readcon-db 0.1.2__tar.gz

readcon_db-0.1.2/.github/workflows/ci.yml

@@ -0,0 +1,58 @@
+name: CI
+
+on:
+  push:
+    branches: [main]
+  pull_request:
+  workflow_dispatch:
+
+concurrency:
+  group: ci-${{ github.ref }}
+  cancel-in-progress: true
+
+permissions:
+  contents: read
+
+env:
+  CARGO_TERM_COLOR: always
+
+jobs:
+  test:
+    name: cargo test (${{ matrix.os }})
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-latest, macos-latest]
+    steps:
+      - uses: actions/checkout@v4
+      - uses: dtolnay/rust-toolchain@stable
+      - name: Cache cargo
+        uses: Swatinem/rust-cache@v2
+      - name: Test (locked)
+        run: cargo test --locked --all-targets
+      - name: Clippy
+        run: cargo clippy --locked --all-targets -- -D warnings
+      - name: Docs
+        run: cargo doc --locked --no-deps
+
+  python:
+    name: maturin develop (ubuntu)
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: dtolnay/rust-toolchain@stable
+      - uses: actions/setup-python@v5
+        with:
+          python-version: "3.12"
+      - name: Cache cargo
+        uses: Swatinem/rust-cache@v2
+      - name: Install maturin
+        run: pip install maturin
+      - name: Build extension
+        working-directory: python
+        run: maturin build --release --features python --out /tmp/wheels
+      - name: Install wheel and smoke import
+        run: |
+          pip install /tmp/wheels/*.whl
+          python -c "import readcon_db; print(readcon_db.__file__)"

readcon_db-0.1.2/.github/workflows/crates_publish.yml

@@ -0,0 +1,66 @@
+# Publish readcon-db to crates.io on version tags.
+# Secret: CARGO_REGISTRY_TOKEN (same owner as crates.io publish).
+name: Publish to crates.io
+
+on:
+  push:
+    tags:
+      - 'v*'
+  workflow_dispatch:
+    inputs:
+      tag:
+        description: 'Tag to publish (e.g. v0.1.2); defaults to ref'
+        required: false
+        type: string
+
+permissions:
+  contents: read
+
+jobs:
+  publish-crates-io:
+    name: Publish to crates.io
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          ref: ${{ inputs.tag || github.ref }}
+
+      - name: Install Rust toolchain
+        uses: dtolnay/rust-toolchain@stable
+
+      - name: Resolve crate version
+        id: check
+        run: |
+          version="$(sed -n 's/^version = "\([^"]*\)"/\1/p' Cargo.toml | head -1)"
+          ref_name="${GITHUB_REF_NAME:-}"
+          if [ -n "${{ inputs.tag }}" ]; then
+            ref_name="${{ inputs.tag }}"
+          fi
+          if [[ "$ref_name" == v* ]]; then
+            tag_ver="${ref_name#v}"
+            if [ "$tag_ver" != "$version" ]; then
+              echo "tag ${ref_name} does not match Cargo.toml version ${version}" >&2
+              exit 1
+            fi
+          fi
+          echo "version=${version}" >> "$GITHUB_OUTPUT"
+          if curl -sfL \
+              -H "User-Agent: readcon-db-release-check (lode-org)" \
+              "https://crates.io/api/v1/crates/readcon-db/${version}" \
+              -o /dev/null; then
+              echo "already_published=true" >> "$GITHUB_OUTPUT"
+              echo "readcon-db ${version} is already published; skipping."
+          else
+              echo "already_published=false" >> "$GITHUB_OUTPUT"
+          fi
+
+      - name: cargo publish
+        if: steps.check.outputs.already_published != 'true'
+        env:
+          CARGO_REGISTRY_TOKEN: ${{ secrets.CARGO_REGISTRY_TOKEN }}
+        run: |
+          if [ -z "${CARGO_REGISTRY_TOKEN:-}" ]; then
+            echo "CARGO_REGISTRY_TOKEN secret is empty; set it on the repo." >&2
+            exit 1
+          fi
+          cargo publish --locked

