grz-cli 0.1.2__tar.gz → 0.1.4__tar.gz

{grz_cli-0.1.2 → grz_cli-0.1.4}/MANIFEST.in

@@ -1 +1,2 @@
 include src/grz_cli/resources/grz-schema.json
+include src/grz_cli/resources/thresholds.json

{grz_cli-0.1.2/src/grz_cli.egg-info → grz_cli-0.1.4}/PKG-INFO

@@ -1,6 +1,6 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.2
 Name: grz-cli
-Version: 0.1.2
+Version: 0.1.4
 Summary: Tool for validation, encryption and upload of MV submissions to GDCs.
 Author-email: Koray Kirli <koraykirli@gmail.com>, Mathias Lesche <mathias.lesche@tu-dresden.de>, "Florian R. Hölzlwimmer" <git.ich@frhoelzlwimmer.de>, Till Hartmann <till.hartmann@bih-charite.de>, Thomas Sell <thomas.sell@bih-charite.de>
 License: MIT
@@ -11,7 +11,6 @@ Classifier: License :: OSI Approved :: MIT License
 Classifier: Operating System :: OS Independent
 Requires-Python: >=3.12
 Description-Content-Type: text/markdown
-License-File: LICENSE
 Requires-Dist: boto3<2,>=1.35.39
 Requires-Dist: click<9,>=8.1.7
 Requires-Dist: crypt4gh<2,>=1.7
@@ -26,7 +25,7 @@ Requires-Dist: pytest-cov<6,>=5.0.0; extra == "test"
 Requires-Dist: pytest-mock<4,>=3.14.0; extra == "test"
 Requires-Dist: moto[s3]<6,>=5.0.16; extra == "test"
 Requires-Dist: pytest-sugar<2,>=1.0.0; extra == "test"
-Requires-Dist: ruff<1,>=0.8.1; extra == "test"
+Requires-Dist: ruff<1,>=0.9.6; extra == "test"
 Requires-Dist: numpy<3,>=2.1.2; extra == "test"
 
 # GRZ CLI

{grz_cli-0.1.2 → grz_cli-0.1.4}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "grz-cli"
-version = "0.1.2"
+version = "0.1.4"
 description = "Tool for validation, encryption and upload of MV submissions to GDCs."
 readme = "README.md"
 license = { text = "MIT" }
@@ -46,7 +46,7 @@ test = [
     "pytest-mock >=3.14.0,<4",
     "moto[s3] >=5.0.16,<6",
     "pytest-sugar >=1.0.0,<2",
-    "ruff >=0.8.1,<1",
+    "ruff >=0.9.6,<1",
     "numpy >=2.1.2,<3"
 ]
 
@@ -76,7 +76,7 @@ exclude = [
     "dist",
     "out"
 ]
-line-length = 88
+line-length = 120
 src = [
     "src",
     "tests"
@@ -149,26 +149,30 @@ convention = "pep257"
 
 [tool.tox]
 requires = ["tox>=4.23"]
-env_list = ["format-check", "lints", "mypy", "3.12"]
+env_list = ["format-check", "lints", "mypy", "3.12", "3.13"]
 allowlist_externals = ["pytest", "ruff"]
 isolated_build = true
 
 [tool.tox.env_run_base]
+runner = "uv-venv-lock-runner"
 description = "run unit tests"
 dependency_groups = ["test"]
 commands = [["pytest", { replace = "posargs", default = ["tests"], extend = true }]]
 
 [tool.tox.env."format-check"]
+runner = "uv-venv-lock-runner"
 skip_install = true
 dependency_groups = ["lint"]
 commands = [["ruff", "format", "--check"]]
 
 [tool.tox.env."lints"]
+runner = "uv-venv-lock-runner"
 skip_install = true
 dependency_groups = ["lint"]
 commands = [["ruff", "check"]]
 
 [tool.tox.env."mypy"]
+runner = "uv-venv-lock-runner"
 skip_install = false
 dependency_groups = ["lint"]
 commands = [["mypy"]]
@@ -177,8 +181,9 @@ commands = [["mypy"]]
 dev-dependencies = [
     "datamodel-code-generator>=0.26.2",
     "mypy>=1.13.0",
-    "ruff>=0.8.1",
+    "ruff>=0.9.6",
     "tox>=4.23.2",
+    "tox-uv>=1.20.1",
     "types-pyyaml>=6.0.12.20240917",
     "types-tqdm>=4.66.0.20240417",
 ]
@@ -188,3 +193,10 @@ python_version = "3.12"
 plugins = "pydantic.mypy"
 packages = "src"
 
