temgym-core 0.1.0__tar.gz

temgym_core-0.1.0/.flake8

@@ -0,0 +1,4 @@
+[flake8]
+max-line-length = 100
+ignore = E24,E121,E123,E126,E128,E133,E226,E241,E242,E704,W503
+exclude = .git,__pycache__,.tox,build,dist,node_modules,TOXENV

temgym_core-0.1.0/.github/dependabot.yml

@@ -0,0 +1,8 @@
+version: 2
+updates:
+  - package-ecosystem: github-actions
+    directory: /
+    schedule:
+      interval: weekly
+    cooldown:
+      default-days: 7      # don't adopt brand-new releases immediately

temgym_core-0.1.0/.github/workflows/ci.yml

@@ -0,0 +1,75 @@
+name: CI
+
+on:
+  push:
+    branches:
+      - main
+      - 'v[0-9]*'
+    tags:
+      - 'v[0-9]*'
+  pull_request:
+
+concurrency: 
+  group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  tests:
+    strategy:
+      matrix:
+        python:
+          - version: "3.11"
+            toxenv: py311
+          - version: "3.12"
+            toxenv: py312
+          - version: "3.13"
+            toxenv: py313
+          - version: "3.14"
+            toxenv: py314
+          # - version: "3.15"
+          #   toxenv: py315
+        os: [ubuntu-latest, windows-latest]
+    runs-on: ${{ matrix.os }}
+    steps:
+      - uses: actions/checkout@v7
+        with:
+          persist-credentials: false
+      - name: Choose Python version ${{ matrix.python.version }}
+        uses: actions/setup-python@v7
+        with:
+          python-version: '${{ matrix.python.version }}'
+          cache: 'pip'
+      - name: install tox
+        run: python3 -m pip install tox tox-uv
+      - name: run tox
+        run: tox -e '${{ matrix.python.toxenv }}'
+      # - name: submit code coverage
+      #   uses: codecov/codecov-action@v4
+      #   env:
+      #     CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
+  mc-tests:
+    strategy:
+      matrix:
+        python_version: ["3.14"]
+        os: [ubuntu-latest]
+    runs-on: ${{ matrix.os }}
+    steps:
+      - uses: actions/checkout@v7
+        with:
+          persist-credentials: false
+      - name: Choose Python version ${{ matrix.python_version }}
+        uses: actions/setup-python@v7
+        with:
+          python-version: '${{ matrix.python_version }}'
+          cache: 'pip'
+      - name: install uv
+        run: python3 -m pip install uv
+      - name: install core
+        run: uv pip install --system .
+      - name: checkout mc
+        run: git clone -b main --single-branch https://github.com/LiberTEM/Microscope-Calibration.git
+      - name: install mc + test
+        working-directory: ./Microscope-Calibration
+        run: |
+          uv pip install --system .[test,common,diffraction,gui]
+          pytest tests/

temgym_core-0.1.0/.github/workflows/release.yml

@@ -0,0 +1,82 @@
+name: Release
+
+on:
+  release:
+    types: [released]        # stable releases only (not drafts or pre-releases)
+
+permissions: {}              # deny by default; each job opts in below
+
+jobs:
+  build:
+    name: Build and verify distributions
+    runs-on: ubuntu-24.04
+    timeout-minutes: 15
+    permissions:
+      contents: read
+    steps:
+      - uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7.0.1
+        with:
+          fetch-depth: 0               # hatch-vcs needs the tags
+          persist-credentials: false
+
+      - uses: astral-sh/setup-uv@c18668ad3cf93ea998bef934396af7bb5c839dc7 # v10.2.0
+        with:
+          enable-cache: false          # no cache in a publishing workflow
+
+      - name: Build sdist and wheel
+        run: uv build                  # builds the wheel from the sdist
+
+      - name: Check package metadata
+        run: uvx twine check --strict dist/*
+
+      - name: Smoke-test wheel and compare version with tag
+        env:
+          TAG: ${{ github.event.release.tag_name }}
+        run: |
+          VERSION=$(uv run --isolated --no-project --with dist/*.whl \
+            python -c "import importlib.metadata as m, temgym_core; print(m.version('temgym-core'))")
+          echo "Built version: $VERSION / release tag: $TAG"
+          test "v$VERSION" = "$TAG"    # assumes tags look like v0.1.0
+
+      - uses: actions/upload-artifact@cf430e030ddbb5b0abf93d22962f4752f3646cd9 # v7.0.2
+        with:
+          name: dist
+          path: dist/
+          if-no-files-found: error
+
+  publish-pypi:
+    name: Publish to PyPI
+    needs: build
+    runs-on: ubuntu-24.04
+    timeout-minutes: 10
+    environment:
+      name: pypi                       # must match the PyPI trusted-publisher entry
+      url: https://pypi.org/project/temgym-core/
+    permissions:
+      id-token: write                  # OIDC for Trusted Publishing; nothing else
+    steps:
+      - uses: actions/download-artifact@3e5f45b2cfb9172054b4087a40e8e0b5a5461e7c # v8.0.1
+        with:
+          name: dist
+          path: dist/
+      - uses: pypa/gh-action-pypi-publish@dc37677b2e1c63e2034f94d8a5b11f265b73ba33 # v1.14.2
+        # attestations (PEP 740) are generated automatically with Trusted Publishing
+
+  attach-to-release:                   # optional
+    name: Attach distributions to the GitHub release
+    needs: publish-pypi
+    runs-on: ubuntu-24.04
+    timeout-minutes: 10
+    permissions:
+      contents: write
+    steps:
+      - uses: actions/download-artifact@3e5f45b2cfb9172054b4087a40e8e0b5a5461e7c # v8.0.1
+        with:
+          name: dist
+          path: dist/
+      - name: Upload assets
+        env:
+          GH_TOKEN: ${{ github.token }}
+          TAG: ${{ github.event.release.tag_name }}
+        run: gh release upload "$TAG" dist/* --repo "$GITHUB_REPOSITORY"
+  

