From 8b1bdeaff6f9a5120bb34e496cb89f0c988b23e6 Mon Sep 17 00:00:00 2001 From: Eric Prestat Date: Thu, 4 May 2023 16:21:34 +0100 Subject: [PATCH 1/5] Add py4dstem --- .github/workflows/release.yml | 2 +- conda_distribution/construct.yaml | 1 + 2 files changed, 2 insertions(+), 1 deletion(-) diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml index e7482de..6b0fa77 100644 --- a/.github/workflows/release.yml +++ b/.github/workflows/release.yml @@ -294,7 +294,7 @@ jobs: WP_EXE: winpython.exe WP_DIR_NAME: WPy64-31090 TEST_DEPS: pytest pytest-qt pytest-xdist pytest-rerunfailures - LIB_TO_INSTALL: abtem ase atomap graphviz hdf5plugin hyperspy[all] hyperspyui kikuchipy lumispy matplotlib-scalebar nglview particlespy pystackreg python-rapidjson pyxem scanning_drift_corr start_jupyter_cm + LIB_TO_INSTALL: abtem ase atomap graphviz hdf5plugin hyperspy[all] hyperspyui kikuchipy lumispy matplotlib-scalebar nglview py4dstem particlespy pystackreg python-rapidjson pyxem scanning_drift_corr start_jupyter_cm LIB_TO_TEST: lumispy pyxem LIB_TO_TEST_SKIP: '' diff --git a/conda_distribution/construct.yaml b/conda_distribution/construct.yaml index d076d0b..1c17eaf 100644 --- a/conda_distribution/construct.yaml +++ b/conda_distribution/construct.yaml @@ -39,6 +39,7 @@ specs: - ovito # [win] - ovito =3.7 # [not win] - particlespy + - py4dstem - pystackreg - python 3.10* - python-graphviz From a7f94bb20e87d426f9c266c513ede7f39df27aab Mon Sep 17 00:00:00 2001 From: Eric Prestat Date: Sat, 6 May 2023 10:35:17 +0100 Subject: [PATCH 2/5] Update minimum version --- .github/workflows/release.yml | 1 - conda_distribution/construct.yaml | 12 +++++------- 2 files changed, 5 insertions(+), 8 deletions(-) diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml index 6b0fa77..82d2f75 100644 --- a/.github/workflows/release.yml +++ b/.github/workflows/release.yml @@ -396,7 +396,6 @@ jobs: MPLBACKEND: 'agg' run: | call "${{ env.WP_DIR_NAME }}\scripts\env.bat" - # Skip these tests until there are fixed pytest --pyargs hyperspy --reruns 3 -n 2 - name: Run other test suites diff --git a/conda_distribution/construct.yaml b/conda_distribution/construct.yaml index 1c17eaf..d7f9781 100644 --- a/conda_distribution/construct.yaml +++ b/conda_distribution/construct.yaml @@ -21,8 +21,8 @@ specs: - dask >=2021.08.1 - dask-labextension - hdf5plugin - - hyperspy >=1.7.4 - - hyperspyui >=1.2.0 + - hyperspy >=1.7.5 + - hyperspyui >=1.3.1 - ipympl - jupyterlab >=3.0.0,<4.0 - kikuchipy >=0.8.4 @@ -44,13 +44,11 @@ specs: - python 3.10* - python-graphviz - python-rapidjson - - pyxem >=0.15 + - pyxem >=0.15.1 - openpyxl - # https://github.com/jupyter/qtconsole/issues/576 - - qtconsole =5.4.1 + - qtconsole >=5.4.3 - scanning_drift_corr - # to use qtconsole 5.4.1 - - spyder =5.4.2 + - spyder >=5.4.3 - start_jupyter_cm - xlrd From dd3887b65cf9be6f29bb2e20b727ab3c3695a0ea Mon Sep 17 00:00:00 2001 From: Eric Prestat Date: Sat, 6 May 2023 10:46:24 +0100 Subject: [PATCH 3/5] Fix Github logo in docs and update `readthedocs.yml` configuration --- .readthedocs.yaml | 11 ++++++----- docs/conf.py | 18 ++++++------------ 2 files changed, 12 insertions(+), 17 deletions(-) diff --git a/.readthedocs.yaml b/.readthedocs.yaml index ce78536..9eda205 100644 --- a/.readthedocs.yaml +++ b/.readthedocs.yaml @@ -5,6 +5,12 @@ # Required version: 2 +# Set the version of Python and other tools you might need +build: + os: "ubuntu-22.04" + tools: + python: "mambaforge-4.10" + # Build documentation in the docs/ directory with Sphinx sphinx: configuration: docs/conf.py @@ -13,10 +19,5 @@ sphinx: formats: - htmlzip -build: - os: "ubuntu-20.04" - tools: - python: "mambaforge-4.10" - conda: environment: conda_environment.yml diff --git a/docs/conf.py b/docs/conf.py index a0f5668..37499bb 100644 --- a/docs/conf.py +++ b/docs/conf.py @@ -65,17 +65,8 @@ html_favicon = '_static/hyperspy.ico' html_theme_options = { + "github_url": "https://github.com/hyperspy/hyperspy-bundle", "icon_links": [ - { - # Label for this link - "name": "GitHub", - # URL where the link will redirect - "url": "https://github.com/hyperspy/hyperspy-bundle", # required - # Icon class (if "type": "fontawesome"), or path to local image (if "type": "local") - "icon": "fab fa-github-square", - # The type of image to be used (see below for details) - "type": "fontawesome", - }, { # Label for this link "name": "HyperSpy", @@ -86,6 +77,11 @@ # The type of image to be used (see below for details) "type": "local", }, + { + "name": "Gitter", + "url": "https://gitter.im/hyperspy/hyperspy", + "icon": "fab fa-gitter", + }, { # Label for this link "name": "Release", @@ -96,8 +92,6 @@ # The type of image to be used (see below for details) "type": "url", }, - - ], "logo": { "text": "HyperSpy-bundle", From c1bfa956bbaddbb6a63075371e5067dd7c9f9f4b Mon Sep 17 00:00:00 2001 From: Eric Prestat Date: Sun, 14 May 2023 10:58:22 +0100 Subject: [PATCH 4/5] Update release text and use "Silicon" instead of "M1" for osx-arm64 build --- .github/workflows/release.yml | 2 +- RELEASE_TEXT.md | 4 ++-- docs/index.rst | 4 ++-- 3 files changed, 5 insertions(+), 5 deletions(-) diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml index 82d2f75..d032538 100644 --- a/.github/workflows/release.yml +++ b/.github/workflows/release.yml @@ -160,7 +160,7 @@ jobs: echo "Original installer name: " $installer_name # Rename installer name according to BLAS_IMPL if [ ${{ matrix.TARGET_PLATFORM }} = osx-arm64 ]; then - CPU=M1 + CPU=Silicon elif [ ${{ matrix.BLAS_IMPL }} = mkl ]; then CPU=Intel else diff --git a/RELEASE_TEXT.md b/RELEASE_TEXT.md index 2243b87..1caf745 100644 --- a/RELEASE_TEXT.md +++ b/RELEASE_TEXT.md @@ -10,11 +10,11 @@ For Windows and Linux, there is the choice between two variants, which are optim For Mac, there are also two variants available: - `Intel` for Mac computers with Intel CPU -- `M1` for Mac computers with Apple Silicon (M1) CPU +- `Silicon` for Mac computers with Apple Silicon (M1, M2, etc.) CPU For included packages, [see documentation](https://hyperspy.org/hyperspy-bundle/index.html#included-software-and-libraries). -This distribution is built using [constructor 3.3.1](https://github.com/conda/constructor). +This distribution is built using [constructor 3.4.3](https://github.com/conda/constructor). ## Portable (Windows only) The portable distribution is based on the [WinPython](https://winpython.github.io) distribution and is a self-extracting archive. Running the installer will install the distribution in the current directory. Since the distribution is portable, it can be moved to any directory or run from an external drive. diff --git a/docs/index.rst b/docs/index.rst index 1813ffe..9902d33 100644 --- a/docs/index.rst +++ b/docs/index.rst @@ -34,8 +34,8 @@ Table of Contents Variants of the HyperSpy-bundle =============================== -It is compatible with Windows, MacOS (Intel or native M1), or Linux and comes -with variants, which are optimised for AMD or Intel processors. +It is compatible with Windows, MacOS (Intel and Apple Silicon), or Linux and comes +with variants, which are optimised for AMD (using openblas) or Intel (using MKL) processors. The portable version is supported on windows only. Standard Version From 849d3db45f5469b16756869af2ff15bb0c48f7ec Mon Sep 17 00:00:00 2001 From: Eric Prestat Date: Sun, 14 May 2023 10:58:41 +0100 Subject: [PATCH 5/5] Update skipping test --- .github/workflows/release.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml index d032538..8d2a109 100644 --- a/.github/workflows/release.yml +++ b/.github/workflows/release.yml @@ -100,7 +100,7 @@ jobs: TARGET_PLATFORM: osx-arm64 env: TEST_DEPS: pytest pytest-qt pytest-xdist pytest-rerunfailures - LIB_TO_TEST: lumispy pyxem + LIB_TO_TEST: lumispy pyxem kikuchipy # Fails on linux-mkl build LIB_TO_TEST_SKIP: '-k "not test_results_dict_to_crystal_map"' DISPLAY: ':0' @@ -295,7 +295,7 @@ jobs: WP_DIR_NAME: WPy64-31090 TEST_DEPS: pytest pytest-qt pytest-xdist pytest-rerunfailures LIB_TO_INSTALL: abtem ase atomap graphviz hdf5plugin hyperspy[all] hyperspyui kikuchipy lumispy matplotlib-scalebar nglview py4dstem particlespy pystackreg python-rapidjson pyxem scanning_drift_corr start_jupyter_cm - LIB_TO_TEST: lumispy pyxem + LIB_TO_TEST: lumispy pyxem kikuchipy LIB_TO_TEST_SKIP: '' steps: