Update dependencies, bump patch versions (#116)

mephenor · web-flow · commit f60553d9e6dc · 2025-07-02T11:10:00.000+02:00
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -49,13 +49,13 @@ repos:
       - id: no-commit-to-branch
         args: [--branch, dev, --branch, int, --branch, main]
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.11.13
+    rev: v0.12.1
     hooks:
       - id: ruff
         args: [--fix, --exit-non-zero-on-fix]
       - id: ruff-format
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v1.16.0
+    rev: v1.16.1
     hooks:
       - id: mypy
         args: [--no-warn-unused-ignores]
diff --git a/.pyproject_generation/pyproject_custom.toml b/.pyproject_generation/pyproject_custom.toml
@@ -1,6 +1,6 @@
 [project]
 name = "fsb"
-version = "5.1.0"
+version = "5.1.1"
 description = "File Services Backend - monorepo housing file services"
 dependencies = [
     "typer >= 0.15",
diff --git a/lock/requirements-dev-template.in b/lock/requirements-dev-template.in
@@ -2,7 +2,7 @@
 
 pytest>=8.3
 pytest-asyncio>=0.26
-pytest-cov>=6
+pytest-cov>=6.1
 snakeviz>=2.2
 logot>=1.3
 
@@ -19,14 +19,14 @@ typer>=0.15
 httpx>=0.28
 pytest-httpx>=0.35
 
-urllib3>=2.3
-requests>=2.31
+urllib3>=2.5
+requests>=2.32.4
 
 casefy>=1.1
 jsonschema2md>=1.5
-setuptools>=78.1
+setuptools>=80.3
 
 # required since switch to pyproject.toml and pip-tools
 tomli_w>=1.2
 
-uv>=0.6.10
+uv>=0.7.2
diff --git a/lock/requirements-dev.in b/lock/requirements-dev.in
@@ -4,4 +4,4 @@
 -r requirements-dev-template.in
 
 # additional requirements can be listed here
-testcontainers[kafka,mongo]>=4.9.2
+testcontainers[kafka,mongo]>=4.10
diff --git a/lock/requirements-dev.txt b/lock/requirements-dev.txt
diff --git a/lock/requirements.txt b/lock/requirements.txt
diff --git a/pyproject.toml b/pyproject.toml
@@ -1,6 +1,6 @@
 [project]
 name = "fsb"
-version = "5.1.0"
+version = "5.1.1"
 description = "File Services Backend - monorepo housing file services"
 dependencies = [
     "typer >= 0.15",
diff --git a/scripts/script_utils/deps.py b/scripts/script_utils/deps.py
@@ -20,7 +20,7 @@
 from pathlib import Path
 from typing import Any
 
-from casefy import kebabcase
+import casefy
 
 
 def exclude_from_dependency_list(*, package_name: str, dependencies: list) -> list:
@@ -44,7 +44,7 @@ def remove_self_dependencies(pyproject: dict) -> dict:
 
     project_metadata = modified_pyproject["project"]
 
-    package_name = kebabcase(project_metadata.get("name"))
+    package_name = casefy.kebabcase(project_metadata.get("name"))
 
     if not package_name:
         raise ValueError("The provided project metadata does not contain a name.")
diff --git a/services/dcs/README.md b/services/dcs/README.md
@@ -43,21 +43,21 @@ We recommend using the provided Docker container.
 
 A pre-built version is available at [docker hub](https://hub.docker.com/repository/docker/ghga/download-controller-service):
 ```bash
-docker pull ghga/download-controller-service:6.1.0
+docker pull ghga/download-controller-service:6.1.1
 ```
 
 Or you can build the container yourself from the [`./Dockerfile`](./Dockerfile):
 ```bash
 # Execute in the repo's root dir:
-docker build -t ghga/download-controller-service:6.1.0 .
+docker build -t ghga/download-controller-service:6.1.1 .
 ```
 
 For production-ready deployment, we recommend using Kubernetes, however,
 for simple use cases, you could execute the service using docker
 on a single server:
 ```bash
 # The entrypoint is preconfigured:
-docker run -p 8080:8080 ghga/download-controller-service:6.1.0 --help
+docker run -p 8080:8080 ghga/download-controller-service:6.1.1 --help
 ```
 
 If you prefer not to use containers, you may install the service from source:
diff --git a/services/dcs/openapi.yaml b/services/dcs/openapi.yaml
@@ -206,7 +206,7 @@ info:
     \ Object Storage. \n\nThis is an implementation of the DRS standard from the Global\
     \ Alliance for Genomics and Health, please find more information at: https://github.com/ga4gh/data-repository-service-schemas"
   title: Download Controller Service
-  version: 6.1.0
+  version: 6.1.1
 openapi: 3.1.0
 paths:
   /health:
diff --git a/services/dcs/pyproject.toml b/services/dcs/pyproject.toml
@@ -21,7 +21,7 @@ classifiers = [
     "Intended Audience :: Developers",
 ]
 name = "dcs"
-version = "6.1.0"
+version = "6.1.1"
 description = "Download Controller Service - a GA4GH DRS-compliant service for delivering files from S3 encrypted according to the GA4GH Crypt4GH standard."
 
 
diff --git a/services/ekss/README.md b/services/ekss/README.md
@@ -65,21 +65,21 @@ We recommend using the provided Docker container.
 
