Merge 0c2544b into 7bb4a48

.github/workflows/python-deploy_to_pypi.yml

@@ -7,15 +7,17 @@ on:
 jobs:
   deploy:
     name: Build and publish to PyPI
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-22.04
     steps:
-    - uses: actions/checkout@v2
-    - name: Set up Python 3.7.6
-      uses: actions/setup-python@v2
+    - uses: actions/checkout@v3
       with:
-        python-version: 3.7.6
+        fetch-depth: 0
+    - name: Set up Python 3.9
+      uses: actions/setup-python@v4
+      with:
+        python-version: 3.9
     - name: Install pypa/build
-      run: pip install build
+      run: pip install build pbr wheel
     - name: Build a binary wheel and a source tarball
       run: python -m build --sdist --wheel --outdir dist/ .
     - name: Publish distribution to PyPI

.github/workflows/python-test.yml

@@ -12,39 +12,37 @@ on:
 jobs:
   pytest:
     name: Run PHOTONAI_neuro tests
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-22.04
 
     steps:
-      - uses: actions/checkout@v2
-      - name: Set up Python 3.7.6
-        uses: actions/setup-python@v2
+      - uses: actions/checkout@v3
+      - name: Set up Python 3.9
+        uses: actions/setup-python@v4
         with:
-          python-version: 3.7.6
+          python-version: 3.9
       - name: Install dependencies
         run: |
           pip install wheel flake8
-          python setup.py egg_info
-          pip install pytest pytest-cov coveralls -r photonai_neuro.egg-info/requires.txt
+          pip install pytest pytest-cov coveralls -r requirements.txt
       - name: Test with pytest
         run: |
-          PYTHONPATH=./ pytest ./test --cov=./photonai_neuro --tb=long
+          PYTHONPATH=./ pytest ./test --cov-report lcov:./coverage/lcov.info --cov=./photonai_neuro --tb=long
       - name: Coveralls
-        run: coveralls
-        env:
-          COVERALLS_REPO_TOKEN: ${{ secrets.COVERALLS_REPO_TOKEN }}
-          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        uses: coverallsapp/github-action@master
+        with:
+          github-token: ${{ secrets.GITHUB_TOKEN }}
 
   deploy:
     name: Build and publish to TestPyPI
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-22.04
     needs: pytest
     if: github.ref == 'refs/heads/master'
     steps:
-      - uses: actions/checkout@v2
-      - name: Set up Python 3.7.6
-        uses: actions/setup-python@v2
+      - uses: actions/checkout@v3
+      - name: Set up Python 3.9
+        uses: actions/setup-python@v4
         with:
-          python-version: 3.7.6
+          python-version: 3.9
       - name: Replace version number with commit hash
         run: |
           dt=$(date '+%Y.%m.%d.%H.%M.%S')

README.md

@@ -1,13 +1,18 @@
+[![PHOTONAI_neuro tests + TestPyPI deployment @master](https://github.com/wwu-mmll/photonai_neuro/actions/workflows/python-test.yml/badge.svg)](https://github.com/wwu-mmll/photonai_neuro/actions/workflows/python-test.yml)
+[![Coverage Status](https://coveralls.io/repos/github/wwu-mmll/photonai_neuro/badge.svg?branch=master)](https://coveralls.io/github/wwu-mmll/photonai_neuro?branch=master)
+[![Quality Gate Status](https://sonarcloud.io/api/project_badges/measure?project=wwu-mmll_photonai_neuro&metric=alert_status)](https://sonarcloud.io/summary/new_code?id=wwu-mmll_photonai_neuro)
+![GitHub](https://img.shields.io/github/license/wwu-mmll/photonai_neuro)
+[![Twitter URL](https://img.shields.io/twitter/url?style=social&url=https%3A%2F%2Ftwitter.com%2Fwwu_mmll)](https://twitter.com/wwu_mmll)
 # PHOTONAI Neuro
 PHOTONAI Neuro is an add-on module to simplify machine learning analyses for multimodal Magnetic Resonance Imaging (MRI) 
 with PHOTONAI.
 Overall, this module combines the functionality of the famous [Nilearn](https://nilearn.github.io) package
 with the pipeline structure of [PHOTONAI](https://photon-ai.com).
 
 ## Project setup
-Install the latest version directly from Github:
+Install the latest version directly via pip:
 ```
-pip install git+https://github.com/wwu-mmll/photonai_neuro
+pip install photonai-neuro
 ```
 
