fix bug of 253 - Githubissues

Summary by Sourcery

Replace the CouchDB backend with a new SQLite-based implementation, introducing advanced extractor tutorials and enhancing the GUI with a slide show feature. Improve testing infrastructure and update CI workflows to support multiple Python versions. Remove obsolete CouchDB-related files and update documentation to reflect these changes.

New Features:

Introduce a new SQLite-based backend to replace the previous CouchDB implementation, enhancing data management and retrieval.
Add support for advanced extractor tutorials, demonstrating how to use style recipes and create metadata data-scientifically.
Implement a new GUI slide show feature to showcase all widgets, facilitating easier testing and demonstration of the user interface.

Bug Fixes:

Fix various issues related to the handling of image data, including validation of JPEG and SVG formats to ensure proper loading and display.
Resolve inconsistencies in the handling of document paths and stacks, improving the reliability of document hierarchy management.

Enhancements:

Refactor the codebase to improve modularity and maintainability, including the separation of string manipulation functions into a dedicated module.
Enhance the testing infrastructure with new tests for GUI components and data export/import functionalities, ensuring robustness and reliability.
Improve the user interface by updating the appearance and functionality of various widgets, including the addition of new themes and styles.

Build:

Update the build system to include new dependencies required for the SQLite backend and enhanced testing capabilities.

CI:

Revise CI workflows to support multiple Python versions and ensure compatibility across different environments.

Deployment:

Remove CouchDB-related deployment scripts and configurations, aligning with the transition to a SQLite-based backend.

Documentation:

Update documentation to reflect changes in the backend architecture and provide guidance on using new features and enhancements.

Tests:

Add comprehensive tests for the new SQLite backend, covering data operations and ensuring consistency with previous functionality.
Introduce tests for the new extractor tutorials, verifying the correct implementation of style recipes and metadata handling.

Chores:

Clean up obsolete files and scripts related to the deprecated CouchDB implementation, streamlining the project structure.

Reviewer's Guide by Sourcery

This pull request implements a major refactoring of the PASTA-ELN project, transitioning from CouchDB to SQLite as the backend database. The changes are extensive, affecting nearly all parts of the codebase, including the core backend functionality, GUI components, installation process, and testing suite.

Class diagram for the refactored serverActions module

classDiagram
    class Backend {
        +checkDB(outputStyle: str, repair: bool)
        +db: SqlLiteDB
    }
    class SqlLiteDB {
        +basePath: Path
        +saveDoc(doc: dict)
        +remove(docID: str)
        +cursor: Cursor
        +connection: Connection
    }
    class serverActions {
        +couchDB2SQLite(userName: str, password: str, database: str, path: str)
        +translateDoc(doc: dict, comment: str) : tuple
        +translateV2_V3(path: str)
        +verifyPasta(projectGroup: str, repair: bool)
        +repairPropertiesDot(projectGroup: str)
        +delete(projectGroup: str, docID: str)
        +__returnBackend__(projectGroup: str) : Backend
    }
    Backend --> SqlLiteDB
    serverActions --> Backend
    serverActions --> SqlLiteDB

Class diagram for the refactored form module

classDiagram
    class Form {
        -comm: Communicate
        -doc: dict
        -flagNewDoc: bool
        -skipKeys: list
        -allHidden: bool
        -allUserElements: list
        +autosave()
        +execute(command: list)
        +textChanged()
        +delTag(_: str, tag: str)
        +addTag(tag: Union[str, int])
        +updateTagsBar()
    }
    class Communicate {
        +backend: Backend
    }
    Form --> Communicate
    Form --> Backend

Class diagram for the refactored installationTools module

classDiagram
    class installationTools {
        +getOS() : str
        +createDefaultConfiguration(pathPasta: Optional[Path]) : dict
        +configuration(command: str, pathData: str) : str
        +exampleData(force: bool, callbackPercent: Optional[Callable], projectGroup: str, outputFormat: str) : str
    }
    class Backend {
        +addData(docType: str, data: dict, newProjID: list)
        +changeHierarchy(projID: str)
        +db: SqlLiteDB
    }
    installationTools --> Backend
    Backend --> SqlLiteDB

File-Level Changes

Change	Details	Files
Replaced CouchDB with SQLite as the backend database	Implemented new SqlLiteDB class to handle database operations Updated all database queries and operations throughout the codebase to work with SQLite Removed CouchDB-specific code and dependencies	`pasta_eln/sqlite.py` `pasta_eln/backend.py` `pasta_eln/GUI/table.py` `pasta_eln/GUI/project.py`
Refactored data model and document structure	Updated document structure to use new field names (e.g., 'id' instead of '_id') Modified how metadata and properties are stored and retrieved Implemented new data hierarchy and definitions system	`pasta_eln/fixedStringsJson.py` `pasta_eln/handleDictionaries.py` `pasta_eln/GUI/form.py`
Updated installation and configuration process	Removed CouchDB installation steps Updated configuration file structure and naming Modified example data creation process to work with new backend	`pasta_eln/installationTools.py` `pasta_eln/GUI/configSetup.py`
Refactored GUI components to work with new backend	Updated form handling and data display in various GUI components Modified project tree view and hierarchy management Implemented new palette system for theming	`pasta_eln/GUI/details.py` `pasta_eln/GUI/projectLeafRenderer.py` `pasta_eln/GUI/palette.py`
Updated and expanded test suite	Added new tests for SQLite backend functionality Updated existing tests to work with new data model Implemented new GUI tests using pytest-qt	`tests/test_01_DefaultExample.py` `tests/test_02_copyMove.py` `tests/test_03_dragDrop.py`
Refactored utility functions and string handling	Moved and updated various utility functions Implemented new string manipulation functions Updated logging and error handling throughout the codebase	`pasta_eln/stringChanges.py` `pasta_eln/miscTools.py`
Updated extractor functionality	Modified extractor interface to work with new data model Updated existing extractors (e.g., PNG, CSV, JSON) to use new style parameter Improved extractor documentation and examples	`pasta_eln/Extractors/extractor_png.py` `pasta_eln/Extractors/extractor_csv.py` `pasta_eln/Extractors/extractor_json.py`

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PASTA-ELN / pasta-eln