Merge branch 'main' into adding-docstrings

linkml · Mar 4, 2024 · ec4fd2c · ec4fd2c
2 parents 7bf5d96 + 9f6ffee
commit ec4fd2c
Show file tree

Hide file tree

Showing 28 changed files with 1,461 additions and 1,061 deletions.
diff --git a/.github/workflows/codespell.yml b/.github/workflows/codespell.yml
@@ -0,0 +1,23 @@
+# Codespell configuration is within pyproject.toml
+---
+name: Codespell
+
+on:
+  push:
+    branches: [main]
+  pull_request:
+    branches: [main]
+
+permissions:
+  contents: read
+
+jobs:
+  codespell:
+    name: Check for spelling errors
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+      - name: Codespell
+        uses: codespell-project/actions-codespell@v2
diff --git a/.github/workflows/main.yaml b/.github/workflows/main.yaml
@@ -72,3 +72,9 @@ jobs:
           path: htmlcov
         # Use always() to always run this step to publish test results when there are test failures
         if: ${{ always() }}
+
+      #----------------------------------------------
+      #           test generate-populate via `make scripts-all`
+      #----------------------------------------------
+      - name: generate-populate via make scripts-all
+        run: make scripts-all
diff --git a/.gitignore b/.gitignore
@@ -1,4 +1,5 @@
 .DS_Store
+target
 
 examples/output
 

diff --git a/Makefile b/Makefile
@@ -105,3 +105,5 @@ docker-publish: docker-build
 
 docker-run:
 	@docker run  -v $(PWD):/work -w /work -ti $(IM):$(VERSION) 
+
+include scripts.makefile
diff --git a/docs/datamodel/types/Objectidentifier.md b/docs/datamodel/types/Objectidentifier.md
@@ -15,5 +15,5 @@ URI: [linkml:Objectidentifier](https://w3id.org/linkml/Objectidentifier)
 
 |  |  |  |
 | --- | --- | --- |
-| **Comments:** | | Used for inheritence and type checking |
+| **Comments:** | | Used for inheritance and type checking |
 
diff --git a/docs/intro/export.md b/docs/intro/export.md
@@ -84,7 +84,7 @@ this guards against accidental overwrites.
 
 schemasheets allows *custom* sheet formats that map to the LinkML standard.
 
-you can use the combination of sheets2linkml and linkml2sheets to convert betweeen two sheet specifications.
+you can use the combination of sheets2linkml and linkml2sheets to convert between two sheet specifications.
 
 For example, let's say for schema1.tsv, you use a spreadsheet with the following headers:
 

diff --git a/docs/intro/mixed-sheets.md b/docs/intro/mixed-sheets.md
@@ -23,4 +23,4 @@ For example:
 |C|ForProfit|||||Organization|||||||
 |C|NonProfit|||||Organization|||Q163740|||foo|
 
- * [personinfo with tyoes](https://docs.google.com/spreadsheets/d/1wVoaiFg47aT9YWNeRfTZ8tYHN8s8PAuDx5i2HUcDpvQ/edit#gid=509198484)
+ * [personinfo with types](https://docs.google.com/spreadsheets/d/1wVoaiFg47aT9YWNeRfTZ8tYHN8s8PAuDx5i2HUcDpvQ/edit#gid=509198484)
diff --git a/examples/output/docs/types/Objectidentifier.md b/examples/output/docs/types/Objectidentifier.md
@@ -15,5 +15,5 @@ URI: [linkml:Objectidentifier](https://w3id.org/linkml/Objectidentifier)
 
 |  |  |  |
 | --- | --- | --- |
-| **Comments:** | | Used for inheritence and type checking |
+| **Comments:** | | Used for inheritance and type checking |
 
diff --git a/examples/output/jsonld/combined.jsonld b/examples/output/jsonld/combined.jsonld
@@ -207,7 +207,7 @@
       "definition_uri": "https://w3id.org/linkml/Objectidentifier",
       "description": "A URI or CURIE that represents an object in the model.",
       "comments": [
-        "Used for inheritence and type checking"
+        "Used for inheritance and type checking"
       ],
       "from_schema": "https://w3id.org/linkml/types",
       "imported_from": "linkml:types",

diff --git a/poetry.lock b/poetry.lock
diff --git a/pyproject.toml b/pyproject.toml
@@ -12,11 +12,11 @@ documentation = "https://github.com/linkml/schemasheets"
 
 [tool.poetry.dependencies]
 python = "^3.9"
-linkml = "^1.4"
-linkml-runtime = "^1.4"
-Jinja2 = "^3.0.3"
+linkml = ">=1.5.0"
+linkml-runtime = ">=1.5.0"
+Jinja2 = ">=3.0.3"
 ontodev-cogs = "^0.3.3"
-bioregistry = ">0.5.0, <0.7.0"
+bioregistry = ">0.5.0"
 
 
 [tool.poetry.dev-dependencies]
@@ -32,3 +32,11 @@ build-backend = "poetry.core.masonry.api"
 sheets2linkml = "schemasheets.schemamaker:convert"
 linkml2sheets = "schemasheets.schema_exporter:export_schema"
 sheets2project = "schemasheets.sheets_to_project:multigen"
+
+linkml2schemasheets-template = 'schemasheets.generate_populate:cli'
+[tool.codespell]
+# Ref: https://github.com/codespell-project/codespell#using-a-config-file
+skip = '.git,*.lock'
+check-hidden = true
+ignore-regex = '\bOTU\b'
+# ignore-words-list = ''
Original file line number	Diff line number	Diff line change
Expand Up		@@ -105,3 +105,5 @@ docker-publish: docker-build

		docker-run:
		@docker run -v $(PWD):/work -w /work -ti $(IM):$(VERSION)

		include scripts.makefile