Merge branch 'release/v0.11.0'

Author: DilumAluthge

.gitignore

@@ -1,10 +1,16 @@
-*.jl.cov
+.DS_Store
+*.aux
+*.ipynb_checkpoints/
 *.jl.*.cov
+*.jl.cov
 *.jl.mem
-deps/deps.jl
-
-.DS_Store
-
+*.log
 data/
+deps/custom_preamble.tex
+deps/deps.jl
+deps/pdf2svg.svg
+deps/showed_warning
+docs/build
 input/
 output/
+scratch.jl

.travis.yml

@@ -22,6 +22,7 @@ addons:
     - gfortran
     - pdf2svg
     - pgf
+    - poppler-utils # provides /usr/bin/pdftoppm
     - texlive-binaries
     - texlive-latex-base
     - texlive-latex-extra

CONTRIBUTING.md

@@ -1,6 +1,6 @@
-# Contributing to AluthgeSinhaBase
+# Contributing to PredictMD
 
-This document provides information on contributing to the AluthgeSinhaBase source code. For information on installing and using AluthgeSinhaBase, please see [README.md](README.md).
+This document provides information on contributing to the PredictMD source code. For information on installing and using PredictMD, please see [README.md](README.md).
 
 <table>
     <thead>
@@ -13,7 +13,10 @@ This document provides information on contributing to the AluthgeSinhaBase sourc
             <td align="left"><a href="#1-prerequisites">1. Prerequisites</a></td>
         </tr>
         <tr>
-            <td align="left"><a href="#2-setting-up-the-aluthgesinhabase-repo">2. Setting up the AluthgeSinhaBase repo</a></td>
+            <td align="left"><a href="#2-setting-up-the-predictmd-repo">2. Setting up the PredictMD repo</a></td>
+        </tr>
+                <tr>
+            <td align="left"><a href="#3-working-with-examples">3. Working with examples</a></td>
         </tr>
     </tbody>
 </table>
@@ -136,20 +139,58 @@ If you do, then go to Step 2. If you instead see an error, download and install
 4. [https://help.github.com/articles/telling-git-about-your-gpg-key/](https://help.github.com/articles/telling-git-about-your-gpg-key/)
 5. [https://help.github.com/articles/associating-an-email-with-your-gpg-key/](https://help.github.com/articles/associating-an-email-with-your-gpg-key/)
 
-## 2. Setting up the AluthgeSinhaBase repo
+## 2. Setting up the PredictMD repo
 
 **Step 1:** Make sure that you have followed all of the instructions in [Section 1 (Prerequisites)](#1-prerequisites).
 
-**Step 2:** Follow the installation instructions in [README.md](README.md) to install AluthgeSinhaBase.
+**Step 2:** Follow the installation instructions in [README.md](README.md) to install PredictMD.
 
-**Step 3:** Open a terminal window and `cd` to the directory containing the AluthgeSinhaBase source code:
+**Step 3:** Open a terminal window and `cd` to the directory containing the PredictMD source code:
 
 ```bash
-cd ~/.julia/v0.6/AluthgeSinhaBase
+cd ~/.julia/v0.6/PredictMD
 ```
 
 **Step 4:** Run the following line:
 
 ```bash
-git config commit.gpgsign true && git checkout master && git checkout develop && git flow init -fd && git checkout develop 
+git config commit.gpgsign true && git remote set-url origin https://github.com/bcbi/PredictMD.jl.git && git remote set-url --push origin git@github.com:bcbi/PredictMD.jl.git && git checkout master && git checkout develop && git flow init -fd && git checkout develop && git fetch --all --prune
+```
+
+## 3. Working with examples
+
+Some of the examples are provided as Jupyter notebooks as a convinient way to visualize and interact with the code. However, we also like to mantain corresponding plain Julia scripts that are in-sync with the notebooks. A convinient way to do so, is to add a post-save hook to your Jupyter configuration file.
+
+1. Open you jupyter configuration file ~/.jupyter/jupyter_notebook_config.py. If the file does not exist you can generate it by running `jupyter notebook --generate-config`
+
+2. Add the following code to the top of the file
+
+```python
+#-----------------------------------------------------------------------------
+# Auto save script version of notebook
+# Reference: https://svds.com/jupyter-notebook-best-practices-for-data-science/
+#-----------------------------------------------------------------------------
+
+import os
+from subprocess import check_call
+
+def post_save(model, os_path, contents_manager):
+    """post-save hook for converting notebooks to .py scripts"""
+    if model['type'] != 'notebook':
+        return # only do this for notebooks
+    d, fname = os.path.split(os_path)
+    check_call(['jupyter', 'nbconvert', '--to', 'script', fname], cwd=d)
+
+c.FileContentsManager.post_save_hook = post_save
+```
+
+**Note:** This behavior is global. If you want to have this saving only when in a particular folder, you can create multiple configuration files as a work-around. First create a new profile name via a bash command line:
+```bash
+export JUPYTER_CONFIG_DIR=~/.jupyter_profile2
+jupyter notebook --generate-config
+```
+This will create a new directory and file at `~/.jupyter_profile2/jupyter_notebook_config.py` Then run jupyter notebook and work as usual. To switch back to your default profile you will have to set (either by hand, shell function, or your .bashrc) back to:  
+
+```bash
+export JUPYTER_CONFIG_DIR=~/.jupyter
 ```

