ncrf 0.5__tar.gz

ncrf-0.5/.git_archival.txt

@@ -0,0 +1,3 @@
+node: $Format:%H$
+node-date: $Format:%cI$
+describe-name: $Format:%(describe:tags=true,match=*[0-9]*)$

ncrf-0.5/.gitattributes

@@ -0,0 +1 @@
+.git_archival.txt  export-subst

ncrf-0.5/.github/labeler.yaml

@@ -0,0 +1,3 @@
+📓 doc:
+  - changed-files:
+      - any-glob-to-any-file: ['docs/*']

ncrf-0.5/.github/workflows/auto-label.yaml

@@ -0,0 +1,18 @@
+name: auto-label
+concurrency:
+  group: ${{ github.workflow }}-${{ github.event.number }}-${{ github.event.ref }}
+  cancel-in-progress: true
+on:  # yamllint disable-line rule:truthy
+- pull_request_target
+
+jobs:
+  labeler:
+    permissions:
+      issues: write
+      contents: read
+      pull-requests: write
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/labeler@v5
+        with:
+          configuration-path: .github/labeler.yaml

ncrf-0.5/.github/workflows/code-quality.yml

@@ -0,0 +1,25 @@
+name: Lint with pre-commit
+
+on: [push, pull_request]
+
+jobs:
+  pre-commit:
+    runs-on: ubuntu-latest
+    steps:
+    - name: Checkout code
+      uses: actions/checkout@v7
+      with:
+        fetch-depth: 0
+
+    - name: Set up Python
+      uses: actions/setup-python@v6.2.0
+      with:
+        python-version: '3.12'
+
+    - name: Install dependencies
+      run: |
+        pip install pre-commit
+
+    - name: Run pre-commit hooks
+      run: |
+        pre-commit run --all-files

ncrf-0.5/.github/workflows/doc.yaml

@@ -0,0 +1,63 @@
+name: doc
+concurrency:
+  group: ${{ github.workflow }}-${{ github.event.number }}-${{ github.event.ref }}
+  cancel-in-progress: true
+on:  # yamllint disable-line rule:truthy
+  pull_request:
+  push:
+    branches:
+      - master
+      - doc*
+  workflow_dispatch:
+
+jobs:
+  build:
+    timeout-minutes: 30
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+      - run: sudo apt update && sudo apt install -y optipng
+      - name: Install Miniconda
+        uses: conda-incubator/setup-miniconda@v3
+        with:
+          auto-update-conda: true
+          miniforge-version: latest
+          environment-file: env-dev.yml
+          activate-environment: ncrf
+          auto-activate-base: false
+      - name: build Neuro-currentRF and doc
+        shell: bash -el {0}
+        run: |
+          python -m pip install -e .[doc]
+          python -c "import ncrf"
+          make -C docs html
+      - name: Prune sphinx environment
+        run: rm -R ./docs/_build/html/.doctrees
+      - uses: actions/upload-artifact@v4
+        with:
+          name: doc-dev
+          path: ./docs/_build/html
+
+  deploy:
+    if: github.event_name == 'push'
+    needs: build
+    timeout-minutes: 10
+    runs-on: ubuntu-latest
+    permissions:
+      contents: write
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/download-artifact@v4
+        with:
+          name: doc-dev
+          path: ./doc-dev
+      - uses: JamesIves/github-pages-deploy-action@v4
+        with:
+          folder: doc-dev
+          # target-folder: ./neuro-currentRF
+          git-config-name: 'github-actions[bot]'
+          git-config-email: 'github-actions[bot]@users.noreply.github.com'
+          single-commit: true
+          force: true

