Update package manager to uv, gh-workflow and bugfix

.github/workflows/openvariant_tester.yml

@@ -24,27 +24,30 @@ jobs:
   build:
 
     runs-on: ubuntu-latest
+    env:
+      UV_LINK_MODE: copy
+      RUFF_FORMAT: github
 
     steps:
-    - uses: actions/checkout@v3
-    - name: Set up the latest Python
-      uses: actions/setup-python@v3
+    - uses: actions/checkout@v4
+
+    - name: Set up Python
+      uses: actions/setup-python@v5
       with:
-        python-version: "3.x"
-    - name: Install dependencies
-      run: |
-        python -m pip install --upgrade pip
-        pip install flake8 pytest pytest-cov
-        pip install -e .
-    - name: Lint with flake8
+        python-version-file: "pyproject.toml"
+
+    - uses: astral-sh/setup-uv@v4
+
+    - name: Lint with Ruff
       run: |
-        # stop the build if there are Python syntax errors or undefined names
-        # flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
-        # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
-        flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
-    - name: Test with pytest
+        uv sync --extra linting --frozen
+        uv run ruff check openvariant
+
+    - name: Test
       run: |
-        pytest --cov .
+        uv sync --extra tests --frozen
+        uv run pytest --cov . 
+
     - name: Upload coverage reports to Codecov with GitHub Action
       uses: codecov/codecov-action@v3
-        
+

.readthedocs.yaml

@@ -3,17 +3,18 @@ version: 2
 build:
   os: "ubuntu-22.04"
   tools:
-    python: "3.12"
+    python: "3.10"
   apt_packages:
     - build-essential
     - libzmq3-dev 
     - gcc
     - g++
-    - python3-dev
+  commands:
+    - asdf plugin add uv
+    - asdf install uv latest
+    - asdf global uv latest
+    - uv sync --extra docs --frozen
+    - uv run -m sphinx -T -b html -d docs/_build/doctrees -D language=en docs $READTHEDOCS_OUTPUT/html
 
 sphinx:
-  configuration: docs/conf.py 
-
-python:
-  install:
-    - requirements: requirements-docs.txt
+  configuration: docs/conf.py 

