PR for 0.3.10

.github/workflows/tests.yml

@@ -28,11 +28,11 @@ jobs:
 
       - name: Install dependencies
         run: |
-          pip install manifix
+          pip install check-manifest
 
       - name: Check MANIFEST.in file
         run: |
-          python setup.py manifix
+          check-manifest
 
   tests:
     name: ${{ matrix.os }}-py${{ matrix.python-version }}${{ matrix.LABEL }}
@@ -42,10 +42,10 @@ jobs:
       fail-fast: false
       matrix:
         os: [ubuntu-latest, macos-latest, windows-latest]
-        python-version: ['3.10', '3.11', '3.12']
+        python-version: ['3.11', '3.12', '3.13']
         include:
           - os: ubuntu-latest
-            python-version: 3.10
+            python-version: '3.10'
             DEPENDENCIES: matplotlib==3.8 numba==0.56.4 pyopencl==2023.1.2
             LABEL: -oldest
     steps:
@@ -67,13 +67,15 @@ jobs:
           pip install ${{ matrix.DEPENDENCIES }}
 
       - name: Install support for multiprocessing and GPU support
-        if: ${{ matrix.os == 'ubuntu-latest' || matrix.os == 'macos-latest' }}
+        if: ${{ matrix.os == 'ubuntu-latest'}} # || matrix.os == 'macos-latest' }}
+        # GitHub RAM limits for macOS are not working properly with Ray > 0.53
+        # I hope to reverse this sometime in the future.
+
         # The second line is redundant but added for testing of pip
         # selectors
         run: |
           pip install -U -e .'[gpu,parallel]'
           pip install -U -e .'[all]'
-
       - name: Display versions of Python, pip and packages
         run: |
           python -V

CHANGELOG.rst

@@ -5,6 +5,24 @@ Changelog
 All notable changes to PyEBSDIndex will be documented in this file. The format is based
 on `Keep a Changelog <https://keepachangelog.com/en/1.1.0>`_.
 
+0.3.10 (2026-05-11)
+==================
+ Added
+-----
+
+Changed
+-------
+- Updated CPU band detection to use more numba-based multi threading.
+- Changed default values for ``ebsd_index.index_pats_distributed()`` for using CPU only indexing.
+- Converted the project from ``setup.py`` to ``pyproject.toml`` and build backend now is hatchling.
+- Package version now located in __version.py to avoid issues with building with hatchling.
+
+
+Fixed
+-----
+- Removed multiprocess (with Ray) testing for macOS on GitHub due to hitting RAM limits. Unclear as to root cause.
+  This was the former root cause of tests failing with Ray versions ``>0.53.1``; however these versions of Ray work
+  perfectly well on local machines.
 
 0.3.9.2 (2026-03-06)
 ==================
@@ -179,7 +197,7 @@ Changed
 
 Removed
 -------
-- Removed ``band_vote`` modual as that is now wrapped into triplevote.
+- Removed ``band_vote`` module as that is now wrapped into triplevote.
 
 Fixed
 -----

README.md

@@ -28,5 +28,5 @@ and contributing guide is available at https://pyebsdindex.readthedocs.io.
 
 ## Installation
 
-See [the documentation](https://pyebsdindex.readthedocs.io/en/stable/installation.html)
+See [the documentation](https://pyebsdindex.readthedocs.io/en/stable/index.html)
 for installation instructions.

RELEASE.rst

@@ -7,7 +7,7 @@ Preparation
 -----------
 - Review the contributor list ``__credits__`` in ``pyebsdindex/__init__.py`` to ensure
   all contributors are included and sorted correctly.
-- Bump ``__version__`` in ``pyebsdindex/__init__.py``, for example to "0.4.2".
+- Bump ``__version__`` in ``pyebsdindex/__version.py``, for example to "0.4.2".
 - Update the changelog ``CHANGELOG.rst``.
 - Let the PR collect comments for a day to ensure that other maintainers are
   comfortable with releasing. Merge.
@@ -25,6 +25,6 @@ Post-release action
 - Monitor the `documentation build
   <https://readthedocs.org/projects/pyebsdindex/builds>`_ to ensure that the new stable
   documentation is successfully built from the release.
-- Make a post-release PR to ``main`` with ``__version__`` in ``__init__.py`` updated (or reverted),
+- Make a post-release PR to ``main`` with ``__version__`` in ``__version.py`` updated (or reverted),
   and in ``CHANGELOG.rst`` e.g. to "0.4.dev0", and any updates to this guide if necessary
 - Tidy up GitHub issues.

pyebsdindex/__init__.py

@@ -1,3 +1,5 @@
+from pyebsdindex.__version import __version__
+
 __author__ = "Dave Rowenhorst"
 __author_email__ = ""
 # Initial committer first, then sorted by line contributions
@@ -7,7 +9,6 @@
 ]
 __description__ = "Python based tool for Radon based EBSD indexing"
 __name__ = "pyebsdindex"
-__version__ = "0.3.9.2"
 
