pixi.toml

[workspace]
name = "mantidimaging"
version = "3.1.0"
description = "Graphical toolkit for tomography and time-of-flight imaging"
authors = [
    "Dolica Akello-Egwel, Jack Allen, Hussam Alhassan, Rachel Baust, James Cornal, Martyn Gigg, Despina Ioannide, Samuel Jones, Rasmia Kulan, Ashley Meigh, Daniel Nixon, Samuel Stock, Will Taylor, Sam Tygier",
]
channels = [
    "conda-forge",
    "astra-toolbox",
    "ccpi",
    "algotom",
    "https://software.repos.intel.com/python/conda",
]
requires-pixi = ">=0.59,<1.0"
platforms = ["linux-64", "win-64"]

[environments]
lint = ["lint", "runtime", "runtime-cpu"]
dev = ["runtime", "runtime-cpu", "dev", "test", "lint"]
dev-gpu = ["runtime", "runtime-gpu", "gpu-verify", "dev", "test", "lint"]
build-cpu = ["runtime", "runtime-cpu", "build"]
build-gpu = ["runtime", "runtime-gpu", "gpu-verify", "build"]

# Linting packages
[feature.lint.dependencies]
mypy = "==1.17"
pyright = "==1.1.391"
yapf = "0.43.*"
ruff = "0.3.7.*"
types-requests = "*"
types-pyyaml = "*"
types-docutils = "*"

# Testing packages
[feature.test.dependencies]
pytest = "7.4.*"
pytest-cov = "4.1.*"
pytest-randomly = "3.15.*"
pytest-xdist = "3.3.*"
testfixtures = "7.2.*"
pyfakefs = "5.3.*"
parameterized = "0.9.*"

# Packages required for development and building
[feature.dev.dependencies]
gitpython = "3.1.*"
coverage = ">=7.0,<7.5"
coveralls = "4.1.*"
pyinstaller = "6.14.*"
make = "==4.3"
pre-commit = "3.5.*"
sphinx = "8.2.*"
pydata-sphinx-theme = "0.16.*"
sphinx-copybutton = "0.5.*"
sphinx-design = "0.6.*"
attrs = ">=19.2.0,<23"         # Pinned due to conflict when installing eyes
setuptools = "72.*"

# pypi only packages for development (not available via conda)
[feature.dev.pypi-dependencies]
eyes-images = "==5.23.*"

# Core packages required at runtime
[feature.runtime.dependencies]
# Core Python and utilities
python = "3.12.*"
pip = "*"
numpy = "1.26.*"
scipy = "1.14.*"
numba = "0.61.*"
numexpr = "2.10.*"
requests = "2.32.*"
psutil = "5.9.*"
pyyaml = "*"

# Data I/O and file handling
h5py = "3.13.*"
hdf5 = ">=1.14.2,<1.15"
tifffile = "2023.7.18.*"
imagecodecs = ">=2023.9,<2025"
imageio = "2.33.*"

# Image processing and scientific libraries
astropy = "7.1.*"
scikit-image = "0.25.*"
jenkspy = "0.4.*"

# Tomography and reconstruction
algotom = "1.6.*"
tomopy = "1.12.*"
cil = "25.0.*"
ccpi-regulariser = "25.0.*"
ccpi-viewer = "25.0.*"

# Visualization and GUI
vtk = { version = ">=9.2.6,<9.4", build = "qt*" }
pyqt = { version = "5.15.11.*", build = "py312h*_2" }
qt-main = "5.15.15.*"
pyqtgraph = "0.13.7.*"
qt-material = "2.14.*"
darkdetect = "0.8.0.*"

# GPU-specific packages - common across all platforms
[feature.runtime-gpu.dependencies]
cudatoolkit = "11.8.*"
cupy = "12.3.*"

# Linux-specific GPU packages - Linux (CUDA-enabled builds)
[feature.runtime-gpu.target.linux-64.dependencies]
astra-toolbox = { version = "2.1.0.*", build = "cuda*" }
libastra = { version = "2.1.0.*", build = "cuda*" }

