ghga-transpiler 2.0.0__tar.gz → 2.1.1__tar.gz

{ghga_transpiler-2.0.0 → ghga_transpiler-2.1.1}/LICENSE

@@ -186,7 +186,7 @@
       same "printed page" as the copyright notice for easier
       identification within third-party archives.
 
-   Copyright 2021 - 2023 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
+   Copyright 2021 - 2024 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");

{ghga_transpiler-2.0.0 → ghga_transpiler-2.1.1}/PKG-INFO

@@ -1,23 +1,22 @@
 Metadata-Version: 2.1
 Name: ghga_transpiler
-Version: 2.0.0
+Version: 2.1.1
 Summary: GHGA-Transpiler - excel to JSON converter
 Author-email: "German Human Genome Phenome Archive (GHGA)" <contact@ghga.de>
 License: Apache 2.0
 Project-URL: Repository, https://github.com/ghga-de/ghga-transpiler
 Classifier: Development Status :: 1 - Planning
 Classifier: Operating System :: POSIX :: Linux
-Classifier: Programming Language :: Python :: 3.9
-Classifier: Programming Language :: Python :: 3.10
-Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.12
 Classifier: License :: OSI Approved :: Apache Software License
 Classifier: Topic :: Internet :: WWW/HTTP :: HTTP Servers
 Classifier: Topic :: Software Development :: Libraries
 Classifier: Intended Audience :: Developers
-Requires-Python: >=3.9
+Requires-Python: >=3.12
 Description-Content-Type: text/markdown
 License-File: LICENSE
-Requires-Dist: typer~=0.9.0
+Requires-Dist: typer>=0.12
 Requires-Dist: openpyxl==3.*,>=3.1.2
 Requires-Dist: defusedxml==0.*,>=0.7
 Requires-Dist: pydantic<3,>=2

ghga_transpiler-2.1.1/pyproject.toml

@@ -0,0 +1,157 @@
+[build-system]
+requires = [
+    "setuptools>=69",
+]
+build-backend = "setuptools.build_meta"
+
+[project]
+readme = "README.md"
+authors = [
+    { name = "German Human Genome Phenome Archive (GHGA)", email = "contact@ghga.de" },
+]
+requires-python = ">=3.12"
+classifiers = [
+    "Development Status :: 1 - Planning",
+    "Operating System :: POSIX :: Linux",
+    "Programming Language :: Python :: 3",
+    "Programming Language :: Python :: 3.12",
+    "License :: OSI Approved :: Apache Software License",
+    "Topic :: Internet :: WWW/HTTP :: HTTP Servers",
+    "Topic :: Software Development :: Libraries",
+    "Intended Audience :: Developers",
+]
+name = "ghga_transpiler"
+version = "2.1.1"
+description = "GHGA-Transpiler - excel to JSON converter"
+dependencies = [
+    "typer >= 0.12",
+    "openpyxl >= 3.1.2, == 3.*",
+    "defusedxml >= 0.7, == 0.*",
+    "pydantic >=2, <3",
+    "PyYAML ~= 6.0",
+    "semver == 3.*",
+]
+
+[project.license]
+text = "Apache 2.0"
+
+[project.urls]
+Repository = "https://github.com/ghga-de/ghga-transpiler"
+
+[project.scripts]
+ghga-transpiler = "ghga_transpiler.__main__:run"
+
+[tool.setuptools.packages.find]
+where = [
+    "src",
+]
+
+[tool.ruff]
+exclude = [
+    ".git",
+    ".devcontainer",
+    "__pycache__",
+    "build",
+    "dist",
+]
+line-length = 88
+src = [
+    "src",
+    "tests",
+    "examples",
+    "scripts",
+]
+target-version = "py312"
+
+[tool.ruff.lint]
+fixable = [
+    "UP",
+    "I",
+    "D",
+]
+ignore = [
+    "E111",
+    "E114",
+    "E116",
+    "PLW",
+    "RUF001",
+    "RUF010",
+    "RUF012",
+    "N818",
+    "B008",
+    "PLR2004",
+    "D205",
+    "D400",
+    "D401",
+    "D107",
+    "D206",
+    "D300",
+    "UP040",
+]
+select = [
+    "C90",
+    "F",
+    "I",
+    "S",
+    "B",
+    "N",
+    "UP",
+    "PL",
+    "RUF",
+    "SIM",
+    "D",
+]
+
+[tool.ruff.lint.mccabe]
+max-complexity = 10
+
+[tool.ruff.lint.per-file-ignores]
+"scripts/*" = [
+    "PL",
+    "S",
+    "SIM",
+    "D",
+]
+"tests/*" = [
+    "S",
+    "SIM",
+    "PLR",
+    "B011",
+]
+".devcontainer/*" = [
+    "S",
+    "SIM",
+    "D",
+]
+"examples/*" = [
+    "S",
+    "D",
+]
+"__init__.py" = [
+    "D",
+]
+
+[tool.ruff.lint.pydocstyle]
+convention = "pep257"
+
+[tool.mypy]
+disable_error_code = "import"
+show_error_codes = true
+exclude = [
+    "build/lib/",
+]
+warn_redundant_casts = true
+warn_unused_ignores = true
+check_untyped_defs = true
+no_site_packages = false
+
+[tool.pytest.ini_options]
+minversion = "8.0"
+asyncio_mode = "strict"
+
+[tool.coverage.paths]
+source = [
+    "src",
+    "/workspace/src",
+    "**/lib/python*/site-packages",
+]

