eon-akmc 2.16.0__tar.gz

eon_akmc-2.16.0/.cargo/config.toml

@@ -0,0 +1,2 @@
+[build]
+rustflags = []

eon_akmc-2.16.0/.clangd

@@ -0,0 +1,28 @@
+CompileFlags:
+  # Replace conda cross-compiler with system clang
+  Compiler: clang++
+  Add:
+    - -std=c++20
+    - -DEON_CHECKS=TRUE
+    - -DQUILL_DISABLE_NON_PREFIXED_MACROS
+  Remove:
+    # Fortran flags that leak from meson's compile DB
+    - -fno-implicit-none
+    - -J*
+    # Conda-specific flags clangd doesn't understand
+    - -fmessage-length=0
+    - -march=nocona
+    - -mtune=haswell
+    - -ftree-vectorize
+    - -fno-plt
+    - -fstack-protector-strong
+    - -fvisibility-inlines-hidden
+
+Diagnostics:
+  Suppress:
+    # Vendored thirdparty code
+    - pp_file_not_found
+  ClangTidy:
+    Remove:
+      - modernize-use-trailing-return-type
+      - readability-identifier-length

eon_akmc-2.16.0/.gitattributes

@@ -0,0 +1,5 @@
+# SCM syntax highlighting & preventing 3-way merges
+pixi.lock merge=binary linguist-language=YAML linguist-generated=true
+*.tar.gz !text !filter !merge !diff
+*.zip !text !filter !merge !diff
+*.pdf !text !filter !merge !diff

eon_akmc-2.16.0/.github/CODEOWNERS

@@ -0,0 +1,17 @@
+# Release / version surfaces — request review when these change.
+# Enable required CODEOWNERS checks on branch protection if desired.
+
+/cog.toml                          @HaoZeke
+/towncrier.toml                    @HaoZeke
+/CHANGELOG.md                      @HaoZeke
+/pyproject.toml                    @HaoZeke
+/pixi.toml                         @HaoZeke
+/scripts/release_assert.py         @HaoZeke
+/docs/source/devdocs/release.md    @HaoZeke
+/docs/newsfragments/               @HaoZeke
+/docs/source/releases/             @HaoZeke
+/.github/workflows/release.yml     @HaoZeke
+/.github/workflows/release-prepare.yml @HaoZeke
+/.github/workflows/towncrier.yml   @HaoZeke
+/SECURITY.md                       @HaoZeke
+/ci/gha/                            @HaoZeke

eon_akmc-2.16.0/.github/workflows/ci_ase.yml

@@ -0,0 +1,42 @@
+name: Build and test eonclient with ASE
+concurrency:
+  group: ${{ github.workflow }}-${{ github.head_ref || github.run_id }}
+  cancel-in-progress: true
+on: [push, pull_request]
+jobs:
+  build_eon:
+    runs-on: ${{ matrix.os }}
+    name: test (${{ matrix.os }})
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-22.04]
+    steps:
+      - uses: actions/checkout@v4
+      - uses: prefix-dev/setup-pixi@v0.9.4
+        with:
+          cache: true
+          cache-write: true
+          activate-environment: true
+          environments: >-
+            dev
+      - name: Install cbindgen
+        shell: bash
+        run: command -v cbindgen || cargo install cbindgen
+      - name: Install ASE
+        shell: pixi run -e dev bash -e {0}
+        run: pip install ase
+      - name: Build eonclient with ASE
+        shell: pixi run -e dev bash -e {0}
+        run: |
+          meson setup bbdir  \
+          --prefix=$CONDA_PREFIX           \
+          --buildtype release              \
+          --libdir=lib                     \
+          -Dwith_ase=True            \
+          -Dwith_tests=True
+          meson install -C bbdir
+      - name: Run tests
+        shell: pixi run -e dev bash -e {0}
+        run: |
+          meson test -C bbdir test_ase_pot