# Windows-specific GPU packages - Windows (CUDA-enabled builds with specific hashes)
[feature.runtime-gpu.target.win-64.dependencies]
astra-toolbox = { version = "2.1.0.*", build = "cudapy312h0f47501_105" }
libastra = { version = "2.1.0.*", build = "cuda11.8hb8fb34d_111" }

# CPU-specific packages (non-CUDA builds)
[feature.runtime-cpu.target.linux-64.dependencies]
astra-toolbox = "2.1.0.*"
libastra = "2.1.0.*"

# Windows-specific CPU packages - Windows (non-CUDA builds with specific hashes)
[feature.runtime-cpu.target.win-64.dependencies]
astra-toolbox = { version = "2.1.0.*", build = "py312h6965d8f_5" }
libastra = { version = "2.1.0.*" }

# GPU verification feature - adds __cuda requirement - needed to ensure GPU builds only go to GPU-capable systems
[feature.gpu-verify.system-requirements]
cuda = "11.8"

# Virtual package to ensure CUDA is available on GPU systems - needed for windows
[feature.gpu-verify.target.win-64.dependencies]
__cuda = "11.8.*"

# Packages required for building and uploading conda packages
[feature.build.dependencies]
boa = "*" #could potentially be removed with the migration to rattler-build
anaconda-client = "*"
conda-build = "*" #could potentially be removed with the migration to pixi
rattler-build = "*"

# Set environment variables for development environment during environment activation
[feature.dev.activation.env]
SOURCE_DIRS = "mantidimaging scripts docs/ext/"
CONDA_DLL_SEARCH_MODIFICATION_ENABLE = "1"

# Set environment variables for build environment during environment activation
[feature.build.activation.env]
UPLOAD_USER = "mantidimaging"
AUTHENTICATION_PARAMS = "--user $UPLOAD_USER --token $ANACONDA_API_TOKEN"

# Linux specific dependencies (to get Qt platform theme working)
[target.linux-64.dependencies]
qt-gtk-platformtheme = "5.15.15.*"

# Windows specific dependencies (to get VS runtime and Intel OpenMP for MKL)
[target.win-64.dependencies]
ipp = { version = "2021.12.*", channel = "https://software.repos.intel.com/python/conda" }

# Platform specific system and screenshot base tasks
[target.linux-64.tasks.test-system-base]
cmd = [
    "bash",
    "-c",
    """
    mkdir -p system_tests_output
    APPLITOOLS_IMAGE_DIR=system_tests_output TEST_RESULT_DIR=system_tests_output python -m pytest -vs -rs -p no:xdist -p no:randomly -p no:repeat -p no:cov -o log_cli=true --durations=10 --run-system-tests mantidimaging/gui/test/
    """,
]
env = { QT_QPA_PLATFORM = "offscreen" }
description = "Run system tests (Linux) without GUI display"

[target.linux-64.tasks.test-system-show-base]
cmd = [
    "bash",
    "-c",
    """
    mkdir -p system_tests_output
    APPLITOOLS_IMAGE_DIR=system_tests_output TEST_RESULT_DIR=system_tests_output python -m pytest -vs -rs -p no:xdist -p no:randomly -p no:repeat -p no:cov -o log_cli=true --run-system-tests-show mantidimaging/gui/test/
    """,
]

[target.linux-64.tasks.test-screenshots-base]
cmd = [
    "bash",
    "-c",
    """
    mkdir -p screenshot_tests_output
    echo "Screenshots directory: screenshot_tests_output"
    APPLITOOLS_API_KEY=local APPLITOOLS_IMAGE_DIR=screenshot_tests_output pytest -p no:xdist -p no:randomly -p no:cov mantidimaging/eyes_tests/ -vs --run-eyes-tests
    echo "Screenshots written to screenshot_tests_output"
    """,
]
env = { QT_QPA_PLATFORM = "offscreen" }
description = "Run screenshot tests (Linux) without GUI display"