{ghga_transpiler-2.0.0 → ghga_transpiler-2.1.1}/src/ghga_transpiler/__init__.py

@@ -1,25 +1,24 @@
-# Copyright 2021 - 2023 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
+# Copyright 2021 - 2024 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");
 # you may not use this file except in compliance with the License.
 # You may obtain a copy of the License at
-#
+
 #     http://www.apache.org/licenses/LICENSE-2.0
-#
+
 # Unless required by applicable law or agreed to in writing, software
 # distributed under the License is distributed on an "AS IS" BASIS,
 # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 # See the License for the specific language governing permissions and
 # limitations under the License.
+#
 
-"""Short description of package"""  # Please adapt to package
-
-from importlib.metadata import version
+"""GHGA metadata transpiler"""
 
 from openpyxl.xml import DEFUSEDXML
 
-__version__ = version(__package__)
+__version__ = "2.1.1"
 
 if not DEFUSEDXML:
     raise RuntimeError(

{ghga_transpiler-2.0.0 → ghga_transpiler-2.1.1}/src/ghga_transpiler/__main__.py

@@ -1,17 +1,18 @@
-# Copyright 2021 - 2023 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
+# Copyright 2021 - 2024 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");
 # you may not use this file except in compliance with the License.
 # You may obtain a copy of the License at
-#
+
 #     http://www.apache.org/licenses/LICENSE-2.0
-#
+
 # Unless required by applicable law or agreed to in writing, software
 # distributed under the License is distributed on an "AS IS" BASIS,
 # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 # See the License for the specific language governing permissions and
 # limitations under the License.
+#
 
 """Entrypoint of the package"""
 

{ghga_transpiler-2.0.0 → ghga_transpiler-2.1.1}/src/ghga_transpiler/cli.py

@@ -1,22 +1,23 @@
-# Copyright 2021 - 2023 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
+# Copyright 2021 - 2024 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");
 # you may not use this file except in compliance with the License.
 # You may obtain a copy of the License at
-#
+
 #     http://www.apache.org/licenses/LICENSE-2.0
-#
+
 # Unless required by applicable law or agreed to in writing, software
 # distributed under the License is distributed on an "AS IS" BASIS,
 # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 # See the License for the specific language governing permissions and
 # limitations under the License.
 #
+#
 """CLI-specific wrappers around core functions."""
+
 import sys
 from pathlib import Path
-from typing import Optional
 
 import typer
 
@@ -43,7 +44,7 @@ def transpile(
         dir_okay=False,
         readable=True,
     ),
-    output_file: Optional[Path] = typer.Argument(
+    output_file: Path | None = typer.Argument(
         None, help="The path to output file (JSON).", dir_okay=False
     ),
     force: bool = typer.Option(

{ghga_transpiler-2.0.0 → ghga_transpiler-2.1.1}/src/ghga_transpiler/config/__init__.py

@@ -1,18 +1,20 @@
-# Copyright 2021 - 2023 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
+# Copyright 2021 - 2024 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");
 # you may not use this file except in compliance with the License.
 # You may obtain a copy of the License at
-#
+
 #     http://www.apache.org/licenses/LICENSE-2.0
-#
+
 # Unless required by applicable law or agreed to in writing, software
 # distributed under the License is distributed on an "AS IS" BASIS,
 # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 # See the License for the specific language governing permissions and
 # limitations under the License.
 #
+#
+
+"""Module to load workbook configurations and convert it to transpiler config"""
 
-"""Module to load workbook configurations and convert it to transpiler config """
 from .config import Config, load_config  # noqa

{ghga_transpiler-2.0.0 → ghga_transpiler-2.1.1}/src/ghga_transpiler/config/config.py

