Try to use latest version of lmfit #411
Workflow file for this run
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| name: Release | |
| on: | |
| workflow_dispatch: | |
| push: | |
| branches: ['*'] | |
| tags: ['*'] | |
| paths-ignore: | |
| - 'docs/**' | |
| pull_request: | |
| branches: [main] | |
| paths-ignore: | |
| - 'docs/**' | |
| permissions: | |
| # needs write permission at workflow level to create release and upload artifacts | |
| contents: write | |
| jobs: | |
| create_release_job: | |
| name: Create Release (on tag only) | |
| runs-on: ubuntu-latest | |
| outputs: | |
| ID: ${{ steps.create_release.outputs.id }} | |
| VERSION: ${{ env.VERSION }} | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Get version (on tag) | |
| if: startsWith(github.ref, 'refs/tags/') | |
| run: | | |
| echo "VERSION=${GITHUB_REF#refs/*/}" >> $GITHUB_ENV | |
| - name: Get version (short hash) | |
| if: ${{ startsWith(github.ref, 'refs/tags/') == false }} | |
| run: | | |
| # Use git short hash instead of tag | |
| echo "VERSION=$(git rev-parse --short HEAD)" >> $GITHUB_ENV | |
| - name: Display version | |
| run: | | |
| echo ${{ env.VERSION }} | |
| - name: Find and Replace | |
| uses: jacobtomlinson/gha-find-replace@a51bbcd94d000df9ca0fcb54ec8be69aad8374b0 | |
| if: startsWith(github.ref, 'refs/tags/') | |
| with: | |
| find: "__TAG__" | |
| replace: ${{ env.VERSION }} | |
| include: "RELEASE_TEXT.md" # Will match all RELEASE_TEXT.md files in any nested directory | |
| - name: Create Release | |
| if: startsWith(github.ref, 'refs/tags/') | |
| id: create_release | |
| uses: softprops/action-gh-release@de2c0eb89ae2a093876385947365aca7b0e5f844 | |
| env: | |
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} # This token is provided by Actions | |
| with: | |
| body_path: "RELEASE_TEXT.md" | |
| draft: true | |
| build: | |
| name: ${{ matrix.TARGET_PLATFORM }}-${{ matrix.BLAS_IMPL }} | |
| needs: create_release_job | |
| runs-on: ${{ matrix.os }}-latest | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| include: | |
| - os: ubuntu | |
| INSTALLER_EXTENSION: sh | |
| BLAS_IMPL: mkl | |
| ARCH: x86_64 | |
| TARGET_PLATFORM: linux-64 | |
| - os: ubuntu | |
| INSTALLER_EXTENSION: sh | |
| BLAS_IMPL: openblas | |
| ARCH: x86_64 | |
| TARGET_PLATFORM: linux-64 | |
| - os: windows | |
| INSTALLER_EXTENSION: exe | |
| BLAS_IMPL: mkl | |
| ARCH: x86_64 | |
| TARGET_PLATFORM: win-64 | |
| - os: windows | |
| INSTALLER_EXTENSION: exe | |
| BLAS_IMPL: openblas | |
| ARCH: x86_64 | |
| TARGET_PLATFORM: win-64 | |
| - os: macos | |
| INSTALLER_EXTENSION: pkg | |
| BLAS_IMPL: mkl | |
| ARCH: x86_64 | |
| TARGET_PLATFORM: osx-64 | |
| - os: macos | |
| INSTALLER_EXTENSION: pkg | |
| BLAS_IMPL: openblas | |
| ARCH: arm64 | |
| TARGET_PLATFORM: osx-arm64 | |
| env: | |
| TEST_DEPS: pytest pytest-qt pytest-xdist pytest-rerunfailures | |
| LIB_TO_TEST: lumispy pyxem kikuchipy | |
| # Fails on linux-mkl build | |
| LIB_TO_TEST_SKIP: '-k "not test_results_dict_to_crystal_map"' | |
| DISPLAY: ':0' | |
| MICROMAMBA_VERSION: '1.5.1' | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - uses: conda-incubator/setup-miniconda@v2 | |
| with: | |
| miniforge-variant: Mambaforge | |
| channels: conda-forge | |
| channel-priority: strict | |
| - shell: bash -l {0} | |
| name: Conda info | |
| run: | | |