eon_akmc-2.16.0/.github/workflows/ci_bench_commenter.yml

@@ -0,0 +1,38 @@
+name: Comment benchmark results
+
+on:
+  workflow_run:
+    workflows: ["Benchmark PR"]
+    types: [completed]
+
+jobs:
+  comment:
+    if: >-
+      github.event.workflow_run.event == 'pull_request' &&
+      github.event.workflow_run.conclusion == 'success'
+    runs-on: ubuntu-latest
+    permissions:
+      pull-requests: write
+      issues: write
+      actions: read
+
+    steps:
+      - name: Download benchmark results
+        uses: actions/download-artifact@v4
+        with:
+          name: benchmark-results
+          path: results/
+          run-id: ${{ github.event.workflow_run.id }}
+          github-token: ${{ secrets.GITHUB_TOKEN }}
+
+      - name: Post benchmark comment
+        uses: HaoZeke/asv-perch@v1
+        with:
+          github-token: ${{ secrets.GITHUB_TOKEN }}
+          comparison-text-file: results/comparison.txt
+          metadata-file: results/metadata.txt
+          regression-threshold: '10'
+          auto-draft-on-regression: 'true'
+          label-before: main
+          label-after: pr
+          runner-info: ubuntu-22.04

eon_akmc-2.16.0/.github/workflows/ci_benchmark.yml

@@ -0,0 +1,124 @@
+name: Benchmark PR
+concurrency:
+  group: ${{ github.workflow }}-${{ github.head_ref || github.run_id }}
+  cancel-in-progress: true
+on:
+  pull_request:
+    branches: [main]
+jobs:
+  benchmark:
+    strategy:
+      fail-fast: false
+      matrix:
+        include:
+          - label: main
+            sha: ${{ github.event.pull_request.base.sha }}
+          - label: pr
+            sha: ${{ github.event.pull_request.head.sha }}
+    runs-on: ubuntu-22.04
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+
+      - name: Checkout target commit
+        run: |
+          mkdir -p /tmp/_bench_preserve
+          cp -r benchmarks/ /tmp/_bench_preserve/
+          cp asv.conf.json /tmp/_bench_preserve/
+          git checkout -f ${{ matrix.sha }}
+          git clean -fd
+          rm -rf benchmarks
+          cp -r /tmp/_bench_preserve/benchmarks/ benchmarks/
+          cp /tmp/_bench_preserve/asv.conf.json asv.conf.json
+
+      - uses: prefix-dev/setup-pixi@v0.9.4
+        with:
+          cache: true
+          cache-write: false
+          activate-environment: true
+
+      - name: Install cbindgen
+        shell: bash
+        run: command -v cbindgen || cargo install cbindgen
+      - uses: astral-sh/setup-uv@v5
+
+      - name: Build
+        run: |
+          pixi run bash -c "meson setup bbdir \
+            --prefix=$CONDA_PREFIX --libdir=lib \
+            --buildtype release --wipe 2>/dev/null \
+            || meson setup bbdir --prefix=$CONDA_PREFIX \
+            --libdir=lib --buildtype release"
+          pixi run meson install -C bbdir
+
+      - name: Run benchmarks
+        run: |
+          pixi run bash -c "pip install asv && asv machine --yes"
+          pixi run asv run -E "existing:$(which python)" \
+            --set-commit-hash ${{ matrix.sha }} \
+            --record-samples --quick
+
+      - name: Upload results
+        uses: actions/upload-artifact@v4
+        with:
+          name: bench-${{ matrix.label }}
+          path: .asv/results/
+          retention-days: 7
+
+  combine:
+    needs: benchmark
+    runs-on: ubuntu-latest
+    steps:
+      - uses: astral-sh/setup-uv@v5
+
+      - name: Download main results
+        uses: actions/download-artifact@v4
+        with:
+          name: bench-main
+          path: results/
+
+      - name: Download PR results
+        uses: actions/download-artifact@v4
+        with:
+          name: bench-pr
+          path: results/
+
+      - name: Find result files and compare
+        run: |
+          BASE_SHA="${{ github.event.pull_request.base.sha }}"
+          PR_SHA="${{ github.event.pull_request.head.sha }}"
+          BASE_PREFIX="${BASE_SHA:0:8}"
+          PR_PREFIX="${PR_SHA:0:8}"
+          BASE_FILE=$(find results -name "${BASE_PREFIX}*.json" | head -1)
+          PR_FILE=$(find results -name "${PR_PREFIX}*.json" | head -1)
+          BCONF=$(find results -name "benchmarks.json" | head -1)
+          echo "Base file: $BASE_FILE"
+          echo "PR file: $PR_FILE"
+          echo "Benchmarks: $BCONF"
+          BCONF_ARG=""
+          if [ -n "$BCONF" ]; then
+            BCONF_ARG="$BCONF"
+          fi
+          # Exit code 1 = regressions detected (expected, not an error)
+          uvx --from "git+https://github.com/airspeed-velocity/asv_spyglass.git" \
+            asv-spyglass compare "$BASE_FILE" "$PR_FILE" $BCONF_ARG \
+            --label-before main --label-after pr \
+            > results/comparison.txt || true
+          if [ ! -s results/comparison.txt ]; then
+            echo "::error::asv-spyglass compare produced no output"
+            exit 1
+          fi
+          cat results/comparison.txt
+
+      - name: Write metadata
+        run: |
+          echo "main_sha=${{ github.event.pull_request.base.sha }}" > results/metadata.txt
+          echo "pr_sha=${{ github.event.pull_request.head.sha }}" >> results/metadata.txt
+
+      - name: Upload combined results
+        uses: actions/upload-artifact@v4
+        with:
+          name: benchmark-results
+          path: results/
+          retention-days: 7