README.md

@@ -1,4 +1,4 @@
-# AluthgeSinhaBase.jl
+# PredictMD.jl
 
 <table>
     <thead>
@@ -9,13 +9,13 @@
     </thead>
     <tbody>
         <tr>
-            <td><a href="https://travis-ci.com/DilumAluthge/AluthgeSinhaBase.jl/branches"><img alt="Build Status (master)" title="Build Status (master)" src="https://travis-ci.com/DilumAluthge/AluthgeSinhaBase.jl.svg?token=dMqeEKHqcnWSXz982pdf&branch=master"></a></td>
-            <td><a href="https://travis-ci.com/DilumAluthge/AluthgeSinhaBase.jl/branches"><img alt="Build Status (develop)" title="Build Status (develop)" src="https://travis-ci.com/DilumAluthge/AluthgeSinhaBase.jl.svg?token=dMqeEKHqcnWSXz982pdf&branch=develop"></a></td>
+            <td><a href="https://travis-ci.org/bcbi/PredictMD.jl/branches"><img alt="Build Status (master)" title="Build Status (master)" src="https://travis-ci.org/bcbi/PredictMD.jl.svg?branch=master"></a></td>
+            <td><a href="https://travis-ci.org/bcbi/PredictMD.jl/branches"><img alt="Build Status (develop)" title="Build Status (develop)" src="https://travis-ci.org/bcbi/PredictMD.jl.svg?branch=develop"></a></td>
         </tr>
     </tbody>
 </table>
 
-AluthgeSinhaBase is a [Julia](https://julialang.org/) package that provides a uniform interface for using multiple different statistics and machine learning packages. This document describes how to install and use AluthgeSinhaBase.
+PredictMD is a [Julia](https://julialang.org/) package that provides a uniform interface for using multiple different statistics and machine learning packages. This document describes how to install and use PredictMD.
 
 <table>
     <thead>
@@ -41,7 +41,7 @@ AluthgeSinhaBase is a [Julia](https://julialang.org/) package that provides a un
 
 ## 1. Prerequisites
 
-In order to run AluthgeSinhaBase, you need to have all of the following software packages installed on your system:
+In order to run PredictMD, you need to have all of the following software packages installed on your system:
 * Julia (version >= 0.6)
 * LaTeX
 * pdf2svg.
@@ -112,20 +112,19 @@ If you receive an error (e.g. "command not found"), download and install pdf2svg
 
 **Step 3:** Paste the following line into Julia and press enter:
 ```julia
-Pkg.update();Pkg.clone("git@github.com:dilumaluthge/AluthgeSinhaBase.jl.git");Pkg.checkout("AluthgeSinhaBase", "master");Pkg.test("AluthgeSinhaBase");
+Pkg.update();Pkg.clone("https://github.com/bcbi/PredictMD.jl.git");Pkg.checkout("PredictMD", "master");Pkg.test("PredictMD");
 ```
-
 You will need to wait several minutes while all of the required packages are installed and all of the tests are run.
 
