From b6da5eded2bdc8fd008410afe8f9a283dedf57d4 Mon Sep 17 00:00:00 2001 From: Matthew Avaylon Date: Fri, 25 Aug 2023 11:21:05 -0700 Subject: [PATCH 01/34] Create validate_schema.yml --- .github/workflows/validate_schema.yml | 26 ++++++++++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100644 .github/workflows/validate_schema.yml diff --git a/.github/workflows/validate_schema.yml b/.github/workflows/validate_schema.yml new file mode 100644 index 0000000..c46e408 --- /dev/null +++ b/.github/workflows/validate_schema.yml @@ -0,0 +1,26 @@ +name: Validate HDMF Dev Compatibility + +on: [push, pull_request, workflow_dispatch] + +jobs: + validate: + 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@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 + pip install pytest + - name: Run HDMF tests + run: | + cd hdmf + pytest tests/unit/common/ From df776c0994ce66eb94ca6724b3c594b184b989ea Mon Sep 17 00:00:00 2001 From: Matthew Avaylon Date: Fri, 25 Aug 2023 11:25:47 -0700 Subject: [PATCH 02/34] Update validate_schema.yml --- .github/workflows/validate_schema.yml | 8 +++----- 1 file changed, 3 insertions(+), 5 deletions(-) diff --git a/.github/workflows/validate_schema.yml b/.github/workflows/validate_schema.yml index c46e408..51db180 100644 --- a/.github/workflows/validate_schema.yml +++ b/.github/workflows/validate_schema.yml @@ -16,11 +16,9 @@ jobs: 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 - pip install pytest - - name: Run HDMF tests + - 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 pytest tests/unit/common/ From dcd1b11879e1cda1bc6e17f674decc78b953556c Mon Sep 17 00:00:00 2001 From: Matthew Avaylon Date: Fri, 25 Aug 2023 11:26:47 -0700 Subject: [PATCH 03/34] Update validate_schema.yml --- .github/workflows/validate_schema.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/validate_schema.yml b/.github/workflows/validate_schema.yml index 51db180..faf7258 100644 --- a/.github/workflows/validate_schema.yml +++ b/.github/workflows/validate_schema.yml @@ -1,6 +1,6 @@ name: Validate HDMF Dev Compatibility -on: [push, pull_request, workflow_dispatch] +on: [pull_request, workflow_dispatch] jobs: validate: From 2ddcc0de75c8d31cefcdb54db3a6c48ef0aed21e Mon Sep 17 00:00:00 2001 From: Matthew Avaylon Date: Fri, 25 Aug 2023 11:28:42 -0700 Subject: [PATCH 04/34] Update validate_schema.yml --- .github/workflows/validate_schema.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/.github/workflows/validate_schema.yml b/.github/workflows/validate_schema.yml index faf7258..a62ecd6 100644 --- a/.github/workflows/validate_schema.yml +++ b/.github/workflows/validate_schema.yml @@ -21,4 +21,5 @@ jobs: 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 . pytest tests/unit/common/ From a5780346dc2f58908f3be8a4909466e1fe26312a Mon Sep 17 00:00:00 2001 From: Matthew Avaylon Date: Mon, 28 Aug 2023 09:54:34 -0700 Subject: [PATCH 05/34] Update namespace.yaml --- common/namespace.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/common/namespace.yaml b/common/namespace.yaml index b174003..5ed4ebe 100644 --- a/common/namespace.yaml +++ b/common/namespace.yaml @@ -23,7 +23,7 @@ namespaces: - doc: data types for different types of sparse matrices source: sparse.yaml title: Sparse data types - version: 1.8.0 + version: 1.8.1 - name: hdmf-experimental doc: Experimental data structures provided by HDMF. These are not guaranteed to be available in the future. @@ -48,4 +48,4 @@ namespaces: - doc: data types for storing references to web accessible resources source: resources.yaml title: Resource reference data types - version: 0.5.0 + version: 0.5.1 From 5bf0fef05a9563191dfb97be1cb8641fc1b16c10 Mon Sep 17 00:00:00 2001 From: Matthew Avaylon Date: Mon, 28 Aug 2023 09:56:11 -0700 Subject: [PATCH 06/34] Update conf.py --- docs/source/conf.