eon_akmc-2.16.0/.github/workflows/ci_build_akmc.yml

@@ -0,0 +1,59 @@
+name: Build basic eon
+concurrency:
+  group: ${{ github.workflow }}-${{ github.head_ref || github.run_id }}
+  cancel-in-progress: true
+on: [push, pull_request]
+jobs:
+  build_eon:
+    runs-on: ${{ matrix.os }}
+    name: test (${{ matrix.os }})
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-22.04, macos-14, windows-latest]
+    steps:
+      - uses: actions/checkout@v4
+      - uses: prefix-dev/setup-pixi@v0.9.4
+        with:
+          cache: true
+          cache-write: true
+      - name: Install cbindgen
+        shell: bash
+        run: command -v cbindgen || cargo install cbindgen
+      - name: Use Homebrew gfortran (macOS)
+        if: runner.os == 'macOS'
+        run: |
+          brew install gcc
+          FC=$(find "$(brew --prefix gcc)/bin" -name 'gfortran-*' | head -1)
+          echo "FC=$FC" >> "$GITHUB_ENV"
+          echo "SDKROOT=$(xcrun --show-sdk-path)" >> "$GITHUB_ENV"
+
+      - name: Compile and install [unix]
+        if: runner.os != 'Windows'
+        shell: pixi run bash -e {0}
+        run: |
+          meson setup bbdir --prefix=$CONDA_PREFIX --libdir=lib --buildtype release
+          meson install -C bbdir
+
+      - name: Activate MSVC (Windows)
+        if: runner.os == 'Windows'
+        uses: ilammy/msvc-dev-cmd@v1
+
+      - name: Compile and install [windows]
+        if: runner.os == 'Windows'
+        shell: pixi run bash -e {0}
+        run: |
+          # Git Bash puts GNU link.exe on PATH which shadows MSVC link.exe
+          export PATH=$(echo "$PATH" | tr ':' '\n' | grep -v '^/usr/bin$' | paste -sd:)
+          # Align with conda-forge/eon-feedstock#15 / build.bat: in-tree Fortran ON
+          # (m2w64/gfortran pots + MSVC C++; /STACK:16M in meson for GAGAFE; CuH2 on).
+          meson setup bbdir --prefix=$CONDA_PREFIX --libdir=lib --buildtype release \
+            --default-library=static -Dwith_fortran=true -Dwith_cuh2=true
+          meson install -C bbdir
+
+      - name: Run tests
+        shell: pixi run bash -e {0}
+        run: |
+          python tests/test_config_metadata.py
+          cd examples/akmc-al
+          python -m eon.server

