diploSHIC 1.0.6__tar.gz → 1.0.7__tar.gz

{diploshic-1.0.6/diploSHIC.egg-info → diploSHIC-1.0.7}/PKG-INFO

@@ -1,22 +1,16 @@
 Metadata-Version: 2.1
 Name: diploSHIC
-Version: 1.0.6
+Version: 1.0.7
 Summary: diploSHIC
 Home-page: https://github.com/kr-colab/diploSHIC
 Author: Andrew Kern
 Author-email: adkern@uoregon.edu
 License: MIT
+Platform: UNKNOWN
+Requires-Python: <3.12,>=3.10
 Description-Content-Type: text/markdown
-License-File: LICENSE
-Requires-Dist: numpy
-Requires-Dist: scipy
-Requires-Dist: matplotlib
-Requires-Dist: pandas
-Requires-Dist: scikit-allel
-Requires-Dist: scikit-learn
-Requires-Dist: tensorflow==2.15.0
-Requires-Dist: keras
 Provides-Extra: dev
+License-File: LICENSE
 
 # diploS/HIC
 This repo contains the implementation for `diploS/HIC` as described in Kern and Schrider (2018; https://doi.org/10.1534/g3.118.200262), along 
@@ -45,7 +39,7 @@ I'm going to focus on the steps involved to install on a linux machine using Ana
 package manager. Assuming you have conda installed, create a new conda env
 
 ```
-$ conda create -n diploshic python=3.9 --yes
+$ conda create -n diploshic python=3.10 --yes
 ```
 
 Note that because I'm using the Anaconda version of python, pip will only install this in the anaconda directory
@@ -69,6 +63,11 @@ You will need to determine if
 you want to use a CPU-only implementation (probably) or a GPU implementation of tensorflow. See
 https://www.tensorflow.org/install/install_linux for install instructions. 
 
+## Mac Installation
+
+1. install new versions of the compilers etc using brew (this seems to be the root of the issue) `brew install gcc gfortran libomp`
+2. set these environment variables export SYSTEM_VERSION_COMPAT=1 \\n && export LDFLAGS="-L/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/lib"
+build the diploshic packge from the root of the repo dir with pip install .
 
 ## Usage
 The main program that you will interface with is `diploSHIC`. This script is installed by default
@@ -359,3 +358,5 @@ the output predictions will be saved in `testEmpirical.preds` and should be stra
 In the interest of showing the user the whole enchilada when it comes to the workflow, I've provided the user
 with a more detailed example on the wiki of this repo. That example can be found here: https://github.com/kern-lab/diploSHIC/wiki/A-soup-to-nuts-example
 
+
+

{diploshic-1.0.6 → diploSHIC-1.0.7}/README.md

@@ -25,7 +25,7 @@ I'm going to focus on the steps involved to install on a linux machine using Ana
 package manager. Assuming you have conda installed, create a new conda env
 
 ```
-$ conda create -n diploshic python=3.9 --yes
+$ conda create -n diploshic python=3.10 --yes
 ```
 
 Note that because I'm using the Anaconda version of python, pip will only install this in the anaconda directory
@@ -49,6 +49,11 @@ You will need to determine if
 you want to use a CPU-only implementation (probably) or a GPU implementation of tensorflow. See
 https://www.tensorflow.org/install/install_linux for install instructions. 
 
+## Mac Installation
+
+1. install new versions of the compilers etc using brew (this seems to be the root of the issue) `brew install gcc gfortran libomp`
+2. set these environment variables export SYSTEM_VERSION_COMPAT=1 \\n && export LDFLAGS="-L/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/lib"
+build the diploshic packge from the root of the repo dir with pip install .
 