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/docs/source/conf.py b/docs/source/conf.py index 3974479..e27dddd 100644 --- a/docs/source/conf.py +++ b/docs/source/conf.py @@ -83,9 +83,9 @@ def setup(app): # built documents. # # The short X.Y version. -version = 'v1.8.0' +version = 'v1.8.1' # The full version, including alpha/beta/rc tags. -release = 'v1.8.0' +release = 'v1.8.1' # The language for content autogenerated by Sphinx. Refer to documentation # for a list of supported languages. From 0fb5dc67c6ac8a372411444c6f798ccda27b0fce Mon Sep 17 00:00:00 2001 From: Matthew Avaylon Date: Mon, 28 Aug 2023 09:57:26 -0700 Subject: [PATCH 07/34] Update hdmf_common_release_notes.rst --- docs/source/hdmf_common_release_notes.rst | 3 +++ 1 file changed, 3 insertions(+) diff --git a/docs/source/hdmf_common_release_notes.rst b/docs/source/hdmf_common_release_notes.rst index 7a7d28d..10eecbb 100644 --- a/docs/source/hdmf_common_release_notes.rst +++ b/docs/source/hdmf_common_release_notes.rst @@ -2,6 +2,9 @@ hdmf-common Release Notes ========================= +1.8.1 (Upcoming) +---------------------- +- Added workflow to validate schema to HDMF dev branch. 1.8.0 (August 4, 2023) ---------------------- From 5f9cbf9a580cb717512150559f078fe92974f976 Mon Sep 17 00:00:00 2001 From: Matthew Avaylon Date: Mon, 28 Aug 2023 09:58:30 -0700 Subject: [PATCH 08/34] Update namespace.yaml --- common/namespace.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/common/namespace.yaml b/common/namespace.yaml index 5ed4ebe..29d69b6 100644 --- a/common/namespace.yaml +++ b/common/namespace.yaml @@ -48,4 +48,4 @@ namespaces: - doc: data types for storing references to web accessible resources source: resources.yaml title: Resource reference data types - version: 0.5.1 + version: 0.5.0 From 9154e4106100d8b71798a067d16139c89428d8c2 Mon Sep 17 00:00:00 2001 From: Matthew Avaylon Date: Mon, 28 Aug 2023 10:13:52 -0700 Subject: [PATCH 09/34] Update conf.py --- docs/source/conf.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/docs/source/conf.py b/docs/source/conf.py index e27dddd..3974479 100644 --- a/docs/source/conf.py +++ b/docs/source/conf.py @@ -83,9 +83,9 @@ def setup(app): # built documents. # # The short X.Y version. -version = 'v1.8.1' +version = 'v1.8.0' # The full version, including alpha/beta/rc tags. -release = 'v1.8.1' +release = 'v1.8.0' # The language for content autogenerated by Sphinx. Refer to documentation # for a list of supported languages. From 36d0d971c8c8ac547ddf0922bb83f85a368a854a Mon Sep 17 00:00:00 2001 From: Matthew Avaylon Date: Mon, 28 Aug 2023 10:14:13 -0700 Subject: [PATCH 10/34] Update namespace.yaml --- common/namespace.