eon_akmc-2.16.0/.github/workflows/ci_build_gprd.yml

@@ -0,0 +1,48 @@
+name: Build eOn with GPRD
+concurrency:
+  group: ${{ github.workflow }}-${{ github.head_ref || github.run_id }}
+  cancel-in-progress: true
+on:
+  push:
+    branches:
+      - main
+jobs:
+  build_eon:
+    runs-on: ubuntu-latest
+    # TODO: the gpr_optim submodule pin (26242c8) is unreadable; this job is
+    # non-blocking until the pin is updated to a valid gpr_optim commit.
+    continue-on-error: true
+    steps:
+      - uses: actions/checkout@v4
+      - name: Setup SSH for private submodule
+        uses: webfactory/ssh-agent@v0.9.0
+        with:
+          ssh-private-key: ${{ secrets.SUBMODULE_PRIVATE }}
+      - name: Pull GPRD submodule
+        run: |
+          git clone git@github.com:TheochemUI/gpr_optim.git subprojects/gpr_optim
+          cd subprojects/gpr_optim
+          git checkout 26242c8e94569ef81103ece4662008c3250ada55
+      - uses: prefix-dev/setup-pixi@v0.9.4
+        with:
+          cache: true
+          cache-write: true
+          activate-environment: true
+          environments: >-
+            dev
+      - name: Install cbindgen
+        shell: bash
+        run: command -v cbindgen || cargo install cbindgen
+      - name: Install eon
+        shell: pixi run bash -e {0}
+        run: |
+          meson setup --reconfigure bbdir  \
+          --prefix=$CONDA_PREFIX           \
+          --buildtype release              \
+          --libdir=lib
+          meson install -C bbdir
+      - name: Integration Tests
+        shell: pixi run bash -e {0}
+        run: |
+          cd client/unit_tests/data/systems/saddle_search/
+          eonclient

eon_akmc-2.16.0/.github/workflows/ci_doc_commenter.yml

@@ -0,0 +1,23 @@
+name: Comment on pull request
+
+on:
+  workflow_run:
+    workflows: ["Build and Deploy Documentation"]
+    types: [completed]
+
+jobs:
+  pr_comment:
+    if: github.event.workflow_run.event == 'pull_request' && github.event.workflow_run.conclusion == 'success'
+    runs-on: ubuntu-latest
+    permissions:
+      pull-requests: write
+      issues: write
+      actions: read
+
+    steps:
+      - uses: HaoZeke/doc-previewer@0e1094735b4f7ee9a2c60a18a34d7a7e5bc6bb63
+        with:
+          workflow_run_id: ${{ github.event.workflow_run.id }}
+          head_sha: ${{ github.event.workflow_run.head_sha }}
+          artifact_name: documentation
+          comment_header: "### eOn Documentation Preview"

