Merge pull request neurodatascience#21 from effigies/tests

TEST: Add tox and GitHub actions

.github/workflows/test.yml

@@ -0,0 +1,88 @@
+name: Build and test
+
+on:
+  push:
+    branches:
+      - main
+    tags:
+      - "*"
+  pull_request:
+    branches:
+      - main
+  # Run weekly to avoid missing deprecations during low activity
+  schedule:
+    - cron: '0 0 * * 1'
+  # Allow job to be triggered manually from GitHub interface
+  workflow_dispatch:
+
+defaults:
+  run:
+    shell: bash
+
+# Force tox and pytest to use color
+env:
+  FORCE_COLOR: true
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+permissions:
+  contents: read
+
+jobs:
+  test:
+    # Check each OS, all supported Python, minimum versions and latest releases
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        os: ['ubuntu-latest']
+        python-version: ["3.8", "3.9", "3.10", "3.11", "3.12"]
+        include:
+          # Basic dependencies only
+          - os: ubuntu-latest
+            python-version: 3.8
+            dependencies: 'min'
+
+    env:
+      DEPENDS: ${{ matrix.dependencies }}
+      ARCH: ${{ !contains(fromJSON('["none", "min"]'), matrix.dependencies) && matrix.architecture }}
+
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          submodules: recursive
+          fetch-depth: 0
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+          architecture: ${{ matrix.architecture }}
+          allow-prereleases: true
+      - name: Display Python version
+        run: python -c "import sys; print(sys.version)"
+      - name: Install tox
+        run: |
+          python -m pip install --upgrade pip
+          python -m pip install tox tox-gh-actions
+      - name: Show tox config
+        run: tox c
+      - name: Run tox
+        run: tox -v --exit-and-dump-after 1200
+
+  publish:
+    runs-on: ubuntu-latest
+    environment: "Package deployment"
+    needs: [test]
+    permissions:
+      # Required for trusted publishing
+      id-token: write
+    if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags/')
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          submodules: recursive
+          fetch-depth: 0
+      - run: pipx run build
+      - uses: pypa/gh-action-pypi-publish@release/v1

pydfc/data_loader.py

@@ -7,7 +7,7 @@
 """
 
 import numpy as np
-import hdf5storage
+import h5py
 import os
 
 from .dfc_utils import intersection, label2network
@@ -59,7 +59,7 @@ def load_from_array(subj_id2load=None, **params):
     returns a dictionary of TIME_SERIES objects
     each corresponding to a session
 
-    - if the file_name is a .mat file, it will be loaded using hdf5storage
+    - if the file_name is a .mat file, it will be loaded using h5py
       if the file_name is a .npy file, it will be loaded using np.load
 
     - the roi locations should be in the same folder and a .npy file
@@ -113,7 +113,8 @@ def load_from_array(subj_id2load=None, **params):
             # LOAD BOLD Data
 
             if params['file_name'][params['file_name'].find('.'):] == '.mat':
-                DATA = hdf5storage.loadmat(params['data_root']+subj_fldr+'/'+params['file_name'])
+                with h5py.File(params['data_root']+subj_fldr+'/'+params['file_name'], 'r') as f:
+                    DATA = {k: np.array(f[k]) for k in f.keys()}
             elif params['file_name'][params['file_name'].find('.'):] == '.npy':
                 DATA = np.load(params['data_root']+subj_fldr+'/'+params['file_name'], allow_pickle='True').item()
             time_series = DATA['ROI_data'] # time_series.shape = (time, roi)
@@ -347,4 +348,4 @@ def load_TS(
 
 
 
-####################################################################################################################################
+####################################################################################################################################

pyproject.toml

@@ -14,7 +14,7 @@ classifiers = [
             "Operating System :: Microsoft :: Windows", #change later
 ]
 dependencies = [
-            'hdf5storage', 
+            'h5py',
             'hmmlearn', 
             'ksvd', 
             'matplotlib', 
@@ -31,4 +31,7 @@ maintainers = [{name = "Mohammad Torabi", email = "mohammad.torabi@mail.mcgill.c
 name = "pydfc"
 readme = "README.rst"
 requires-python = ">=3.8"
-keywords = ['python', 'dFC package', 'neuroimaging']
+keywords = ['python', 'dFC package', 'neuroimaging']
+
+[project.optional-dependencies]
+test = ["pytest"]

tests/test_data_loader.py

@@ -0,0 +1,35 @@
+import pytest
+
+import nibabel as nb
+import numpy as np
+
+from pydfc.data_loader import nifti2timeseries
+
+
+# @pytest.fixture(scope="session")
+# def rest_file(tmp_path_factory):
+#     URL = "https://s3.amazonaws.com/openneuro.org/ds002785/derivatives/fmriprep/sub-0001/func/sub-0001_task-restingstate_acq-mb3_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz?versionId=UfCs4xtwIEPDgmb32qFbtMokl_jxLUKr"
+#     tmpdir = tmp_path_factory.mktemp("data")
+#     file_path = tmpdir / "sub-0001_task-restingstate_acq-mb3_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz"
+#     with httpx.stream("GET", URL) as response:
+#         with file_path.open("wb") as f:
+#             for chunk in response.iter_bytes():
+#                 f.write(chunk)
+#
+#     return file_path
+
+
+@pytest.fixture
+def simulated_bold_data(tmp_path):
+    img = nb.Nifti1Image(np.random.rand(10, 10, 10, 100), np.eye(4))
+    img.to_filename(tmp_path / "simulated_bold.nii.gz")
+    return tmp_path / "simulated_bold.nii.gz"
+
+
+def test_load(simulated_bold_data):
+    timeseries = nifti2timeseries(
+        nifti_file=str(simulated_bold_data),
+        n_rois=100,
+        Fs=1 / 0.75,
+        subj_id="sub-0001",
+    )

tox.ini

@@ -0,0 +1,76 @@
+# This file encodes a lot of our intended support range, as well as some
+# details about dependency availability.
+#
+# The majority of the information is contained in tox.envlist and testenv.deps.
+[tox]
+requires =
+  tox>=4
+envlist =
+  py3{8,9,10,11,12}
+  py38-min
+skip_missing_interpreters = true
+
+# Configuration that allows us to split tests across GitHub runners effectively
+[gh-actions]
+python =
+  3.8: py38
+  3.9: py39
+  3.10: py310
+  3.11: py311
+  3.12: py312
+
+[gh-actions:env]
+DEPENDS =
+  min: min
+
+[testenv]
+description = Pytest with coverage
+labels = test
+pass_env =
+  # getpass.getuser() sources for Windows:
+  LOGNAME
+  USER
+  LNAME
+  USERNAME
+  # Pass user color preferences through
+  PY_COLORS
+  FORCE_COLOR
+  NO_COLOR
+  CLICOLOR
+  CLICOLOR_FORCE
+extras = test
+
+commands =
+  pytest -sv tests
+
+[testenv:spellcheck]
+description = Check spelling
+labels = check
+deps =
+  codespell[toml]
+skip_install = true
+commands =
+  codespell . {posargs}
+
+[testenv:build{,-strict}]
+labels =
+  check
+  pre-release
+deps =
+  build
+  twine
+skip_install = true
+set_env =
+  build-strict: PYTHONWARNINGS=error
+commands =
+  python -m build
+  python -m twine check dist/*
+
+[testenv:publish]
+depends = build
+labels = release
+deps =
+  twine
+skip_install = true
+commands =
+  python -m twine upload dist/*