Merge pull request #952 from weixuanfu/python3_only

Drop supports for python < 3.5 in TPOT v0.11

.appveyor.yml

@@ -18,7 +18,7 @@ install:
   - conda config --set always_yes yes --set changeps1 no
   - conda update -q conda
   - conda info -a
-  - conda create -q -n test-environment python=%PYTHON_VERSION% numpy scipy scikit-learn nose cython pandas pywin32 joblib
+  - conda create -q -n test-environment python=%PYTHON_VERSION% numpy scipy scikit-learn nose cython pandas joblib
   - activate test-environment
   - pip install deap tqdm update_checker stopit xgboost dask[delayed] dask[dataframe] cloudpickle==0.5.6 fsspec>=0.3.3 dask_ml==%DASK_ML_VERSION%
 

README.md

@@ -6,8 +6,7 @@ Development status: [![Development Build Status - Mac/Linux](https://travis-ci.o
 [![Development Build Status - Windows](https://ci.appveyor.com/api/projects/status/b7bmpwpkjhifrm7v/branch/development?svg=true)](https://ci.appveyor.com/project/weixuanfu/tpot?branch=development)
 [![Development Coverage Status](https://coveralls.io/repos/github/EpistasisLab/tpot/badge.svg?branch=development)](https://coveralls.io/github/EpistasisLab/tpot?branch=development)
 
-Package information: [![Python 2.7](https://img.shields.io/badge/python-2.7-blue.svg)](https://www.python.org/download/releases/2.7/)
-[![Python 3.7](https://img.shields.io/badge/python-3.7-blue.svg)](https://www.python.org/downloads/release/python-370/)
+Package information: [![Python 3.7](https://img.shields.io/badge/python-3.7-blue.svg)](https://www.python.org/downloads/release/python-370/)
 [![License: LGPL v3](https://img.shields.io/badge/license-LGPL%20v3-blue.svg)](http://www.gnu.org/licenses/lgpl-3.0)
 [![PyPI version](https://badge.fury.io/py/TPOT.svg)](https://badge.fury.io/py/TPOT)
 

docs/404.html

@@ -13,12 +13,11 @@
 
   <link rel="stylesheet" href="/tpot/css/theme.css" type="text/css" />
   <link rel="stylesheet" href="/tpot/css/theme_extra.css" type="text/css" />
-  <link rel="stylesheet" href="//cdnjs.cloudflare.com/ajax/libs/highlight.js/9.12.0/styles/github.min.css">
+  <link rel="stylesheet" href="/tpot/css/highlight.css">
 
-  <script src="/tpot/js/jquery-2.1.1.min.js" defer></script>
-  <script src="/tpot/js/modernizr-2.8.3.min.js" defer></script>
-  <script src="//cdnjs.cloudflare.com/ajax/libs/highlight.js/9.12.0/highlight.min.js"></script>
-  <script>hljs.initHighlightingOnLoad();</script> 
+  <script src="/tpot/js/jquery-2.1.1.min.js"></script>
+  <script src="/tpot/js/modernizr-2.8.3.min.js"></script>
+  <script type="text/javascript" src="/tpot/js/highlight.pack.js"></script> 
 
 </head>
 
@@ -29,10 +28,10 @@
 
     <nav data-toggle="wy-nav-shift" class="wy-nav-side stickynav">
       <div class="wy-side-nav-search">
-        <a href="/tpot/." class="icon icon-home"> TPOT</a>
+        <a href="/tpot/" class="icon icon-home"> TPOT</a>
         <div role="search">
   <form id ="rtd-search-form" class="wy-form" action="/tpot/search.html" method="get">
-    <input type="text" name="q" placeholder="Search docs" title="Type search term here" />
+    <input type="text" name="q" placeholder="Search docs" />
   </form>
 </div>
       </div>
@@ -43,7 +42,7 @@
 
             <li class="toctree-l1">
 
-    <a class="" href="/tpot/.">Home</a>
+    <a class="" href="/tpot/">Home</a>
 	    </li>
 
