Merge pull request #192 from JesseLivezey/1.0.0

1.0.0

Author: pssachdeva

.flake8

@@ -1,4 +1,3 @@
 [flake8]
 ignore = E401,W503,W504
 max-line-length = 80
-exclude = bin/run_uoinmf.py

.travis.yml

@@ -1,7 +1,6 @@
 language: python
 os: linux
 python:
-  - 3.5
   - 3.6
   - 3.7
 matrix:

README.md

@@ -3,7 +3,7 @@
 
 <img src="https://travis-ci.org/BouchardLab/PyUoI.svg?branch=master"> [![codecov](https://codecov.io/gh/BouchardLab/PyUoI/branch/master/graph/badge.svg)](https://codecov.io/gh/BouchardLab/PyUoI)
 [![Documentation Status](https://readthedocs.org/projects/pyuoi/badge/?version=latest)](https://pyuoi.readthedocs.io/en/latest/?badge=latest)
-![PyPI](https://img.shields.io/pypi/v/pyuoi)
+![PyPI](https://img.shields.io/pypi/v/pyuoi)[![Anaconda-Server Badge](https://anaconda.org/conda-forge/pyuoi/badges/installer/conda.svg)](https://conda.anaconda.org/conda-forge)
 
 PyUoI contains implementations of Union of Intersections framework for a variety
 of penalized generalized linear models as well as dimensionality reductions
@@ -23,13 +23,13 @@ Further details on the UoI framework can be found in the NeurIPS paper (<a href=
 
 # Installation
 
-PyUoI is available for Python>=3.5 on PyPI:
+PyUoI is available for Python 3 on PyPI:
 
 ```
 pip install pyuoi
 ```
 
-and will soon be through conda-forge:
+and through conda-forge:
 
 ```
 conda install pyuoi -c conda-forge

bin/generate_build.sh

@@ -1,6 +1,6 @@
 eval "$(conda shell.bash hook)"
 mkdir dist
-for py in 3.5 3.6 3.7; do
+for py in 3.6 3.7; do
   git clone https://github.com/BouchardLab/pyuoi.git
   cd pyuoi
   conda create -y -n temp_build_env python=$py

docs/source/installation.rst

@@ -4,13 +4,13 @@
 Installation
 ============
 
-PyUoI is available for Python>=3.5 on PyPI:
+PyUoI is available for Python 3 on PyPI:
 
 .. code-block:: bash
 
     $ pip install pyuoi
 
-and will soon be through conda-forge:
+and through conda-forge:
 
 .. code-block:: bash
 

paper/paper.md

@@ -100,7 +100,7 @@ y = \boldsymbol{\beta}^T \mathbf{x} + \epsilon
 \end{equation}
 
 where $\epsilon \sim \mathcal{N}(0, \sigma^2)$ for each sample. When the true
-$\boldsymbol{\beta}$ is thought to be sparse (i.e., some subset of the $\beta$
+$\boldsymbol{\beta}$ is thought to be sparse (i.e., some subset of the $\boldsymbol{\beta}$
 are exactly zero), an estimate of $\boldsymbol{\beta}$ can be found by solving a
 constrained optimization problem of the form
 
@@ -124,7 +124,7 @@ intersection (compressive) operations and model estimation through union
 selection profiles that are more robust and parameter estimates that have less bias. This can be
 contrasted with a typical Lasso fit wherein parameter selection and estimation are performed
 simultaneously. The Lasso procedure can lead to selection profiles that are not robust
-to data resampling and estimates that are biased by the penalty on $\beta$. For
+to data resampling and estimates that are biased by the penalty on $\boldsymbol{\beta}$. For
 UoI~Lasso~, the procedure is as follows (see Algorithm 1 for a more detailed pseudocode):
 
 * **Model Selection:** For each $\lambda_j$ in the Lasso path, generate estimates on $N_S$
@@ -148,7 +148,7 @@ and the degree of feature expansion via unions (quantified by $N_E$) can be bala
 prediction accuracy for the response variable $y$.
 
 \begin{algorithm}[t]
-    \caption{\textsc{UoI-Lasso}}
+    \caption{\textsc{UoI$_\textsc{Lasso}$}}
     \label{alg:uoi}
     \hspace*{\algorithmicindent} \textbf{Input}:
     $X \in \mathbb{R}^{N\times p}$ design matrix \\

setup.py

@@ -46,7 +46,7 @@ def finalize_options(self):
     # Versions should comply with PEP440.  For a discussion on single-sourcing
     # the version across setup.py and the project code, see
     # https://packaging.python.org/en/latest/single_source_version.html
-    version='0.99.0',
+    version='1.0.0',
 
     description='The Union of Intersections framework in Python.',
     long_description=long_description,
@@ -75,9 +75,9 @@ def finalize_options(self):
         # Specify the Python versions you support here. In particular, ensure
         # that you indicate whether you support Python 2, Python 3 or both.
         'Programming Language :: Python :: 3',
-        'Programming Language :: Python :: 3.5',
         'Programming Language :: Python :: 3.6',
         'Programming Language :: Python :: 3.7',
+        'Programming Language :: Python :: 3.8',
     ],
 
     # What does your project relate to?