hdeeg-snpm 0.4.0__tar.gz

hdeeg_snpm-0.4.0/CHANGELOG.md

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+# Changelog
+
+## 0.4.0 (2026-10-24)
+
+First public release, and the first on PyPI.
+
+Changed, in step with the MATLAB toolbox:
+- The corrected p of the t-tests and correlations is now b/N. The observed labelling is one of
+  the N permutations and is counted once; it used to be counted twice, which made p slightly
+  conservative (by less than 1/(N+1)); for a one-sided paired test on 5 subjects the smallest p
+  was 2/33 instead of 1/32, so it could not reach 0.05.
+  Group designs, mixed models and circular analyses keep (b+1)/(N+1). A supplied `perms` matrix
+  without the observed labelling is refused.
+- Mixed model: +-Inf in a model column counts as missing; an effect naming no coefficient or term
+  is refused, listing the available ones; a within-subject shuffle of an effect that is constant
+  within subject is refused; under group relabelling a channel with one value on every trial is
+  excluded and a response constant within subject is refused; reference levels and coefficient
+  names follow MATLAB's fitlme (text columns not converted to categorical keep their order of
+  first appearance).
+- circ_corrAngLinear: the exclusion reason no longer mentions groups.
+
+## 0.3.0 (2026-10-20)
+
+Mixed linear model (`mixedmodel`) with a random intercept per subject.
+
+## 0.2.0 (2026-10-19)
+
+Circular phase analyses: circ_phase_group, circ_phase_group_u2, circ_corrAngLinear.
+
+## 0.1.0 (2026-10-18)
+
+t-tests, Pearson and Spearman correlation with covariates, group designs (anova1, ancova,
+regression, rmanova, mixed2way), results file, Excel workbook, scalp maps and HTML report, and
+an optional reader for TurtleWave event databases.

hdeeg_snpm-0.4.0/LICENSE

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+MIT License
+
+Copyright (c) 2026 Tancy Kao
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

hdeeg_snpm-0.4.0/MANIFEST.in

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+include CHANGELOG.md
+include tests/conftest.py tests/parity_util.py
+recursive-include tests/data *
+recursive-include examples *.toml *.csv