             <li class="toctree-l1">
@@ -101,15 +100,15 @@
 
       <nav class="wy-nav-top" role="navigation" aria-label="top navigation">
         <i data-toggle="wy-nav-top" class="fa fa-bars"></i>
-        <a href="/tpot/.">TPOT</a>
+        <a href="/tpot/">TPOT</a>
       </nav>
 
 
       <div class="wy-nav-content">
         <div class="rst-content">
           <div role="navigation" aria-label="breadcrumbs navigation">
   <ul class="wy-breadcrumbs">
-    <li><a href="/tpot/.">Docs</a> &raquo;</li>
+    <li><a href="/tpot/">Docs</a> &raquo;</li>
 
 
     <li class="wy-breadcrumbs-aside">
@@ -161,8 +160,9 @@ <h1 id="404-page-not-found">404</h1>
     </span>
 </div>
     <script>var base_url = '/tpot';</script>
-    <script src="/tpot/js/theme.js" defer></script>
-      <script src="/tpot/search/main.js" defer></script>
+    <script src="/tpot/js/theme.js"></script>
+      <script src="/tpot/search/require.js"></script>
+      <script src="/tpot/search/search.js"></script>
 
 </body>
 </html>

docs/api/index.html

@@ -13,19 +13,18 @@
 
   <link rel="stylesheet" href="../css/theme.css" type="text/css" />
   <link rel="stylesheet" href="../css/theme_extra.css" type="text/css" />
-  <link rel="stylesheet" href="//cdnjs.cloudflare.com/ajax/libs/highlight.js/9.12.0/styles/github.min.css">
+  <link rel="stylesheet" href="../css/highlight.css">
 
   <script>
     // Current page data
     var mkdocs_page_name = "TPOT API";
     var mkdocs_page_input_path = "api.md";
-    var mkdocs_page_url = "/tpot/api/";
+    var mkdocs_page_url = "/api/";
   </script>
 
-  <script src="../js/jquery-2.1.1.min.js" defer></script>
-  <script src="../js/modernizr-2.8.3.min.js" defer></script>
-  <script src="//cdnjs.cloudflare.com/ajax/libs/highlight.js/9.12.0/highlight.min.js"></script>
-  <script>hljs.initHighlightingOnLoad();</script> 
+  <script src="../js/jquery-2.1.1.min.js"></script>
+  <script src="../js/modernizr-2.8.3.min.js"></script>
+  <script type="text/javascript" src="../js/highlight.pack.js"></script> 
 
 </head>
 
@@ -39,7 +38,7 @@
         <a href=".." class="icon icon-home"> TPOT</a>
         <div role="search">
   <form id ="rtd-search-form" class="wy-form" action="../search.html" method="get">
-    <input type="text" name="q" placeholder="Search docs" title="Type search term here" />
+    <input type="text" name="q" placeholder="Search docs" />
   </form>
 </div>
       </div>
@@ -167,14 +166,14 @@ <h1 id="classification">Classification</h1>
 The TPOTClassifier will also search over the hyperparameters of all objects in the pipeline.</p>
 <p>By default, TPOTClassifier will search over a broad range of supervised classification algorithms, transformers, and their parameters.
 However, the algorithms, transformers, and hyperparameters that the TPOTClassifier searches over can be fully customized using the <code>config_dict</code> parameter.</p>
-<p>Read more in the <a href="using/#tpot-with-code">User Guide</a>.</p>
+<p>Read more in the <a href="../using/#tpot-with-code">User Guide</a>.</p>
 <table>
 <tr>
 <td width="20%" style="vertical-align:top; background:#F5F5F5;"><strong>Parameters:</strong></td>
 <td width="80%" style="background:white;">
-<strong>generations</strong>: int, optional (default=100)
+<strong>generations</strong>: int or None optional (default=100)
 <blockquote>
-Number of iterations to the run pipeline optimization process. Must be a positive number.
+Number of iterations to the run pipeline optimization process. It must be a positive number or None. If None, the parameter <em>max_time_mins</em> must be defined as the runtime limit.
 <br /><br />
 Generally, TPOT will work better when you give it more generations (and therefore time) to optimize the pipeline.
 <br /><br />
@@ -220,8 +219,6 @@ <h1 id="classification">Classification</h1>
 <br /><br/>
 If you would like to use a custom scorer, you can pass the callable object/function with signature <em>scorer(estimator, X, y)</em>.
 <br /><br/>
-If you would like to use a metric function, you can pass the callable function to this parameter with the signature <em>score_func(y_true, y_pred)</em>. TPOT assumes that any function with "error" or "loss" in the function name is meant to be minimized, whereas any other functions will be maximized. This scoring type was deprecated in version 0.9.1 and will be removed in version 0.11.
-<br /><br/>
 See the section on <a href="../using/#scoring-functions">scoring functions</a> for more details.
 