@@ -1,24 +1,25 @@
-# Copyright 2021 - 2023 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
+# Copyright 2021 - 2024 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");
 # you may not use this file except in compliance with the License.
 # You may obtain a copy of the License at
-#
+
 #     http://www.apache.org/licenses/LICENSE-2.0
-#
+
 # Unless required by applicable law or agreed to in writing, software
 # distributed under the License is distributed on an "AS IS" BASIS,
 # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 # See the License for the specific language governing permissions and
 # limitations under the License.
 #
+#
 
 """Module to process config file"""
 
 from collections import Counter
+from collections.abc import Callable
 from importlib import resources
-from typing import Callable, Optional
 
 import yaml
 from pydantic import BaseModel, model_validator
@@ -40,18 +41,18 @@ class WorksheetSettings(BaseModel):
     """A data model for the per-worksheet settings of a transpiler config"""
 
     name: str
-    header_row: Optional[int] = None
-    start_row: Optional[int] = None
-    start_column: Optional[int] = None
-    end_column: Optional[int] = None
-    transformations: Optional[dict[str, Callable]] = None
+    header_row: int | None = None
+    start_row: int | None = None
+    start_column: int | None = None
+    end_column: int | None = None
+    transformations: dict[str, Callable] | None = None
 
 
 class Worksheet(BaseModel):
     """A data model for worksheets in the transpiler config"""
 
     sheet_name: str
-    settings: Optional[WorksheetSettings]
+    settings: WorksheetSettings | None
 
 
 class Config(BaseModel):

{ghga_transpiler-2.0.0 → ghga_transpiler-2.1.1}/src/ghga_transpiler/config/exceptions.py

@@ -1,18 +1,19 @@
-# Copyright 2021 - 2023 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
+# Copyright 2021 - 2024 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");
 # you may not use this file except in compliance with the License.
 # You may obtain a copy of the License at
-#
+
 #     http://www.apache.org/licenses/LICENSE-2.0
-#
+
 # Unless required by applicable law or agreed to in writing, software
 # distributed under the License is distributed on an "AS IS" BASIS,
 # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 # See the License for the specific language governing permissions and
 # limitations under the License.
 #
+#
 
 """Module to collect custom exceptions"""
 

{ghga_transpiler-2.0.0 → ghga_transpiler-2.1.1}/src/ghga_transpiler/configs/__init__.py

@@ -1,15 +1,16 @@
-# Copyright 2021 - 2023 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
+# Copyright 2021 - 2024 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");
 # you may not use this file except in compliance with the License.
 # You may obtain a copy of the License at
-#
+
 #     http://www.apache.org/licenses/LICENSE-2.0
-#
+
 # Unless required by applicable law or agreed to in writing, software
 # distributed under the License is distributed on an "AS IS" BASIS,
 # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 # See the License for the specific language governing permissions and
 # limitations under the License.
 #
+#

{ghga_transpiler-2.0.0 → ghga_transpiler-2.1.1}/src/ghga_transpiler/core.py

@@ -1,22 +1,24 @@
-# Copyright 2021 - 2023 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
+# Copyright 2021 - 2024 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");
 # you may not use this file except in compliance with the License.
 # You may obtain a copy of the License at
-#
+
 #     http://www.apache.org/licenses/LICENSE-2.0
-#
+
 # Unless required by applicable law or agreed to in writing, software
 # distributed under the License is distributed on an "AS IS" BASIS,
 # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 # See the License for the specific language governing permissions and
 # limitations under the License.
 #
+#
 
 """This module contains functionalities for processing excel sheets into json object."""
+
+from collections.abc import Callable
 from importlib import resources
-from typing import Callable, Optional, Union
 
 import semver
 from openpyxl import Workbook
@@ -59,10 +61,10 @@ class GHGAWorkbook:
 
 def get_worksheet_rows(
     worksheet,
-    min_row: Union[int, None],
+    min_row: int | None,
     max_row: int,
-    min_col: Union[int, None],
-    max_col: Union[int, None],
+    min_col: int | None,
+    max_col: int | None,
 ) -> list:
     """Function to create a list of rows of a worksheet"""
     return list(
@@ -76,9 +78,9 @@ def get_worksheet_rows(
 
 def get_header(
     worksheet,
-    header_row: Union[int, None],
-    min_col: Union[int, None],
-    max_col: Union[int, None],
+    header_row: int | None,
+    min_col: int | None,
+    max_col: int | None,
 ) -> list[str]:
     """Function to return a list column names of a worksheet"""
     return list(
@@ -95,7 +97,7 @@ def convert_rows(header, rows) -> list[dict]:
     return [
         {
             key: value
-            for key, value in zip(header, row)
+            for key, value in zip(header, row, strict=False)
             if value is not None and value != ""
         }
         for row in rows
@@ -103,7 +105,7 @@ def convert_rows(header, rows) -> list[dict]:
 
 
 def transform_rows(
-    rows: list[dict], transformations: Optional[dict[str, Callable]]
+    rows: list[dict], transformations: dict[str, Callable] | None
 ) -> list[dict]:
     """Transforms row values if it is applicable with a given function"""
     transformed = []

