vineetb-pyEQL 1.4.0rc9__tar.gz

vineetb_pyeql-1.4.0rc9/.coveragerc

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+# .coveragerc to control coverage.py
+[run]
+branch = True
+source = pyEQL
+# 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__.:

vineetb_pyeql-1.4.0rc9/.gitattributes

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+# Auto detect text files and perform LF normalization
+#* text=auto
+
+# Custom for Visual Studio
+*.cs     diff=csharp
+
+# Standard to msysgit
+*.doc	 diff=astextplain
+*.DOC	 diff=astextplain
+*.docx diff=astextplain
+*.DOCX diff=astextplain
+*.dot  diff=astextplain
+*.DOT  diff=astextplain
+*.pdf  diff=astextplain
+*.PDF	 diff=astextplain
+*.rtf	 diff=astextplain
+*.RTF	 diff=astextplain

vineetb_pyeql-1.4.0rc9/.github/dependabot.yml

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+version: 2
+updates:
+  # Maintain dependencies for GitHub Actions
+  - package-ecosystem: "github-actions"
+    directory: "/"
+    schedule:
+      interval: "weekly"
+    groups:
+      actions:
+        patterns:
+          - "*"

vineetb_pyeql-1.4.0rc9/.github/pull_request_template.md

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+## Summary
+
+Major changes:
+
+- feature 1: ...
+- fix 1: ...
+
+## Todos
+
+If this is work in progress, what else needs to be done?
+
+- feature 2: ...
+- fix 2:
+
+## Checklist
+
+- [ ] Google format doc strings added.
+- [ ] Code linted with `ruff`. (For guidance in fixing rule violates, see [rule list](https://beta.ruff.rs/docs/rules/))
+- [ ] Type annotations included. Check with `mypy`.
+- [ ] Tests added for new features/fixes.
+- [ ] I have run the tests locally and they passed.
+<!-- - [ ] If applicable, new classes/functions/modules have [`duecredit`](https://github.com/duecredit/duecredit) `@due.dcite` decorators to reference relevant papers by DOI ([example](https://github.com/materialsproject/pymatgen/blob/91dbe6ee9ed01d781a9388bf147648e20c6d58e0/pymatgen/core/lattice.py#L1168-L1172)) -->
+
+Tip: Install `pre-commit` hooks to auto-check types and linting before every commit:
+
+```sh
+pip install -U pre-commit
+pre-commit install
+```

vineetb_pyeql-1.4.0rc9/.github/release.yml

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+changelog:
+  exclude:
+    authors: [dependabot, github-actions, pre-commit-ci]
+  categories:
+    - title: 🎉 New Features
+      labels: [feature]
+    - title: 🐛 Bug Fixes
+      labels: [fix]
+    - title: 🛠 Enhancements
+      labels: [enhancement, DX, UX]
+    - title: 📖 Documentation
+      labels: [docs]
+    - title: 🧹 House-Keeping
+      labels: [housekeeping]
+    - title: 🚀 Performance
+      labels: [performance]
+    - title: 💡 Refactoring
+      labels: [refactor]
+    - title: 🧪 Tests
+      labels: [tests]
+    - title: 💥 Breaking Changes
+      labels: [breaking]
+    - title: 🔒 Security Fixes
+      labels: [security]
+    - title: 🏥 Package Health
+      labels: [pkg]
+    - title: 🤷‍♂️ Other Changes
+      labels: ["*"]