 </blockquote>
@@ -255,7 +252,7 @@ <h1 id="classification">Classification</h1>
 <blockquote>
 How many minutes TPOT has to optimize the pipeline.
 <br /><br />
-If not None, this setting will override the <em>generations</em> parameter and allow TPOT to run until <em>max_time_mins</em> minutes elapse.
+If not None, this setting will allow TPOT to run until <em>max_time_mins</em> minutes elapsed and then stop. TPOT will stop earlier if <em>generations</em> is set and all generations are already evaluated.
 </blockquote>
 
 <strong>max_eval_time_mins</strong>: float, optional (default=5)
@@ -639,14 +636,14 @@ <h1 id="regression">Regression</h1>
 The TPOTRegressor will also search over the hyperparameters of all objects in the pipeline.</p>
 <p>By default, TPOTRegressor will search over a broad range of supervised regression models, transformers, and their hyperparameters.
 However, the models, transformers, and parameters that the TPOTRegressor searches over can be fully customized using the <code>config_dict</code> parameter.</p>
-<p>Read more in the <a href="using/#tpot-with-code">User Guide</a>.</p>
+<p>Read more in the <a href="../using/#tpot-with-code">User Guide</a>.</p>
 <table>
 <tr>
 <td width="20%" style="vertical-align:top; background:#F5F5F5;"><strong>Parameters:</strong></td>
 <td width="80%" style="background:white;">
-<strong>generations</strong>: int, optional (default=100)
+<strong>generations</strong>: int or None, optional (default=100)
 <blockquote>
-Number of iterations to the run pipeline optimization process. Must be a positive number.
+Number of iterations to the run pipeline optimization process. It must be a positive number or None. If None, the parameter <em>max_time_mins</em> must be defined as the runtime limit.
 <br /><br />
 Generally, TPOT will work better when you give it more generations (and therefore time) to optimize the pipeline.
 <br /><br />
@@ -693,8 +690,6 @@ <h1 id="regression">Regression</h1>
 <br /><br/>
 If you would like to use a custom scorer, you can pass the callable object/function with signature <em>scorer(estimator, X, y)</em>.
 <br /><br/>
-If you would like to use a metric function, you can pass the callable function to this parameter with the signature <em>score_func(y_true, y_pred)</em>. TPOT assumes that any function with "error" or "loss" in the function name is meant to be minimized, whereas any other functions will be maximized. This scoring type was deprecated in version 0.9.1 and will be removed in version 0.11.
-<br /><br/>
 See the section on <a href="../using/#scoring-functions">scoring functions</a> for more details.
 </blockquote>
 
@@ -728,7 +723,7 @@ <h1 id="regression">Regression</h1>
 <blockquote>
 How many minutes TPOT has to optimize the pipeline.
 <br /><br />
-If not None, this setting will override the <em>generations</em> parameter and allow TPOT to run until <em>max_time_mins</em> minutes elapse.
+If not None, this setting will allow TPOT to run until <em>max_time_mins</em> minutes elapsed and then stop. TPOT will stop earlier if <em>generations</em> is set and all generations are already evaluated.
 </blockquote>
 
 <strong>max_eval_time_mins</strong>: float, optional (default=5)
@@ -1098,8 +1093,9 @@ <h1 id="regression">Regression</h1>
     </span>
 </div>
     <script>var base_url = '..';</script>
-    <script src="../js/theme.js" defer></script>
-      <script src="../search/main.js" defer></script>
+    <script src="../js/theme.js"></script>
+      <script src="../search/require.js"></script>
+      <script src="../search/search.js"></script>
 