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/common/namespace.yaml b/common/namespace.yaml index 29d69b6..b174003 100644 --- a/common/namespace.yaml +++ b/common/namespace.yaml @@ -23,7 +23,7 @@ namespaces: - doc: data types for different types of sparse matrices source: sparse.yaml title: Sparse data types - version: 1.8.1 + version: 1.8.0 - name: hdmf-experimental doc: Experimental data structures provided by HDMF. These are not guaranteed to be available in the future. From 2dd3d21c94792b0280f725bfde9988b2c191ce60 Mon Sep 17 00:00:00 2001 From: Matthew Avaylon Date: Mon, 28 Aug 2023 10:14:40 -0700 Subject: [PATCH 11/34] Update hdmf_common_release_notes.rst --- docs/source/hdmf_common_release_notes.rst | 4 ---- 1 file changed, 4 deletions(-) diff --git a/docs/source/hdmf_common_release_notes.rst b/docs/source/hdmf_common_release_notes.rst index 10eecbb..268b4c7 100644 --- a/docs/source/hdmf_common_release_notes.rst +++ b/docs/source/hdmf_common_release_notes.rst @@ -2,10 +2,6 @@ hdmf-common Release Notes ========================= -1.8.1 (Upcoming) ----------------------- -- Added workflow to validate schema to HDMF dev branch. - 1.8.0 (August 4, 2023) ---------------------- - No change in the hdmf-common namespace. See :ref:`here ` for changes to the From 64a28aa73146ce8a1d73a2d8e19d960c132a7b6c Mon Sep 17 00:00:00 2001 From: Matthew Avaylon Date: Mon, 28 Aug 2023 10:14:59 -0700 Subject: [PATCH 12/34] Update hdmf_common_release_notes.rst --- docs/source/hdmf_common_release_notes.rst | 1 + 1 file changed, 1 insertion(+) diff --git a/docs/source/hdmf_common_release_notes.rst b/docs/source/hdmf_common_release_notes.rst index 268b4c7..7a7d28d 100644 --- a/docs/source/hdmf_common_release_notes.rst +++ b/docs/source/hdmf_common_release_notes.rst @@ -2,6 +2,7 @@ hdmf-common Release Notes ========================= + 1.8.0 (August 4, 2023) ---------------------- - No change in the hdmf-common namespace. See :ref:`here ` for changes to the From e1999266854098be29b4c663470cca172d21a4fb Mon Sep 17 00:00:00 2001 From: Matthew Avaylon Date: Fri, 8 Sep 2023 18:07:40 -0700 Subject: [PATCH 13/34] Rename validate_schema.yml to hdmf_compatibility_schema.yml --- .../{validate_schema.yml => hdmf_compatibility_schema.yml} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename .github/workflows/{validate_schema.yml => hdmf_compatibility_schema.yml} (100%) diff --git a/.github/workflows/validate_schema.yml b/.github/workflows/hdmf_compatibility_schema.yml similarity index 100% rename from .github/workflows/validate_schema.yml rename to .github/workflows/hdmf_compatibility_schema.yml From 9f0ed7b3e39025d645a6c4e701393e07add1b1de Mon Sep 17 00:00:00 2001 From: Matthew Avaylon Date: Fri, 8 Sep 2023 18:10:05 -0700 Subject: [PATCH 14/34] Create validate_schema.yaml --- .github/workflows/validate_schema.yaml | 21 +++++++++++++++++++++ 1 file changed, 21 insertions(+) create mode 100644 .github/workflows/validate_schema.yaml diff --git a/.github/workflows/validate_schema.yaml b/.github/workflows/validate_schema.yaml new file mode 100644 index 0000000..d53a4eb --- /dev/null +++ b/.github/workflows/validate_schema.yaml @@ -0,0 +1,21 @@ +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 3.10 + uses: actions/setup-python@v4 + with: + python-version: "3.10" + - 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 From 1fe5a3e305f938094ca2f926a8068e11af1151ab Mon Sep 17 00:00:00 2001 From: Matthew Avaylon Date: Fri, 8 Sep 2023 18:16:26 -0700 Subject: [PATCH 15/34] Create hdmf-common.schema.json --- hdmf-common.schema.json | 280 ++++++++++++++++++++++++++++++++++++++++ 1 file changed, 280 insertions(+) create mode 100644 hdmf-common.schema.json diff --git a/hdmf-common.schema.json b/hdmf-common.schema.json new file mode 100644 index 0000000..fc0f381 --- /dev/null +++ b/hdmf-common.schema.json @@ -0,0 +1,280 @@ +{ + "$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."