grz-cli 1.5.1__tar.gz → 1.6.0__tar.gz

{grz_cli-1.5.1 → grz_cli-1.6.0}/CHANGELOG.md

@@ -1,5 +1,29 @@
 # Changelog
 
+## [1.6.0](https://github.com/BfArM-MVH/grz-tools/compare/grz-cli-v1.5.1...grz-cli-v1.6.0) (2026-05-11)
+
+
+### Features
+
+* **grz-cli,grz-common:** Add version checks to upload/submit ([#477](https://github.com/BfArM-MVH/grz-tools/issues/477)) ([289683d](https://github.com/BfArM-MVH/grz-tools/commit/289683d6154df7fb175ad4db9671f28e1cdd0eb3))
+* **grz-cli,grzctl,grz-common,grz-check:** use grz check python bindings ([#554](https://github.com/BfArM-MVH/grz-tools/issues/554)) ([5dce167](https://github.com/BfArM-MVH/grz-tools/commit/5dce16733e549e92de546f298d821f6202bcee9f))
+* **grz-cli,grzctl,grz-common:** use grz-check python bindings instead ([5dce167](https://github.com/BfArM-MVH/grz-tools/commit/5dce16733e549e92de546f298d821f6202bcee9f))
+* **grzctl,grz-cli,grz-common:** Merge multiple configuration files ([#490](https://github.com/BfArM-MVH/grz-tools/issues/490)) ([8ae881d](https://github.com/BfArM-MVH/grz-tools/commit/8ae881d4f65882ae5d8823bdb00971eec246a395))
+
+
+### Bug Fixes
+
+* **grz-check:** actually calculate checksums in python exposed API ([5dce167](https://github.com/BfArM-MVH/grz-tools/commit/5dce16733e549e92de546f298d821f6202bcee9f))
+* **grz-check:** add return types to public python functions ([5dce167](https://github.com/BfArM-MVH/grz-tools/commit/5dce16733e549e92de546f298d821f6202bcee9f))
+* **grz-check:** do not silently ignore pair errors ([5dce167](https://github.com/BfArM-MVH/grz-tools/commit/5dce16733e549e92de546f298d821f6202bcee9f))
+* **grz-check:** expose validate_raw* functions that also return a ([5dce167](https://github.com/BfArM-MVH/grz-tools/commit/5dce16733e549e92de546f298d821f6202bcee9f))
+* **grz-check:** set source.name as path in report as a fallback ([5dce167](https://github.com/BfArM-MVH/grz-tools/commit/5dce16733e549e92de546f298d821f6202bcee9f))
+* **grz-check:** use 8MB as buffer size to match python codebase defaults ([5dce167](https://github.com/BfArM-MVH/grz-tools/commit/5dce16733e549e92de546f298d821f6202bcee9f))
+* **grz-common,grzctl,grz-cli:** add pynacl to dependencies, update crypt4gh ([#560](https://github.com/BfArM-MVH/grz-tools/issues/560)) ([9060876](https://github.com/BfArM-MVH/grz-tools/commit/9060876094d9f2a97ea7d351e0adcfc34a6bbd39))
+* **grz-common,grzctl,grz-cli:** update crypt4gh dependency version ([9060876](https://github.com/BfArM-MVH/grz-tools/commit/9060876094d9f2a97ea7d351e0adcfc34a6bbd39))
+* **grz-common:** add pynacl to dependencies ([9060876](https://github.com/BfArM-MVH/grz-tools/commit/9060876094d9f2a97ea7d351e0adcfc34a6bbd39))
+* **repo:** Update dependencies ([#498](https://github.com/BfArM-MVH/grz-tools/issues/498)) ([368dfdb](https://github.com/BfArM-MVH/grz-tools/commit/368dfdbaa703f17f0c290ea051be30f9be4bebf3))
+
 ## [1.5.1](https://github.com/BfArM-MVH/grz-tools/compare/grz-cli-v1.5.0...grz-cli-v1.5.1) (2025-12-04)
 
 

