Update authorship and licence

.all-contributorsrc

@@ -29,6 +29,17 @@
         "infra"
       ]
     },
+    {
+      "login": "beccaclements99",
+      "name": "Becca Clements",
+      "avatar_url": "https://avatars.githubusercontent.com/u/95257798?v=4",
+      "profile": "https://github.com/beccaclements99",
+      "contributions": [
+        "bug",
+        "code",
+        "userTesting"
+      ]
+    },
     {
       "login": "avigotsky",
       "name": "Andrew Vigotsky",
@@ -38,6 +49,16 @@
         "code"
       ]
     },
+    {
+      "login": "ccomellalue",
+      "name": "ccomellalue",
+      "avatar_url": "https://avatars.githubusercontent.com/u/209748720?v=4",
+      "profile": "https://github.com/ccomellalue",
+      "contributions": [
+        "code",
+        "ideas"
+      ]
+    },
     {
       "login": "merelvdthiel",
       "name": "merelvdthiel",

CHANGELOG.md

@@ -1,3 +1,38 @@
+# 0.28.3 (Thu Mar 12 2026)
+
+:tada: This release contains work from a new contributor! :tada:
+
+Thank you, Becca Clements ([@beccaclements99](https://github.com/beccaclements99)), for all your work!
+
+#### 🐛 Bug Fix
+
+- Fix usage of previously computed lag maps to run a (new) lagged regression [#154](https://github.com/smoia/phys2cvr/pull/154) ([@beccaclements99](https://github.com/beccaclements99) [@pre-commit-ci[bot]](https://github.com/pre-commit-ci[bot]) [@smoia](https://github.com/smoia))
+- Give an error message if peaks are not provided AND comp_endtidal is True [#156](https://github.com/smoia/phys2cvr/pull/156) ([@beccaclements99](https://github.com/beccaclements99))
+
+#### ⚠️ Pushed to `master`
+
+- tests: Reorganise tests, remove or mark xfails the failing ones ([@smoia](https://github.com/smoia))
+- docs: update licenses ([@smoia](https://github.com/smoia))
+- docs: Fix logos ([@smoia](https://github.com/smoia))
+
+#### ⚠️ Tests
+
+- Fix workflow halting on missing peaks when they are not required (i.e. when skipping end-tidal convolution) [#153](https://github.com/smoia/phys2cvr/pull/153) ([@smoia](https://github.com/smoia) [@beccaclements99](https://github.com/beccaclements99) [@pre-commit-ci[bot]](https://github.com/pre-commit-ci[bot]))
+
+#### 🏠 Internal
+
+- [pre-commit.ci] pre-commit autoupdate [#152](https://github.com/smoia/phys2cvr/pull/152) ([@pre-commit-ci[bot]](https://github.com/pre-commit-ci[bot]))
+- Bump actions/checkout from 5 to 6 [#151](https://github.com/smoia/phys2cvr/pull/151) ([@dependabot[bot]](https://github.com/dependabot[bot]))
+
+#### Authors: 4
+
+- [@dependabot[bot]](https://github.com/dependabot[bot])
+- [@pre-commit-ci[bot]](https://github.com/pre-commit-ci[bot])
+- Becca Clements ([@beccaclements99](https://github.com/beccaclements99))
+- Stefano Moia ([@smoia](https://github.com/smoia))
+
+---
+
 # 0.28.2 (Wed Nov 19 2025)
 
 #### 🐛 Bug Fix

README.md

@@ -20,7 +20,7 @@ phys2cvr
 [![Supports python version](https://img.shields.io/pypi/pyversions/phys2cvr?style=shield&logo=python)](https://pypi.org/project/phys2cvr/)
 
 <!-- ALL-CONTRIBUTORS-BADGE:START - Do not remove or modify this section -->
-[![All Contributors](https://img.shields.io/badge/all_contributors-5-orange.svg?style=flat)](#contributors)
+[![All Contributors](https://img.shields.io/badge/all_contributors-7-orange.svg?style=flat)](#contributors)
 <!-- ALL-CONTRIBUTORS-BADGE:END -->
 