 
 # Try to import only once - also will perform check that at least one GPU is found.

pyebsdindex/__version.py

@@ -0,0 +1 @@
+__version__ = "0.3.9.2"

pyebsdindex/_ebsd_index_parallel.py

@@ -321,7 +321,7 @@ def index_pats_distributed(
             #ncpu = max(1,min(os.cpu_count(), int(len(indexer.phaseLib)*16)))
             # this is a heuristic, and may be highly dependent on hardware
         else:
-            ncpu = max(1,os.cpu_count()//4)
+            ncpu = min(4,os.cpu_count())#max(1,os.cpu_count()//4)
     if ncpu != -1:
         n_cpu_nodes = int(ncpu)
 
@@ -361,7 +361,7 @@ def index_pats_distributed(
         ncpucpu_per_worker = 0.5 - 1.0e-3
         ncpugpu_per_wrker = 0.5 - 1.0e-3
         if chunksize <= 0:
-            chunksize = 1000
+            chunksize = 256
     ncpuwrker = n_cpu_nodes
 
     PCpat = indexer._fillPCarray(PC, npats)

pyebsdindex/_ebsd_index_single.py

@@ -50,6 +50,7 @@
 else:
     from pyebsdindex import band_detect as band_detect
 
+from pyebsdindex import gnomonic_correction
 
 RADEG = 180.0 / np.pi
 
@@ -80,6 +81,7 @@ def index_pats(
     verbose=0,
     chunksize=528,
     gpu_id=None,
+    useCPU = False,
     **kwargs,
 ):
     """Index EBSD patterns on a single thread.
@@ -229,6 +231,7 @@ def index_pats(
             nBands=nBands,
             patDim=pdim,
             gpu_id=gpu_id,
+            useCPU=useCPU,
         )
     else:
         indexer = ebsd_indexer_obj
@@ -406,6 +409,9 @@ def __init__(
             )
 
         self.nband_earlyexit = nband_earlyexit
+
+        self.gnomonic = gnomonic_correction.GnomoicCorrection(radonPlan=self.bandDetectPlan.radonPlan, PC=self.PC)
+
         self.dataTemplate = np.dtype(
             [
                 ("quat", np.float64, 4),
@@ -554,6 +560,7 @@ def index_pats(
         except:
             pass
 
+        self.gnomonic.calccorrection(PCpat)
         banddata, bandnorm = self._detectbands(pats, PCpat, xyloc=xyloc, clparams=clparams, verbose=verbose,
                                                chunksize=chunksize, gpu_id=gpuid)
         tic = timer()
@@ -695,8 +702,11 @@ def _getpats(self, patsin=None, patstart=0, npats=-1, xyloc=None):
     def _detectbands(self, pats, PC, xyloc=None, clparams=None, verbose=0, chunksize=528, gpu_id=None):
 
         banddata = self.bandDetectPlan.find_bands(
-            pats, clparams=clparams, verbose=verbose, chunksize=chunksize, gpu_id=gpu_id,
+            pats, verbose=verbose, chunksize=chunksize, clparams=clparams, gpu_id=gpu_id,
         )
+
+        #banddata = self.gnomonic.applycorrection(banddata, self.bandDetectPlan.rSigma)
+
         #  shpBandDat = banddata.shape
         if PC is None:
             PC_0 = self.PC
@@ -719,6 +729,7 @@ def _indexbandsphase(self, banddata, bandnorm, verbose=0):
         indxData = np.zeros((nPhases + 1, npoints), dtype=self.dataTemplate)
         #bandmatchindex = np.zeros((nPhases, npoints,shpBandDat[-1],2), dtype=np.int32)-100
         bandmatchindex = np.zeros((npoints,nBands, nPhases), dtype=np.int32)-100
+        bandfit_out = np.zeros((npoints,nBands, nPhases), dtype=np.float64)+180
         banddataout = banddata.copy()
 
         indxData["phase"] = -1
@@ -775,6 +786,7 @@ def _indexbandsphase(self, banddata, bandnorm, verbose=0):
                 nMatch,
                 matchAttempts,
                 totvotes,
+                bandfit,
             ) = self.phaseLib[j].bandindex(
                         bandnorm[p2do, ...],
                         band_intensity=adj_intensity[p2do, ...],
@@ -792,6 +804,7 @@ def _indexbandsphase(self, banddata, bandnorm, verbose=0):
                 indxData["matchattempts"][j, whgood2] = matchAttempts[whgood, ...]
                 indxData["totvotes"][j, whgood2] = totvotes[whgood]
                 bandmatchindex[whgood2, ..., j] = bandmatch[whgood, ...].reshape(whgood.size,nBands )
+                bandfit_out[whgood2, ..., j] = bandfit[whgood, ...].reshape(whgood.size, nBands)
 
 
 
@@ -804,6 +817,7 @@ def _indexbandsphase(self, banddata, bandnorm, verbose=0):
         indxData["quat"][0:nPhases, :, :] = q
         indxData[-1, :] = indxData[0, :]
         banddataout['band_match_index'][:,:, 0:nPhases] = bandmatchindex[:,:,:]#.squeeze()
+        banddataout['bandfit'][:,:, 0:nPhases] = bandfit_out[:,:,:]
         if nPhases > 1:
             for j in range(1, nPhases):
                 # indxData[-1, :] = np.where(