diploSHIC 1.0.7__tar.gz → 1.1.0__tar.gz

{diploSHIC-1.0.7 → diploshic-1.1.0}/MANIFEST.in

@@ -1,5 +1,3 @@
-include diploshic/shicstats.pyf
 include diploshic/testEmpirical.fvec
 include diploshic/testing/*
 include diploshic/training/*
-include diploshic/utils.c

{diploSHIC-1.0.7/diploSHIC.egg-info → diploshic-1.1.0}/PKG-INFO

@@ -1,16 +1,41 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.4
 Name: diploSHIC
-Version: 1.0.7
-Summary: diploSHIC
-Home-page: https://github.com/kr-colab/diploSHIC
-Author: Andrew Kern
-Author-email: adkern@uoregon.edu
+Version: 1.1.0
+Summary: A deep learning tool for identifying hard and soft selective sweeps in population genomic data
+Author-email: Andrew Kern <adkern@uoregon.edu>
+Maintainer-email: Andrew Kern <adkern@uoregon.edu>
 License: MIT
-Platform: UNKNOWN
-Requires-Python: <3.12,>=3.10
+Project-URL: Homepage, https://github.com/kr-colab/diploSHIC
+Project-URL: Documentation, https://github.com/kr-colab/diploSHIC/wiki
+Project-URL: Repository, https://github.com/kr-colab/diploSHIC.git
+Project-URL: Issues, https://github.com/kr-colab/diploSHIC/issues
+Keywords: population genetics,selective sweeps,deep learning,CNN,genomics,evolution
+Classifier: Development Status :: 5 - Production/Stable
+Classifier: Intended Audience :: Science/Research
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Operating System :: OS Independent
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Requires-Python: >=3.10
 Description-Content-Type: text/markdown
-Provides-Extra: dev
 License-File: LICENSE
+Requires-Dist: numpy>=1.20
+Requires-Dist: scipy>=1.7
+Requires-Dist: matplotlib>=3.5
+Requires-Dist: pandas>=1.3
+Requires-Dist: scikit-allel>=1.3
+Requires-Dist: scikit-learn>=1.0
+Requires-Dist: tensorflow<3.0,>=2.13
+Requires-Dist: keras>=2.13
+Requires-Dist: numba>=0.56
+Provides-Extra: dev
+Requires-Dist: pytest>=7.0; extra == "dev"
+Requires-Dist: pytest-cov>=4.0; extra == "dev"
+Requires-Dist: ruff>=0.1; extra == "dev"
+Dynamic: license-file
 
 # 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 
@@ -23,51 +48,38 @@ using simulation. 2) `diploS/HIC` training and performance evaluation. 3) Calcul
 genetic simulations must be performed using separate software such as discoal (https://github.com/kern-lab/discoal) 
 
 ## Installation
-`diploS/HIC` has a number of dependencies that should be straightforward to install using python package managers
-such as `conda` or `pip`. The complete list of dependencies looks like this:
-
-- numpy
-- scipy
-- pandas
-- scikit-allel
-- scikit-learn
-- tensorflow
-- keras
 
-## Install on linux
-I'm going to focus on the steps involved to install on a linux machine using Anaconda as our python source / main
-package manager. Assuming you have conda installed, create a new conda env
+`diploS/HIC` requires Python 3.10+ and has the following main dependencies:
 
-```
-$ conda create -n diploshic python=3.10 --yes
-```
+- numpy, scipy, pandas
+- scikit-allel, scikit-learn
+- tensorflow, keras
+- numba
 
-Note that because I'm using the Anaconda version of python, pip will only install this in the anaconda directory
-which is a good thing. Now we are ready to install `diploS/HIC` itself. We recommend using the binarys that
-we have packaged using pip. Simply type
+### Install from PyPI (recommended)
 
-```
+```bash
 pip install diploshic
 ```
 
-or if you prefer you can clone and build the repo yourself
+Or using [uv](https://docs.astral.sh/uv/):
 
+```bash
+uv pip install diploshic
 ```
-$ git clone https://github.com/kern-lab/diploSHIC.git
-$ cd diploSHIC 
-$ pip install .
-```
 