eon_akmc-2.16.0/.github/workflows/ci_docs.yml

@@ -0,0 +1,76 @@
+name: Build and Deploy Documentation
+
+concurrency:
+  group: "pages"
+  cancel-in-progress: true
+
+on:
+  push:
+    branches: [main]
+    tags: ["*"]
+  pull_request:
+    # Check all PR
+  schedule:
+    - cron: '0 8 * * 1' # run every Monday at 8am UTC
+
+env:
+  # Execute notebook cells on cache miss; reuse outputs on hit (local default remains force in conf.py).
+  NB_EXECUTION_MODE: cache
+
+jobs:
+  build_docs:
+    name: Build documentation
+    runs-on: ubuntu-latest
+    permissions:
+      contents: write
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v4
+        with:
+          # gitversion.py only needs `git log -1`
+          fetch-depth: 1
+
+      - uses: prefix-dev/setup-pixi@v0.9.4
+        with:
+          cache: true
+          cache-write: true
+          activate-environment: true
+          environments: >-
+            docs-mta
+
+      - name: Restore myst-nb execution cache
+        uses: actions/cache@v4
+        with:
+          path: docs/source/.jupyter_cache
+          key: mystnb-${{ runner.os }}-${{ hashFiles('docs/source/**/*.md', 'docs/source/conf.py', 'eon/**/*.py') }}
+          restore-keys: |
+            mystnb-${{ runner.os }}-
+
+      - name: Ensure cbindgen
+        shell: bash
+        run: command -v cbindgen || cargo install --root "$CONDA_PREFIX" cbindgen
+
+      - name: Generate Docs
+        shell: pixi run -e docs-mta bash -e {0}
+        env:
+          NB_EXECUTION_MODE: ${{ env.NB_EXECUTION_MODE }}
+        run: |
+          # One meson build/install only (eonclient + python package into pixi prefix).
+          # Do not pip install . here — that would re-run meson-python and compile twice.
+          meson setup bbdir --prefix=$CONDA_PREFIX --libdir=lib --buildtype release \
+            -Dwith_metatomic=True -Dtorch_version=2.10 -Dpip_metatomic=True
+          meson install -C bbdir
+          sphinx-build -b html -j auto docs/source docs/build/html
+
+      - name: Upload artifact
+        uses: actions/upload-artifact@v4
+        with:
+          name: documentation
+          path: docs/build/html/
+
+      - name: Deploy
+        if: github.event_name == 'push'
+        uses: peaceiris/actions-gh-pages@v4
+        with:
+          github_token: ${{ secrets.GITHUB_TOKEN }}
+          publish_dir: docs/build/html/

eon_akmc-2.16.0/.github/workflows/ci_metatomic.yml

@@ -0,0 +1,49 @@
+name: Build and test eonclient with Metatomic
+concurrency:
+  group: ${{ github.workflow }}-${{ github.head_ref || github.run_id }}
+  cancel-in-progress: true
+on: [push, pull_request]
+jobs:
+  build_eon:
+    runs-on: ${{ matrix.os }}
+    name: test (${{ matrix.os }})
+    strategy:
+      fail-fast: false
+      matrix:
+        # TODO(rg): Handle the windows-2022 later, issues linking fmt
+        os: [ubuntu-22.04, macos-14]
+    steps:
+      - uses: actions/checkout@v4
+      - uses: prefix-dev/setup-pixi@v0.9.4
+        with:
+          cache: true
+          cache-write: true
+          activate-environment: true
+          environments: >-
+            dev-mta
+      - name: Install cbindgen
+        shell: bash
+        run: command -v cbindgen || cargo install cbindgen
+      - name: Use Homebrew gfortran (macOS)
+        if: runner.os == 'macOS'
+        run: |
+          brew install gcc
+          FC=$(find "$(brew --prefix gcc)/bin" -name 'gfortran-*' | head -1)
+          echo "FC=$FC" >> "$GITHUB_ENV"
+          echo "SDKROOT=$(xcrun --show-sdk-path)" >> "$GITHUB_ENV"
+      - name: Install eon
+        shell: pixi run bash -e {0}
+        run: |
+          meson setup --reconfigure bbdir  \
+          --prefix=$CONDA_PREFIX           \
+          --buildtype release              \
+          --libdir=lib                     \
+          -Dwith_metatomic=True            \
+          -Dtorch_version=2.10             \
+          -Dwith_tests=True                \
+          -Dpip_metatomic=True
+          meson install -C bbdir
+      - name: Run tests
+        shell: bash -el {0}
+        run: |
+          meson test -C bbdir

eon_akmc-2.16.0/.github/workflows/ci_precommit.yml

@@ -0,0 +1,30 @@
+name: lints
+concurrency:
+  group: ${{ github.workflow }}-${{ github.head_ref || github.run_id }}
+  cancel-in-progress: true
+on: [push, pull_request]
+jobs:
+  lints:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v4
+    - name: Install uv
+      uses: astral-sh/setup-uv@v6
+    - name: Run prek (faster pre-commit)
+      run: |
+        uvx prek -a
+    # Autonomy: release/prepare/towncrier YAML must match ci/gha/*.ncl (when nickel available).
+    - name: GHA nickel drift (release workflows)
+      run: |
+        set -euo pipefail
+        if command -v nickel >/dev/null 2>&1; then
+          bash ci/gha/check-drift.sh
+        elif command -v pixi >/dev/null 2>&1; then
+          pixi r -e cigen gha-drift
+        else
+          echo "nickel/pixi not on runner; skip gha-drift (enforced on release-prepare + local cigen)"
+        fi
+    - name: Audit for large files
+      uses: HaoZeke/large-file-auditor@v0.1.0
+      with:
+        file-size-threshold: "3M"