ncrf-0.5/.github/workflows/test-posix.yml

@@ -0,0 +1,59 @@
+name: Python Package using Conda on linux and macos
+
+on:
+  push:
+    branches:
+      - master
+      - maint*
+  pull_request:
+    branches: [ "master" ]
+
+jobs:
+  build-posix:
+    name: build-${{ matrix.os }}
+    runs-on: ${{ matrix.os }}
+    # runs-on: ubuntu-latest
+    strategy:
+      max-parallel: 5
+      matrix:
+        os: [ubuntu-latest, macos-latest]
+        python-version: ['3.12']  # oldest Python with conda builds of Eelbrain pre-releases
+        include:
+          - os: ubuntu-latest
+            cv: 1
+          - os: macos-latest
+            cc: 1
+
+    steps:
+    - uses: actions/checkout@v4
+      with:
+        fetch-depth: 0
+    - name: Install Miniconda
+      uses: conda-incubator/setup-miniconda@v3
+      with:
+        auto-update-conda: true
+        miniforge-version: latest
+        python-version: ${{ matrix.python-version }}
+        environment-file: env-dev.yml
+        activate-environment: ncrf
+        auto-activate-base: false
+    - name: build Neuro-currentRF
+      shell: bash -el {0}
+      run: |
+        python -m pip install .[test]
+        rm -rf ncrf
+    - if: ${{ matrix.cc }}
+      name: Test with pytest and code-cov
+      shell: bash -el {0}
+      run: |
+        pytest --cov --cov-report=xml --pyargs ncrf  # namespace vs module import?
+    - if: ${{ matrix.cc }}
+      name: Upload coverage to Codecov  
+      uses: codecov/codecov-action@v4
+      with:
+        token: ${{ secrets.CODECOV_TOKEN }}
+    - if: ${{ matrix.cv }}
+      name: Test with pytest and cv
+      shell: bash -el {0}
+      run: |
+        pytest --crossvalidation=True --pyargs ncrf

ncrf-0.5/.github/workflows/test-windows.yml

@@ -0,0 +1,32 @@
+name: Python Package using Conda on windows
+
+on:
+  push:
+    branches:
+      - master
+      - maint*
+  pull_request:
+    branches: [ "master" ]
+
+jobs:
+  build-windows-latest:
+    runs-on: windows-latest
+
+    steps:
+    - uses: actions/checkout@v4
+      with:
+        fetch-depth: 0
+    - name: Install Miniconda
+      uses: conda-incubator/setup-miniconda@v3
+      with:
+        auto-update-conda: false
+        environment-file: env-dev.yml
+        activate-environment: ncrf
+    - name: build Neuro-currentRF
+      shell: bash -el {0}
+      run: |
+        pip install -e .[test]
+    - name: Test with pytest
+      shell: bash -el {0}
+      run: |
+        pytest  --crossvalidation=True

ncrf-0.5/.github/workflows/wheels.yml

@@ -0,0 +1,89 @@
+name: Build wheels
+
+# Adapted from Eelbrain
+
+on:
+  push:
+    branches:
+      - master
+    tags:
+      - "v*"
+  pull_request:
+    branches:
+      - master
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  build:
+    name: Build sdist and wheel
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v7
+        with:
+          fetch-depth: 0
+      - name: Build sdist and wheel
+        run: pipx run build
+      - uses: actions/upload-artifact@v7
+        with:
+          name: dist
+          path: ./dist/*
+
+  test-sdist:
+    name: Test sdist
+    needs: [build]
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v7  # for env-dev.yml
+      - uses: actions/download-artifact@v8
+        with:
+          name: dist
+          path: ./dist
+      - name: Install Miniconda
+        uses: conda-incubator/setup-miniconda@v3
+        with:
+          auto-update-conda: true
+          miniforge-version: latest
+          environment-file: env-dev.yml
+          activate-environment: ncrf
+          auto-activate-base: false
+      - name: Install sdist
+        shell: bash -el {0}
+        run: |
+          pip install "$(ls dist/*.tar.gz)[test]"
+          rm -rf ncrf
+      - name: Check version
+        shell: bash -el {0}
+        run: |
+          python -c "import ncrf; v = ncrf.__version__; assert v != '0.0.0' and v[0].isdigit(), f'Bad version: {v!r}'"
+      - name: Run tests
+        shell: bash -el {0}
+        run: pytest -m "not slow" -rsx -v --pyargs ncrf
+
+  pre-publish:
+    runs-on: ubuntu-latest
+    needs: [test-sdist]
+    steps:
+      - uses: actions/download-artifact@v8
+        with:
+          name: dist
+          path: dist/
+      - run: ls -lR dist/
+      - run: pipx run twine check dist/*
+
+  publish:
+    runs-on: ubuntu-latest
+    environment: "Package deployment"
+    permissions:
+      id-token: write  # for trusted publishing
+    needs: [pre-publish]
+    if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags/')
+    steps:
+      - uses: actions/download-artifact@v8
+        with:
+          name: dist
+          path: dist/
+      - run: ls -lR dist/
+      - uses: pypa/gh-action-pypi-publish@release/v1

