From 7b6a251d4cfaf81c7ae82c9c44bbc4ef237e129f Mon Sep 17 00:00:00 2001 From: Harshad Hegde Date: Tue, 21 Jun 2022 14:31:55 -0500 Subject: [PATCH 1/7] moved schema into proj_name folder --- src/{ => neat_ml_schema}/schema/neat_ml_schema.yaml | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename src/{ => neat_ml_schema}/schema/neat_ml_schema.yaml (100%) diff --git a/src/schema/neat_ml_schema.yaml b/src/neat_ml_schema/schema/neat_ml_schema.yaml similarity index 100% rename from src/schema/neat_ml_schema.yaml rename to src/neat_ml_schema/schema/neat_ml_schema.yaml From bedc1101c492c844ee577d0077db477209838d0c Mon Sep 17 00:00:00 2001 From: Harshad Hegde Date: Tue, 21 Jun 2022 14:40:37 -0500 Subject: [PATCH 2/7] added missing files --- src/__init__.py | 0 src/neat_ml_schema/__init__.py | 1 + 2 files changed, 1 insertion(+) create mode 100644 src/__init__.py create mode 100644 src/neat_ml_schema/__init__.py diff --git a/src/__init__.py b/src/__init__.py new file mode 100644 index 0000000..e69de29 diff --git a/src/neat_ml_schema/__init__.py b/src/neat_ml_schema/__init__.py new file mode 100644 index 0000000..a5814f3 --- /dev/null +++ b/src/neat_ml_schema/__init__.py @@ -0,0 +1 @@ +from .datamodel.neat_ml_schema import * \ No newline at end of file From 9309d38719e049a3d7cda807631e005f012e4378 Mon Sep 17 00:00:00 2001 From: Harshad Hegde Date: Tue, 21 Jun 2022 14:41:02 -0500 Subject: [PATCH 3/7] format --- src/neat_ml_schema/__init__.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/neat_ml_schema/__init__.py b/src/neat_ml_schema/__init__.py index a5814f3..71b0b8d 100644 --- a/src/neat_ml_schema/__init__.py +++ b/src/neat_ml_schema/__init__.py @@ -1 +1 @@ -from .datamodel.neat_ml_schema import * \ No newline at end of file +from .datamodel.neat_ml_schema import * From c09fc81eadb5d373200e406282ad1fb0918ef49d Mon Sep 17 00:00:00 2001 From: Harshad Hegde Date: Tue, 21 Jun 2022 14:42:57 -0500 Subject: [PATCH 4/7] changed paths accordingly --- tests/test_neat_ml_schema.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tests/test_neat_ml_schema.py b/tests/test_neat_ml_schema.py index 1fec7e2..585672a 100644 --- a/tests/test_neat_ml_schema.py +++ b/tests/test_neat_ml_schema.py @@ -20,7 +20,7 @@ def setUpClass(cls) -> None: def setUp(self) -> None: """More setup.""" cwd = os.path.dirname(__file__) - self.project_dir = os.path.join(os.getcwd(), "src/schema/") + self.project_dir = os.path.join(os.getcwd(), "src/neat_ml_schema/schema/") self.resource_dir = os.path.join(cwd, "resources") self.GOOD_YAML_FILENAME = "test_good.yaml" self.BAD_YAML_FILENAME = "test_bad.yaml" From 19d2b61af992bcdffde9647cbf62159dae9ab4dc Mon Sep 17 00:00:00 2001 From: Harshad Hegde Date: Tue, 21 Jun 2022 14:43:52 -0500 Subject: [PATCH 5/7] formatted and paths changed. --- .github/workflows/doc_pages.yml | 2 +- Makefile | 2 +- README.md | 2 +- about.yaml | 2 +- docs/about.md | 2 +- src/docs/about.md | 2 +- tests/test_neat_ml_schema.py | 4 +++- 7 files changed, 9 insertions(+), 7 deletions(-) diff --git a/.github/workflows/doc_pages.yml b/.github/workflows/doc_pages.yml index 04ec5ba..3878b00 100644 --- a/.github/workflows/doc_pages.yml +++ b/.github/workflows/doc_pages.yml @@ -26,5 +26,5 @@ jobs: - name: Build documentation. run: | touch docs/.nojekyll - poetry run gen-doc -d docs src/schema/neat_ml_schema.yaml + poetry run gen-doc -d docs src/neat_ml_schema/schema/neat_ml_schema.yaml poetry run mkdocs gh-deploy \ No newline at end of file diff --git a/Makefile b/Makefile index ef0a48a..f2cb934 100644 --- a/Makefile +++ b/Makefile @@ -94,7 +94,7 @@ git-init-add: git-init git-add git-commit git-status git-init: git init git-add: - git add .gitignore .github Makefile LICENSE *.md examples utils about.yaml mkdocs.yml poetry.lock project.Makefile pyproject.toml src/schema/*yaml src/*/datamodel/*py src/data + git add .gitignore .github Makefile LICENSE *.md examples utils about.yaml mkdocs.yml poetry.lock project.Makefile pyproject.toml src/neat_ml_schema/schema/*yaml src/*/datamodel/*py src/data git add $(patsubst %, project/%, $(PROJECT_FOLDERS)) git-commit: git commit -m 'Initial commit' -a diff --git a/README.md b/README.md index e0ddbf8..bcbc7b3 100644 --- a/README.md +++ b/README.md @@ -1,5 +1,5 @@ # Neat-ml schema -Neat-ml schema defines the schema in the form of a [YAML file](https://github.com/Knowledge-Graph-Hub/neat-ml-schema/blob/main/neat_ml_schema/src/schema/neat-ml-schema.yaml) for data going into graph ML pipelines (specifically [NEAT](https://github.com/Knowledge-Graph-Hub/neat-ml)). This