eon_akmc-2.16.0/.github/workflows/ci_rgpot.yml

@@ -0,0 +1,58 @@
+name: Build and test eonclient with Rgpot
+concurrency:
+  group: ${{ github.workflow }}-${{ github.head_ref || github.run_id }}
+  cancel-in-progress: true
+on: [push, pull_request]
+jobs:
+  build_rgpot:
+    runs-on: ${{ matrix.os }}
+    name: test (${{ matrix.os }})
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-22.04]
+    steps:
+      - uses: actions/checkout@v4
+      - uses: prefix-dev/setup-pixi@v0.9.4
+        with:
+          cache: true
+          cache-write: true
+          activate-environment: true
+          environments: >-
+            serve
+      - name: Install cbindgen
+        shell: bash
+        run: command -v cbindgen || cargo install cbindgen
+      - name: Build with rgpot potential
+        shell: pixi run bash -e {0}
+        run: |
+          meson setup bbdir \
+            --prefix=$CONDA_PREFIX \
+            --libdir=lib \
+            --buildtype release \
+            -Dwith_rgpot=true \
+            -Dwith_tests=true
+          meson compile -C bbdir
+      - name: Build rgpot fake engines
+        shell: pixi run bash -e {0}
+        run: |
+          # Compile the rgpot fake engines directly: rgpot's meson test targets
+          # need Catch2, which the serve env does not carry. The cpmdc fake
+          # uses the capnp header generated during the eonclient build.
+          cc -shared -fPIC -O2 \
+            -I subprojects/rgpot/CppCore/rgpot/NWChemPot \
+            subprojects/rgpot/CppCore/tests/nwchemc_fake_engine.c \
+            -o libnwchemc_fake_engine.so
+          c++ -shared -fPIC -O2 \
+            -I subprojects/rgpot/CppCore \
+            -I subprojects/rgpot/CppCore/rgpot/CPMDPot \
+            -I bbdir/subprojects/rgpot/CppCore \
+            subprojects/rgpot/CppCore/tests/cpmdc_fake_engine.cc \
+            -lcapnp -lkj \
+            -o libcpmdc_fake_engine.so
+      - name: Run rgpot potential tests
+        shell: pixi run bash -e {0}
+        run: |
+          export NWCHEMC_LIBRARY=$PWD/libnwchemc_fake_engine.so
+          export CPMDC_LIBRARY=$PWD/libcpmdc_fake_engine.so
+          meson test -C bbdir --suite rgpot --print-errorlogs

eon_akmc-2.16.0/.github/workflows/ci_serve.yml

@@ -0,0 +1,39 @@
+name: Build and test serve mode
+concurrency:
+  group: ${{ github.workflow }}-${{ github.head_ref || github.run_id }}
+  cancel-in-progress: true
+on: [push, pull_request]
+jobs:
+  build_serve:
+    runs-on: ${{ matrix.os }}
+    name: test (${{ matrix.os }})
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-22.04]
+    steps:
+      - uses: actions/checkout@v4
+      - uses: prefix-dev/setup-pixi@v0.9.4
+        with:
+          cache: true
+          cache-write: true
+          activate-environment: true
+          environments: >-
+            serve
+      - name: Install cbindgen
+        shell: bash
+        run: command -v cbindgen || cargo install cbindgen
+      - name: Build with serve mode
+        shell: pixi run bash -e {0}
+        run: |
+          meson setup bbdir \
+            --prefix=$CONDA_PREFIX \
+            --libdir=lib \
+            --buildtype release \
+            -Dwith_serve=true \
+            -Dwith_tests=true
+          meson compile -C bbdir
+      - name: Run serve mode tests
+        shell: pixi run bash -e {0}
+        run: |
+          meson test -C bbdir test_serve_spec