Merge pull request #225 from pycroscopy/fitter_refactored

Fitter refactored, and the TODO items have all been done, although generation of a fit dataset is to be done externally for now using the internal reconstruct_function() method - simply use this with the existing metadata on a fit object to derive the fitted dataset. Still need to make a notebook to show how to use all of the features of the new fitter class.

Author: ramav87

.github/workflows/actions.yml

@@ -34,6 +34,8 @@ jobs:
         sudo apt-get update -qq
         python -m pip install --upgrade pip
         python -m pip install flake8 pytest coveralls
+        python -m pip install ".[test]"
+        python -m pip show SciFiReaders
         if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
         
     - name: install package

extras_require.txt

@@ -1 +1,4 @@
-mpi4py
+extras_require={
+    'MPI': ["mpi4py"],
+    'test': ["pytest", "pytest-cov", "SciFiReaders"],
+},

setup.cfg

@@ -10,4 +10,10 @@ universal=1
 test=pytest
 
 [tool:pytest]
-testpaths = tests docs
+testpaths = tests docs
+
+[options.extras_require]
+test =
+    pytest
+    pytest-cov
+    SciFiReaders

setup.py

@@ -15,6 +15,7 @@
                 'toolz',  # dask installation failing without this
                 'cytoolz',  # dask installation failing without this
                 'dask',
+                'dask-ml',
                 'h5py>=2.6.0',
                 'matplotlib>=2.0.0',
                 'distributed>=2.0.0',
@@ -60,7 +61,7 @@
     author_email='pycroscopy@gmail.com',
     install_requires=requirements,
 
-    tests_require=['pytest'],
+    tests_require=['pytest', 'SciFiReaders'],
     platforms=['Linux', 'Mac OSX', 'Windows 11/10'],
     # package_data={'sample':['dataset_1.dat']}
     test_suite='pytest',
@@ -69,7 +70,7 @@
     include_package_data=True,
     # https://setuptools.readthedocs.io/en/latest/setuptools.html#declaring-dependencies
     extras_require={
-        'MPI': ["mpi4py"]
+        'MPI': ["mpi4py"], 'test': ["pytest", "pytest-cov", "SciFiReaders"]
     },
     # If there are data files included in your packages that need to be
     # installed, specify them here.  If using Python 2.6 or less, then these

sidpy/proc/__init__.py

@@ -3,5 +3,6 @@
 """
 
 from . import fitter
+from . import fitter_refactor
 
-__all__ = ['fitter']
+__all__ = ['fitter', 'fitter_refactor']