physdes-py 0.1__tar.gz

physdes_py-0.1/.coveragerc

@@ -0,0 +1,28 @@
+# .coveragerc to control coverage.py
+[run]
+branch = True
+source = physdes
+# omit = bad_file.py
+
+[paths]
+source =
+    src/
+    */site-packages/
+
+[report]
+# Regexes for lines to exclude from consideration
+exclude_lines =
+    # Have to re-enable the standard pragma
+    pragma: no cover
+
+    # Don't complain about missing debug-only code:
+    def __repr__
+    if self\.debug
+
+    # Don't complain if tests don't hit defensive assertion code:
+    raise AssertionError
+    raise NotImplementedError
+
+    # Don't complain if non-runnable code isn't run:
+    if 0:
+    if __name__ == .__main__.:

physdes_py-0.1/.flake8

@@ -0,0 +1,3 @@
+# Autoformatter friendly flake8 config (all formatting rules disabled)
+[flake8]
+extend-ignore = E1, E2, E3, E501, W1, W2, W3, W5

physdes_py-0.1/.github/workflows/jekyll-gh-pages.yml

@@ -0,0 +1,51 @@
+# Sample workflow for building and deploying a Jekyll site to GitHub Pages
+name: Deploy Jekyll with GitHub Pages dependencies preinstalled
+
+on:
+  # Runs on pushes targeting the default branch
+  push:
+    branches: ["main"]
+
+  # Allows you to run this workflow manually from the Actions tab
+  workflow_dispatch:
+
+# Sets permissions of the GITHUB_TOKEN to allow deployment to GitHub Pages
+permissions:
+  contents: read
+  pages: write
+  id-token: write
+
+# Allow only one concurrent deployment, skipping runs queued between the run in-progress and latest queued.
+# However, do NOT cancel in-progress runs as we want to allow these production deployments to complete.
+concurrency:
+  group: "pages"
+  cancel-in-progress: false
+
+jobs:
+  # Build job
+  build:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+      - name: Setup Pages
+        uses: actions/configure-pages@v4
+      - name: Build with Jekyll
+        uses: actions/jekyll-build-pages@v1
+        with:
+          source: ./
+          destination: ./_site
+      - name: Upload artifact
+        uses: actions/upload-pages-artifact@v3
+
+  # Deployment job
+  deploy:
+    environment:
+      name: github-pages
+      url: ${{ steps.deployment.outputs.page_url }}
+    runs-on: ubuntu-latest
+    needs: build
+    steps:
+      - name: Deploy to GitHub Pages
+        id: deployment
+        uses: actions/deploy-pages@v4

physdes_py-0.1/.github/workflows/multi-platforms.yml

@@ -0,0 +1,38 @@
+name: Multi-Platforms
+on: [push]
+
+jobs:
+  miniconda:
+    name: Miniconda ${{ matrix.os }} for Python ${{ matrix.version }}
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        os: ["ubuntu-latest", "windows-latest"]
+        version: ["3.10", "3.12"]
+    steps:
+      - uses: actions/checkout@v2
+      - uses: conda-incubator/setup-miniconda@v2
+        with:
+          activate-environment: test
+          environment-file: environment.yml
+          python-version: ${{ matrix.version }}
+          auto-activate-base: false
+      - shell: bash -l {0}
+        run: |
+          conda info
+          conda list
+      - name: Lint
+        shell: bash -l {0}
+        run: |
+          conda install flake8
+          python -m flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
+          python -m flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
+      - name: Run pytest
+        shell: bash -l {0}
+        run: |
+          conda install pytest
+          python -m pip install --upgrade pip
+          if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
+          pip install git+https://github.com/luk036/lds-gen.git
+          python setup.py develop
+          pytest

