Merge pull request #560 from microbiomedata/559-bump-schema-version-f…

…rom-1030-to-1054

Bump `nmdc-schema` from `10.3.0` to `10.5.5`

Makefile

@@ -3,14 +3,22 @@ init:
 	pip install -r requirements/dev.txt
 	pip install --editable .[dev]
 
+# Updates Python dependencies based upon the contents of the `requirements/main.in` and `requirements/dev.in` files.
+#
+# To omit the `--upgrade` option (included by default) when running `pip-compile`:
+# ```
+# $ make update-deps UPDATE_DEPS_MAIN_UPGRADE_OPT='' UPDATE_DEPS_DEV_UPGRADE_OPT=''
+# ```
+UPDATE_DEPS_MAIN_UPGRADE_OPT ?= --upgrade
+UPDATE_DEPS_DEV_UPGRADE_OPT ?= --upgrade
 update-deps:
     # --allow-unsafe pins packages considered unsafe: distribute, pip, setuptools.
 	pip install --upgrade pip-tools pip setuptools
-	pip-compile --upgrade --build-isolation \
+	pip-compile $(UPDATE_DEPS_MAIN_UPGRADE_OPT) --build-isolation \
 		--allow-unsafe --resolver=backtracking --strip-extras \
 		--output-file requirements/main.txt \
 		requirements/main.in
-	pip-compile --allow-unsafe --upgrade --build-isolation \
+	pip-compile --allow-unsafe $(UPDATE_DEPS_DEV_UPGRADE_OPT) --build-isolation \
 		--allow-unsafe --resolver=backtracking --strip-extras \
 		--output-file requirements/dev.txt \
 		requirements/dev.in

nmdc_runtime/util.py

@@ -16,7 +16,7 @@
 import requests
 from frozendict import frozendict
 from jsonschema.validators import Draft7Validator
-from nmdc_schema.nmdc_schema_accepting_legacy_ids import Database as NMDCDatabase
+from nmdc_schema.nmdc import Database as NMDCDatabase
 from nmdc_schema.get_nmdc_view import ViewGetter
 from pydantic import Field, BaseModel
 from pymongo.database import Database as MongoDatabase