readcon_db-0.1.2/.github/workflows/pages.yml

@@ -0,0 +1,43 @@
+name: Pages
+on:
+  push:
+    branches: [main]
+  workflow_dispatch:
+permissions:
+  contents: read
+  pages: write
+  id-token: write
+concurrency:
+  group: pages
+  cancel-in-progress: true
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
+        with:
+          python-version: "3.12"
+      - name: Sphinx HTML
+        run: |
+          pip install -r docs/requirements.txt
+          sphinx-build -b html docs/source docs/_build/html
+      - name: Assemble site
+        run: |
+          mkdir -p _site
+          cp -a website/. _site/
+          mkdir -p _site/docs
+          cp -a docs/_build/html/. _site/docs/
+          cp -a assets _site/assets
+      - uses: actions/upload-pages-artifact@v3
+        with:
+          path: _site
+  deploy:
+    needs: build
+    runs-on: ubuntu-latest
+    environment:
+      name: github-pages
+      url: ${{ steps.deployment.outputs.page_url }}
+    steps:
+      - id: deployment
+        uses: actions/deploy-pages@v4

readcon_db-0.1.2/.github/workflows/python_wheels.yml

@@ -0,0 +1,113 @@
+name: Python wheels
+
+on:
+  push:
+    tags:
+      - 'v*'
+  pull_request:
+    paths:
+      - 'src/**'
+      - 'Cargo.toml'
+      - 'Cargo.lock'
+      - 'python/**'
+      - '.github/workflows/python_wheels.yml'
+  workflow_dispatch:
+
+concurrency:
+  group: python-wheels-${{ github.ref }}
+  cancel-in-progress: ${{ !startsWith(github.ref, 'refs/tags/') }}
+
+permissions:
+  contents: read
+
+env:
+  CARGO_HTTP_MULTIPLEXING: "false"
+  CARGO_NET_RETRY: "10"
+  CARGO_HTTP_TIMEOUT: "120"
+  RUSTFLAGS: "-C link-arg=-fuse-ld=bfd"
+  CARGO_TARGET_X86_64_UNKNOWN_LINUX_GNU_LINKER: "cc"
+
+jobs:
+  sdist:
+    name: Build sdist
+    runs-on: ubuntu-latest
+    defaults:
+      run:
+        working-directory: python
+    steps:
+      - uses: actions/checkout@v4
+      - name: Build sdist
+        uses: PyO3/maturin-action@v1
+        with:
+          command: sdist
+          args: --out ../dist
+          working-directory: python
+      - name: Validate sdist
+        run: pipx run twine check --strict ../dist/*
+        working-directory: python
+      - uses: actions/upload-artifact@v4
+        with:
+          name: sdist
+          path: dist/*.tar.gz
+          if-no-files-found: error
+
+  wheels:
+    name: Wheel (${{ matrix.os }}, ${{ matrix.target }})
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        include:
+          - os: ubuntu-latest
+            target: x86_64
+          - os: macos-14
+            target: aarch64
+          - os: macos-15
+            target: x86_64
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
+        with:
+          python-version: "3.12"
+      - name: Build wheels
+        uses: PyO3/maturin-action@v1
+        with:
+          target: ${{ matrix.target }}
+          manylinux: auto
+          working-directory: python
+          args: --release --out ../dist --features python --find-interpreter
+          docker-options: >-
+            -e CARGO_HTTP_MULTIPLEXING=false
+            -e CARGO_NET_RETRY=10
+            -e CARGO_HTTP_TIMEOUT=120
+      - name: Validate wheels
+        if: matrix.target != 'aarch64' || runner.os != 'Linux'
+        run: pipx run twine check --strict dist/*
+      - uses: actions/upload-artifact@v4
+        with:
+          name: wheels-${{ matrix.os }}-${{ matrix.target }}
+          path: dist/*.whl
+          if-no-files-found: error
+
+  publish:
+    name: Publish to PyPI
+    needs: [sdist, wheels]
+    runs-on: ubuntu-latest
+    if: startsWith(github.ref, 'refs/tags/v')
+    environment:
+      name: pypi
+      url: https://pypi.org/p/readcon-db
+    permissions:
+      id-token: write
+    steps:
+      - uses: actions/download-artifact@v4
+        with:
+          pattern: '{sdist,wheels-*}'
+          merge-multiple: true
+          path: dist/
+      - name: List artifacts
+        run: ls -la dist/
+      - name: Publish to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          skip-existing: true