physdes_py-0.1/.github/workflows/python-app.yml

@@ -0,0 +1,47 @@
+# This workflow will install Python dependencies, run tests and lint with a single version of Python
+# For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions
+
+name: Python application (new)
+
+on:
+  push:
+    branches: [main]
+  pull_request:
+    branches: [main]
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v2
+      - name: Set up Python 3.10
+        uses: actions/setup-python@v2
+        with:
+          python-version: "3.10"
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install flake8 pytest
+          if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
+          pip install git+https://github.com/luk036/lds-gen.git
+          python setup.py develop
+
+      - name: Lint with flake8
+        run: |
+          # stop the build if there are Python syntax errors or undefined names
+          flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
+          # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
+          flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
+      - name: Test with pytest
+        run: |
+          pytest --cov=src/
+      - name: Codecov
+        # You may pin to the exact commit or the version.
+        # uses: codecov/codecov-action@29386c70ef20e286228c72b668a06fd0e8399192
+        uses: codecov/codecov-action@v1.5.2
+        with:
+          # Repository upload token - get it from codecov.io. Required only for private repositories
+          token: ${{ secrets.CODECOV_TOKEN }}
+          # Comma-separated list of files to upload
+          fail_ci_if_error: true

physdes_py-0.1/.github/workflows/python-publish.yml

@@ -0,0 +1,70 @@
+# This workflow will upload a Python Package to PyPI when a release is created
+# For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python#publishing-to-package-registries
+
+# This workflow uses actions that are not certified by GitHub.
+# They are provided by a third-party and are governed by
+# separate terms of service, privacy policy, and support
+# documentation.
+
+name: Upload Python Package
+
+on:
+  release:
+    types: [published]
+
+permissions:
+  contents: read
+
+jobs:
+  release-build:
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: actions/setup-python@v5
+        with:
+          python-version: "3.x"
+
+      - name: Build release distributions
+        run: |
+          # NOTE: put your own distribution build steps here.
+          python -m pip install build
+          python -m build
+
+      - name: Upload distributions
+        uses: actions/upload-artifact@v4
+        with:
+          name: release-dists
+          path: dist/
+
+  pypi-publish:
+    runs-on: ubuntu-latest
+    needs:
+      - release-build
+    permissions:
+      # IMPORTANT: this permission is mandatory for trusted publishing
+      id-token: write
+
+    # Dedicated environments with protections for publishing are strongly recommended.
+    # For more information, see: https://docs.github.com/en/actions/deployment/targeting-different-environments/using-environments-for-deployment#deployment-protection-rules
+    environment:
+      name: pypi
+      # OPTIONAL: uncomment and update to include your PyPI project URL in the deployment status:
+      # url: https://pypi.org/p/YOURPROJECT
+      #
+      # ALTERNATIVE: if your GitHub Release name is the PyPI project version string
+      # ALTERNATIVE: exactly, uncomment the following line instead:
+      # url: https://pypi.org/project/YOURPROJECT/${{ github.event.release.name }}
+
+    steps:
+      - name: Retrieve release distributions
+        uses: actions/download-artifact@v4
+        with:
+          name: release-dists
+          path: dist/
+
+      - name: Publish release distributions to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          packages-dir: dist/

physdes_py-0.1/.gitignore

@@ -0,0 +1,178 @@
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+cover/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+.pybuilder/
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+#   For a library or package, you might want to ignore these files since the code is
+#   intended to run in multiple environments; otherwise, check them in:
+# .python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# poetry
+#   Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control.
+#   This is especially recommended for binary packages to ensure reproducibility, and is more
+#   commonly ignored for libraries.
+#   https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control
+#poetry.lock
+
+# pdm
+#   Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control.
+#pdm.lock
+#   pdm stores project-wide configurations in .pdm.toml, but it is recommended to not include it
+#   in version control.
+#   https://pdm.fming.dev/#use-with-ide
+.pdm.toml
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+# pytype static type analyzer
+.pytype/
+
+# Cython debug symbols
+cython_debug/
+
+# PyCharm
+#  JetBrains specific template is maintained in a separate JetBrains.gitignore that can
+#  be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
+#  and can be added to the global gitignore or merged into this file.  For a more nuclear
+#  option (not recommended) you can uncomment the following to ignore the entire idea folder.
+#.idea/
+
+# Build and docs folder/files
+build/*
+dist/*
+sdist/*
+docs/api/*
+docs/_rst/*
+docs/_build/*
+cover/*
+MANIFEST
+
+# Per-project virtualenvs
+.venv*/
+.conda*/
+.python-version
+
+# my stuffs
+.hypothesis

