Refact/reorganize modules

.devcontainer/Dockerfile

@@ -0,0 +1,22 @@
+FROM ghcr.io/astral-sh/uv:latest AS uv
+
+FROM mcr.microsoft.com/devcontainers/base:2-ubuntu24.04
+
+# install needed packages
+RUN apt-get update && export DEBIAN_FRONTEND=noninteractive \
+    && apt-get -y install \
+    build-essential \
+    cmake \
+    gcc \
+    gdb \
+    libgmp-dev \
+    ninja-build
+
+COPY tools/install-deps.sh /usr/local/bin/install-deps.sh
+
+RUN /usr/local/bin/install-deps.sh \
+    && apt-get autoremove -y \
+    && apt-get clean -y \
+    && rm -rf /var/lib/apt/lists/*
+
+COPY --from=uv --chown=vscode /uv /uvx /bin/

.devcontainer/devcontainer.json

@@ -0,0 +1,57 @@
+{
+  "name": "PauliEngine development environment",
+  "build": {
+    "dockerfile": "Dockerfile",
+    "context": ".."
+  },
+  "capAdd": [
+    "SYS_PTRACE"
+  ],
+  "securityOpt": [
+    "seccomp=unconfined"
+  ],
+  "remoteUser": "vscode",
+  "customizations": {
+    "vscode": {
+      "settings": {
+        "python.defaultInterpreterPath": "${containerEnv:UV_PROJECT_ENVIRONMENT}/bin/python",
+        "python.terminal.activateEnvInCurrentTerminal": true,
+        "terminal.integrated.defaultProfile.linux": "zsh",
+        "terminal.integrated.profiles.linux": {
+          "zsh": {
+            "path": "/bin/zsh"
+          }
+        }
+      },
+      "extensions": [
+        "MS-vsliveshare.vsliveshare",
+        "benjamin-simmonds.pythoncpp-debug",
+        "charliermarsh.ruff",
+        "cschlosser.doxdocgen",
+        "ms-python.python",
+        "ms-toolsai.jupyter",
+        "ms-vscode.cmake-tools",
+        "ms-vscode.cpptools",
+        "ms-vscode.cpptools-themes",
+        "mutantdino.resourcemonitor",
+        "njpwerner.autodocstring",
+        "streetsidesoftware.code-spell-checker",
+        "streetsidesoftware.code-spell-checker-scientific-terms",
+        "tamasfe.even-better-toml",
+        "vivaxy.vscode-conventional-commits"
+      ]
+    }
+  },
+  "containerEnv": {
+    "PYTHONUNBUFFERED": "True",
+    "WORKSPACE": "${containerWorkspaceFolder}",
+    "UV_LINK_MODE": "copy",
+    "UV_PROJECT_ENVIRONMENT": "/home/vscode/.venv"
+  },
+  "postCreateCommand": "./.devcontainer/postCreateCommand.sh",
+  "postStartCommand": "./.devcontainer/postStartCommand.sh",
+  "hostRequirements": {
+    "cpus": 4,
+    "memory": "6gb"
+  }
+}

.devcontainer/postCreateCommand.sh

@@ -0,0 +1,18 @@
+#!/usr/bin/env bash
+
+set -euxo pipefail
+
+# install uv and uvx shell completions
+echo 'eval "$(uv generate-shell-completion zsh)"' >> /home/vscode/.zshrc
+echo 'eval "$(uvx --generate-shell-completion zsh)"' >> /home/vscode/.zshrc
+
+# set up GDB to view contents of STL containers
+gcc_version="$(gcc --version | awk 'NR==1 {print $NF}')"
+cat <<EOT >> ~/.gdbinit
+python
+import sys
+sys.path.insert(0, "/usr/share/gcc-$gcc_version/python")
+from libstdcxx.v6.printers import register_libstdcxx_printers
+register_libstdcxx_printers (None)
+end
+EOT

