Merge pull request #297 from microbiomedata/feat-nmdc-schema-python-d…

…ependency

Declare `nmdc-schema` as a Python dependency

.github/workflows/test_pages_build.yaml

@@ -54,7 +54,7 @@ jobs:
           poetry run mkdocs build -d dist
       
       - name: Upload artifact
-        uses: actions/upload-pages-artifact@v1
+        uses: actions/upload-pages-artifact@v3
         with:
           path: dist
 

README.md

@@ -22,28 +22,14 @@ Note that the while this repo is named `submission-schema`, the generated artifa
 
 ### Updating the submission schema
 
-Here's how you can update the submission schema to use a new version of `nmdc-schema`:
-
-1. Update the one occurrence of the `nmdc-schema` version number in `project.Makefile`:
-
-    ```diff
-    local/nmdc.yaml:
-    -        wget -O $@ https://raw.githubusercontent.com/microbiomedata/nmdc-schema/v11.0.1/nmdc_schema/nmdc_materialized_patterns.yaml
-    +        wget -O $@ https://raw.githubusercontent.com/microbiomedata/nmdc-schema/v11.1.0/nmdc_schema/nmdc_materialized_patterns.yaml
-    ```
-
-2. Update all the `nmdc-schema` version numbers in `sheets_and_friends/tsv_in/import_slots_regardless.tsv`
-
-    ```diff
-    - Biosample	https://raw.githubusercontent.com/microbiomedata/nmdc-schema/v11.0.1/nmdc_schema/nmdc_materialized_patterns.yaml	abs_air_humidity ...
-    + Biosample	https://raw.githubusercontent.com/microbiomedata/nmdc-schema/v11.1.0/nmdc_schema/nmdc_materialized_patterns.yaml	abs_air_humidity ...
-    ```
-    > That is one of the _many_ occurrences in that file.
-    >
-    > **Note:** The above search-and-replacement (of all occurrences in that file) can be done inside Vim via:
-    > ```vim
-    > :%s/nmdc-schema\/v11.0.1/nmdc-schema\/v11.1.0/g
-    > ```
+The version of `nmdc-schema` used as a basis when building the submission schema is controlled by a dependency in the `dev` group, specified in `pyproject.toml`. You can update the version used by running:
+
+```shell
+poetry add nmdc-schema==X.Y.Z --group dev  # replace X.Y.Z with the desired version
+```
+
+> [!NOTE]  
+> It is important to use the `==` version constraint to ensure the exact version is installed. 
 
 ### Building the submission schema
 

project.Makefile

@@ -34,7 +34,7 @@ sheets_and_friends-clean:
 	rm -rf sheets_and_friends/yaml_out/with_shuttles.yaml
 
 local/with_shuttles.yaml: src/nmdc_submission_schema/schema/nmdc_submission_schema_base.yaml \
-sheets_and_friends/tsv_in/import_slots_regardless.tsv
+sheets_and_friends/tsv_in/import_slots_regardless.tsv local/nmdc.yaml
 		$(RUN) do_shuttle \
 			--config_tsv  $(word 2,$^) \
 			--recipient_model $(word 1,$^) \
@@ -148,8 +148,8 @@ local/with_shuttles_yq.yaml: local/with_shuttles.yaml
 modifications-clean:
 	rm -rf sheets_and_friends/yaml_out/with_modifications.yaml
 
-local/nmdc.yaml:
-	wget -O $@ https://raw.githubusercontent.com/microbiomedata/nmdc-schema/v11.3.0/nmdc_schema/nmdc_materialized_patterns.yaml
+local/nmdc.yaml: poetry.lock
+	$(RUN) python src/nmdc_submission_schema/scripts/export_nmdc_schema.py -o $@
 
 # sheets-for-nmdc-submission-schema_validation_converter_empty.tsv
 local/with_modifications.yaml: local/with_shuttles_yq.yaml \

pyproject.toml

@@ -12,29 +12,25 @@ include = [
     { path = "src/nmdc_submission_schema/project/**/*", format = ["sdist", "wheel"] }
 ]
 
-# note that the nmdc-schema is not imported as a module,
-#   but one file from the nmdc-schema is accessed via sheets_and_friends/tsv_in/import_slots_regardless.tsv
-#   and project.Makefile
-#   look for strings like
-#   https://raw.githubusercontent.com/microbiomedata/nmdc-schema/v7.7.2/nmdc_schema/nmdc_materialized_patterns.yaml
 [tool.poetry.dependencies]
 python = "^3.9"
 linkml-runtime = "^1.6.2"
 
 [tool.poetry.group.dev.dependencies]
-gsheets = "^0.6.1"
 db-dtypes = "^1.3.1"
 duckdb = "^1.1.3"
 duckdb-engine = "^0.13.6"
 exhaustion-check = "^0.1.3"
 google-cloud-bigquery = "^3.27.0"
+gsheets = "^0.6.1"
 inflection = "^0.5.1"
 jupyter = "^1.1.1"
 jupyter-datatables = "^0.3.9"
 linkml = "^1.7.10"
 matplotlib = "^3.9.2"
 mkdocs-material = "^9.1.2"
 mkdocs-mermaid2-plugin = "^1.1.0"
+nmdc-schema = "11.4.0rc1"
 oaklib = "^0.6.1" # was using 0.5.6 up to 2024-12-10
 pymongo = "^4.10.1"
 pytest = "^8.3.4"