[target.linux-64.tasks.test-screenshots-ci-base]
cmd = [
    "xvfb-run",
    "--auto-servernum",
    "bash",
    "-c",
    """
    mkdir -p screenshot_tests_output
    echo "Screenshots directory: screenshot_tests_output"
    APPLITOOLS_IMAGE_DIR=screenshot_tests_output pytest -p no:xdist -p no:randomly -p no:cov mantidimaging/eyes_tests/ -vs --run-eyes-tests
    echo "Screenshots written to screenshot_tests_output"
    """,
]
env = { QT_QPA_PLATFORM = "offscreen" }
description = "Run screenshot tests (Linux) in CI mode (requires APPLITOOLS_API_KEY, uses xvfb)"

[target.win-64.tasks.test-system-base]
cmd = [
    "cmd",
    "/c",
    "mkdir system_tests_output 2>nul & set TEST_RESULT_DIR=system_tests_output & set APPLITOOLS_IMAGE_DIR=system_tests_output & python -m pytest -vs -rs -p no:xdist -p no:randomly -p no:repeat -p no:cov -o log_cli=true --durations=10 --run-system-tests mantidimaging/gui/test/",
]
env = { QT_QPA_PLATFORM = "offscreen" }
description = "Run system tests (Windows)"

[target.win-64.tasks.test-screenshots-base]
cmd = [
    "cmd",
    "/c",
    "mkdir screenshot_tests_output 2>nul & set APPLITOOLS_API_KEY=local & set APPLITOOLS_IMAGE_DIR=%CD%\\screenshot_tests_output & pytest -p no:xdist -p no:randomly -p no:cov mantidimaging/eyes_tests/ -vs --run-eyes-tests",
]
description = "Run screenshot tests (Windows)"

[target.win-64.tasks.test-system-show-base]
cmd = [
    "cmd",
    "/c",
    "mkdir system_tests_output 2>nul & set TEST_RESULT_DIR=system_tests_output & set APPLITOOLS_IMAGE_DIR=system_tests_output & python -m pytest -vs -rs -p no:xdist -p no:randomly -p no:repeat -p no:cov -o log_cli=true --run-system-tests-show mantidimaging/gui/test/",
]
description = "Run system tests with GUI display (Windows)"

# System test variants for CPU and GPU
[tasks.test-system-cpu]
depends-on = [{ task = "test-system-base", environment = "dev" }]
description = "Run system tests (CPU)"

[tasks.test-system-gpu]
depends-on = [{ task = "test-system-base", environment = "dev-gpu" }]
description = "Run system tests (GPU)"

[tasks.test-system-show-cpu]
depends-on = [{ task = "test-system-show-base", environment = "dev" }]
description = "Run system tests with GUI display (CPU)"

[tasks.test-system-show-gpu]
depends-on = [{ task = "test-system-show-base", environment = "dev-gpu" }]
description = "Run system tests with GUI display (GPU)"

[tasks.test-screenshots-cpu]
depends-on = [{ task = "test-screenshots-base", environment = "dev" }]
description = "Run screenshot tests (CPU)"

[tasks.test-screenshots-cpu-ci]
depends-on = [{ task = "test-screenshots-ci-base", environment = "dev" }]
description = "Run screenshot tests in CI (CPU) - CI mode (requires APPLITOOLS_API_KEY)"

[tasks.test-screenshots-gpu]
depends-on = [{ task = "test-screenshots-base", environment = "dev-gpu" }]
description = "Run screenshot tests (GPU)"

# Combined linting task
[feature.lint.tasks]
# Base linting tasks (run in lint environment) - FAIL FAST (no || true)
mypy-base = { cmd = "python -m mypy --ignore-missing-imports $SOURCE_DIRS", description = "Run mypy type checks (fail on error)" }
pyright-base = { cmd = "python -m pyright", description = "Run pyright type checks (fail on error)" }
yapf-base = { cmd = "python -m yapf --parallel --diff --recursive $SOURCE_DIRS", description = "Check code formatting with yapf (fail on error)" }
yapf-staged-base = { cmd = "python -m yapf --parallel --diff", description = "Check formatting of staged files with yapf (for pre-commit)" }  
ruff-base = { cmd = "ruff check $SOURCE_DIRS", description = "Run ruff linter (fail on error)" }
ruff-staged-base = { cmd = "ruff check", description = "Run ruff on staged files (for pre-commit)" }