hdeeg_snpm-0.4.0/PKG-INFO

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+Metadata-Version: 2.4
+Name: hdeeg-snpm
+Version: 0.4.0
+Summary: Permutation statistics (TFCE and cluster correction) for high-density EEG scalp topographies
+Author: Tancy Kao
+License-Expression: MIT
+Project-URL: Homepage, https://github.com/TancyKao/hdEEG-SnPM-py
+Project-URL: Documentation, https://github.com/TancyKao/hdEEG-SnPM-py/tree/main/docs
+Project-URL: Changelog, https://github.com/TancyKao/hdEEG-SnPM-py/blob/main/CHANGELOG.md
+Project-URL: MATLAB toolbox, https://github.com/TancyKao/hdEEG-SnPM
+Requires-Python: >=3.10
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: numpy>=1.26
+Requires-Dist: scipy>=1.10
+Requires-Dist: pandas>=2.0
+Requires-Dist: matplotlib>=3.5
+Requires-Dist: openpyxl>=3.1
+Requires-Dist: jinja2>=3.1
+Requires-Dist: tomli>=2.0; python_version < "3.11"
+Provides-Extra: turtlewave
+Requires-Dist: turtlewave-hdeeg>=4.6; extra == "turtlewave"
+Provides-Extra: dev
+Requires-Dist: pytest>=7; extra == "dev"
+Requires-Dist: ruff>=0.4; extra == "dev"
+Requires-Dist: mne>=1.0; extra == "dev"
+Requires-Dist: statsmodels>=0.14; extra == "dev"
+Dynamic: license-file
+
+# hdeeg-snpm (Python)
+
+Permutation statistics for high-density EEG scalp topographies: a statistic per channel,
+threshold-free cluster enhancement (TFCE) and cluster correction over the channel-neighbour
+graph, and a max-statistic permutation null for family-wise error control.
+
+This is the Python port of the MATLAB toolbox [hdEEG-SnPM](https://github.com/TancyKao/hdEEG-SnPM).
+The MATLAB toolbox is the reference: an analysis here counts as validated only once it reproduces
+the MATLAB statistic maps and corrected p-values on shared inputs using the same permutation
+indices.
+
+**Status: v0.4.0, beta. It reproduces the MATLAB toolbox on the parity fixtures (phases 1 to 3); the MATLAB toolbox stays the reference. Changes: [CHANGELOG.md](https://github.com/TancyKao/hdEEG-SnPM-py/blob/main/CHANGELOG.md).**
+
+| Piece | State |
+|---|---|
+| Recording systems (EGI 256 HydroCel, Compumedics 257 Neuvo) | ported; Compumedics checked against MATLAB on anova1, correlationP, pairedT, unpairedT |
+| TFCE and cluster finding | ported; equal to MATLAB on 206 stored maps |
+| Paired, unpaired, one-sample t-tests; Pearson and Spearman correlation with covariates | ported; reproduces MATLAB on 33 reference runs |
+| Group designs: anova1, ancova, regression, rmanova, mixed2way | ported; reproduces MATLAB on 8 reference runs (37 permutation loops) |
+| Results file, Excel workbook, scalp maps, HTML report, `snpm run` | written; Excel workbook matches MATLAB's numbers on 9 reference runs |
+| TurtleWave `neural_events.db` reader | written; density checked only in TurtleWave's environment (below) |
+| Circular phase analyses: circ_phase_group, circ_phase_group_u2, circ_corrAngLinear | ported in phase 2 (v0.2.0); reproduces MATLAB on 8 reference runs |
+| Mixed linear model (`mixedmodel`), random intercept `(1\|Subject)` only | ported in phase 3 (v0.3.0); agrees with MATLAB on 6 reference runs within the fit tolerances (except a few permuted fits where MATLAB's optimiser stops short), correction exact |
+| GUI, spectral-power folders, other random structures | not ported |
+
+How agreement with MATLAB is checked, and where the two differ on purpose:
+[docs/explanation/parity-with-matlab.md](https://github.com/TancyKao/hdEEG-SnPM-py/blob/main/docs/explanation/parity-with-matlab.md).
+All documentation: [docs/README.md](https://github.com/TancyKao/hdEEG-SnPM-py/blob/main/docs/README.md).
+
+## Install
+
+    pip install hdeeg-snpm
+
+## Use
+
+    snpm run examples/paired_t.toml
+
+writes a results file, a summary, an Excel workbook and a self-contained HTML report. The example
+files are in this repository, under `examples/`.
+
+## Install (development)
+
+    uv venv && uv pip install -e ".[dev]"
+    .venv/bin/pytest -q
+
+Event density from TurtleWave databases is computed by TurtleWave itself, so its tests are
+skipped in this environment. Before a release, run them in TurtleWave's environment from the
+repository root, with TurtleWave-hdEEG checked out beside this repository:
+
+    PYTHONPATH=src ../TurtleWave-hdEEG/.venv/bin/python -m pytest -q tests/test_turtlewave.py
+
+Every test must pass with none skipped.