-This should automatically install all the dependencies including tensorflow.
-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. 
+### Install from source
+
+```bash
+git clone https://github.com/kr-colab/diploSHIC.git
+cd diploSHIC
+pip install .
+```
 
-## Mac Installation
+### GPU support
 
-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 .
+By default, TensorFlow installs with CPU support. For GPU acceleration, see
+the [TensorFlow GPU installation guide](https://www.tensorflow.org/install/gpu)
 
 ## Usage
 The main program that you will interface with is `diploSHIC`. This script is installed by default
@@ -145,6 +157,14 @@ optional arguments:
                         information (marked by 'N'). If specified, simulations
                         will be masked in a manner mirroring windows drawn
                         from this file.
+  --vcfForMaskFileName VCFFORMASKFILENAME
+                        Path to a VCF file that contains genotype information. This will be used to mask genotypes in a manner that mirrors how the true data are masked.
+  --popForMask POPFORMASK
+                        The label of the population for which we should draw genotype information from the VCF for masking purposes.
+  --sampleToPopFileName SAMPLETOPOPFILENAME
+                        Path to tab delimited file with population assignments (used for genotype masking); format: SampleID popID
+  --unmaskedGenoFracCutoff UNMASKEDGENOFRACCUTOFF
+                        Fraction of unmasked genotypes required to retain a site (default=0.75)
   --chrArmsForMasking CHRARMSFORMASKING
                         A comma-separated list (no spaces) of chromosome arms
                         from which we want to draw masking information (or
@@ -358,5 +378,3 @@ 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-1.0.7 → diploshic-1.1.0}/README.md

@@ -9,51 +9,38 @@ using simulation. 2) `diploS/HIC` training and performance evaluation. 3) Calcul
 genetic simulations must be performed using separate software such as discoal (https://github.com/kern-lab/discoal) 
 
 ## Installation
-`diploS/HIC` has a number of dependencies that should be straightforward to install using python package managers
-such as `conda` or `pip`. The complete list of dependencies looks like this:
 
-- numpy
-- scipy
-- pandas
-- scikit-allel
-- scikit-learn
-- tensorflow
-- keras
+`diploS/HIC` requires Python 3.10+ and has the following main dependencies:
 
-## Install on linux
-I'm going to focus on the steps involved to install on a linux machine using Anaconda as our python source / main
-package manager. Assuming you have conda installed, create a new conda env
+- numpy, scipy, pandas
+- scikit-allel, scikit-learn
+- tensorflow, keras
+- numba
 
-```
-$ conda create -n diploshic python=3.10 --yes
-```
+### Install from PyPI (recommended)
 
-Note that because I'm using the Anaconda version of python, pip will only install this in the anaconda directory
-which is a good thing. Now we are ready to install `diploS/HIC` itself. We recommend using the binarys that
-we have packaged using pip. Simply type
-
-```
+```bash
 pip install diploshic
 ```
 
-or if you prefer you can clone and build the repo yourself
+Or using [uv](https://docs.astral.sh/uv/):
 
+```bash
+uv pip install diploshic
 ```
-$ git clone https://github.com/kern-lab/diploSHIC.git
-$ cd diploSHIC 
-$ pip install .
-```
 
-This should automatically install all the dependencies including tensorflow.
-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. 
+### Install from source
+
+```bash
+git clone https://github.com/kr-colab/diploSHIC.git
+cd diploSHIC
+pip install .
+```
 
-## Mac Installation
+### GPU support
 
-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 .
+By default, TensorFlow installs with CPU support. For GPU acceleration, see
+the [TensorFlow GPU installation guide](https://www.tensorflow.org/install/gpu)
 
