From e9137ac31db449ee24fcd8cda4afd2415d7c412c Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?H=C3=A5kon=20Wiik=20=C3=85nes?= Date: Sun, 23 Jul 2023 08:48:04 -0700 Subject: [PATCH 1/9] List explicit support for Python 3.11 MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Signed-off-by: Håkon Wiik Ånes --- setup.py | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/setup.py b/setup.py index 2c5a9072..b274f6eb 100644 --- a/setup.py +++ b/setup.py @@ -49,7 +49,7 @@ "nlopt", "panel", # Used in the docs by PyVista "pydata-sphinx-theme", - "pyebsdindex >= 0.1.1", + "pyebsdindex ~= 0.1", "pyvista", "sphinx >= 3.0.2", "sphinx-codeautolink[ipython] < 0.14", @@ -103,6 +103,7 @@ "Programming Language :: Python :: 3.8", "Programming Language :: Python :: 3.9", "Programming Language :: Python :: 3.10", + "Programming Language :: Python :: 3.11", "Development Status :: 4 - Beta", "Intended Audience :: Science/Research", ( @@ -153,7 +154,7 @@ "numba >= 0.55", "numpy >= 1.19", "orix >= 0.11.1", - "pooch >= 0.13", + "pooch >= 1.3.0", "pyyaml", "tqdm >= 0.5.2", "scikit-image >= 0.16.2", From 5f8c6f0e93418f7f5b529951775a78f9b7dc9c98 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?H=C3=A5kon=20Wiik=20=C3=85nes?= Date: Sun, 23 Jul 2023 08:48:20 -0700 Subject: [PATCH 2/9] List explicit support for Python 3.11 in changelog MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Signed-off-by: Håkon Wiik Ånes --- CHANGELOG.rst | 2 ++ 1 file changed, 2 insertions(+) diff --git a/CHANGELOG.rst b/CHANGELOG.rst index 7f1e0139..ba1b684e 100644 --- a/CHANGELOG.rst +++ b/CHANGELOG.rst @@ -18,6 +18,8 @@ Unreleased Added ----- +- Explicit support for Python 3.11. + (`#645 `_) Changed ------- From 04034ccaa5102c7d0b5cd7e138f0afed6a997e20 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?H=C3=A5kon=20Wiik=20=C3=85nes?= Date: Sun, 23 Jul 2023 08:48:40 -0700 Subject: [PATCH 3/9] Use Python 3.11 to build docs on readthedocs MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Signed-off-by: Håkon Wiik Ånes --- readthedocs.yaml | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/readthedocs.yaml b/readthedocs.yaml index 66d0509a..b0d2b5f5 100644 --- a/readthedocs.yaml +++ b/readthedocs.yaml @@ -13,7 +13,7 @@ sphinx: build: os: ubuntu-22.04 tools: - python: "3.10" + python: "3.11" nodejs: "19" # See https://docs.pyvista.org/user-guide/jupyter/panel.html#configuration-considerations. # Some of these packages are needed by PyVista/panel to render 3D @@ -35,4 +35,3 @@ python: path: . extra_requirements: - doc - - viz From b84c00efd09a8c017cc29e57cece8c1883364c53 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?H=C3=A5kon=20Wiik=20=C3=85nes?= Date: Sun, 23 Jul 2023 08:49:03 -0700 Subject: [PATCH 4/9] Make Binder use Python 3.11 MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Signed-off-by: Håkon Wiik Ånes --- environment.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/environment.yml b/environment.yml index 07a50c99..4f7f9576 100644 --- a/environment.yml +++ b/environment.yml @@ -2,7 +2,7 @@ name: doc-dependencies-for-binder channels: - conda-forge dependencies: - - python=3.9 + - python=3.11 - pip - pip: - --editable .