Docs update for release 1.1.0

[ramosv]

Docs update for release 1.1.0
Condensed a lot of the repetitiveness

[Copilot]

Pull Request Overview

This PR updates the documentation and metadata for the upcoming 1.1.0 release, consolidating repetitive sections and bumping version settings across configuration, source, and example files.

• Updated package version to 1.1.0 in setup.cfg, conf.py, init.py, notebooks, and README.
• Refactored and condensed multiple .rst docs (installation, index, gnn, clustering, downstream tasks, FAQ) for consistency and clarity.
• Extended changelog with 1.1.0 entries, added new API autosummaries, and removed obsolete notebook cells.

Reviewed Changes

Copilot reviewed 16 out of 18 changed files in this pull request and generated no comments.

Show a summary per file

File	Description
setup.cfg	Bump version to 1.1.0
docs/source/installation.rst	Revised installation instructions and formatting
docs/source/index.rst	Updated landing page text, quick-start, and images
docs/source/gnns.rst	Condensed GNN overview and feature descriptions
docs/source/faq.rst	Expanded FAQ answers and updated license info
docs/source/downstream_tasks.rst	Reorganized downstream tasks section
docs/source/conf.py	Bump Sphinx release to 1.1.0
docs/source/clustering.rst	Rewrote clustering docs to key features
docs/source/_autosummary/bioneuralnet.utils.preprocess.rst	Removed deprecated entries from autosummary
docs/source/_autosummary/bioneuralnet.utils.graph.rst	Added get_logger to autosummary
docs/source/Quick_Start.ipynb	Bumped displayed version to 1.1.0
docs/jupyter_execute/TCGA-BRCA_Dataset.ipynb	Removed display/warning suppression helper cell
docs/jupyter_execute/Quick_Start.ipynb	Bumped displayed version to 1.1.0
bioneuralnet/init.py	Bump __version__ to 1.1.0
README.md	Updated welcome header to 1.1.0
CHANGELOG.md	Added 1.1.0 changelog sections (Added/Changed/Fixed)

Comments suppressed due to low confidence (2)

docs/source/installation.rst:50

• The R code block indentation is inconsistent under the .. code-block:: r directive. Align all lines at the same indent level (typically 4 spaces) to ensure correct rendering.

        install.packages(c("dplyr", "jsonlite"))

docs/jupyter_execute/TCGA-BRCA_Dataset.ipynb:60

• The helper cell that sets pandas display options and suppresses warnings/logging was removed. Confirm this change won't introduce unwanted warnings or formatting issues in the rendered notebook.

    "- [Direct Download BRCA](http://firebrowse.org/?cohort=BRCA&download_dialog=true)\n"

[ramosv]

This PR only contains updates to the documentation. Also completes the release project from 1.0.0 to 1.1.0

All changes are incorporated in the change log. Since no code updates were made. I will push this without a review.