 ## Usage
 The main program that you will interface with is `diploSHIC`. This script is installed by default
@@ -131,6 +118,14 @@ optional arguments:
                         information (marked by 'N'). If specified, simulations
                         will be masked in a manner mirroring windows drawn
                         from this file.
+  --vcfForMaskFileName VCFFORMASKFILENAME
+                        Path to a VCF file that contains genotype information. This will be used to mask genotypes in a manner that mirrors how the true data are masked.
+  --popForMask POPFORMASK
+                        The label of the population for which we should draw genotype information from the VCF for masking purposes.
+  --sampleToPopFileName SAMPLETOPOPFILENAME
+                        Path to tab delimited file with population assignments (used for genotype masking); format: SampleID popID
+  --unmaskedGenoFracCutoff UNMASKEDGENOFRACCUTOFF
+                        Fraction of unmasked genotypes required to retain a site (default=0.75)
   --chrArmsForMasking CHRARMSFORMASKING
                         A comma-separated list (no spaces) of chromosome arms
                         from which we want to draw masking information (or

{diploSHIC-1.0.7 → diploshic-1.1.0/diploSHIC.egg-info}/PKG-INFO

@@ -1,16 +1,41 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.4
 Name: diploSHIC
-Version: 1.0.7
-Summary: diploSHIC
-Home-page: https://github.com/kr-colab/diploSHIC
-Author: Andrew Kern
-Author-email: adkern@uoregon.edu
+Version: 1.1.0
+Summary: A deep learning tool for identifying hard and soft selective sweeps in population genomic data
+Author-email: Andrew Kern <adkern@uoregon.edu>
+Maintainer-email: Andrew Kern <adkern@uoregon.edu>
 License: MIT
-Platform: UNKNOWN
-Requires-Python: <3.12,>=3.10
+Project-URL: Homepage, https://github.com/kr-colab/diploSHIC
+Project-URL: Documentation, https://github.com/kr-colab/diploSHIC/wiki
+Project-URL: Repository, https://github.com/kr-colab/diploSHIC.git
+Project-URL: Issues, https://github.com/kr-colab/diploSHIC/issues
+Keywords: population genetics,selective sweeps,deep learning,CNN,genomics,evolution
+Classifier: Development Status :: 5 - Production/Stable
+Classifier: Intended Audience :: Science/Research
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Operating System :: OS Independent
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Requires-Python: >=3.10
 Description-Content-Type: text/markdown
-Provides-Extra: dev
 License-File: LICENSE
+Requires-Dist: numpy>=1.20
+Requires-Dist: scipy>=1.7
+Requires-Dist: matplotlib>=3.5
+Requires-Dist: pandas>=1.3
+Requires-Dist: scikit-allel>=1.3
+Requires-Dist: scikit-learn>=1.0
+Requires-Dist: tensorflow<3.0,>=2.13
+Requires-Dist: keras>=2.13
+Requires-Dist: numba>=0.56
+Provides-Extra: dev
+Requires-Dist: pytest>=7.0; extra == "dev"
+Requires-Dist: pytest-cov>=4.0; extra == "dev"
+Requires-Dist: ruff>=0.1; extra == "dev"
+Dynamic: license-file
 
 # 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 
@@ -23,51 +48,38 @@ using simulation. 2) `diploS/HIC` training and performance evaluation. 3) Calcul
 genetic simulations must be performed using separate software such as discoal (https://github.com/kern-lab/discoal) 
 
 ## Installation
-`diploS/HIC` has a number of dependencies that should be straightforward to install using python package managers
-such as `conda` or `pip`. The complete list of dependencies looks like this:
-
-- numpy
-- scipy
-- pandas
-- scikit-allel
-- scikit-learn
-- tensorflow
-- keras
 
-## Install on linux
-I'm going to focus on the steps involved to install on a linux machine using Anaconda as our python source / main
-package manager. Assuming you have conda installed, create a new conda env
+`diploS/HIC` requires Python 3.10+ and has the following main dependencies:
 
-```
-$ conda create -n diploshic python=3.10 --yes
-```
+- numpy, scipy, pandas
+- scikit-allel, scikit-learn
+- tensorflow, keras
+- numba
 
-Note that because I'm using the Anaconda version of python, pip will only install this in the anaconda directory
-which is a good thing. Now we are ready to install `diploS/HIC` itself. We recommend using the binarys that
-we have packaged using pip. Simply type
+### Install from PyPI (recommended)
 
