From 7a367e9fbfe9c17776f6ba529b04582db90176d0 Mon Sep 17 00:00:00 2001 From: Cooper Gamble Date: Tue, 25 Jul 2023 18:04:29 -0500 Subject: [PATCH] pair repo with fixes to algorithms --- GANDLF/__init__.py | 5 ----- {GANDLF => GANDLF_modules}/README.md | 0 {GANDLF/data/patch_miner => GANDLF_modules}/__init__.py | 0 {GANDLF => GANDLF_modules}/anonymize/__init__.py | 0 {GANDLF => GANDLF_modules}/anonymize/convert_to_nifti.py | 0 {GANDLF => GANDLF_modules}/cli/__init__.py | 0 {GANDLF => GANDLF_modules}/cli/config_generator.py | 0 {GANDLF => GANDLF_modules}/cli/deploy.py | 0 {GANDLF => GANDLF_modules}/cli/generate_metrics.py | 0 {GANDLF => GANDLF_modules}/cli/main_run.py | 0 {GANDLF => GANDLF_modules}/cli/patch_extraction.py | 0 .../cli/post_training_model_optimization.py | 0 {GANDLF => GANDLF_modules}/cli/preprocess_and_save.py | 0 {GANDLF => GANDLF_modules}/cli/recover_config.py | 0 {GANDLF => GANDLF_modules}/compute/__init__.py | 0 {GANDLF => GANDLF_modules}/compute/forward_pass.py | 0 {GANDLF => GANDLF_modules}/compute/generic.py | 0 {GANDLF => GANDLF_modules}/compute/inference_loop.py | 0 {GANDLF => GANDLF_modules}/compute/loss_and_metric.py | 0 {GANDLF => GANDLF_modules}/compute/step.py | 0 {GANDLF => GANDLF_modules}/compute/training_loop.py | 0 {GANDLF => GANDLF_modules}/data/ImagesFromDataFrame.py | 0 {GANDLF => GANDLF_modules}/data/__init__.py | 0 {GANDLF => GANDLF_modules}/data/augmentation/README.md | 0 {GANDLF => GANDLF_modules}/data/augmentation/__init__.py | 0 .../data/augmentation/blur_enhanced.py | 0 {GANDLF => GANDLF_modules}/data/augmentation/hed_augs.py | 0 .../data/augmentation/noise_enhanced.py | 0 {GANDLF => GANDLF_modules}/data/augmentation/rgb_augs.py | 0 {GANDLF => GANDLF_modules}/data/augmentation/rotations.py | 0 {GANDLF => GANDLF_modules}/data/augmentation/wrap_torchio.py | 0 .../data/inference_dataloader_histopath.py | 0 {GANDLF => GANDLF_modules}/data/patch_miner/README.md | 0 GANDLF_modules/data/patch_miner/__init__.py | 1 + {GANDLF => GANDLF_modules}/data/patch_miner/opm/__init__.py | 0 {GANDLF => GANDLF_modules}/data/patch_miner/opm/config.yml | 0 {GANDLF => GANDLF_modules}/data/patch_miner/opm/patch.py | 0 .../data/patch_miner/opm/patch_manager.py | 0 {GANDLF => GANDLF_modules}/data/patch_miner/opm/utils.py | 0 {GANDLF => GANDLF_modules}/data/post_process/README.md | 0 {GANDLF => GANDLF_modules}/data/post_process/__init__.py | 0 {GANDLF => GANDLF_modules}/data/post_process/morphology.py | 0 {GANDLF => GANDLF_modules}/data/post_process/tensor.py | 0 {GANDLF => GANDLF_modules}/data/preprocessing/README.md | 0 {GANDLF => GANDLF_modules}/data/preprocessing/__init__.py | 0 .../data/preprocessing/crop_zero_planes.py | 0 .../data/preprocessing/non_zero_normalize.py | 0 .../data/preprocessing/normalize_rgb.py | 0 .../data/preprocessing/resample_minimum.py | 0 .../data/preprocessing/rgb_conversion.py | 0 .../data/preprocessing/template_matching/README.md | 0 .../data/preprocessing/template_matching/__init__.py | 0 .../data/preprocessing/template_matching/base.py | 0 .../preprocessing/template_matching/histogram_matching.py | 0 .../data/preprocessing/template_matching/stain_extractors.py | 0 .../data/preprocessing/template_matching/stain_normalizer.py | 0 .../data/preprocessing/template_matching/utils.py | 0 .../data/preprocessing/threshold_and_clip.py | 0 {GANDLF => GANDLF_modules}/grad_clipping/__init__.py | 0 .../grad_clipping/adaptive_gradient_clipping.py | 0 {GANDLF => GANDLF_modules}/grad_clipping/clip_gradients.py | 0 {GANDLF => GANDLF_modules}/grad_clipping/grad_scaler.py | 0 {GANDLF => GANDLF_modules}/inference_manager.py | 0 {GANDLF => GANDLF_modules}/logger.py | 0 {GANDLF => GANDLF_modules}/losses/README.md | 0 {GANDLF => GANDLF_modules}/losses/__init__.py | 0 {GANDLF => GANDLF_modules}/losses/hybrid.py | 0 {GANDLF => GANDLF_modules}/losses/regression.py | 0 {GANDLF => GANDLF_modules}/losses/segmentation.py | 0 {GANDLF => GANDLF_modules}/metrics/README.md | 0 {GANDLF => GANDLF_modules}/metrics/__init__.py | 0 {GANDLF => GANDLF_modules}/metrics/classification.py | 0 {GANDLF => GANDLF_modules}/metrics/generic.py | 0 {GANDLF => GANDLF_modules}/metrics/regression.py | 0 {GANDLF => GANDLF_modules}/metrics/segmentation.py | 0 {GANDLF => GANDLF_modules}/metrics/synthesis.py | 0 {GANDLF => GANDLF_modules}/models/MSDNet.py | 0 {GANDLF => GANDLF_modules}/models/Readme.md | 0 {GANDLF => GANDLF_modules}/models/__init__.py | 0 {GANDLF => GANDLF_modules}/models/brain_age.py | 0 {GANDLF => GANDLF_modules}/models/deep_unet.py | 0 {GANDLF => GANDLF_modules}/models/densenet.py | 0 {GANDLF => GANDLF_modules}/models/efficientnet.py | 0 {GANDLF => GANDLF_modules}/models/fcn.py | 0 {GANDLF => GANDLF_modules}/models/imagenet_unet.py | 0 {GANDLF => GANDLF_modules}/models/imagenet_vgg.py | 0 {GANDLF => GANDLF_modules}/models/light_unet.py | 0 {GANDLF => GANDLF_modules}/models/light_unet_multilayer.py | 0 {GANDLF => GANDLF_modules}/models/modelBase.py | 0 {GANDLF => GANDLF_modules}/models/resnet.py | 0 {GANDLF => GANDLF_modules}/models/sdnet.py | 0 .../models/seg_modules/DecodingModule.py | 0 .../models/seg_modules/DownsamplingModule.py | 0 .../models/seg_modules/EncodingModule.py | 0 .../models/seg_modules/FCNUpsamplingModule.py | 0 {GANDLF => GANDLF_modules}/models/seg_modules/IncConv.py | 0 .../models/seg_modules/IncDownsamplingModule.py | 0 {GANDLF => GANDLF_modules}/models/seg_modules/IncDropout.py | 0 .../models/seg_modules/IncUpsamplingModule.py | 0 .../models/seg_modules/InceptionModule.py | 0 {GANDLF => GANDLF_modules}/models/seg_modules/InitialConv.py | 0 {GANDLF => GANDLF_modules}/models/seg_modules/Interpolate.py | 0 {GANDLF => GANDLF_modules}/models/seg_modules/Readme.md | 0 .../models/seg_modules/ResNetModule.py | 0 .../models/seg_modules/UpsamplingModule.py | 0 {GANDLF => GANDLF_modules}/models/seg_modules/__init__.py | 0 .../models/seg_modules/add_conv_block.py | 0 .../models/seg_modules/add_downsample_conv_block.py | 0 .../models/seg_modules/average_pool.py | 0 {GANDLF => GANDLF_modules}/models/seg_modules/out_conv.py | 0 {GANDLF => GANDLF_modules}/models/transunet.py | 0 {GANDLF => GANDLF_modules}/models/uinc.py | 0 {GANDLF => GANDLF_modules}/models/unet.py | 0 {GANDLF => GANDLF_modules}/models/unet_multilayer.py | 0 {GANDLF => GANDLF_modules}/models/unetr.py | 0 {GANDLF => GANDLF_modules}/models/vgg.py | 0 {GANDLF => GANDLF_modules}/optimizers/README.md | 0 {GANDLF => GANDLF_modules}/optimizers/__init__.py | 0 {GANDLF => GANDLF_modules}/optimizers/wrap_torch.py | 0 {GANDLF => GANDLF_modules}/parseConfig.py | 0 {GANDLF => GANDLF_modules}/schedulers/README.md | 0 {GANDLF => GANDLF_modules}/schedulers/__init__.py | 0 {GANDLF => GANDLF_modules}/schedulers/wrap_torch.py | 0 {GANDLF => GANDLF_modules}/training_manager.py | 0 {GANDLF => GANDLF_modules}/utils/__init__.py | 0 {GANDLF => GANDLF_modules}/utils/exceptions.py | 0 {GANDLF => GANDLF_modules}/utils/generic.py | 0 {GANDLF => GANDLF_modules}/utils/handle_collisions.py | 0 {GANDLF => GANDLF_modules}/utils/imaging.py | 0 {GANDLF => GANDLF_modules}/utils/modelbase.py | 0 {GANDLF => GANDLF_modules}/utils/modelio.py | 0 {GANDLF => GANDLF_modules}/utils/parameter_processing.py | 0 {GANDLF => GANDLF_modules}/utils/tensor.py | 0 {GANDLF => GANDLF_modules}/utils/write_parse.py | 0 {GANDLF => GANDLF_modules}/version.py | 0 135 files changed, 1 insertion(+), 5 deletions(-) delete mode 100644 GANDLF/__init__.py rename {GANDLF => GANDLF_modules}/README.md (100%) rename {GANDLF/data/patch_miner => GANDLF_modules}/__init__.py (100%) rename {GANDLF => GANDLF_modules}/anonymize/__init__.py (100%) rename {GANDLF => GANDLF_modules}/anonymize/convert_to_nifti.py (100%) rename {GANDLF => GANDLF_modules}/cli/__init__.py (100%) rename {GANDLF => GANDLF_modules}/cli/config_generator.py (100%) rename {GANDLF => GANDLF_modules}/cli/deploy.py (100%) rename {GANDLF => GANDLF_modules}/cli/generate_metrics.py (100%) rename {GANDLF => GANDLF_modules}/cli/main_run.py (100%) rename {GANDLF => GANDLF_modules}/cli/patch_extraction.py (100%) rename {GANDLF => GANDLF_modules}/cli/post_training_model_optimization.py (100%) rename {GANDLF => GANDLF_modules}/cli/preprocess_and_save.py (100%) rename {GANDLF => GANDLF_modules}/cli/recover_config.py (100%) rename {GANDLF => GANDLF_modules}/compute/__init__.py (100%) rename {GANDLF => GANDLF_modules}/compute/forward_pass.py (100%) rename {GANDLF => GANDLF_modules}/compute/generic.py (100%) rename {GANDLF => GANDLF_modules}/compute/inference_loop.py (100%) rename {GANDLF => GANDLF_modules}/compute/loss_and_metric.py (100%) rename {GANDLF => GANDLF_modules}/compute/step.py (100%) rename {GANDLF => GANDLF_modules}/compute/training_loop.py (100%) rename {GANDLF => GANDLF_modules}/data/ImagesFromDataFrame.py (100%) rename {GANDLF => GANDLF_modules}/data/__init__.py (100%) rename {GANDLF => GANDLF_modules}/data/augmentation/README.md (100%) rename {GANDLF => GANDLF_modules}/data/augmentation/__init__.py (100%) rename {GANDLF => GANDLF_modules}/data/augmentation/blur_enhanced.py (100%) rename {GANDLF => GANDLF_modules}/data/augmentation/hed_augs.py (100%) rename {GANDLF => GANDLF_modules}/data/augmentation/noise_enhanced.py (100%) rename {GANDLF => GANDLF_modules}/data/augmentation/rgb_augs.py (100%) rename {GANDLF => GANDLF_modules}/data/augmentation/rotations.py (100%) rename {GANDLF => GANDLF_modules}/data/augmentation/wrap_torchio.py (100%) rename {GANDLF => GANDLF_modules}/data/inference_dataloader_histopath.py (100%) rename {GANDLF => GANDLF_modules}/data/patch_miner/README.md (100%) create mode 100644 GANDLF_modules/data/patch_miner/__init__.py rename {GANDLF => GANDLF_modules}/data/patch_miner/opm/__init__.py (100%) rename {GANDLF => GANDLF_modules}/data/patch_miner/opm/config.yml (100%) rename {GANDLF => GANDLF_modules}/data/patch_miner/opm/patch.py (100%) rename {GANDLF => GANDLF_modules}/data/patch_miner/opm/patch_manager.py (100%) rename {GANDLF => GANDLF_modules}/data/patch_miner/opm/utils.py (100%) rename {GANDLF => GANDLF_modules}/data/post_process/README.md (100%) rename {GANDLF => GANDLF_modules}/data/post_process/__init__.py (100%) rename {GANDLF => GANDLF_modules}/data/post_process/morphology.py (100%) rename {GANDLF => GANDLF_modules}/data/post_process/tensor.py (100%) rename {GANDLF => GANDLF_modules}/data/preprocessing/README.md (100%) rename {GANDLF => GANDLF_modules}/data/preprocessing/__init__.py (100%) rename {GANDLF => GANDLF_modules}/data/preprocessing/crop_zero_planes.py (100%) rename {GANDLF => GANDLF_modules}/data/preprocessing/non_zero_normalize.py (100%) rename {GANDLF => GANDLF_modules}/data/preprocessing/normalize_rgb.py (100%) rename {GANDLF => GANDLF_modules}/data/preprocessing/resample_minimum.py (100%) rename {GANDLF => GANDLF_modules}/data/preprocessing/rgb_conversion.py (100%) rename {GANDLF => GANDLF_modules}/data/preprocessing/template_matching/README.md (100%) rename {GANDLF => GANDLF_modules}/data/preprocessing/template_matching/__init__.py (100%) rename {GANDLF => GANDLF_modules}/data/preprocessing/template_matching/base.py (100%) rename {GANDLF => GANDLF_modules}/data/preprocessing/template_matching/histogram_matching.py (100%) rename {GANDLF => GANDLF_modules}/data/preprocessing/template_matching/stain_extractors.py (100%) rename {GANDLF => GANDLF_modules}/data/preprocessing/template_matching/stain_normalizer.py (100%) rename {GANDLF => GANDLF_modules}/data/preprocessing/template_matching/utils.py (100%) rename {GANDLF => GANDLF_modules}/data/preprocessing/threshold_and_clip.py (100%) rename {GANDLF => GANDLF_modules}/grad_clipping/__init__.py (100%) rename {GANDLF => GANDLF_modules}/grad_clipping/adaptive_gradient_clipping.py (100%) rename {GANDLF => GANDLF_modules}/grad_clipping/clip_gradients.py (100%) rename {GANDLF => GANDLF_modules}/grad_clipping/grad_scaler.py (100%) rename {GANDLF => GANDLF_modules}/inference_manager.py (100%) rename {GANDLF => GANDLF_modules}/logger.py (100%) rename {GANDLF => GANDLF_modules}/losses/README.md (100%) rename {GANDLF => GANDLF_modules}/losses/__init__.py (100%) rename {GANDLF => GANDLF_modules}/losses/hybrid.py (100%) rename {GANDLF => GANDLF_modules}/losses/regression.py (100%) rename {GANDLF => GANDLF_modules}/losses/segmentation.py (100%) rename {GANDLF => GANDLF_modules}/metrics/README.md (100%) rename {GANDLF => GANDLF_modules}/metrics/__init__.py (100%) rename {GANDLF => GANDLF_modules}/metrics/classification.py (100%) rename {GANDLF => GANDLF_modules}/metrics/generic.py (100%) rename {GANDLF => GANDLF_modules}/metrics/regression.py (100%) rename {GANDLF => GANDLF_modules}/metrics/segmentation.py (100%) rename {GANDLF => GANDLF_modules}/metrics/synthesis.py (100%) rename {GANDLF => GANDLF_modules}/models/MSDNet.py (100%) rename {GANDLF => GANDLF_modules}/models/Readme.md (100%) rename {GANDLF => GANDLF_modules}/models/__init__.py (100%) rename {GANDLF => GANDLF_modules}/models/brain_age.py (100%) rename {GANDLF => GANDLF_modules}/models/deep_unet.py (100%) rename {GANDLF => GANDLF_modules}/models/densenet.py (100%) rename {GANDLF => GANDLF_modules}/models/efficientnet.py (100%) rename {GANDLF => GANDLF_modules}/models/fcn.py (100%) rename {GANDLF => GANDLF_modules}/models/imagenet_unet.py (100%) rename {GANDLF => GANDLF_modules}/models/imagenet_vgg.py (100%) rename {GANDLF => GANDLF_modules}/models/light_unet.py (100%) rename {GANDLF => GANDLF_modules}/models/light_unet_multilayer.py (100%) rename {GANDLF => GANDLF_modules}/models/modelBase.py (100%) rename {GANDLF => GANDLF_modules}/models/resnet.py (100%) rename {GANDLF => GANDLF_modules}/models/sdnet.py (100%) rename {GANDLF => GANDLF_modules}/models/seg_modules/DecodingModule.py (100%) rename {GANDLF => GANDLF_modules}/models/seg_modules/DownsamplingModule.py (100%) rename {GANDLF => GANDLF_modules}/models/seg_modules/EncodingModule.py (100%) rename {GANDLF => GANDLF_modules}/models/seg_modules/FCNUpsamplingModule.py (100%) rename {GANDLF => GANDLF_modules}/models/seg_modules/IncConv.py (100%) rename {GANDLF => GANDLF_modules}/models/seg_modules/IncDownsamplingModule.py (100%) rename {GANDLF => GANDLF_modules}/models/seg_modules/IncDropout.py (100%) rename {GANDLF => GANDLF_modules}/models/seg_modules/IncUpsamplingModule.py (100%) rename {GANDLF => GANDLF_modules}/models/seg_modules/InceptionModule.py (100%) rename {GANDLF => GANDLF_modules}/models/seg_modules/InitialConv.py (100%) rename {GANDLF => GANDLF_modules}/models/seg_modules/Interpolate.py (100%) rename {GANDLF => GANDLF_modules}/models/seg_modules/Readme.md (100%) rename {GANDLF => GANDLF_modules}/models/seg_modules/ResNetModule.py (100%) rename {GANDLF => GANDLF_modules}/models/seg_modules/UpsamplingModule.py (100%) rename {GANDLF => GANDLF_modules}/models/seg_modules/__init__.py (100%) rename {GANDLF => GANDLF_modules}/models/seg_modules/add_conv_block.py (100%) rename {GANDLF => GANDLF_modules}/models/seg_modules/add_downsample_conv_block.py (100%) rename {GANDLF => GANDLF_modules}/models/seg_modules/average_pool.py (100%) rename {GANDLF => GANDLF_modules}/models/seg_modules/out_conv.py (100%) rename {GANDLF => GANDLF_modules}/models/transunet.py (100%) rename {GANDLF => GANDLF_modules}/models/uinc.py (100%) rename {GANDLF => GANDLF_modules}/models/unet.py (100%) rename {GANDLF => GANDLF_modules}/models/unet_multilayer.py (100%) rename {GANDLF => GANDLF_modules}/models/unetr.py (100%) rename {GANDLF => GANDLF_modules}/models/vgg.py (100%) rename {GANDLF => GANDLF_modules}/optimizers/README.md (100%) rename {GANDLF => GANDLF_modules}/optimizers/__init__.py (100%) rename {GANDLF => GANDLF_modules}/optimizers/wrap_torch.py (100%) rename {GANDLF => GANDLF_modules}/parseConfig.py (100%) rename {GANDLF => GANDLF_modules}/schedulers/README.md (100%) rename {GANDLF => GANDLF_modules}/schedulers/__init__.py (100%) rename {GANDLF => GANDLF_modules}/schedulers/wrap_torch.py (100%) rename {GANDLF => GANDLF_modules}/training_manager.py (100%) rename {GANDLF => GANDLF_modules}/utils/__init__.py (100%) rename {GANDLF => GANDLF_modules}/utils/exceptions.py (100%) rename {GANDLF => GANDLF_modules}/utils/generic.py (100%) rename {GANDLF => GANDLF_modules}/utils/handle_collisions.py (100%) rename {GANDLF => GANDLF_modules}/utils/imaging.py (100%) rename {GANDLF => GANDLF_modules}/utils/modelbase.py (100%) rename {GANDLF => GANDLF_modules}/utils/modelio.py (100%) rename {GANDLF => GANDLF_modules}/utils/parameter_processing.py (100%) rename {GANDLF => GANDLF_modules}/utils/tensor.py (100%) rename {GANDLF => GANDLF_modules}/utils/write_parse.py (100%) rename {GANDLF => GANDLF_modules}/version.py (100%) diff --git a/GANDLF/__init__.py b/GANDLF/__init__.py deleted file mode 100644 index af28be2be..000000000 --- a/GANDLF/__init__.py +++ /dev/null @@ -1,5 +0,0 @@ -#!/usr/bin/env python3 -# -*- coding: UTF-8 -*- -from .version import __version__ - -version = __version__ # alias diff --git a/GANDLF/README.md b/GANDLF_modules/README.md similarity index 100% rename from GANDLF/README.md rename to GANDLF_modules/README.md diff --git a/GANDLF/data/patch_miner/__init__.py b/GANDLF_modules/__init__.py similarity index 100% rename from GANDLF/data/patch_miner/__init__.py rename to GANDLF_modules/__init__.py diff --git a/GANDLF/anonymize/__init__.py b/GANDLF_modules/anonymize/__init__.py similarity index 100% rename from GANDLF/anonymize/__init__.py rename to GANDLF_modules/anonymize/__init__.py diff --git a/GANDLF/anonymize/convert_to_nifti.py b/GANDLF_modules/anonymize/convert_to_nifti.py similarity index 100% rename from GANDLF/anonymize/convert_to_nifti.py rename to GANDLF_modules/anonymize/convert_to_nifti.py diff --git a/GANDLF/cli/__init__.py b/GANDLF_modules/cli/__init__.py similarity index 100% rename from GANDLF/cli/__init__.py rename to GANDLF_modules/cli/__init__.py diff --git a/GANDLF/cli/config_generator.py b/GANDLF_modules/cli/config_generator.py similarity index 100% rename from GANDLF/cli/config_generator.py rename to GANDLF_modules/cli/config_generator.py diff --git a/GANDLF/cli/deploy.py b/GANDLF_modules/cli/deploy.py similarity index 100% rename from GANDLF/cli/deploy.py rename to GANDLF_modules/cli/deploy.py diff --git a/GANDLF/cli/generate_metrics.py b/GANDLF_modules/cli/generate_metrics.py similarity index 100% rename from GANDLF/cli/generate_metrics.py rename to GANDLF_modules/cli/generate_metrics.py diff --git a/GANDLF/cli/main_run.py b/GANDLF_modules/cli/main_run.py similarity index 100% rename from GANDLF/cli/main_run.py rename to GANDLF_modules/cli/main_run.py diff --git a/GANDLF/cli/patch_extraction.py b/GANDLF_modules/cli/patch_extraction.py similarity index 100% rename from GANDLF/cli/patch_extraction.py rename to GANDLF_modules/cli/patch_extraction.py