Bring changes from v7.12.0.7 to main

.env

@@ -12,21 +12,18 @@ DATABASE_NAME=specify
 # This user should already be setup before running Specify.
 MASTER_NAME=root
 MASTER_PASSWORD=password
-MASTER_HOST=%
 
 # MIGRATOR Database User 
 # User with elevated privileges to perform migrations (create/drop/modify tables, etc.), for Django migration steps.
 # Make sure that the user is unique to just one database, otherwise use master.
 MIGRATOR_NAME=specify_migrator
 MIGRATOR_PASSWORD=specify_migrator
-MIGRATOR_HOST=%
 
 # APP Database User
 # Normal runtime database user that performs application-level operations.
 # Make sure that the user is unique to just one database, otherwise use master.
 APP_USER_NAME=specify_user
 APP_USER_PASSWORD=specify_user
-APP_HOST=%
 
 # Enabling this option allows administrators with access to the
 # backend Specify instance to log in as any user for support

.github/workflows/test.yml

@@ -78,7 +78,22 @@ jobs:
           - 6379
 
     steps:
-      - uses: actions/checkout@v4
+      - name: Checkout Copy of Repo
+        uses: actions/checkout@v4
+        with:
+          # We're not making any writes to the repo, so there's no need to
+          # store the credentials in git config
+          persist-credentials: false
+          # Ugh, don't like fetching the entire copy of the Specify 7 repo
+          # here, but this was needed because the details of the most recent
+          # tag was required from the build version Make target
+          # The backend tests can be run on a branch that can be some arbitrary
+          # distance from the most recent tag, so we can't realistically set a
+          # reasonable fetch depth here.
+          # There might be some Git command to do this, will need to look into
+          # that if we want to somewhat speed up the backend tests
+          fetch-depth: 0
+
 
       - name: Install ubuntu dependencies
         run: |

CHANGELOG.md

@@ -4,6 +4,92 @@ All notable changes to this project will be documented in this file.
 
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/).
 
