Refactors logging and display architecture (#107)

* Converts print statements to logging

* Refactors plotting module to display module

* Refines parameter handling and logging functionality

* Refines CIF serialization and updates docs

* Refines renderer architecture and error handling

* Refines logging and utils import structure

* Refines table rendering and error handling logic

* Enhances logging with customizable rich formatting

* Refactors plotting modules and updates test expectations

* Refactors logger and environment detection functions

* Switches logging from log to console

* Improves axis scaling for asciichartpy

* Refactors logging utility with enhanced features

* Renames utils module for clarity

* Enhances display and tracking in analysis module

* Disable Jupyter notebook output scrolling

* Rename environment checks for clarity

* Remove redundant type ignores and streamline exception handling

* Improves console width detection for flexible environments

* Refactors logging modes and console output methods

* Enhances logging utilities with improved docs

* Removes unused imports and obsolete functions

* Refactors logging architecture for clarity

* Removes unused show_index parameter

* Refactors logger configuration setup

* Reorders render_table arguments for clarity

* Refactors parameter table rendering and identity handling

* Removes redundant header handling in render_table

* Adds structure refinement example scripts

* Refactors test environment detection logic

* Enhances table styling with padding and font size

* Refactors logger imports and removes lazy loading

* Suppresses user warnings in pytest configuration

* Adds SPDX license headers to utils.py

* Reorganizes display and logging structure

* Refines logging initialization and aliases

* Activates commented pre-commit hooks

* Adds SPDX license identifiers to init files

* Enhances Pandas table styling

* Removes Jupyter-specific logic from CIF renderer

* Updates deps

* Temporarily disable Jupyter scroll in MkDocs

* Improves table styling for enhanced readability

* Add conditional doc build for branch environments

Author: AndrewSazonov

.github/workflows/docs.yaml

@@ -137,7 +137,14 @@ jobs:
       # Input: docs/ directory containing the Markdown files
       # Output: site/ directory containing the generated HTML files
       - name: Build site with MkDocs
-        run: pixi run docs-build
+        run: |
+          if [[ "${CI_BRANCH}" == "develop" || "${CI_BRANCH}" == "master" || "${CI_BRANCH}" == "main" ]]; then
+            echo "📘 Building production docs for ${CI_BRANCH}"
+            pixi run docs-build
+          else
+            echo "📗 Building local docs for ${CI_BRANCH}"
+            pixi run docs-local
+          fi
 
       # Set up the Pages action to configure the static files to be deployed
       # NOTE: The repository must have GitHub Pages enabled and configured to build using GitHub Actions

.pre-commit-config.yaml

@@ -49,9 +49,9 @@ repos:
         pass_filenames: false
         stages: [pre-push]
 
-      #- id: pixi-unit-tests
-      #  name: pixi run unit-tests
-      #  entry: pixi run unit-tests
-      #  language: system
-      #  pass_filenames: false
-      #  stages: [pre-push]
+      - id: pixi-unit-tests
+        name: pixi run unit-tests
+        entry: pixi run unit-tests
+        language: system
+        pass_filenames: false
+        stages: [pre-push]

docs/api-reference/display.md

@@ -0,0 +1 @@
+::: easydiffraction.display

docs/api-reference/index.md

@@ -13,7 +13,7 @@ available in EasyDiffraction:
   space groups, and symmetry operations.
 - [utils](utils.md) – Miscellaneous utility functions for formatting,
   decorators, and general helpers.
-- [plotting](plotting.md) – Tools for visualizing data and fitting results.
+- [display](display.md) – Tools for plotting data and rendering tables.
 - [project](project.md) – Defines the project and manages its state.
 - [sample_models](sample_models.md) – Defines sample models, such as
   crystallographic structures, and manages their properties.