 A pre-built version is available at [docker hub](https://hub.docker.com/repository/docker/ghga/encryption-key-store-service):
 ```bash
-docker pull ghga/encryption-key-store-service:3.1.0
+docker pull ghga/encryption-key-store-service:3.1.1
 ```
 
 Or you can build the container yourself from the [`./Dockerfile`](./Dockerfile):
 ```bash
 # Execute in the repo's root dir:
-docker build -t ghga/encryption-key-store-service:3.1.0 .
+docker build -t ghga/encryption-key-store-service:3.1.1 .
 ```
 
 For production-ready deployment, we recommend using Kubernetes, however,
 for simple use cases, you could execute the service using docker
 on a single server:
 ```bash
 # The entrypoint is preconfigured:
-docker run -p 8080:8080 ghga/encryption-key-store-service:3.1.0 --help
+docker run -p 8080:8080 ghga/encryption-key-store-service:3.1.1 --help
 ```
 
 If you prefer not to use containers, you may install the service from source:
diff --git a/services/ekss/openapi.yaml b/services/ekss/openapi.yaml
@@ -234,7 +234,7 @@ info:
   description: A service managing storage and retrieval of symmetric keys in a HashiCorp
     Vault.
   title: Encryption Key Store Service
-  version: 3.1.0
+  version: 3.1.1
 openapi: 3.1.0
 paths:
   /health:
diff --git a/services/ekss/pyproject.toml b/services/ekss/pyproject.toml
@@ -6,7 +6,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "ekss"
-version = "3.1.0"
+version = "3.1.1"
 description = "Encryption Key Store Service - providing crypt4gh file secret extraction, storage and envelope generation"
 readme = "README.md"
 authors = [
diff --git a/services/fis/README.md b/services/fis/README.md
@@ -15,21 +15,21 @@ We recommend using the provided Docker container.
 
 A pre-built version is available at [docker hub](https://hub.docker.com/repository/docker/ghga/file-ingest-service):
 ```bash
-docker pull ghga/file-ingest-service:8.1.0
+docker pull ghga/file-ingest-service:8.1.1
 ```
 
 Or you can build the container yourself from the [`./Dockerfile`](./Dockerfile):
 ```bash
 # Execute in the repo's root dir:
-docker build -t ghga/file-ingest-service:8.1.0 .
+docker build -t ghga/file-ingest-service:8.1.1 .
 ```
 
 For production-ready deployment, we recommend using Kubernetes, however,
 for simple use cases, you could execute the service using docker
 on a single server:
 ```bash
 # The entrypoint is preconfigured:
-docker run -p 8080:8080 ghga/file-ingest-service:8.1.0 --help
+docker run -p 8080:8080 ghga/file-ingest-service:8.1.1 --help
 ```
 
 If you prefer not to use containers, you may install the service from source:
diff --git a/services/fis/openapi.yaml b/services/fis/openapi.yaml
@@ -108,7 +108,7 @@ info:
   description: A service to ingest s3 file upload metadata produced by the data-steward-kit
     upload command
   title: File Ingest Service
-  version: 8.1.0
+  version: 8.1.1
 openapi: 3.1.0
 paths:
   /federated/ingest_metadata:
diff --git a/services/fis/pyproject.toml b/services/fis/pyproject.toml
@@ -6,7 +6,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "fis"
-version = "8.1.0"
+version = "8.1.1"
 description = "File Ingest Service - A lightweight service to propagate file upload metadata to the GHGA file backend services"
 readme = "README.md"
 authors = [
diff --git a/services/ifrs/README.md b/services/ifrs/README.md
@@ -36,21 +36,21 @@ We recommend using the provided Docker container.
 
 A pre-built version is available at [docker hub](https://hub.docker.com/repository/docker/ghga/internal-file-registry-service):
 ```bash
-docker pull ghga/internal-file-registry-service:5.1.0
+docker pull ghga/internal-file-registry-service:5.1.1
 ```
 
 Or you can build the container yourself from the [`./Dockerfile`](./Dockerfile):
 ```bash
 # Execute in the repo's root dir:
-docker build -t ghga/internal-file-registry-service:5.1.0 .
+docker build -t ghga/internal-file-registry-service:5.1.1 .
 ```
 
 For production-ready deployment, we recommend using Kubernetes, however,
 for simple use cases, you could execute the service using docker
 on a single server:
 ```bash
 # The entrypoint is preconfigured:
-docker run -p 8080:8080 ghga/internal-file-registry-service:5.1.0 --help
+docker run -p 8080:8080 ghga/internal-file-registry-service:5.1.1 --help
 ```
 
 If you prefer not to use containers, you may install the service from source:
diff --git a/services/ifrs/pyproject.toml b/services/ifrs/pyproject.toml
@@ -6,7 +6,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "ifrs"
-version = "5.1.0"
+version = "5.1.1"
 description = "Internal File Registry Service - This service acts as a registry for the internal location and representation of files."
 readme = "README.md"
 authors = [
diff --git a/services/irs/README.md b/services/irs/README.md
@@ -14,21 +14,21 @@ We recommend using the provided Docker container.
 
