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HatPdotS
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removed 3.9 compatibility due to pytorch numpy conflicts
1 parent 0906c4d commit f53eda6

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Lines changed: 284 additions & 2 deletions

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‎pyproject.toml‎

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@@ -7,7 +7,7 @@ name = "torchref"
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version = "0.4.1"
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description = "Pytorch based crystallographic refinement"
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readme = "README.md"
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requires-python = ">=3.9"
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requires-python = ">=3.10"
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license = "MIT"
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authors = [
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{name = "HansPeterSeidel"},
@@ -88,7 +88,7 @@ torchref = ["data/*.csv", "data/*.json", "data/*.pt", "data/monomer_library/**/*
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[tool.black]
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line-length = 88
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target-version = ["py39"]
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target-version = ["py310"]
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[tool.isort]
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profile = "black"

‎tox.ini‎

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[tox]
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envlist =
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# Major Python versions with latest packages
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py310-latest
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py311-latest
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py312-latest
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py313-latest
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# NumPy 2.x version boundaries
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py311-numpy2x
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py312-numpy2x
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# Numba version tests
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py311-numba061
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py312-numba063
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# Minimum viable modern stack
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py310-minimum
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py311-minimum
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# PyTorch version tests
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py311-torch24
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py311-torch26
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# Pandas version tests
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py311-pandas20
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py311-pandas22
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# Crystallography stack tests
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py311-gemmi-min
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# Lower bounds test
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py310-lowerbounds
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py311-lowerbounds
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isolated_build = True
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skip_missing_interpreters = True
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[testenv]
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description = Run tests with {basepython}
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changedir = {toxinidir}
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setenv =
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PYTHONPATH = {toxinidir}
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deps =
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pytest>=6.0.0
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pytest-cov>=2.12.0
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# Base dependencies for all environments
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tqdm>=4.61.0
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gemmi>=0.5.0
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matplotlib>=3.4.0
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reciprocalspaceship>=0.9.0
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pyarrow>=4.0.0
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commands =
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python -c "import sys; print(f'Python: {sys.version}')"
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python -c "import numpy; print(f'numpy: {numpy.__version__}')"
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python -c "import pandas; print(f'pandas: {pandas.__version__}')"
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python -c "import torch; print(f'torch: {torch.__version__}')"
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python -c "import numba; print(f'numba: {numba.__version__}')"
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python -c "import scipy; print(f'scipy: {scipy.__version__}')"
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python -c "import torchref; print(f'torchref: {getattr(torchref, \"__version__\", \"unknown\")}')"
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pytest tests/ -v --tb=short -m "not gpu and not slow" {posargs}
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# =============================================================================
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# Python 3.10 - Minimum supported version
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# =============================================================================
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[testenv:py310-latest]
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description = Python 3.10 with latest packages
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basepython = python3.10
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deps =
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{[testenv]deps}
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numpy
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pandas
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torch
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numba
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scipy
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[testenv:py310-minimum]
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description = Python 3.10 with minimum viable versions (numpy 2.0 + torch 2.4)
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basepython = python3.10
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deps =
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{[testenv]deps}
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numpy==2.0.0
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pandas==2.0.0
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torch==2.4.0
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numba==0.61.0
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scipy==1.13.0
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[testenv:py310-lowerbounds]
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description = Python 3.10 testing lower version bounds
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basepython = python3.10
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deps =
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pytest>=6.0.0
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pytest-cov>=2.12.0
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numpy==2.0.0
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pandas==2.0.0
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torch==2.4.0
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tqdm==4.61.0
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numba==0.59.0
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gemmi==0.5.0
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scipy==1.10.0
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matplotlib==3.7.0
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reciprocalspaceship==0.9.18
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pyarrow==12.0.0
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# =============================================================================
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# Python 3.11 - Well-supported middle ground
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# =============================================================================
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[testenv:py311-latest]
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description = Python 3.11 with latest packages
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basepython = python3.11
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deps =
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{[testenv]deps}
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numpy
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pandas
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torch
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numba
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scipy
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[testenv:py311-numpy2x]
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description = Python 3.11 with NumPy 2.x
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basepython = python3.11
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deps =
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{[testenv]deps}
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numpy>=2.0.0
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pandas>=2.2.0
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torch>=2.4.0
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numba>=0.61.0
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scipy>=1.13.0
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[testenv:py311-numba061]
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description = Python 3.11 with numba 0.61 (first NumPy 2.x support)
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basepython = python3.11
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deps =
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{[testenv]deps}
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numpy>=2.0.0,<2.1.0
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pandas>=2.1.0
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torch>=2.4.0,<2.5.0
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numba>=0.61.0,<0.62.0
