Merge pull request #251 from rsagroup/cython

Cython port of core similarity computation

Author: HeikoSchuett

.github/workflows/pull_request.yml

@@ -1,28 +1,96 @@
-name: pull_request_tests
+name: pull_request_builds
 
 on:
   pull_request:
     types: [opened, synchronize, reopened]
 
 jobs:
+
   tests:
+    runs-on: ubuntu-22.04
+    steps:
+    - uses: actions/checkout@v3
+    - uses: actions/setup-python@v4
+      with:
+        python-version: '3.10'
+    - name: Python Version
+      run: python --version
+    - name: Update Pip
+      run: python -m pip install --upgrade pip
+    - name: Install dependencies
+      run: pip install -r requirements.txt
+    - name: Install rsatoolbox
+      run: pip install .
+    - name: Install test dependencies
+      run: pip install -r tests/requirements.txt
+    - name: Unit tests
+      run: pytest
 
-    runs-on: ubuntu-latest
+  source:
+    needs: tests
+    runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        python-version: [3.7, 3.8, 3.9]
-
+        python-version: ['3.7', '3.8', '3.9', '3.10']
+        os: [ubuntu-latest, macos-latest, windows-latest]
     steps:
-    - uses: actions/checkout@v2
-    - name: Setup Python
-      uses: actions/setup-python@v2
+    - uses: actions/checkout@v3
+    - uses: actions/setup-python@v4
       with:
         python-version: ${{ matrix.python-version }}
-    - name: Update pip
+    - name: Python Version
+      run: python --version
+    - name: Update Pip
       run: python -m pip install --upgrade pip
-    - name: Install dependencies
+    - name: Install Build
+      run: pip install build
+    - name: Build package
+      run: python -m build --sdist
+    - name: Install rsatoolbox (Linux, Mac)
+      run: pip install dist/*
+      if: matrix.os != 'windows-latest'
+    - name: Install rsatoolbox (Windows)
       run: |
-        pip install -r requirements.txt
-        pip install -r tests/requirements.txt
+        $sdistfname = Get-ChildItem dist -Name
+        pip install dist/$sdistfname
+      if: matrix.os == 'windows-latest'
+    - name: Install test dependencies
+      run: pip install -r tests/requirements.txt
     - name: Unit tests
-      run: pytest tests
+      run: pytest
+    - name: Store artifact
+      uses: actions/upload-artifact@v3
+      with:
+        name: source
+        path: dist/*
+        if-no-files-found: error
+        retention-days: 1
+
+  binaries:
+    needs: tests
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        os: [ubuntu-latest, macos-latest, windows-latest]
+    steps:
+    - uses: actions/checkout@v3
+    - uses: actions/setup-python@v4
+      with:
+        python-version: '3.10'
+    - name: Python Version
+      run: python --version
+    - name: Update Pip
+      run: python -m pip install --upgrade pip
+    - name: Build package
+      uses: pypa/[email protected]
+      with:
+        output-dir: dist
+    - name: Install test dependencies
+      run: pip install -r tests/requirements.txt
+    - name: Store artifact
+      uses: actions/upload-artifact@v3
+      with:
+        name: wheels-${{ matrix.os }}
+        path: dist/*.whl
+        if-no-files-found: error
+        retention-days: 1

.gitignore

@@ -1,5 +1,25 @@
+# Debug and profile files
+debug*.py
+*.Result
+
+# c files resulting from cython
+src/rsatoolbox/cengine/*.c
+src/rsatoolbox/cengine/*.html
+
+# data files from tutorials & demos
+cadena_ploscb_data.pkl
 fmri_data
-allendata
+demos/allendata
+
+# stats files
+stats/**/*.npz
+stats/**/*.hdf5
+stats/**/*.npy
+stats/**/*.txt
+stats/**/*.csv
+stats/boc
+stats/illustrations
+stats/figures
 
