pydmoo 0.0.8__tar.gz → 0.0.9__tar.gz

pydmoo-0.0.9/.github/workflows/docs.yml

@@ -0,0 +1,71 @@
+name: Deploy Documentation
+
+on:
+  push:
+    branches: [main]
+  pull_request:
+    branches: [main]
+
+jobs:
+  test:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v5
+
+      - name: Set up Python
+        uses: actions/setup-python@v6
+        with:
+          python-version: "3.12"
+
+      - name: Cache pip
+        uses: actions/cache@v4
+        with:
+          path: ~/.cache/pip
+          key: ${{ runner.os }}-pip-${{ hashFiles('requirements.txt') }}
+          restore-keys: |
+            ${{ runner.os }}-pip-
+
+      - name: Install dependencies
+        run: |
+          pip install mkdocs mkdocs-autorefs mkdocs-material mkdocs-material-extensions mkdocstrings[python] mkdocs-minify-plugin mkdocs-redirects
+
+      - name: Generate API docs
+        run: python generate_docs.py
+
+      - name: Build documentation (strict)
+        run: mkdocs build --strict
+
+  deploy:
+    if: github.event_name == 'push' && github.ref == 'refs/heads/main'
+    runs-on: ubuntu-latest
+    needs: test
+    steps:
+      - uses: actions/checkout@v5
+
+      - name: Set up Python
+        uses: actions/setup-python@v6
+        with:
+          python-version: "3.12"
+
+      - name: Cache pip
+        uses: actions/cache@v4
+        with:
+          path: ~/.cache/pip
+          key: ${{ runner.os }}-pip-${{ hashFiles('requirements.txt') }}
+          restore-keys: |
+            ${{ runner.os }}-pip-
+
+      - name: Install dependencies
+        run: |
+          pip install mkdocs mkdocs-autorefs mkdocs-material mkdocs-material-extensions mkdocstrings[python] mkdocs-minify-plugin mkdocs-redirects
+
+      - name: Generate API docs
+        run: python generate_docs.py
+
+      - name: Configure Git
+        run: |
+          git config user.name "GitHub Actions"
+          git config user.email "actions@github.com"
+
+      - name: Deploy to GitHub Pages
+        run: mkdocs gh-deploy --force --remote-branch gh-pages

{pydmoo-0.0.8 → pydmoo-0.0.9}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: pydmoo
-Version: 0.0.8
+Version: 0.0.9
 Summary: pydmoo
 Project-URL: Homepage, https://github.com/dynoptimization/pydmoo
 Project-URL: Repository, https://github.com/dynoptimization/pydmoo

pydmoo-0.0.9/docs/api-auto/pydmoo.md

@@ -0,0 +1,12 @@
+# pydmoo API Reference
+
+pydmoo is a dynamic multi-objective optimization library providing various optimization algorithms and tools.
+
+## Module Overview
+
+::: pydmoo
+    options:
+      show_root_heading: false
+      show_submodules: true
+      heading_level: 3
+      show_source: false

pydmoo-0.0.9/docs/api-auto/response.ar_model.md

@@ -0,0 +1,9 @@
+# response.ar_model
+
+::: pydmoo.response.ar_model
+    options:
+      show_root_heading: false
+      show_submodules: true
+      heading_level: 2
+      show_source: true
+      show_category_heading: true

pydmoo-0.0.9/docs/api-auto/response.tca_model.md

@@ -0,0 +1,9 @@
+# response.tca_model
+
+::: pydmoo.response.tca_model
+    options:
+      show_root_heading: false
+      show_submodules: true
+      heading_level: 2
+      show_source: true
+      show_category_heading: true

pydmoo-0.0.9/docs/api-auto.md

@@ -0,0 +1,10 @@
+# API Reference
+
+This is the complete API reference documentation for the pydmoo library.
+
+## Module List
+
+### Root Modules
+
+- [response.ar_model](api-auto/response.ar_model.md)
+- [response.tca_model](api-auto/response.tca_model.md)

