mef3io 0.3.0__tar.gz

mef3io-0.3.0/.github/workflows/bump-version.yml

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+name: bump-version
+
+# Manual release trigger: bumps the repo-root VERSION file (the single source
+# of truth for Python, C++, and later MATLAB), commits, tags vX.Y.Z, and
+# dispatches the release workflow on that tag.
+on:
+  workflow_dispatch:
+    inputs:
+      bump:
+        description: "patch | minor | major, or an explicit version like 1.2.3"
+        required: true
+        default: "patch"
+
+permissions:
+  contents: write
+  actions: write
+
+jobs:
+  bump:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Compute new version
+        id: ver
+        run: |
+          cur=$(tr -d ' \n' < VERSION)
+          IFS=. read -r major minor patch <<< "$cur"
+          case "${{ inputs.bump }}" in
+            patch) new="$major.$minor.$((patch + 1))" ;;
+            minor) new="$major.$((minor + 1)).0" ;;
+            major) new="$((major + 1)).0.0" ;;
+            *)
+              new="${{ inputs.bump }}"
+              [[ "$new" =~ ^[0-9]+\.[0-9]+\.[0-9]+([a-z0-9.]*)?$ ]] || { echo "bad version: $new"; exit 1; }
+              ;;
+          esac
+          echo "current $cur -> new $new"
+          echo "new=$new" >> "$GITHUB_OUTPUT"
+
+      - name: Commit VERSION and tag
+        run: |
+          new="${{ steps.ver.outputs.new }}"
+          echo "$new" > VERSION
+          git config user.name "github-actions[bot]"
+          git config user.email "github-actions[bot]@users.noreply.github.com"
+          git add VERSION
+          git commit -m "Release v$new"
+          git tag "v$new"
+          git push origin "HEAD:${{ github.ref_name }}" "refs/tags/v$new"
+
+      # Tags pushed with GITHUB_TOKEN do not trigger push events (recursion
+      # guard), so start the release run on the new tag explicitly.
+      - name: Dispatch release workflow
+        env:
+          GH_TOKEN: ${{ github.token }}
+        run: gh workflow run release.yml --ref "v${{ steps.ver.outputs.new }}"

mef3io-0.3.0/.github/workflows/ci.yml

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+name: ci
+
+on:
+  push:
+    branches: [main, dev]
+  pull_request:
+  workflow_dispatch:
+
+jobs:
+  cpp-tests:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - name: Build and run C++ unit tests
+        run: |
+          cmake -S core -B build-core -DMEF3IO_BUILD_TESTS=ON
+          cmake --build build-core -j
+          ctest --test-dir build-core --output-on-failure
+
+  python-tests:
+    name: pytest ${{ matrix.os }} / py${{ matrix.python-version }}
+    strategy:
+      fail-fast: false
+      matrix:
+        include:
+          - { os: ubuntu-latest, python-version: "3.10" }
+          - { os: ubuntu-latest, python-version: "3.12" }
+          - { os: ubuntu-latest, python-version: "3.13" }
+          - { os: macos-latest, python-version: "3.13" }
+    runs-on: ${{ matrix.os }}
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Install package with the oracle test stack
+        run: |
+          python -m pip install --upgrade pip
+          pip install ".[test]"
+      - name: Version sanity (single source of truth)
+        run: |
+          python -c "import mef3io; print('mef3io', mef3io.__version__)"
+          python -c "import mef3io, pathlib; v = pathlib.Path('VERSION').read_text().strip(); assert mef3io.__version__ == v, (mef3io.__version__, v)"
+      - name: Run test suite
+        run: python -m pytest tests -q
+
+  # Windows has no reliable pymef oracle build; verify compile + import + the
+  # oracle-free subset instead. Full Windows coverage happens in cibuildwheel.
+  windows-smoke:
+    runs-on: windows-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
+        with:
+          python-version: "3.13"
+      - name: Install and smoke-test
+        run: |
+          python -m pip install --upgrade pip
+          pip install .
+          python -c "import mef3io; assert mef3io.have_cpp_backend(); print('cpp backend OK,', mef3io.__version__)"
+
+  # Newest CPython, oracle-free (the legacy pymef stack may lag new Pythons):
+  # compile, import, and a full write/read round trip.
+  python-latest-smoke:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
+        with:
+          python-version: "3.14"
+      - name: Install and round-trip
+        run: |
+          python -m pip install --upgrade pip
+          pip install .
+          python -c "
+          import tempfile
+          import numpy as np
+          import mef3io
+          p = tempfile.mkdtemp() + '/s.mefd'
+          w = mef3io.Writer(p, overwrite=True)
+          d = np.sin(np.arange(1000) / 9)
+          d[100:200] = np.nan
+          w.write('ch', d, 1577836800000000, 256.0, precision=3)
+          w.close()
+          r = mef3io.Reader(p)
+          x = r.read('ch')
+          assert len(x) == 1000 and np.isnan(x[100:200]).all()
+          ok = ~np.isnan(d)
+          assert np.allclose(x[ok], np.round(d[ok], 3))
+          print('py3.14 round trip OK,', mef3io.__version__)
+          "

