netoptim 0.1__tar.gz → 0.3__tar.gz

{netoptim-0.1 → netoptim-0.3}/.github/workflows/ci.bak

@@ -8,7 +8,7 @@ on:
   push:
     # Avoid using all the resources/limits available by checking only
     # relevant branches and tags. Other branches can be checked via PRs.
-    branches: [master]
+    branches: [ master, dev ]
     tags: ['v[0-9]*', '[0-9]+.[0-9]+*']  # Match tags that resemble a version
   pull_request:  # Run in every PR
   workflow_dispatch:  # Allow manually triggering the workflow

{netoptim-0.1 → netoptim-0.3}/.github/workflows/multi-platforms.yml

@@ -8,10 +8,10 @@ jobs:
     strategy:
       matrix:
         os: ["ubuntu-latest", "windows-latest"]
-        version: ["3.9", "3.12"]
+        version: ["3.9", "3.11"]
     steps:
-      - uses: actions/checkout@v2
-      - uses: conda-incubator/setup-miniconda@v2
+      - uses: actions/checkout@v3
+      - uses: conda-incubator/setup-miniconda@v3
         with:
           activate-environment: test
           environment-file: environment.yml
@@ -31,10 +31,11 @@ jobs:
         shell: bash -l {0}
         run: |
           conda install pytest
-          python -m pip install --upgrade pip
+          conda install pip
+          conda install setuptools wheel setuptools_scm
           if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
-          pip install git+https://github.com/luk036/mywheel.git
           pip install git+https://github.com/luk036/ellalgo.git
+          pip install git+https://github.com/luk036/mywheel.git
           pip install git+https://github.com/luk036/digraphx.git
-          python setup.py develop
+          pip install -e .
           pytest

{netoptim-0.1 → netoptim-0.3}/.github/workflows/python-app.yml

@@ -5,9 +5,9 @@ name: Python application
 
 on:
   push:
-    branches: [master]
+    branches: [ master, dev ]
   pull_request:
-    branches: [master]
+    branches: [ master, dev ]
 
 jobs:
   build:

{netoptim-0.1 → netoptim-0.3}/.github/workflows/python-package.yml

@@ -5,9 +5,9 @@ name: Python package
 
 on:
   push:
-    branches: [master]
+    branches: [ master, dev ]
   pull_request:
-    branches: [master]
+    branches: [ master, dev ]
 
 jobs:
   build:
@@ -15,7 +15,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ["3.9", "3.12"]
+        python-version: ["3.9", "3.11"]
 
     steps:
       - uses: actions/checkout@v2

{netoptim-0.1 → netoptim-0.3}/.gitignore

@@ -176,3 +176,7 @@ MANIFEST
 
 # my stuffs
 .hypothesis
+
+# Cache dirs
+.ruff_cache/
+.benchmarks/

{netoptim-0.1 → netoptim-0.3}/.pre-commit-config.yaml

@@ -14,8 +14,10 @@ repos:
       - id: debug-statements
       - id: end-of-file-fixer
       - id: requirements-txt-fixer
+        exclude: "requirements[.]txt$"
       - id: mixed-line-ending
         args: ["--fix=auto"] # replace 'auto' with 'lf' to enforce Linux/Mac line endings or 'crlf' for Windows
+        exclude: "requirements[.]txt$"
 
   ## If you want to automatically "modernize" your Python code:
   # - repo: https://github.com/asottile/pyupgrade

{netoptim-0.1 → netoptim-0.3}/.readthedocs.yml

@@ -9,7 +9,7 @@ version: 2
 build:
   os: ubuntu-22.04
   tools:
-    python: "3.12"
+    python: "3.11"
     # You can also specify other tool versions:
     # nodejs: "19"
     # rust: "1.64"

netoptim-0.3/.vscode/settings.json

@@ -0,0 +1,4 @@
+{
+    "python-envs.defaultEnvManager": "ms-python.python:conda",
+    "python-envs.defaultPackageManager": "ms-python.python:conda"
+}