pydmoo-0.0.9/docs/index.md

@@ -0,0 +1,2 @@
+
+pydmoo: Dynamic Multi-Objective Optimization in Python

pydmoo-0.0.9/docs/reference/algorithms/diversity-based.md

@@ -0,0 +1 @@
+# Diversity-Based Algorithms

pydmoo-0.0.9/docs/reference/algorithms/index.md

@@ -0,0 +1 @@
+# Algorithms

pydmoo-0.0.9/docs/reference/applications/index.md

@@ -0,0 +1 @@
+# Applications

pydmoo-0.0.9/docs/reference/index.md

@@ -0,0 +1 @@
+# Reference

pydmoo-0.0.9/docs/reference/metrics/index.md

@@ -0,0 +1 @@
+# Metrics

pydmoo-0.0.9/docs/reference/problems/benchmarks.md

@@ -0,0 +1 @@
+# Benchmarks

pydmoo-0.0.9/docs/reference/problems/index.md

@@ -0,0 +1 @@
+# Problems

pydmoo-0.0.9/docs/users-guide/bug-report.md

@@ -0,0 +1 @@
+# Bug report

pydmoo-0.0.9/docs/users-guide/installation.md

@@ -0,0 +1,19 @@
+# Installation
+
+## [uv](https://docs.astral.sh/uv/)
+
+```shell
+uv add pydmoo
+```
+
+## [poetry](https://python-poetry.org/)
+
+```shell
+poetry add pydmoo
+```
+
+## [pip](https://pip.pypa.io/en/stable/)
+
+```shell
+pip install pydmoo
+```