mef3io-0.3.0/.github/workflows/docs.yml

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+name: docs
+
+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"
+      - run: pip install "mkdocs-material>=9,<10" "mkdocs>=1.6,<2"
+      - run: mkdocs build --strict
+      - 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

mef3io-0.3.0/.github/workflows/release.yml

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+name: release
+
+# Builds wheels for every supported platform/arch and publishes to PyPI.
+# Triggered by a version tag (created by the bump-version workflow, which also
+# dispatches this workflow explicitly — tags pushed with GITHUB_TOKEN do not
+# fire tag-push events). A plain workflow_dispatch on a branch is a dry run:
+# wheels are built and uploaded as artifacts, but publishing is skipped.
+on:
+  push:
+    tags: ["v*"]
+  workflow_dispatch:
+
+jobs:
+  wheels:
+    name: wheels ${{ matrix.label }}
+    strategy:
+      fail-fast: false
+      matrix:
+        include:
+          - { os: ubuntu-latest, label: linux-x86_64 }
+          - { os: ubuntu-24.04-arm, label: linux-aarch64 }
+          - { os: windows-latest, label: windows-amd64 }
+          # CPython ships official Windows-on-ARM binaries from 3.11.
+          - { os: windows-11-arm, label: windows-arm64, cibw_build: "cp311-* cp312-* cp313-* cp314-*" }
+          # One macOS runner builds both arm64 and x86_64 (see pyproject).
+          - { os: macos-latest, label: macos }
+    runs-on: ${{ matrix.os }}
+    steps:
+      - uses: actions/checkout@v4
+      - name: Build wheels
+        uses: pypa/cibuildwheel@v3.4.1
+        env:
+          CIBW_BUILD: ${{ matrix.cibw_build || '' }}
+      - uses: actions/upload-artifact@v4
+        with:
+          name: wheels-${{ matrix.label }}
+          path: ./wheelhouse/*.whl
+
+  sdist:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - name: Build sdist
+        run: pipx run build --sdist
+      - uses: actions/upload-artifact@v4
+        with:
+          name: sdist
+          path: dist/*.tar.gz
+
+  # MATLAB MEX binaries for the platforms MATLAB supports. Free MathWorks
+  # licensing on GitHub-hosted runners applies to public repos; on a private
+  # repo these jobs need a MathWorks batch token (they don't block PyPI).
+  mex:
+    name: mex ${{ matrix.label }}
+    strategy:
+      fail-fast: false
+      matrix:
+        include:
+          - { os: ubuntu-latest, label: linux-x86_64 }   # mexa64
+          - { os: windows-latest, label: windows-amd64 } # mexw64
+          - { os: macos-latest, label: macos-arm64 }     # mexmaca64
+    runs-on: ${{ matrix.os }}
+    steps:
+      - uses: actions/checkout@v4
+      - uses: matlab-actions/setup-matlab@v2
+        with:
+          release: latest
+      - name: Build and test the MEX
+        uses: matlab-actions/run-command@v2
+        with:
+          command: cd('matlab'); build_mex; test_mef3io
+      - uses: actions/upload-artifact@v4
+        with:
+          name: mex-${{ matrix.label }}
+          path: matlab/*.mex*
+
+  publish:
+    if: startsWith(github.ref, 'refs/tags/')
+    needs: [wheels, sdist]
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/download-artifact@v4
+        with:
+          path: dist
+          merge-multiple: true
+      - uses: actions/setup-python@v5
+        with:
+          python-version: "3.12"
+      - name: Publish to PyPI
+        env:
+          TWINE_USERNAME: __token__
+          TWINE_PASSWORD: ${{ secrets.PYPI_Token_General }}
+        run: |
+          python -m pip install --upgrade pip twine
+          twine upload --skip-existing dist/*.whl dist/*.tar.gz
+
+  # GitHub release with the MEX binaries attached (their extensions are
+  # platform-unique: mexa64 / mexw64 / mexmaca64, so they upload flat).
+  github-release:
+    if: startsWith(github.ref, 'refs/tags/')
+    needs: [mex]
+    permissions:
+      contents: write
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/download-artifact@v4
+        with:
+          pattern: "mex-*"
+          path: mexbin
+          merge-multiple: true
+      - name: Create release and attach MEX binaries
+        env:
+          GH_TOKEN: ${{ github.token }}
+        run: |
+          gh release create "$GITHUB_REF_NAME" --repo "$GITHUB_REPOSITORY" \
+            --title "$GITHUB_REF_NAME" --generate-notes || true
+          gh release upload "$GITHUB_REF_NAME" --repo "$GITHUB_REPOSITORY" \
+            --clobber mexbin/*.mex*

