diploSHIC 1.0.5__tar.gz → 1.0.6__tar.gz

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (37) hide show
  1. {diploSHIC-1.0.5/diploSHIC.egg-info → diploshic-1.0.6}/PKG-INFO +2 -2
  2. {diploSHIC-1.0.5 → diploshic-1.0.6/diploSHIC.egg-info}/PKG-INFO +2 -2
  3. {diploSHIC-1.0.5 → diploshic-1.0.6}/diploSHIC.egg-info/requires.txt +1 -1
  4. {diploSHIC-1.0.5 → diploshic-1.0.6}/diploshic/diploSHIC +5 -5
  5. {diploSHIC-1.0.5 → diploshic-1.0.6}/setup.py +2 -2
  6. {diploSHIC-1.0.5 → diploshic-1.0.6}/LICENSE +0 -0
  7. {diploSHIC-1.0.5 → diploshic-1.0.6}/MANIFEST.in +0 -0
  8. {diploSHIC-1.0.5 → diploshic-1.0.6}/README.md +0 -0
  9. {diploSHIC-1.0.5 → diploshic-1.0.6}/diploSHIC.egg-info/SOURCES.txt +0 -0
  10. {diploSHIC-1.0.5 → diploshic-1.0.6}/diploSHIC.egg-info/dependency_links.txt +0 -0
  11. {diploSHIC-1.0.5 → diploshic-1.0.6}/diploSHIC.egg-info/not-zip-safe +0 -0
  12. {diploSHIC-1.0.5 → diploshic-1.0.6}/diploSHIC.egg-info/top_level.txt +0 -0
  13. {diploSHIC-1.0.5 → diploshic-1.0.6}/diploshic/__init__.py +0 -0
  14. {diploSHIC-1.0.5 → diploshic-1.0.6}/diploshic/fvTools.py +0 -0
  15. {diploSHIC-1.0.5 → diploshic-1.0.6}/diploshic/generateSimLaunchScript.py +0 -0
  16. {diploSHIC-1.0.5 → diploshic-1.0.6}/diploshic/makeFeatureVecsForChrArmFromVcfDiploid.py +0 -0
  17. {diploSHIC-1.0.5 → diploshic-1.0.6}/diploshic/makeFeatureVecsForChrArmFromVcf_ogSHIC.py +0 -0
  18. {diploSHIC-1.0.5 → diploshic-1.0.6}/diploshic/makeFeatureVecsForSingleMsDiploid.py +0 -0
  19. {diploSHIC-1.0.5 → diploshic-1.0.6}/diploshic/makeFeatureVecsForSingleMs_ogSHIC.py +0 -0
  20. {diploSHIC-1.0.5 → diploshic-1.0.6}/diploshic/makeTrainingSets.py +0 -0
  21. {diploSHIC-1.0.5 → diploshic-1.0.6}/diploshic/misc.py +0 -0
  22. {diploSHIC-1.0.5 → diploshic-1.0.6}/diploshic/msTools.py +0 -0
  23. {diploSHIC-1.0.5 → diploshic-1.0.6}/diploshic/setup.py +0 -0
  24. {diploSHIC-1.0.5 → diploshic-1.0.6}/diploshic/shicstats.pyf +0 -0
  25. {diploSHIC-1.0.5 → diploshic-1.0.6}/diploshic/testing/hard.fvec +0 -0
  26. {diploSHIC-1.0.5 → diploshic-1.0.6}/diploshic/testing/linkedHard.fvec +0 -0
  27. {diploSHIC-1.0.5 → diploshic-1.0.6}/diploshic/testing/linkedSoft.fvec +0 -0
  28. {diploSHIC-1.0.5 → diploshic-1.0.6}/diploshic/testing/neut.fvec +0 -0
  29. {diploSHIC-1.0.5 → diploshic-1.0.6}/diploshic/testing/soft.fvec +0 -0
  30. {diploSHIC-1.0.5 → diploshic-1.0.6}/diploshic/training/hard.fvec +0 -0
  31. {diploSHIC-1.0.5 → diploshic-1.0.6}/diploshic/training/linkedHard.fvec +0 -0
  32. {diploSHIC-1.0.5 → diploshic-1.0.6}/diploshic/training/linkedSoft.fvec +0 -0
  33. {diploSHIC-1.0.5 → diploshic-1.0.6}/diploshic/training/neut.fvec +0 -0
  34. {diploSHIC-1.0.5 → diploshic-1.0.6}/diploshic/training/soft.fvec +0 -0
  35. {diploSHIC-1.0.5 → diploshic-1.0.6}/diploshic/utils.c +0 -0
  36. {diploSHIC-1.0.5 → diploshic-1.0.6}/pyproject.toml +0 -0
  37. {diploSHIC-1.0.5 → diploshic-1.0.6}/setup.cfg +0 -0
{diploSHIC-1.0.5/diploSHIC.egg-info → diploshic-1.0.6}/PKG-INFO RENAMED
@@ -1,6 +1,6 @@
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  Metadata-Version: 2.1
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  Name: diploSHIC
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- Version: 1.0.5
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+ Version: 1.0.6
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  Summary: diploSHIC
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  Home-page: https://github.com/kr-colab/diploSHIC
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  Author: Andrew Kern
@@ -14,7 +14,7 @@ Requires-Dist: matplotlib
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  Requires-Dist: pandas
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  Requires-Dist: scikit-allel
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  Requires-Dist: scikit-learn
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- Requires-Dist: tensorflow
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+ Requires-Dist: tensorflow==2.15.0
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  Requires-Dist: keras
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  Provides-Extra: dev
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{diploSHIC-1.0.5 → diploshic-1.0.6/diploSHIC.egg-info}/PKG-INFO RENAMED
@@ -1,6 +1,6 @@
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  Metadata-Version: 2.1
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  Name: diploSHIC
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- Version: 1.0.5
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+ Version: 1.0.6
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  Summary: diploSHIC
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  Home-page: https://github.com/kr-colab/diploSHIC
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  Author: Andrew Kern
@@ -14,7 +14,7 @@ Requires-Dist: matplotlib
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  Requires-Dist: pandas
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  Requires-Dist: scikit-allel
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  Requires-Dist: scikit-learn
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- Requires-Dist: tensorflow
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+ Requires-Dist: tensorflow==2.15.0
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  Requires-Dist: keras
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  Provides-Extra: dev
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{diploSHIC-1.0.5 → diploshic-1.0.6}/diploSHIC.egg-info/requires.txt RENAMED
@@ -4,7 +4,7 @@ matplotlib
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  pandas
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  scikit-allel
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  scikit-learn
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- tensorflow
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+ tensorflow==2.15.0