 ## Usage
 The main program that you will interface with is `diploSHIC`. This script is installed by default

{diploshic-1.0.6 → diploSHIC-1.0.7/diploSHIC.egg-info}/PKG-INFO

@@ -1,22 +1,16 @@
 Metadata-Version: 2.1
 Name: diploSHIC
-Version: 1.0.6
+Version: 1.0.7
 Summary: diploSHIC
 Home-page: https://github.com/kr-colab/diploSHIC
 Author: Andrew Kern
 Author-email: adkern@uoregon.edu
 License: MIT
+Platform: UNKNOWN
+Requires-Python: <3.12,>=3.10
 Description-Content-Type: text/markdown
-License-File: LICENSE
-Requires-Dist: numpy
-Requires-Dist: scipy
-Requires-Dist: matplotlib
-Requires-Dist: pandas
-Requires-Dist: scikit-allel
-Requires-Dist: scikit-learn
-Requires-Dist: tensorflow==2.15.0
-Requires-Dist: keras
 Provides-Extra: dev
+License-File: LICENSE
 
 # diploS/HIC
 This repo contains the implementation for `diploS/HIC` as described in Kern and Schrider (2018; https://doi.org/10.1534/g3.118.200262), along 
@@ -45,7 +39,7 @@ I'm going to focus on the steps involved to install on a linux machine using Ana
 package manager. Assuming you have conda installed, create a new conda env
 
 ```
-$ conda create -n diploshic python=3.9 --yes
+$ conda create -n diploshic python=3.10 --yes
 ```
 
 Note that because I'm using the Anaconda version of python, pip will only install this in the anaconda directory
@@ -69,6 +63,11 @@ You will need to determine if
 you want to use a CPU-only implementation (probably) or a GPU implementation of tensorflow. See
 https://www.tensorflow.org/install/install_linux for install instructions. 
 
+## Mac Installation
+
+1. install new versions of the compilers etc using brew (this seems to be the root of the issue) `brew install gcc gfortran libomp`
+2. set these environment variables export SYSTEM_VERSION_COMPAT=1 \\n && export LDFLAGS="-L/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/lib"
+build the diploshic packge from the root of the repo dir with pip install .
 
 ## Usage
 The main program that you will interface with is `diploSHIC`. This script is installed by default
@@ -359,3 +358,5 @@ the output predictions will be saved in `testEmpirical.preds` and should be stra
 In the interest of showing the user the whole enchilada when it comes to the workflow, I've provided the user
 with a more detailed example on the wiki of this repo. That example can be found here: https://github.com/kern-lab/diploSHIC/wiki/A-soup-to-nuts-example
 
+
+

{diploshic-1.0.6 → diploSHIC-1.0.7}/diploshic/fvTools.py

@@ -252,6 +252,7 @@ def readFa(faFileName, upper=False):
         fopen = open
     with fopen(faFileName, "rt") as faFile:
         reading = False
+        currChr = None
         for line in faFile:
             if line.startswith(">"):
                 if reading:
@@ -493,6 +494,10 @@ def readMaskDataForTraining(
     readingMasks = False
     isAccessible, isAccessibleArm = [], []
     genoMaskInfo = []
+    currChr = None
+    genos = None
+    positions = None
+    positions2SnpIndices = None
     with fopen(maskFileName, "rt") as maskFile:
         for line in maskFile:
             if line.startswith(">"):
@@ -916,7 +921,7 @@ def calcAndAppendStatValDiplo(
             - statVals["pi"][instanceIndex][subWinIndex]
         )
     elif statName == "HapCount":
-        statVals[statName][instanceIndex].append(len(hapsInSubWin.distinct()))
+        statVals[statName][instanceIndex].append(len(genosInSubWin.distinct()))
     elif statName == "nDiplos":
         diplotypeCounts = dps.getHaplotypeFreqSpec(genosNAlt)
         nDiplos = diplotypeCounts[genosNAlt.shape[1]]
@@ -1021,7 +1026,7 @@ def calcAndAppendStatValForScanDiplo(
         )
     elif statName == "HapCount":
         # AK: undefined variables
-        statVals[statName].append(len(hapsInSubWin.distinct()))
+        statVals[statName].append(len(genosInSubWin.distinct()))
     elif statName == "nDiplos":
         diplotypeCounts = dps.getHaplotypeFreqSpec(genosNAlt)
         nDiplos = diplotypeCounts[genosNAlt.shape[1]]