{ghga_transpiler-2.0.0 → ghga_transpiler-2.1.1}/src/ghga_transpiler/io.py

@@ -1,18 +1,19 @@
-# Copyright 2021 - 2023 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
+# Copyright 2021 - 2024 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");
 # you may not use this file except in compliance with the License.
 # You may obtain a copy of the License at
-#
+
 #     http://www.apache.org/licenses/LICENSE-2.0
-#
+
 # Unless required by applicable law or agreed to in writing, software
 # distributed under the License is distributed on an "AS IS" BASIS,
 # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 # See the License for the specific language governing permissions and
 # limitations under the License.
 #
+#
 
 """IO related functionality"""
 
@@ -20,7 +21,7 @@ import json
 import sys
 from importlib import resources
 from pathlib import Path
-from typing import Optional, TextIO
+from typing import TextIO
 
 from openpyxl import load_workbook
 
@@ -39,7 +40,7 @@ def _write_json(data: dict, file: TextIO):
     json.dump(obj=data, fp=file, ensure_ascii=False, indent=4)
 
 
-def write_json(data: dict, path: Optional[Path], force: bool) -> None:
+def write_json(data: dict, path: Path | None, force: bool) -> None:
     """Write the data provided as a dictionary to the specified output path or
     to stdout if the path is None.
     """

{ghga_transpiler-2.0.0 → ghga_transpiler-2.1.1}/src/ghga_transpiler/transformations.py

@@ -1,22 +1,23 @@
-# Copyright 2021 - 2023 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
+# Copyright 2021 - 2024 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");
 # you may not use this file except in compliance with the License.
 # You may obtain a copy of the License at
-#
+
 #     http://www.apache.org/licenses/LICENSE-2.0
-#
+
 # Unless required by applicable law or agreed to in writing, software
 # distributed under the License is distributed on an "AS IS" BASIS,
 # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 # See the License for the specific language governing permissions and
 # limitations under the License.
 #
+#
 
 """Module containing transformation functions"""
 
-from typing import Callable
+from collections.abc import Callable
 
 
 def split_by_semicolon(value: str) -> list[str]:
@@ -35,7 +36,7 @@ def to_attributes() -> Callable:
     def split_one(value: str) -> dict:
         """Returns a dictionary with key, value as keys, splitted string as values"""
         splitted = (elem.strip() for elem in value.split("="))
-        return dict(zip(("key", "value"), splitted))
+        return dict(zip(("key", "value"), splitted, strict=False))
 
     def split_mult(value: str) -> list[dict]:
         """Converts string to attributes"""

{ghga_transpiler-2.0.0 → ghga_transpiler-2.1.1}/src/ghga_transpiler.egg-info/PKG-INFO

@@ -1,23 +1,22 @@
 Metadata-Version: 2.1
-Name: ghga-transpiler
-Version: 2.0.0
+Name: ghga_transpiler
+Version: 2.1.1
 Summary: GHGA-Transpiler - excel to JSON converter
 Author-email: "German Human Genome Phenome Archive (GHGA)" <contact@ghga.de>
 License: Apache 2.0
 Project-URL: Repository, https://github.com/ghga-de/ghga-transpiler
 Classifier: Development Status :: 1 - Planning
 Classifier: Operating System :: POSIX :: Linux
-Classifier: Programming Language :: Python :: 3.9
-Classifier: Programming Language :: Python :: 3.10
-Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.12
 Classifier: License :: OSI Approved :: Apache Software License
 Classifier: Topic :: Internet :: WWW/HTTP :: HTTP Servers
 Classifier: Topic :: Software Development :: Libraries
 Classifier: Intended Audience :: Developers
-Requires-Python: >=3.9
+Requires-Python: >=3.12
 Description-Content-Type: text/markdown
 License-File: LICENSE
-Requires-Dist: typer~=0.9.0
+Requires-Dist: typer>=0.12
 Requires-Dist: openpyxl==3.*,>=3.1.2
 Requires-Dist: defusedxml==0.*,>=0.7
 Requires-Dist: pydantic<3,>=2

{ghga_transpiler-2.0.0 → ghga_transpiler-2.1.1}/src/ghga_transpiler.egg-info/requires.txt

