scd-edition 0.1.0__tar.gz

scd_edition-0.1.0/CHANGELOG.md

@@ -0,0 +1,18 @@
+# Changelog
+
+All notable changes to SCD Edition are documented here.
+
+## 0.1.0 — 2026-09-19
+
+First public release.
+
+- Configure and decompose surface and intramuscular EMG recordings.
+- Load OT Bioelettronica, Intan, MATLAB, HDF5, NumPy and CSV data.
+- Inspect unfamiliar MATLAB/HDF5 layouts in the GUI and reuse the selected
+  array path and orientation through saved configurations.
+- Convert proprietary recordings to a documented portable SCD HDF5 format.
+- Review, edit, quality-check and save motor-unit spike trains.
+- Visualise rasters, discharge rates, cumulative spike trains and quality metrics.
+- Open raw Swarm-Contrastive Decomposition output for downstream editing.
+- Include a configured example recording through `scd-edition --example`.
+- Distribute a self-contained Windows application with tagged releases.

scd_edition-0.1.0/CITATION.cff

@@ -0,0 +1,66 @@
+cff-version: 1.2.0
+type: software
+message: "If you use SCD Edition, please cite this software and the relevant method papers."
+authors:
+  - family-names: "Grison"
+    given-names: "Agnese"
+    orcid: "https://orcid.org/0009-0001-5981-3589"
+    email: "agnese.grison@outlook.it"
+    affiliation: "Imperial College London"
+title: "SCD Edition"
+version: "0.1.0"
+date-released: "2026-09-19"
+license: BSD-3-Clause
+repository-code: "https://github.com/AgneGris/scd-edition"
+url: "https://github.com/AgneGris/scd-edition"
+keywords:
+  - electromyography
+  - motor units
+  - signal decomposition
+  - spike editing
+  - neurophysiology
+references:
+  - type: article
+    authors:
+      - family-names: "Grison"
+        given-names: "Agnese"
+      - family-names: "Clarke"
+        given-names: "Alexander Kenneth"
+      - family-names: "Muceli"
+        given-names: "Silvia"
+      - family-names: "Ibáñez"
+        given-names: "Jaime"
+      - family-names: "Kundu"
+        given-names: "Aritra"
+      - family-names: "Farina"
+        given-names: "Dario"
+    doi: "10.1109/TBME.2024.3446806"
+    journal: "IEEE Transactions on Biomedical Engineering"
+    title: "A Particle Swarm Optimised Independence Estimator for Blind Source Separation of Neurophysiological Time Series"
+    volume: "72"
+    issue: "1"
+    start: "227"
+    end: "237"
+    year: 2025
+  - type: article
+    authors:
+      - family-names: "Grison"
+        given-names: "Agnese"
+      - family-names: "Mendez Guerra"
+        given-names: "Irene"
+      - family-names: "Clarke"
+        given-names: "Alexander Kenneth"
+      - family-names: "Muceli"
+        given-names: "Silvia"
+      - family-names: "Ibáñez"
+        given-names: "Jaime"
+      - family-names: "Farina"
+        given-names: "Dario"
+    doi: "10.1113/JP287913"
+    journal: "The Journal of Physiology"
+    title: "Unlocking the full potential of high-density surface EMG: novel non-invasive high-yield motor unit decomposition"
+    volume: "603"
+    issue: "8"
+    start: "2281"
+    end: "2300"
+    year: 2025

scd_edition-0.1.0/CONTRIBUTING.md

@@ -0,0 +1,74 @@
+# Contributing to SCD Edition
+
+Thank you for helping improve SCD Edition. Bug reports, loader requests,
+documentation improvements and focused pull requests are welcome.
+
+## Report a problem
+
+Use the appropriate GitHub issue form. Include:
+
+- SCD Edition version or commit;
+- installation method, operating system and Python version;
+- CPU or GPU model and, for CUDA problems, driver information;
+- acquisition system and file format;
+- exact steps, expected behaviour, actual behaviour and the complete traceback.
+
+Do not upload participant recordings, identifying metadata or confidential lab
+data to a public issue. If a minimal reproducer is necessary, use synthetic or
+explicitly redistributable data.
+
+## Development setup
+
+Install [uv](https://docs.astral.sh/uv/), clone the repository, and create an
+environment using either the CPU or CUDA dependency source:
+
+```bash
+uv sync --extra cpu
+```
+
+```bash
+uv sync --extra cuda
+```
+
+On Windows, add `--python 3.13 --managed-python` if the system Python comes
+from Conda or otherwise causes Qt DLL conflicts.
+
+Run the checks before opening a pull request:
+
+```bash
+uv run ruff check src tests scripts docs
+uv run ruff format --check src tests scripts docs
+uv run pytest
+```
+
+The GUI smoke tests run headlessly by setting `QT_QPA_PLATFORM=offscreen`.
+Changes to loaders should include a small synthetic fixture and tests for
+malformed input. Changes to scientific calculations should include numerical
+regression tests and a clear source or rationale.
+
+For a new acquisition format, first read the
+[data-import guide](docs/importing-data.md). Generic MATLAB/HDF5 layouts should
+use the inspector; a built-in loader is most useful when the format has stable
+metadata, units and channel-order semantics that the generic path cannot
+capture.
+
+## Pull requests
+
+Keep each pull request focused. Explain the user-visible change, tests run and
+any compatibility implications for existing `.pkl` sessions. Update the README
+or quick-start when behaviour or supported formats change.
+
+The files under `src/scd_app/_vendor/` come from Motor Unit Toolbox and should
+not be edited casually. If they need updating, record the new upstream commit,
+preserve its MIT licence, and compare the affected numerical outputs against
+the previous version.
+
+## Releases
+
+1. Update the version in `pyproject.toml`, `CITATION.cff` and `CHANGELOG.md`.
+2. Run the full test suite and `python -m build` from a clean checkout.
+3. Run `python scripts/check_distribution.py`.
+4. Push a matching tag such as `v0.1.0`.
+5. Approve the protected `pypi` environment when the release workflow asks.
+6. After Zenodo archives the GitHub release, add its concept DOI to the README
+   and `CITATION.cff`.

scd_edition-0.1.0/LICENSE

@@ -0,0 +1,29 @@
+BSD 3-Clause License
+
+Copyright (c) 2026, Agnese Grison and contributors
+All rights reserved.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+1. Redistributions of source code must retain the above copyright notice,
+   this list of conditions and the following disclaimer.
+
+2. Redistributions in binary form must reproduce the above copyright notice,
+   this list of conditions and the following disclaimer in the documentation
+   and/or other materials provided with the distribution.
+
+3. Neither the name of the copyright holder nor the names of its
+   contributors may be used to endorse or promote products derived from
+   this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

scd_edition-0.1.0/MANIFEST.in

@@ -0,0 +1,8 @@
+include CITATION.cff
+include CONTRIBUTING.md
+include CHANGELOG.md
+include SUPPORT.md
+include THIRD_PARTY_NOTICES.md
+recursive-include docs *.gif *.ipynb *.md
+recursive-include scripts *.py
+recursive-include src/scd_app/resources/examples *.json *.mat *.md