 # IDEs
 .vscode/
@@ -18,8 +38,10 @@ __pycache__/
 
 # C extensions
 *.so
+src/rsatoolbox/*.html
 
 # Distribution / packaging
+wheelhouse/
 .Python
 build/
 develop-eggs/

MANIFEST.in

@@ -1,2 +1,9 @@
-recursive-include rsatoolbox *.mplstyle
+recursive-include src/rsatoolbox *.mplstyle
 include requirements.txt
+include tests/requirements.txt
+recursive-exclude *.yml
+prune .github
+prune demos
+prune docs
+prune tests
+prune wiki

consistencytests.py

@@ -0,0 +1,64 @@
+from rsatoolbox.model import ModelInterpolate, ModelWeighted
+from rsatoolbox.model.fitter import fit_regress, fit_optimize_positive
+from rsatoolbox.rdm import concat, compare
+from rsatoolbox.data import Dataset
+from rsatoolbox.rdm import calc_rdm
+from rsatoolbox.rdm import concat
+import numpy as np
+
+
+
+rdms = []
+for _ in range(5):
+    data = np.random.rand(6, 20)
+    data_s = Dataset(data)
+    rdms.append(calc_rdm(data_s))
+rdms = concat(rdms)
+
+#def test_two_rdms_nan
+
+for i_method in ['corr_cov']: #['cosine', 'corr', 'cosine_cov', 'corr_cov']:
+
+    for i in range(200):
+        rdms = []
+        for _ in range(5):
+            data = np.random.rand(6, 20)
+            data_s = Dataset(data)
+            rdms.append(calc_rdm(data_s))
+        rdms = concat(rdms)
+        rdms = rdms.subsample_pattern('index', [0, 1, 1, 3, 4, 5])
+        model_rdms = concat([rdms[0], rdms[1]])
+        model_weighted = ModelWeighted(
+            'm_weighted',
+            model_rdms)
+        model_interpolate = ModelInterpolate(
+            'm_interpolate',
+            model_rdms)
+        # theta_m_i = model_interpolate.fit(rdms, method=i_method)
+        theta_m_w = model_weighted.fit(rdms, method=i_method)
+        # theta_m_w_pos = fit_optimize_positive(
+        #     model_weighted, rdms, method=i_method)
+        theta_m_w_linear = fit_regress(model_weighted, rdms, method=i_method)
+        # eval_m_i = np.mean(compare(model_weighted.predict_rdm(
+        #     theta_m_i), rdms, method=i_method))
+        eval_m_w = np.mean(compare(
+            model_weighted.predict_rdm(theta_m_w),
+            rdms,
+            method=i_method
+        ))
+        # eval_m_w_pos = np.mean(compare(model_weighted.predict_rdm(
+        #     theta_m_w_pos), rdms, method=i_method))
+        eval_m_w_linear = np.mean(compare(
+            model_weighted.predict_rdm(theta_m_w_linear),
+            rdms,
+            method=i_method
+        ))
+        #rdiff_wei_int = (eval_m_i - eval_m_w_pos) / eval_m_w_pos
+        rdiff_reg_opt = (eval_m_w - eval_m_w_linear) / eval_m_w_linear
+        assert np.all(theta_m_w > 0)
+        if np.all(theta_m_w > 0):
+            # does it only happen with negative theta?
+            assert abs(rdiff_reg_opt) < 0.002
+        # assert False
+        #assert abs(rdiff_reg_opt) < 0.02
+

docs/source/conf.py

@@ -26,7 +26,7 @@
 # The short X.Y version
 version = '0.0'
 # The full version, including alpha/beta/rc tags
-release = '0.0.4'
+release = '0.0.5'
 
