atomscale 0.7.0__tar.gz

atomscale-0.7.0/.github/workflows/release.yml

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+name: Publish
+
+on:
+  release:
+    types: [published]
+  workflow_dispatch:
+
+jobs:
+  build_wheels:
+    name: Build wheels (${{ matrix.os }})
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-latest, macos-latest, windows-latest]  # macos-latest provides Apple Silicon runners
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: actions/setup-python@v5
+        with:
+          python-version: "3.11"   # host Python; cibuildwheel builds for multiple Pythons
+
+      # QEMU only needed for cross-arch Linux wheels
+      - name: Set up QEMU (Linux only)
+        if: runner.os == 'Linux'
+        uses: docker/setup-qemu-action@v3
+        with:
+          platforms: arm64
+
+      - name: Install SSL
+        if: runner.os == 'Linux'
+        run: |
+          sudo apt-get update || true
+          sudo apt-get install -y libcurl4-openssl-dev libssl-dev --fix-missing
+
+      # Install Rust toolchain on host (macOS/Windows builds run on host)
+      - name: Install Rust toolchain (host)
+        if: runner.os != 'Linux'
+        uses: dtolnay/rust-toolchain@stable
+
+      - name: Upgrade pip & install build tooling
+        run: |
+          python -m pip install --upgrade pip
+          python -m pip install cibuildwheel==2.* setuptools setuptools-rust wheel build
+
+      - name: Build wheels with cibuildwheel
+        env:
+          # Build CPython for version 3.x . Adjust as needed.
+          CIBW_BUILD: "cp3{10,11,12}-*"
+          # Skip 32-bit, PyPy, and musllinux
+          CIBW_SKIP: "pp* *-manylinux_i686 *-musllinux_*"
+          # Architectures
+          CIBW_ARCHS_LINUX: "x86_64"
+          CIBW_ARCHS_MACOS: "arm64"
+          CIBW_ARCHS_WINDOWS: "AMD64"
+          # Ensure Rust is present inside manylinux Docker images
+          CIBW_BEFORE_ALL_LINUX: |
+            set -euo pipefail
+            if command -v dnf >/dev/null 2>&1; then
+              dnf -y update || true
+              dnf -y install openssl-devel pkgconfig perl make gcc
+            else
+              yum -y update || true
+              yum -y install openssl-devel pkgconfig perl make gcc
+            fi
+
+            # Install Rust inside the manylinux container
+            curl https://sh.rustup.rs -sSf | sh -s -- -y
+          CIBW_ENVIRONMENT_LINUX: 'PATH="$HOME/.cargo/bin:$PATH"'
+          CIBW_ENVIRONMENT_MACOS: >
+              MACOSX_DEPLOYMENT_TARGET=11.0
+          # Make sure setuptools-rust is available in the build env
+          CIBW_BEFORE_BUILD: "python -m pip install -U pip setuptools setuptools-rust wheel"
+          # (Optional) If extra  system deps, use CIBW_BEFORE_ALL_* hooks per OS.
+        run: python -m cibuildwheel --output-dir dist
+
+      - name: Upload built wheels (artifact)
+        uses: actions/upload-artifact@v4
+        with:
+          # make the name unique per matrix entry
+          name: wheels-${{ matrix.os }}
+          path: dist/*.whl
+          if-no-files-found: error
+
+  sdist:
+    name: Build sdist
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: actions/setup-python@v5
+        with:
+          python-version: "3.11"
+
+      - name: Build sdist
+        run: |
+          python -m pip install --upgrade pip build
+          python -m build --sdist
+        env:
+          # If PEP 517 backend pulls in setuptools-rust, pip will handle it.
+          # Otherwise: PIP_PRE=1 and explicit deps as needed.
+          PIP_DISABLE_PIP_VERSION_CHECK: "1"
+
+      - name: Upload sdist (artifact)
+        uses: actions/upload-artifact@v4
+        with:
+          name: sdist
+          path: dist/*.tar.gz
+
+  publish:
+    needs: [build_wheels, sdist]
+    runs-on: ubuntu-latest
+    steps:
+      - name: Download wheels
+        uses: actions/download-artifact@v4
+        with:
+          pattern: wheels-*
+          merge-multiple: true    # puts everything under ./
+          path: dist
+
+      - name: Download sdist
+        uses: actions/download-artifact@v4
+        with:
+          name: sdist
+          path: dist
+
+      - name: Publish package
+        uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          user: __token__
+          password: ${{ secrets.PYPI_TOKEN }}
+          packages_dir: dist
+
+  docs:
+    runs-on: ubuntu-latest
+    needs:
+      - publish
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: actions/setup-python@v5
+        with:
+          python-version: "3.11"
+
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install -r requirements/requirements-ubuntu-latest_py3.11.txt
+          pip install -r requirements/requirements-ubuntu-latest_py3.11_extras.txt
+          pip install sphinx
+          pip install -e .
+
+      - name: Build docs
+        run: sphinx-build ./docs ./docs/_build
+
+      - name: Deploy docs
+        uses: peaceiris/actions-gh-pages@v3.8.0
+        with:
+          github_token: ${{ secrets.GH_TOKEN }}
+          publish_dir: ./docs/_build

