✨ make relative outputs and path work better in streamlit

[enryH]

Now this works and can be run from the docs folder using:

cd docs
vuegen -c example_config_files/Basic_example_vuegen_demo_notebook_config.yaml -output_dir ../tests/report_examples/Basic_example_vuegen_demo_notebook_cfg
streamlit run ../tests/report_examples/Basic_example_vuegen_demo_notebook_cfg/streamlit_report/sections/report_manager.py

Solution to be implemented for relative paths:

One or both options:

• unify root path for relative imports in StreamlitReportView class to init. This will allow to make changes to the logic relatively easy.
• set relative path w.r.t. to entry point of the script
• store information of from where the report was executed in order to make the entire folder 'movevable'

[Copilot]

Pull Request Overview

This PR refactors how the generated Streamlit report handles relative paths by introducing a consistent section_dir, updating all section scripts to compute file paths via pathlib, and recording the report’s execution context.

• Introduce sections_dir parameter and self.section_dir attribute in StreamlitReportView
• Change all generated Python section files to import Path, set section_dir, and compute plot_file_path/file_path via (section_dir / …).resolve().as_posix()
• Update CI workflow, docs, Makefile, and config files to point to the new docs/images/logo/ path and validate report generation in tests

Reviewed Changes

Copilot reviewed 27 out of 27 changed files in this pull request and generated no comments.

Show a summary per file

File	Description
src/vuegen/streamlit_reportview.py	Added sections_dir init param; use self.section_dir for relative imports and README
src/vuegen/report_generator.py	Pass sections_dir to view; drop explicit output_dir args
tests/report_examples/**/streamlit_report/sections//.py (all section scripts)	Import Path, define section_dir, and build file paths via section_dir
tests/report_examples/**/streamlit_report/static/Man_Example.html	No change in logic, static HTML moved under correct static dir
gui/Makefile	Updated pyinstaller add-data path to docs/images/logo/vuegen_logo.png
.github/workflows/cdci.yml	Added a step to regenerate and check Streamlit report
docs/vuegen_basic_case_study_configfile.md	Updated logo URL to .../docs/images/logo/...
docs/example_config_files/*.yaml	Updated logo and graphical_abstract URLs to new logo/ path
docs/split_readme.py	Pointed VueGen logo to new logo/ directory
docs/**/README.md and .ipynb	Updated image paths and notebook metadata versions

Comments suppressed due to low confidence (3)

src/vuegen/streamlit_reportview.py:53

• [nitpick] The parameter name sections_dir is inconsistent with the attribute self.section_dir; consider renaming the parameter to section_dir to match and avoid confusion.

        sections_dir: str = SECTIONS_DIR,

src/vuegen/streamlit_reportview.py:92

• The docstring still refers to a default of SECTIONS_DIR; update it to explain that output_dir is now optional and defaults to the configured section_dir when None.

    def generate_report(self, output_dir: str = None) -> None:

src/vuegen/report_generator.py:113

• [nitpick] Since generate_report no longer accepts an explicit output_dir, ensure callers relying on output_dir continue to work; consider logging a warning if the CLI passed an --output_dir flag.

        st_report.generate_report()