+[tool.pytest.ini_options]
+addopts = [
+    "--import-mode=importlib",
+]
+
+[tool.setuptools]
+license-files = []

{grz_cli-0.1.2 → grz_cli-0.1.4}/src/grz_cli/cli.py

@@ -48,9 +48,7 @@ DIR_RW_C = click.Path(
     writable=True,
     resolve_path=True,
 )
-FILE_R_E = click.Path(
-    exists=True, file_okay=True, dir_okay=False, readable=True, resolve_path=True
-)
+FILE_R_E = click.Path(exists=True, file_okay=True, dir_okay=False, readable=True, resolve_path=True)
 
 submission_dir = click.option(
     "--submission-dir",

{grz_cli-0.1.2 → grz_cli-0.1.4}/src/grz_cli/download.py

@@ -74,10 +74,7 @@ class S3BotoDownloadWorker:
 
         # configure proxies if proxy_url is defined
         proxy_url = empty_str_to_none(self._config.s3_options.proxy_url)
-        if proxy_url is not None:
-            config = Boto3Config(proxies={"http": proxy_url, "https": proxy_url})
-        else:
-            config = None
+        config = Boto3Config(proxies={"http": proxy_url, "https": proxy_url}) if proxy_url is not None else None
 
         # Initialize S3 client for uploading
         self._s3_client: boto3.session.Session.client = boto3_client(
@@ -149,9 +146,7 @@ class S3BotoDownloadWorker:
             if filesize / MULTIPART_CHUNKSIZE > MULTIPART_MAX_CHUNKS
             else MULTIPART_CHUNKSIZE
         )
-        self.__log.debug(
-            f"Using a chunksize of: {chunksize / 1024**2}MiB, results in {filesize/chunksize} chunks"
-        )
+        self.__log.debug(f"Using a chunksize of: {chunksize / 1024**2}MiB, results in {filesize / chunksize} chunks")
 
         config = TransferConfig(
             multipart_threshold=MULTIPART_THRESHOLD,
@@ -160,9 +155,7 @@ class S3BotoDownloadWorker:
         )
 
         transfer = S3Transfer(self._s3_client, config)
-        progress_bar = tqdm(
-            total=filesize, unit="B", unit_scale=True, unit_divisor=1024
-        )
+        progress_bar = tqdm(total=filesize, unit="B", unit_scale=True, unit_divisor=1024)
         transfer.download_file(
             self._config.s3_options.bucket,
             s3_object_id,
@@ -192,15 +185,11 @@ class S3BotoDownloadWorker:
                     file_path = Path(file_key).relative_to(encrypted_files_key_prefix)
                     full_path = encrypted_submission.encrypted_files_dir / file_path
                     if full_path not in encrypted_submission.encrypted_files:
-                        raise DownloadError(
-                            f"File {file_path} not listed in metadata.json"
-                        )
+                        raise DownloadError(f"File {file_path} not listed in metadata.json")
                     file_metadata = encrypted_submission.encrypted_files[full_path]
                     logged_state = progress_logger.get_state(full_path, file_metadata)
 
-                    if (logged_state is None) or not logged_state.get(
-                        "download_successful", False
-                    ):
+                    if (logged_state is None) or not logged_state.get("download_successful", False):
                         self.__log.info(
                             "Download file: '%s' -> '%s'",
                             file_key,
@@ -208,9 +197,7 @@ class S3BotoDownloadWorker:
                         )
 
                         try:
-                            full_path.parent.mkdir(
-                                mode=0o770, parents=True, exist_ok=True
-                            )
+                            full_path.parent.mkdir(mode=0o770, parents=True, exist_ok=True)
                             self.download_file(str(full_path), file_key, file["Size"])
 
                             self.__log.info(f"Download complete for {str(full_path)}. ")
@@ -225,9 +212,7 @@ class S3BotoDownloadWorker:
                             progress_logger.set_state(
                                 full_path,
                                 file_metadata,
-                                state=DownloadState(
-                                    download_successful=False, errors=[str(e)]
-                                ),
+                                state=DownloadState(download_successful=False, errors=[str(e)]),
                             )
 
                             raise e

{grz_cli-0.1.2 → grz_cli-0.1.4}/src/grz_cli/fastq_validation.py

@@ -29,9 +29,7 @@ def is_gzipped(file_path: str | PathLike) -> bool:
 
 
 @contextmanager
-def open_fastq(
-    file_path: str | PathLike, progress=True
-) -> Generator[TextIO, None, None]:
+def open_fastq(file_path: str | PathLike, progress=True) -> Generator[TextIO, None, None]:
     """
     Open a FASTQ file, handling both regular and gzipped formats.
 