netoptim-0.3/CHANGELOG.md

@@ -0,0 +1,22 @@
+# Changelog
+
+## Version 0.3 (2026-07-16)
+
+### Documentation
+- **plot_directive with network flow examples**: Enabled matplotlib plot_directive for auto-generated figures. Added network flow and network oracle example plots. (#4ae94a8)
+
+### Bug Fixes
+- **mypy type annotation fixes**: Annotated `NegCycleFinder` with `float Domain` to prevent `int` default. Fixed `NetworkOracle.__init__` parameter types to `Dict[Any, float]`. (#336ef29)
+- **Float literal normalization**: Normalized integer literals to float in test graph data across cycle_finder, ratio, and stress_optscaling tests for type consistency. (#30f5d7a)
+- **Re-enabled disabled tests**: Fixed type annotations in `test_delay_padding` and re-enabled `test_maximize_slack`, `test_maximize_effective_slack`. (#8a76500)
+
+### Testing & Code Quality
+- **Delay padding implementation**: Added delay padding with enhanced cycle finder test cases. (#9df6788)
+- **Additional cycle finder tests**: Added extra test cases for cycle finder algorithms. (#9df6788)
+
+### Code Cleanup
+- **Removed PyScaffold boilerplate**: Deleted `skeleton.py`/`test_skeleton.py`, removed Python < 3.9 compat, dead entry points, stale `IFLOW.md`, duplicate `LICENSE`. (#4cd5756)
+
+### Build & CI
+- **CI repair**: Fixed broken entry_points and remaining skeleton imports. (#c2bf0d3)
+- **Dependency fixes**: Added explicit `mywheel` dep, PyPI-compatible version pins, removed redundant git+https installs. (#81b59c8, #2d232b7, #f07e1bf)

{netoptim-0.1 → netoptim-0.3}/CONTRIBUTING.md

@@ -69,27 +69,29 @@ by adding missing information and correcting mistakes.
 This means that the docs are kept in the same repository as the project code, and
 that any documentation update is done in the same way was a code contribution.
 
-```{todo} Don't forget to mention which markup language you are using.
+```{todo}
+Don't forget to mention which markup language you are using.
 
-    e.g.,  [reStructuredText] or [CommonMark] with [MyST] extensions.
+e.g.,  [reStructuredText] or [CommonMark] with [MyST] extensions.
 ```
 
-```{todo} If your project is hosted on GitHub, you can also mention the following tip:
-
-   :::{tip}
-      Please notice that the [GitHub web interface] provides a quick way of
-      propose changes in `netoptim`'s files. While this mechanism can
-      be tricky for normal code contributions, it works perfectly fine for
-      contributing to the docs, and can be quite handy.
-
-      If you are interested in trying this method out, please navigate to
-      the `docs` folder in the source [repository], find which file you
-      would like to propose changes and click in the little pencil icon at the
-      top, to open [GitHub's code editor]. Once you finish editing the file,
-      please write a message in the form at the bottom of the page describing
-      which changes have you made and what are the motivations behind them and
-      submit your proposal.
-   :::
+```{todo}
+If your project is hosted on GitHub, you can also mention the following tip:
+
+:::{tip}
+   Please notice that the [GitHub web interface] provides a quick way of
+   propose changes in `netoptim`'s files. While this mechanism can
+   be tricky for normal code contributions, it works perfectly fine for
+   contributing to the docs, and can be quite handy.
+
+   If you are interested in trying this method out, please navigate to
+   the `docs` folder in the source [repository], find which file you
+   would like to propose changes and click in the little pencil icon at the
+   top, to open [GitHub's code editor]. Once you finish editing the file,
+   please write a message in the form at the bottom of the page describing
+   which changes have you made and what are the motivations behind them and
+   submit your proposal.
+:::
 ```
 