atomscale-0.7.0/.github/workflows/testing.yml

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+name: Testing
+
+on:
+  push:
+    branches: [main]
+
+  pull_request:
+    branches: [main]
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  lint:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.11"
+
+      - name: Install Python dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install -r requirements/requirements-ubuntu-latest_py3.11.txt
+          pip install -r requirements/requirements-ubuntu-latest_py3.11_extras.txt
+
+      - name: Install dependencies
+        run: |
+          pip install pre-commit
+
+      - name: Run pre-commit
+        run: |
+          pre-commit run --all-files --show-diff-on-failure
+
+      - name: Run mypy
+        run: |
+          mypy --version
+          rm -rf .mypy_cache
+          mypy src/atomicds
+
+  test:
+    needs: lint
+    strategy:
+      max-parallel: 3
+      matrix:
+        os: [ubuntu-latest, windows-latest, macos-latest]
+        python-version: ["3.10", "3.11", "3.12"]
+
+    runs-on: ${{ matrix.os }}
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Install Python dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install -r requirements/requirements-${{ matrix.os }}_py${{ matrix.python-version }}.txt
+          pip install -r requirements/requirements-${{ matrix.os }}_py${{ matrix.python-version }}_extras.txt
+
+      - name: Set SSL_CERT_FILE (Linux/MacOS)
+        if: matrix.os == 'ubuntu-latest' || matrix.os == 'macos-latest'
+        run: echo "SSL_CERT_FILE=$(python -m certifi)" >> $GITHUB_ENV
+
+      - name: Set SSL_CERT_FILE (Windows)
+        if: matrix.os == 'windows-latest'
+        run: echo "SSL_CERT_FILE=$(python -m certifi)" | Out-File -FilePath $Env:GITHUB_ENV -Encoding utf8 -Append
+
+      - name: Test with pytest
+        env:
+          AS_API_KEY: ${{ secrets.ADS_API_KEY }}
+          AS_API_ENDPOINT: "https://api.atomscale.ai"
+        run: |
+          pip install -e .
+          pytest -x
+
+  auto-gen-release:
+    needs: test
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_TOKEN: ${{ secrets.GH_TOKEN }}
+    steps:
+      - uses: rymndhng/release-on-push-action@v0.28.0
+        with:
+          bump_version_scheme: norelease

atomscale-0.7.0/.github/workflows/upgrade_dependencies.yml

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+name: Upgrade Dependencies
+
+on:
+  workflow_dispatch:
+
+jobs:
+  upgrade:
+    name: ${{ matrix.package }} (${{ matrix.os }}/py${{ matrix.python-version }})
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        os: ['ubuntu-latest', 'macos-latest', 'windows-latest']
+        package: ["atomicds"]
+        python-version: ["3.10", "3.11", "3.12"]
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+      - uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+          cache: 'pip'
+      - name: Upgrade Python dependencies
+        shell: bash
+        run: |
+          python -m pip install --upgrade pip pip-tools
+          python -m piptools compile -q --upgrade --resolver=backtracking -o requirements/requirements-${{ matrix.os }}_py${{ matrix.python-version }}.txt pyproject.toml
+          python -m piptools compile -q --upgrade --resolver=backtracking --all-extras -o requirements/requirements-${{ matrix.os }}_py${{ matrix.python-version }}_extras.txt pyproject.toml
+      - name: Detect changes
+        id: changes
+        shell: bash
+        run: |
+          echo "count=$(git diff-index HEAD | wc -l | xargs)" >> $GITHUB_OUTPUT
+          echo "files=$(git ls-files --exclude-standard --others | wc -l | xargs)" >> $GITHUB_OUTPUT
+      - name: commit & push changes
+        if: steps.changes.outputs.count > 0 || steps.changes.outputs.files > 0
+        shell: bash
+        run: |
+          git config user.name github-actions
+          git config user.email github-actions@github.com
+          git add requirements/requirements-${{ matrix.os }}_py${{ matrix.python-version }}.txt
+          git add requirements/requirements-${{ matrix.os }}_py${{ matrix.python-version }}_extras.txt
+          git commit -m "Update ${{ matrix.os }} dependencies for ${{ matrix.package }}"
+          git push -f origin ${{ github.ref_name }}:auto-dependency-upgrades-${{ matrix.package }}-${{ matrix.os }}-py${{ matrix.python-version }}
+
+  pull_request:
+    name: Merge all branches and open PR
+    runs-on: ubuntu-latest
+    needs: upgrade
+    strategy:
+      matrix:
+        python-version: ["3.11"]
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+      - uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: detect auto-upgrade-dependency branches
+        id: changes
+        run: echo "count=$(git branch -r | grep auto-dependency-upgrades- | wc -l | xargs)" >> $GITHUB_OUTPUT
+      - name: merge all auto-dependency-upgrades branches
+        if: steps.changes.outputs.count > 0
+        run: |
+          git config user.name github-actions
+          git config user.email github-actions@github.com
+          git checkout -b auto-dependency-upgrades
+          git branch -r | grep auto-dependency-upgrades- | xargs -I {} git merge {}
+          git rebase ${GITHUB_REF##*/}
+          git push -f origin auto-dependency-upgrades
+          git branch -r | grep auto-dependency-upgrades- | cut -d/ -f2 | xargs -I {} git push origin :{}
+      - name: Open pull request if needed
+        if: steps.changes.outputs.count > 0
+        env:
+          GH_TOKEN: ${{ secrets.GH_TOKEN }}
+        # Only open a PR if the branch is not attached to an existing one
+        run: |
+          PR=$(gh pr list --head auto-dependency-upgrades --json number -q '.[0].number')
+          if [ -z $PR ]; then
+            gh pr create \
+            --head auto-dependency-upgrades \
+            --title "Automated dependency upgrades" \
+            --body "Full log: https://github.com/${{ github.repository }}/actions/runs/${{ github.run_id }} (THIS IS AN AUTOMATED COMMENT)"
+          else
+            echo "Pull request already exists, won't create a new one."
+          fi