@@ -103,9 +101,7 @@ def validate_fastq_file(fastq_file: str | PathLike) -> tuple[int, set[int], list
 
     # Check if the number of lines in a FASTQ file is a multiple of 4.
     if num_lines % 4 != 0:
-        errors.append(
-            f"{fastq_file}: Number of lines is not a multiple of 4! Found {num_lines} lines."
-        )
+        errors.append(f"{fastq_file}: Number of lines is not a multiple of 4! Found {num_lines} lines.")
     else:
         log.debug("%s: %s lines", fastq_file, num_lines)
 
@@ -132,9 +128,7 @@ def validate_single_end_reads(fastq_file: str | PathLike) -> Generator[str]:
     yield from errors
 
 
-def validate_paired_end_reads(
-    fastq_file1: str | PathLike, fastq_file2: str | PathLike
-) -> Generator[str]:
+def validate_paired_end_reads(fastq_file1: str | PathLike, fastq_file2: str | PathLike) -> Generator[str]:
     """
     Validate two paired-end FASTQ files.
 

{grz_cli-0.1.2 → grz_cli-0.1.4}/src/grz_cli/file_operations.py

@@ -69,9 +69,7 @@ def calculate_md5(file_path, chunk_size=2**16, progress=True) -> str:
     md5_hash = hashlib.md5()  # noqa: S324
     with open(file_path, "rb") as f:
         if progress and (total_size > chunk_size):
-            with tqdm(
-                total=total_size, unit="B", unit_scale=True, desc="Calculating MD5"
-            ) as pbar:
+            with tqdm(total=total_size, unit="B", unit_scale=True, desc="Calculating MD5") as pbar:
                 while chunk := f.read(chunk_size):
                     md5_hash.update(chunk)
                     pbar.update(len(chunk))
@@ -117,9 +115,7 @@ def read_multiple_json(input: TextIO, buffer_size=65536, max_buffer_size=1342177
         raise ValueError("Remaining data is not empty. Is there invalid JSON?")
 
 
-def is_relative_subdirectory(
-    relative_path: str | PathLike, root_directory: str | PathLike
-) -> bool:
+def is_relative_subdirectory(relative_path: str | PathLike, root_directory: str | PathLike) -> bool:
     """
     Check if the target path is a subdirectory of the root path
     using os.path.commonpath() without checking the file system.
@@ -223,9 +219,7 @@ class Crypt4GH:
         if passphrase:
             passphrase_callback = lambda: passphrase
         else:
-            passphrase_callback = partial(
-                getpass, prompt=f"Passphrase for {seckey_path}: "
-            )
+            passphrase_callback = partial(getpass, prompt=f"Passphrase for {seckey_path}: ")
 
         return crypt4gh.keys.get_private_key(seckeypath, passphrase_callback)
 
@@ -254,9 +248,7 @@ class Crypt4GH:
             ) as pbar_in_fd,
         ):
             crypt4gh.lib.decrypt(
-                keys=[
-                    (0, private_key, None)
-                ],  # list of (method, privkey, recipient_pubkey=None),
+                keys=[(0, private_key, None)],  # list of (method, privkey, recipient_pubkey=None),
                 infile=pbar_in_fd,
                 outfile=out_fd,
             )

{grz_cli-0.1.2 → grz_cli-0.1.4}/src/grz_cli/models/config.py

@@ -97,22 +97,14 @@ class ConfigModel(StrictBaseModel):
     @field_validator("grz_public_key")
     @classmethod
     def check_grz_public_key(cls, v):
-        if (
-            v is not None
-            and "BEGIN CRYPT4GH PUBLIC KEY" not in v
-            and "END CRYPT4GH PUBLIC KEY" not in v
-        ):
+        if v is not None and "BEGIN CRYPT4GH PUBLIC KEY" not in v and "END CRYPT4GH PUBLIC KEY" not in v:
             raise ValueError("Invalid public key format")
         return v
 
     @model_validator(mode="after")
     def validate_grz_public_key(self) -> Self:
         if self.grz_public_key is None and self.grz_public_key_path is None:
-            raise ValueError(
-                "Either grz_public_key or grz_public_key_path must be set."
-            )
+            raise ValueError("Either grz_public_key or grz_public_key_path must be set.")
         if self.grz_public_key is not None and self.grz_public_key_path is not None:
-            raise ValueError(
-                "Only one of grz_public_key or grz_public_key_path must be set."
-            )
+            raise ValueError("Only one of grz_public_key or grz_public_key_path must be set.")
         return self