 ## Features

photonai_neuro/__init__.py

@@ -1,23 +1,39 @@
 import os
-from datetime import datetime
-
+from photonai.base import PhotonRegistry
 from photonai.photonlogger import logger
 
 from .util import register_photonai_neuro
-
-
-# REGISTRATION
-current_path = os.path.dirname(os.path.abspath(__file__))
-registered_file = os.path.join(current_path, "registered")
-logger.info("Checking Neuro Module Registration")
-if not os.path.isfile(registered_file):
-    logger.info("Registering Neuro Module")
-    register_photonai_neuro()
-    with open(os.path.join(registered_file), "w") as f:
-        f.write(str(datetime.now()))
+from .version import __version__
 
 from .atlas_mapper import AtlasMapper
 from .brain_mask import BrainMask
 from .brain_atlas import BrainAtlas
 from .atlas_library import AtlasLibrary
 from .neuro_branch import NeuroBranch
+
+
+# REGISTRATION
+def do_register(current_path, registered_file):  # pragma: no cover
+    reg = PhotonRegistry()
+    reg.add_module(os.path.join(current_path, "photonai_neuro.json"))
+    with open(os.path.join(registered_file), "w") as f:
+        f.write(str(__version__))
+
+
+def register():  # pragma: no cover
+    current_path = os.path.dirname(os.path.abspath(__file__))
+    registered_file = os.path.join(current_path, "registered")
+    logger.info("Checking Neuro Module Registration")
+    if not os.path.isfile(registered_file):  # pragma: no cover
+        logger.info("Registering Neuro Module")
+        do_register(current_path=current_path, registered_file=registered_file)
+    else:
+        with open(os.path.join(registered_file), "r") as f:
+            if f.read() == __version__:
+                logger.info("Current version already registered")
+            else:
+                logger.info("Updating Neuro Module")
+                do_register(current_path=current_path, registered_file=registered_file)
+
+
+register()

photonai_neuro/neuro_branch.py

@@ -49,6 +49,10 @@ def __iadd__(self, pipe_element: PipelineElement):
             self
 
         """
+        if pipe_element.name not in NeuroBranch.NEURO_ELEMENTS:
+            # reload
+            PhotonRegistry.ELEMENT_DICTIONARY = PhotonRegistry().get_package_info()
+            NeuroBranch.NEURO_ELEMENTS = PhotonRegistry().get_package_info(['photonai_neuro'])
         if pipe_element.name in NeuroBranch.NEURO_ELEMENTS:
             # as the neuro branch is parallelized and processes several images subsequently on
             # different cores, we need to stop the children to process on several cores as well

photonai_neuro/version.py

@@ -0,0 +1,3 @@
+from pbr.version import VersionInfo
+
+__version__ = VersionInfo('photonai_neuro').release_string()

requirements.txt

@@ -7,3 +7,4 @@ pandas
 photonai
 scikit-learn
 scikit-image
+pbr

setup.cfg

@@ -0,0 +1,24 @@
+[metadata]
+name = photonai_neuro
+description-file  =  README.md
+author = PHOTONAI Team
+author_email = hahnt@uni-muenster.de
+url = https://www.photon-ai.com/
+license = GPLv3
+long_description_content_type = text/markdown
+project_urls:
+    Source Code = https://github.com/wwu-mmll/photonai_neuro
+    Bug Tracker = https://github.com/wwu-mmll/photonai_neuro/issues
+download_url = https://pypi.org/project/photonai_neuro/#files
+keywords =
+    machine learning
+    neuroimaging
+    MRI
+classifiers =
+    License :: OSI Approved :: GNU General Public License v3 (GPLv3)
+    Topic :: Software Development :: Libraries :: Python Modules
+    Topic :: Scientific/Engineering :: Artificial Intelligence
+    Intended Audience :: Science/Research
+
+[files]
+package = photonai_neuro

setup.py

@@ -1,33 +1,5 @@
-try:
-    from setuptools import setup, find_packages
-except ImportError:
-    from ez_setup import use_setuptools
-    use_setuptools()
-    from setuptools import setup, find_packages
-
-
-__version__ = '0.1.0'
+from setuptools import setup
 
 setup(
-    name='photonai_neuro',
-    packages=find_packages(),
-    include_package_data=True,
-    version=__version__,
-    description="""
-PHOTONAI NEURO
-The Neuro Module enables loading and preprocessing neuroimaging data such as structural and 
-functional Magnetic Resonance Imaging (MRI) data. 
-In addition, it supports a range of advanced feature extraction and feature engineering as well as atlas-based analyses. 
-""",
-    author='PHOTONAI Team',
-    author_email='hahnt@wwu.de',
-    url='https://github.com/mmll-wwu/photonai_neuro.git',
-    download_url='https://github.com/wwu-mmll/photonai_neuro/archive/' + __version__ + '.tar.gz',
-    keywords=['machine learning', 'neuroimaging', 'MRI'],
-    classifiers=[],
-    install_requires=[
-        'photonai',
-        'nibabel',
-        'nilearn',
-        'scikit-image']
+    pbr=True
 )

test/test_atlas_mapper.py

@@ -32,11 +32,13 @@ def create_hyperpipe(self):
     @staticmethod
     def create_data():
         n_subjects = 20
-        dataset_files = fetch_oasis_vbm(n_subjects=n_subjects)
-        _ = dataset_files.ext_vars['age'].astype(float)
-        gender = dataset_files.ext_vars['mf'].astype(str)
-        y = np.array(gender)
-        X = np.array(dataset_files.gray_matter_maps)
+        y = [0]
+        while len(np.unique(y)) == 1:
+            dataset_files = fetch_oasis_vbm(n_subjects=n_subjects)
+            _ = dataset_files.ext_vars['age'].astype(float)
+            gender = dataset_files.ext_vars['mf'].astype(str)
+            y = np.array(gender)
+            X = np.array(dataset_files.gray_matter_maps)
         return X, y
 
     def test_fit_reload_all(self):