nmdc-runtime 2.3.0__tar.gz → 2.4.0__tar.gz

{nmdc_runtime-2.3.0 → nmdc_runtime-2.4.0}/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

{nmdc_runtime-2.3.0/nmdc_runtime.egg-info → nmdc_runtime-2.4.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.2
 Name: nmdc_runtime
-Version: 2.3.0
+Version: 2.4.0
 Summary: A runtime system for NMDC data management and orchestration
 Home-page: https://github.com/microbiomedata/nmdc-runtime
 Author: Donny Winston
@@ -37,7 +37,7 @@ houses the LinkML schema specification, as well as generated artifacts (e.g. JSO
 * [nmdc-server](https://github.com/microbiomedata/nmdc-server)
 houses code specific to the data portal -- its database, back-end API, and front-end application.
 
-* [workflow_documentation](https://nmdc-workflow-documentation.readthedocs.io/en/latest/index.html)
+* [workflow_documentation](https://docs.microbiomedata.org/workflows/)
 references workflow code spread across several repositories, that take source data and produce computed data.
 
 * This repo (nmdc-runtime)

{nmdc_runtime-2.3.0 → nmdc_runtime-2.4.0}/README.md

@@ -15,7 +15,7 @@ houses the LinkML schema specification, as well as generated artifacts (e.g. JSO
 * [nmdc-server](https://github.com/microbiomedata/nmdc-server)
 houses code specific to the data portal -- its database, back-end API, and front-end application.
 
-* [workflow_documentation](https://nmdc-workflow-documentation.readthedocs.io/en/latest/index.html)
+* [workflow_documentation](https://docs.microbiomedata.org/workflows/)
 references workflow code spread across several repositories, that take source data and produce computed data.
 
 * This repo (nmdc-runtime)

{nmdc_runtime-2.3.0 → nmdc_runtime-2.4.0}/db/migrations/notebooks/.notebook.env.example

@@ -1,4 +1,4 @@
-# Paths to folders in which the notebook will store Mongo dumps.
+# Paths to existing folders in which the notebook will store Mongo dumps.
 PATH_TO_ORIGIN_MONGO_DUMP_FOLDER = "./mongodump.origin.out"
 PATH_TO_TRANSFORMER_MONGO_DUMP_FOLDER = "./mongodump.transformer.out"
 
@@ -12,7 +12,7 @@ PATH_TO_MONGOSH_BINARY = "__REPLACE_ME__"  # e.g. "/Users/Alice/Downloads/mongos
 #       to migrate. It is where the "E" and "L" in "ETL" will take place.
 ORIGIN_MONGO_HOST="__REPLACE_ME__"
 ORIGIN_MONGO_PORT="__REPLACE_ME__"
-ORIGIN_MONGO_USERNAME="__REPLACE_ME__"
+ORIGIN_MONGO_USERNAME="__REPLACE_ME__"  # e.g. "app.migrator"
 ORIGIN_MONGO_PASSWORD="__REPLACE_ME__"
 ORIGIN_MONGO_DATABASE_NAME="__REPLACE_ME__"  # e.g. "nmdc"
 

nmdc_runtime-2.4.0/db/migrations/notebooks/migrate_11_2_1_to_11_3_0.ipynb

@@ -0,0 +1,50 @@
+{
+ "cells": [
+  {
+   "metadata": {},
+   "cell_type": "markdown",
+   "source": "# Migrate MongoDB database from `nmdc-schema` `v11.2.1` to `v11.3.0`",
+   "id": "d05efc6327778f9c"
+  },
+  {
+   "metadata": {},
+   "cell_type": "markdown",
+   "source": "There are no migrators associated with any schema changes between schema versions `v11.2.1` and `v11.3.0`. So, this notebook is a \"no op\" (i.e. \"no operation\").",
+   "id": "b99d5924e825b9a2"
+  },
+  {
+   "cell_type": "code",
+   "id": "initial_id",
+   "metadata": {
+    "collapsed": true,
+    "jupyter": {
+     "is_executing": true
+    }
+   },
+   "source": "# no op",
+   "outputs": [],
+   "execution_count": null
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 3",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 2
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython2",
+   "version": "2.7.6"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 5
+}