mef3io-0.3.0/.gitignore

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+build/
+build-core/
+dist/
+wheelhouse/
+*.egg-info/
+__pycache__/
+*.pyc
+.pytest_cache/
+python/mef3io/_mef3io*.so
+python/mef3io/_mef3io*.pyd
+# reference sources (meflib/pymef/mef3_dump), kept next to the repo but untracked
+../reference_files/
+reference_files/
+.idea/
+matlab/*.mex*
+site/

mef3io-0.3.0/CLAUDE.md

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+# mef3io — assistant context
+
+A single C++17/20 core for **MEF 3.0** read+write, wrapped for Python via
+nanobind. The high-level semantics of the legacy `mef_tools` (float scaling,
+NaN discontinuities, precision inference, the int32-counts + conversion-factor
+primitive path) live in **C++** so all bindings behave identically. Video is out
+of scope. The legacy `mef_tools`/`pymef` stack is the correctness oracle.
+
+Status: read + write complete, cross-validated **both directions** vs
+pymef/mef_tools (values, NaN gaps, times, encryption none/L1+L2, fractional fs,
+records). In-segment append + per-segment map implemented. ~112 Python tests +
+standalone C++ Catch2 tests. Wheel builds via `python -m build`. Parallel
+decode/encode, byte-deterministic across threads.
+
+## Build & test (use the active conda env for everything)
+
+```bash
+scripts/dev_build.sh              # builds build/dev, symlinks _mef3io*.so into python/mef3io/
+python -m pytest tests            # conftest.py sets up paths; pymef needed as oracle
+# C++ unit tests:
+cmake -S core -B build-core -DMEF3IO_BUILD_TESTS=ON && cmake --build build-core && ctest --test-dir build-core
+python -m build --wheel           # wheel
+```
+
+This is the standalone mef3io repo (github.com/bnelair/mef3io), migrated out of
+the original `mef_tools` repo in July 2026. The legacy `mef_tools` oracle now
+comes from the pip-installed `mef-tools` package (`pip install mef3io[test]`);
+`tests/conftest.py` still prefers a local checkout if one exists in a parent
+directory. `reference_files/` (meflib/pymef/mef3_dump) stayed in the old repo.
+
+## Module map
+
+`core/` (C++): `types` (aliases + format constants), `byteio` (LE field IO, no
+packed-struct casts), `crc` (Koopman-32), `crypto` (SHA-256, AES-128-ECB,
+two-level password), `headers` (UniversalHeader, MetadataSection1/2/3,
+TimeSeriesIndex, RedBlockHeader — parse/serialize by explicit offset),
+`metadata` (.tmet loader: CRC→password→decrypt), `red` (decode + encode),
+`session` (lazy .mefd/.timd/.segd tree, indexed reads, `collect_blocks`),
+`reader` (gridding, NaN fill, scaling, parallel decode), `records` (read+write),
+`writer` (segment writer), `session_writer` (precision inference, quantization,
+NaN splitting, segments), `parallel.hpp`.
+
+`python/mef3io/`: `Reader`, `Writer` (incl. `write_annotations`), `compat`
+(mef_tools.io drop-in; `MefReader`/`MefWriter` are also re-exported at the top
+level — `from mef3io import MefReader, MefWriter` — via lazy `__getattr__`),
+`cache` (opt-in warm start), `pure` (stub). `bindings/python/mef3io_ext.cpp` =
+nanobind. `matlab/` = MEX + `+mef3io` classes. `examples/` = runnable scripts
+(write/read, int32, append, segment map, annotations, encryption, legacy
+style). Docs site: MkDocs Material from `docs/` (`mkdocs.yml`; nav pages
+index/install/python/matlab/cpp/examples/releasing + the reference docs),
+deployed to GitHub Pages by `.github/workflows/docs.yml` on push to main —
+keep `mkdocs build --strict` green; `for_agents/` (repo root) holds agent handoff docs, outside the site. `docs/design.md` = full design; `docs/encryption_model.md` = crypto
+model; `docs/mef3_format.md` = format reference.
+
+## Format gotchas (do NOT relearn the hard way)
+
+- **Times are stored NEGATED on disk** as meflib's "recording-time-offset
+  applied" marker. User uUTC = `(t>=0)?t:(-t+rto)` (read), `disk = rto-absolute`
+  (write). Applies to UH start/end AND block/record times. rto=0 in fixtures.
+  Missing this makes every time-range read return 0 samples.
+- **Encryption is all-or-nothing pairing**: section 2 → L1 key, section 3 → L2
+  key, by password presence. "Level-1 only" is not a valid file. Decrypt a
+  section only when its stored level is strictly positive; unencrypted files