| conda info | |
| conda list | |
| - shell: bash -l {0} | |
| name: Install constructor | |
| run: | | |
| mamba install constructor jinja2 conda-libmamba-solver | |
| - shell: bash -l {0} | |
| if: matrix.ARCH == 'arm64' | |
| name: Install micromamba | |
| run: | | |
| TEMP_DIR=$(mktemp -d) | |
| mkdir "${TEMP_DIR}/micromamba" | |
| pushd "${TEMP_DIR}/micromamba" | |
| curl -L -O "https://anaconda.org/conda-forge/micromamba/${{ env.MICROMAMBA_VERSION }}/download/${{ matrix.TARGET_PLATFORM }}/micromamba-${{ env.MICROMAMBA_VERSION }}-0.tar.bz2" | |
| bsdtar -xf "micromamba-${{ env.MICROMAMBA_VERSION }}-0.tar.bz2" | |
| echo "MICROMAMBA_FILE=${PWD}/bin/micromamba" >> $GITHUB_ENV | |
| ls ${PWD} | |
| ls ${PWD}/bin | |
| popd | |
| - shell: bash -l {0} | |
| name: Build distribution | |
| env: | |
| VERSION: ${{ needs.create_release_job.outputs.VERSION }} | |
| BLAS_IMPL: ${{ matrix.BLAS_IMPL }} | |
| CONDA_SOLVER: 'libmamba' | |
| run: | | |
| if [ ${{ matrix.TARGET_PLATFORM }} == osx-arm64 ]; then | |
| constructor -v conda_distribution --platform ${{ matrix.TARGET_PLATFORM }} --conda-exe ${{ env.MICROMAMBA_FILE }} | |
| else | |
| constructor -v conda_distribution | |
| fi | |
| - shell: bash -l {0} | |
| name: Set asset name | |
| env: | |
| ext: ${{ matrix.INSTALLER_EXTENSION }} | |
| run: | | |
| installer_name=(HyperSpy-*.${{ env.ext }}) | |
| echo "Original installer name: " $installer_name | |
| # Rename installer name according to BLAS_IMPL | |
| if [ ${{ matrix.TARGET_PLATFORM }} = osx-arm64 ]; then | |
| CPU=Silicon | |
| elif [ ${{ matrix.BLAS_IMPL }} = mkl ]; then | |
| CPU=Intel | |
| else | |
| CPU=AMD | |
| fi | |
| new_installer_name=$(basename $installer_name .${{ env.ext }})-$CPU.${{ env.ext }} | |
| mv $installer_name $new_installer_name | |
| echo "asset_name=$new_installer_name" >> $GITHUB_ENV | |
| echo "Installer name: "$new_installer_name | |
| ls | |
| - name: Get hash | |
| run: | | |
| shasum -a 256 ${{ env.asset_name }} | |
| - name: Install new distribution (Linux) | |
| if: runner.os == 'linux' | |
| env: | |
| install_dir: '${{ github.workspace }}/new_distribution' | |
| run: | | |
| echo "install_dir=${{ env.install_dir }}" >> $GITHUB_ENV | |
| bash ${{ env.asset_name }} -b -p ${{ env.install_dir }} | |
| - name: Install new distribution (MacOS) | |
| if: runner.os == 'macos' && matrix.ARCH == 'x86_64' | |
| run: | | |
| echo "install_dir=/Users/runner" >> $GITHUB_ENV | |
| installer -pkg ${{ env.asset_name }} -target CurrentUserHomeDirectory | |
| - name: Install new distribution (Windows) | |
| if: runner.os == 'windows' | |
| env: | |
| install_dir: '${{ github.workspace }}\nd' | |
| shell: bash | |
| run: | | |
| echo "install_dir=${{ env.install_dir }}" >> $GITHUB_ENV | |
| - name: Install new distribution (Windows) | |
| if: runner.os == 'windows' | |
| shell: powershell | |
| run: | | |
| Start-Process -Wait -FilePath ${{ env.asset_name }} -ArgumentList "/S /AddToPath=0 /RegisterPython=0 /NoScripts=1 /D=${{ env.install_dir }}" | |
| - name: Upload artifact | |
| if: startsWith(github.ref, 'refs/tags/') != true | |
| uses: actions/upload-artifact@v3 | |
| with: | |
| path: ${{ env.asset_name }} | |
| name: ${{ env.asset_name }} | |
| - shell: bash -l {0} | |
| if: matrix.ARCH == 'x86_64' | |
| name: Info new distribution | |
| run: | | |
