Significant update v0.2 (#47)

Introduces non-cubic phases, improved support for input file types, and provides initial output file types. Many other bug fixes and improvement. See change log.
---------

Signed-off-by: Håkon Wiik Ånes <hwaanes@gmail.com>
Co-authored-by: Håkon Wiik Ånes <hwaanes@gmail.com>

.github/workflows/publish.yml

@@ -1,15 +1,20 @@
 # This workflows runs when a tagged release is created or it is triggered manually.
+#
 # For more information see:
-# - Python docs: https://packaging.python.org/en/latest/guides/publishing-package-distribution-releases-using-github-actions-ci-cd-workflows/
+# - Python docs: https://packaging.python.org/en/latest/guides/publishing-package-distribution-releases-using-github-actions-ci-cd-workflows
 # - GitHub action: https://github.com/marketplace/actions/pypi-publish
 # - GitHub docs: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python#publishing-to-package-registries
+#
 # The source distribution (sdist) is built with the `build` package
 # (https://pypa-build.readthedocs.io/en/stable/index.html).
+#
 # The sdist is uploaded to:
 # - TestPyPI whenever the workflow is run
 # - PyPI when the current commit is tagged
+#
+# Trusted publishing to PyPI within GitHub without using an API token: https://blog.pypi.org/posts/2023-04-20-introducing-trusted-publishers
 
-name: Upload to PyPI
+name: Upload package to PyPI
 
 on:
   release:
@@ -20,28 +25,31 @@ on:
 jobs:
   deploy:
     runs-on: ubuntu-latest
+    permissions:
+      # IMPORTANT: this permission is mandatory for trusted publishing:
+      id-token: write
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v3
+
     - name: Set up Python
-      uses: actions/setup-python@v2
+      uses: actions/setup-python@v4
       with:
         python-version: '3.x'
+
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
         pip install build
+
     - name: Build package
       run: |
         python -m build
+
     - name: Publish package to TestPyPI
-      uses: pypa/gh-action-pypi-publish@27b31702a0e7fc50959f5ad993c78deac1bdfc29
+      uses: pypa/gh-action-pypi-publish@release/v1
+      continue-on-error: true
       with:
-        user: __token__
-        password: ${{ secrets.TEST_PYPI_API_TOKEN }}
         repository_url: https://test.pypi.org/legacy/
+
     - name: Publish package to PyPI
-      if: startsWith(github.ref, 'refs/tags')
-      uses: pypa/gh-action-pypi-publish@27b31702a0e7fc50959f5ad993c78deac1bdfc29
-      with:
-        user: __token__
-        password: ${{ secrets.PYPI_API_TOKEN }}
+      uses: pypa/gh-action-pypi-publish@release/v1

.github/workflows/build.yml → .github/workflows/tests.yml

@@ -1,4 +1,4 @@
-name: Build
+name: Tests
 
 
 on:
@@ -24,7 +24,7 @@ jobs:
 
       - uses: actions/setup-python@v4
         with:
-          python-version: '3.10'
+          python-version: '3.11'
 
       - name: Install dependencies
         run: |
@@ -42,11 +42,10 @@ jobs:
       fail-fast: false
       matrix:
         os: [ubuntu-latest, macos-latest, windows-latest]
-        python-version: [3.9, '3.10']
+        python-version: ['3.10', '3.11']
         include:
           - os: ubuntu-latest
             python-version: 3.7
-            OLDEST_SUPPORTED_VERSION: true
             DEPENDENCIES: matplotlib==3.3 numba==0.52 numpy==1.19 ray[default]==1.13
             LABEL: -oldest
     steps:
@@ -63,7 +62,7 @@ jobs:
           pip install -U -e .'[tests]'
 
       - name: Install oldest supported version
-        if: ${{ matrix.OLDEST_SUPPORTED_VERSION }}
+        if: contains(matrix.LABEL, 'oldest')
         run: |
           pip install ${{ matrix.DEPENDENCIES }}
 

