Restructure project into a named package

Author: mdraw

Diff for: LICENSE

@@ -1,6 +1,6 @@
 MIT License
 
-Copyright (c) 2021 Martin Drawitsch
+Copyright (c) 2021 - 2022 Martin Drawitsch
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

Diff for: __init__.py renamed to emcaps/__init__.py

@@ -33,8 +33,8 @@
 from elektronn3.data import transforms
 from elektronn3.models.unet import UNet
 
-from analysis.radial_patchlineplots import measure_outer_disk_radius
-import utils
+from emcaps.analysis.radial_patchlineplots import measure_outer_disk_radius
+from emcaps import utils
 
 
 def eul(paths):

Diff for: analysis/__init__.py renamed to emcaps/analysis/__init__.py

@@ -15,13 +15,11 @@
 
 import imageio
 import matplotlib.pyplot as plt
-import yaml
 import torch
 import numpy as np
 import pandas as pd
 from tqdm import tqdm
-from sklearn.metrics import confusion_matrix, ConfusionMatrixDisplay
-
+from sklearn.metrics import confusion_matrix
 
 # Don't move this stuff, it needs to be run this early to work
 import elektronn3
@@ -31,10 +29,7 @@
 from elektronn3.data import transforms
 from elektronn3.inference import Predictor
 
-from training.tifdirdata import UPatches
-
-from models.effnetv2 import effnetv2_s, effnetv2_m
-from analysis.cf_matrix import plot_confusion_matrix
+from emcaps.analysis.cf_matrix import plot_confusion_matrix
 
 parser = argparse.ArgumentParser(description='Evaluate a network.')
 parser.add_argument(

Diff for: analysis/average_patches.py renamed to emcaps/analysis/average_patches.py

@@ -26,7 +26,7 @@
 from elektronn3.data import transforms
 
 
-from utils import get_old_enctype, get_v5_enctype, OLDNAMES_TO_V5NAMES, clean_int, ensure_not_inverted, get_meta
+from emcaps.utils import get_old_enctype, get_v5_enctype, OLDNAMES_TO_V5NAMES, clean_int, ensure_not_inverted, get_meta
 
 
 # torch.backends.cudnn.benchmark = True

Diff for: analysis/cf_matrix.py renamed to emcaps/analysis/cf_matrix.py

@@ -48,11 +48,9 @@
 import cv2; cv2.setNumThreads(0); cv2.ocl.setUseOpenCL(False)
 import albumentations
 
-from training.tifdirdata import EncPatchData
-
-from models.effnetv2 import effnetv2_s, effnetv2_m
-
-import utils
+from emcaps.training.tifdirdata import EncPatchData
+from emcaps.models.effnetv2 import effnetv2_s, effnetv2_m
+from emcaps import utils
 
 
 parser = argparse.ArgumentParser(description='Train a network.')

Diff for: analysis/encari.py renamed to emcaps/analysis/encari.py

@@ -51,8 +51,8 @@
 
 from tqdm import tqdm
 
-from training.tifdirdata import EncSegData
-from utils import V5NAMES_TO_OLDNAMES
+from emcaps.training.tifdirdata import EncSegData
+from emcaps.utils import V5NAMES_TO_OLDNAMES
 
 
 # @dataclass
@@ -150,7 +150,7 @@
 else:
     DATA_SELECTION_V5NAMES = [args.constraintype]
 
-DATA_SELECTION = [V5NAMES_TO_OLDNAMES[n] for n in DATA_SELECTION_V5NAMES]
+DATA_SELECTION = [utils.V5NAMES_TO_OLDNAMES[n] for n in DATA_SELECTION_V5NAMES]
 
 
 

Diff for: analysis/naparivis.py renamed to emcaps/analysis/naparivis.py

@@ -17,7 +17,7 @@
 from skimage import morphology as sm
 from torch.utils import data
 
-import utils
+from emcaps import utils
 
 logger = logging.getLogger('elektronn3log')
 

Diff for: analysis/radial_patchlineplots.py renamed to emcaps/analysis/radial_patchlineplots.py

@@ -0,0 +1 @@
+from emcaps.utils.utils import *

Diff for: analysis/size_analysis.py renamed to emcaps/analysis/size_analysis.py

@@ -11,7 +11,7 @@
 import pandas as pd
 from skimage import measure
 
-from utils import get_meta, get_path_prefix, get_image_resources
+from emcaps.utils import get_meta, get_path_prefix, get_image_resources
 
 
 # Load original image sheet

Diff for: class_info.yaml renamed to emcaps/class_info.yaml

@@ -0,0 +1,3 @@
+[build-system]
+requires = ["setuptools", "setuptools-scm"]
+build-backend = "setuptools.build_meta"

Diff for: inference/__init__.py renamed to emcaps/inference/__init__.py

@@ -0,0 +1,24 @@
+[metadata]
+name = emcaps
+version = 0.1.0
+description = Code for the paper Genetically encoded barcodes for correlative volume electron microscopy
+long_description = file: README.md
+long_description_content_type = text/markdown
+license = MIT license
+classifiers =
+    Programming Language :: Python :: 3
+
+[options]
+packages = find:
+zip_safe = True
+include_package_data = True
+install_requires =
+    pandas == 1.4.1
+
+[options.entry_points]
+console_scripts =
+    emcaps-seginference = emcaps.inference.inference:main
+
+
+[options.package_data]
+* = README.md, *.yaml

Diff for: inference/patchifyseg.py renamed to emcaps/inference/patchifyseg.py

@@ -0,0 +1,5 @@
+# Just for `pip install -e` support until it works without setup.py
+
+from setuptools import setup
+
+setup()