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scipy>=1.13.0,<1.14.0
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[testenv:py311-minimum]
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description = Python 3.11 with minimum viable versions (numpy 2.0 + torch 2.4)
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basepython = python3.11
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deps =
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{[testenv]deps}
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numpy==2.0.0
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pandas==2.0.0
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torch==2.4.0
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numba==0.61.0
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scipy==1.13.0
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# =============================================================================
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# Python 3.12 - Latest stable Python
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# =============================================================================
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[testenv:py312-latest]
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description = Python 3.12 with latest packages
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basepython = python3.12
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deps =
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{[testenv]deps}
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numpy
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pandas
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torch
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numba
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scipy
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[testenv:py312-numpy2x]
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description = Python 3.12 with NumPy 2.x stack
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basepython = python3.12
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deps =
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{[testenv]deps}
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numpy>=2.0.0
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pandas>=2.2.0
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torch>=2.4.0
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numba>=0.61.0
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scipy>=1.13.0
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[testenv:py312-numba063]
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description = Python 3.12 with numba 0.63 (latest)
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basepython = python3.12
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deps =
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{[testenv]deps}
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numpy>=2.0.0
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pandas>=2.2.0
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torch>=2.5.0
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numba>=0.63.0
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scipy>=1.14.0
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# =============================================================================
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# Python 3.13 - Latest Python
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# =============================================================================
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[testenv:py313-latest]
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description = Python 3.13 with latest packages
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basepython = python3.13
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deps =
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{[testenv]deps}
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numpy
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pandas
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torch
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numba
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scipy
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# =============================================================================
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# PyTorch Version Tests
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# =============================================================================
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[testenv:py311-torch24]
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description = Python 3.11 with PyTorch 2.4 (minimum supported)
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basepython = python3.11
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deps =
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{[testenv]deps}
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numpy>=2.0.0,<2.1.0
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pandas>=2.1.0,<2.3.0
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torch>=2.4.0,<2.5.0
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numba>=0.61.0,<0.62.0
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scipy>=1.13.0,<1.14.0
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[testenv:py311-torch26]
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description = Python 3.11 with PyTorch 2.6
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basepython = python3.11
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deps =
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{[testenv]deps}
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numpy>=2.1.0,<2.2.0
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pandas>=2.2.0,<2.3.0
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torch>=2.6.0,<2.7.0
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numba>=0.61.0,<0.62.0
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scipy>=1.14.0,<1.15.0
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# =============================================================================
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# Pandas Version Tests
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# =============================================================================
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[testenv:py311-pandas20]
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description = Python 3.11 with Pandas 2.0
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basepython = python3.11
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deps =
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{[testenv]deps}
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numpy>=2.0.0,<2.1.0
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pandas>=2.0.0,<2.1.0
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torch>=2.4.0,<2.5.0
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numba>=0.61.0,<0.62.0
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scipy>=1.13.0,<1.14.0
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[testenv:py311-pandas22]
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description = Python 3.11 with Pandas 2.2
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basepython = python3.11
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deps =
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{[testenv]deps}
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numpy>=2.0.0,<2.2.0
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pandas>=2.2.0,<2.3.0
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torch>=2.4.0,<2.6.0
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numba>=0.61.0,<0.62.0
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scipy>=1.13.0,<1.15.0
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# =============================================================================
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# Crystallography Stack Tests
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# =============================================================================
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[testenv:py311-gemmi-min]
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description = Python 3.11 with gemmi 0.5.0 (declared minimum)
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basepython = python3.11
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deps =
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pytest>=6.0.0
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pytest-cov>=2.12.0
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tqdm>=4.61.0
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gemmi==0.5.0
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matplotlib>=3.4.0
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reciprocalspaceship>=0.9.0,<1.0.0
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pyarrow>=4.0.0
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numpy>=2.0.0,<2.1.0
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pandas>=2.0.0,<2.2.0
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torch>=2.4.0,<2.5.0
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numba>=0.61.0,<0.62.0
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scipy>=1.13.0,<1.14.0
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# =============================================================================
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# Lower Bounds Test - Test declared minimums from pyproject.toml
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# =============================================================================
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[testenv:py311-lowerbounds]
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description = Python 3.11 testing lower version bounds
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basepython = python3.11
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deps =
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pytest>=6.0.0
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pytest-cov>=2.12.0
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numpy==2.0.0
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pandas==2.0.0
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torch==2.4.0
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tqdm==4.61.0
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numba==0.59.0
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gemmi==0.5.0
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scipy==1.10.0
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matplotlib==3.7.0
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reciprocalspaceship==0.9.18
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pyarrow==12.0.0

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