} + } + } + } + } +} From f73ab87aa3b5347a954f15bf9e9ff16437bba4b6 Mon Sep 17 00:00:00 2001 From: Matthew Avaylon Date: Mon, 11 Sep 2023 17:22:28 -0700 Subject: [PATCH 16/34] Update hdmf_compatibility_schema.yml --- .github/workflows/hdmf_compatibility_schema.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/hdmf_compatibility_schema.yml b/.github/workflows/hdmf_compatibility_schema.yml index a62ecd6..468d74b 100644 --- a/.github/workflows/hdmf_compatibility_schema.yml +++ b/.github/workflows/hdmf_compatibility_schema.yml @@ -1,4 +1,4 @@ -name: Validate HDMF Dev Compatibility +name: Check HDMF Dev Compatibility on: [pull_request, workflow_dispatch] From dd42bb482d8ad5ec2fcbc78e366b0fd6488e4719 Mon Sep 17 00:00:00 2001 From: Matthew Avaylon Date: Mon, 11 Sep 2023 17:23:51 -0700 Subject: [PATCH 17/34] Update validate_schema.yaml --- .github/workflows/validate_schema.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/validate_schema.yaml b/.github/workflows/validate_schema.yaml index d53a4eb..f9ae464 100644 --- a/.github/workflows/validate_schema.yaml +++ b/.github/workflows/validate_schema.yaml @@ -9,10 +9,10 @@ jobs: runs-on: ubuntu-latest steps: - uses: actions/checkout@v3 - - name: Set up Python 3.10 + - name: Set up Python 3.11 uses: actions/setup-python@v4 with: - python-version: "3.10" + python-version: "3.11" - name: Install dev branch of HDMF run: | pip install git+https://github.com/hdmf-dev/hdmf.git From 0ab5ed92fff7da04e5970029e6e82033b539c2d4 Mon Sep 17 00:00:00 2001 From: Matthew Avaylon Date: Mon, 11 Sep 2023 17:29:59 -0700 Subject: [PATCH 18/34] Update validate_schema.yaml --- .github/workflows/validate_schema.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/validate_schema.yaml b/.github/workflows/validate_schema.yaml index f9ae464..774eadc 100644 --- a/.github/workflows/validate_schema.yaml +++ b/.github/workflows/validate_schema.yaml @@ -1,6 +1,6 @@ name: Validate schema -on: [push, pull_request, workflow_dispatch] +on: [pull_request, workflow_dispatch] jobs: validate: From 9a1b061a783bdcbf38b47aad1a9ed7a1f7d21f53 Mon Sep 17 00:00:00 2001 From: Matthew Avaylon Date: Mon, 11 Sep 2023 17:56:44 -0700 Subject: [PATCH 19/34] Update hdmf_compatibility_schema.yml --- .github/workflows/hdmf_compatibility_schema.yml | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/.github/workflows/hdmf_compatibility_schema.yml b/.github/workflows/hdmf_compatibility_schema.yml index 468d74b..425a2e0 100644 --- a/.github/workflows/hdmf_compatibility_schema.yml +++ b/.github/workflows/hdmf_compatibility_schema.yml @@ -11,7 +11,9 @@ jobs: with: all_but_latest: true access_token: ${{ github.token }} - - uses: actions/checkout@v3 + - uses: actions/checkout@v4 + with: + ref: ${{ github.ref }} # checkout branch - name: Set up Python 3.11 uses: actions/setup-python@v4 with: From f099e8b5e31267a197e65331bee9db0719b9fa73 Mon Sep 17 00:00:00 2001 From: Matthew Avaylon Date: Mon, 11 Sep 2023 18:01:49 -0700 Subject: [PATCH 20/34] Update hdmf_compatibility_schema.yml --- .github/workflows/hdmf_compatibility_schema.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/hdmf_compatibility_schema.yml b/.github/workflows/hdmf_compatibility_schema.yml index 425a2e0..65fdf20 100644 --- a/.github/workflows/hdmf_compatibility_schema.yml +++ b/.github/workflows/hdmf_compatibility_schema.yml @@ -3,7 +3,7 @@ name: Check HDMF Dev Compatibility on: [pull_request, workflow_dispatch] jobs: - validate: + check_compatibility: runs-on: ubuntu-latest steps: - name: Cancel non-latest runs From 82c6672d9029ca0a7eac9779e73560b3de26c4c1 Mon Sep 17 00:00:00 2001 From: Matthew Avaylon Date: Mon, 11 Sep 2023 18:04:19 -0700 Subject: [PATCH 21/34] Update validate_schema.yaml --- .github/workflows/validate_schema.