| conda activate "${{ env.install_dir }}" | |
| conda info | |
| conda config --show channels | |
| conda config --show channel_priority | |
| conda list | |
| - shell: bash -l {0} | |
| if: matrix.ARCH == 'x86_64' | |
| name: Check latest available hyperspy version | |
| run: | | |
| conda activate "${{ env.install_dir }}" | |
| python check_hyperspy_latest.py | |
| - name: Install xvfb | |
| if: runner.os == 'linux' && always() | |
| run: | | |
| sudo apt-get install -y xvfb libxkbcommon-x11-0 libxcb-icccm4 libxcb-image0 libxcb-keysyms1 libxcb-randr0 libxcb-render-util0 libxcb-xinerama0 libxcb-xinput0 libxcb-xfixes0 | |
| - name: Start xvfb | |
| if: runner.os == 'linux' && always() | |
| run: | | |
| sudo /usr/bin/Xvfb ${{ env.DISPLAY }} -screen 0 1280x1024x24 & | |
| - shell: bash -l {0} | |
| name: Install test dependencies | |
| if: matrix.ARCH == 'x86_64' && always() | |
| run: | | |
| conda activate "${{ env.install_dir }}" | |
| mamba install ${{ env.TEST_DEPS }} | |
| - shell: bash -l {0} | |
| # TODO: revisit at some point, to get it to work on linux (hyperspyui CI works fine...) | |
| if: runner.os != 'linux' && matrix.ARCH == 'x86_64' && always() | |
| name: Test new distribution (HyperSpyUI) | |
| run: | | |
| conda activate "${{ env.install_dir }}" | |
| pytest --pyargs hyperspyui | |
| - shell: bash -l {0} | |
| name: Test hyperspy | |
| if: matrix.ARCH == 'x86_64' && always() | |
| env: | |
| MPLBACKEND: 'agg' | |
| run: | | |
| conda activate "${{ env.install_dir }}" | |
| # Skip these tests until there are fixed | |
| pytest --pyargs hyperspy --reruns 3 -n 2 -k "not test_find_peaks2D" | |
| - shell: bash -l {0} | |
| name: Run other test suites | |
| if: matrix.ARCH == 'x86_64' && always() | |
| env: | |
| MPLBACKEND: 'agg' | |
| run: | | |
| conda activate "${{ env.install_dir }}" | |
| # Skip these tests until there are fixed | |
| pytest --pyargs ${{ env.LIB_TO_TEST }} ${{ env.LIB_TO_TEST_SKIP }} | |
| - name: Upload Release Asset | |
| if: startsWith(github.ref, 'refs/tags/') | |
| uses: softprops/action-gh-release@de2c0eb89ae2a093876385947365aca7b0e5f844 | |
| env: | |
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| with: | |
| files: ${{ env.asset_name }} | |
| draft: true | |
| build_portable: | |
| name: windows (Portable) | |
| needs: create_release_job | |
| runs-on: windows-latest | |
| env: | |
| WP_URL: https://github.com/winpython/winpython/releases/download/7.0.20230928/Winpython64-3.11.5.0mkl.exe | |
| WP_SHA256: 0b2037660064589dd73a58ac17f44d9e657cfc5fcea92cec9223185243a0a3bc | |
| WP_EXE: winpython.exe | |
| WP_DIR_NAME: WPy64-31150 | |
| 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 py4dstem pymatgen pystackreg python-rapidjson pyxem scanning_drift_corr start_jupyter_cm | |
| LIB_TO_TEST: lumispy pyxem kikuchipy | |
| LIB_TO_TEST_SKIP: '' | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Download Winpython | |
| run: | | |
| Invoke-WebRequest -OutFile ${{ env.WP_EXE }} ${{ env.WP_URL }} | |
| ls | |
| $file_hash = (Get-FileHash ${{ env.WP_EXE }} ).Hash | |
| $file_hash | |
| if ($file_hash -ne "${{ env.WP_SHA256 }}") { exit(1) } | |
| - name: Install Winpython | |
| run: | | |
| .\${{ env.WP_EXE }} -y | Out-Null | |
| ls | |
| ls ${{ env.WP_DIR_NAME }} | |
| - name: Install libraries | |
| shell: cmd | |
| run: | | |
| call "${{ env.WP_DIR_NAME }}\scripts\env.bat" | |
