SurfaceTopography 0.0.0__tar.gz

surfacetopography-0.0.0/.check_mufft_capabilities.py

@@ -0,0 +1,13 @@
+import sys
+
+import muGrid
+
+mpi_required = sys.argv[1] in ["yes", "1"]
+
+print('`muGrid` imported successfully')
+print(f'muGrid version: {muGrid.__version__}')
+
+if mpi_required:
+    # Make sure that we have the parallel version running
+    assert muGrid.has_mpi, "MPI support is required but muGrid.has_mpi is False"
+    print('MPI support: enabled')

surfacetopography-0.0.0/.gitattributes

@@ -0,0 +1,3 @@
+# Meson dist uses git to create the package - we don't want file format
+# examples in the packages as those are > 100 MB.
+test/file_format_examples export-ignore

surfacetopography-0.0.0/.github/workflows/flake8.yml

@@ -0,0 +1,31 @@
+name: Check coding conventions with flake8
+
+on:
+  push:
+    branches:
+      - '**'
+    tags:
+      - '**'
+  pull_request:
+    branches:
+      - '**'
+
+jobs:
+  tests:
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v6
+      with:
+        fetch-depth: 0
+
+        submodules: recursive
+
+    - name: Install dependencies
+      run: |
+        sudo apt-get update -qy
+        sudo apt-get install -y flake8
+
+    - name: Flake8
+      run: |
+        flake8 SurfaceTopography test

surfacetopography-0.0.0/.github/workflows/publish.yml

@@ -0,0 +1,80 @@
+name: Publish
+
+on:
+  push:
+    branches:
+      - master
+    tags:
+      - '*'
+
+jobs:
+  build:
+    runs-on: ubuntu-24.04
+
+    steps:
+      - uses: actions/checkout@v6
+        with:
+          fetch-depth: 0
+          submodules: recursive
+
+      - name: Installing Python
+        run: |
+          sudo apt-get update -qy
+          sudo apt-get install -y \
+            python3-dev \
+            python3-pip \
+            python3-venv \
+            meson \
+            ninja-build
+          python3 -m venv ../venv
+          source ../venv/bin/activate
+          pip install build
+
+      - name: Build package
+        run: |
+          source ../venv/bin/activate
+          python3 -m build . -s
+
+      - name: Install extension module
+        run: |
+          source ../venv/bin/activate
+          pip install dist/*.tar.gz
+
+      - name: Install sphinx
+        run: |
+          source ../venv/bin/activate
+          pip install sphinx sphinx_rtd_theme
+
+      - name: Build documentation
+        run: |
+          source ../venv/bin/activate
+          cd docs
+          sphinx-apidoc -o source/ ../SurfaceTopography
+          make html
+          cd ..
+
+      - name: Commit documentation changes
+        run: |
+          git clone https://github.com/ContactEngineering/SurfaceTopography.git --branch gh-pages --single-branch gh-pages
+          cp -r docs/_build/html/* gh-pages/
+          cd gh-pages
+          git config --local user.email "action@github.com"
+          git config --local user.name "GitHub Action"
+          git add .
+          git commit -m "Update documentation" -a || true
+          # The above command will fail if no changes were present, so we ignore
+          # that.
+
+      - name: Push documentation changes
+        uses: ad-m/github-push-action@master
+        with:
+          branch: gh-pages
+          directory: gh-pages
+          github_token: ${{ secrets.GITHUB_TOKEN }}
+
+      - name: Publish package
+        if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags')
+        uses: pypa/gh-action-pypi-publish@master
+        with:
+          user: __token__
+          password: ${{ secrets.PYPI_PASSWORD }}