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/validate_schema.yaml b/.github/workflows/validate_schema.yaml index 774eadc..f9ae464 100644 --- a/.github/workflows/validate_schema.yaml +++ b/.github/workflows/validate_schema.yaml @@ -1,6 +1,6 @@ name: Validate schema -on: [pull_request, workflow_dispatch] +on: [push, pull_request, workflow_dispatch] jobs: validate: From 2c173d4573803db1c0de4d4d07cc78513606201a Mon Sep 17 00:00:00 2001 From: Matthew Avaylon Date: Mon, 11 Sep 2023 20:17:24 -0700 Subject: [PATCH 22/34] Update hdmf_compatibility_schema.yml --- .github/workflows/hdmf_compatibility_schema.yml | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/.github/workflows/hdmf_compatibility_schema.yml b/.github/workflows/hdmf_compatibility_schema.yml index 65fdf20..c301786 100644 --- a/.github/workflows/hdmf_compatibility_schema.yml +++ b/.github/workflows/hdmf_compatibility_schema.yml @@ -12,8 +12,6 @@ jobs: all_but_latest: true access_token: ${{ github.token }} - uses: actions/checkout@v4 - with: - ref: ${{ github.ref }} # checkout branch - name: Set up Python 3.11 uses: actions/setup-python@v4 with: @@ -24,4 +22,8 @@ jobs: 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.ref }} # checkout branch + cd + cd hdmf pytest tests/unit/common/ From 150ad4f79ef5d038ca217de28401e7912abcb4fb Mon Sep 17 00:00:00 2001 From: Matthew Avaylon Date: Mon, 11 Sep 2023 20:20:27 -0700 Subject: [PATCH 23/34] Update hdmf_compatibility_schema.yml --- .github/workflows/hdmf_compatibility_schema.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/.github/workflows/hdmf_compatibility_schema.yml b/.github/workflows/hdmf_compatibility_schema.yml index c301786..7d745a7 100644 --- a/.github/workflows/hdmf_compatibility_schema.yml +++ b/.github/workflows/hdmf_compatibility_schema.yml @@ -23,6 +23,7 @@ jobs: python -m pip install -r requirements-dev.txt -r requirements.txt python -m pip install -e . cd src/hdmf/common/hdmf-common-schema + git fetch git checkout ${{ github.ref }} # checkout branch cd cd hdmf From a478b44808457132cdb3705230dd810d8a2d450e Mon Sep 17 00:00:00 2001 From: Matthew Avaylon Date: Mon, 11 Sep 2023 20:36:47 -0700 Subject: [PATCH 24/34] Update hdmf_compatibility_schema.yml --- .github/workflows/hdmf_compatibility_schema.yml | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/.github/workflows/hdmf_compatibility_schema.yml b/.github/workflows/hdmf_compatibility_schema.yml index 7d745a7..26fccc7 100644 --- a/.github/workflows/hdmf_compatibility_schema.yml +++ b/.github/workflows/hdmf_compatibility_schema.yml @@ -23,8 +23,9 @@ jobs: python -m pip install -r requirements-dev.txt -r requirements.txt python -m pip install -e . cd src/hdmf/common/hdmf-common-schema + git remote update git fetch - git checkout ${{ github.ref }} # checkout branch + git checkout -b ${{ github.ref }} # checkout branch cd cd hdmf pytest tests/unit/common/ From b99948aad1e5b5abf699df1f3d7bbc0b09b3db1f Mon Sep 17 00:00:00 2001 From: Matthew Avaylon Date: Mon, 11 Sep 2023 20:54:55 -0700 Subject: [PATCH 25/34] Update hdmf_compatibility_schema.yml --- .github/workflows/hdmf_compatibility_schema.yml | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/.github/workflows/hdmf_compatibility_schema.yml