openvariant/tasks/plugin.py

@@ -31,49 +31,49 @@ def _add_action(name: str) -> None:
         init_file.write(f"import .{name} from {context_name}\n")
         init_file.close()
     with open(f"{path}/{name}/{name}.py", 'w') as plugin_file:
-        plugin_file.write(f"from openvariant.plugins.context import Context\n")
-        plugin_file.write(f"from openvariant.plugins.plugin import Plugin\n\n\n")
+        plugin_file.write("from openvariant.plugins.context import Context\n")
+        plugin_file.write("from openvariant.plugins.plugin import Plugin\n\n\n")
         plugin_file.write(f"class {context_name}(Context):\n")
-        plugin_file.write(f"\t\"\"\"\n")
+        plugin_file.write("\t\"\"\"\n")
         plugin_file.write(f"\t{context_name} class generated by OpenVariant\n\n")
-        plugin_file.write(f"\tAttributes\n")
-        plugin_file.write(f"\t-------\n")
-        plugin_file.write(f"\trow : dict\n")
-        plugin_file.write(f"\t\tMain method to execute data transformation in each row.\n")
-        plugin_file.write(f"\tfield_name : str\n")
-        plugin_file.write(f"\t\tName of the corresponding column that was described on the annotation schema.\n")
-        plugin_file.write(f"\tfile_path : str\n")
-        plugin_file.write(f"\t\tPath of the Input file that is being parsed.\n")
-        plugin_file.write(f"\t\"\"\"\n\n")
-        plugin_file.write(f"\tdef __init__(self, row: dict, field_name: str, file_path: str) -> None:\n")
-        plugin_file.write(f"\t\tsuper().__init__(row, field_name, file_path)\n")
-        plugin_file.write(f"\n\n")
+        plugin_file.write("\tAttributes\n")
+        plugin_file.write("\t-------\n")
+        plugin_file.write("\trow : dict\n")
+        plugin_file.write("\t\tMain method to execute data transformation in each row.\n")
+        plugin_file.write("\tfield_name : str\n")
+        plugin_file.write("\t\tName of the corresponding column that was described on the annotation schema.\n")
+        plugin_file.write("\tfile_path : str\n")
+        plugin_file.write("\t\tPath of the Input file that is being parsed.\n")
+        plugin_file.write("\t\"\"\"\n\n")
+        plugin_file.write("\tdef __init__(self, row: dict, field_name: str, file_path: str) -> None:\n")
+        plugin_file.write("\t\tsuper().__init__(row, field_name, file_path)\n")
+        plugin_file.write("\n\n")
         plugin_file.write(f"class {plugin_name}(Plugin):\n")
-        plugin_file.write(f"\t\"\"\"\n")
+        plugin_file.write("\t\"\"\"\n")
         plugin_file.write(f"\t{plugin_name} class generated by OpenVariant\n\n")
-        plugin_file.write(f"\tMethods\n")
-        plugin_file.write(f"\t-------\n")
+        plugin_file.write("\tMethods\n")
+        plugin_file.write("\t-------\n")
         plugin_file.write(f"\trun(context: {context_name})\n")
-        plugin_file.write(f"\t\tMain method to execute data transformation in each row.\n")
-        plugin_file.write(f"\t\"\"\"\n\n")
+        plugin_file.write("\t\tMain method to execute data transformation in each row.\n")
+        plugin_file.write("\t\"\"\"\n\n")
         plugin_file.write(f"\tdef run(self, context: {context_name}) -> dict:\n")
-        plugin_file.write(f"\t\t\"\"\"\n")
-        plugin_file.write(f"\t\tData transformation of a single row\n\n")
-        plugin_file.write(f"\t\tParameters\n")
-        plugin_file.write(f"\t\t-------\n")
+        plugin_file.write("\t\t\"\"\"\n")
+        plugin_file.write("\t\tData transformation of a single row\n\n")
+        plugin_file.write("\t\tParameters\n")
+        plugin_file.write("\t\t-------\n")
         plugin_file.write(f"\t\tcontext : {context_name}\n")
-        plugin_file.write(f"\t\t\tRepresentation of the row to be parsed.\n")
-        plugin_file.write(f"\t\t\n")
-        plugin_file.write(f"\t\tReturns\n")
-        plugin_file.write(f"\t\t-------\n")
-        plugin_file.write(f"\t\tfloat or int or str\n")
-        plugin_file.write(f"\t\t\tThe value of the field transformed.\n")
-        plugin_file.write(f"\t\t\"\"\"\n")
-        plugin_file.write(f"\n")
-        plugin_file.write(f"\t\t# This is an example code, modify if as you wish\n")
-        plugin_file.write(f"\t\tcontext.row[context.field_name] = \"Hello world! file:\" + context.file_path\n")
-        plugin_file.write(f"\n")
-        plugin_file.write(f"\t\treturn context.row[context.field_name]\n")
+        plugin_file.write("\t\t\tRepresentation of the row to be parsed.\n")
+        plugin_file.write("\t\t\n")
+        plugin_file.write("\t\tReturns\n")
+        plugin_file.write("\t\t-------\n")
+        plugin_file.write("\t\tfloat or int or str\n")
+        plugin_file.write("\t\t\tThe value of the field transformed.\n")
+        plugin_file.write("\t\t\"\"\"\n")
+        plugin_file.write("\n")
+        plugin_file.write("\t\t# This is an example code, modify if as you wish\n")
+        plugin_file.write("\t\tcontext.row[context.field_name] = \"Hello world! file:\" + context.file_path\n")
+        plugin_file.write("\n")
+        plugin_file.write("\t\treturn context.row[context.field_name]\n")
 
 
 class PluginActions(Enum):

openvariant/variant/variant.py

@@ -94,13 +94,18 @@ def _extract_header(file_path: str, original_header: list, annotation: Annotatio
 
     for field, ann in mapping_fields:
         ann_type = ann[0]
-        header_schema.update({field: AnnotationTypesProcess[ann_type].value(ann, original_header, file_path,
-                                                                            header_schema)})
+
+        class_name = ann_type
+        module_name = "openvariant.annotation.process"
+        ClassAnnotation = import_class_from_module(module_name, class_name)
+        instance = ClassAnnotation()
+
+        header_schema.update({field: instance(ann, original_header, file_path, header_schema)})
     return header_schema, annotation.columns
 
 
 @lru_cache(maxsize=256)
-def _parse_field(value: float or int or str, func: Callable) -> str:
+def _parse_field(value: float | int | str, func: Callable) -> str:
     """Getting the value of a specific annotation field. Cached with LRU policy"""
     result = func(value)
     return result if result is not None else str(float('nan'))

openvariant/variant/where.py

@@ -52,9 +52,9 @@ def _parse_where(where: str or None) -> List:
                         WhereAttributesKeys.FIELD.value: wh[0],
                         WhereAttributesKeys.VALUE.value: wh[2]}
             except KeyError:
-                raise ValueError(f"Unknown \"where\" syntax.")
+                raise ValueError("Unknown \"where\" syntax.")
         else:
-            raise ValueError(f"Unknown where syntax.")
+            raise ValueError("Unknown where syntax.")
     return [stmt]
 