{diploshic-1.0.6 → diploSHIC-1.0.7}/pyproject.toml

@@ -1,4 +1,4 @@
 [build-system]
 build-backend = "setuptools.build_meta"
-requires = ["setuptools", "numpy"]
+requires = ["setuptools<60.0.0", "numpy"]
 

diploSHIC-1.0.7/setup.py

@@ -0,0 +1,47 @@
+from setuptools import setup
+from numpy.distutils.core import Extension, setup
+
+with open("README.md", "r") as fh:
+    long_description = fh.read()
+
+shic_stats = Extension(
+    "diploshic.shicstats",
+    sources=["diploshic/shicstats.pyf", "diploshic/utils.c"],
+)
+setup(
+    name="diploSHIC",
+    version="1.0.7",
+    description="diploSHIC",
+    python_requires="<3.12,>=3.10",
+    long_description=long_description,
+    long_description_content_type="text/markdown",
+    url="https://github.com/kr-colab/diploSHIC",
+    author="Andrew Kern",
+    author_email="adkern@uoregon.edu",
+    license="MIT",
+    packages=["diploshic"],
+    install_requires=[
+        "numpy",
+        "scipy",
+        "matplotlib",
+        "pandas",
+        "scikit-allel",
+        "scikit-learn",
+        "tensorflow==2.15.0",
+        "keras",
+    ],
+    scripts=[
+        "diploshic/diploSHIC",
+        "diploshic/makeFeatureVecsForChrArmFromVcfDiploid.py",
+        "diploshic/makeFeatureVecsForChrArmFromVcf_ogSHIC.py",
+        "diploshic/makeFeatureVecsForSingleMsDiploid.py",
+        "diploshic/makeFeatureVecsForSingleMs_ogSHIC.py",
+        "diploshic/makeTrainingSets.py",
+    ],
+    zip_safe=False,
+    extras_require={
+        "dev": [],
+    },
+    setup_requires=[],
+    ext_modules=[shic_stats],
+)

diploshic-1.0.6/setup.py

@@ -1,41 +0,0 @@
-from setuptools import setup
-from numpy.distutils.core import Extension, setup
-
-with open("README.md", "r") as fh:
-    long_description = fh.read()
-
-shic_stats = Extension("diploshic.shicstats",
-                       sources=["diploshic/shicstats.pyf",
-                                "diploshic/utils.c"],
-                      )
-setup(name='diploSHIC',
-      version='1.0.6',
-      description='diploSHIC',
-      long_description=long_description,
-      long_description_content_type="text/markdown",
-      url='https://github.com/kr-colab/diploSHIC',
-      author='Andrew Kern',
-      author_email='adkern@uoregon.edu',
-      license='MIT',
-      packages=['diploshic'],
-      install_requires=['numpy',
-                        'scipy',
-                        'matplotlib',
-                        'pandas',
-                        'scikit-allel',
-                        'scikit-learn',
-                        'tensorflow==2.15.0',
-                        'keras'],
-      scripts=['diploshic/diploSHIC',
-              'diploshic/makeFeatureVecsForChrArmFromVcfDiploid.py',
-              'diploshic/makeFeatureVecsForChrArmFromVcf_ogSHIC.py',
-              'diploshic/makeFeatureVecsForSingleMsDiploid.py',
-              'diploshic/makeFeatureVecsForSingleMs_ogSHIC.py',
-              'diploshic/makeTrainingSets.py'],
-      zip_safe=False,
-      extras_require={
-          'dev': [],
-      },
-      setup_requires=[],
-      ext_modules=[shic_stats]
-)