 
 # -- General configuration ---------------------------------------------------

pyproject.toml

@@ -0,0 +1,54 @@
+[build-system]
+requires = [
+    "setuptools~=65.3",
+    "setuptools-scm",
+    "wheel",
+    "numpy>=1.21.2",
+    "scipy",
+    "cython~=3.0.0a11"
+]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "rsatoolbox"
+description = "Representational Similarity Analysis (RSA) in Python"
+requires-python = ">=3.7,<3.11"
+version = "0.0.5"
+authors = [
+    {name="rsatoolbox authors"},
+]
+keywords = ["neuroscience "]
+license = {file = "LICENSE"}
+classifiers = [
+      'Programming Language :: Python',
+      'License :: OSI Approved :: MIT License',
+      'Operating System :: OS Independent',
+      'Development Status :: 4 - Beta',
+      'Topic :: Scientific/Engineering',
+      'Intended Audience :: Science/Research',
+      'Programming Language :: Python :: 3.7',
+      'Programming Language :: Python :: 3.8',
+      'Programming Language :: Python :: 3.9',
+      'Programming Language :: Python :: 3.10',
+]
+dynamic = ["readme", "dependencies"]
+
+[tool.setuptools]
+packages = ["rsatoolbox"]
+package-dir = {"" = "src"}
+
+[tool.setuptools.dynamic]
+readme = {file = "README.md"}
+dependencies = {file = "requirements.txt"}
+
+[tool.pytest.ini_options]
+testpaths = [
+    "tests"
+]
+python_files = "*.py"
+
+[tool.cibuildwheel]
+test-requires = "pytest"
+test-command = "pytest {project}/tests"
+before-test = "pip install -r tests/requirements.txt"
+skip = ["*-win32", "*-manylinux_i686", "*-musllinux_*", "pp*"]

requirements.txt

@@ -7,5 +7,4 @@ tqdm
 h5py
 matplotlib
 joblib
-petname==2.2
 pandas

setup.py

@@ -1,42 +1,20 @@
-from setuptools import setup, find_packages
-
-requires = []
-with open('requirements.txt') as reqfile:
-    requires = reqfile.read().splitlines()
+from setuptools import setup, Extension
+from Cython.Build import build_ext ## missing dev time req
+from os.path import isfile
 
 test_requires = []
-with open('tests/requirements.txt') as reqfile:
-    test_requires = reqfile.read().splitlines()
-
-with open('README.md', encoding='utf-8') as readmefile:
-    long_description = readmefile.read()
-
+if isfile('tests/requirements.txt'):
+    with open('tests/requirements.txt') as reqfile:
+        test_requires = reqfile.read().splitlines()
 
 setup(
-    name='rsatoolbox',
-    version='0.0.4',
-    description='Representational Similarity Analysis (RSA) in Python',
-    url='https://github.com/rsagroup/rsatoolbox',
-    long_description=long_description,
-    long_description_content_type='text/markdown',
-    classifiers=[
-        'Programming Language :: Python',
-        'License :: OSI Approved :: MIT License',
-        'Operating System :: OS Independent',
-        'Development Status :: 4 - Beta',
-        'Topic :: Scientific/Engineering',
-        'Intended Audience :: Science/Research',
-        'Programming Language :: Python :: 3.7',
-        'Programming Language :: Python :: 3.8',
-        'Programming Language :: Python :: 3.9',
-    ],
-    author='rsatoolbox authors',
-    author_email='',
-    keywords='neuroscience ',
-    packages=find_packages(),
-    include_package_data=True,
-    zip_safe=False,
-    install_requires=requires,
     tests_require=test_requires,
     test_suite='tests',
+    url = "https://github.com/rsagroup/rsatoolbox",
+    zip_safe = False,
+    ext_modules = [
+        Extension(
+            "rsatoolbox.cengine.similarity",
+            ["src/rsatoolbox/cengine/similarity.pyx"])],
+    cmdclass={'build_ext': build_ext}
 )

rsatoolbox/__init__.py renamed to src/rsatoolbox/__init__.py

@@ -3,6 +3,7 @@
 """ Top level package: Only imports and organisation
 """
 
+from . import cengine
 from . import data
 from . import inference
 from . import model

src/rsatoolbox/cengine/__init__.pxd

@@ -0,0 +1 @@
+from .similarity cimport similarity

src/rsatoolbox/cengine/__init__.py

@@ -0,0 +1 @@
+from .similarity import similarity, calc_one