ncrf-0.5/.gitignore

@@ -0,0 +1,22 @@
+docs/_build
+docs/generated
+docs/auto_examples
+docs/sg_execution_times.rst
+ncrf.egg-info
+fit_ncrf/*.log
+*.out
+*.so
+fit_ncrf/*.pickled
+*egg-info
+.idea/
+build/
+dist/
+__pycache__/
+ncrf/__pycache__/
+ncrf-testing-data
+*.html
+ncrf_data
+.pytest_cache
+.DS_Store
+*.ipynb
+*/.ipynb_checkpoints/*

ncrf-0.5/.pre-commit-config.yaml

@@ -0,0 +1,29 @@
+repos:
+- repo: https://github.com/asottile/pyupgrade
+  rev: v3.19.1
+  hooks:
+    - id: pyupgrade
+      args: [--py310-plus]
+- repo: https://github.com/PyCQA/autoflake
+  rev: v2.3.3
+  hooks:
+    - id: autoflake
+      args:
+        - --remove-all-unused-imports
+        - --in-place
+        - --remove-unused-variables
+        - --ignore-init-module-imports
+- repo: https://github.com/ikamensh/flynt/
+  rev: 1.0.6
+  hooks:
+    - id: flynt
+- repo: https://github.com/hhatto/autopep8
+  rev: v2.3.2
+  hooks:
+    - id: autopep8
+      files: 'ncrf/'
+- repo: https://github.com/PyCQA/flake8
+  rev: 7.3.0
+  hooks:
+    - id: flake8
+      files: 'ncrf/'

ncrf-0.5/LICENSE.txt

@@ -0,0 +1,7 @@
+Copyright 2019-2025, Proloy Das
+
+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.