-```
+```bash
 pip install diploshic
 ```
 
-or if you prefer you can clone and build the repo yourself
+Or using [uv](https://docs.astral.sh/uv/):
 
+```bash
+uv pip install diploshic
 ```
-$ git clone https://github.com/kern-lab/diploSHIC.git
-$ cd diploSHIC 
-$ pip install .
-```
 
-This should automatically install all the dependencies including tensorflow.
-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. 
+### Install from source
+
+```bash
+git clone https://github.com/kr-colab/diploSHIC.git
+cd diploSHIC
+pip install .
+```
 
-## Mac Installation
+### GPU support
 
-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 .
+By default, TensorFlow installs with CPU support. For GPU acceleration, see
+the [TensorFlow GPU installation guide](https://www.tensorflow.org/install/gpu)
 
 ## Usage
 The main program that you will interface with is `diploSHIC`. This script is installed by default
@@ -145,6 +157,14 @@ optional arguments:
                         information (marked by 'N'). If specified, simulations
                         will be masked in a manner mirroring windows drawn
                         from this file.
+  --vcfForMaskFileName VCFFORMASKFILENAME
+                        Path to a VCF file that contains genotype information. This will be used to mask genotypes in a manner that mirrors how the true data are masked.
+  --popForMask POPFORMASK
+                        The label of the population for which we should draw genotype information from the VCF for masking purposes.
+  --sampleToPopFileName SAMPLETOPOPFILENAME
+                        Path to tab delimited file with population assignments (used for genotype masking); format: SampleID popID
+  --unmaskedGenoFracCutoff UNMASKEDGENOFRACCUTOFF
+                        Fraction of unmasked genotypes required to retain a site (default=0.75)
   --chrArmsForMasking CHRARMSFORMASKING
                         A comma-separated list (no spaces) of chromosome arms
                         from which we want to draw masking information (or
@@ -358,5 +378,3 @@ 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-1.0.7 → diploshic-1.1.0}/diploSHIC.egg-info/SOURCES.txt

@@ -2,11 +2,9 @@ LICENSE
 MANIFEST.in
 README.md
 pyproject.toml
-setup.py
 diploSHIC.egg-info/PKG-INFO
 diploSHIC.egg-info/SOURCES.txt
 diploSHIC.egg-info/dependency_links.txt
-diploSHIC.egg-info/not-zip-safe
 diploSHIC.egg-info/requires.txt
 diploSHIC.egg-info/top_level.txt
 diploshic/__init__.py
@@ -20,9 +18,8 @@ diploshic/makeFeatureVecsForSingleMs_ogSHIC.py
 diploshic/makeTrainingSets.py
 diploshic/misc.py
 diploshic/msTools.py
+diploshic/numba_stats.py
 diploshic/setup.py
-diploshic/shicstats.pyf
-diploshic/utils.c
 diploshic/testing/hard.fvec
 diploshic/testing/linkedHard.fvec
 diploshic/testing/linkedSoft.fvec
@@ -32,4 +29,5 @@ diploshic/training/hard.fvec
 diploshic/training/linkedHard.fvec
 diploshic/training/linkedSoft.fvec
 diploshic/training/neut.fvec
-diploshic/training/soft.fvec
+diploshic/training/soft.fvec
+tests/test_regression.py

diploshic-1.1.0/diploSHIC.egg-info/requires.txt

@@ -0,0 +1,14 @@
+numpy>=1.20
+scipy>=1.7
+matplotlib>=3.5
+pandas>=1.3
+scikit-allel>=1.3
+scikit-learn>=1.0
+tensorflow<3.0,>=2.13
+keras>=2.13
+numba>=0.56
+
+[dev]
+pytest>=7.0
+pytest-cov>=4.0
+ruff>=0.1

{diploSHIC-1.0.7 → diploshic-1.1.0}/diploshic/__init__.py

@@ -1,3 +1,3 @@
 from diploshic.fvTools import *
 from diploshic.msTools import *
-from diploshic.shicstats import *
+from diploshic.numba_stats import *