# Base linting tasks - CONTINUE ON ERROR (with || true)
mypy-base-continue = { cmd = "python -m mypy --ignore-missing-imports $SOURCE_DIRS || true", description = "Run mypy type checks (continue on error)" }
pyright-base-continue = { cmd = "python -m pyright || true", description = "Run pyright type checks (continue on error)" }
yapf-base-continue = { cmd = "python -m yapf --parallel --diff --recursive $SOURCE_DIRS || true", description = "Check code formatting with yapf (continue on error)" }
ruff-base-continue = { cmd = "ruff check $SOURCE_DIRS || true", description = "Run ruff linter (continue on error)" }
[feature.lint.activation.env]
SOURCE_DIRS = "mantidimaging scripts docs/ext/"

[feature.dev.tasks]
# Documentation base tasks
build-docs-base = { cmd = "python -c 'import shutil; shutil.rmtree(\"docs/api\", ignore_errors=True)' && sphinx-apidoc -f -M -e -T -d 3 mantidimaging '**/test' '**/test_helpers' '**/eyes_tests' '**/tests' 'mantidimaging/ipython' -o docs/api/ && sphinx-build -b html docs/ docs/build/html", cwd = ".", description = "Base task to build Sphinx documentation" }
build-docs-headless-base = { cmd = "python -c 'import shutil; shutil.rmtree(\"docs/api\", ignore_errors=True)' && sphinx-apidoc -f -M -e -T -d 3 mantidimaging '**/test' '**/test_helpers' '**/eyes_tests' '**/tests' 'mantidimaging/ipython' -o docs/api/ && sphinx-build -b html docs/ docs/build/html", cwd = ".", env = { QT_QPA_PLATFORM = "offscreen" }, description = "Base task to build Sphinx documentation in headless mode" }
serve-docs-base = { cmd = "python -m http.server 8000", cwd = "docs/build/html", description = "Base task to serve built documentation on http://localhost:8000" }
release-notes-base = { cmd = "python setup.py release_notes", description = "Base task to generate release notes" }
mypy-staged-base = { cmd = "python -m mypy --ignore-missing-imports", description = "Run mypy on staged files (for pre-commit)" }  
pyright-staged-base = { cmd = "python -m pyright", description = "Run pyright on staged files (for pre-commit)" }  
check-licenses = { cmd = "python -m CheckLicensesInFiles" }
check-release-notes-format = { cmd = "python -m CheckReleaseNoteFormat" }

setup-pre-commit = { cmd = "pre-commit install", description = "Install the Git pre-commit hook" }

[tasks]
#Run Mantid Imaging Application
MI-base = { cmd = "python -m mantidimaging", description = "Base task to launch Mantid Imaging GUI (used by other tasks)" }
MI-cpu = { depends-on = [{ task = "MI-base", environment = "dev" }], description = "Launch Mantid Imaging GUI with CPU support" }
MI-gpu = { depends-on = [{ task = "MI-base", environment = "dev-gpu" }], description = "Launch Mantid Imaging GUI with GPU support" }

MI-debug-base = { cmd = "python -X faulthandler -W default -m mantidimaging --log-level DEBUG", description = "Base task to launch Mantid Imaging GUI in debug mode (used by other tasks)" }
MI-debug-cpu = { depends-on = [{ task = "MI-debug-base", environment = "dev" }], description = "Launch Mantid Imaging GUI in debug mode with CPU support" }
MI-debug-gpu = { depends-on = [{ task = "MI-debug-base", environment = "dev-gpu" }], description = "Launch Mantid Imaging GUI in debug mode with GPU support" }