 When working on documentation changes in your local machine, you can

netoptim-0.3/GEMINI.md

@@ -0,0 +1,64 @@
+# Gemini Code Assistant Context
+
+## Project Overview
+
+This is a Python project for **Network Optimization**. It uses `networkx` for graph-related operations. The project is set up using `PyScaffold`, and the packaging is configured in `setup.cfg`.
+
+The project's source code is located in the `src` directory, and the tests are in the `tests` directory.
+
+## Building and Running
+
+### Dependencies
+
+The main dependencies are:
+- `networkx`
+- `ellalgo`
+- `mywheel`
+- `digraphx`
+- `numpy`
+
+To install all the necessary dependencies, you can use the `requirements.txt` file:
+
+```bash
+pip install -r requirements.txt
+```
+
+### Running Tests
+
+The project uses `pytest` for testing. To run the tests, use the following command:
+
+```bash
+pytest
+```
+
+You can also use `tox` to run the tests in an isolated environment:
+
+```bash
+tox
+```
+
+### Building the Project
+
+To build the project, you can use the `build` environment in `tox`:
+
+```bash
+tox -e build
+```
+
+This will create a `dist` directory with the built package.
+
+## Development Conventions
+
+### Code Style
+
+The project uses the following tools to maintain code quality:
+
+- **Formatting:** `black` is used for code formatting.
+- **Import Sorting:** `isort` is used to sort imports automatically.
+- **Linting:** `flake8` is used for linting the code.
+
+These tools are configured in the `.pre-commit-config.yaml` file and are run automatically before each commit.
+
+### Contribution Guidelines
+
+The `CONTRIBUTING.md` file provides guidelines for contributing to the project. It is recommended to read this file before making any contributions.

{netoptim-0.1 → netoptim-0.3}/LICENSE.txt

@@ -1,6 +1,6 @@
 The MIT License (MIT)
 
-Copyright (c) 2023 Wai-Shing Luk
+Copyright (c) 2025 Wai-Shing Luk
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

{netoptim-0.1/src/netoptim.egg-info → netoptim-0.3}/PKG-INFO

@@ -1,18 +1,24 @@
 Metadata-Version: 2.4
 Name: netoptim
-Version: 0.1
+Version: 0.3
 Summary: Network Optimization Python Code
 Home-page: https://github.com/luk036/netoptim
 Author: Wai-Shing Luk
 Author-email: luk036@gmail.com
 License: MIT
-Project-URL: Documentation, https://pyscaffold.org/
+Project-URL: Documentation, https://netoptim.readthedocs.io/
+Project-URL: Source, https://github.com/luk036/netoptim
+Project-URL: Changelog, https://github.com/luk036/netoptim/blob/main/CHANGELOG.md
+Project-URL: Tracker, https://github.com/luk036/netoptim/issues
 Platform: any
 Classifier: Development Status :: 4 - Beta
 Classifier: Programming Language :: Python
+Requires-Python: >=3.9
 Description-Content-Type: text/markdown; charset=UTF-8; variant=GFM
 License-File: LICENSE.txt
-Requires-Dist: importlib-metadata; python_version < "3.9"
+Requires-Dist: digraphx>=0.3
+Requires-Dist: ellalgo>=0.4
+Requires-Dist: mywheel>=0.3
 Requires-Dist: networkx
 Provides-Extra: testing
 Requires-Dist: setuptools; extra == "testing"
@@ -20,6 +26,7 @@ Requires-Dist: pytest; extra == "testing"
 Requires-Dist: pytest-cov; extra == "testing"
 Requires-Dist: networkx; extra == "testing"
 Requires-Dist: numpy; extra == "testing"
+Requires-Dist: icecream; extra == "testing"
 Dynamic: license-file
 
 <!-- These are examples of badges you might want to add to your README:
@@ -38,9 +45,9 @@ Dynamic: license-file
 [![Documentation Status](https://readthedocs.org/projects/netoptim/badge/?version=latest)](https://netoptim.readthedocs.io/en/latest/?badge=latest)
 [![codecov](https://codecov.io/gh/luk036/netoptim/graph/badge.svg?token=BqErpMZbCK)](https://codecov.io/gh/luk036/netoptim)
 
-# 🖧 netoptim
+# 🌊 netoptim
 
-> Network Optimization Python Code
+> Network Flow Optimization Python Code
 
 A longer description of your project goes here...
 