vineetb_pyeql-1.4.0rc9/.github/workflows/release.yml

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+name: release
+
+on:
+  release:
+    types: [published]
+
+jobs:
+
+  build_sdist:
+    name: Build source
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v6
+      with:
+        fetch-depth: 0
+        ref: ${{ github.event.release.tag_name }}
+
+    - name: Build source
+      run: |
+        python -m pip install pip --upgrade
+        pip install build --upgrade
+        python -m build --sdist --outdir=wheelhouse
+
+    - name: Upload sdist to github
+      uses: actions/upload-artifact@v6
+      with:
+        name: wheels-sdist
+        path: wheelhouse/*.tar.gz
+        if-no-files-found: error
+
+  build_wheels:
+    name: Build wheel on ${{ matrix.os }} for ${{ matrix.cibw_archs }}
+    needs: [build_sdist]
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        include:
+          - os: ubuntu-latest
+            cibw_archs: "x86_64"
+          - os: ubuntu-24.04-arm
+            cibw_archs: "auto"
+          - os: windows-2022
+            cibw_archs: "auto64"
+          # macos-15-intel for Intel and maos-latest for Apple Silicon
+          - os: macos-15-intel
+            cibw_archs: "x86_64"
+          - os: macos-latest
+            cibw_archs: "arm64"
+
+    steps:
+    - uses: actions/checkout@v6
+      with:
+        fetch-depth: 0
+        ref: ${{ github.event.release.tag_name }}
+
+    - name: Build wheels
+      uses: pypa/cibuildwheel@v3.3
+      with:
+        config-file: cibuildwheel.toml
+        output-dir: wheelhouse
+      env:
+        CIBW_ENVIRONMENT_MACOS: CMAKE_OSX_ARCHITECTURES=${{ matrix.cibw_archs }}
+
+    - name: Upload artifacts to github
+      uses: actions/upload-artifact@v6
+      with:
+        name: wheels-${{ runner.os }}-${{ matrix.cibw_archs }}
+        path: ./wheelhouse/*.whl
+        if-no-files-found: error
+
+  publish_to_pypi:
+    name: Publish wheels to PyPi
+    needs: [build_sdist, build_wheels]
+    runs-on: ubuntu-latest
+    steps:
+      - name: Download packages
+        uses: actions/download-artifact@v7
+        with:
+          pattern: wheels-*
+          path: dist
+          merge-multiple: true
+
+      - name: Print out packages
+        run: ls -la dist/*
+
+      - name: Upload wheels to pypi
+        if: false
+        env:
+          TWINE_USERNAME: __token__
+          TWINE_PASSWORD: ${{ secrets.pypi_password }}
+        run: |
+          python -m pip install --upgrade twine
+          twine upload dist/*

vineetb_pyeql-1.4.0rc9/.github/workflows/testing-pinned.yaml

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+name: testing-pinned
+
+on:
+  pull_request:
+    branches:
+      - main
+    paths-ignore:
+      - CHANGELOG.md
+
+jobs:
+  test:
+    strategy:
+      matrix:
+        # We only test on min. and max. supported Python versions here.
+        python-version: ["3.10", "3.13"]
+        os:
+          - ubuntu-latest
+          - macos-latest
+          - macos-14
+          - windows-latest
+
+    runs-on: ${{ matrix.os }}
+
+    steps:
+      - uses: actions/checkout@v6
+
+      - name: Setup Python
+        uses: actions/setup-python@v6
+        with:
+          python-version: ${{ matrix.python-version }}${{ matrix.dev }}
+
+      - name: Install requirements
+        run: |
+          python -m pip install --upgrade pip
+          pip install -r requirements.txt
+          pip install -e . --no-deps
+
+      - name: Run tests
+        run: |
+          pytest -n auto --cov=src/pyEQL --cov-report=xml --dist=loadscope

vineetb_pyeql-1.4.0rc9/.github/workflows/testing.yaml

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+name: testing
+
+on:
+  pull_request:
+    branches:
+      - main
+      - pourbaix
+    paths-ignore:
+      - CHANGELOG.md
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: false
+
+jobs:
+  lint:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v6
+        with:
+          fetch-depth: 0
+
+      - name: Set up Python
+        uses: actions/setup-python@v6
+        with:
+          python-version: "3.12"
+
+      - name: Run pre-commit
+        run: |
+          pip install pre-commit
+          pre-commit run
+
+  test:
+    needs: lint
+    strategy:
+      matrix:
+        python-version: ["3.10", "3.11", "3.12","3.13"]
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v6
+
+      - name: Setup Python
+        uses: actions/setup-python@v6
+        with:
+          python-version: ${{ matrix.python-version }}${{ matrix.dev }}
+
+      - name: Install test requirements
+        run: |
+          python -m pip install --upgrade pip
+          pip install -e ".[testing]"
+
+      - name: List installed requirements
+        run: |
+          pip freeze
+
+      - name: Run tests
+        run: |
+          if [[ "${{ matrix.python-version }}" == "3.12" ]]; then
+            pytest -n auto --cov=src/pyEQL --cov-report=xml --dist=loadscope
+          else
+            pytest -n auto --dist=loadscope
+          fi
+
+      - uses: codecov/codecov-action@v5
+        if: matrix.python-version == '3.12'
+        with:
+          token: ${{ secrets.CODECOV_TOKEN }}
+          file: ./coverage.xml
+
+  docs:
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v6
+
+      - name: Setup Python
+        uses: actions/setup-python@v6
+        with:
+          python-version: "3.11"
+
+      - name: Install tox
+        run: |
+          python -m pip install tox
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - name: Build docs
+        run: tox -e docs
+
+      - name: Check links
+        run: tox -e links