# Tests (suitable for CI as they do not require GUI)
test-base = { cmd = "python -m pytest -n auto --maxprocesses=4 --dist loadgroup", env = { QT_QPA_PLATFORM = "offscreen" }, description = "Base task to run unit tests (used by other tasks)" }
test-cpu = { depends-on = [{ task = "test-base", environment = "dev" }], description = "Run unit tests with CPU support" }
test-gpu = { depends-on = [{ task = "test-base", environment = "dev-gpu" }], description = "Run unit tests with GPU support" }
test-verbose-base = { cmd = "python -m pytest -vs -o log_cli=true", env = { QT_QPA_PLATFORM = "offscreen" }, description = "Base task to run tests with verbose output (used by other tasks)" }
test-verbose-cpu = { depends-on = [{ task = "test-verbose-base", environment = "dev" }], description = "Run tests with verbose output (CPU)" }
test-verbose-gpu = { depends-on = [{ task = "test-verbose-base", environment = "dev-gpu" }], description = "Run tests with verbose output (GPU)" }

# PyInstaller packaging tasks
package-pyinstaller-base = { cmd = "python PackageWithPyInstaller.py", cwd = "packaging", description = "Build PyInstaller package" }
package-pyinstaller-cpu = { depends-on = [{ task = "package-pyinstaller-base", environment = "dev" }], description = "Build PyInstaller package (CPU)" }
package-pyinstaller-gpu = { depends-on = [{ task = "package-pyinstaller-base", environment = "dev-gpu" }], description = "Build PyInstaller package (GPU)" }

# Static analysis tasks - FAIL FAST (stop on first error)
mypy = { depends-on = [{ task = "mypy-base", environment = "dev" }], description = "Run mypy type checks (fail on error)" }
pyright = { depends-on = [{ task = "pyright-base", environment = "dev" }], description = "Run pyright type checks (fail on error)" }
yapf = { depends-on = [{ task = "yapf-base", environment = "lint" }], description = "Check code formatting with yapf (fail on error)" }
ruff = { depends-on = [{ task = "ruff-base", environment = "lint" }], description = "Run ruff linter (fail on error)" }

# Static analysis tasks - CONTINUE ON ERROR (run all checks)
mypy-continue = { depends-on = [{ task = "mypy-base-continue", environment = "dev" }], description = "Run mypy type checks (continue on error)" }
pyright-continue = { depends-on = [{ task = "pyright-base-continue", environment = "dev" }], description = "Run pyright type checks (continue on error)" }
yapf-continue = { depends-on = [{ task = "yapf-base-continue", environment = "lint" }], description = "Check code formatting with yapf (continue on error)" }
ruff-continue = { depends-on = [{ task = "ruff-base-continue", environment = "lint" }], description = "Run ruff linter (continue on error)" }

# Utility task to apply yapf formatting
yapf-apply = { depends-on = [{ task = "yapf-apply-base", environment = "lint" }], description = "Apply yapf formatting" }

# Combined linting tasks - FAIL FAST (stop on first failure)
typecheck = { depends-on = ["mypy", "pyright"], description = "Run all type checks (stop on first error)" }
format-check = { depends-on = ["yapf", "ruff"], description = "Run all code format checks (stop on first error)" }
lint-all = { depends-on = ["mypy", "pyright", "yapf", "ruff"], description = "Run all linting checks (stop on first error)" }

# Combined linting tasks - CONTINUE ON ERROR (run all checks regardless of failures)
typecheck-continue = { depends-on = ["mypy-continue", "pyright-continue"], description = "Run all type checks (continue on error)" }
format-check-continue = { depends-on = ["yapf-continue", "ruff-continue"], description = "Run all code format checks (continue on error)" }
lint-all-continue = { depends-on = ["mypy-continue", "pyright-continue", "yapf-continue", "ruff-continue"], description = "Run all linting checks (continue on error)" }

# Documentation tasks
build-docs = { depends-on = [{ task = "build-docs-base", environment = "dev" }], description = "Build Sphinx documentation" }
build-docs-headless = { depends-on = [{ task = "build-docs-headless-base", environment = "dev" }], description = "Build Sphinx documentation in headless mode" }
release-notes = { depends-on = [{ task = "release-notes-base", environment = "dev" }], description = "Generate release notes" }
serve-docs = { depends-on = [{ task = "serve-docs-base", environment = "dev" }], description = "Serve built documentation on http://localhost:8000" }