surfacetopography-0.0.0/.github/workflows/test-code-functionality.yml

@@ -0,0 +1,86 @@
+name: Test code functionality
+
+on:
+  push:
+    branches:
+      - '**'
+    tags:
+      - '**'
+  pull_request:
+    branches:
+      - '**'
+  schedule:
+    - cron: "0 2 * * 5"  
+jobs:
+  tests:
+    runs-on: ubuntu-24.04
+    timeout-minutes: 45
+
+    strategy:
+      matrix:
+        mpi: ['no', 'mpi']
+        python-version: ['3.10', '3.11', '3.12', '3.13', '3.14']
+        mpi4py-version: [4.0.3]
+
+    steps:
+      - uses: actions/checkout@v6
+        with:
+          fetch-depth: 0
+          submodules: recursive
+
+      - name: Set up python3 ${{ matrix.python-version }}
+        uses: actions/setup-python@v6
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Install dependencies
+        run: |
+          sudo apt-get update -qy
+          python3 -m venv venv
+          source venv/bin/activate
+          python3 -m pip install --upgrade pip pip-tools meson build
+          if [ "${{ matrix.mpi }}" == "yes" ]; then
+            sudo apt-get install -y \
+              openmpi-bin \
+              libopenmpi-dev \
+              libfftw3-dev \
+              libfftw3-mpi-dev \
+              libhdf5-mpi-dev \
+              libpnetcdf-dev \
+              libnetcdf-pnetcdf-dev \
+              meson \
+              ninja-build
+            # Compute mpi4py, numpy and muGrid versions
+            pip-compile pyproject.toml
+            NUMPY_VERSION=$(grep 'numpy==' requirements.txt)
+            MUGRID_VERSION=$(grep 'mugrid==' requirements.txt)
+            echo "numpy version: ${NUMPY_VERSION}"
+            echo "muGrid version: ${MUGRID_VERSION}"
+            # Install numpy
+            pip install -v ${NUMPY_VERSION}
+            # Install mpi4py
+            echo "Installing mpi4py==${{ matrix.mpi4py-version }}"
+            CC=mpicc python3 -m pip install -v \
+              --no-binary mpi4py \
+              mpi4py==${{ matrix.mpi4py-version }}
+            # Manually install muGrid with MPI enabled
+            echo "Installing ${MUGRID_VERSION}"
+            pip install -v --no-binary muGrid ${MUGRID_VERSION}
+          else
+            sudo apt-get install -y \
+              libfftw3-dev \
+              libhdf5-dev \
+              libnetcdf-dev
+          fi
+          python3 -m pip list
+
+      - name: Install extension module
+        run: |
+          source venv/bin/activate
+          python3 -m pip install .[test]
+
+      - name: Test with pytest
+        run: |
+          source venv/bin/activate
+          python3 .check_mufft_capabilities.py ${{ matrix.mpi }}
+          if [ "${{ matrix.mpi }}" == "yes" ]; then python3 run-tests.py --no-build --verbose --full-trace; else python3 -m pytest --verbose --full-trace -s; fi

surfacetopography-0.0.0/.github/workflows/test-source-package.yml

@@ -0,0 +1,43 @@
+name: Test build and install of source package
+
+on:
+  push:
+    branches:
+      - '**'
+    tags:
+      - '**'
+  pull_request:
+    branches:
+      - '**'
+
+jobs:
+  tests:
+    runs-on: ubuntu-24.04
+
+    steps:
+      - uses: actions/checkout@v6
+        with:
+          fetch-depth: 0
+          submodules: recursive
+
+      - name: Installing Python
+        run: |
+          sudo apt-get update -qy
+          sudo apt-get install -y \
+            python3-dev \
+            python3-pip \
+            python3-venv \
+            ninja-build
+          python3 -m venv ../venv
+          source ../venv/bin/activate
+          python3 -m pip install --upgrade pip pip-tools meson build
+
+      - name: Build package
+        run: |
+          source ../venv/bin/activate
+          python3 -m build . -s
+
+      - name: Install package
+        run: |
+          source ../venv/bin/activate
+          pip install -v dist/*.tar.gz