pydmoo-0.0.9/docs/users-guide/pull-request.md

@@ -0,0 +1 @@
+# Pull Requests

pydmoo-0.0.9/generate_docs.py

@@ -0,0 +1,255 @@
+#!/usr/bin/env python3
+
+"""
+Documentation Generation Script.
+
+This script is used to automatically generate API documentation for the pydmoo library.
+It scans the source code directory and generates corresponding Markdown files for MkDocs build.
+"""
+
+import os
+import sys
+from pathlib import Path
+from typing import Any, Dict, List
+
+
+class DocGenerator:
+    """Documentation generator class."""
+
+    def __init__(self, source_dir: str = "pydmoo", docs_dir: str = "docs"):
+        """
+        Initialize the documentation generator.
+
+        Parameters
+        ----------
+        source_dir : str
+            Python source code directory
+        docs_dir : str
+            Documentation output directory
+        """
+        self.source_dir = Path(source_dir)
+        self.docs_dir = Path(docs_dir)
+        self.api_dir = self.docs_dir / "api-auto"
+
+        # Create necessary directories
+        self.api_dir.mkdir(parents=True, exist_ok=True)
+
+    def discover_modules(self) -> List[Path]:
+        """
+        Discover all Python modules.
+
+        Returns
+        -------
+        List[Path]
+            List of found Python module paths
+        """
+        modules = []
+
+        for py_file in self.source_dir.rglob("*.py"):
+            # Skip __pycache__ directories and test files
+            if "__pycache__" in str(py_file) or "test" in str(py_file).lower():
+                continue
+
+            # Skip empty files and __init__.py files (handled separately)
+            if py_file.name == "__init__.py":
+                continue
+
+            modules.append(py_file)
+
+        return modules
+
+    def get_module_info(self, module_path: Path) -> Dict[str, Any]:
+        """
+        Get module information.
+
+        Parameters
+        ----------
+        module_path : Path
+            Module file path
+
+        Returns
+        -------
+        Dict[str, Any]
+            Module information dictionary
+        """
+        # Calculate relative import path
+        relative_path = module_path.relative_to(self.source_dir)
+        module_name = str(relative_path).replace("/", ".").replace("\\", ".").replace(".py", "")
+
+        return {
+            "path": module_path,
+            "name": module_name,
+            "import_path": f"pydmoo.{module_name}",
+            "doc_path": self.api_dir / f"{module_name}.md"
+        }
+
+    def generate_module_doc(self, module_info: Dict[str, Any]) -> str:
+        """
+        Generate documentation content for a single module.
+
+        Parameters
+        ----------
+        module_info : Dict[str, Any]
+            Module information
+
+        Returns
+        -------
+        str
+            Markdown formatted documentation content
+        """
+        module_name = module_info["name"]
+        import_path = module_info["import_path"]
+
+        content = [
+            f"# {module_name}",
+            "",
+            f"::: {import_path}",
+            "    options:",
+            "      show_root_heading: false",
+            "      show_submodules: true",
+            "      heading_level: 2",
+            "      show_source: true",
+            "      show_category_heading: true",
+            ""
+        ]
+
+        return "\n".join(content)
+
+    def generate_package_doc(self) -> str:
+        """
+        Generate documentation for the main package.
+
+        Returns
+        -------
+        str
+            Main package documentation content
+        """
+        content = [
+            "# pydmoo API Reference",
+            "",
+            "pydmoo is a dynamic multi-objective optimization library providing various optimization algorithms and tools.",
+            "",
+            "## Module Overview",
+            "",
+            "::: pydmoo",
+            "    options:",
+            "      show_root_heading: false",
+            "      show_submodules: true",
+            "      heading_level: 3",
+            "      show_source: false",
+            ""
+        ]
+
+        return "\n".join(content)
+
+    def generate_api_index(self) -> str:
+        """
+        Generate API index page.
+
+        Returns
+        -------
+        str
+            Index page content
+        """
+        modules = self.discover_modules()
+        module_infos = [self.get_module_info(module) for module in modules]
+
+        content = [
+            "# API Reference",
+            "",
+            "This is the complete API reference documentation for the pydmoo library.",
+            "",
+            "## Module List",
+            ""
+        ]
+
+        # Group modules by directory
+        modules_by_dir = {}
+        for info in module_infos:
+            dir_path = str(Path(info["name"]).parent)
+            if dir_path == ".":
+                dir_path = "Root Modules"
+            if dir_path not in modules_by_dir:
+                modules_by_dir[dir_path] = []
+            modules_by_dir[dir_path].append(info)
+
+        # Generate directory structure
+        for dir_name in sorted(modules_by_dir.keys()):
+            content.append(f"### {dir_name}")
+            content.append("")
+
+            for info in sorted(modules_by_dir[dir_name], key=lambda x: x["name"]):
+                module_name = info["name"]
+                doc_file = f"api-auto/{module_name}.md"
+                content.append(f"- [{module_name}]({doc_file})")
+
+            content.append("")
+
+        return "\n".join(content)
+
+    def write_file(self, filepath: Path, content: str) -> None:
+        """
+        Write content to file.
+
+        Parameters
+        ----------
+        filepath : Path
+            File path
+        content : str
+            File content
+        """
+        # Ensure directory exists
+        filepath.parent.mkdir(parents=True, exist_ok=True)
+
+        with open(filepath, "w", encoding="utf-8") as f:
+            f.write(content)
+
+        print(f"✓ Generated documentation: {filepath}")
+
+    def generate_all(self) -> None:
+        """Generate all documentation."""
+        print("Starting API documentation generation...")
+
+        # Generate documentation for individual modules
+        modules = self.discover_modules()
+        print(f"Found {len(modules)} modules")
+
+        for module_path in modules:
+            module_info = self.get_module_info(module_path)
+            doc_content = self.generate_module_doc(module_info)
+            self.write_file(module_info["doc_path"], doc_content)
+
+        # Generate API index
+        api_index_content = self.generate_api_index()
+        self.write_file(self.docs_dir / "api-auto.md", api_index_content)
+
+        # Generate main package documentation
+        package_content = self.generate_package_doc()
+        self.write_file(self.api_dir / "pydmoo.md", package_content)
+
+        print("Documentation generation completed!")
+
+
+def main():
+    try:
+        # Check if source code directory exists
+        if not os.path.exists("pydmoo"):
+            print("Error: pydmoo directory not found")
+            print("Please ensure you are running this script from the project root directory")
+            sys.exit(1)
+
+        # Generate documentation
+        generator = DocGenerator()
+        generator.generate_all()
+
+        # Verify generated files
+        api_files = list(Path("docs/api").glob("*.md"))
+        print(f"Generated {len(api_files)} API documentation files")
+
+    except Exception as e:
+        print(f"Error generating documentation: {e}")
+        sys.exit(1)
+
+
+if __name__ == "__main__":
+    main()

pydmoo-0.0.9/mkdocs.yml

@@ -0,0 +1,150 @@
+# Project information
+site_name: pydmoo Documentations
+site_url: https://github.com/dynoptimization/pydmoo
+site_author: DynOpt
+site_description: >-
+  Dynamic Multi-Objective Optimization in Python (pydmoo)
+
+# Repository
+repo_url: https://github.com/dynoptimization/pydmoo
+repo_name: dynoptimization/pydmoo
+
+# Copyright
+copyright: Copyright © 2025 - 2025 DynOpt
+
+# Configuration
+theme:
+  name: material
+  features:
+    - announce.dismiss
+    # - content.action.edit
+    # - content.action.view
+    - content.code.annotate
+    - content.code.copy
+    # - content.code.select
+    # - content.footnote.tooltips
+    # - content.tabs.link
+    - content.tooltips
+    # - header.autohide
+    # - navigation.expand
+    - navigation.footer
+    - navigation.indexes
+    # - navigation.instant
+    # - navigation.instant.prefetch
+    # - navigation.instant.progress
+    # - navigation.prune
+    - navigation.sections
+    - navigation.tabs
+    # - navigation.tabs.sticky
+    - navigation.top
+    - navigation.tracking
+    - search.highlight
+    - search.share
+    - search.suggest
+    - toc.follow
+    # - toc.integrate
+  palette:
+    - scheme: default
+      primary: teal
+      accent: purple
+      toggle:
+        icon: material/brightness-7
+        name: Switch to dark mode
+    - scheme: slate
+      primary: teal
+      accent: purple
+      toggle:
+        icon: material/brightness-4
+        name: Switch to light mode
+
+plugins:
+  - search:
+      lang: en
+      separator: '[\s\u200b\-_,:!=\[\]()"`/]+|\.(?!\d)|&[lg]t;|(?!\b)(?=[A-Z][a-z])'
+  - autorefs
+  - mkdocstrings:
+      default_handler: python
+      handlers:
+        python:
+          paths: [pydmoo]
+          options:
+            docstring_style: numpy
+            show_root_heading: true
+            show_source: true
+            show_category_heading: true
+            separate_signature: true
+            merge_init_into_class: true
+  - minify:
+      minify_html: true
+
+# Extensions
+markdown_extensions:
+  - abbr
+  - admonition
+  - attr_list
+  - def_list
+  - footnotes
+  - md_in_html
+  - toc:
+      permalink: true
+  - pymdownx.arithmatex:
+      generic: true
+  - pymdownx.betterem:
+      smart_enable: all
+  - pymdownx.caret
+  - pymdownx.details
+  - pymdownx.emoji:
+      emoji_generator: !!python/name:material.extensions.emoji.to_svg
+      emoji_index: !!python/name:material.extensions.emoji.twemoji
+  - pymdownx.highlight:
+      anchor_linenums: true
+      line_spans: __span
+      pygments_lang_class: true
+  - pymdownx.inlinehilite
+  - pymdownx.keys
+  - pymdownx.magiclink:
+      normalize_issue_symbols: true
+      repo_url_shorthand: true
+      user: squidfunk
+      repo: mkdocs-material
+  - pymdownx.mark
+  - pymdownx.smartsymbols
+  - pymdownx.snippets:
+      auto_append:
+        - includes/mkdocs.md
+  - pymdownx.superfences:
+      custom_fences:
+        - name: mermaid
+          class: mermaid
+          format: !!python/name:pymdownx.superfences.fence_code_format
+  - pymdownx.tabbed:
+      alternate_style: true
+      combine_header_slug: true
+      slugify: !!python/object/apply:pymdownx.slugs.slugify
+        kwds:
+          case: lower
+  - pymdownx.tasklist:
+      custom_checkbox: true
+  - pymdownx.tilde
+
+nav:
+  - Home: index.md
+
+  - Getting Started:
+      - Installation: users-guide/installation.md
+
+  - API:
+      - pydmoo: api-auto/pydmoo.md
+      - API reference: api-auto.md
+
+  - Reference:
+      - reference/index.md
+      - Benchmarks: reference/problems/benchmarks.md
+      - Algorithms: reference/algorithms/diversity-based.md
+      - Metrics: reference/metrics/index.md
+      - Applications: reference/applications/index.md
+
+  - Community:
+      - Contributing:
+          - Reporting a bug: users-guide/bug-report.md
+          - Making a pull request: users-guide/pull-request.md