| where python | |
| where pip | |
| pip install ${{ env.LIB_TO_INSTALL }} | |
| # lmfit version seems to be old | |
| pip install --upgrade lmfit | |
| - name: Pip list | |
| shell: cmd | |
| run: | | |
| call "${{ env.WP_DIR_NAME }}\scripts\env.bat" | |
| pip list | |
| - shell: bash -l {0} | |
| name: Set installer name | |
| env: | |
| VERSION: ${{ needs.create_release_job.outputs.VERSION }} | |
| run: | | |
| installer_name=HyperSpy-bundle-${{ env.VERSION }}-Windows-x86_64-Portable.exe | |
| echo "asset_name=$installer_name" >> $GITHUB_ENV | |
| echo $installer_name | |
| - name: Run pyclean in distribution folder | |
| shell: cmd | |
| run: | | |
| where pip | |
| pip install pyclean | |
| where pyclean | |
| pyclean ${{ env.WP_DIR_NAME }} | |
| - name: Create installer | |
| run: | | |
| 7z -mx5 -sfx a ${{ env.asset_name }} ${{ env.WP_DIR_NAME }} | |
| ls | |
| - name: Upload artifact | |
| if: startsWith(github.ref, 'refs/tags/') != true | |
| uses: actions/upload-artifact@v3 | |
| with: | |
| path: ${{ env.asset_name }} | |
| name: ${{ env.asset_name }} | |
| - name: Install new distribution | |
| run: | | |
| Remove-Item -recurse ${{ env.WP_DIR_NAME }} | |
| ls | |
| .\${{ env.asset_name }} -y | Out-Null | |
| echo "After installation" | |
| ls | |
| echo ${{ env.asset_name }} | |
| - name: Check latest available hyperspy version | |
| shell: cmd | |
| run: | | |
| call "${{ env.WP_DIR_NAME }}\scripts\env.bat" | |
| python check_hyperspy_latest.py | |
| - name: Install testing libraries | |
| if: always() | |
| shell: cmd | |
| run: | | |
| call "${{ env.WP_DIR_NAME }}\scripts\env.bat" | |
| pip install ${{ env.TEST_DEPS }} | |
| - name: Run test suite (HyperSpyUI) | |
| if: always() | |
| shell: cmd | |
| run: | | |
| call "${{ env.WP_DIR_NAME }}\scripts\env.bat" | |
| pytest --pyargs hyperspyui | |
| - name: Run test hyperspy | |
| if: always() | |
| shell: cmd | |
| env: | |
| MPLBACKEND: 'agg' | |
| run: | | |
| call "${{ env.WP_DIR_NAME }}\scripts\env.bat" | |
| # Remove for 1.7.6 release | |
| del WPy64-31150/python-3.11.5.amd64/Lib/site-packages/hyperspy/tests/signals/test_find_peaks2D.py | |
| pytest --pyargs hyperspy --reruns 3 -n 2 -k "not test_find_peaks2D" | |
| - name: Run other test suites | |
| if: always() | |
| shell: cmd | |
| env: | |
| MPLBACKEND: 'agg' | |
| run: | | |
| call "${{ env.WP_DIR_NAME }}\scripts\env.bat" | |
| # Skip these tests until there are fixed | |
| pytest --pyargs ${{ env.LIB_TO_TEST }} ${{ env.LIB_TO_TEST_SKIP }} | |
| - name: Upload Release Asset | |
| if: startsWith(github.ref, 'refs/tags/') | |
| uses: softprops/action-gh-release@de2c0eb89ae2a093876385947365aca7b0e5f844 | |
| env: | |
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| with: | |
| files: ${{ env.asset_name }} | |
| draft: true | |
| publish_release_job: | |
| # Set build, build_portable are needed, so that it runs when they are finished | |
| needs: [create_release_job, build, build_portable] | |
| if: startsWith(github.ref, 'refs/tags/') | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Finalise release | |
| # Publish draft release | |
| uses: eregon/publish-release@46913fa2b3f7edc7345ae3c17f6d1b093a54916d | |
| env: | |
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| with: | |
| release_id: ${{ needs.create_release_job.outputs.ID }} |