surfacetopography-0.0.0/.github/workflows/wheels.yml

@@ -0,0 +1,95 @@
+name: Wheels
+
+on:
+  push:
+    branches:
+      - '**'
+    tags:
+      - '**'
+  pull_request:
+    branches:
+      - '**'
+
+jobs:
+  build_wheels:
+    name: Build wheel for ${{ matrix.python }}-${{ matrix.buildplat[1] }} ${{ matrix.buildplat[2] }}
+    runs-on: ${{ matrix.buildplat[0] }}
+    strategy:
+      matrix:
+        buildplat:
+        - [ubuntu-22.04, manylinux, x86_64]
+        - [ubuntu-22.04, manylinux, aarch64]
+        - [macos-14, macosx, arm64]
+        - [windows-2022, win, AMD64]
+        - [windows-2022, win, ARM64]
+        python: ["cp310", "cp311", "cp312", "cp313", "cp314"]
+      fail-fast: false
+
+    env:
+      IS_32_BIT: ${{ matrix.buildplat[2] == 'x86' }}
+      MACOSX_DEPLOYMENT_TARGET: "14.0"
+
+    steps:
+      - if: matrix.buildplat[2] == 'aarch64'
+        uses: docker/setup-qemu-action@v3
+        with:
+          platforms: all
+
+      - uses: actions/checkout@v6
+        with:
+          fetch-depth: 0
+          submodules: recursive
+
+      - uses: actions/setup-python@v6
+        with:
+          python-version: '3.14'
+
+      - name: Get version from DiscoverVersion
+        id: get_version
+        run: |
+          pip install DiscoverVersion
+          echo "version=$(python -m DiscoverVersion)" >> $GITHUB_OUTPUT
+        shell: bash
+
+      - name: Build wheels
+        uses: pypa/cibuildwheel@v3.3.1
+        env:
+          CIBW_BUILD: ${{ matrix.python }}-${{ matrix.buildplat[1] }}*
+          CIBW_ARCHS: ${{ matrix.buildplat[2] }}
+          CIBW_ENVIRONMENT: DISCOVER_VERSION=${{ steps.get_version.outputs.version }}
+          CIBW_ENVIRONMENT_PASS_LINUX: RUNNER_OS DISCOVER_VERSION
+          CIBW_BEFORE_BUILD_WINDOWS: pip install delvewheel
+          CIBW_REPAIR_WHEEL_COMMAND_WINDOWS: delvewheel repair -w {dest_dir} {wheel}
+          CIBW_TEST_COMMAND: python -c "import SurfaceTopography; print(SurfaceTopography.__version__)"
+          CIBW_TEST_SKIP: "*-*linux_{aarch64,ppc64le,s390x}"
+
+      - uses: actions/upload-artifact@v6
+        with:
+          path: ./wheelhouse/*.whl
+          name: ${{ matrix.python }}-${{ matrix.buildplat[1] }}-${{ matrix.buildplat[2] }}
+
+      - name: Release wheels
+        uses: softprops/action-gh-release@v2
+        if: startsWith(github.ref, 'refs/tags/')
+        with:
+          files: wheelhouse/*.whl
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+
+      - name: Check tag
+        id: check-tag
+        run: |
+          if [[ ${{ github.ref }} =~ ^refs/tags/[0-9]+\.[0-9]+\.[0-9]+$ ]]; then
+              echo ::set-output name=match::true
+          fi
+        shell: bash
+
+      - name: Deploy to PyPI
+        if: steps.check-tag.outputs.match == 'true'
+        run: |
+          pip install twine
+          twine upload wheelhouse/*.whl
+        env:
+          TWINE_USERNAME: __token__
+          TWINE_PASSWORD: ${{ secrets.PYPI_PASSWORD }}
+        shell: bash

surfacetopography-0.0.0/.gitignore

@@ -0,0 +1,29 @@
+*~
+*.pyc
+*.cpython*.so
+__pycache__
+../build
+dist
+*egg-info
+/tests/*.png
+/helpers/*.png
+/helpers/*.png.pdf
+/helpers/figs.pdf
+/notes/*/_region_*
+/notes/*/auto
+/notes/*/*.aux
+/notes/*/*.bbl
+/notes/*/*.blg
+/notes/*/*.log
+/notes/power_spectrum/power_spectrum.pdf
+/notes/power_spectrum/prv*
+/notes/auto/biblio.el
+/helpers/.ipynb_checkpoints/
+*.pyc
+.eggs
+.idea
+.vscode
+build
+docs/_build
+/subprojects/*
+!/subprojects/*.wrap

surfacetopography-0.0.0/.pre-commit-config.yaml

@@ -0,0 +1,11 @@
+repos:
+  - repo: https://github.com/pycqa/flake8
+    rev: '7.0.0'
+    hooks:
+    - id: flake8
+      name: flake8 (check python code style)
+  - repo: https://github.com/pycqa/isort
+    rev: '5.13.2'
+    hooks:
+      - id: isort
+        name: isort (check imports)

surfacetopography-0.0.0/AUTHORS

@@ -0,0 +1,14 @@
+Lintao Fang <michaelfanglt@gmail.com>
+Kai Haase <k.o.haase@googlemail.com>
+Johannes Hörmann <johannes.hoermann@imtek.uni-freiburg.de>
+Till Junge <till.junge@altermail.ch>
+Till Junge <till.junge@kit.edu>
+Till Junge <junge@Festwemse-3>
+Till Junge <junge@cmsjunge>
+Lars Pastewka <lars.pastewka@kit.edu>
+Lars Pastewka <lars.pastewka@imtek.uni-freiburg.de>
+Lars Pastewka <lars.pastewka@surface.design>
+Michael Röttger <info@michael-roettger.de>
+Antoine Sanner <antoine.sanner@imtek.uni-freiburg.de>
+Antoine Sanner <asanner@ethz.ch>
+Paul Strauch <paul-strauch@gmx.de>