 A pre-built version is available at [docker hub](https://hub.docker.com/repository/docker/ghga/interrogation-room-service):
 ```bash
-docker pull ghga/interrogation-room-service:6.1.0
+docker pull ghga/interrogation-room-service:6.1.1
 ```
 
 Or you can build the container yourself from the [`./Dockerfile`](./Dockerfile):
 ```bash
 # Execute in the repo's root dir:
-docker build -t ghga/interrogation-room-service:6.1.0 .
+docker build -t ghga/interrogation-room-service:6.1.1 .
 ```
 
 For production-ready deployment, we recommend using Kubernetes, however,
 for simple use cases, you could execute the service using docker
 on a single server:
 ```bash
 # The entrypoint is preconfigured:
-docker run -p 8080:8080 ghga/interrogation-room-service:6.1.0 --help
+docker run -p 8080:8080 ghga/interrogation-room-service:6.1.1 --help
 ```
 
 If you prefer not to use containers, you may install the service from source:
diff --git a/services/irs/pyproject.toml b/services/irs/pyproject.toml
@@ -6,7 +6,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "irs"
-version = "6.1.0"
+version = "6.1.1"
 description = "Interrogation Room Service"
 readme = "README.md"
 authors = [
diff --git a/services/pcs/README.md b/services/pcs/README.md
@@ -26,21 +26,21 @@ We recommend using the provided Docker container.
 
 A pre-built version is available at [docker hub](https://hub.docker.com/repository/docker/ghga/purge-controller-service):
 ```bash
-docker pull ghga/purge-controller-service:4.1.0
+docker pull ghga/purge-controller-service:4.1.1
 ```
 
 Or you can build the container yourself from the [`./Dockerfile`](./Dockerfile):
 ```bash
 # Execute in the repo's root dir:
-docker build -t ghga/purge-controller-service:4.1.0 .
+docker build -t ghga/purge-controller-service:4.1.1 .
 ```
 
 For production-ready deployment, we recommend using Kubernetes, however,
 for simple use cases, you could execute the service using docker
 on a single server:
 ```bash
 # The entrypoint is preconfigured:
-docker run -p 8080:8080 ghga/purge-controller-service:4.1.0 --help
+docker run -p 8080:8080 ghga/purge-controller-service:4.1.1 --help
 ```
 
 If you prefer not to use containers, you may install the service from source:
diff --git a/services/pcs/openapi.yaml b/services/pcs/openapi.yaml
@@ -38,7 +38,7 @@ info:
   description: A service exposing an external API to commission file deletionsfrom
     the wholefile backend.
   title: Purge Controller Service
-  version: 4.1.0
+  version: 4.1.1
 openapi: 3.1.0
 paths:
   /files/{file_id}:
diff --git a/services/pcs/pyproject.toml b/services/pcs/pyproject.toml
@@ -6,7 +6,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "pcs"
-version = "4.1.0"
+version = "4.1.1"
 description = "Purge Controller Service - a service to commission file deletions"
 readme = "README.md"
 authors = [
diff --git a/services/ucs/README.md b/services/ucs/README.md
@@ -15,21 +15,21 @@ We recommend using the provided Docker container.
 
 A pre-built version is available at [docker hub](https://hub.docker.com/repository/docker/ghga/upload-controller-service):
 ```bash
-docker pull ghga/upload-controller-service:6.1.0
+docker pull ghga/upload-controller-service:6.1.1
 ```
 
 Or you can build the container yourself from the [`./Dockerfile`](./Dockerfile):
 ```bash
 # Execute in the repo's root dir:
-docker build -t ghga/upload-controller-service:6.1.0 .
+docker build -t ghga/upload-controller-service:6.1.1 .
 ```
 
 For production-ready deployment, we recommend using Kubernetes, however,
 for simple use cases, you could execute the service using docker
 on a single server:
 ```bash
 # The entrypoint is preconfigured:
-docker run -p 8080:8080 ghga/upload-controller-service:6.1.0 --help
+docker run -p 8080:8080 ghga/upload-controller-service:6.1.1 --help
 ```
 
 If you prefer not to use containers, you may install the service from source:
diff --git a/services/ucs/openapi.yaml b/services/ucs/openapi.yaml
@@ -417,7 +417,7 @@ info:
   description: A service managing uploads of file objects to an S3-compatible Object
     Storage.
   title: Upload Controller Service
-  version: 6.1.0
+  version: 6.1.1
 openapi: 3.1.0
 paths:
   /files/{file_id}:
diff --git a/services/ucs/pyproject.toml b/services/ucs/pyproject.toml
@@ -6,7 +6,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "ucs"
-version = "6.1.0"
+version = "6.1.1"
 description = "Upload Controller Service - manages uploads to an S3 inbox bucket."
 readme = "README.md"
 authors = [