[doc,all] \ No newline at end of file From 6bebe718a415587de8344ad3e7aef91efd5239fa Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?H=C3=A5kon=20Wiik=20=C3=85nes?= Date: Sun, 23 Jul 2023 08:49:34 -0700 Subject: [PATCH 5/9] Replace Python 3.9 test run with 3.11 MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Signed-off-by: Håkon Wiik Ånes --- .github/workflows/tests.yml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml index fc1b8336..bc0b2a31 100644 --- a/.github/workflows/tests.yml +++ b/.github/workflows/tests.yml @@ -39,7 +39,7 @@ jobs: - uses: actions/setup-python@v4 with: - python-version: '3.10' + python-version: '3.11' - name: Install dependencies run: | @@ -57,14 +57,14 @@ jobs: fail-fast: false matrix: os: [ubuntu-latest, windows-latest, macos-latest] - python-version: [3.9, '3.10'] + python-version: ['3.10', '3.11'] include: - os: ubuntu-latest python-version: 3.7 - DEPENDENCIES: dask==2021.8.1 diffsims==0.5.0 hyperspy==1.7.3 matplotlib==3.3 numba==0.55 numpy==1.19 orix==0.11.1 scikit-image==0.16.2 + DEPENDENCIES: dask==2021.8.1 diffsims==0.5.0 hyperspy==1.7.3 matplotlib==3.3 numba==0.55 numpy==1.19 orix==0.11.1 pooch==1.3.0 scikit-image==0.16.2 LABEL: -oldest - os: ubuntu-latest - python-version: 3.10 + python-version: 3.11 LABEL: -minimum_requirement steps: - uses: actions/checkout@v3 From ba3cf7b2cf9a51be839f62effffa54fc984a71ed Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?H=C3=A5kon=20Wiik=20=C3=85nes?= Date: Sun, 23 Jul 2023 08:50:02 -0700 Subject: [PATCH 6/9] Use Python 3.11 when running nbval to test notebooks MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Signed-off-by: Håkon Wiik Ånes --- .github/workflows/test_documentation_notebooks.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/test_documentation_notebooks.yml b/.github/workflows/test_documentation_notebooks.yml index 2bbee6c8..702798e3 100644 --- a/.github/workflows/test_documentation_notebooks.yml +++ b/.github/workflows/test_documentation_notebooks.yml @@ -19,7 +19,7 @@ jobs: - name: Set up Python uses: actions/setup-python@v4 with: - python-version: '3.10' + python-version: '3.11' - name: Install package and dependencies shell: bash From 2fb66143a01b84fe5835df350d86e32eb3471422 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?H=C3=A5kon=20Wiik=20=C3=85nes?= Date: Sun, 23 Jul 2023 08:50:28 -0700 Subject: [PATCH 7/9] Fix link to dark logo in docs MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Signed-off-by: Håkon Wiik Ånes --- doc/conf.py | 8 +++++++- 1 file changed, 7 insertions(+), 1 deletion(-) diff --git a/doc/conf.py b/doc/conf.py index 30a47733..5a830d0a 100644 --- a/doc/conf.py +++ b/doc/conf.py @@ -112,7 +112,7 @@ ], "logo": { "alt_text": "kikuchipy", - "image_dark": "logo/plasma_banner_dark.png", + "image_dark": "_static/logo/plasma_banner_dark.png", }, "navigation_with_keys": False, "show_toc_level": 2, @@ -351,3 +351,9 @@ def _str_examples(self): print("[kikuchipy] Downloading example datasets (if not found in cache)") _ = kp.data.nickel_ebsd_large(allow_download=True) _ = kp.data.si_ebsd_moving_screen(0, allow_download=True) + + +def setup(app): + # Ignore .ipynb and .html files (see https://github.com/executablebooks/MyST-NB/issues/363). + app.registry.source_suffix.pop(".ipynb", None) + app.registry.source_suffix.pop(".html", None) From 462f9734117a511b1a158bf4d04a51876f695cbb Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?H=C3=A5kon=20Wiik=20=C3=85nes?