{netoptim-0.1 → netoptim-0.3}/README.md

@@ -14,9 +14,9 @@
 [![Documentation Status](https://readthedocs.org/projects/netoptim/badge/?version=latest)](https://netoptim.readthedocs.io/en/latest/?badge=latest)
 [![codecov](https://codecov.io/gh/luk036/netoptim/graph/badge.svg?token=BqErpMZbCK)](https://codecov.io/gh/luk036/netoptim)
 
-# 🖧 netoptim
+# 🌊 netoptim
 
-> Network Optimization Python Code
+> Network Flow Optimization Python Code
 
 A longer description of your project goes here...
 

{netoptim-0.1 → netoptim-0.3}/docs/api/netoptim.rst

@@ -9,29 +9,21 @@ netoptim.network\_oracle module
 
 .. automodule:: netoptim.network_oracle
    :members:
-   :undoc-members:
    :show-inheritance:
+   :undoc-members:
 
 netoptim.optscaling\_oracle module
 ----------------------------------
 
 .. automodule:: netoptim.optscaling_oracle
    :members:
-   :undoc-members:
    :show-inheritance:
-
-netoptim.skeleton module
-------------------------
-
-.. automodule:: netoptim.skeleton
-   :members:
    :undoc-members:
-   :show-inheritance:
 
 Module contents
 ---------------
 
 .. automodule:: netoptim
    :members:
-   :undoc-members:
    :show-inheritance:
+   :undoc-members:

{netoptim-0.1 → netoptim-0.3}/docs/conf.py

@@ -9,7 +9,6 @@
 
 import os
 import sys
-import shutil
 
 # -- Path setup --------------------------------------------------------------
 
@@ -28,31 +27,6 @@ sys.path.insert(0, os.path.join(__location__, "../src"))
 # setup.py install" in the RTD Advanced Settings.
 # Additionally it helps us to avoid running apidoc manually
 
-try:  # for Sphinx >= 1.7
-    from sphinx.ext import apidoc
-except ImportError:
-    from sphinx import apidoc
-
-output_dir = os.path.join(__location__, "api")
-module_dir = os.path.join(__location__, "../src/netoptim")
-try:
-    shutil.rmtree(output_dir)
-except FileNotFoundError:
-    pass
-
-try:
-    import sphinx
-
-    cmd_line = f"sphinx-apidoc --implicit-namespaces -f -o {output_dir} {module_dir}"
-
-    args = cmd_line.split(" ")
-    if tuple(sphinx.__version__.split(".")) >= ("1", "7"):
-        # This is a rudimentary parse_version to avoid external dependencies
-        args = args[1:]
-
-    apidoc.main(args)
-except Exception as e:
-    print("Running `sphinx-apidoc` failed!\n{}".format(e))
 
 # -- General configuration ---------------------------------------------------
 
@@ -62,6 +36,7 @@ except Exception as e:
 # Add any Sphinx extension module names here, as strings. They can be extensions
 # coming with Sphinx (named 'sphinx.ext.*') or your custom ones.
 extensions = [
+    "sphinx.ext.apidoc",
     "sphinx.ext.autodoc",
     "sphinx.ext.intersphinx",
     "sphinx.ext.todo",
@@ -72,6 +47,20 @@ extensions = [
     "sphinx.ext.ifconfig",
     "sphinx.ext.mathjax",
     "sphinx.ext.napoleon",
+    "sphinxcontrib.svgbob",
+    "matplotlib.sphinxext.plot_directive",
+]
+
+# -- matplotlib.sphinxext.plot_directive configuration -----------------------
+plot_html_show_source_link = True
+plot_html_show_formats = False
+plot_include_source = True
+plot_working_directory = os.path.join(__location__, "examples")
+plot_pre_code = [
+    "import matplotlib.pyplot as plt",
+    "import networkx as nx",
+    "import numpy as np",
+    "plt.rcParams['figure.dpi'] = 100",
 ]
 