 A python-based tool to generate regressor for and/or estimate CVR maps and their lag.
@@ -92,7 +92,11 @@ Thanks goes to these wonderful people ([emoji key](https://allcontributors.org/d
     <tr>
       <td align="center" valign="top" width="20%"><a href="https://github.com/smoia"><img src="https://avatars3.githubusercontent.com/u/35300580?v=4?s=100" width="100px;" alt="Stefano Moia"/><br /><sub><b>Stefano Moia</b></sub></a><br /><a href="https://github.com/smoia/phys2cvr/commits?author=smoia" title="Code">💻</a> <a href="#ideas-smoia" title="Ideas, Planning, & Feedback">🤔</a> <a href="#infra-smoia" title="Infrastructure (Hosting, Build-Tools, etc)">🚇</a> <a href="#projectManagement-smoia" title="Project Management">📆</a></td>
       <td align="center" valign="top" width="20%"><a href="https://github.com/kristinazvolanek"><img src="https://avatars3.githubusercontent.com/u/54590158?v=4?s=100" width="100px;" alt="Kristina Zvolanek"/><br /><sub><b>Kristina Zvolanek</b></sub></a><br /><a href="https://github.com/smoia/phys2cvr/commits?author=kristinazvolanek" title="Code">💻</a> <a href="https://github.com/smoia/phys2cvr/issues?q=author%3Akristinazvolanek" title="Bug reports">🐛</a> <a href="#infra-kristinazvolanek" title="Infrastructure (Hosting, Build-Tools, etc)">🚇</a></td>
+      <td align="center" valign="top" width="20%"><a href="https://github.com/beccaclements99"><img src="https://avatars.githubusercontent.com/u/95257798?v=4?s=100" width="100px;" alt="Becca Clements"/><br /><sub><b>Becca Clements</b></sub></a><br /><a href="https://github.com/smoia/phys2cvr/issues?q=author%3Abeccaclements99" title="Bug reports">🐛</a> <a href="https://github.com/smoia/phys2cvr/commits?author=beccaclements99" title="Code">💻</a> <a href="#userTesting-beccaclements99" title="User Testing">📓</a></td>
       <td align="center" valign="top" width="20%"><a href="https://github.com/avigotsky"><img src="https://avatars.githubusercontent.com/u/904218?v=4?s=100" width="100px;" alt="Andrew Vigotsky"/><br /><sub><b>Andrew Vigotsky</b></sub></a><br /><a href="https://github.com/smoia/phys2cvr/commits?author=avigotsky" title="Code">💻</a></td>
+      <td align="center" valign="top" width="20%"><a href="https://github.com/ccomellalue"><img src="https://avatars.githubusercontent.com/u/209748720?v=4?s=100" width="100px;" alt="ccomellalue"/><br /><sub><b>ccomellalue</b></sub></a><br /><a href="https://github.com/smoia/phys2cvr/commits?author=ccomellalue" title="Code">💻</a> <a href="#ideas-ccomellalue" title="Ideas, Planning, & Feedback">🤔</a></td>
+    </tr>
+    <tr>
       <td align="center" valign="top" width="20%"><a href="https://github.com/merelvdthiel"><img src="https://avatars.githubusercontent.com/u/72999546?v=4?s=100" width="100px;" alt="merelvdthiel"/><br /><sub><b>merelvdthiel</b></sub></a><br /><a href="https://github.com/smoia/phys2cvr/commits?author=merelvdthiel" title="Documentation">📖</a></td>
       <td align="center" valign="top" width="20%"><a href="https://github.com/RazkinMalen"><img src="https://avatars.githubusercontent.com/u/147508933?v=4?s=100" width="100px;" alt="razkin"/><br /><sub><b>razkin</b></sub></a><br /><a href="#design-RazkinMalen" title="Design">🎨</a> <a href="https://github.com/smoia/phys2cvr/commits?author=RazkinMalen" title="Documentation">📖</a> <a href="https://github.com/smoia/phys2cvr/commits?author=RazkinMalen" title="Tests">⚠️</a></td>
     </tr>
@@ -108,7 +112,7 @@ Thanks goes to these wonderful people ([emoji key](https://allcontributors.org/d
 License
 -------
 
-Copyright 2021-2025, Stefano Moia & phys2cvr contributors.
+Copyright 2021-2026, Stefano Moia & phys2cvr contributors.
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.

phys2cvr/cli/run.py

@@ -701,7 +701,7 @@ def _check_opt_conf(parser):
 
 
 """
-Copyright 2021-2025, Stefano Moia & phys2cvr contributors.
+Copyright 2021-2026, Stefano Moia & phys2cvr contributors.
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.