= Date: Sun, 23 Jul 2023 08:51:16 -0700 Subject: [PATCH 8/9] Minor updates to versions, application paper links and related proj. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Signed-off-by: Håkon Wiik Ånes --- doc/user/applications.rst | 12 ++++++++---- doc/user/installation.rst | 10 +++++----- doc/user/related_projects.rst | 9 ++++++--- 3 files changed, 19 insertions(+), 12 deletions(-) diff --git a/doc/user/applications.rst b/doc/user/applications.rst index e09b09dc..dabe62d6 100644 --- a/doc/user/applications.rst +++ b/doc/user/applications.rst @@ -16,16 +16,18 @@ Most of these works are also listed when searching for ``"kikuchipy"`` `on Googl ==== - A. V. Bugten, L. Michels, R. B. Brurok, C. Hartung, E. Ott, L. Vines, Y. Li, L. Arnberg and M. Di Sabatino, "The Role of Boron in Low Copper Spheroidal Graphite - Irons," *Metallurgical and Materials Transactions A* (2023). + Irons," *Metallurgical and Materials Transactions A* **54** (2023). https://doi.org/10.1007/s11661-023-07014-y. - O. W. Sandvik, A. M. Müller, H. W. Ånes, M. Zahn, J. He, M. Fiebig, T. Lottermoser, - Th. Rojac, D. Meier and J. Schultheiß, "Pressure-control of non-ferroelastic - ferroelectric domains in ErMnO3," *arXiv* (2023). - https://doi.org/10.48550/arXiv.2304.08423. + Th. Rojac, D. Meier and J. Schultheiß, "Pressure Control of Nonferroelastic + Ferroelectric Domains in ErMnO3," *Nano Letters* (2023). + https://doi.org/10.1021/acs.nanolett.3c01638. + (`arXiv `__.) - H. W. Ånes, A. T. J. van Helvoort and K. Marthinsen, "Orientation dependent pinning of (sub)grains by dispersoids during recovery and recrystallization in an Al-Mn alloy," *Acta Materialia* **248** (2023). https://doi.org/10.1016/j.actamat.2023.118761. + (`arXiv `__.) - T. Bergh, H. W. Ånes, R. Aune, S. Wenner, R. Holmestad, X. Ren and P. E. Vullum, "Intermetallic Phase Layers in Cold Metal Transfer Aluminium-Steel Welds with an Al-Si–Mn Filler Alloy," *Materials Transactions* **64(2)** (2023). @@ -41,10 +43,12 @@ Most of these works are also listed when searching for ``"kikuchipy"`` `on Googl particle analysis of a recovered Al-Mn alloy by directly combining EBSD and backscatter electron imaging," *Materials Characterization* **193** (2022). https://doi.org/10.1016/j.matchar.2022.112228. + (`arXiv `__.) - J. Schultheiß, F. Xue, E. Roede, H. W. Ånes, F. H. Danmo, S. M. Selbach, L.-Q. Chen and D. Meier, "Confinement-driven inverse domain scaling in polycrystalline ErMnO3," *Advanced Materials*, **34** (2022). https://doi.org/10.1002/adma.202203449. + (`arXiv `__.) 