Merge pull request #317 from AKUMAR0019/master

Changes to README and nidm_linreg

Author: dbkeator

README.rst

@@ -18,6 +18,10 @@ Dependencies
 * OS-X: `brew install graphviz`
 * Datalad (optional): `pip install datalad`
 * Git-Annex (optional): <https://git-annex.branchable.com/>
+* Sklearn: `pip install sklearn`
+* Statsmodels: `pip install statsmodels`
+* Statistics: `pip install statistics`
+* Patsy: `pip install patsy`
 
 Installation
 ============
@@ -33,8 +37,12 @@ macOS
 -----  
 .. code-block:: bash
 
+	$ ruby -e "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/master/install)"
+	$ brew install miniconda --cask
+	$ conda init
+	$ conda update conda
 	$ conda create -n pynidm_py3 python=3
-	$ source activate pynidm_py3
+	$ conda activate pynidm_py3
 	$ cd PyNIDM
  	$ pip install datalad
 	$ pip install neurdflib

nidm/experiment/tools/nidm_linreg.py

@@ -7,7 +7,7 @@
 #  License: Apache License, Version 2.0
 # *******************************************************************************************************
 # *******************************************************************************************************
-# Date: 10-09-21                 Coded by: Ashmita Kumar (ashmita.kumar@gmail.com)
+# Date: 07-26-22                 Coded by: Ashmita Kumar (ashmita.kumar@gmail.com)
 # Filename: nidm_linreg.py
 #
 # Program description:  This program provides a tool to complete a linear regression on nidm files
@@ -43,47 +43,24 @@
 from nidm.experiment.tools.click_base import cli
 from nidm.experiment.tools.rest import RestParser
 import numpy as np
-try:
-    from sklearn.linear_model import LinearRegression
-    from sklearn import preprocessing
-    from sklearn.linear_model import Ridge
-    from sklearn.linear_model import Lasso
-    from sklearn.model_selection import cross_val_score
-except:
-    system('python -m pip install --upgrade pip sklearn')
-    from sklearn.linear_model import LinearRegression
-    from sklearn import preprocessing
-    from sklearn.linear_model import Ridge
-    from sklearn.linear_model import Lasso
-    from sklearn.model_selection import cross_val_score
-
-try:
-    import statsmodels.api as sm
-    from statsmodels.formula.api import ols
-except:
-    system('python -m pip install --upgrade pip statsmodels')
-    import statsmodels.api as sm
-    from statsmodels.formula.api import ols
-
-try:
-    from statistics import mean
-except:
-    system('python -m pip install --upgrade pip statistics')
-    from statistics import mean
-
-try:
-    from patsy.contrasts import Treatment
-    from patsy.contrasts import ContrastMatrix
-    from patsy.contrasts import Sum
-    from patsy.contrasts import Diff
-    from patsy.contrasts import Helmert
-except:
-    system('python -m pip install --upgrade pip patsy')
-    from patsy.contrasts import Treatment
-    from patsy.contrasts import ContrastMatrix
-    from patsy.contrasts import Sum
-    from patsy.contrasts import Diff
-    from patsy.contrasts import Helmert
+from sklearn.linear_model import LinearRegression
+from sklearn import preprocessing
+from sklearn.linear_model import Ridge
+from sklearn.linear_model import Lasso
+from sklearn.model_selection import cross_val_score
+
+import statsmodels.api as sm
+from statsmodels.formula.api import ols
+
+
+from statistics import mean
+
+from patsy.contrasts import Treatment
+from patsy.contrasts import ContrastMatrix
+from patsy.contrasts import Sum
+from patsy.contrasts import Diff
+from patsy.contrasts import Helmert
+
 
 MAX_ALPHA = 700
 #Defining the parameters of the commands.

nidm/version.py

@@ -57,5 +57,5 @@
 VERSION = __version__
 INSTALL_REQUIRES = ["prov", "graphviz", "pydotplus", "pydot", "validators", "requests", "rapidfuzz", "pygithub",
                     "pandas", "pybids>=0.12.4", "duecredit", "pytest", "graphviz", "click", "rdflib-jsonld",
-                    "pyld==1.0.5", "rdflib", "datalad", "ontquery==0.2.3", "orthauth>=0.0.12","tabulate", "joblib", "cognitiveatlas", "numpy>=1.16.5", "etelemetry","click-option-group","patsy"]
+                    "pyld==1.0.5", "rdflib", "datalad", "ontquery==0.2.3", "orthauth>=0.0.12","tabulate", "joblib", "cognitiveatlas", "numpy>=1.16.5", "etelemetry","click-option-group","patsy","sklearn","statsmodels","statistics"]
 SCRIPTS = ["bin/nidm_query", "bin/bidsmri2nidm", "bin/csv2nidm","bin/nidm_utils"]