project itself is generated using the command `linkml-ws new` derived from the [linkML](https://github.com/linkml/linkml) project. +Neat-ml schema defines the schema in the form of a [YAML file](https://github.com/Knowledge-Graph-Hub/neat-ml-schema/blob/main/neat_ml_schema/src/neat_ml_schema/schema/neat-ml-schema.yaml) for data going into graph ML pipelines (specifically [NEAT](https://github.com/Knowledge-Graph-Hub/neat-ml)). This project itself is generated using the command `linkml-ws new` derived from the [linkML](https://github.com/linkml/linkml) project. [Documentation](https://knowledge-graph-hub.github.io/neat-ml-schema/) diff --git a/about.yaml b/about.yaml index 3b26531..af22ec9 100644 --- a/about.yaml +++ b/about.yaml @@ -1,3 +1,3 @@ name: neat_ml_schema description: Schema for driving NEAT -source_schema_path: neat_ml_schema/src/schema/neat_ml_schema.yaml +source_schema_path: neat_ml_schema/src/neat_ml_schema/schema/neat_ml_schema.yaml diff --git a/docs/about.md b/docs/about.md index f47c324..f9a07f1 100644 --- a/docs/about.md +++ b/docs/about.md @@ -1,3 +1,3 @@ # About NEAT schema -This project defines the schema in the form of a [YAML file](https://github.com/Knowledge-Graph-Hub/neat_ml_schema/blob/main/src/schema/neat_ml_schema.yaml) for data going into graph ML pipelines (specifically [NEAT](https://github.com/Knowledge-Graph-Hub/NEAT)). NEAT schema itself is generated from a [linkML](https://github.com/linkml/linkml) template. +This project defines the schema in the form of a [YAML file](https://github.com/Knowledge-Graph-Hub/neat_ml_schema/blob/main/src/neat_ml_schema/schema/neat_ml_schema.yaml) for data going into graph ML pipelines (specifically [NEAT](https://github.com/Knowledge-Graph-Hub/NEAT)). NEAT schema itself is generated from a [linkML](https://github.com/linkml/linkml) template. diff --git a/src/docs/about.md b/src/docs/about.md index f47c324..f9a07f1 100644 --- a/src/docs/about.md +++ b/src/docs/about.md @@ -1,3 +1,3 @@ # About NEAT schema -This project defines the schema in the form of a [YAML file](https://github.com/Knowledge-Graph-Hub/neat_ml_schema/blob/main/src/schema/neat_ml_schema.yaml) for data going into graph ML pipelines (specifically [NEAT](https://github.com/Knowledge-Graph-Hub/NEAT)). NEAT schema itself is generated from a [linkML](https://github.com/linkml/linkml) template. +This project defines the schema in the form of a [YAML file](https://github.com/Knowledge-Graph-Hub/neat_ml_schema/blob/main/src/neat_ml_schema/schema/neat_ml_schema.yaml) for data going into graph ML pipelines (specifically [NEAT](https://github.com/Knowledge-Graph-Hub/NEAT)). NEAT schema itself is generated from a [linkML](https://github.com/linkml/linkml) template. diff --git a/tests/test_neat_ml_schema.py b/tests/test_neat_ml_schema.py index 585672a..b1892ae 100644 --- a/tests/test_neat_ml_schema.py +++ b/tests/test_neat_ml_schema.py @@ -20,7 +20,9 @@ def setUpClass(cls) -> None: def setUp(self) -> None: """More setup.""" cwd = os.path.dirname(__file__) - self.project_dir = os.path.join(os.getcwd(), "src/neat_ml_schema/schema/") + self.project_dir = os.path.join( + os.getcwd(), "src/neat_ml_schema/schema/" + ) self.resource_dir = os.path.join(cwd, "resources") self.GOOD_YAML_FILENAME = "test_good.yaml" self.BAD_YAML_FILENAME = "test_bad.yaml" From cbce8745322448a0c7dc4d4a59adca1f8bbd27ba Mon Sep 17 00:00:00 2001 From: Harshad Hegde Date: Tue, 21 Jun 2022 14:50:16 -0500 Subject: [PATCH 6/7] test qc --- .github/workflows/qc.yml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/.github/workflows/qc.yml b/.github/workflows/qc.yml index c235d2e..0f7a13f 100644 --- a/.github/workflows/qc.yml +++ b/.github/workflows/qc.yml @@ -28,9 +28,9 @@ jobs: #---------------------------------------------- - name: Install Poetry uses: snok/install-poetry@v1.3 - with: - virtualenvs-create: true - virtualenvs-in-project: true + # with: + # virtualenvs-create: true + # virtualenvs-in-project: true #---------------------------------------------- # load cached venv if cache exists From 7e2eceb6369af97c19664b1d6f75e0bb2d1c03c9 Mon Sep 17 00:00:00 2001 From: Harshad Hegde Date: Tue, 21 Jun 2022 14:56:22 -0500 Subject: [PATCH 7/7] added another __init__ --- src/neat_ml_schema/datamodel/__init__.py | 0 1 file changed, 0 insertions(+), 0 deletions(-) create mode 100644 src/neat_ml_schema/datamodel/__init__.py diff --git a/src/neat_ml_schema/datamodel/__init__.py b/src/neat_ml_schema/datamodel/__init__.py new file mode 100644 index 0000000..e69de29