ncrf-0.5/PKG-INFO

@@ -0,0 +1,133 @@
+Metadata-Version: 2.4
+Name: ncrf
+Version: 0.5
+Summary: add-on module to eelbrain for neural current RF estimation
+Author-email: Proloy Das <proloyd94@gmail.com>
+Maintainer: Christian Brodbeck
+Maintainer-email: Proloy Das <proloyd94@gmail.com>
+License-Expression: MIT
+Project-URL: documentation, https://proloyd.github.io/neuro-currentRF
+Project-URL: homepage, https://github.com/proloyd/neuro-currentRF
+Project-URL: source, https://github.com/proloyd/neuro-currentRF
+Project-URL: tracker, https://github.com/proloyd/neuro-currentRF/issues
+Keywords: meg,eeg,source localization,python
+Classifier: Natural Language :: English
+Classifier: Operating System :: MacOS
+Classifier: Operating System :: Microsoft :: Windows
+Classifier: Operating System :: Unix
+Classifier: Programming Language :: Python :: 3 :: Only
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Requires-Python: >=3.11
+Description-Content-Type: text/markdown
+License-File: LICENSE.txt
+Requires-Dist: eelbrain>=0.43.0b3
+Requires-Dist: numpy<3,>=1.23
+Provides-Extra: all
+Requires-Dist: ncrf[style]; extra == "all"
+Requires-Dist: ncrf[test]; extra == "all"
+Requires-Dist: ncrf[doc]; extra == "all"
+Provides-Extra: full
+Requires-Dist: ncrf[all]; extra == "full"
+Provides-Extra: style
+Requires-Dist: codespell[toml]>=2.2.4; extra == "style"
+Requires-Dist: ruff>=0.6.0; extra == "style"
+Requires-Dist: toml-sort; extra == "style"
+Requires-Dist: yamllint; extra == "style"
+Provides-Extra: doc
+Requires-Dist: dipy; extra == "doc"
+Requires-Dist: numpydoc; extra == "doc"
+Requires-Dist: furo; extra == "doc"
+Requires-Dist: matplotlib; extra == "doc"
+Requires-Dist: sphinx-copybutton; extra == "doc"
+Requires-Dist: sphinx-design; extra == "doc"
+Requires-Dist: sphinx-gallery; extra == "doc"
+Requires-Dist: sphinx-issues; extra == "doc"
+Requires-Dist: sphinxcontrib-bibtex; extra == "doc"
+Requires-Dist: intersphinx_registry; extra == "doc"
+Requires-Dist: memory-profiler; extra == "doc"
+Provides-Extra: test
+Requires-Dist: flake8; extra == "test"
+Requires-Dist: pytest-cov; extra == "test"
+Requires-Dist: pytest<8.1.1,>=8.0; extra == "test"
+Requires-Dist: pytest-faulthandler; extra == "test"
+Requires-Dist: seaborn; extra == "test"
+Dynamic: license-file
+
+# Build Status
+![test-posix](https://github.com/proloyd/neuro-currentRF/actions/workflows/test-posix.yml/badge.svg)
+
+![test-windows](https://github.com/proloyd/neuro-currentRF/actions/workflows/test-windows.yml/badge.svg)
+
+
+# NCRF   
+The magnetoencephalography (MEG) response to continuous auditory stimuli, such as speech, is commonly described using a linear filter, the auditory temporal response function (TRF). Though components of the sensor level TRFs have been well characterized, the cortical distributions of  the underlying neural responses are not well-understood. In our recent work, we provide a unified framework for determining the TRFs of neural sources directly from the MEG data, by integrating the TRF and distributed forward  source models into one, and casting the joint estimation task as a Bayesian optimization problem. Though the resulting  problem emerges as non-convex, we propose efficient solutions that leverage recent advances in evidence maximization. For more details please refer to [1], [2].
+
+This repository contains the implementation of our direct TRF estimation algorithm in Python.
+
+For code examples using real datasets, see the [Example gallery](https://eelbrain.github.io/neuro-currentRF/auto_examples/index.html).
+
+The optimization algorithm is configurable independently of the forward model.
+For a prepared `RegressionData` dataset, the lower-level API is:
+
+```python
+from ncrf import ChampLasso, NCRFEstimator
+
+estimator = NCRFEstimator.from_lead_field(lead_field, noise_covariance)
+solver = ChampLasso(mu='auto', n_iter=30, n_iterc=10, n_iterf=100)
+result = estimator.fit(data, solver)
+```
+
+All solvers return a common predictive `NCRF` in `result.model`; training explained variance
+is available as `result.scores['explained_variance']`. To score other data,
+`result.model.evaluate(data, [explained_variance, l2_error])` predicts once and
+returns all requested metrics. Solver-specific state is available as
+`result.solver_fit`.
+
+
+## How to use:
+run
+```python
+result = fit_ncrf(meg, stim, lead_field, noise_covariance, mu='auto', tstop=1.0, basis_stride=2, n_splits=3, scale='l1')
+```