{grz_cli-1.5.1 → grz_cli-1.6.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: grz-cli
-Version: 1.5.1
+Version: 1.6.0
 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
@@ -15,14 +15,13 @@ Classifier: Programming Language :: Python :: 3
 Requires-Python: >=3.12
 Requires-Dist: boto3<2,>=1.36
 Requires-Dist: click<9,>=8.2
-Requires-Dist: crypt4gh<2,>=1.7
+Requires-Dist: crypt4gh<2,>=1.8.6
 Requires-Dist: grz-common<2,>=1.5.0
 Requires-Dist: grz-pydantic-models<3,>=2.5
 Requires-Dist: jsonschema<5,>=4.23.0
 Requires-Dist: platformdirs<5,>=4.3.6
 Requires-Dist: pydantic-settings<3,>=2.11
 Requires-Dist: pydantic<3,>=2.12
-Requires-Dist: pysam==0.23.*
 Requires-Dist: pyyaml<7,>=6.0.2
 Requires-Dist: requests<3,>=2.32.3
 Requires-Dist: rich==13.*

{grz_cli-1.5.1 → grz_cli-1.6.0}/pyproject.toml

@@ -15,7 +15,7 @@ dynamic = ["version"]
 dependencies = [
     "boto3 >=1.36,<2",
     "click >=8.2,<9",
-    "crypt4gh >=1.7,<2",
+    "crypt4gh >=1.8.6,<2",
     "jsonschema >=4.23.0,<5",
     "pyyaml >=6.0.2,<7",
     "tqdm >=4.66.5,<5",
@@ -23,7 +23,6 @@ dependencies = [
     "pydantic-settings >=2.11,<3",
     "platformdirs >=4.3.6,<5",
     "grz-pydantic-models >=2.5,<3",
-    "pysam ==0.23.*",
     "rich ==13.*",
     "requests >=2.32.3,<3",
     "grz-common >=1.5.0,<2",
@@ -38,9 +37,7 @@ keywords = ["GRZ", "GDC", "S3"]
 [dependency-groups]
 dev = ["tox", "tox-uv"]
 
-[tool.uv.sources]
-grz-common = { path = "../grz-common", editable = true }
-grz-pydantic-models = { path = "../grz-pydantic-models", editable = true }
+
 
 [project.urls]
 Homepage = "https://github.com/BfArM-MVH/grz-tools"

grz_cli-1.6.0/src/grz_cli/__init__.py

@@ -0,0 +1 @@
+__version__ = "1.6.0"

{grz_cli-1.5.1 → grz_cli-1.6.0}/src/grz_cli/cli.py

@@ -2,16 +2,18 @@
 CLI module for handling command-line interface operations.
 """
 
-import logging
 import logging.config
 import shutil
 import subprocess
 import sys
 from importlib.metadata import version
+from pathlib import Path
 from textwrap import dedent
 
 import click
 import grz_pydantic_models.submission.metadata
+from grz_common.cli import config_file
+from grz_common.cli.dump_config import dump_config
 from grz_common.logging import setup_cli_logging
 
 from .commands.encrypt import encrypt
@@ -52,7 +54,7 @@ def build_cli():
         grz-pydantic-models v{version("grz-pydantic-models")}
         """)
         + (
-            subprocess.run(["grz-check", "--version"], capture_output=True, text=True).stdout.strip()  # noqa: S603, S607
+            subprocess.run(["grz-check", "--version"], capture_output=True, text=True).stdout.strip()  # noqa: S607
             if shutil.which("grz-check") is not None
             else ""
         ),
@@ -64,7 +66,9 @@ def build_cli():
         type=click.Choice(["DEBUG", "INFO", "WARNING", "ERROR", "CRITICAL"]),
         help="Set the log level (default: INFO)",
     )
-    def cli(log_file: str | None = None, log_level: str = "INFO"):
+    @config_file
+    @click.pass_context
+    def cli(ctx, config_file: tuple[Path], log_file: str | None = None, log_level: str = "INFO"):
         """
         Command-line interface function for setting up logging.
 