temgym_core-0.1.0/.gitignore

@@ -0,0 +1,41 @@
+*.swp
+*.pyc
+*.bib.bak
+*.bib.sav
+__pycache__
+.tox
+docs/build/
+.ipynb_checkpoints/
+*.egg-info
+htmlcov
+coverage.xml
+.coverage*
+.pytest_cache
+node_modules
+build
+dist
+*.AppImage
+dask-worker-space
+AppDir
+Miniconda3-latest-Linux-x86_64.sh
+MANIFEST
+.vscode
+pip-wheel-metadata
+data
+*Thumbs.db
+*.DS_Store
+*.idea
+.mypy_cache/
+.benchmarks
+junit.xml
+.vscode-server
+*.sif
+examples/generated/
+dist/
+*.lprof
+*.png
+*nsys-rep
+*.npy
+examples/fourdstem_example/fourdstem_array.npy
+.ruff_cache/
+*.cfg

temgym_core-0.1.0/.pre-commit-config.yaml

@@ -0,0 +1,28 @@
+# See https://pre-commit.com for more information
+# See https://pre-commit.com/hooks.html for more hooks
+repos:
+- repo: https://github.com/pre-commit/pre-commit-hooks
+  rev: v5.0.0
+  hooks:
+  - id: trailing-whitespace
+    files: ^src/
+  - id: end-of-file-fixer
+    files: ^src/
+  - id: check-yaml
+  - id: check-added-large-files
+- repo: https://github.com/pycqa/flake8
+  rev: 7.1.1
+  hooks:
+  - id: flake8
+    files: ^src/
+# - repo: https://github.com/regebro/pyroma
+#   rev: "4.2"
+#   hooks:
+#   - id: pyroma
+#     exclude: ^examples/
+- repo: https://github.com/asottile/pyupgrade
+  rev: v3.19.0
+  hooks:
+    - id: pyupgrade
+      args: ["--py37-plus"]
+      exclude: ^examples/

temgym_core-0.1.0/.readthedocs.yaml

@@ -0,0 +1,17 @@
+version: 2
+
+build:
+  os: "ubuntu-22.04"
+  tools:
+    python: "3.9"
+
+sphinx:
+  configuration: docs/conf.py
+  formats:
+  - epub
+  - pdf
+
+python:
+  install:
+    - requirements: requirements-doc.txt
+

temgym_core-0.1.0/CITATION.cff

@@ -0,0 +1,55 @@
+cff-version: 1.2.0
+message: "If you use this software, please cite it using the metadata from this file."
+type: software
+title: "TemGymCore"
+abstract: >-
+  A differentiable ray tracing package for transmission electron microscopy
+  built on JAX. Optical systems are described through the Jacobian (ABCD ray
+  transfer matrices) or Taylor-expansion coefficients of the ray coordinates
+  through the system, enabling, for example, the verification of coordinate
+  systems and descan error in 4D STEM shadow-image experiments.
+authors:
+  - family-names: Landers
+    given-names: David
+    email: davidlandersresearch@gmail.com
+    orcid: "https://orcid.org/0000-0002-3295-9473"
+    affiliation: "Univ. Grenoble Alpes, CEA, IRIG, MEM, LEMMA, 17 avenue des Martyrs, Grenoble, 38000, France"
+  - family-names: Bryan
+    given-names: Matthew
+    email: matthewbryan52@gmail.com
+    orcid: "https://orcid.org/0000-0001-9134-384X"
+    affiliation: "CEA LETI, France"
+  - family-names: Weber
+    given-names: Dieter
+    email: d.weber@fz-juelich.de
+    orcid: "https://orcid.org/0000-0001-6635-9567"
+    affiliation: "Ernst Ruska-Centre for Microscopy and Spectroscopy with Electrons, Forschungszentrum Jülich, 52425 Jülich, Germany"
+repository-code: "https://github.com/TemGym/TemGymCore"
+url: "https://github.com/TemGym/TemGymCore"
+license: GPL-3.0-only   # must match the SPDX license in pyproject.toml
+keywords:
+  - electron microscopy
+  - virtual twin
+  - ray tracing
+  - differentiable programming
+  - JAX
+  - 4D STEM
+references:
+  - type: article
+    authors:
+      - family-names: Landers
+        given-names: David
+      - family-names: Clancy
+        given-names: Ian
+      - family-names: Weber
+        given-names: Dieter
+      - family-names: Dunin-Borkowski
+        given-names: Rafal E.
+      - family-names: Stewart
+        given-names: Andrew
+    title: "TEMGYM Basic: transmission electron microscopy simulation software for teaching and training of microscope operation"
+    journal: "Journal of Applied Crystallography"
+    volume: 56
+    issue: 4
+    year: 2023
+    doi: "10.1107/S1600576723005174"