# Cross-platform Tasks for building and uploading conda packages
#
# Build tasks requiring authentication check usage require environment variables:
#   export UPLOAD_USER="mantidimaging"
#   export ANACONDA_API_TOKEN="your-token-here"
#
# Local builds (no authentication):
#   pixi run build-conda-package-cpu
#   pixi run build-conda-package-gpu
#
# Authenticated builds (upload to Anaconda):
#   pixi run build-conda-package-nightly-cpu  # Uploads to nightly channel
#   pixi run build-conda-package-nightly-gpu  # Uploads to nightly channel
#   pixi run build-conda-package-release-cpu  # Uploads to main channel
#   pixi run build-conda-package-release-gpu  # Uploads to main channel
[feature.build.tasks]
# Check required environment variables for upload
check-upload-user = "python -c \"import os, sys; sys.exit(0 if os.environ.get('UPLOAD_USER') else (print('Environment variable UPLOAD_USER not set!', file=sys.stderr) or 1))\""
check-anaconda-api = "python -c \"import os, sys; sys.exit(0 if os.environ.get('ANACONDA_API_TOKEN') else (print('Environment variable ANACONDA_API_TOKEN not set!', file=sys.stderr) or 1))\""

# Base build commands (no authentication needed)
build-conda-package-base ="rattler-build build -r conda/recipe.yaml --experimental --output-dir output/unstable --config-file conda/recipe_config.toml"

# Build with authentication (for nightly/release)
build-conda-package-nightly-base = "python -c \"import os, subprocess, sys; user = os.environ.get('UPLOAD_USER', ''); token = os.environ.get('ANACONDA_API_TOKEN', ''); cmd = ['conda-build', 'conda', '--user', user, '--token', token, '--label', 'nightly']; sys.exit(subprocess.call(cmd))\""
build-conda-package-release-base = "python -c \"import os, subprocess, sys; user = os.environ.get('UPLOAD_USER', ''); token = os.environ.get('ANACONDA_API_TOKEN', ''); cmd = ['conda-build', 'conda', '--user', user, '--token', token]; sys.exit(subprocess.call(cmd))\""

# CPU and GPU build task variants
[tasks.build-conda-package-cpu]
depends-on = [{ task = "build-conda-package-base", environment = "build-cpu" }]
description = "Build conda package (CPU) - no upload"

[tasks.build-conda-package-gpu]
depends-on = [{ task = "build-conda-package-base", environment = "build-gpu" }]
description = "Build conda package (GPU) - no upload"

[tasks.build-conda-package-nightly-cpu]
depends-on = [
    { task = "check-upload-user", environment = "build-cpu" },
    { task = "check-anaconda-api", environment = "build-cpu" },
    { task = "build-conda-package-nightly-base", environment = "build-cpu" },
]
description = "Build nightly conda package (CPU)"

[tasks.build-conda-package-nightly-gpu]
depends-on = [
    { task = "check-upload-user", environment = "build-gpu" },
    { task = "check-anaconda-api", environment = "build-gpu" },
    { task = "build-conda-package-nightly-base", environment = "build-gpu" },
]
description = "Build nightly conda package (GPU)"

[tasks.build-conda-package-release-cpu]
depends-on = [
    { task = "check-upload-user", environment = "build-cpu" },
    { task = "check-anaconda-api", environment = "build-cpu" },
    { task = "build-conda-package-release-base", environment = "build-cpu" },
]
description = "Build release conda package (CPU)"

[tasks.build-conda-package-release-gpu]
depends-on = [
    { task = "check-upload-user", environment = "build-gpu" },
    { task = "check-anaconda-api", environment = "build-gpu" },
    { task = "build-conda-package-release-base", environment = "build-gpu" },
]
description = "Build release conda package (GPU)"