.gitignore

@@ -20,7 +20,7 @@ dist/
 *.code-workspace
 
 # Line coverage
-.coverage
+.coverage*
 
 # Sphinx
 doc/build

.readthedocs.yaml

@@ -1,4 +1,4 @@
-# ..readthedocs.yaml
+# .readthedocs.yaml
 # Read the Docs configuration file
 # See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
 
@@ -11,9 +11,9 @@ sphinx:
 
 # Set the version of Python and other tools you might need
 build:
-  os: ubuntu-20.04
+  os: ubuntu-22.04
   tools:
-    python: "3.9"
+    python: "3.11"
 
 # Build doc in all formats (HTML, PDF and ePub)
 formats:

CHANGELOG.rst

@@ -5,28 +5,45 @@ 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>`_.
 
-Unreleased
-==========
+0.2.0 (2023-08-08)
+==================
 
 Added
 -----
+- Initial support for uncompressed EBSP files from Oxford systems.
+- Significant improvement in the particle swarm optimization for pattern center
+  optimization.
+- Initial support for non-cubic phases. Hexagonal verified with EDAX convention.
+  Others are untested.
+- Significant improvements in phase differentiation.
+- NLPAR support for Oxford HDF5 and EBSP.
+- Initial support for Oxford .h5oina files
+- Added IPF coloring/legends for hexagonal phases
+- Data output files in .ang and EDAX .oh5 files
+- Explicit support for Python 3.11.
 
 Changed
 -------
-
-Deprecated
-----------
+- CRITICAL! All ``ebsd_pattern.EBSDPatternFiles.read_data()`` calls will now return TWO
+  arguments. The patterns (same as previous), and an nd.array of the x,y location within
+  the scan of the patterns. The origin is the center of the scan, and reported in
+  microns.
+- ``ebsd_index.index_pats_distributed()`` now will auto optimize the number of patterns
+  processed at a time depending on GPU capability, and is set as the default.
+- Updated tutorials for new features.
 
 Removed
 -------
+- Removed requirement for installation of pyswarms.
+- Removed any references to np.floats and replaced with float() or np.float32/64.
 
 Fixed
 -----
-- Hough transform figure when ``verbose=2`` is passed to various indexing methods is now
+- Radon transform figure when ``verbose=2`` is passed to various indexing methods is now
   plotted in its own figure.
-
-Security
---------
+- Several bug fixes with NLPAR file reading/writing.
+- Complete rewrite of the scheduling for ``ebsd_index.index_pats_distributed()``
+  function to be compatible with NVIDIA cards.
 
 0.1.1 (2022-10-25)
 ==================

MANIFEST.in

@@ -3,6 +3,8 @@ include CHANGELOG.rst
 include CONTRIBUTING.rst
 include IPFCubic.pdf
 include IPFCubic.png
+include IPFHex.pdf
+include IPFHex.png
 include License
 include MANIFEST.in
 include README.md

README.md

@@ -1,6 +1,6 @@
 # PyEBSDIndex
 
-Python based tool for Hough/Radon based EBSD orientation indexing.
+Python based tool for Radon based EBSD orientation indexing.
 
 [![Build status](https://github.com/USNavalResearchLaboratory/PyEBSDIndex/actions/workflows/build.yml/badge.svg)](https://github.com/USNavalResearchLaboratory/PyEBSDIndex/actions/workflows/build.yml)
 [![Documentation status](https://readthedocs.org/projects/pyebsdindex/badge/?version=latest)](https://pyebsdindex.readthedocs.io/en/latest/)

doc/index.rst

@@ -2,7 +2,7 @@
 PyEBSDIndex |release| documentation
 ===================================
 
-Python based tool for Hough/Radon based EBSD orientation indexing.
+Python based tool for Radon based EBSD orientation indexing.
 
 The pattern processing is based on a GPU pipeline, and is based on the work of S. I.
 Wright and B. L. Adams. Metallurgical Transactions A-Physical Metallurgy and Materials

doc/reference/index.rst

@@ -32,3 +32,4 @@ Functionality is inteded to be imported like this:
     ebsd_index
     nlpar
     pcopt
+    tripletvote