requirements/dev.txt

@@ -9,11 +9,11 @@ attrs==23.2.0
     #   -c requirements/main.txt
     #   cattrs
     #   requests-cache
-black==24.2.0
-    # via
-    #   -c requirements/main.txt
-    #   -r requirements/dev.in
-build==1.1.1
+backports-tarfile==1.2.0
+    # via jaraco-context
+black==24.4.2
+    # via -r requirements/dev.in
+build==1.2.1
     # via pip-tools
 cattrs==23.2.3
     # via
@@ -23,10 +23,6 @@ certifi==2024.2.2
     # via
     #   -c requirements/main.txt
     #   requests
-cffi==1.16.0
-    # via
-    #   -c requirements/main.txt
-    #   cryptography
 charset-normalizer==3.3.2
     # via
     #   -c requirements/main.txt
@@ -36,30 +32,24 @@ click==8.1.7
     #   -c requirements/main.txt
     #   black
     #   pip-tools
-coverage==7.4.3
+coverage==7.5.3
     # via
     #   -r requirements/dev.in
     #   pytest-cov
-cryptography==42.0.5
-    # via
-    #   -c requirements/main.txt
-    #   secretstorage
-docutils==0.20.1
-    # via
-    #   -c requirements/main.txt
-    #   readme-renderer
+docutils==0.21.2
+    # via readme-renderer
 exceptiongroup==1.2.0
     # via
     #   -c requirements/main.txt
     #   cattrs
     #   pytest
-flake8==7.0.0
+flake8==7.1.0
     # via -r requirements/dev.in
 idna==3.6
     # via
     #   -c requirements/main.txt
     #   requests
-importlib-metadata==7.0.1
+importlib-metadata==7.1.0
     # via
     #   keyring
     #   twine
@@ -69,13 +59,13 @@ iniconfig==2.0.0
     #   pytest
 invoke==2.2.0
     # via -r requirements/dev.in
-jaraco-classes==3.3.1
+jaraco-classes==3.4.0
     # via keyring
-jeepney==0.8.0
-    # via
-    #   keyring
-    #   secretstorage
-keyring==24.3.1
+jaraco-context==5.3.0
+    # via keyring
+jaraco-functools==4.0.1
+    # via keyring
+keyring==25.2.1
     # via twine
 markdown-it-py==3.0.0
     # via
@@ -87,13 +77,13 @@ mdurl==0.1.2
     # via
     #   -c requirements/main.txt
     #   markdown-it-py
-more-itertools==10.2.0
-    # via jaraco-classes
-mypy-extensions==1.0.0
+more-itertools==10.3.0
     # via
-    #   -c requirements/main.txt
-    #   black
-nh3==0.2.15
+    #   jaraco-classes
+    #   jaraco-functools
+mypy-extensions==1.0.0
+    # via black
+nh3==0.2.17
     # via readme-renderer
 packaging==23.2
     # via
@@ -105,9 +95,9 @@ pathspec==0.12.1
     # via
     #   -c requirements/main.txt
     #   black
-pip-tools==7.4.0
+pip-tools==7.4.1
     # via -r requirements/dev.in
-pkginfo==1.9.6
+pkginfo==1.11.1
     # via twine
 platformdirs==4.2.0
     # via
@@ -118,22 +108,16 @@ pluggy==1.4.0
     # via
     #   -c requirements/main.txt
     #   pytest
-pycodestyle==2.11.1
+pycodestyle==2.12.0
     # via flake8
-pycparser==2.21
-    # via
-    #   -c requirements/main.txt
-    #   cffi
 pyflakes==3.2.0
-    # via
-    #   -c requirements/main.txt
-    #   flake8
+    # via flake8
 pygments==2.17.2
     # via
     #   -c requirements/main.txt
     #   readme-renderer
     #   rich
-pyproject-hooks==1.0.0
+pyproject-hooks==1.1.0
     # via
     #   build
     #   pip-tools
@@ -143,9 +127,9 @@ pytest==8.0.2
     #   -r requirements/dev.in
     #   pytest-asyncio
     #   pytest-cov
-pytest-asyncio==0.23.5
+pytest-asyncio==0.23.7
     # via -r requirements/dev.in
-pytest-cov==4.1.0
+pytest-cov==5.0.0
     # via -r requirements/dev.in
 readme-renderer==43.0
     # via twine
@@ -160,7 +144,7 @@ requests-cache==1.2.0
     # via
     #   -c requirements/main.txt
     #   -r requirements/dev.in
-requests-mock==1.11.0
+requests-mock==1.12.1
     # via -r requirements/dev.in
 requests-toolbelt==1.0.0
     # via
@@ -172,12 +156,9 @@ rich==13.7.1
     # via
     #   -c requirements/main.txt
     #   twine
-secretstorage==3.3.3
-    # via keyring
 six==1.16.0
     # via
     #   -c requirements/main.txt
-    #   requests-mock
     #   url-normalize
 tomli==2.0.1
     # via
@@ -186,9 +167,8 @@ tomli==2.0.1
     #   build
     #   coverage
     #   pip-tools
-    #   pyproject-hooks
     #   pytest
-twine==5.0.0
+twine==5.1.0
     # via -r requirements/dev.in
 typing-extensions==4.10.0
     # via
@@ -205,9 +185,9 @@ urllib3==2.0.7
     #   requests
     #   requests-cache
     #   twine
-wheel==0.42.0
+wheel==0.43.0
     # via pip-tools
-zipp==3.17.0
+zipp==3.19.2
     # via importlib-metadata
 
 # The following packages are considered to be unsafe in a requirements file:

requirements/main.in

@@ -24,7 +24,7 @@ mkdocs-jupyter
 mkdocs-material
 mkdocs-mermaid2-plugin
 motor
-nmdc-schema==10.3.0
+nmdc-schema==10.5.5
 openpyxl
 pandas
 passlib[bcrypt]