grz-cli 1.0.2__tar.gz → 1.1.0__tar.gz

{grz_cli-1.0.2 → grz_cli-1.1.0}/CHANGELOG.md

@@ -1,5 +1,29 @@
 # Changelog
 
+## [1.1.0](https://github.com/BfArM-MVH/grz-tools/compare/grz-cli-v1.0.3...grz-cli-v1.1.0) (2025-07-21)
+
+
+### Features
+
+* **grz-cli,grzctl,grz-check:** Add grz-check ([#240](https://github.com/BfArM-MVH/grz-tools/issues/240)) ([57048f6](https://github.com/BfArM-MVH/grz-tools/commit/57048f66888cb566887e627a2b973c3f8b1b83c5))
+
+
+### Bug Fixes
+
+* **grz-cli,grzctl:** bump deps to make VCFs optional ([#291](https://github.com/BfArM-MVH/grz-tools/issues/291)) ([fe4ac2f](https://github.com/BfArM-MVH/grz-tools/commit/fe4ac2f8230b804ad9ec2c6d2102207ab97b0365))
+
+## [1.0.3](https://github.com/BfArM-MVH/grz-tools/compare/grz-cli-v1.0.2...grz-cli-v1.0.3) (2025-07-14)
+
+
+### Bug Fixes
+
+* **grzctl,grz-cli:** bump grz-pydantic-models for end-to-end tests ([#274](https://github.com/BfArM-MVH/grz-tools/issues/274)) ([a1ed791](https://github.com/BfArM-MVH/grz-tools/commit/a1ed791f1f9fce52d08f8e70fba12a674336d250))
+
+
+### Documentation
+
+* **grz-cli:** fix Conda update instructions ([#277](https://github.com/BfArM-MVH/grz-tools/issues/277)) ([fd6e054](https://github.com/BfArM-MVH/grz-tools/commit/fd6e054a8f8e80e1d3ab659ca1b9906199030c18))
+
 ## [1.0.2](https://github.com/BfArM-MVH/grz-tools/compare/grz-cli-v1.0.1...grz-cli-v1.0.2) (2025-07-04)
 
 

{grz_cli-1.0.2 → grz_cli-1.1.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: grz-cli
-Version: 1.0.2
+Version: 1.1.0
 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
@@ -16,8 +16,8 @@ Requires-Python: >=3.12
 Requires-Dist: boto3<2,>=1.36
 Requires-Dist: click<9,>=8.2
 Requires-Dist: crypt4gh<2,>=1.7
-Requires-Dist: grz-common<2,>=1.0.2
-Requires-Dist: grz-pydantic-models<3,>=2.0.2
+Requires-Dist: grz-common<2,>=1.0.3
+Requires-Dist: grz-pydantic-models<3,>=2.1.1
 Requires-Dist: jsonschema<5,>=4.23.0
 Requires-Dist: platformdirs<5,>=4.3.6
 Requires-Dist: pydantic-settings<2.10,>=2.9.0
@@ -115,10 +115,12 @@ conda create -n grz-tools -c conda-forge -c bioconda "grz-cli"
 conda activate grz-tools
 ```
 
-##### Update instructions:
+##### Update instructions
+
 Use the following command to update the tool:
+
 ```bash
-conda update -n grz-tools "grz-cli"
+conda update -n grz-tools -c conda-forge -c bioconda grz-cli
 ```
 
 
@@ -139,6 +141,7 @@ pip upgrade grz-cli
 #### Docker
 Docker images are available via biocontainers at [https://biocontainers.pro/tools/grz-cli](https://biocontainers.pro/tools/grz-cli).
 
+The build process can take at least a few days after the Bioconda release, so double-check that the latest version in Bioconda is also the latest Docker image version.
 
 ## Usage
 

{grz_cli-1.0.2 → grz_cli-1.1.0}/README.md

@@ -84,10 +84,12 @@ conda create -n grz-tools -c conda-forge -c bioconda "grz-cli"
 conda activate grz-tools
 ```
 
-##### Update instructions:
+##### Update instructions
+
 Use the following command to update the tool:
+
 ```bash
-conda update -n grz-tools "grz-cli"
+conda update -n grz-tools -c conda-forge -c bioconda grz-cli
 ```
 
 
@@ -108,6 +110,7 @@ pip upgrade grz-cli
 #### Docker
 Docker images are available via biocontainers at [https://biocontainers.pro/tools/grz-cli](https://biocontainers.pro/tools/grz-cli).
 
+The build process can take at least a few days after the Bioconda release, so double-check that the latest version in Bioconda is also the latest Docker image version.
 
 ## Usage
 

{grz_cli-1.0.2 → grz_cli-1.1.0}/pyproject.toml

@@ -22,11 +22,11 @@ dependencies = [
     "pydantic >=2.9.2,<2.10",
     "pydantic-settings >=2.9.0,<2.10",
     "platformdirs >=4.3.6,<5",
-    "grz-pydantic-models >=2.0.2,<3",
+    "grz-pydantic-models >=2.1.1,<3",
     "pysam ==0.23.*",
     "rich ==13.*",
     "requests >=2.32.3,<3",
-    "grz-common >=1.0.2,<2",
+    "grz-common >=1.0.3,<2",
 ]
 classifiers = [
     "Programming Language :: Python :: 3",

grz_cli-1.1.0/src/grz_cli/__init__.py

@@ -0,0 +1 @@
+__version__ = "1.1.0"

{grz_cli-1.0.2 → grz_cli-1.1.0}/src/grz_cli/commands/validate.py

@@ -5,7 +5,7 @@ from pathlib import Path
 
 import click
 from grz_cli.models.config import ValidateConfig
-from grz_common.cli import config_file, force, submission_dir
+from grz_common.cli import config_file, force, submission_dir, threads
 from grz_common.workers.worker import Worker
 
 log = logging.getLogger(__name__)
@@ -15,7 +15,15 @@ log = logging.getLogger(__name__)
 @submission_dir
 @config_file
 @force
-def validate(submission_dir, config_file, force):
+@threads
+@click.option(
+    "--with-grz-check/--no-grz-check",
+    "with_grz_check",
+    default=True,
+    hidden=True,
+    help="Whether to use grz-check to perform validation",
+)
+def validate(submission_dir, config_file, force, threads, with_grz_check):
     """
     Validate the submission.
 
@@ -33,7 +41,8 @@ def validate(submission_dir, config_file, force):
         files_dir=submission_dir / "files",
         log_dir=submission_dir / "logs",
         encrypted_files_dir=submission_dir / "encrypted_files",
+        threads=threads,
     )
-    worker_inst.validate(identifiers=config.identifiers, force=force)
+    worker_inst.validate(identifiers=config.identifiers, force=force, with_grz_check=with_grz_check)
 
     log.info("Validation finished!")

grz_cli-1.0.2/src/grz_cli/__init__.py

@@ -1 +0,0 @@
-__version__ = "1.0.2"