+  carry -1/-2 (`0xFF`/`0xFE`). See docs/encryption_model.md.
+- **Password scheme**: bytes = terminal byte of each UTF-8 char, 16, zero-pad.
+  L1 field = SHA256(L1)[:16]; L2 field = SHA256(L2)[:16] XOR L1. L2 access
+  derives putative L1 = SHA256(pwd)[:16] XOR L2field, checks its hash.
+- **RED data blocks are UNENCRYPTED** even in encrypted sessions (meflib
+  default); only metadata s2/s3 and record bodies are encrypted.
+- **Index file_offset is FILE-relative** (includes the 1024 B UH); first block
+  offset = 1024. Windowed reads must read only the needed byte range
+  (`collect_blocks` uses `read_file_range`), not the whole `.tdat`.
+- **RED encode**: first emitted byte is junk (meflib overwrites stats[255] then
+  restores) → drop emitted[0], payload = emitted[1:] at offset 304; stored
+  difference_bytes = generated+1. Lossless no-detrend/no-scale, pymef-readable.
+  Constants: TOP_VALUE 0x80000000, CARRY_CHECK 0x7F800000, SHIFT_BITS 23,
+  EXTRA_BITS 7, BOTTOM_VALUE 0x800000, PAD_BYTE 0x7e, 8-byte alignment.
+- **Records**: header 24 B (crc@0,type[4]@4,vmaj@9,vmin@10,enc@11,bytes@12,
+  time@16). Body padded to 16-byte multiple with 0x7e. L2-encrypted when the
+  session is encrypted. `.ridx` entry 24 B (type@0,vmaj@5,vmin@6,enc@7,
+  offset@8,time@16). file_offset FILE-relative.
+- **Oracle**: use `pymef` `read_ts_channels_sample([ch],[0,nsamp])` for decoded
+  int32 (no gap NaN) and `read_ts_channels_uutc` for gap-filled. `mef3_dump` is
+  NOT usable (reads the encryption sentinel byte unsigned). Manifest `nsamp` !=
+  stored nsamp (it's get_raw_data length incl. gaps) — compare vs pymef
+  basic_info.
+
+## Known limitations / next steps
+
+- **In-segment append implemented** (`append_time_series_segment` +
+  `SessionWriter` hydration): non-first writes extend the channel's last
+  segment in place (.tdat streamed-CRC append, .tidx extend, .tmet s2 rewrite);
+  `new_segment=True` forces a fresh segment. Appends validate fs/ufact/start
+  time vs on-disk metadata (`WriteConflictError` → Python RuntimeError); float
+  appends reuse the segment's precision. `Reader.segments(ch)` maps what data
+  is where per segment. First appended block keeps discontinuity=true (readers
+  are time-gridded so contiguous appends stay seamless).
+- **Do NOT `pip install -e .` for C++ dev** — scikit-build-core's editable hook
+  loads an install-time extension snapshot that shadows the dev_build symlink
+  (meta-path beats sys.path). Keep mef3io uninstalled; use scripts/dev_build.sh.
+- Pure-Python backend is a stub. Records write covers Note/EDFA/SyLg/Seiz.
+  Cache is Python-level (a C++ warm-start is future).
+- **MATLAB binding implemented**: flat C ABI (`core/include/mef3io/c_api.h`,
+  Catch2-tested) → single command-dispatch MEX (`matlab/mef3io_mex.cpp`) →
+  `+mef3io` Reader/Writer classes. Build with `matlab/build_mex.m` (C++20
+  compiler; do NOT add -fvisibility=hidden — it hides the MEX version symbols
+  → "not supported in current release"). `matlab/test_mef3io.m` = round trip;
+  validated cross-language both directions vs Python/pymef with R2026a.
+  Append-overlap check has half-a-sample-period slack (per-block half-us time
+  rounding can store a segment end ~1 us past the grid-exact end).
+- Distribution: **version single source of truth = repo-root `VERSION` file**
+  (pyproject regex provider → wheel metadata; CMake → `mef3io::version()` and
+  the extension's `__version__`; `mef3io.__version__` prefers installed dist
+  metadata). Release flow: manually run the `bump-version` workflow
+  (patch/minor/major or explicit) → commits VERSION, tags vX.Y.Z, dispatches
+  `release.yml` → cibuildwheel on linux x86_64+aarch64, windows AMD64+ARM64
+  (cp311+ on ARM), macOS arm64+x86_64, + sdist → twine upload using the
+  `PYPI_Token_General` secret. `ci.yml` = tests on push/PR (main, dev). PyPI
+  name not yet reserved. Then: benchmark vs legacy, cut mef_tools 3.0 as a
+  compat re-export. Keep mef3io brand-neutral; brainmaze-mef3-server should
+  depend on it (see docs/design.md).
+
+Benchmarks: `benchmarks/mef_benchmark.py` (write/open/seq/parallel vs mef_tools
+& NWB-Zarr) and `benchmarks/compression_test.py` (file size / compression).