+to perform a 3-fold cross-validation and then construct the model for 1s long TRF with the regularization weight among the given range that gives least generalization error. The signature of the ``meg`` and ``stim`` could be as follows:
+
+    [        megA (case, sensor, time),                       megB (case, sensor, time),               ...]
+    [[featA1 (case, time), featA2 (case, time), ...], [featB1 (case, time), featB2 (case, time), ...], ...]
+
+For more options, please look at the docstring. The learned TRF, `h` can be retrieved using:
+```python
+h = result.model.h
+```
+
+## Results
+We applied the algorithm on a subset of MEG data collected from 17 adults (aged 18-27 years) under an auditory task described in the papers. In short, during the task, the participants listened to `1 min` long segments from an audio-book recording of [The Legend of Sleepy Hollow by Washington Irving](https://librivox.org/the-legend-of-sleepy-hollow-by-washington-irving/), narrated by a male speaker. We consider localizing the TRFs using a total of `6 min` data from each participant. MNE-python 0.14 was used in pre-processing the raw data to automatically detect and discard flat channels, remove  extraneous artifacts, and to band-pass filter the data in the range `1 - 80 Hz`. The six `1 min` long data epochs were then down-sampled to `200 Hz`. As the stimulus variable, we used the speech envelope reflecting the momentary acoustic power, by averaging the auditory spectrogram representation (generated using a model of the 
+auditory periphery) across the frequency bands, sampled at `200 Hz`.  A volume source space for individual subjects was defined on a 3D regular grid with a resolution of `7 mm` in each direction. The lead-field matrix was then computed by placing free orientation virtual dipoles on the resulting `3322` grid points. The consistent components of our estimated `1 s`-long 3D TRFs across all `17` subjects looks like following:
+
+![Demo](https://user-images.githubusercontent.com/28169943/49410670-bf51c500-f733-11e8-9894-43880aa8d49e.gif)
+
+Isn't that cool? Do expect to see something like that with any other source localization method? If you realize you could use this method on your data, please feel free to use the codes. You can reach me at proloy@umd.edu if you have any issues with the codes. And don't forget to go over the papers/ posters before applying the algorithm. 
+
+## Versioning and releases
+The version is derived from git tags by [setuptools_scm](https://setuptools-scm.readthedocs.io); it is not stored in the source. A commit tagged `v0.5.0` builds as `0.5.0`; later commits build as a development version of the next release, e.g. `0.5.1.dev3+g1a2b3c4`. The installed version is available as `ncrf.__version__`.
+
+To release, [create a release on GitHub](https://github.com/Eelbrain/neuro-currentRF/releases/new) with a new tag of the form `v0.5.0`. Publishing the release creates the tag and triggers the `wheels` workflow, which builds and tests the sdist and wheel and publishes them to [PyPI](https://pypi.org/project/ncrf/). Clones need the tags for the version to resolve (`git fetch --tags`); `pip install -e .` must be re-run for `ncrf.__version__` to reflect new tags.
+
+The files involved:
+
+- `pyproject.toml`: declares the version as dynamic and enables setuptools_scm (`[tool.setuptools_scm]`), which computes it from git at build time.
+- `ncrf/__init__.py`: reads the version of the installed package from its metadata into `ncrf.__version__`.
+- `.git_archival.txt` and `.gitattributes`: let GitHub archive downloads (`.zip`/`.tar.gz`), which have no git history, still carry the tag information.
+- `.github/workflows/wheels.yml`: builds, tests and publishes the sdist and wheel; the other workflows check out the full history (`fetch-depth: 0`) so tags are available.
+- `docs/conf.py`: takes the documentation version from `ncrf.__version__`.
+
+## References
+[1] P. Das, C. Brodbeck, J. Z. Simon, B. Babadi, [Direct Cortical Localization of the MEG Auditory Temporal Response 
+Function: a Non-Convex Optimization Approach](https://isr.umd.edu/Labs/CSSL/simonlab/pubs/SFN2018.pdf); Proceedings 
+of the 47th Annual Neuroscience Meeting (SfN 2018), Nov. 2-7, San Diego, CA.
+
+[2] P. Das, C. Brodbeck, J. Z. Simon, B. Babadi, [Cortical Localization of the Auditory Temporal Response Function from 
+MEG via Non-Convex Optimization](https://isr.umd.edu/Labs/CSSL/simonlab/pubs/Asilomar2018.pdf); 2018 Asilomar Conference
+ on Signals, Systems, and Computers, Oct. 28–31, Pacific Grove, CA (invited)
+

