grz-cli 3.0.0__tar.gz → 3.0.1__tar.gz

{grz_cli-3.0.0 → grz_cli-3.0.1}/CHANGELOG.md

@@ -1,5 +1,12 @@
 # Changelog
 
+## [3.0.1](https://github.com/BfArM-MVH/grz-tools/compare/grz-cli-v3.0.0...grz-cli-v3.0.1) (2026-10-22)
+
+
+### Bug Fixes
+
+* **grz-cli,grzctl:** require grz-common 4.0.2 ([#737](https://github.com/BfArM-MVH/grz-tools/issues/737)) ([6bc5d89](https://github.com/BfArM-MVH/grz-tools/commit/6bc5d8942bf3568ba1037a52f8fa0a97ace71b50))
+
 ## [3.0.0](https://github.com/BfArM-MVH/grz-tools/compare/grz-cli-v2.0.0...grz-cli-v3.0.0) (2026-09-26)
 
 

{grz_cli-3.0.0 → grz_cli-3.0.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.5
 Name: grz-cli
-Version: 3.0.0
+Version: 3.0.1
 Summary: Tool for validation, encryption and upload of MV submissions to GDCs.
 Project-URL: Homepage, https://github.com/BfArM-MVH/grz-tools
 Project-URL: Repository, https://github.com/BfArM-MVH/grz-tools
@@ -13,7 +13,7 @@ Keywords: GDC,GRZ,S3
 Classifier: Operating System :: OS Independent
 Classifier: Programming Language :: Python :: 3
 Requires-Python: >=3.12
-Requires-Dist: grz-common<5,>=4
+Requires-Dist: grz-common<5,>=4.0.2
 Requires-Dist: packaging<27,>=23
 Description-Content-Type: text/markdown
 
@@ -21,7 +21,6 @@ Description-Content-Type: text/markdown
 
 A command-line tool for validating, encrypting, and uploading submissions to a genomDE Model Project GDC (Genome Data Center).
 
-
 ## Table of Contents
 
 - [Installation](#installation)
@@ -38,7 +37,6 @@ A command-line tool for validating, encrypting, and uploading submissions to a g
 - [License](#license)
 - [Acknowledgements](#acknowledgements)
 
-
 ## Installation
 
 ### Requirements
@@ -53,7 +51,6 @@ For example:
 - Docker container
 - Windows Subsystem for Linux
 
-
 ### Using [Conda](https://conda.io) (recommended)
 
 If Conda is not yet available on your system, we recommend to install it through the [Miniforge Conda installer](https://github.com/conda-forge/miniforge) by running the following commands:
@@ -79,7 +76,6 @@ Use the following command to update the tool:
 conda update -n grz-tools -c conda-forge -c bioconda grz-cli
 ```
 
-
 ### Using pip (not recommended)
 
 While installation via `pip` is possible, it is not recommended because users should create/manage a Python virtual environment and must ensure that the correct Python version is being used.
@@ -96,7 +92,6 @@ Use the following command to update the tool:
 pip upgrade grz-cli
 ```
 
-
 ### Using Docker
 
 Docker images are available via biocontainers at [https://biocontainers.pro/tools/grz-cli](https://biocontainers.pro/tools/grz-cli).
@@ -120,7 +115,7 @@ The S3 secrets can either be directly within the config file or as defined with
 
 It is recommended to have the following folder structure for a single submission:
 
-```
+```text
 EXAMPLE_SUBMISSION
 ├── files
 │   ├── aaaaaaaa00000000aaaaaaaa00000000_blood_normal.read1.fastq.gz
@@ -138,7 +133,6 @@ The only requirements are that `metadata/metadata.json` exists and the `files/`
 Data files may be nested under subfolders inside `files/` for better organization.
 For example, each donor could have their own folder for files.
 