.devcontainer/postStartCommand.sh

@@ -0,0 +1,7 @@
+#!/usr/bin/env bash
+
+# install project with all dependencies
+uv sync --all-groups --all-extras
+
+# install pre-commit hooks
+# uv run pre-commit install --install-hooks

.git_archival.txt

@@ -0,0 +1,3 @@
+node: $Format:%H$
+node-date: $Format:%cI$
+describe-name: $Format:%(describe:tags=true,match=*[0-9]*)$

.github/workflows/deploy.yml

@@ -0,0 +1,181 @@
+name: Publish PauliEngine Python sdist and wheels to PyPI
+
+on:
+  workflow_dispatch:
+    inputs:
+      force-upload:
+        description: 'Upload artifacts without a corresponding release'
+        required: false
+        default: false
+        type: boolean
+  release:
+    types:
+      - published
+  pull_request:
+    # PRs trigger for the "opened", "reopened", "synchronize" events (default) and
+    # "ready_for_review"
+    paths:
+      - .github/workflows/deploy.yml
+    types:
+      - opened
+      - reopened
+      - synchronize # when new commits are pushed to the PR
+      - ready_for_review # when the PR is un-drafted
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+env:
+  COLUMNS: 120
+  FORCE_COLOR: 3
+
+jobs:
+  build-sdist:
+    name: Build source distribution
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v6
+        with:
+          fetch-depth: 0  # such that setuptools_scm can do its job correctly
+
+      - name: Build SDist
+        run: |
+          pipx install uv
+          pipx run build --verbose --sdist --installer=uv
+
+      - uses: actions/upload-artifact@v6
+        with:
+          name: cibw-sdist
+          path: dist/*.tar.gz
+
+  build-wheels:
+    # in combination with the PR types selection, this top-level if statement
+    # skips running the workflow for Draft PRs
+    if: ${{ github.event_name == 'push' || !github.event.pull_request.draft }}
+    name: Build Python wheels for ${{ matrix.os }}
+    runs-on: ${{ matrix.runs-on }}
+    strategy:
+      matrix:
+        os: [ linux-intel, linux-arm, macos-arm, windows-intel, windows-arm]
+        include:
+          - archs: native
+            platform: auto
+          - os: linux-intel
+            runs-on: ubuntu-latest
+          - os: linux-arm
+            runs-on: ubuntu-24.04-arm
+          - os: macos-arm
+            runs-on: macos-latest
+          - os: windows-intel
+            runs-on: windows-latest
+          - os: windows-arm
+            runs-on: windows-latest
+    steps:
+      - uses: actions/checkout@v6
+        with:
+          fetch-depth: 0
+
+      - uses: pypa/cibuildwheel@v3.3.1
+        with:
+          extras: "uv"
+        env:
+          # target platform
+          CIBW_PLATFORM: ${{ matrix.platform }}
+          # architectures to build
+          CIBW_ARCHS: ${{ matrix.archs }}
+          # use uv and build
+          CIBW_BUILD_FRONTEND: "build[uv]"
+          # increase pip debugging output
+          CIBW_BUILD_VERBOSITY: 1
+          CIBW_DEBUG_TRACEBACK: TRUE
+          CIBW_BEFORE_ALL_LINUX: |
+            dnf install -y gmp gmp-devel ninja-build
+            # install symengine
+            ./tools/install-deps.sh 
+          CIBW_BEFORE_ALL_MACOS: |
+            brew install gmp
+            # install symengine
+            PREFIX="${SYMEMENGINE_PREFIX:-$HOME/.local}"
+            ./tools/install-deps.sh "$PREFIX"
+          CIBW_BEFORE_ALL_WINDOWS: |
+            pip install delvewheel
+          # do not activate architecture-dependent compiler flags