ncrf-0.5/README.md

@@ -0,0 +1,76 @@
+# Build Status
+![test-posix](https://github.com/proloyd/neuro-currentRF/actions/workflows/test-posix.yml/badge.svg)
+
+![test-windows](https://github.com/proloyd/neuro-currentRF/actions/workflows/test-windows.yml/badge.svg)
+
+
+# NCRF   
+The magnetoencephalography (MEG) response to continuous auditory stimuli, such as speech, is commonly described using a linear filter, the auditory temporal response function (TRF). Though components of the sensor level TRFs have been well characterized, the cortical distributions of  the underlying neural responses are not well-understood. In our recent work, we provide a unified framework for determining the TRFs of neural sources directly from the MEG data, by integrating the TRF and distributed forward  source models into one, and casting the joint estimation task as a Bayesian optimization problem. Though the resulting  problem emerges as non-convex, we propose efficient solutions that leverage recent advances in evidence maximization. For more details please refer to [1], [2].
+
+This repository contains the implementation of our direct TRF estimation algorithm in Python.
+
+For code examples using real datasets, see the [Example gallery](https://eelbrain.github.io/neuro-currentRF/auto_examples/index.html).
+
+The optimization algorithm is configurable independently of the forward model.
+For a prepared `RegressionData` dataset, the lower-level API is:
+
+```python
+from ncrf import ChampLasso, NCRFEstimator
+
+estimator = NCRFEstimator.from_lead_field(lead_field, noise_covariance)
+solver = ChampLasso(mu='auto', n_iter=30, n_iterc=10, n_iterf=100)
+result = estimator.fit(data, solver)
+```
+
+All solvers return a common predictive `NCRF` in `result.model`; training explained variance
+is available as `result.scores['explained_variance']`. To score other data,
+`result.model.evaluate(data, [explained_variance, l2_error])` predicts once and
+returns all requested metrics. Solver-specific state is available as
+`result.solver_fit`.
+
+
+## How to use:
+run
+```python
+result = fit_ncrf(meg, stim, lead_field, noise_covariance, mu='auto', tstop=1.0, basis_stride=2, n_splits=3, scale='l1')
+```
+to perform a 3-fold cross-validation and then construct the model for 1s long TRF with the regularization weight among the given range that gives least generalization error. The signature of the ``meg`` and ``stim`` could be as follows:
+
+    [        megA (case, sensor, time),                       megB (case, sensor, time),               ...]
+    [[featA1 (case, time), featA2 (case, time), ...], [featB1 (case, time), featB2 (case, time), ...], ...]
+
+For more options, please look at the docstring. The learned TRF, `h` can be retrieved using:
+```python
+h = result.model.h
+```
+
+## Results
+We applied the algorithm on a subset of MEG data collected from 17 adults (aged 18-27 years) under an auditory task described in the papers. In short, during the task, the participants listened to `1 min` long segments from an audio-book recording of [The Legend of Sleepy Hollow by Washington Irving](https://librivox.org/the-legend-of-sleepy-hollow-by-washington-irving/), narrated by a male speaker. We consider localizing the TRFs using a total of `6 min` data from each participant. MNE-python 0.14 was used in pre-processing the raw data to automatically detect and discard flat channels, remove  extraneous artifacts, and to band-pass filter the data in the range `1 - 80 Hz`. The six `1 min` long data epochs were then down-sampled to `200 Hz`. As the stimulus variable, we used the speech envelope reflecting the momentary acoustic power, by averaging the auditory spectrogram representation (generated using a model of the 
+auditory periphery) across the frequency bands, sampled at `200 Hz`.  A volume source space for individual subjects was defined on a 3D regular grid with a resolution of `7 mm` in each direction. The lead-field matrix was then computed by placing free orientation virtual dipoles on the resulting `3322` grid points. The consistent components of our estimated `1 s`-long 3D TRFs across all `17` subjects looks like following:
+
+![Demo](https://user-images.githubusercontent.com/28169943/49410670-bf51c500-f733-11e8-9894-43880aa8d49e.gif)
+
+Isn't that cool? Do expect to see something like that with any other source localization method? If you realize you could use this method on your data, please feel free to use the codes. You can reach me at proloy@umd.edu if you have any issues with the codes. And don't forget to go over the papers/ posters before applying the algorithm. 
+
+## Versioning and releases
+The version is derived from git tags by [setuptools_scm](https://setuptools-scm.readthedocs.io); it is not stored in the source. A commit tagged `v0.5.0` builds as `0.5.0`; later commits build as a development version of the next release, e.g. `0.5.1.dev3+g1a2b3c4`. The installed version is available as `ncrf.__version__`.
+
+To release, [create a release on GitHub](https://github.com/Eelbrain/neuro-currentRF/releases/new) with a new tag of the form `v0.5.0`. Publishing the release creates the tag and triggers the `wheels` workflow, which builds and tests the sdist and wheel and publishes them to [PyPI](https://pypi.org/project/ncrf/). Clones need the tags for the version to resolve (`git fetch --tags`); `pip install -e .` must be re-run for `ncrf.__version__` to reflect new tags.
+
+The files involved:
+
+- `pyproject.toml`: declares the version as dynamic and enables setuptools_scm (`[tool.setuptools_scm]`), which computes it from git at build time.
+- `ncrf/__init__.py`: reads the version of the installed package from its metadata into `ncrf.__version__`.
+- `.git_archival.txt` and `.gitattributes`: let GitHub archive downloads (`.zip`/`.tar.gz`), which have no git history, still carry the tag information.
+- `.github/workflows/wheels.yml`: builds, tests and publishes the sdist and wheel; the other workflows check out the full history (`fetch-depth: 0`) so tags are available.
+- `docs/conf.py`: takes the documentation version from `ncrf.__version__`.
+
+## References
+[1] P. Das, C. Brodbeck, J. Z. Simon, B. Babadi, [Direct Cortical Localization of the MEG Auditory Temporal Response 
+Function: a Non-Convex Optimization Approach](https://isr.umd.edu/Labs/CSSL/simonlab/pubs/SFN2018.pdf); Proceedings 
+of the 47th Annual Neuroscience Meeting (SfN 2018), Nov. 2-7, San Diego, CA.
+
+[2] P. Das, C. Brodbeck, J. Z. Simon, B. Babadi, [Cortical Localization of the Auditory Temporal Response Function from 
+MEG via Non-Convex Optimization](https://isr.umd.edu/Labs/CSSL/simonlab/pubs/Asilomar2018.pdf); 2018 Asilomar Conference
+ on Signals, Systems, and Computers, Oct. 28–31, Pacific Grove, CA (invited)
+