 # Add any paths that contain templates here, relative to this directory.
@@ -249,7 +238,7 @@ htmlhelp_basename = "netoptim-doc"
 
 # -- Options for LaTeX output ------------------------------------------------
 
-latex_elements = {
+latex_elements: dict[str, str] = {
     # The paper size ("letterpaper" or "a4paper").
     # "papersize": "letterpaper",
     # The font size ("10pt", "11pt" or "12pt").

netoptim-0.3/docs/examples/plot_network_flow.py

@@ -0,0 +1,36 @@
+"""
+Network Flow Graph
+==================
+
+Visualization of a directed flow network with edge capacities.
+"""
+import matplotlib.pyplot as plt
+import networkx as nx
+
+g = nx.DiGraph()
+edges = [
+    ("s", "a", 10),
+    ("s", "b", 5),
+    ("a", "b", 15),
+    ("a", "t", 10),
+    ("b", "t", 10),
+]
+for u, v, c in edges:
+    g.add_edge(u, v, capacity=c)
+
+plt.figure(figsize=(7, 5))
+pos = nx.spring_layout(g, seed=42)
+nx.draw(
+    g,
+    pos,
+    with_labels=True,
+    node_color="lightgreen",
+    node_size=800,
+    arrowsize=25,
+    font_weight="bold",
+    font_size=14,
+)
+edge_labels = {(u, v): f'cap={d["capacity"]}' for u, v, d in g.edges(data=True)}
+nx.draw_networkx_edge_labels(g, pos, edge_labels=edge_labels, font_size=11)
+plt.title("Flow Network with Edge Capacities")
+plt.grid(True, alpha=0.3)

netoptim-0.3/docs/examples/plot_network_oracle.py

@@ -0,0 +1,35 @@
+"""
+Network Oracle Example
+======================
+
+Demonstrates a parametric network with an oracle for cutting-plane optimization.
+"""
+import matplotlib.pyplot as plt
+import networkx as nx
+
+gra = {
+    "v1": {"v2": {"w": 3}, "v3": {"w": 4}},
+    "v2": {"v1": {"w": -2}, "v3": {"w": 1}},
+    "v3": {"v1": {"w": -3}, "v2": {"w": -2}},
+}
+
+g = nx.DiGraph()
+for u, neighbors in gra.items():
+    for v, attr in neighbors.items():
+        g.add_edge(u, v, w=attr["w"])
+
+plt.figure(figsize=(7, 5))
+pos = nx.spring_layout(g, seed=42)
+nx.draw(
+    g,
+    pos,
+    with_labels=True,
+    node_color="lightblue",
+    node_size=800,
+    arrowsize=25,
+    font_weight="bold",
+)
+edge_labels = {(u, v): f"w={d['w']}" for u, v, d in g.edges(data=True)}
+nx.draw_networkx_edge_labels(g, pos, edge_labels=edge_labels)
+plt.title("Parametric Network Oracle Graph")
+plt.grid(True, alpha=0.3)

netoptim-0.3/docs/figures_demo.md

@@ -0,0 +1,25 @@
+# Figures Demo
+
+Auto-generated figures demonstrating netoptim functionality.
+
+## Network Flow Graph
+
+```{plot} examples/plot_network_flow.py
+```
+
+## Network Oracle Example
+
+```{plot} examples/plot_network_oracle.py
+```
+
+### Inline Plot Example
+
+```{plot}
+import matplotlib.pyplot as plt
+import numpy as np
+
+x = np.linspace(0, 2 * np.pi, 100)
+plt.plot(x, np.sin(x))
+plt.title("Simple Sine Wave")
+plt.grid(True, alpha=0.3)
+```