physdes_py-0.1/.gitpod.Dockerfile

@@ -0,0 +1,78 @@
+FROM gitpod/workspace-full
+
+USER root
+# Install util tools.
+
+RUN apt-get update \
+ && apt-get install -y \
+  apt-utils \
+  aria2 \
+# utilities (not ripgrep, gh) \
+  asciinema \
+  bat \
+  byobu \
+  curl \
+  elinks \
+  fd-find \
+  fish \
+  mdp \
+  ncdu \
+  neofetch \
+  patat \
+  pkg-config \
+  ranger \
+  w3m \
+# just for fun (not cmatrix) \
+  cowsay \
+  figlet \
+  fortune \
+  toilet \
+  tty-clock
+
+RUN mkdir -p /workspace/data \
+    && chown -R gitpod:gitpod /workspace/data
+
+RUN mkdir /home/gitpod/.conda
+# Install conda
+RUN wget --quiet https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh -O ~/miniconda.sh && \
+    /bin/bash ~/miniconda.sh -b -p /opt/conda && \
+    rm ~/miniconda.sh && \
+    ln -s /opt/conda/etc/profile.d/conda.sh /etc/profile.d/conda.sh && \
+    echo ". /opt/conda/etc/profile.d/conda.sh" >> ~/.bashrc && \
+    echo "conda activate base" >> ~/.bashrc
+
+RUN /opt/conda/bin/conda config --set always_yes yes --set changeps1 no \
+    && /opt/conda/bin/conda update -q conda \
+    && /opt/conda/bin/conda info -a
+
+RUN /opt/conda/bin/conda install -y -c conda-forge \
+    pandoc-crossref \
+    pandoc
+
+# RUN /opt/conda/bin/pip install \
+#     codecov \
+#     coverage \
+#     coveralls \
+#     cvxpy \
+#     jupyter \
+#     matplotlib \
+#     networkx \
+#     numexpr \
+#     numpy \
+#     scipy \
+#     flake8 \
+#     mypy \
+#     pre-commit \
+#     pyqt5 \
+#     pytest-benchmark \
+#     pytest-cov \
+#     pytest \
+#     yapf \
+#     lolcat
+
+RUN chown -R gitpod:gitpod /opt/conda \
+    && chmod -R 777 /opt/conda \
+    && chown -R gitpod:gitpod /home/gitpod/.conda \
+    && chmod -R 777 /home/gitpod/.conda
+
+RUN apt-get clean && rm -rf /var/cache/apt/* && rm -rf /var/lib/apt/lists/* && rm -rf /tmp/*

physdes_py-0.1/.gitpod.yml

@@ -0,0 +1,15 @@
+ports:
+  - port: 8050
+    onOpen: open-preview
+  - port: 8888
+    onOpen: open-browser
+tasks:
+  - command: >
+      pip3 install -r ./requirements.txt &&
+      python3 setup.py develop
+# image:
+#   file: .gitpod.Dockerfile
+
+vscode:
+  extensions:
+    - njpwerner.autodocstring

physdes_py-0.1/.hadolint.yaml

@@ -0,0 +1,4 @@
+# Following source doesn't work in most setups
+ignored:
+  - SC1090
+  - SC1091