surfacetopography-0.0.0/LICENSE.md

@@ -0,0 +1,19 @@
+### MIT license
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

surfacetopography-0.0.0/MANIFEST.in

@@ -0,0 +1,4 @@
+prune test
+include examples/*.py
+include examples/*.ipynb
+include c/*.h

surfacetopography-0.0.0/PKG-INFO

@@ -0,0 +1,99 @@
+Metadata-Version: 2.1
+Name: SurfaceTopography
+Version: 0.0.0
+Summary: Read and analyze surface topographies
+Author-Email: Lars Pastewka <lars.pastewka@imtek.uni-freiburg.de>, Kai Haase <k.o.haase@googlemail.com>, =?utf-8?q?Johannes_H=C3=B6rmann?= <johannes.hoermann@imtek.uni-freiburg.de>, Till Junge <till.junge@altermail.ch>, =?utf-8?q?Michael_R=C3=B6ttger?= <info@michael-roettger.de>, Antoine Sanner <antoine.sanner@imtek.uni-freiburg.de>
+License: ### MIT license
+         
+         Permission is hereby granted, free of charge, to any person obtaining a copy
+         of this software and associated documentation files (the "Software"), to deal
+         in the Software without restriction, including without limitation the rights
+         to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+         copies of the Software, and to permit persons to whom the Software is
+         furnished to do so, subject to the following conditions:
+         
+         The above copyright notice and this permission notice shall be included in
+         all copies or substantial portions of the Software.
+         
+         THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+         IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+         FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+         AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+         LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+         OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+         SOFTWARE.
+         
+Classifier: Development Status :: 5 - Production/Stable
+Classifier: Programming Language :: Python
+Project-URL: documentation, https://contactengineering.github.io/SurfaceTopography/
+Project-URL: repository, https://github.com/ContactEngineering/SurfaceTopography
+Project-URL: changelog, https://github.com/ContactEngineering/SurfaceTopography/blob/master/SurfaceTopography/ChangeLog.md
+Requires-Python: >=3.10.0
+Requires-Dist: numpy>=2.0.0
+Requires-Dist: scipy>=1.9.0
+Requires-Dist: defusedxml
+Requires-Dist: h5py
+Requires-Dist: igor2
+Requires-Dist: matplotlib>=1.0.0
+Requires-Dist: muGrid>=0.103.0
+Requires-Dist: NuMPI>=0.9.0
+Requires-Dist: numpyencoder
+Requires-Dist: openpyxl
+Requires-Dist: Pillow
+Requires-Dist: python-dateutil
+Requires-Dist: pyyaml
+Requires-Dist: requests
+Requires-Dist: tiffile
+Requires-Dist: xmltodict
+Requires-Dist: pandas
+Requires-Dist: pydantic
+Requires-Dist: zstandard
+Provides-Extra: test
+Requires-Dist: flake8<8; extra == "test"
+Requires-Dist: pytest; extra == "test"
+Requires-Dist: pytest-cov; extra == "test"
+Requires-Dist: pytest-flake8; extra == "test"
+Requires-Dist: runtests; extra == "test"
+Description-Content-Type: text/markdown
+
+[![Build Status](https://github.com/ContactEngineering/SurfaceTopography/actions/workflows/test-code-functionality.yml/badge.svg)](https://github.com/ContactEngineering/SurfaceTopography/actions/workflows/tests.yml)
+
+[![Ask DeepWiki](https://deepwiki.com/badge.svg)](https://deepwiki.com/ContactEngineering/SurfaceTopography)
+
+SurfaceTopography
+=================
+
+*Read and analyze surface topographies with Python.* This code implements basic classes for handling uniform and
+nonuniform surface topography data. It contains a rich set of import filters for experimental surface topography data.
+Surface topographies can be easily analyzed using standard (rms height, power spectrum, ...) and some special purpose
+(autocorrelation function, variable bandwidth analysis, ...) statistical techniques. 
+
+If you use this code, please cite:
+* [Jacobs, Junge, Pastewka, Surf. Topogr. Metrol. Prop. 1, 013001 (2017)](https://doi.org/10.1088/2051-672X/aa51f8)
+* [Röttger el al., Surf. Topogr. Metrol. Prop. 10, 035032 (2022)](https://doi.org/10.1088/2051-672X/ac860a) 
+
+Documentation
+-------------
+
+This README file contains a brief introduction into the code. The full documentation can be found at https://contactengineering.github.io/SurfaceTopography/.
+
+Installation
+------------
+
+Detailed instruction for the installation are provided in the [documentation](https://contactengineering.github.io/SurfaceTopography/installation.html?highlight=installation). If you want to install from source
+you need to run `git submodule update --init` after a fresh checkout.
+
+The most basic configuration of SurfaceTopography installs all requirements autonomously `python3 -m pip install SurfaceTopgography`
+
+If you need an editable install (e.g. for development purposes), make sure you disable build isolation:
+
+    python3 -m pip install --no-build-isolation -e .
+
+You need to manually install `ninja`, `meson-python`, `pytest`, `runtests`, `DiscoverVersion` and `numpy` before:
+
+    python3 -m pip install ninja meson-python pytest runtests DiscoverVersion numpy
+
+Funding
+-------
+
+Development of this project is funded by the [European Research Council](https://erc.europa.eu) within [Starting Grant 757343](https://cordis.europa.eu/project/id/757343) and by the [Deutsche Forschungsgemeinschaft](https://www.dfg.de/en) within projects [PA 2023/2](https://gepris.dfg.de/gepris/projekt/258153560) and [EXC 2193](https://gepris.dfg.de/gepris/projekt/390951807).