vineetb_pyeql-1.4.0rc9/.gitignore

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+# Temporary and binary files
+*~
+*.py[cod]
+*.so
+*.cfg
+!.isort.cfg
+!setup.cfg
+*.orig
+*.log
+*.pot
+__pycache__/*
+.cache/*
+.*.swp
+*/.ipynb_checkpoints/*
+.DS_Store
+
+# Project files
+.ropeproject
+.project
+.pydevproject
+.settings
+.idea
+.vscode
+tags
+
+# Package files
+*.egg
+*.eggs/
+.installed.cfg
+*.egg-info
+
+# Unittest and coverage
+htmlcov/*
+.coverage
+.coverage.*
+.tox
+junit*.xml
+coverage.xml
+.pytest_cache/
+
+# Build and docs folder/files
+build/*
+dist/*
+sdist/*
+docs/_build/*
+docs/_static/*
+docs/api/*
+cover/*
+MANIFEST
+
+# Per-project virtualenvs
+.venv*/
+.conda*/
+
+# setuptools-scm managed version file
+src/pyEQL/_version.py

vineetb_pyeql-1.4.0rc9/.pre-commit-config.yaml

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+exclude: ^(docs/conf\.py|src/pyEQL/phreeqc/ext|tests/phreeqc/.*\.dat)
+
+default_stages: [pre-commit]
+
+default_install_hook_types: [pre-commit, commit-msg]
+
+ci:
+  autoupdate_schedule: monthly
+  # skip: [mypy]
+  autofix_commit_msg: pre-commit auto-fixes
+  autoupdate_commit_msg: pre-commit autoupdate
+
+repos:
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.12.7
+    hooks:
+      # Run the linter. filters are to exclude .ipynb files
+      - id: ruff-check
+        types_or: [ python, pyi ]
+        args: [--fix, --ignore, "D,E501", --show-fixes]
+      # Run the formatter. This WILL run on .ipynb files
+      - id: ruff-format
+
+  - repo: https://github.com/codespell-project/codespell
+    rev: v2.4.1
+    hooks:
+      - id: codespell
+        stages: [pre-commit, commit-msg]
+        exclude_types: [html, svg, jupyter]
+        additional_dependencies: [tomli] # needed to read pyproject.toml below py3.11
+
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v5.0.0
+    hooks:
+      - id: check-case-conflict
+      - id: check-symlinks
+      - id: destroyed-symlinks
+      - id: end-of-file-fixer
+      - id: mixed-line-ending
+        exclude_types: [svg]
+      - id: trailing-whitespace
+        exclude_types: [svg]
+      - id: check-yaml
+      - id: check-json
+      - id: pretty-format-json
+        exclude_types: [jupyter]
+        args: [--autofix, --indent=4]

vineetb_pyeql-1.4.0rc9/.readthedocs.yml

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+# 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"
+
+# Build documentation in the docs/ directory with Sphinx
+sphinx:
+  configuration: docs/conf.py
+
+# Build documentation with MkDocs
+#mkdocs:
+#  configuration: mkdocs.yml
+
+# Optionally build your docs in additional formats such as PDF
+formats:
+  - pdf
+
+python:
+  install:
+    - requirements: docs/requirements.txt

vineetb_pyeql-1.4.0rc9/.zenodo.json

@@ -0,0 +1,25 @@
+{
+    "creators": [
+        {
+            "affiliation": "Princeton University",
+            "name": "Kingsbury, Ryan",
+            "orcid": "0000-0002-7168-3967"
+        }
+    ],
+    "rights": [
+        {
+            "description": {
+                "en": ""
+            },
+            "id": "lgpl-3.0-only",
+            "props": {
+                "scheme": "spdx",
+                "url": "https://www.gnu.org/licenses/lgpl-3.0-standalone.html"
+            },
+            "title": {
+                "en": "GNU Lesser General Public License v3.0 only"
+            }
+        }
+    ],
+    "title": "pyEQL: A python library for water chemistry"
+}

vineetb_pyeql-1.4.0rc9/AUTHORS.md

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+# Contributors
+
+pyEQL was originally written by Prof. Ryan Kingsbury (@rkingsbury) and is primarily
+developed and maintained by the Kingsbury Lab at Princeton University.
+
+Other contributors, listed alphabetically, are:
+
+- Arpit Bhardwaj (@abhardwaj73)
+- Nikhil Dhruv (@NikhilDhruv)
+- Dhruv Duseja (@DhruvDuseja)
+- @githubalexliu
+- Hernan Grecco (@hgrecco)
+- @Ouriel Ndalamba (@Ouriel-N)
+- Ugo Nwosu (@ugognw)
+- Yitong Pan (@YitongPan1)
+- Jaebeom Park (@Jaebeom-P)
+- Kirill Pushkarev (@kirill-push)
+- Andrew Rosen (@arosen93)
+- Sui Xiong Tay (@SuixiongTay)
+
+(If you think that your name belongs here, please let the maintainer know)