readcon_db-0.1.2/.gitignore

@@ -0,0 +1,11 @@
+/target
+**/*.rs.bk
+.python-version
+.venv
+dist/
+*.so
+*.a
+__pycache__/
+.pytest_cache/
+docs/.venv/
+docs/_build/

readcon_db-0.1.2/CHANGELOG.md

@@ -0,0 +1,38 @@
+# Changelog
+
+## 0.1.2 - 2026-06-28
+
+### Documentation
+- Install docs reflect crates.io / PyPI / Pages (no path-only wording)
+- Package metadata: homepage and documentation URLs
+
+### Continuous integration
+- CI (test, clippy, maturin smoke), crates.io publish workflow, Python wheels + PyPI on tags
+
+### Packaging
+- Align `python/pyproject.toml` version with crate **0.1.2**
+
+## 0.1.1 - 2026-06-28
+### Features
+- Optional RCSO cooked SoA tier (`frames_soa`) with cook/delete/numeric getters
+- C/Python/CLI/Fortran exposure for cook and positions/forces fast path
+- User docs: `docs/orgmode/cooked-soa.org` (CON authority; RCSO not fully equivalent)
+
+### Documentation
+- Dual-tier rules in architecture Sphinx summaries and README pointer
+
+
+## 0.1.0 — 2026-06-27
+
+### Added
+- Heed/LMDB `ConCorpus` with trajectory ingest, SoA-agnostic CON text blobs via `readcon-core`
+- Secondary indexes: `idx_natoms`, `idx_symbol`
+- **xxHash3-128** exact content identity: `frame_by_hash` / `hash_by_frame`, `Select::exact_hash`, `find_by_hash`
+- C ABI (`rkrdb_*`) in `cdylib`/`staticlib`; `include/readcon-db.h` with C++ `readcon_db::Corpus`
+- Optional PyO3 module (`--features python`), maturin project under `python/`
+- Fortran `bind(C)` module under `fortran/ReadConDb`
+- Example `ingest_select`
+- **CLI** `readcon-db` (`ingest`, `ingest-dir`, `select`, `dedup-export`, `hash-file`)
+- **`export_extxyz`** / **`ingest_directory`** / **`unique_frame_keys`** for metatrain-style pipelines
+- Workflow docs: `examples/workflows/metatrain_from_con.md` + YAML snippet
+- Sphinx docs, marketing `website/`, logo kit under `assets/logo/`

readcon_db-0.1.2/CITATION.cff

@@ -0,0 +1,18 @@
+cff-version: 1.2.0
+title: "readcon-db: mmap CON corpus store with multi-language bindings"
+message: "If you use readcon-db, please cite it using the metadata below."
+type: software
+authors:
+  - given-names: Rohit
+    family-names: Goswami
+    email: rgoswami@ieee.org
+    orcid: "https://orcid.org/0000-0002-2393-8056"
+license: MIT
+repository-code: "https://github.com/lode-org/readcon-db"
+version: 0.1.0
+date-released: "2026-06-27"
+keywords:
+  - CON
+  - LMDB
+  - trajectory
+  - molecular dynamics