Release 0.9

.github/workflows/test.yml

@@ -20,89 +20,47 @@ on:
 jobs:
   build-linux:
     runs-on: ubuntu-latest
+    defaults:
+      run:
+        shell: bash -el {0}
     strategy:
       max-parallel: 10
       fail-fast: false
       matrix:
         python-version:
-          - "3.8"
           - "3.9"
           - "3.10"
           - "3.11"
           - "3.12"
+          - "3.13"
         conda-env:
           - "core"
           - "full"
     name: Python ${{ matrix.python-version }} and ${{ matrix.conda-env }} dependencies
     steps:
     - name: Checkout
       uses: actions/checkout@v4
-    - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v5
+    - uses: conda-incubator/setup-miniconda@v3
       with:
-        python-version:  ${{ matrix.python-version }}
-    - name: Add conda to system path
-      run: |
-        # $CONDA is an environment variable pointing to the root of the miniconda directory
-        echo $CONDA/bin >> $GITHUB_PATH
-        conda --version
-        conda info
-    - name: Make sure conda is updated
-      run: |
-        conda update conda
-        conda --version
+        auto-update-conda: true
+        auto-activate-base: false
+        conda-remove-defaults: true
+        channels: conda-forge
+        activate-environment: ptypy_env
+        python-version: ${{ matrix.python-version }}
+        miniforge-version: latest
     - name: Install ${{ matrix.conda-env }} dependencies
       run: |
-        # replace python version in dependencies
         sed -i 's/python/python=${{ matrix.python-version }}/' dependencies_${{ matrix.conda-env }}.yml
-        if [ ${{ matrix.conda-env }} == 'full' ] && [ ${{ matrix.python-version }} == '3.12' ]; then
-          sed -i '/- pyfftw/d' dependencies_${{ matrix.conda-env }}.yml
-        fi
-        # if [ ${{ matrix.conda-env }} == 'full' ] && [ ${{ matrix.python-version }} == '3.8' ]; then
-        #   sed -i '/- mpi4py/d' dependencies_${{ matrix.conda-env }}.yml
-        # fi
-        # if [ ${{ matrix.conda-env }} == 'full' ] && [ ${{ matrix.python-version }} == '3.9' ]; then
-        #   sed -i '/- mpi4py/d' dependencies_${{ matrix.conda-env }}.yml
-        # fi
-        conda install --solver=classic mpich
-        conda env update --file dependencies_${{ matrix.conda-env }}.yml --name base
-        conda install --solver=classic flake8 pytest pytest-cov
-        conda list	
+        conda install -c conda-forge mpich
+        conda env update --file dependencies_${{ matrix.conda-env }}.yml --name ptypy_env
+        conda install -c conda-forge flake8 pytest pytest-cov
+        conda list
     - name: Prepare ptypy
-      run: |
-        # Install ptypy
-        pip install .
+      run: pip install .
     - name: Lint with flake8
       run: |
         # stop the build if there are Python syntax errors or undefined names
-        flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
-        # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
-        # flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
+        flake8 . --count --select=E9,F63,F7,F82 --ignore=F824 --show-source --statistics
     - name: Test with pytest
-      run: |
-        # pytest ptypy/test -v --doctest-modules --junitxml=junit/test-results.xml --cov=ptypy --cov-report=xml --cov-report=html --cov-config=.coveragerc
-        pytest -v
-#    - name: cobertura-report
-#      if: github.event_name == 'pull_request' && (github.event.action == 'opened' || github.event.action == 'reopened' || github.event.action == 'synchronize')
-#      uses: 5monkeys/cobertura-action@v7
-#      with:
-#        # The GITHUB_TOKEN for this repo
-#        repo_token:  ${{ secrets.GITHUB_TOKEN }}
-#        # Path to the cobertura file.
-#        path: coverage.xml
-#        # If files with 100% should be skipped from report.
-#        skip_covered: true
-#        # Minimum allowed coverage percentage as an integer.
-#        minimum_coverage: 90
-#        only_changed_files: true
-#    - name: Junit Report to Annotations
-#      uses: ashley-taylor/junit-report-annotations-action@master
-#      with:
-#        # github token
-#        access-token: ${{ secrets.GITHUB_TOKEN }}
-#        # glob to junit xml files
-#        path: junit/test-results.xml
-#        # include summary annotation
-#        includeSummary: true
-#        # max number of failed tests to include
-#        numFailures: 10
+      run: pytest -v

cufft/extensions.py

@@ -4,8 +4,8 @@
 import os, re
 import subprocess
 import sysconfig
-from distutils.unixccompiler import UnixCCompiler
-from distutils.command.build_ext import build_ext
+from setuptools._distutils.unixccompiler import UnixCCompiler
+from setuptools.command.build_ext import build_ext
 
 
 def find_in_path(name, path):
@@ -116,6 +116,7 @@ def _compile(self, obj, src, ext, cc_args, extra_postargs, pp_opts):
         compiler_command = [self.CUDA["nvcc"]] + self.NVCC_FLAGS + self.OPTFLAGS + ["-Xcompiler"] + self.CXXFLAGS + CPPFLAGS
         compiler_exec = " ".join(compiler_command)
         self.set_executable('compiler_so', compiler_exec)
+        self.set_executable('compiler_so_cxx', compiler_exec)
         postargs = [] # we don't actually have any postargs
         super(NvccCompiler, self)._compile(obj, src, ext, cc_args, postargs, pp_opts) # the _compile method
         # reset the default compiler_so, which we might have changed for cuda