b/.github/workflows/hdmf_compatibility_schema.yml index 26fccc7..fa9bff5 100644 --- a/.github/workflows/hdmf_compatibility_schema.yml +++ b/.github/workflows/hdmf_compatibility_schema.yml @@ -26,6 +26,8 @@ jobs: git remote update git fetch git checkout -b ${{ github.ref }} # checkout branch - cd - cd hdmf + cd .. + cd .. + cd .. + cd .. pytest tests/unit/common/ From af56adc9dc393fe08905db1fe5e198aaf8179b4b Mon Sep 17 00:00:00 2001 From: Matthew Avaylon Date: Mon, 11 Sep 2023 20:57:10 -0700 Subject: [PATCH 26/34] Update hdmf_compatibility_schema.yml --- .github/workflows/hdmf_compatibility_schema.yml | 5 +---- 1 file changed, 1 insertion(+), 4 deletions(-) diff --git a/.github/workflows/hdmf_compatibility_schema.yml b/.github/workflows/hdmf_compatibility_schema.yml index fa9bff5..8fdd259 100644 --- a/.github/workflows/hdmf_compatibility_schema.yml +++ b/.github/workflows/hdmf_compatibility_schema.yml @@ -26,8 +26,5 @@ jobs: git remote update git fetch git checkout -b ${{ github.ref }} # checkout branch - cd .. - cd .. - cd .. - cd .. + cd pytest tests/unit/common/ From 1089c4f9791ad8a05270dc0dbe6052ebe3807727 Mon Sep 17 00:00:00 2001 From: Matthew Avaylon Date: Mon, 11 Sep 2023 20:58:33 -0700 Subject: [PATCH 27/34] Update hdmf_compatibility_schema.yml --- .github/workflows/hdmf_compatibility_schema.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/hdmf_compatibility_schema.yml b/.github/workflows/hdmf_compatibility_schema.yml index 8fdd259..21dd547 100644 --- a/.github/workflows/hdmf_compatibility_schema.yml +++ b/.github/workflows/hdmf_compatibility_schema.yml @@ -27,4 +27,4 @@ jobs: git fetch git checkout -b ${{ github.ref }} # checkout branch cd - pytest tests/unit/common/ + pytest hdmf/tests/unit/common/ From fb609e1f704abaa7879d398110edb18e1f390085 Mon Sep 17 00:00:00 2001 From: Matthew Avaylon Date: Mon, 11 Sep 2023 21:04:03 -0700 Subject: [PATCH 28/34] Update hdmf_compatibility_schema.yml --- .github/workflows/hdmf_compatibility_schema.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/hdmf_compatibility_schema.yml b/.github/workflows/hdmf_compatibility_schema.yml index 21dd547..42b738f 100644 --- a/.github/workflows/hdmf_compatibility_schema.yml +++ b/.github/workflows/hdmf_compatibility_schema.yml @@ -26,5 +26,5 @@ jobs: git remote update git fetch git checkout -b ${{ github.ref }} # checkout branch - cd + cd .. 4 pytest hdmf/tests/unit/common/ From 7417ee4e303d719a31d249e256f84a9000757d78 Mon Sep 17 00:00:00 2001 From: Matthew Avaylon Date: Mon, 11 Sep 2023 21:05:49 -0700 Subject: [PATCH 29/34] Update hdmf_compatibility_schema.yml --- .github/workflows/hdmf_compatibility_schema.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/hdmf_compatibility_schema.yml b/.github/workflows/hdmf_compatibility_schema.yml index 42b738f..3e12056 100644 --- a/.github/workflows/hdmf_compatibility_schema.yml +++ b/.github/workflows/hdmf_compatibility_schema.yml @@ -26,5 +26,5 @@ jobs: git remote update git fetch git checkout -b ${{ github.ref }} # checkout branch - cd .. 