Update dependencies, fix overwrite flag and update license headers (#112)

Author: mephenor

.devcontainer/license_header.txt

@@ -1,4 +1,4 @@
-Copyright 2021 - 2024 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
+Copyright 2021 - 2025 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
 for the German Human Genome-Phenome Archive (GHGA)
 
 Licensed under the Apache License, Version 2.0 (the "License");

.pre-commit-config.yaml

@@ -45,7 +45,7 @@ repos:
       - id: no-commit-to-branch
         args: [--branch, dev, --branch, int, --branch, main]
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.11.0
+    rev: v0.11.11
     hooks:
       - id: ruff
         args: [--fix, --exit-non-zero-on-fix]

.pyproject_generation/README.md

@@ -1,5 +1,5 @@
 <!--
- Copyright 2021 - 2024 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
+ Copyright 2021 - 2025 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
  for the German Human Genome-Phenome Archive (GHGA)
 
  Licensed under the Apache License, Version 2.0 (the "License");

.pyproject_generation/pyproject_custom.toml

@@ -1,13 +1,13 @@
 [project]
 name = "ghga_connector"
-version = "1.7.1"
+version = "1.7.2"
 description = "GHGA Connector - A CLI client application for interacting with the GHGA system."
 dependencies = [
     "typer~=0.15",
     "crypt4gh>=1.6, <2",
-    "ghga-service-commons[crypt]>=3.1.1, <4",
-    "hexkit[s3]>=3",
-    "rich>=13.7.1, <14",
+    "ghga-service-commons[crypt]>=4.1.0",
+    "hexkit[s3]>=5.1",
+    "rich>=14.0, <15",
     "tenacity >=9.0.0, <10",
     "hishel>=0.1.1, < 0.2",
 ]

.readme_generation/README.md

@@ -1,5 +1,5 @@
 <!--
- Copyright 2021 - 2024 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
+ Copyright 2021 - 2025 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
  for the German Human Genome-Phenome Archive (GHGA)
 
  Licensed under the Apache License, Version 2.0 (the "License");

.readme_generation/readme_template.md

@@ -13,7 +13,7 @@ $description
 
 We recommend using the provided Docker container.
 
-A pre-build version is available at [docker hub](https://hub.docker.com/repository/docker/ghga/$name):
+A pre-built version is available at [docker hub](https://hub.docker.com/repository/docker/ghga/$name):
 ```bash
 docker pull ghga/$name:$version
 ```
@@ -50,11 +50,11 @@ $config_description
 
 ### Usage:
 
-A template YAML for configurating the service can be found at
+A template YAML for configuring the service can be found at
 [`./example-config.yaml`](./example-config.yaml).
-Please adapt it, rename it to `.$shortname.yaml`, and place it into one of the following locations:
-- in the current working directory were you are execute the service (on unix: `./.$shortname.yaml`)
-- in your home directory (on unix: `~/.$shortname.yaml`)
+Please adapt it, rename it to `.$shortname.yaml`, and place it in one of the following locations:
+- in the current working directory where you execute the service (on Linux: `./.$shortname.yaml`)
+- in your home directory (on Linux: `~/.$shortname.yaml`)
 
 The config yaml will be automatically parsed by the service.
 
@@ -68,7 +68,7 @@ e.g. for the `host` set an environment variable named `${shortname}_host`
 (you may use both upper or lower cases, however, it is standard to define all env
 variables in upper cases).
 
-To using file secrets please refer to the
+To use file secrets, please refer to the
 [corresponding section](https://pydantic-docs.helpmanual.io/usage/settings/#secret-support)
 of the pydantic documentation.
 
@@ -95,8 +95,8 @@ This will give you a full-fledged, pre-configured development environment includ
 - a pre-configured debugger
 - automatic license-header insertion
 
-Moreover, inside the devcontainer, a convenience commands `dev_install` is available.
-It installs the service with all development dependencies, installs pre-commit.
+Moreover, inside the devcontainer, a command `dev_install` is available for convenience.
+It installs the service with all development dependencies, and it installs pre-commit.
 
 The installation is performed automatically when you build the devcontainer. However,
 if you update dependencies in the [`./pyproject.toml`](./pyproject.toml) or the

.template/README.md

@@ -1,5 +1,5 @@
 <!--
- Copyright 2021 - 2024 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
+ Copyright 2021 - 2025 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
  for the German Human Genome-Phenome Archive (GHGA)
 
  Licensed under the Apache License, Version 2.0 (the "License");

.template/static_files_ignore.txt

@@ -13,3 +13,6 @@ scripts/update_pyproject.py
 .github/workflows/tests.yaml
 .pyproject_generation/pyproject_template.toml
 .devcontainer/Dockerfile
+
+# ignore for now due to some python 3.9 incompatibilities with required urrlib and botocore
+lock/requirements-dev-template.in

Dockerfile

@@ -1,4 +1,4 @@
-# Copyright 2021 - 2024 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
+# Copyright 2021 - 2025 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
 # for the German Human Genome-Phenome Archive (GHGA)
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
@@ -13,7 +13,7 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
-# Copyright 2021 - 2024 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
+# Copyright 2021 - 2025 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
 # for the German Human Genome-Phenome Archive (GHGA)
 #
 # Licensed under the Apache License, Version 2.0 (the "License");

Dockerfile.debian

@@ -1,4 +1,4 @@
-# Copyright 2021 - 2024 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
+# Copyright 2021 - 2025 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
 # for the German Human Genome-Phenome Archive (GHGA)
 #
 # Licensed under the Apache License, Version 2.0 (the "License");