phys2cvr/io.py

@@ -119,6 +119,7 @@ def load_txt(fname, shape=None):
         '.txt': ' ',
         '.1d': ' ',
         '.par': ' ',
+        '': ' ',
     }
 
     mtx = np.genfromtxt(fname, delimiter=delimiter_map.get(ext))
@@ -235,10 +236,11 @@ def load_array(fname, shape=''):
     """
     _, _, ext = utils.check_ext(EXT_ARRAY, fname, scan=True, remove=True)
 
-    if ext.lower() in EXT_1D:
-        return load_txt(fname, shape=shape)
-    if ext.lower() in EXT_MAT:
-        return load_mat(fname, shape=shape)
+    if ext:
+        if ext.lower() in EXT_1D:
+            return load_txt(fname, shape=shape)
+        if ext.lower() in EXT_MAT:
+            return load_mat(fname, shape=shape)
 
     raise NotImplementedError(
         f'{fname} file extension {ext} was not found or is not supported yet'
@@ -268,7 +270,7 @@ def load_physio(fname):
 
 
 def export_regressor(
-    regressors_matrix, ntp, outname, suffix='petco2hrf', ext='.1D', axis=-1
+    regressors_matrix, ntp, outprefix, suffix='petco2hrf', ext='.1D', axis=-1
 ):
     """
     Export generated regressors for fMRI analysis.
@@ -279,7 +281,7 @@ def export_regressor(
         The regressors that needs to be exported, in its original sample
     ntp : int
         The number of fMRI timepoints
-    outname : str or path
+    outprefix : str or path
         Prefix of the output file - can contain a path.
     suffix : str, optional
         The suffix of the output file.
@@ -301,7 +303,7 @@ def export_regressor(
     regressors_demeaned = regressors_matrix - regressors_matrix.mean(
         axis=axis, keepdims=True
     )
-    np.savetxt(f'{outname}_{suffix}{ext}', regressors_demeaned, fmt='%.6f')
+    np.savetxt(f'{outprefix}_{suffix}{ext}', regressors_demeaned, fmt='%.6f')
     return regressors_demeaned
 
 
@@ -324,7 +326,7 @@ def export_nifti(data, img, fname):
 
 
 """
-Copyright 2021-2025, Stefano Moia & phys2cvr contributors.
+Copyright 2021-2026, Stefano Moia & phys2cvr contributors.
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.

phys2cvr/regressors.py

@@ -100,7 +100,7 @@ def compute_petco2hrf(
             'Arrays with more than 2 dimensions are not supported.'
         )
 
-    if comp_endtidal:
+    if comp_endtidal and pidx is not None:
         petco2 = endtidal_interpolation(co2, pidx, axis=-1)
 
         # Plot PetCO2 vs CO2
@@ -111,6 +111,10 @@ def compute_petco2hrf(
         # Demean and export
         petco2 = petco2 - petco2.mean()
         np.savetxt(f'{outprefix}_petco2.1D', petco2, fmt='%.18f')
+    elif comp_endtidal and pidx is None:
+        raise ValueError(
+            'End-tidal interpolation was requested, but peaks were not provided.'
+        )
     else:
         LGR.info(
             'Skipping End Tidal interpolation of PetCO2 trace (if you provided raw CO2 '
@@ -412,7 +416,7 @@ def create_physio_regressor(
 
 
 """
-Copyright 2021-2025, Stefano Moia & phys2cvr contributors.
+Copyright 2021-2026, Stefano Moia & phys2cvr contributors.
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.

phys2cvr/signal.py

@@ -70,7 +70,7 @@ def create_hrf(freq=40):
     u = np.arange(0, p[6] / dt + 1, 1) - p[5] / dt
 
     a1 = p[0] / p[2]
-    b1 = 1 / p[3]
+    b1 = 1 / p[2]
     a2 = p[1] / p[3]
     b2 = 1 / p[3]
 
@@ -325,7 +325,7 @@ def resample_signal_freqs(ts, freq1, freq2, axis=-1):
 
 
 """
-Copyright 2021-2025, Stefano Moia & phys2cvr contributors.
+Copyright 2021-2026, Stefano Moia & phys2cvr contributors.
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.

phys2cvr/stats.py

@@ -365,7 +365,7 @@ def regression(
 
 
 """
-Copyright 2021-2025, Stefano Moia & phys2cvr contributors.
+Copyright 2021-2026, Stefano Moia & phys2cvr contributors.
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.

phys2cvr/tests/test_io.py

@@ -2,9 +2,14 @@
 """Tests for io."""
 