{netoptim-0.1 → netoptim-0.3}/docs/index.md

@@ -22,6 +22,7 @@ Contributions & Help <contributing>
 License <license>
 Authors <authors>
 Changelog <changelog>
+Figures Demo <figures_demo>
 Module Reference <api/modules>
 ```
 

{netoptim-0.1 → netoptim-0.3}/docs/requirements.txt

@@ -1,6 +1,10 @@
+digraphx
+ellalgo
 # Requirements file for ReadTheDocs, check .readthedocs.yml.
 # To build the module reference correctly, make sure every external package
 # under `install_requires` in `setup.cfg` is also listed here!
 # sphinx_rtd_theme
 myst-parser[linkify]
+numpy
 sphinx>=3.2.1
+sphinxcontrib-svgbob

{netoptim-0.1 → netoptim-0.3}/environment.yml

@@ -5,3 +5,4 @@ dependencies:
   - pytest
   - pytest-benchmark
   - networkx
+  - icecream

{netoptim-0.1 → netoptim-0.3}/mypy.ini

@@ -5,19 +5,14 @@ warn_unused_configs = True
 [mypy-setuptools.*]
 ignore_missing_imports = True
 
-[mypy-networkx.*]
 ignore_missing_imports = True
 
-[mypy-numpy.*]
 ignore_missing_imports = True
 
-[mypy-scipy.*]
 ignore_missing_imports = True
 
-[mypy-Cython.*]
 ignore_missing_imports = True
 
-[mypy-json.*]
 ignore_missing_imports = True
 
 [mypy-matplotlib.*]

{netoptim-0.1 → netoptim-0.3}/requirements/default.txt

@@ -1,3 +1,4 @@
 decorator>=4.1.0
+icecream>=1.0
 networkx>=2.1
 numpy>=1.12.0

{netoptim-0.1 → netoptim-0.3}/requirements/doc.txt

@@ -1,2 +1,3 @@
 sphinx>=1.6.3
 sphinx_rtd_theme>=0.2.4
+sphinxcontrib-svgbob>=1.0.0

{netoptim-0.1 → netoptim-0.3}/setup.cfg

@@ -9,7 +9,10 @@ long_description = file: README.md
 long_description_content_type = text/markdown; charset=UTF-8; variant=GFM
 url = https://github.com/luk036/netoptim
 project_urls = 
-	Documentation = https://pyscaffold.org/
+	Documentation = https://netoptim.readthedocs.io/
+	Source = https://github.com/luk036/netoptim
+	Changelog = https://github.com/luk036/netoptim/blob/main/CHANGELOG.md
+	Tracker = https://github.com/luk036/netoptim/issues
 platforms = any
 classifiers = 
 	Development Status :: 4 - Beta
@@ -21,8 +24,11 @@ packages = find_namespace:
 include_package_data = True
 package_dir = 
 	=src
+python_requires = >=3.9
 install_requires = 
-	importlib-metadata; python_version<"3.9"
+	digraphx>=0.3
+	ellalgo>=0.4
+	mywheel>=0.3
 	networkx
 
 [options.packages.find]
@@ -37,8 +43,7 @@ testing =
 	pytest-cov
 	networkx
 	numpy
-
-[options.entry_points]
+	icecream
 
 [tool:pytest]
 addopts = 

netoptim-0.3/src/netoptim/__init__.py

@@ -0,0 +1,16 @@
+"""Network Flow Optimization Package.
+
+Provides tools for solving parametric network flow problems
+using cutting-plane methods and ellipsoid algorithms.
+"""
+
+from importlib.metadata import PackageNotFoundError, version  # pragma: no cover
+
+try:
+    # Change here if project is renamed and does not equal the package name
+    dist_name = __name__
+    __version__ = version(dist_name)
+except PackageNotFoundError:  # pragma: no cover
+    __version__ = "unknown"
+finally:
+    del version, PackageNotFoundError