filter out some unuseful warnings; prevent talismac dupes

Author: SandyRogers

.pre-commit-config.yaml

@@ -24,3 +24,20 @@ repos:
     hooks:
       - id: talisman-commit
         entry: cmd --githook pre-commit
+  - repo: local
+    hooks:
+      - id: talismanrc-no-duplicate-filenames
+        name: Fail on duplicate filenames in .talismanrc
+        entry: >-
+          bash -c '
+          dupes=$(grep -E "^[[:space:]]*- filename:" .talismanrc \
+            | sed -E "s/^[[:space:]]*- filename:[[:space:]]*//" \
+            | sort | uniq -d);
+          if [ -n "$dupes" ]; then
+            echo "Duplicate filename entries in .talismanrc:";
+            echo "$dupes";
+            exit 1;
+          fi'
+        language: system
+        files: ^\.talismanrc$
+        pass_filenames: false

.talismanrc

@@ -1,7 +1,4 @@
 fileignoreconfig:
-- filename: slurm-dev-environment/configs/jwt_hs256.key
-  checksum: cf9887754600f97f20b4afb223bcd666c3b0aa47dab9b067669c24997f398c26
-
 - filename: .github/workflows/release_k8s.yml
   checksum: 0e93196d244417801fd40ad6bfa01f53a6bf04257371378a1dc3e14cbc7a04d8
 
@@ -54,7 +51,7 @@ fileignoreconfig:
   checksum: 3afe465b36e4e141124bd84c8459c5aa81332eedf49b691eff22c74df63a0f18
 
 - filename: emgapiv2/settings.py
-  checksum: ab0fa7cdb6cd720aedd0a4f6bb9e2940187f9de91a39967e93ed4b91ca5050c5
+  checksum: 4113e9045da277c139530cbf71de334dc83b49a4f93a570b559e694bdd5cb0c8
 
 - filename: emgapiv2/settings_test.py
   checksum: ded898400b4eda7e3cf75694af1b66235975a85eb5b8f49f3a2c708163a7aad4
@@ -65,6 +62,12 @@ fileignoreconfig:
 - filename: emgapiv2/widgets.py
   allowed_patterns: [key]
 
+- filename: pyproject.toml
+  allowed_patterns: [Config key]
+
+- filename: slurm-dev-environment/configs/jwt_hs256.key
+  checksum: cf9887754600f97f20b4afb223bcd666c3b0aa47dab9b067669c24997f398c26
+
 - filename: slurm-dev-environment/configs/private-data-nginx.conf
   checksum: e3bb31e2a0f97c62ee684dd7124e5b72db364c52088ddd98331310909c6a0493
 
@@ -155,9 +158,6 @@ fileignoreconfig:
 - filename: workflows/flows/update_ena_accession_from_json_flow.py
   allowed_patterns: [total_missing_key_or_parse_error]
 
-- filename: workflows/flows/upload_assembly.py
-  checksum: f82f92058dabd50b9b6caf557d4eadae227ec4f6a0233135653251c20cf3c64b
-
 - filename: workflows/prefect_utils/env_context.py
   checksum: 8f5e11c7e0038bc4a648dc61ec657a679356857f77e557f744e2dd769ad88def
   ignore_detectors: [filename]
@@ -186,9 +186,6 @@ fileignoreconfig:
 - filename: workflows/data_io_utils/schemas/base.py
   checksum: 27b03a470da785c58f8294d2aa0aa3ef5f4e5ec5cffd97984ab446a5b8a9f337
 
-- filename: Taskfile.yaml
-  checksum: 592e19dbbafe04c136aa73a4921ac04b2d0473e654416b08d09e81d7544b8b09
-
 - filename: workflows/data_io_utils/schemas/assembly.py
   checksum: 12b45869a636431bb6e1bfe193f02f301a6b484a0c4503bc793f5450c36c932a
 

emgapiv2/config.py

@@ -4,7 +4,10 @@
 
 from pydantic import AnyHttpUrl, BaseModel, Field
 from pydantic.networks import MongoDsn, MySQLDsn
-from pydantic_settings import BaseSettings
+from pydantic_settings import (
+    BaseSettings,
+    SettingsConfigDict,
+)
 
 from workflows.ena_utils.abstract import ENAPortalDataPortal
 
@@ -346,7 +349,7 @@ class EMGConfig(BaseSettings):
     genomes: GenomeConfig = GenomeConfig()
     darwin_core_archive: DarwinCoreArchiveConfig = DarwinCoreArchiveConfig()
 
-    model_config = {
-        "env_prefix": "emg_",
-        "env_nested_delimiter": "__",
-    }
+    model_config = SettingsConfigDict(
+        env_prefix="emg_",
+        env_nested_delimiter="__",
+    )

emgapiv2/settings.py

@@ -12,9 +12,18 @@
 
 import logging
 import os
+import warnings
 from datetime import timedelta
 from pathlib import Path
 
+# Suppress pydantic-settings warnings that are raised because the sources for toml and pyproject.toml
+# are not explicitly configured, but they are included in pydantic-settings' default model_config.
+warnings.filterwarnings(
+    "ignore",
+    message="Config key `(pyproject_toml_table_header|toml_file)` is set in model_config but will be ignored",
+    category=UserWarning,
+)
+
 import dj_database_url
 from django.templatetags.static import static
 from django.urls import reverse_lazy

pyproject.toml

@@ -1,5 +1,5 @@
 [project]
-version = "2025.6.13"
+version = "2026.3.01"
 name = "emgapi-v2"
 requires-python = ">= 3.11"
 
@@ -17,7 +17,10 @@ env = [
     "PREFECT_SQLALCHEMY_POOL_SIZE=20",
     "PREFECT_SERVER_DATABASE_SQLALCHEMY_POOL_SIZE=20"
 ]
-filterwarnings = "ignore:.*is deprecated:DeprecationWarning"
+filterwarnings = [
+    "ignore:.*is deprecated:DeprecationWarning",
+    "ignore:Config key `(pyproject_toml_table_header|toml_file)` is set in model_config but will be ignored:UserWarning"
+]
 asyncio_mode = "auto"
 asyncio_default_fixture_loop_scope = "function"
 cache_dir = "/app/.pytest-cache"