0 deletions .github/workflows/hdmf_compatibility_schema.yml
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name: Check HDMF Dev Compatibility

on: [pull_request, workflow_dispatch]

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/
21 changes: 21 additions & 0 deletions .github/workflows/validate_schema.yaml
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name: Validate schema

on: [push, pull_request, workflow_dispatch]

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
280 changes: 280 additions & 0 deletions 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."}
}
}
}
}
}

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