-
 ### Example submission procedure
 
 After preparing your submission as outlined above, you can use the following command to validate, encrypt and upload the submission:
@@ -167,7 +161,6 @@ It combines the `validate`, `encrypt`, and `upload` commands (see below).
 grz-cli submit --submission-dir foo
 ```
 
-
 ### validate
 
 It is recommended to run this command before continuing with encryption and upload.
@@ -228,7 +221,7 @@ We recommend using Conda or [Pixi](https://pixi.sh/latest).
 
 After cloning the desired branch of the `grz-tools` repo locally, you can run `grz-cli` directly from the repo using:
 
-```
+```text
 uv run --project path/to/cloned/grz-tools grz-cli --help
 ```
 

{grz_cli-3.0.0 → grz_cli-3.0.1}/README.md

@@ -2,7 +2,6 @@
 
 A command-line tool for validating, encrypting, and uploading submissions to a genomDE Model Project GDC (Genome Data Center).
 
-
 ## Table of Contents
 
 - [Installation](#installation)
@@ -19,7 +18,6 @@ A command-line tool for validating, encrypting, and uploading submissions to a g
 - [License](#license)
 - [Acknowledgements](#acknowledgements)
 
-
 ## Installation
 
 ### Requirements
@@ -34,7 +32,6 @@ For example:
 - Docker container
 - Windows Subsystem for Linux
 
-
 ### Using [Conda](https://conda.io) (recommended)
 
 If Conda is not yet available on your system, we recommend to install it through the [Miniforge Conda installer](https://github.com/conda-forge/miniforge) by running the following commands:
@@ -60,7 +57,6 @@ Use the following command to update the tool:
 conda update -n grz-tools -c conda-forge -c bioconda grz-cli
 ```
 
-
 ### Using pip (not recommended)
 
 While installation via `pip` is possible, it is not recommended because users should create/manage a Python virtual environment and must ensure that the correct Python version is being used.
@@ -77,7 +73,6 @@ Use the following command to update the tool:
 pip upgrade grz-cli
 ```
 
-
 ### Using Docker
 
 Docker images are available via biocontainers at [https://biocontainers.pro/tools/grz-cli](https://biocontainers.pro/tools/grz-cli).
@@ -101,7 +96,7 @@ The S3 secrets can either be directly within the config file or as defined with
 
 It is recommended to have the following folder structure for a single submission:
 
-```
+```text
 EXAMPLE_SUBMISSION
 ├── files
 │   ├── aaaaaaaa00000000aaaaaaaa00000000_blood_normal.read1.fastq.gz
@@ -119,7 +114,6 @@ The only requirements are that `metadata/metadata.json` exists and the `files/`
 Data files may be nested under subfolders inside `files/` for better organization.
 For example, each donor could have their own folder for files.
 
-
 ### Example submission procedure
 
 After preparing your submission as outlined above, you can use the following command to validate, encrypt and upload the submission:
@@ -148,7 +142,6 @@ It combines the `validate`, `encrypt`, and `upload` commands (see below).
 grz-cli submit --submission-dir foo
 ```
 
-
 ### validate
 
 It is recommended to run this command before continuing with encryption and upload.
@@ -209,7 +202,7 @@ We recommend using Conda or [Pixi](https://pixi.sh/latest).
 
 After cloning the desired branch of the `grz-tools` repo locally, you can run `grz-cli` directly from the repo using:
 
-```
+```text
 uv run --project path/to/cloned/grz-tools grz-cli --help
 ```
 