@@ -81,6 +85,7 @@ def build_cli():
     cli.add_command(upload)
     cli.add_command(submit)
     cli.add_command(get_id)
+    cli.add_command(dump_config)
 
     return cli
 

{grz_cli-1.5.1 → grz_cli-1.6.0}/src/grz_cli/commands/encrypt.py

@@ -4,9 +4,10 @@ import logging
 import sys
 from pathlib import Path
 from tempfile import NamedTemporaryFile
+from typing import Any
 
 import click
-from grz_common.cli import config_file, force, submission_dir
+import grz_common.cli as grzcli
 from grz_common.workers.worker import Worker
 
 from ..models.config import EncryptConfig
@@ -15,23 +16,23 @@ log = logging.getLogger(__name__)
 
 
 @click.command()
-@submission_dir
-@config_file
-@force
+@grzcli.configuration
+@grzcli.submission_dir
+@grzcli.force
 @click.option(
     "--check-validation-logs/--no-check-validation-logs",
     "check_validation_logs",
     default=True,
     help="Check validation logs before encrypting.",
 )
-def encrypt(submission_dir, config_file, force, check_validation_logs):
+def encrypt(configuration: dict[str, Any], submission_dir, force, check_validation_logs, **kwargs):
     """
     Encrypt a submission.
 
     Encryption is done with the recipient's public key.
     Sub-folders 'encrypted_files' and 'logs' are created within the submission directory.
     """
-    config = EncryptConfig.from_path(config_file)
+    config = EncryptConfig.model_validate(configuration)
 
     submitter_privkey_path = config.keys.submitter_private_key_path
     if submitter_privkey_path == "":

{grz_cli-1.5.1 → grz_cli-1.6.0}/src/grz_cli/commands/submit.py

@@ -3,6 +3,7 @@
 import logging
 
 import click
+from grz_cli.utils.version_check import check_version_and_exit_if_needed
 
 from .encrypt import encrypt
 from .upload import upload
@@ -10,14 +11,16 @@ from .validate import validate
 
 log = logging.getLogger(__name__)
 
-from grz_common.cli import config_file, force, submission_dir, threads
+import grz_common.cli as grzcli
+
+from ..models.config import UploadConfig
 
 
 @click.command("submit")
-@submission_dir
-@config_file
-@threads
-@force
+@grzcli.submission_dir
+@grzcli.config_file
+@grzcli.threads
+@grzcli.force
 @click.pass_context
 def submit(ctx, submission_dir, config_file, threads, force):
     """
@@ -28,6 +31,9 @@ def submit(ctx, submission_dir, config_file, threads, force):
     2. Encrypt the submission
     3. Upload the encrypted submission
     """
+    config = UploadConfig.from_path(config_file)
+    check_version_and_exit_if_needed(config.s3)
+
     click.echo("Starting submission process...")
     ctx.invoke(validate, submission_dir=submission_dir, config_file=config_file, force=force)
     ctx.invoke(encrypt, submission_dir=submission_dir, config_file=config_file, force=force, check_validation_logs=True)

{grz_cli-1.5.1 → grz_cli-1.6.0}/src/grz_cli/commands/upload.py

@@ -2,30 +2,34 @@
 
 import logging
 from pathlib import Path
+from typing import Any
 
 import click
 from grz_common.workers.worker import Worker
 
 log = logging.getLogger(__name__)
 
-from grz_common.cli import config_file, submission_dir, threads
+import grz_common.cli as grzcli
+from grz_cli.utils.version_check import check_version_and_exit_if_needed
 
 from ..models.config import UploadConfig
 
 
 @click.command()
-@submission_dir
-@config_file
-@threads
+@grzcli.submission_dir
+@grzcli.threads
+@grzcli.configuration
 def upload(
+    configuration: dict[str, Any],
     submission_dir,
-    config_file,
     threads,
+    **kwargs,
 ):
     """
     Upload a submission to a GRZ/GDC.
     """
-    config = UploadConfig.from_path(config_file)
+    config = UploadConfig.model_validate(configuration)
+    check_version_and_exit_if_needed(config.s3)
 
     log.info("Starting upload...")
 

{grz_cli-1.5.1 → grz_cli-1.6.0}/src/grz_cli/commands/validate.py

@@ -2,35 +2,43 @@
 
 import logging
 from pathlib import Path
+from typing import Any
 
 import click
+import grz_common.cli as grzcli
 from grz_cli.models.config import ValidateConfig
-from grz_common.cli import config_file, force, submission_dir, threads
 from grz_common.workers.worker import Worker
 
 log = logging.getLogger(__name__)
 
 
 @click.command()
-@submission_dir
-@config_file
-@force
-@threads
+@grzcli.configuration
+@grzcli.submission_dir
+@grzcli.force
+@grzcli.threads
 @click.option(
-    "--with-grz-check/--no-grz-check",
-    "with_grz_check",
+    "--mmap/--no-mmap",
+    "mmap",
     default=True,
     hidden=True,
-    help="Whether to use grz-check to perform validation",
+    help="Whether to use mmap.",
 )
-def validate(submission_dir, config_file, force, threads, with_grz_check):
+def validate(
+    configuration: dict[str, Any],
+    submission_dir,
+    force,
+    threads,
+    mmap,
+    **kwargs,
+):
     """
     Validate the submission.
 