hdeeg_snpm-0.4.0/README.md

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+# hdeeg-snpm (Python)
+
+Permutation statistics for high-density EEG scalp topographies: a statistic per channel,
+threshold-free cluster enhancement (TFCE) and cluster correction over the channel-neighbour
+graph, and a max-statistic permutation null for family-wise error control.
+
+This is the Python port of the MATLAB toolbox [hdEEG-SnPM](https://github.com/TancyKao/hdEEG-SnPM).
+The MATLAB toolbox is the reference: an analysis here counts as validated only once it reproduces
+the MATLAB statistic maps and corrected p-values on shared inputs using the same permutation
+indices.
+
+**Status: v0.4.0, beta. It reproduces the MATLAB toolbox on the parity fixtures (phases 1 to 3); the MATLAB toolbox stays the reference. Changes: [CHANGELOG.md](https://github.com/TancyKao/hdEEG-SnPM-py/blob/main/CHANGELOG.md).**
+
+| Piece | State |
+|---|---|
+| Recording systems (EGI 256 HydroCel, Compumedics 257 Neuvo) | ported; Compumedics checked against MATLAB on anova1, correlationP, pairedT, unpairedT |
+| TFCE and cluster finding | ported; equal to MATLAB on 206 stored maps |
+| Paired, unpaired, one-sample t-tests; Pearson and Spearman correlation with covariates | ported; reproduces MATLAB on 33 reference runs |
+| Group designs: anova1, ancova, regression, rmanova, mixed2way | ported; reproduces MATLAB on 8 reference runs (37 permutation loops) |
+| Results file, Excel workbook, scalp maps, HTML report, `snpm run` | written; Excel workbook matches MATLAB's numbers on 9 reference runs |
+| TurtleWave `neural_events.db` reader | written; density checked only in TurtleWave's environment (below) |
+| Circular phase analyses: circ_phase_group, circ_phase_group_u2, circ_corrAngLinear | ported in phase 2 (v0.2.0); reproduces MATLAB on 8 reference runs |
+| Mixed linear model (`mixedmodel`), random intercept `(1\|Subject)` only | ported in phase 3 (v0.3.0); agrees with MATLAB on 6 reference runs within the fit tolerances (except a few permuted fits where MATLAB's optimiser stops short), correction exact |
+| GUI, spectral-power folders, other random structures | not ported |
+
+How agreement with MATLAB is checked, and where the two differ on purpose:
+[docs/explanation/parity-with-matlab.md](https://github.com/TancyKao/hdEEG-SnPM-py/blob/main/docs/explanation/parity-with-matlab.md).
+All documentation: [docs/README.md](https://github.com/TancyKao/hdEEG-SnPM-py/blob/main/docs/README.md).
+
+## Install
+
+    pip install hdeeg-snpm
+
+## Use
+
+    snpm run examples/paired_t.toml
+
+writes a results file, a summary, an Excel workbook and a self-contained HTML report. The example
+files are in this repository, under `examples/`.
+
+## Install (development)
+
+    uv venv && uv pip install -e ".[dev]"
+    .venv/bin/pytest -q
+
+Event density from TurtleWave databases is computed by TurtleWave itself, so its tests are
+skipped in this environment. Before a release, run them in TurtleWave's environment from the
+repository root, with TurtleWave-hdEEG checked out beside this repository:
+
+    PYTHONPATH=src ../TurtleWave-hdEEG/.venv/bin/python -m pytest -q tests/test_turtlewave.py
+
+Every test must pass with none skipped.

hdeeg_snpm-0.4.0/examples/circ_phase_group.toml

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+# Two-group preferred-phase comparison (Hotelling T^2 on the cos/sin embedding, adjusted for
+# log(event count) per channel) on the synthetic example data in examples/data, copied from the
+# MATLAB toolbox's example_data: 16 + 16 subjects, a mean-direction shift planted near E129.
+# Angle units and the zero convention are required and have no default.
+comparison      = "circ_phase_group"
+channels        = "egi"
+data1_file      = "data/circ_phase_groupA.csv"
+data2_file      = "data/circ_phase_groupB.csv"
+count1_file     = "data/circ_phase_countsA.csv"
+count2_file     = "data/circ_phase_countsB.csv"
+circ_units      = "rad"
+circ_convention = "literature_uppeak0"
+permutations    = 1000
+seed            = 20261013
+output_path     = "../example_output"

hdeeg_snpm-0.4.0/examples/data/circ_anglinear_angles.csv

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