 import os
+import sys
 
 import nibabel as nib
 import numpy as np
+import peakdet as pk
+import pymatreader
+import pytest
+from scipy.io import savemat
 
 from phys2cvr import io
 
@@ -27,8 +32,78 @@ def test_load_nifti_get_mask(nifti_data, nifti_mask):
     assert isinstance(img, nib.nifti1.Nifti1Image)
 
 
+@pytest.mark.parametrize(
+    'extension, delimiter',
+    [
+        ['.csv', ','],
+        ['.csv.gz', ','],
+        ['.tsv', '\t'],
+        ['.tsv.gz', '\t'],
+        ['.txt', ' '],
+        ['.1d', ' '],
+        ['.par', ' '],
+        ['', ' '],
+    ],
+)
+def test_load_txt(extension, delimiter, testdir):
+    """Test load_txt."""
+    a = np.random.randn(5)
+    n = os.join.path(testdir, f'zoe{extension}')
+    np.savetxt(n, a, delimiter=delimiter)
+    b = io.load_txt(n)
+
+    assert (a == b).all()
+    os.remove(n)
+
+
+def test_load_mat():
+    """Test load_mat."""
+    a = np.random.randn(5)
+    b = 'likealeaf'
+    n = 'inthewind'
+
+    savemat(n, {'data': a, 'other': b})
+
+    c = io.load_mat(n)
+
+    assert (a == c).all()
+    os.remove(n)
+
+
+def test_load_array():
+    """Test load_mat."""
+    a = np.random.randn(5)
+    b = 'likealeaf'
+    n = 'inthewind.mat'
+    m = 'zoe.txt'
+    np.savetxt(m, a)
+
+    savemat(n, {'data': a, 'other': b})
+
+    d = io.load_array(n)
+    e = io.load_array(m)
+
+    assert (a == d).all()
+    assert (a == e).all()
+    os.remove(n)
+    os.remove(m)
+
+
+def test_load_physio():
+    d = pk.Physio(np.random.randn(40), fs=10)
+    d = pk.peakfind_physio(d)
+    n = 'kaylee.phys'
+    pk.save_physio(n, d)
+    p = io.load_physio(n)
+
+    assert (p[0] == d.data).all()
+    assert (p[1] == d.peaks).all()
+    assert p[2] == 10
+    os.remove(n)
+
+
 def test_export_regressor(testdir):
-    petco2hrf_shift = np.random.rand(10)
+    petco2hrf_shift = np.random.randn(10)
     ntp = 10
     outname = os.path.join(testdir, 'test_regressor')
     suffix = 'petco2hrf'
@@ -49,7 +124,7 @@ def test_export_regressor(testdir):
 
 def test_export_nifti(testdir):
     # create some test data
-    data = np.random.rand(10, 10, 10)
+    data = np.random.randn(10, 10, 10)
     affine = np.eye(4)
     header = nib.Nifti1Header()
     img = nib.Nifti1Image(data, affine, header)
@@ -66,8 +141,39 @@ def test_export_nifti(testdir):
     assert np.allclose(out_img.get_fdata(), data, atol=1e-6, rtol=0)
     assert np.allclose(out_img.affine, affine, atol=1e-6, rtol=0)
     assert out_img.header.__dict__.keys() == header.__dict__.keys()
+    os.remove(fname)
     # Eventually check that headers have the same content (although they don't now
     # for good reasons!)
 
 
 # ## Break tests
+def test_break_load_mat():
+    """Break load_mat."""
+    sys.modules['pymatreader'] = None
+    with pytest.raises(ImportError) as errorinfo:
+        io.load_mat('simon')
+    assert 'is required' in str(errorinfo.value)
+    sys.modules['pymatreader'] = pymatreader
+
+    a = 'heart'
+    n = 'ofgold'
+    savemat(n, {'data': a})
+
+    with pytest.raises(EOFError) as errorinfo:
+        io.load_mat(n)
+    assert f'{n} does not seem' in str(errorinfo.value)
+    os.remove(n)
+
+
+def test_break_load_xls():
+    """Break load_xls."""
+    with pytest.raises(NotImplementedError) as errorinfo:
+        io.load_xls('firefly')
+    assert 'loading is not' in str(errorinfo.value)
+
+
+def test_break_load_array():
+    """Break load_xls."""
+    with pytest.raises(NotImplementedError) as errorinfo:
+        io.load_array('firefly.leaf')
+    assert 'file extension' in str(errorinfo.value)