pydmoo-0.0.9/pydmoo/response/ar_model.py

@@ -0,0 +1,96 @@
+import numpy as np
+
+
+class ARModel:
+    """
+    Autoregressive (AR) model implementation from scratch.
+
+    Parameters
+    ----------
+    p : int
+        Order of the AR model (number of lagged observations)
+    """
+
+    def __init__(self, p):
+        self.p = p  # AR order
+        self.coef_ = None  # Model coefficients (including intercept if present)
+        self.resid_ = None  # Residuals after fitting
+
+    def fit(self, y, trend="c"):
+        """
+        Fit AR model to time series data.
+
+        Parameters
+        ----------
+        y : ndarray, shape (M,)
+            Time series data of length M
+        trend : str, optional
+            'c' for constant (default), 'n' for no intercept
+
+        Returns
+        -------
+        self : returns an instance of self
+        """
+        M = len(y)
+        if M <= self.p:
+            raise ValueError(f"Time series length M={M} must be > order p={self.p}")
+
+        # Construct design matrix X and target vector Y
+        X = np.zeros((M - self.p, self.p))
+        for i in range(self.p):
+            X[:, i] = y[(self.p - i - 1) : (M - i - 1)]
+
+        Y = y[self.p :]
+
+        # Add intercept if specified
+        if trend == "c":
+            X = np.column_stack([np.ones(X.shape[0]), X])
+
+        # Solve least squares problem
+        self.coef_ = np.linalg.lstsq(X, Y, rcond=None)[0]
+
+        # Store residuals
+        self.resid_ = Y - X @ self.coef_
+
+        return self
+
+    def predict(self, y, steps=1):
+        """
+        Predict future values using the fitted AR model.
+
+        Parameters
+        ----------
+        y : ndarray, shape (K,)
+            Input sequence (K >= p)
+        steps : int, optional
+            Number of steps to predict (default=1)
+
+        Returns
+        -------
+        predictions : ndarray, shape (steps,)
+            Predicted values
+        """
+        if len(y) < self.p:
+            raise ValueError(f"Input length {len(y)} must be >= model order {self.p}")
+        if self.coef_ is None:
+            raise ValueError("Model must be fitted before prediction")
+
+        predictions = np.zeros(steps)
+        history = y[-self.p :].copy()  # Last p observations
+
+        for i in range(steps):
+            # Prepare input vector
+            x = history[-self.p :][::-1]  # Latest p observations in reverse order
+
+            # Add intercept if present (coef[0] is intercept)
+            if len(self.coef_) == self.p + 1:
+                x = np.insert(x, 0, 1)
+
+            # Make prediction
+            pred = np.dot(x, self.coef_)
+            predictions[i] = pred
+
+            # Update history
+            history = np.append(history, pred)
+
+        return predictions