 

pyproject.toml

@@ -0,0 +1,142 @@
+[build-system]
+requires = ["hatchling", "setuptools"]
+build-backend = "hatchling.build"
+
+[project]
+name = "open-variant"
+version = "1.0.1"
+description = "OpenVariant provides different functionalities to read, parse and operate different multiple input file formats, being able to customize the output."
+authors = [
+    { name = "BBGLab (Barcelona Biomedical Genomics Lab)", email = "[email protected]" }
+]
+dependencies = [
+    "pyyaml==6.0.1",
+    "tqdm==4.66.3",
+    "click==8.1.3",
+    "pyliftover==0.4.1",
+    "appdirs==1.4.4",
+]
+readme = "README.md"
+requires-python = ">=3.10"
+license = { file = "LICENSE" }
+keywords = ["bioinformatics", "openvariant", "openvar", "bbglab"]
+
+
+[project.urls]
+Homepage = "https://github.com/bbglab/openvariant"
+Documentation = "https://openvariant.readthedocs.io/"
+Repository = "https://github.com/bbglab/openvariant"
+Issues = "https://github.com/bbglab/openvariant/issues"
+
+
+[project.scripts]
+"openvar" = "openvariant.commands.openvar:openvar"
+
+[project.optional-dependencies]
+docs = [
+    "alabaster==0.7.12",
+    "asttokens==2.0.5",
+    "attrs==22.1.0",
+    "babel==2.10.3",
+    "backcall==0.2.0",
+    "beautifulsoup4==4.11.1",
+    "bleach==5.0.1",
+    "charset-normalizer==2.1.0",
+    "click==8.1.3",
+    "decorator==5.1.1",
+    "defusedxml==0.7.1",
+    "docutils==0.17.1",
+    "entrypoints==0.4",
+    "executing==0.9.1",
+    "fastjsonschema==2.16.1",
+    "idna==3.7",
+    "imagesize==1.4.1",
+    "jedi==0.18.1",
+    "jinja2==3.1.4",
+    "jsonschema==4.8.0",
+    "jupyter-client==7.3.4",
+    "jupyter-core==4.11.2",
+    "jupyterlab-pygments==0.2.2",
+    "markupsafe==2.1.1",
+    "matplotlib-inline==0.1.3",
+    "nbclient==0.6.6",
+    "nbformat==5.4.0",
+    "nbsphinx==0.8.9",
+    "nest-asyncio==1.5.5",
+    "open-variant==1.0.0",
+    "packaging==21.3",
+    "pandocfilters==1.5.0",
+    "parso==0.8.3",
+    "pexpect==4.8.0",
+    "pickleshare==0.7.5",
+    "prompt-toolkit==3.0.30",
+    "ptyprocess==0.7.0",
+    "pure-eval==0.2.2",
+    "pydata-sphinx-theme==0.8.1",
+    "pygments==2.15.0",
+    "pyparsing==3.0.9",
+    "pyrsistent==0.18.1",
+    "python-dateutil==2.8.2",
+    "pytz==2022.1",
+    "pyyaml==6.0.1",
+    "pyzmq==26.2.0",
+    "requests==2.32.2",
+    "ruamel-yaml==0.16.13",
+    "six==1.16.0",
+    "snowballstemmer==2.2.0",
+    "soupsieve==2.3.2.post1",
+    "sphinx-copybutton==0.5.0",
+    "sphinx==4.5.0",
+    "sphinx-gallery==0.10.1",
+    "sphinx-panels==0.6.0",
+    "sphinxcontrib-applehelp==1.0.2",
+    "sphinxcontrib-autoyaml==1.0.0",
+    "sphinxcontrib-devhelp==1.0.2",
+    "sphinxcontrib-htmlhelp==2.0.0",
+    "sphinxcontrib-jsmath==1.0.1",
+    "sphinxcontrib-qthelp==1.0.3",
+    "sphinxcontrib-serializinghtml==1.1.5",
+    "stack-data==0.3.0",
+    "tinycss2==1.1.1",
+    "tornado==6.4.2",
+    "tqdm==4.66.3",
+    "traitlets==5.3.0",
+    "urllib3==1.26.19",
+    "wcwidth==0.2.5",
+    "webencodings==0.5.1",
+    "ipython>=8.18.0",
+    "nbconvert==7.0.0rc0",
+    "mistune==2.0.3",
+    "sphinxcontrib-bibtex==2.6.3",
+    "setuptools>=58.2.0",
+]
+linting = [
+    "flake8>=7.1.1",
+    "ruff>=0.8.3",
+]
+tests = [
+    "coverage>=7.6.9",
+    "pytest-cov>=6.0.0",
+    "pytest>=8.3.4",
+]
+
+[tool.hatch.metadata]
+allow-direct-references = true
+
+[tool.hatch.build.targets.wheel]
+packages = ["openvariant"]
+
+[tool.uv.sources]
+open-variant = { workspace = true }
+
+[tool.ruff.lint]
+select = ["F"]
+ignore = ["F401"]
+
+[tool.ruff]
+line-length = 127
+
+[tool.ruff.format]
+quote-style = "single"
+indent-style = "space"
+docstring-code-format = true