2021 ==== diff --git a/doc/user/installation.rst b/doc/user/installation.rst index 692b4cad..475b6b80 100644 --- a/doc/user/installation.rst +++ b/doc/user/installation.rst @@ -22,9 +22,9 @@ To update kikuchipy to the latest release:: pip install --upgrade kikuchipy -To install a specific version of kikuchipy (say version 0.5.8):: +To install a specific version of kikuchipy (say version 0.8.5):: - pip install kikuchipy==0.5.8 + pip install kikuchipy==0.8.5 .. _optional-dependencies: @@ -59,7 +59,7 @@ To install with Anaconda, we recommend you install it in a `Miniconda distribution `__. To create an environment and activate it, run the following:: - conda create --name kp-env python=3.9 + conda create --name kp-env python=3.11 conda activate kp-env If you prefer a graphical interface to manage packages and environments, you can install @@ -73,9 +73,9 @@ To update kikuchipy to the latest release:: conda update kikuchipy -To install a specific version of kikuchipy (say version 0.5.8):: +To install a specific version of kikuchipy (say version 0.8.5):: - conda install kikuchipy==0.5.8 + conda install kikuchipy==0.8.5 .. _install-with-hyperspy-bundle: diff --git a/doc/user/related_projects.rst b/doc/user/related_projects.rst index 0c0d7c5c..7fcca904 100644 --- a/doc/user/related_projects.rst +++ b/doc/user/related_projects.rst @@ -23,13 +23,16 @@ EBSD data that users of kikuchipy might find useful: kikuchipy depends on this library for Hough indexing. - `OpenECCI `__: GUI-based software for controlled Electron Channelling Contrast Imaging (ECCI) analysis of crystal defects in an SEM. -- `MTEX `__: Matlab toolbox for analyzing and modeling +- `MTEX `__: MATLAB toolbox for analyzing and modeling crystallographic textures by means of EBSD or pole figure data. -- `AstroEBSD `__: Matlab package with +- `Dream.3D `__: C++ library to reconstruct, instatiate, + quantify, mesh, handle, and visualize multidimensional (3D), multimodal data (mainly + EBSD orientation data). +- `AstroEBSD `__: MATLAB package with indexing tools for EBSD patterns. - :doc:`xcdskd `: Python library with tools for Kikuchi Diffraction in the SEM, with example Jupyter Notebooks. -- `OpenXY `_: Matlab tool for +- `OpenXY `_: MATLAB tool for cross-correlation analysis of EBSD patterns. - :doc:`DefDAP `: Python package for correlating EBSD and high-resolution digital image correlation data. From 565c4309d32e515648c82a291d4a54f9943440bb Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?H=C3=A5kon=20Wiik=20=C3=85nes?= Date: Sun, 23 Jul 2023 09:14:19 -0700 Subject: [PATCH 9/9] Increase minimal versions of diffsims, NumPy and Matplotlib MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Signed-off-by: Håkon Wiik Ånes --- .github/workflows/tests.yml | 2 +- CHANGELOG.rst | 2 ++ doc/conf.py | 6 ------ doc/user/applications.rst | 16 ++++++++-------- setup.py | 6 +++--- 5 files changed, 14 insertions(+), 18 deletions(-) diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml index bc0b2a31..6084e0c6 100644 --- a/.github/workflows/tests.yml +++ b/.github/workflows/tests.yml @@ -61,7 +61,7 @@ jobs: include: - os: ubuntu-latest python-version: 3.7 - DEPENDENCIES: dask==2021.8.1 diffsims==0.5.0 hyperspy==1.7.3 matplotlib==3.3 numba==0.55 numpy==1.19 orix==0.11.1 pooch==1.3.0 scikit-image==0.16.2 + DEPENDENCIES: dask==2021.8.1 diffsims==0.5.1 hyperspy==1.7.3 matplotlib==3.5 numba==0.55 numpy==1.21.6 orix==0.11.1 pooch==1.3.0 scikit-image==0.16.2 LABEL: -oldest - os: ubuntu-latest python-version: 3.11 diff --git a/CHANGELOG.rst b/CHANGELOG.rst index ba1b684e..2d645ac3 100644 --- a/CHANGELOG.rst +++ b/CHANGELOG.rst @@ -28,6 +28,8 @@ Changed internally to set the default color to white