atomscale-0.7.0/.gitignore

@@ -0,0 +1,188 @@
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# venvs
+.venvs/
+
+# development
+.vscode/
+
+# PROJECT SPECIFIC
+mp4tojpg/
+*local_overrides*
+lightning_logs/
+backend/migrations/local_dev/*
+
+# Model Checkpoints and WandB
+*.ckpt
+wandb/
+artifacts/
+
+# Profiling outputs
+profiling/*.bin
+
+# C extensions
+*.so
+
+# cache
+cache/*
+
+# Linux trash
+*.un~
+
+# Mac stuff
+*DS_Store
+
+# Typescript
+node_modules/
+react-frontend/.next/
+react-frontend/.yarn/*
+!react-frontend/.yarn/patches/
+!react-frontend/.yarn/plugins/
+!react-frontend/.yarn/releases/
+!react-frontend/.yarn/sdks/
+!react-frontend/.yarn/versions/
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+# lib/
+# lib64/
+parts/
+sdist/
+var/
+wheels/
+pip-wheel-metadata/
+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/
+*.prof
+
+# 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/
+docs/_autosummary/
+
+# 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
+.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
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow
+__pypackages__/
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.env.*
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+cypress.env.json
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# CDK Context & Staging files
+cdk.context.json
+.cdk.staging/
+cdk.out/
+*.tabl.json
+
+# Pyre type checker
+.pyre/
+
+# pytype static type analyzer
+.pytype/
+
+# Cython debug symbols
+cython_debug/
+
+# Ruff cache
+.ruff_cache

atomscale-0.7.0/.pre-commit-config.yaml

@@ -0,0 +1,42 @@
+default_stages: [pre-commit]
+default_install_hook_types: [pre-commit, commit-msg]
+
+ci:
+  autoupdate_commit_msg: "chore: update pre-commit hooks"
+
+repos:
+  - repo: https://github.com/psf/black
+    rev: 23.9.1
+    hooks:
+      - id: black
+
+  - repo: https://github.com/asottile/blacken-docs
+    rev: "1.16.0"
+    hooks:
+      - id: blacken-docs
+        additional_dependencies: [black>=23.7.0]
+
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.5.0
+    hooks:
+      - id: check-case-conflict
+      - id: check-symlinks
+      - id: check-yaml
+      - id: destroyed-symlinks
+      - id: end-of-file-fixer
+      - id: mixed-line-ending
+      - id: trailing-whitespace
+
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.3.4
+    hooks:
+      - id: ruff
+        args: [--fix, --show-fixes]
+
+  - repo: https://github.com/codespell-project/codespell
+    rev: v2.2.6
+    hooks:
+      - id: codespell
+        stages: [pre-commit, commit-msg]
+        exclude_types: [json, bib, svg]
+        args: [--ignore-words-list, "mater,fwe,te"]

atomscale-0.7.0/CHANGELOG.md

@@ -0,0 +1,11 @@
+# Changelog
+
+All notable changes to this project will be documented in this file.
+
+The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/), and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
+
+## [0.0.1]
+
+### Added
+
+- The initial release!