 </body>
 </html>

docs/citing/index.html

@@ -13,19 +13,18 @@
 
   <link rel="stylesheet" href="../css/theme.css" type="text/css" />
   <link rel="stylesheet" href="../css/theme_extra.css" type="text/css" />
-  <link rel="stylesheet" href="//cdnjs.cloudflare.com/ajax/libs/highlight.js/9.12.0/styles/github.min.css">
+  <link rel="stylesheet" href="../css/highlight.css">
 
   <script>
     // Current page data
     var mkdocs_page_name = "Citing";
     var mkdocs_page_input_path = "citing.md";
-    var mkdocs_page_url = "/tpot/citing/";
+    var mkdocs_page_url = "/citing/";
   </script>
 
-  <script src="../js/jquery-2.1.1.min.js" defer></script>
-  <script src="../js/modernizr-2.8.3.min.js" defer></script>
-  <script src="//cdnjs.cloudflare.com/ajax/libs/highlight.js/9.12.0/highlight.min.js"></script>
-  <script>hljs.initHighlightingOnLoad();</script> 
+  <script src="../js/jquery-2.1.1.min.js"></script>
+  <script src="../js/modernizr-2.8.3.min.js"></script>
+  <script type="text/javascript" src="../js/highlight.pack.js"></script> 
 
 </head>
 
@@ -39,7 +38,7 @@
         <a href=".." class="icon icon-home"> TPOT</a>
         <div role="search">
   <form id ="rtd-search-form" class="wy-form" action="../search.html" method="get">
-    <input type="text" name="q" placeholder="Search docs" title="Type search term here" />
+    <input type="text" name="q" placeholder="Search docs" />
   </form>
 </div>
       </div>
@@ -224,8 +223,9 @@
     </span>
 </div>
     <script>var base_url = '..';</script>
-    <script src="../js/theme.js" defer></script>
-      <script src="../search/main.js" defer></script>
+    <script src="../js/theme.js"></script>
+      <script src="../search/require.js"></script>
+      <script src="../search/search.js"></script>
 
 </body>
 </html>

docs/contributing/index.html

@@ -13,19 +13,18 @@
 
   <link rel="stylesheet" href="../css/theme.css" type="text/css" />
   <link rel="stylesheet" href="../css/theme_extra.css" type="text/css" />
-  <link rel="stylesheet" href="//cdnjs.cloudflare.com/ajax/libs/highlight.js/9.12.0/styles/github.min.css">
+  <link rel="stylesheet" href="../css/highlight.css">
 
   <script>
     // Current page data
     var mkdocs_page_name = "Contributing";
     var mkdocs_page_input_path = "contributing.md";
-    var mkdocs_page_url = "/tpot/contributing/";
+    var mkdocs_page_url = "/contributing/";
   </script>
 
-  <script src="../js/jquery-2.1.1.min.js" defer></script>
-  <script src="../js/modernizr-2.8.3.min.js" defer></script>
-  <script src="//cdnjs.cloudflare.com/ajax/libs/highlight.js/9.12.0/highlight.min.js"></script>
-  <script>hljs.initHighlightingOnLoad();</script> 
+  <script src="../js/jquery-2.1.1.min.js"></script>
+  <script src="../js/modernizr-2.8.3.min.js"></script>
+  <script type="text/javascript" src="../js/highlight.pack.js"></script> 
 
 </head>
 
@@ -39,7 +38,7 @@
         <a href=".." class="icon icon-home"> TPOT</a>
         <div role="search">
   <form id ="rtd-search-form" class="wy-form" action="../search.html" method="get">
-    <input type="text" name="q" placeholder="Search docs" title="Type search term here" />
+    <input type="text" name="q" placeholder="Search docs" />
   </form>
 </div>
       </div>
@@ -305,8 +304,9 @@ <h2 id="after-submitting-your-pull-request">After submitting your pull request</
     </span>
 </div>
     <script>var base_url = '..';</script>
-    <script src="../js/theme.js" defer></script>
-      <script src="../search/main.js" defer></script>
+    <script src="../js/theme.js"></script>
+      <script src="../search/require.js"></script>
+      <script src="../search/search.js"></script>
 
 </body>
 </html>