ncrf-0.5/conftest.py

@@ -0,0 +1,14 @@
+import pytest
+
+_Dict = {'True': True, 'False': False}
+
+# decide on cross-validation test from command line
+def pytest_addoption(parser):
+    parser.addoption(
+        "--crossvalidation", action="store", default="False", help="run crossvalidation? True or False"
+    )
+
+
+@pytest.fixture
+def cmdopt(request):
+    return _Dict.get(request.config.getoption("--crossvalidation"), None)

ncrf-0.5/docs/Makefile

@@ -0,0 +1,36 @@
+# Minimal makefile for Sphinx documentation
+#
+
+SPHINXOPTS    ?= -nWT --keep-going
+SPHINXBUILD   ?= sphinx-build
+
+.PHONY: help Makefile clean html html-noplot linkcheck linkcheck-grep view
+
+first_target: help
+
+help:
+	@echo "Please use \`make <target>' where <target> is one of"
+	@echo "  html             to make standalone HTML files"
+	@echo "  html-noplot      to make standalone HTML files without plotting"
+	@echo "  clean            to clean HTML files"
+	@echo "  linkcheck        to check all external links for integrity"
+	@echo "  linkcheck-grep   to grep the linkcheck result"
+	@echo "  view             to view the built HTML"
+
+html:
+	$(SPHINXBUILD) . _build/html -b html $(SPHINXOPTS)
+
+html-noplot:
+	$(SPHINXBUILD) . _build/html -b html $(SPHINXOPTS) -D plot_gallery=0
+
+clean:
+	rm -rf _build generated
+
+linkcheck:
+	$(SPHINXBUILD) . _build/linkcheck -b linkcheck -D plot_gallery=0
+
+linkcheck-grep:
+	@! grep -h "^.*:.*: \[\(\(local\)\|\(broken\)\)\]" _build/linkcheck/output.txt
+
+view:
+	@python -c "import webbrowser; webbrowser.open_new_tab('file://$(PWD)/_build/html/index.html')"