Bump nmdc-schema from 11.3.0 to 11.4.0 without updating Dagster

In this commit, I bumped `nmdc-schema` in `main.in`, then ran: ``` make update-deps \ UPDATE_DEPS_MAIN_UPGRADE_OPT='' UPDATE_DEPS_DEV_UPGRADE_OPT='' ``` When those two options are included, the underlying `pip-compile` command does not include the `--upgrade` option. As a result, `pip-compile` does not try to upgrade all dependencies to their latest versions. I did this because, when the `--upgrade` option was being passed to `pip-compile`, the automated test suite in GitHub Actions was failing due to something related to Dagster, which did get updated in a way that has breaking changes documented in its changelog. This is my attempt to avoid that for now (kick the can down the road).
microbiomedata · Feb 14, 2025 · 85942d9 · 85942d9
1 parent 497fccb
commit 85942d9
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diff --git a/Makefile b/Makefile
@@ -5,7 +5,7 @@ init:
 
 # Updates Python dependencies based upon the contents of the `requirements/main.in` and `requirements/dev.in` files.
 #
-# Note: To omit the `--upgrade` option (included by default) when running `pip-compile`:
+# Note: To omit the `--upgrade` option (included by default) from the constituent `pip-compile` commands:
 #       ```
 #       $ make update-deps UPDATE_DEPS_MAIN_UPGRADE_OPT='' UPDATE_DEPS_DEV_UPGRADE_OPT=''
 #       ```
@@ -14,6 +14,10 @@ init:
 #       ```sh
 #       $ docker compose run --rm --no-deps fastapi sh -c 'make update-deps'
 #       ```
+#       To omit the `--upgrade` option (included by default) from the constituent `pip-compile` commands:
+#       ```sh
+#       $ docker compose run --rm --no-deps fastapi sh -c '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

diff --git a/requirements/main.in b/requirements/main.in
@@ -25,7 +25,7 @@ mkdocs-jupyter
 mkdocs-material
 mkdocs-mermaid2-plugin
 motor
-nmdc-schema==11.3.0
+nmdc-schema==11.4.0
 openpyxl
 pandas
 passlib[bcrypt]

diff --git a/requirements/main.txt b/requirements/main.txt
@@ -85,15 +85,19 @@ click==8.1.8
     # via
     #   -r requirements/main.in
     #   beanie
+    #   click-log
     #   dagster
     #   dagster-webserver
     #   json-flattener
     #   linkml
     #   linkml-runtime
     #   mkdocs
+    #   nmdc-schema
     #   prefixcommons
     #   typer
     #   uvicorn
+click-log==0.4.0
+    # via nmdc-schema
 colorama==0.4.6
     # via mkdocs-material
 coloredlogs==14.0
@@ -104,9 +108,10 @@ comm==0.2.2
     #   ipywidgets
 cryptography==44.0.0
     # via python-jose
-curies==0.10.2
+curies==0.9.2
     # via
     #   linkml-runtime
+    #   nmdc-schema
     #   prefixmaps
 dagit==1.9.9
     # via -r requirements/main.in
@@ -135,7 +140,9 @@ defusedxml==0.7.1
 dependency-injector==4.45.0
     # via -r requirements/main.in
 deprecated==1.2.15
-    # via linkml-runtime
+    # via
+    #   linkml-runtime
+    #   nmdc-schema
 dnspython==2.7.0
     # via
     #   email-validator
@@ -281,6 +288,7 @@ jsonasobj2==1.0.4
     #   -r requirements/main.in
     #   linkml
     #   linkml-runtime
+    #   nmdc-schema
 jsonpatch==1.33
     # via linkml-dataops
 jsonpath-ng==1.7.0
@@ -296,6 +304,7 @@ jsonschema==4.23.0
     #   linkml
     #   linkml-runtime
     #   nbformat
+    #   nmdc-schema
 jsonschema-specifications==2024.10.1
     # via jsonschema
 jupyter==1.1.1
@@ -400,8 +409,6 @@ mkdocs==1.6.1
     #   mkdocs-jupyter
     #   mkdocs-material
     #   mkdocs-mermaid2-plugin
-    #   mkdocs-redirects
-    #   nmdc-schema
 mkdocs-get-deps==0.2.0
     # via mkdocs
 mkdocs-jupyter==0.25.1
@@ -414,11 +421,7 @@ mkdocs-material==9.5.50
 mkdocs-material-extensions==1.3.1
     # via mkdocs-material
 mkdocs-mermaid2-plugin==0.6.0
-    # via
-    #   -r requirements/main.in
-    #   nmdc-schema
-mkdocs-redirects==1.2.2
-    # via nmdc-schema
+    # via -r requirements/main.in
 motor==3.6.1
     # via
     #   -r requirements/main.in
@@ -440,7 +443,7 @@ nbformat==5.10.4
     #   nbconvert
 nest-asyncio==1.6.0
     # via ipykernel
-nmdc-schema==11.3.0
+nmdc-schema==11.4.0
     # via -r requirements/main.in
 notebook==7.3.2
     # via jupyter
@@ -589,6 +592,7 @@ python-dotenv==1.0.1
     # via
     #   -r requirements/main.in
     #   dagster
+    #   nmdc-schema
     #   uvicorn
 python-jose==3.3.0
     # via -r requirements/main.in
@@ -614,6 +618,7 @@ pyyaml==6.0.2
     #   mkdocs
     #   mkdocs-get-deps
     #   mkdocs-mermaid2-plugin
+    #   nmdc-schema
     #   prefixcommons
     #   prefixmaps
     #   pymdown-extensions
@@ -627,11 +632,12 @@ pyzmq==26.2.0
     #   jupyter-client
     #   jupyter-console
     #   jupyter-server
-rdflib==7.1.3
+rdflib==6.2.0
     # via
     #   cfgraph
     #   linkml
     #   linkml-runtime
+    #   nmdc-schema
     #   rdflib-jsonld
     #   rdflib-shim
     #   sparqlslurper
@@ -663,6 +669,7 @@ requests==2.32.3
     #   linkml-runtime
     #   mkdocs-material
     #   mkdocs-mermaid2-plugin
+    #   nmdc-schema
     #   prefixcommons
     #   pyshex
     #   requests-cache
@@ -693,9 +700,7 @@ rpds-py==0.22.3
 rsa==4.9
     # via python-jose
 ruamel-yaml==0.18.10
-    # via
-    #   linkml-dataops
-    #   nmdc-schema
+    # via linkml-dataops
 ruamel-yaml-clib==0.2.12
     # via ruamel-yaml
 s3transfer==0.11.1
@@ -881,4 +886,5 @@ setuptools==75.8.0
     #   dagster
     #   jupyterlab
     #   mkdocs-mermaid2-plugin
+    #   rdflib
     #   setuptools-scm