diff --git a/GANDLF/cli/post_training_model_optimization.py b/GANDLF_modules/cli/post_training_model_optimization.py similarity index 100% rename from GANDLF/cli/post_training_model_optimization.py rename to GANDLF_modules/cli/post_training_model_optimization.py diff --git a/GANDLF/cli/preprocess_and_save.py b/GANDLF_modules/cli/preprocess_and_save.py similarity index 100% rename from GANDLF/cli/preprocess_and_save.py rename to GANDLF_modules/cli/preprocess_and_save.py diff --git a/GANDLF/cli/recover_config.py b/GANDLF_modules/cli/recover_config.py similarity index 100% rename from GANDLF/cli/recover_config.py rename to GANDLF_modules/cli/recover_config.py diff --git a/GANDLF/compute/__init__.py b/GANDLF_modules/compute/__init__.py similarity index 100% rename from GANDLF/compute/__init__.py rename to GANDLF_modules/compute/__init__.py diff --git a/GANDLF/compute/forward_pass.py b/GANDLF_modules/compute/forward_pass.py similarity index 100% rename from GANDLF/compute/forward_pass.py rename to GANDLF_modules/compute/forward_pass.py diff --git a/GANDLF/compute/generic.py b/GANDLF_modules/compute/generic.py similarity index 100% rename from GANDLF/compute/generic.py rename to GANDLF_modules/compute/generic.py diff --git a/GANDLF/compute/inference_loop.py b/GANDLF_modules/compute/inference_loop.py similarity index 100% rename from GANDLF/compute/inference_loop.py rename to GANDLF_modules/compute/inference_loop.py diff --git a/GANDLF/compute/loss_and_metric.py b/GANDLF_modules/compute/loss_and_metric.py similarity index 100% rename from GANDLF/compute/loss_and_metric.py rename to GANDLF_modules/compute/loss_and_metric.py diff --git a/GANDLF/compute/step.py b/GANDLF_modules/compute/step.py similarity index 100% rename from GANDLF/compute/step.py rename to GANDLF_modules/compute/step.py diff --git a/GANDLF/compute/training_loop.py b/GANDLF_modules/compute/training_loop.py similarity index 100% rename from GANDLF/compute/training_loop.py rename to GANDLF_modules/compute/training_loop.py diff --git 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b/GANDLF_modules/utils/modelbase.py similarity index 100% rename from GANDLF/utils/modelbase.py rename to GANDLF_modules/utils/modelbase.py diff --git a/GANDLF/utils/modelio.py b/GANDLF_modules/utils/modelio.py similarity index 100% rename from GANDLF/utils/modelio.py rename to GANDLF_modules/utils/modelio.py diff --git a/GANDLF/utils/parameter_processing.py b/GANDLF_modules/utils/parameter_processing.py similarity index 100% rename from GANDLF/utils/parameter_processing.py rename to GANDLF_modules/utils/parameter_processing.py diff --git a/GANDLF/utils/tensor.py b/GANDLF_modules/utils/tensor.py similarity index 100% rename from GANDLF/utils/tensor.py rename to GANDLF_modules/utils/tensor.py diff --git a/GANDLF/utils/write_parse.py b/GANDLF_modules/utils/write_parse.py similarity index 100% rename from GANDLF/utils/write_parse.py rename to GANDLF_modules/utils/write_parse.py diff --git a/GANDLF/version.py b/GANDLF_modules/version.py similarity index 100% rename from GANDLF/version.py rename to GANDLF_modules/version.py