physdes_py-0.1/.isort.cfg

@@ -0,0 +1,3 @@
+[settings]
+profile = black
+known_first_party = physdes

physdes_py-0.1/.markdownlint.yaml

@@ -0,0 +1,10 @@
+# Autoformatter friendly markdownlint config (all formatting rules disabled)
+default: true
+blank_lines: false
+bullet: false
+html: false
+indentation: false
+line_length: false
+spaces: false
+url: false
+whitespace: false

physdes_py-0.1/.pre-commit-config.yaml

@@ -0,0 +1,53 @@
+exclude: "^docs/conf.py"
+
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.4.0
+    hooks:
+      - id: trailing-whitespace
+      - id: check-added-large-files
+      - id: check-ast
+      - id: check-json
+      - id: check-merge-conflict
+      - id: check-xml
+      - id: check-yaml
+      - id: debug-statements
+      - id: end-of-file-fixer
+      - id: requirements-txt-fixer
+      - id: mixed-line-ending
+        args: ["--fix=auto"] # replace 'auto' with 'lf' to enforce Linux/Mac line endings or 'crlf' for Windows
+
+  ## If you want to avoid flake8 errors due to unused vars or imports:
+  # - repo: https://github.com/myint/autoflake
+  #   rev: v1.4
+  #   hooks:
+  #   - id: autoflake
+  #     args: [
+  #       --in-place,
+  #       --remove-all-unused-imports,
+  #       --remove-unused-variables,
+  #     ]
+
+  - repo: https://github.com/pycqa/isort
+    rev: 5.12.0
+    hooks:
+      - id: isort
+
+  - repo: https://github.com/psf/black
+    rev: 23.7.0
+    hooks:
+      - id: black
+        language_version: python3
+
+  ## If like to embrace black styles even in the docs:
+  # - repo: https://github.com/asottile/blacken-docs
+  #   rev: v1.12.0
+  #   hooks:
+  #   - id: blacken-docs
+  #     additional_dependencies: [black]
+  - repo: https://github.com/PyCQA/flake8
+    rev: 6.1.0
+    hooks:
+      - id: flake8
+    ## You can add flake8 plugins via `additional_dependencies`:
+    #  additional_dependencies: [flake8-bugbear]

physdes_py-0.1/.readthedocs.yml

@@ -0,0 +1,32 @@
+# .readthedocs.yaml
+# Read the Docs configuration file
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+# Required
+version: 2
+
+# Set the OS, Python version and other tools you might need
+build:
+  os: ubuntu-22.04
+  tools:
+    python: "3.11"
+    # You can also specify other tool versions:
+    # nodejs: "19"
+    # rust: "1.64"
+    # golang: "1.19"
+
+# Build documentation in the "docs/" directory with Sphinx
+sphinx:
+  configuration: docs/conf.py
+
+# Optionally build your docs in additional formats such as PDF and ePub
+formats:
+   - pdf
+
+# Optional but recommended, declare the Python requirements required
+# to build your documentation
+# See https://docs.readthedocs.io/en/stable/guides/reproducible-builds.html
+python:
+  install:
+    - requirements: docs/requirements.txt
+    - { path: ., method: pip }

physdes_py-0.1/.shellcheckrc

@@ -0,0 +1,3 @@
+# Following source doesn't work in most setups
+disable=SC1090
+disable=SC1091

physdes_py-0.1/AUTHORS.rst

@@ -0,0 +1,5 @@
+============
+Contributors
+============
+
+* Wai-Shing Luk <luk036@gmail.com>

physdes_py-0.1/CHANGELOG.rst

@@ -0,0 +1,10 @@
+=========
+Changelog
+=========
+
+Version 0.1
+===========
+
+- Feature A added
+- FIX: nasty bug #1729 fixed
+- add your changes here!

physdes_py-0.1/LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2020 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
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

physdes_py-0.1/LICENSE.txt

@@ -0,0 +1,21 @@
+The MIT License (MIT)
+
+Copyright (c) 2022 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
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.