     This validates the submission by checking its checksums, as well as performing basic sanity checks on the supplied metadata.
     Must be executed before calling `encrypt` and `upload`.
     """
-    config = ValidateConfig.from_path(config_file)
+    config = ValidateConfig.model_validate(configuration)
 
     log.info("Starting validation...")
 
@@ -43,6 +51,6 @@ def validate(submission_dir, config_file, force, threads, with_grz_check):
         encrypted_files_dir=submission_dir / "encrypted_files",
         threads=threads,
     )
-    worker_inst.validate(identifiers=config.identifiers, force=force, with_grz_check=with_grz_check)
+    worker_inst.validate(identifiers=config.identifiers, force=force, no_mmap=not mmap)
 
     log.info("Validation finished!")

grz_cli-1.6.0/src/grz_cli/utils/version_check.py

@@ -0,0 +1,89 @@
+import logging
+import sys
+from datetime import UTC, datetime
+from importlib.metadata import version
+
+from grz_common.models.s3 import S3Options
+from grz_common.models.version import VersionFile, VersionInfo
+from packaging import version as pkg_version
+
+logger = logging.getLogger(__name__)
+
+
+def _select_active_policy(
+    policies: list[VersionInfo],
+    now: datetime,
+) -> VersionInfo | None:
+    """Select the version policy that is active for the given datetime.
+
+    :param policies: A non-empty list of available version policies.
+                     Each policy defines version constraints and an
+                     enforcement start datetime.
+    :param now: The reference datetime used to determine which policy
+                is currently active (typically ``datetime.now(UTC)``).
+    :returns: The policy that should be applied for the given datetime.
+    :raises ValueError: If policies is empty.
+    """
+    if not policies:
+        return None
+
+    applicable = [p for p in policies if p.enforced_from <= now]
+
+    if not applicable:
+        return None
+
+    return max(applicable, key=lambda p: p.enforced_from)
+
+
+def check_version_and_exit_if_needed(
+    s3_options: S3Options,
+    version_file_key: str = "version.json",
+) -> None:
+    """Validate the installed grz-cli version against the policy defined in version.json."""
+    version_file = VersionFile.from_s3(s3_options, version_file_key)
+
+    current_version = pkg_version.Version(version("grz-cli"))
+    now = datetime.now(UTC)
+
+    policy = _select_active_policy(version_file.grzcli_version, now)
+
+    if policy is None:
+        logger.debug("No active version policy found — skipping version check.")
+        return
+
+    minimal_version = policy.minimal_version
+    recommended_version = policy.recommended_version
+    max_version = policy.max_version
+    enforced_from = policy.enforced_from
+
+    logger.debug(f"Current grz-cli version: {current_version}")
+    logger.debug(
+        f"Active policy: "
+        f"minimal={minimal_version}, "
+        f"recommended={recommended_version}, "
+        f"max_version={max_version}, "
+        f"enforced_from={enforced_from}"
+    )
+
+    # old version
+    if current_version < minimal_version:
+        logger.error(
+            f"Your grz-cli version ({current_version}) is not supported. Minimum required version is {minimal_version}."
+        )
+        sys.exit(1)
+
+    # supported but behind recommended — skip if recommended_version not set
+    if recommended_version is not None and minimal_version <= current_version < recommended_version:
+        logger.warning(
+            f"You are using grz-cli {current_version}, but the recommended version is "
+            f"{recommended_version}. Upgrading is strongly recommended."
+        )
+        return
+
+    # too new — skip if max_version not set
+    if max_version is not None and current_version > max_version:
+        logger.error(f"grz-cli version {current_version} is newer than the maximum supported version ({max_version}).")
+        sys.exit(1)
+
+    # best case
+    logger.info(f"grz-cli {current_version} is within the supported and tested range.")

grz_cli-1.5.1/src/grz_cli/__init__.py

@@ -1 +0,0 @@
-__version__ = "1.5.1"