+## [7.12.0.7](https://github.com/specify/specify7/compare/v7.12.0.6...v7.12.0.7) (28 July 2026)
+
+### Updated
+
+* The [International Chronostratigraphic Chart](https://stratigraphy.org/chart/) graphic, published by the International Commission on Stratigraphy, has been updated to version `2026/06` ([#8248](https://github.com/specify/specify7/pull/8248))
+   * The default data for the Chronostratigraphy tree (`GeologicTimePeriod`) has been updated to reflect these new values.
+
+### Fixed
+
+* Improves the initial database setup script ([#8156](https://github.com/specify/specify7/pull/8156))
+    * More reliable DB provisioning, privilege verification and clearer failure diagnostics.
+    * Fixed single-use-iterable bug affecting uniqueness rule creation.
+    * Improved legacy-permissions detection and safer role/user assignment during initialization.
+    * Startup validates DB alias and logs connection fallbacks.
+    * Migration initialization now respects override behavior; container startup can skip automatic migrations. 
+    * Credentials/config now come from environment variables with chained defaults.
+    * Setup scripts run in stricter shell mode for safer execution. 
+* Schema config and migration fixes ([#8154](https://github.com/specify/specify7/pull/8154))
+    * Fixes model capitalizations and case sensitivity issues across schema config table labels and descriptions
+    * Fixes Picklist Type filtering to use the correct type during database migrations
+    * Fixes an issue where `SpLocaleItemStr` records were not created when generating Schema Config records for tables
+    * Fixes incorrect Discipline to TectonicUnit tree definition pairing when resolving links
+    * Fixes handling of synonymized root nodes during tree reverse migrations
+    * Fixes handling of custom Tectonic Unit trees when reverting migrations
+    * Fixes a case where the business rules app was not ready but migrations attempted to run
+    * Fixes `MultipleObjectsReturned` errors by simplifying exception handling during schema repairs
+    * Fixes localized string deduplication to scope by language, preventing cross-language string conflicts
+    * Fixes catalog-number uniqueness shadowing in collection functions during migration
+    * Fixes the `DisciplineType` PickList being created when creating a new Collection
+    * Fixes `DisciplineType` picklist assignment for newly created Disciplines
+    * Fixes partially migrated disciplines that could not be repaired due to exclusion logic
+    * Fixes reuse prevention when pairing tree definitions with disciplines
+    * Fixes discipline tree definition links being set before skipping rank creation
+    * Fixes several schema migration reversibility issues (0021, 0023, 0027, 0033, 0040) to ensure safe rollbacks
+    * Fixes `reverse_hide_component_fields` defaulting incorrectly
+    * Fixes a typo in the `UserRole` description
+    * Fixes component catalog number cache typing for consistency
+    * Fixes an issue where `SP7_DEBUG` was not correctly set in all environments
+    * Fixes validation of `AUDIT_LIFESPAN_MONTHS` before executing purge SQL to prevent unsafe operations
+    * Fixes key escaping when fetching remote preferences to prevent injection vulnerabilities
+    * Fixes comparison of full uniqueness rule definitions before deletion to prevent data loss
+    * Fixes an issue where existing rows were not flipped back to `isDatabaseConstraint=True` where needed
+    * Fixes the `Migrator` user being used for all migration key operations
+    * Fixes the `is_sp6_user_permissions_migrated` check being re-introduced for proper legacy permission handling
+    * Fixes database connection handling to use the correct alias for migration connections
+    * Fixes `set_discipline_for_taxon_treedefs` being reduced to a single database query for improved performance
+    * Fixes `fix_taxon_treedef_discipline_links` being optimized to a single query for improved performance
+    * Fixes admin check ordering to evaluate common cases first for faster permission checks
+    * Fixes use of Django defaults in `get_or_create` for Role creation
+    * Fixes database connection used as a context manager for permission operations
+    * Fixes `fix_global_rules` helper function being simplified for better migration performance
+* Fixes missing data model relationships for attachments that could cause issues with record linking ([#8182](https://github.com/specify/specify7/pull/8182))
+* Regex field-formatter fixes ([#8152](https://github.com/specify/specify7/pull/8152))
+    * Fixes expression boundary markers being incorrectly inserted
+    * Fixes handling of outer parentheses in regex expressions
+    * Fixes regex trimming to intelligently handle ambiguous patterns
+    * Adds `ariaLabel` and `placeholder` attributes for improved accessibility
+* Schema config defaults hardening ([#8329](https://github.com/specify/specify7/pull/8329))
+    * Introduces `SchemaWriter` and `SchemaReader` utility classes for consistent and optimized schema config operations
+    * Introduces `ReadonlyDict` to prevent accidental mutation of schema default values, ensuring migration predictability
+    * Fixes `QueryValues` list flattening in migrations 0035 and 0040
+    * Fixes case-insensitive lookups in schema config helper functions
+    * Improves fallback logic to use `schema_localization_en.json` defaults when generating localized strings
+    * Ensures all passed-in default values are always respected during schema config creation
+    * Eliminates redundant database hits when creating Schema Config records sequentially
+* Database setup and permissions hardening ([#8313](https://github.com/specify/specify7/pull/8313))
+    * Reverts automatic migrator privilege grants when the user already exists to avoid permission conflicts
+    * Prevents access to collections belonging to disciplines that are still being created
+    * Fixes regular expressions used when checking database permissions
+    * Defaults `DATABASE_PORT` to 3306 for more reliable out-of-the-box configuration
+    * Removes unused environment variables and host configuration from default `.env`
+    * Fixes character escaping and host direction when creating database users
+* Batch edit fixes ([#8317](https://github.com/specify/specify7/pull/8317))
+    * Disables attachment relationships in batch edit mode to prevent invalid record linking
+* Tree management improvements ([#8312](https://github.com/specify/specify7/pull/8312), [#8243](https://github.com/specify/specify7/pull/8243))
+    * Allows deletion of unused tree ranks ([#8312](https://github.com/specify/specify7/pull/8312))
+    * Replaces child and synonym `LEFT JOIN`s with scalar subqueries for significantly faster tree queries ([#8243](https://github.com/specify/specify7/pull/8243))
+* Paleo discipline visibility fixes
+    * Unhides PaleoContext, Chronostrat, and Lithostrat trees by default in paleo disciplines (Geology, InvertPaleo, Paleobotany, VertPaleo)
+    * Fixes tree visibility and table descriptions across all disciplines for consistency
+    * Fixes incorrect picklist name for Determination → nameUsages
+    * Fixes null `catalogNumber` format specification
+* Migration test suite ([#8225](https://github.com/specify/specify7/pull/8225))
+    * Adds test coverage for `run_key_migration_functions` and discipline directory cleanup functions
+    * Removes reliance on mocking in several migration tests for more reliable validation
+
 ## [7.12.0.6](https://github.com/specify/specify7/compare/v7.12.0.5...v7.12.0.6) (21 May 2026)
 
 * Fix aggregated relation parsing for stored queries ([#8059](https://github.com/specify/specify7/pull/8059))