surfacetopography-0.0.0/README.md

@@ -0,0 +1,41 @@
+[![Build Status](https://github.com/ContactEngineering/SurfaceTopography/actions/workflows/test-code-functionality.yml/badge.svg)](https://github.com/ContactEngineering/SurfaceTopography/actions/workflows/tests.yml)
+
+[![Ask DeepWiki](https://deepwiki.com/badge.svg)](https://deepwiki.com/ContactEngineering/SurfaceTopography)
+
+SurfaceTopography
+=================
+
+*Read and analyze surface topographies with Python.* This code implements basic classes for handling uniform and
+nonuniform surface topography data. It contains a rich set of import filters for experimental surface topography data.
+Surface topographies can be easily analyzed using standard (rms height, power spectrum, ...) and some special purpose
+(autocorrelation function, variable bandwidth analysis, ...) statistical techniques. 
+
+If you use this code, please cite:
+* [Jacobs, Junge, Pastewka, Surf. Topogr. Metrol. Prop. 1, 013001 (2017)](https://doi.org/10.1088/2051-672X/aa51f8)
+* [Röttger el al., Surf. Topogr. Metrol. Prop. 10, 035032 (2022)](https://doi.org/10.1088/2051-672X/ac860a) 
+
+Documentation
+-------------
+
+This README file contains a brief introduction into the code. The full documentation can be found at https://contactengineering.github.io/SurfaceTopography/.
+
+Installation
+------------
+
+Detailed instruction for the installation are provided in the [documentation](https://contactengineering.github.io/SurfaceTopography/installation.html?highlight=installation). If you want to install from source
+you need to run `git submodule update --init` after a fresh checkout.
+
+The most basic configuration of SurfaceTopography installs all requirements autonomously `python3 -m pip install SurfaceTopgography`
+
+If you need an editable install (e.g. for development purposes), make sure you disable build isolation:
+
+    python3 -m pip install --no-build-isolation -e .
+
+You need to manually install `ninja`, `meson-python`, `pytest`, `runtests`, `DiscoverVersion` and `numpy` before:
+
+    python3 -m pip install ninja meson-python pytest runtests DiscoverVersion numpy
+
+Funding
+-------
+
+Development of this project is funded by the [European Research Council](https://erc.europa.eu) within [Starting Grant 757343](https://cordis.europa.eu/project/id/757343) and by the [Deutsche Forschungsgemeinschaft](https://www.dfg.de/en) within projects [PA 2023/2](https://gepris.dfg.de/gepris/projekt/258153560) and [EXC 2193](https://gepris.dfg.de/gepris/projekt/390951807).

surfacetopography-0.0.0/SurfaceTopography/CLI/ShowTopography.py

@@ -0,0 +1,17 @@
+import argparse
+
+from matplotlib import pyplot as plt
+
+from SurfaceTopography.IO import read_topography
+
+
+def main():
+    parser = argparse.ArgumentParser(
+        prog="show-topography", description="Visualize a surface topography"
+    )
+    parser.add_argument('filename')
+    args = parser.parse_args()
+
+    t = read_topography(args.filename)
+    t.plot()
+    plt.show()

surfacetopography-0.0.0/SurfaceTopography/CLI/meson.build

@@ -0,0 +1,13 @@
+# https://mesonbuild.com/Python-module.html
+
+# Pure Python sources
+python_sources = [
+    '__init__.py',
+    'ShowTopography.py'
+]
+
+# Install pure Python
+python.install_sources(
+    python_sources,
+    subdir: 'SurfaceTopography/CLI'
+)