Merge release branch for v2.0.0#23
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…aining typing issues; add some to-do's.
Co-authored-by: Copilot Autofix powered by AI <175728472+Copilot@users.noreply.github.com>
IM2Deep 2.0 API
…hen multiconformer prediction
Fix calibration logic by removing error and multiconformer output in csv
…to release/2.0
Replace blanket type: ignore directives with proper type narrowing (profiler None check, dict key access) and add ty-specific suppression for the optional wandb import.
Add num_threads argument to predict for Torch CPU parallelization
Set up Sphinx with RTD theme, autodoc, sphinx-click, and intersphinx. Auto-generate API reference for public modules and CLI docs from Click decorators. Expand README installation section and use LaTeX math formatting in utils docstrings.
Add Sphinx documentation
…table 2.0 release
Prepare for stable 2.0 release
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Added
coremodule withpredictandpredict_and_calibrateas main public APIcalibrationmodule replacingcalibrate, withCalibrationandLinearCCSCalibrationclassesconstantsmodule for default model paths and configurationexceptionsmodule (public, replacing private_exceptions)_model_opsmodule for PyTorch model loading and inference_io_helpersmodule (split fromutils) for file parsing and I/O_architectures) with modular components: activations, blocks, callbacks, losses, helpersIM2DeepMulti)num_threadsargument to control Torch CPU parallelization--profileflag)Changed
predict_ccs/linear_calibrationtopredict/predict_and_calibrate.ckpt)predictas default commanddeeplcdependency todeeplc>=4.0.0b1,<5Removed
im2deep.pymodule (replaced bycore.py)calibrate.pymodule (replaced bycalibration.py)predict_multi.pymodule (functionality merged into architecture subpackage)numpy==1.26.0dependencyim2deeptraineroptional dependency