Makefile

@@ -15,7 +15,7 @@ pip_requirements:
 	$(PIP) install --upgrade -r requirements.txt
 
 django_migrations:
-	$(PYTHON) manage.py base_specify_migration --database=migrations
+	$(PYTHON) manage.py base_specify_migration --use-override --database=migrations
 	$(PYTHON) manage.py migrate --database=migrations
 
 specifyweb/settings/build_version.py: .FORCE
@@ -53,6 +53,6 @@ MYPY_TARGETS = \
 	specifyweb/backend/context/user_resources.py
 
 typecheck:
-	$(MYPY) --follow-imports silent $(MYPY_TARGETS)
+	$(MYPY) --follow-imports=silent --show-traceback $(MYPY_TARGETS)
 
 .FORCE:

config/bird/schema_overrides.json

@@ -1,7 +1,6 @@
 {
   "collectingevent": {
     "ishidden": false,
-    "desc": "Collecting Event",
     "items": [
       {"stationFieldNumber": {"ishidden": false, "name": "Field Number", "desc": "Field Number"}},
       {"method": {"ishidden": false, "name": "Method", "desc": "Method"}},
@@ -11,7 +10,6 @@
   },
   "collectionobjectattribute": {
     "ishidden": false,
-    "desc": "Collection Object Attribute",
     "items": [
       {"text5": {"ishidden": false, "name": "Stomach", "desc": "Stomach"}},
       {"text3": {"ishidden": false, "name": "ReproCondition", "desc": "ReproCondition"}},
@@ -25,7 +23,6 @@
   },
   "determination": {
     "ishidden": false,
-    "desc": "Determination",
     "items": [
       {"typeStatusName": {"ishidden": false, "name": "Type Status", "desc": "Type Status"}}
     ]

config/botany/schema_overrides.json

@@ -1,15 +1,13 @@
 {
   "collectingevent": {
     "ishidden": false,
-    "desc": "Collecting Event",
     "items": [
       {"stationfieldnumber": {"ishidden": false, "name": "Collector Number", "desc": "Collector Number"}},
       {"remarks": {"ishidden": false, "name": "Locality and Habitat Notes", "desc": "Locality and Habitat Notes"}}
     ]
   },
   "collectionobject": {
     "ishidden": false,
-    "desc": "Collection Object",
     "items": [
       {"text1": {"ishidden": false, "picklistname": "Phenology", "name": "Phenology", "desc": "Phenology"}},
       {"description": {"ishidden": false, "name": "Specimen Description", "desc": "Specimen Description"}},

config/common/global_picklists.json

@@ -448,6 +448,85 @@
         { "title": "Fossil record", "value": "Fossil record" },
         { "title": "Radiometric (adjacent)", "value": "Radiometric (adjacent)" }
       ]
+    },
+    {
+      "name": "DisciplineType",
+      "formatter": null,
+      "issystem": true,
+      "readonly": true,
+      "sizelimit": -1,
+      "sorttype": 1,
+      "tablename": null,
+      "type": 0,
+      "version": 0,
+      "items": [
+        {
+          "ordinal": 1,
+          "title": "Ichthyology",
+          "value": "fish",
+          "version": 0
+        },
+        {
+          "ordinal": 2,
+          "title": "Herpetology",
+          "value": "herpetology",
+          "version": 0
+        },
+        {
+          "ordinal": 3,
+          "title": "Paleobotany",
+          "value": "paleobotany",
+          "version": 0
+        },
+        {
+          "ordinal": 4,
+          "title": "Invertebrate Paleontology",
+          "value": "invertpaleo",
+          "version": 0
+        },
+        {
+          "ordinal": 5,
+          "title": "Vertebrate Paleontology",
+          "value": "vertpaleo",
+          "version": 0
+        },
+        {
+          "ordinal": 6,
+          "title": "Ornithology",
+          "value": "bird",
+          "version": 0
+        },
+        {
+          "ordinal": 7,
+          "title": "Mammalogy",
+          "value": "mammal",
+          "version": 0
+        },
+        {
+          "ordinal": 8,
+          "title": "Entomology",
+          "value": "insect",
+          "version": 0
+        },
+        {
+          "ordinal": 9,
+          "title": "Botany",
+          "value": "botany",
+          "version": 0
+        },
+        {
+          "ordinal": 10,
+          "title": "Invertebrate Zoology",
+          "value": "invertebrate",
+          "version": 0
+        },
+        {
+          "ordinal": 11,
+          "title": "Geology",
+          "value": "geology",
+          "version": 0
+        }
+      ]
     }
   ]
 }