anymore, but uses ``fc`` (facecolor) instead. This change was necessary to improve handling of other keyword arguments. (`#643 `_) +- Increase minimal versions of diffsims, NumPy, and Matplotlib to 0.5.1, 1.21.6, and + 3.5 respectively. (`#645 `_) Deprecated ---------- diff --git a/doc/conf.py b/doc/conf.py index 5a830d0a..e25ec13c 100644 --- a/doc/conf.py +++ b/doc/conf.py @@ -351,9 +351,3 @@ def _str_examples(self): print("[kikuchipy] Downloading example datasets (if not found in cache)") _ = kp.data.nickel_ebsd_large(allow_download=True) _ = kp.data.si_ebsd_moving_screen(0, allow_download=True) - - -def setup(app): - # Ignore .ipynb and .html files (see https://github.com/executablebooks/MyST-NB/issues/363). - app.registry.source_suffix.pop(".ipynb", None) - app.registry.source_suffix.pop(".html", None) diff --git a/doc/user/applications.rst b/doc/user/applications.rst index dabe62d6..4ca9959b 100644 --- a/doc/user/applications.rst +++ b/doc/user/applications.rst @@ -21,13 +21,13 @@ Most of these works are also listed when searching for ``"kikuchipy"`` `on Googl - O. W. Sandvik, A. M. Müller, H. W. Ånes, M. Zahn, J. He, M. Fiebig, T. Lottermoser, Th. Rojac, D. Meier and J. Schultheiß, "Pressure Control of Nonferroelastic Ferroelectric Domains in ErMnO3," *Nano Letters* (2023). - https://doi.org/10.1021/acs.nanolett.3c01638. - (`arXiv `__.) + https://doi.org/10.1021/acs.nanolett.3c01638 + (`arXiv `__). - H. W. Ånes, A. T. J. van Helvoort and K. Marthinsen, "Orientation dependent pinning of (sub)grains by dispersoids during recovery and recrystallization in an Al-Mn alloy," *Acta Materialia* **248** (2023). - https://doi.org/10.1016/j.actamat.2023.118761. - (`arXiv `__.) + https://doi.org/10.1016/j.actamat.2023.118761 + (`arXiv `__). - T. Bergh, H. W. Ånes, R. Aune, S. Wenner, R. Holmestad, X. Ren and P. E. Vullum, "Intermetallic Phase Layers in Cold Metal Transfer Aluminium-Steel Welds with an Al-Si–Mn Filler Alloy," *Materials Transactions* **64(2)** (2023). @@ -42,13 +42,13 @@ Most of these works are also listed when searching for ``"kikuchipy"`` `on Googl - H. W. Ånes, A. T. J. van Helvoort and K. Marthinsen, "Correlated subgrain and particle analysis of a recovered Al-Mn alloy by directly combining EBSD and backscatter electron imaging," *Materials Characterization* **193** (2022). - https://doi.org/10.1016/j.matchar.2022.112228. - (`arXiv `__.) + https://doi.org/10.1016/j.matchar.2022.112228 + (`arXiv `__). - J. Schultheiß, F. Xue, E. Roede, H. W. Ånes, F. H. Danmo, S. M. Selbach, L.-Q. Chen and D. Meier, "Confinement-driven inverse domain scaling in polycrystalline ErMnO3," *Advanced Materials*, **34** (2022). - https://doi.org/10.1002/adma.202203449. - (`arXiv `__.) + https://doi.org/10.1002/adma.202203449 + (`arXiv `__). 2021 ==== diff --git a/setup.py b/setup.py index b274f6eb..5cf150f0 100644 --- a/setup.py +++ b/setup.py @@ -146,13 +146,13 @@ install_requires=[ "dask[array] >= 2021.8.1", "diffpy.structure >= 3", - "diffsims >= 0.5", + "diffsims >= 0.5.1", "hyperspy >= 1.7.3", "h5py >= 2.10", "imageio", - "matplotlib >= 3.3", + "matplotlib >= 3.5", "numba >= 0.55", - "numpy >= 1.19", + "numpy >= 1.21.6", "orix >= 0.11.1", "pooch >= 1.3.0", "pyyaml",