docs/api-reference/io.md

@@ -0,0 +1 @@
+::: easydiffraction.io

docs/api-reference/plotting.md

@@ -32,6 +32,7 @@
 │   │   ├── 📄 reporting.py
 │   │   │   └── 🏷️ class FitResults
 │   │   └── 📄 tracking.py
+│   │       ├── 🏷️ class _TerminalLiveHandle
 │   │       └── 🏷️ class FitProgressTracker
 │   ├── 📁 minimizers
 │   │   ├── 📄 __init__.py
@@ -93,6 +94,37 @@
 │   ├── 📄 __init__.py
 │   ├── 📄 crystallography.py
 │   └── 📄 space_groups.py
+├── 📁 display
+│   ├── 📁 plotters
+│   │   ├── 📄 __init__.py
+│   │   ├── 📄 ascii.py
+│   │   │   └── 🏷️ class AsciiPlotter
+│   │   ├── 📄 base.py
+│   │   │   └── 🏷️ class PlotterBase
+│   │   └── 📄 plotly.py
+│   │       └── 🏷️ class PlotlyPlotter
+│   ├── 📁 tablers
+│   │   ├── 📄 __init__.py
+│   │   ├── 📄 base.py
+│   │   │   └── 🏷️ class TableBackendBase
+│   │   ├── 📄 pandas.py
+│   │   │   └── 🏷️ class PandasTableBackend
+│   │   └── 📄 rich.py
+│   │       └── 🏷️ class RichTableBackend
+│   ├── 📄 __init__.py
+│   ├── 📄 base.py
+│   │   ├── 🏷️ class RendererBase
+│   │   └── 🏷️ class RendererFactoryBase
+│   ├── 📄 plotting.py
+│   │   ├── 🏷️ class PlotterEngineEnum
+│   │   ├── 🏷️ class Plotter
+│   │   └── 🏷️ class PlotterFactory
+│   ├── 📄 tables.py
+│   │   ├── 🏷️ class TableEngineEnum
+│   │   ├── 🏷️ class TableRenderer
+│   │   └── 🏷️ class TableRendererFactory
+│   └── 📄 utils.py
+│       └── 🏷️ class JupyterScrollManager
 ├── 📁 experiments
 │   ├── 📁 categories
 │   │   ├── 📁 background
@@ -192,19 +224,6 @@
 │       ├── 📄 handler.py
 │       │   └── 🏷️ class CifHandler
 │       └── 📄 serialize.py
-├── 📁 plotting
-│   ├── 📁 plotters
-│   │   ├── 📄 __init__.py
-│   │   ├── 📄 plotter_ascii.py
-│   │   │   └── 🏷️ class AsciiPlotter
-│   │   ├── 📄 plotter_base.py
-│   │   │   └── 🏷️ class PlotterBase
-│   │   └── 📄 plotter_plotly.py
-│   │       └── 🏷️ class PlotlyPlotter
-│   ├── 📄 __init__.py
-│   └── 📄 plotting.py
-│       ├── 🏷️ class Plotter
-│       └── 🏷️ class PlotterFactory
 ├── 📁 project
 │   ├── 📄 __init__.py
 │   ├── 📄 project.py
@@ -236,9 +255,14 @@
 │       └── 🏷️ class Summary
 ├── 📁 utils
 │   ├── 📄 __init__.py
-│   ├── 📄 formatting.py
+│   ├── 📄 environment.py
 │   ├── 📄 logging.py
-│   │   └── 🏷️ class Logger
+│   │   ├── 🏷️ class IconifiedRichHandler
+│   │   ├── 🏷️ class ConsoleManager
+│   │   ├── 🏷️ class LoggerConfig
+│   │   ├── 🏷️ class ExceptionHookManager
+│   │   ├── 🏷️ class Logger
+│   │   └── 🏷️ class ConsolePrinter
 │   └── 📄 utils.py
 ├── 📄 __init__.py
 └── 📄 __main__.py

docs/architecture/package-structure-full.md

@@ -46,6 +46,22 @@
 │   ├── 📄 __init__.py
 │   ├── 📄 crystallography.py
 │   └── 📄 space_groups.py
+├── 📁 display
+│   ├── 📁 plotters
+│   │   ├── 📄 __init__.py
+│   │   ├── 📄 ascii.py
+│   │   ├── 📄 base.py
+│   │   └── 📄 plotly.py
+│   ├── 📁 tablers
+│   │   ├── 📄 __init__.py
+│   │   ├── 📄 base.py
+│   │   ├── 📄 pandas.py
+│   │   └── 📄 rich.py
+│   ├── 📄 __init__.py
+│   ├── 📄 base.py
+│   ├── 📄 plotting.py
+│   ├── 📄 tables.py
+│   └── 📄 utils.py
 ├── 📁 experiments
 │   ├── 📁 categories
 │   │   ├── 📁 background
@@ -96,14 +112,6 @@
 │   └── 📁 cif
 │       ├── 📄 handler.py
 │       └── 📄 serialize.py
-├── 📁 plotting
-│   ├── 📁 plotters
-│   │   ├── 📄 __init__.py
-│   │   ├── 📄 plotter_ascii.py
-│   │   ├── 📄 plotter_base.py
-│   │   └── 📄 plotter_plotly.py
-│   ├── 📄 __init__.py
-│   └── 📄 plotting.py
 ├── 📁 project
 │   ├── 📄 __init__.py
 │   ├── 📄 project.py
@@ -125,7 +133,7 @@
 │   └── 📄 summary.py
 ├── 📁 utils
 │   ├── 📄 __init__.py
-│   ├── 📄 formatting.py
+│   ├── 📄 environment.py
 │   ├── 📄 logging.py
 │   └── 📄 utils.py
 ├── 📄 __init__.py

docs/architecture/package-structure-short.md

@@ -86,12 +86,13 @@ nav:
           - 2025 DMSC: tutorials/dmsc-summer-school-2025_analysis-powder-diffraction.ipynb
   - API Reference:
       - API Reference: api-reference/index.md
+      - analysis: api-reference/analysis.md
       - core: api-reference/core.md
       - crystallography: api-reference/crystallography.md
-      - utils: api-reference/utils.md
-      - plotting: api-reference/plotting.md
+      - display: api-reference/display.md
+      - experiments: api-reference/experiments.md
+      - io: api-reference/io.md
       - project: api-reference/project.md
       - sample_models: api-reference/sample_models.md
-      - experiments: api-reference/experiments.md
-      - analysis: api-reference/analysis.md
       - summary: api-reference/summary.md
+      - utils: api-reference/utils.md