Merge branch 'main' into 529_add_NCBI_biosample_and_project_ids_to_NE…

…ON_soil

.github/workflows/build-and-push-docker-images.yml

@@ -1,8 +1,15 @@
 name: build-and-push-docker-images
 on:
+  workflow_dispatch:
   push:
     branches:
       - main
+    paths:
+      - '.github/workflows/build-and-push-docker-images.yml'
+      - 'Makefile'
+      - '**.Dockerfile'
+      - '**.py'
+      - 'requirements/main.txt'
 
 jobs:
   docker:

.github/workflows/release-to-pypi.yml

@@ -0,0 +1,30 @@
+name: Publish Python Package
+
+on:
+  release:
+    types: [created]
+
+jobs:
+  build-n-publish:
+    name: Build and publish Python 🐍 distributions 📦 to PyPI
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Set up Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: '3.10'
+
+      - name: Build source and wheel archives
+        run: |
+          make init
+          python -m build
+
+      - name: Publish distribution 📦 to PyPI
+        if: github.repository == 'microbiomedata/nmdc-runtime'
+        uses: pypa/gh-action-pypi-publish@master
+        with:
+          user: __token__
+          password: ${{ secrets.PYPI_PASSWORD }}

README.md

@@ -144,3 +144,12 @@ desired and does not break over time.
 
 [For hints on how to write tests for solids and pipelines in Dagster, see their documentation
 tutorial on Testing](https://docs.dagster.io/tutorial/testable).
+
+
+## Release to PyPI
+
+```
+rm -rf dist
+python -m build
+twine upload dist/*
+```

RELEASES.md

@@ -13,6 +13,10 @@ Use <https://en.wikipedia.org/wiki/ISO_8601> to express the current date and tim
 time offset for New York on standard time (EST). "−08:00" would be for California.
 
 ## Release Log
+* 2023-11-07T19:45:00-08:00 update nmdc-schema package from 9.0.4 to 9.1.0
+* 2023-11-07T19:30:00-08:00 update nmdc-schema package from 8.1.2 to 9.0.4
+* 2023-11-07T17:30:00-08:00 update nmdc-schema package from 8.0.0 to 8.1.2
+* (missing entries)
 * 2023-08-31T22:15:00-07:00 update nmdc-schema package from 7.7.2 to 7.8.0
 * 2023-01-27T13:13:09-05:00 return 201 on activity creation
 * 2023-01-25T13:13:09-05:00 all typecodes for minter

components/nmdc_runtime/workflow_execution_activity/core.py

@@ -94,7 +94,7 @@ def insert_into_keys(
     workflow: Workflow, data_objects: list[DataObject]
 ) -> dict[str, Any]:
     """Insert data object url into correct workflow input field."""
-    workflow_dict = workflow.dict()
+    workflow_dict = workflow.model_dump()
     for key in workflow_dict["inputs"]:
         for do in data_objects:
             if workflow_dict["inputs"][key] == str(do.data_object_type):

demo/metadata_migration/notebooks/.mongo.yaml.example

@@ -15,6 +15,14 @@
 #      mongodb://root:pass@localhost:27017/?authSource=admin
 #      ```
 #
+#    Example:
+#      Assuming the same scenario as in the previous example, but without
+#      access control enabled (i.e. no username/password),
+#      the value of `uri` would be:
+#      ```
+#      mongodb://localhost:27017/
+#      ```
+#
 #    Reference: 
 #      https://www.mongodb.com/docs/database-tools/mongodump/#std-option-mongodump.--uri
 #