mef3io-0.3.0/CMakeLists.txt

@@ -0,0 +1,26 @@
+# Top-level build for the mef3io Python extension (driven by scikit-build-core).
+cmake_minimum_required(VERSION 3.26)
+
+# Single source of truth for the version (shared with the wheel metadata via
+# pyproject.toml's regex provider, and with C++ via mef3io/version.hpp).
+file(STRINGS "${CMAKE_CURRENT_SOURCE_DIR}/VERSION" MEF3IO_VERSION LIMIT_COUNT 1)
+project(mef3io VERSION ${MEF3IO_VERSION} LANGUAGES CXX)
+
+add_subdirectory(core)
+
+# --- nanobind extension ---
+find_package(Python 3.10 REQUIRED COMPONENTS Interpreter Development.Module)
+
+# Locate nanobind's CMake config via the installed package.
+execute_process(
+  COMMAND "${Python_EXECUTABLE}" -m nanobind --cmake_dir
+  OUTPUT_STRIP_TRAILING_WHITESPACE
+  OUTPUT_VARIABLE NB_DIR)
+list(APPEND CMAKE_PREFIX_PATH "${NB_DIR}")
+find_package(nanobind CONFIG REQUIRED)
+
+nanobind_add_module(_mef3io STABLE_ABI bindings/python/mef3io_ext.cpp)
+target_link_libraries(_mef3io PRIVATE mef3io_core)
+target_compile_features(_mef3io PRIVATE cxx_std_20)
+
+install(TARGETS _mef3io LIBRARY DESTINATION mef3io)

mef3io-0.3.0/LICENSE

@@ -0,0 +1,202 @@
+                                 Apache License
+                           Version 2.0, January 2004
+                        http://www.apache.org/licenses/
+
+   TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION
+
+   1. Definitions.
+
+      "License" shall mean the terms and conditions for use, reproduction,
+      and distribution as defined by Sections 1 through 9 of this document.
+
+      "Licensor" shall mean the copyright owner or entity authorized by
+      the copyright owner that is granting the License.
+
+      "Legal Entity" shall mean the union of the acting entity and all
+      other entities that control, are controlled by, or are under common
+      control with that entity. For the purposes of this definition,
+      "control" means (i) the power, direct or indirect, to cause the
+      direction or management of such entity, whether by contract or
+      otherwise, or (ii) ownership of fifty percent (50%) or more of the
+      outstanding shares, or (iii) beneficial ownership of such entity.
+
+      "You" (or "Your") shall mean an individual or Legal Entity
+      exercising permissions granted by this License.
+
+      "Source" form shall mean the preferred form for making modifications,
+      including but not limited to software source code, documentation
+      source, and configuration files.
+
+      "Object" form shall mean any form resulting from mechanical
+      transformation or translation of a Source form, including but
+      not limited to compiled object code, generated documentation,
+      and conversions to other media types.
+
+      "Work" shall mean the work of authorship, whether in Source or
+      Object form, made available under the License, as indicated by a
+      copyright notice that is included in or attached to the work
+      (an example is provided in the Appendix below).
+
+      "Derivative Works" shall mean any work, whether in Source or Object
+      form, that is based on (or derived from) the Work and for which the
+      editorial revisions, annotations, elaborations, or other modifications
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+      of this License, Derivative Works shall not include works that remain
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+      the Work and Derivative Works thereof.
+
+      "Contribution" shall mean any work of authorship, including
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+      to that Work or Derivative Works thereof, that is intentionally
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