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  keras
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  [dev]
{diploSHIC-1.0.5 → diploshic-1.0.6}/diploshic/diploSHIC RENAMED
@@ -321,7 +321,7 @@ if argsDict["mode"] in ["train", "predict"]:
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  from keras.layers import Dense, Dropout, Activation, Flatten, Input
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  from keras.layers import Conv2D, MaxPooling2D, concatenate
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  from sklearn.model_selection import train_test_split
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- from keras.preprocessing.image import ImageDataGenerator
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+ from tensorflow.keras.preprocessing.image import ImageDataGenerator
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  from keras.callbacks import EarlyStopping, ModelCheckpoint
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  import keras.backend as K
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  import fnmatch
@@ -495,7 +495,7 @@ if argsDict["mode"] == "train":
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  model_json = model.to_json()
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  with open(outputModel + ".json", "w") as json_file:
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  json_file.write(model_json)
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- modWeightsFilepath = outputModel + ".weights.hdf5"
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+ modWeightsFilepath = outputModel + ".weights.h5"
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  checkpoint = ModelCheckpoint(
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  modWeightsFilepath,
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  monitor="val_accuracy",
@@ -514,16 +514,16 @@ if argsDict["mode"] == "train":
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  start = time.time()
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  model.fit(
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  datagen.flow(X_train, Y_train, batch_size=32),
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- steps_per_epoch=len(X_train) / 32,
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+ steps_per_epoch=int(len(X_train) / 32),
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  epochs=epochOption,
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  verbose=1,
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  callbacks=callbacks_list,
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  validation_data=validation_gen.flow(X_valid, Y_valid, batch_size=32),
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- validation_steps=len(X_test) / 32,
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+ validation_steps=int(len(X_test) / 32),
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  )
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  # model.fit(X_train, Y_train, batch_size=32, epochs=100,validation_data=(X_test,Y_test),callbacks=callbacks_list, verbose=1)
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  score = model.evaluate(
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- test_gen.flow(X_test, Y_test, batch_size=32), steps=len(Y_test) / 32
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+ test_gen.flow(X_test, Y_test, batch_size=32), steps=int(len(Y_test) / 32)
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  )
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  sys.stderr.write(
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  "total time spent fitting and evaluating: %f secs\n"
{diploSHIC-1.0.5 → diploshic-1.0.6}/setup.py RENAMED
@@ -9,7 +9,7 @@ shic_stats = Extension("diploshic.shicstats",
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  "diploshic/utils.c"],
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  )
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  setup(name='diploSHIC',
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- version='1.0.5',
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+ version='1.0.6',
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  description='diploSHIC',
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  long_description=long_description,
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  long_description_content_type="text/markdown",
@@ -24,7 +24,7 @@ setup(name='diploSHIC',
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  'pandas',
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  'scikit-allel',
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  'scikit-learn',
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- 'tensorflow',
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+ 'tensorflow==2.15.0',
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  'keras'],
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  scripts=['diploshic/diploSHIC',
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  'diploshic/makeFeatureVecsForChrArmFromVcfDiploid.py',
{diploSHIC-1.0.5 → diploshic-1.0.6}/LICENSE RENAMED
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{diploSHIC-1.0.5 → diploshic-1.0.6}/MANIFEST.in RENAMED
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{diploSHIC-1.0.5 → diploshic-1.0.6}/README.md RENAMED
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{diploSHIC-1.0.5 → diploshic-1.0.6}/diploshic/misc.py RENAMED
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{diploSHIC-1.0.5 → diploshic-1.0.6}/diploshic/setup.py RENAMED
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{diploSHIC-1.0.5 → diploshic-1.0.6}/diploshic/utils.c RENAMED
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{diploSHIC-1.0.5 → diploshic-1.0.6}/pyproject.toml RENAMED
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{diploSHIC-1.0.5 → diploshic-1.0.6}/setup.cfg RENAMED
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