@@ -1,4 +1,4 @@
-typer~=0.9.0
+typer>=0.12
 openpyxl==3.*,>=3.1.2
 defusedxml==0.*,>=0.7
 pydantic<3,>=2

{ghga_transpiler-2.0.0 → ghga_transpiler-2.1.1}/tests/test_convert_workbook.py

@@ -1,18 +1,19 @@
-# Copyright 2021 - 2023 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
+# Copyright 2021 - 2024 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");
 # you may not use this file except in compliance with the License.
 # You may obtain a copy of the License at
-#
+
 #     http://www.apache.org/licenses/LICENSE-2.0
-#
+
 # Unless required by applicable law or agreed to in writing, software
 # distributed under the License is distributed on an "AS IS" BASIS,
 # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 # See the License for the specific language governing permissions and
 # limitations under the License.
 #
+#
 
 """Tests for converting the workbook"""
 

{ghga_transpiler-2.0.0 → ghga_transpiler-2.1.1}/tests/test_create_config.py

@@ -1,18 +1,19 @@
-# Copyright 2021 - 2023 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
+# Copyright 2021 - 2024 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");
 # you may not use this file except in compliance with the License.
 # You may obtain a copy of the License at
-#
+
 #     http://www.apache.org/licenses/LICENSE-2.0
-#
+
 # Unless required by applicable law or agreed to in writing, software
 # distributed under the License is distributed on an "AS IS" BASIS,
 # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 # See the License for the specific language governing permissions and
 # limitations under the License.
 #
+#
 
 """Tests for creating the config"""
 

{ghga_transpiler-2.0.0 → ghga_transpiler-2.1.1}/tests/test_io.py

@@ -1,18 +1,19 @@
-# Copyright 2021 - 2023 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
+# Copyright 2021 - 2024 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");
 # you may not use this file except in compliance with the License.
 # You may obtain a copy of the License at
-#
+
 #     http://www.apache.org/licenses/LICENSE-2.0
-#
+
 # Unless required by applicable law or agreed to in writing, software
 # distributed under the License is distributed on an "AS IS" BASIS,
 # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 # See the License for the specific language governing permissions and
 # limitations under the License.
 #
+#
 
 """IO functionality tests"""
 

{ghga_transpiler-2.0.0 → ghga_transpiler-2.1.1}/tests/test_process_workbook.py

@@ -1,18 +1,19 @@
-# Copyright 2021 - 2023 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
+# Copyright 2021 - 2024 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");
 # you may not use this file except in compliance with the License.
 # You may obtain a copy of the License at
-#
+
 #     http://www.apache.org/licenses/LICENSE-2.0
-#
+
 # Unless required by applicable law or agreed to in writing, software
 # distributed under the License is distributed on an "AS IS" BASIS,
 # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 # See the License for the specific language governing permissions and
 # limitations under the License.
 #
+#
 """Unit tests for core functions"""
 
 import pytest

ghga_transpiler-2.0.0/pyproject.toml

@@ -1,45 +0,0 @@
-[build-system]
-requires = ["setuptools>=67.7.2"]
-build-backend = "setuptools.build_meta"
-
-[project]
-# please adapt to package name
-name = "ghga_transpiler"
-version = "2.0.0"
-description = "GHGA-Transpiler - excel to JSON converter"
-readme = "README.md"
-authors = [
-    { name = "German Human Genome Phenome Archive (GHGA)", email = "contact@ghga.de" },
-]
-requires-python = ">=3.9"
-license = { text = "Apache 2.0" }
-classifiers = [
-    "Development Status :: 1 - Planning",
-    "Operating System :: POSIX :: Linux",
-    "Programming Language :: Python :: 3.9",
-    "Programming Language :: Python :: 3.10",
-    "Programming Language :: Python :: 3.11",
-    "License :: OSI Approved :: Apache Software License",
-    "Topic :: Internet :: WWW/HTTP :: HTTP Servers",
-    "Topic :: Software Development :: Libraries",
-    "Intended Audience :: Developers",
-]
-dependencies = [
-    "typer ~= 0.9.0",
-    "openpyxl >= 3.1.2, == 3.*",
-    "defusedxml >= 0.7, == 0.*",
-    "pydantic >=2, <3",
-    "PyYAML ~= 6.0",
-    "semver == 3.*"
-]
-
-[project.urls]
-# please adapt to package name
-Repository = "https://github.com/ghga-de/ghga-transpiler"
-
-[project.scripts]
-# please adapt to package name
-ghga-transpiler = "ghga_transpiler.__main__:run"
-
-[tool.setuptools.packages.find]
-where = ["src"]