+          # 4 jobs in parallel, but do not start new ones if load average exceeds 5
+          CIBW_ENVIRONMENT_LINUX: >
+            CIBW="true"
+            SKBUILD_BUILD_TOOL_ARGS="-j4;-l5"
+            # CMAKE_PREFIX_PATH="$HOME/.local"
+          # set deployment target for C++20 compatibility
+          # make brew-installed OpenMP discoverable by CMake
+          # do not activate architecture-dependent compiler flags
+          # 4 jobs in parallel, but do not start new ones if load average exceeds 5
+          CIBW_ENVIRONMENT_MACOS: >
+             CIBW="true"
+             MACOSX_DEPLOYMENT_TARGET=15.0
+             GMP_PREFIX="$(brew --prefix gmp)"
+             CPPFLAGS="-I${GMP_PREFIX}/include ${CPPFLAGS}"
+             CFLAGS="-I${GMP_PREFIX}/include ${CFLAGS}"
+             CXXFLAGS="-I${GMP_PREFIX}/include ${CXXFLAGS}"
+             LDFLAGS="-L${GMP_PREFIX}/lib ${LDFLAGS}"
+             PKG_CONFIG_PATH="${GMP_PREFIX}/lib/pkgconfig:${PKG_CONFIG_PATH}"
+             CMAKE_PREFIX_PATH="${GMP_PREFIX}:$HOME/.local:${CMAKE_PREFIX_PATH}"
+          CIBW_ENVIRONMENT_WINDOWS: >
+            CIBW="true"
+          # build 3.10, 3.11, 3.12, 3.13 (with GIL), and 3.14 (with GIL)
+          CIBW_BUILD: "cp310-* cp311-* cp312-* cp313-* cp314-*"
+          # skip musl builds, and PyPy builds
+          CIBW_SKIP: "*-musllinux_*"
+          # use abi3audit to catch issues with Limited API wheels
+          CIBW_REPAIR_WHEEL_COMMAND_LINUX: |
+            auditwheel repair -w {dest_dir} {wheel}
+            if [[ "{wheel}" == *abi3* ]]; then
+              pipx run abi3audit --strict --report {wheel}
+            else
+              echo "{wheel} is not abi3, skipping abi3audit"
+            fi
+          # use abi3audit to catch issues with Limited API wheels
+          CIBW_REPAIR_WHEEL_COMMAND_MACOS: |
+            delocate-wheel --require-archs {delocate_archs} -w {dest_dir} -v {wheel}
+            if [[ "{wheel}" == *abi3* ]]; then
+              pipx run abi3audit --strict --report {wheel}
+            else
+              echo "{wheel} is not abi3, skipping abi3audit"
+            fi
+          CIBW_REPAIR_WHEEL_COMMAND_WINDOWS: |
+            delvewheel repair -w {dest_dir} {wheel}
+            if [[ "{wheel}" == *abi3* ]]; then
+              pipx run abi3audit --strict --report {wheel}
+            else
+              echo "{wheel} is not abi3, skipping abi3audit"
+            fi
+          CIBW_TEST_COMMAND: python -m pytest {package}/tests
+          CIBW_TEST_GROUPS: "test"
+
+      - name: Upload wheels
+        uses: actions/upload-artifact@v6
+        with:
+          name: cibw-wheels-${{ matrix.os }}-${{ strategy.job-index }}
+          path: wheelhouse/*.whl
+
+  # upload_all:
+  #   name: Upload if release
+  #   needs:
+  #     - build_wheels
+  #     - build_sdist
+  #   environment: pypi
+  #   permissions:
+  #     id-token: write
+  #   runs-on: ubuntu-latest
+  #     #if: github.event_name == 'release' && github.event.action == 'published'
+
+  #   steps:
+  #     - uses: actions/download-artifact@v4
+  #       with:
+  #         pattern: cibw-*
+  #         path: dist
+  #         merge-multiple: true
+
+  #     - uses: pypa/gh-action-pypi-publish@release/v1
+  #       with:
+  #         repository-url: https://test.pypi.org/legacy/

.gitignore

@@ -9,4 +9,6 @@ Thumbs.db
 .bat
 .cmake
 .env
-config.json
+config.json
+
+__pycache__/