grz_cli-3.0.1/docs/version-compatibility-check.md

@@ -0,0 +1,63 @@
+# Version compatibility check
+
+When you run `grz-cli`, it automatically checks whether your installed version is compatible with the current requirements.
+If your version is too old, too new, or simply behind the recommended release, you will be informed before any submission processing tasks begin.
+
+## What happens when you run grz-cli
+
+On startup, the tool fetches a version policy from a central location and compares it against your installed version.
+Depending on the result, one of four things will happen:
+
+| Situation                                           | What you'll see      | Does execution continue? |
+| --------------------------------------------------- | -------------------- | ------------------------ |
+| Your version is too old                             | Error message        | No                       |
+| Your version works but is behind the recommendation | Warning message      | Yes                      |
+| Your version is newer than the supported maximum    | Error message        | No                       |
+| Your version is within the supported range          | Confirmation message | Yes                      |
+
+If no policy is currently in effect, the check is silently skipped and execution continues normally.
+
+## What the messages mean
+
+**"Your grz-cli version is not supported"**
+
+Your installed version is below the minimum required.
+You must upgrade before you can continue.
+
+```text
+Example message: Your grz-cli version (1.2.0) is not supported. Minimum required version is 1.5.0.
+```
+
+**"Upgrading is strongly recommended"**
+
+Your version meets the minimum requirement but is behind the recommended release.
+You can continue, but upgrading is advised.
+
+```text
+Example message: You are using grz-cli 1.5.0, but the recommended version is 1.7.0.
+Upgrading is strongly recommended.
+```
+
+**"grz-cli is within the supported and tested range"**
+
+Your version is fully compatible.
+No action is needed.
+
+```text
+Example message: grz-cli 1.7.0 is within the supported and tested range.
+```
+
+**"Version is newer than the maximum supported version"**
+
+Your version is ahead of what has been tested and approved.
+You must downgrade before you can continue.
+
+```text
+Example message: grz-cli version 2.1.0 is newer than the maximum supported version (2.0.0).
+```
+
+## Why is there a maximum version limit?
+
+Most tools only enforce a minimum version.
+`grz-cli` also enforces an upper bound to prevent untested releases from being used in regulated submission workflows, where the exact toolchain version may need to match what was validated.
+If you have installed a pre-release or a newer version than your organisation currently supports, downgrade to the approved version before submitting.

{grz_cli-3.0.0 → grz_cli-3.0.1}/pyproject.toml

@@ -14,7 +14,7 @@ authors = [
 dynamic = ["version"]
 dependencies = [
     "packaging >=23,<27",
-    "grz-common >=4,<5",
+    "grz-common >=4.0.2,<5",
 ]
 classifiers = [
     "Programming Language :: Python :: 3",

grz_cli-3.0.1/src/grz_cli/__init__.py

@@ -0,0 +1 @@
+__version__ = "3.0.1"

grz_cli-3.0.0/docs/version-compatibility-check.md

@@ -1,56 +0,0 @@
-# Version compatibility check
-
-When you run `grz-cli`, it automatically checks whether your installed version is compatible with the current requirements. If your version is too old, too new, or simply behind the recommended release, you will be informed before any submission processing tasks begin.
-
-## What happens when you run grz-cli
-
-On startup, the tool fetches a version policy from a central location and compares it against your installed version. Depending on the result, one of four things will happen:
-
-| Situation | What you'll see | Does execution continue? |
-|---|---|---|
-| Your version is too old | Error message | No |
-| Your version works but is behind the recommendation | Warning message | Yes |
-| Your version is newer than the supported maximum | Error message | No |
-| Your version is within the supported range | Confirmation message | Yes |
-
-If no policy is currently in effect, the check is silently skipped and execution continues normally.
-
-## What the messages mean
-
-**"Your grz-cli version is not supported"**
-
-Your installed version is below the minimum required. You must upgrade before you can continue.
-
-```
-Example message: Your grz-cli version (1.2.0) is not supported. Minimum required version is 1.5.0.
-```
-
-**"Upgrading is strongly recommended"**
-
-Your version meets the minimum requirement but is behind the recommended release. You can continue, but upgrading is advised.
-
-```
-Example message: You are using grz-cli 1.5.0, but the recommended version is 1.7.0.
-Upgrading is strongly recommended.
-```
-
-**"grz-cli is within the supported and tested range"**
-
-Your version is fully compatible. No action is needed.
-
-```
-Example message: grz-cli 1.7.0 is within the supported and tested range.
-```
-
-**"Version is newer than the maximum supported version"**
-
-Your version is ahead of what has been tested and approved. You must downgrade before you can continue.
-
-```
-Example message: grz-cli version 2.1.0 is newer than the maximum supported version (2.0.0).
-```
-
-
-## Why is there a maximum version limit?
-
-Most tools only enforce a minimum version. `grz-cli` also enforces an upper bound to prevent untested releases from being used in regulated submission workflows, where the exact toolchain version may need to match what was validated. If you have installed a pre-release or a newer version than your organisation currently supports, downgrade to the approved version before submitting.

grz_cli-3.0.0/src/grz_cli/__init__.py

@@ -1 +0,0 @@
-__version__ = "3.0.0"