cufft/setup.py

@@ -2,7 +2,7 @@
 
 # we should aim to remove the distutils dependency
 import setuptools
-from distutils.core import setup, Extension
+from setuptools import setup, Extension
 import os
 
 ext_modules = []

dependencies_dev.yml

@@ -10,6 +10,7 @@ dependencies:
   - pyzmq
   - pep8
   - mpi4py
+  - packaging
   - pillow
   - pyfftw
   - pip

dependencies_full.yml

@@ -9,6 +9,7 @@ dependencies:
   - h5py
   - pyzmq
   - mpi4py
+  - packaging
   - pillow
   - pyfftw
   - pyyaml

doc/script2rst.py

@@ -1,5 +1,6 @@
 import sys
 import io
+from importlib.resources import files
 import contextlib
 import os
 
@@ -9,13 +10,12 @@
            'simupod.py',
            'ownengine.py',
            'subclassptyscan.py']
+_ptypy_dir = files('ptypy')
 
 if len(sys.argv) == 1:
-    import pkg_resources
-
     for script in scripts:
-        scr = pkg_resources.resource_filename('ptypy', tutorial_dir+script)
-        if not os.path.exists(scr):
+        scr = _ptypy_dir / (tutorial_dir + script)
+        if not scr.exists():
             print('Using backup tutorial for %s' % script)
             scr = '../tutorial/'+script
         #subprocess.call(['python',sys.argv[0]+' '+scr]) # doesn't work
@@ -50,13 +50,13 @@ def stdoutIO(stdout=None):
 frst.write("""
 .. note::
    This tutorial was generated from the python source
-   :file:`[ptypy_root]/tutorial/%(fname)s` using :file:`ptypy/doc/%(this)s`. 
+   :file:`[ptypy_root]/tutorial/%(fname)s` using :file:`ptypy/doc/%(this)s`.
    You are encouraged to modify the parameters and rerun the tutorial with::
-   
+
      $ python [ptypy_root]/tutorial/%(fname)s
 
 """ % {'fname': os.path.split(script_name)[-1], 'this': sys.argv[0]})
- 
+
 was_comment = True
 
 while True:
@@ -86,7 +86,7 @@ def stdoutIO(stdout=None):
             frst.write('   '+line2[1:].strip()+'\n')
         frst.write('\n')
         continue
-        
+
     if line.startswith('"""'):
         frst.write('.. parsed-literal::\n\n')
         while True:
@@ -95,11 +95,11 @@ def stdoutIO(stdout=None):
                 break
             frst.write('   ' + line2)
         continue
-    
+
     decorator = False
     indent = False
     for key in indent_keys:
-        if line.startswith(key): 
+        if line.startswith(key):
             indent = True
             break
 
@@ -125,12 +125,12 @@ def stdoutIO(stdout=None):
             pt = fpy.tell()
         exec(func+'\n')
         continue
-        
+
     wline = line.strip()
     if not wline:
         frst.write('\n')
         continue
-    
+
     with stdoutIO() as sout:
         exec(wline)
         out = sout.getvalue()
@@ -150,15 +150,15 @@ def stdoutIO(stdout=None):
             if was_comment:
                 wline = '\n::\n\n'+wline
                 was_comment = False
-                
+
             frst.write(wline+'\n')
-        
+
         #print out
         if out.strip():
             print(out)
             for l in out.split('\n'):
                 frst.write(' '*3+l+'\n')
             out = ''
 
-    
+
 

ptypy/accelerate/base/array_utils.py

@@ -70,14 +70,20 @@ def complex_gaussian_filter(input, mfs):
     '''
     takes 2D and 3D arrays. Complex input, complex output. mfs has len 0<x<=2
     '''
-    if len(mfs) > 2:
+    if isinstance(mfs, list) and len(mfs) > 2:
         raise NotImplementedError("Only batches of 2D arrays allowed!")
+    if isinstance(mfs, (int, float)):
+        mfs_list = [mfs, mfs]
+        if input.ndim == 3:
+            mfs_list = [0, mfs, mfs]
+    elif isinstance(mfs, (list,tuple)):
+        mfs_list = list(mfs)
+        if input.ndim == 3:
+            mfs_list.insert(0,0)
+    else:
+        raise NotImplementedError(f"Cannot interpret mfs of type {type(mfs)}")
 
-    if input.ndim == 3:
-        mfs = np.insert(mfs, 0, 0)
-
-    return (ndi.gaussian_filter(np.real(input), mfs) + 1j * ndi.gaussian_filter(np.imag(input), mfs)).astype(
-        input.dtype)
+    return (ndi.gaussian_filter(np.real(input), mfs_list).astype(input.dtype) + 1j * ndi.gaussian_filter(np.imag(input), mfs_list))
 
 
 def complex_gaussian_filter_fft(input, mfs):