4 - pytest hdmf/tests/unit/common/ + cd ../../../.. + pytest tests/unit/common/ From 5a639b1b7e5cc60567a26bf6a96805bba5c653a4 Mon Sep 17 00:00:00 2001 From: Matthew Avaylon Date: Mon, 11 Sep 2023 21:08:01 -0700 Subject: [PATCH 30/34] Update hdmf_compatibility_schema.yml --- .github/workflows/hdmf_compatibility_schema.yml | 1 - 1 file changed, 1 deletion(-) diff --git a/.github/workflows/hdmf_compatibility_schema.yml b/.github/workflows/hdmf_compatibility_schema.yml index 3e12056..9c6b57c 100644 --- a/.github/workflows/hdmf_compatibility_schema.yml +++ b/.github/workflows/hdmf_compatibility_schema.yml @@ -23,7 +23,6 @@ jobs: python -m pip install -r requirements-dev.txt -r requirements.txt python -m pip install -e . cd src/hdmf/common/hdmf-common-schema - git remote update git fetch git checkout -b ${{ github.ref }} # checkout branch cd ../../../.. From dcdf049e547dbbbb6b90739d0e146eb620461692 Mon Sep 17 00:00:00 2001 From: Matthew Avaylon Date: Mon, 11 Sep 2023 21:11:27 -0700 Subject: [PATCH 31/34] Update hdmf_compatibility_schema.yml --- .github/workflows/hdmf_compatibility_schema.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/hdmf_compatibility_schema.yml b/.github/workflows/hdmf_compatibility_schema.yml index 9c6b57c..40c041b 100644 --- a/.github/workflows/hdmf_compatibility_schema.yml +++ b/.github/workflows/hdmf_compatibility_schema.yml @@ -24,6 +24,6 @@ jobs: python -m pip install -e . cd src/hdmf/common/hdmf-common-schema git fetch - git checkout -b ${{ github.ref }} # checkout branch + git checkout ${{ github.ref }} # checkout branch cd ../../../.. pytest tests/unit/common/ From 0cb6ecf36a11127c9f14b51180585855049148f7 Mon Sep 17 00:00:00 2001 From: Matthew Avaylon Date: Mon, 11 Sep 2023 21:17:17 -0700 Subject: [PATCH 32/34] Update hdmf_compatibility_schema.yml --- .github/workflows/hdmf_compatibility_schema.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/.github/workflows/hdmf_compatibility_schema.yml b/.github/workflows/hdmf_compatibility_schema.yml index 40c041b..87d2893 100644 --- a/.github/workflows/hdmf_compatibility_schema.yml +++ b/.github/workflows/hdmf_compatibility_schema.yml @@ -23,6 +23,7 @@ jobs: python -m pip install -r requirements-dev.txt -r requirements.txt python -m pip install -e . cd src/hdmf/common/hdmf-common-schema + git remote update git fetch git checkout ${{ github.ref }} # checkout branch cd ../../../.. From 01f4503c0b5664f08cd46c63f5268ccf327cd609 Mon Sep 17 00:00:00 2001 From: Matthew Avaylon Date: Mon, 11 Sep 2023 21:22:43 -0700 Subject: [PATCH 33/34] Update hdmf_compatibility_schema.yml --- .github/workflows/hdmf_compatibility_schema.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/hdmf_compatibility_schema.yml b/.github/workflows/hdmf_compatibility_schema.yml index 87d2893..7dbbf06 100644 --- a/.github/workflows/hdmf_compatibility_schema.yml +++ b/.github/workflows/hdmf_compatibility_schema.yml @@ -25,6 +25,6 @@ jobs: cd src/hdmf/common/hdmf-common-schema git remote update git fetch - git checkout ${{ github.ref }} # checkout branch + git checkout ${{ github.head_ref }} # checkout branch cd ../../../.. pytest tests/unit/common/ From 0276ec76675b5916ff3b83bc0e6e8b3d83b70932 Mon Sep 17 00:00:00 2001 From: Matthew Avaylon Date: Mon, 11 Sep 2023 21:25:14 -0700 Subject: [PATCH 34/34] Update hdmf_compatibility_schema.yml --- .github/workflows/hdmf_compatibility_schema.yml | 2 -- 1 file changed, 2 deletions(-) diff --git a/.github/workflows/hdmf_compatibility_schema.yml b/.github/workflows/hdmf_compatibility_schema.yml index 7dbbf06..dc76f68 100644 --- a/.github/workflows/hdmf_compatibility_schema.yml +++ b/.github/workflows/hdmf_compatibility_schema.yml @@ -23,8 +23,6 @@ jobs: python -m pip install -r requirements-dev.txt -r requirements.txt python -m pip install -e . cd src/hdmf/common/hdmf-common-schema - git remote update - git fetch git checkout ${{ github.head_ref }} # checkout branch cd ../../../.. pytest tests/unit/common/