-If you receive the message "INFO: AluthgeSinhaBase tests passed", then you have successfully installed AluthgeSinhaBase. If the tests do not pass or if you see an error message, then do the following:
+If you receive the message "INFO: PredictMD tests passed", then you have successfully installed PredictMD. If the tests do not pass or if you see an error message, then do the following:
 1. Close your Julia session (e.g. type ```quit()``` and press enter).
 2. Open a new terminal window, type ```mv ~/.julia ~/.julia.backup-$(date +"%Y%m%d-%H%M%S")```, and press enter.
 3. Repeat Steps 2 and 3 above.
 
-If the tests still do not pass or if you still receive an error message, go to [https://github.com/dilumaluthge/AluthgeSinhaBase.jl/issues/new](https://github.com/dilumaluthge/AluthgeSinhaBase.jl/issues/new) and submit a new issue. Please include a screenshot of the error.
+If the tests still do not pass or if you still receive an error message, go to [https://github.com/bcbi/PredictMD.jl/issues/new](https://github.com/bcbi/PredictMD.jl/issues/new) and submit a new issue. Please include a screenshot of the error.
 
 ## 3. Examples
-The `examples/` folder contains several files that illustrate the usage of AluthgeSinhaBase:
+The `examples/` folder contains several files that illustrate the usage of PredictMD:
 
 ### 3.1. Machine Learning Examples
 
@@ -156,4 +155,4 @@ The `examples/` folder contains several files that illustrate the usage of Aluth
 
 ## 4. Contributing
 
-If you would like to contribute to the AluthgeSinhaBase source code, please see [CONTRIBUTING.md](CONTRIBUTING.md).
+If you would like to contribute to the PredictMD source code, please see [CONTRIBUTING.md](CONTRIBUTING.md).

REQUIRE

@@ -1,102 +1,30 @@
 julia 0.6
 
-Adapt 0.2
-ArgCheck 0.4
-ArgParse 0.5
-ArrayFire 0.1
 Atom 0.6
-AutoGrad 0.0.10
-BenchmarkTools 0.2
-BioMedQuery 0.3
-Blink 0.6
-CLArrays 0.1
 CSV 0.2
-CUDAapi
-CUDAdrv
-CUDAnative
-CUDNN
-CategoricalArrays 0.3
 ClassImbalance 0.2
-Clustering 0.9
-ColorBrewer 0.3
-ColorSchemes 1.5
-ColorTypes 0.6
-Colors 0.8
-CuArrays 0.4
-DataFlow 0.3
+Crayons 0.4
 DataFrames 0.11
-DataFramesMeta 0.3
-DataStreams 0.3
 DecisionTree 0.6
-Devectorize 0.4
-Discretizers 2.1
-Distributions 0.15
-Documenter 0.13
 FileIO 0.6
 Flux 0.4
-ForwardDiff 0.7
 GLM 0.10
-GLMNet 0.3
-GPUArrays 0.2
 GZip 0.3
-GroupedErrors 0.1
-HypothesisTests 0.6
-IterTools 0.2
-IterableTables 0.6
 JLD2 0.0.5
-JuMP 0.18
-Juno 0.4
-KernelDensity 0.4
 Knet 0.9
-LARS 0.0.3
-LIBLINEAR 0.3
 LIBSVM 0.1
 LaTeXStrings 0.3
-Lasso 0.1
-Lazy 0.12
-LearnBase 0.1
-LearningStrategies 0.2
-LightGraphs 0.11
-Loess 0.3
-LossFunctions 0.2
 MLBase 0.7
-MNIST 0.0.2
-MacroTools 0.4
-Merlin 0.0.3
-Missings 0.2
-MultivariateStats 0.4
 NNlib 0.2
 NumericalIntegration 0.0.3
-OhMyREPL
-OpenCL 0.7
 PGFPlots 2.2
 PGFPlotsX 0.2
 PackageCompiler 0.3
-PenaltyFunctions 0.0.2
-PlotRecipes 0.3
-PlotThemes 0.2
-Plots 0.15
 ProgressMeter 0.5
-QuadGK 0.2
-Query 0.9
-RData 0.3
 RDatasets 0.3
-REPLCompletions
-Rmath 0.3
 ROCAnalysis 0.2
-RecipesBase 0.2
-Reel 1.0
-Reinforce 0.0.1
 Requires 0.4
-ReverseDiff 0.2
-ReverseDiffSource 0.3
-ScikitLearnBase 0.3
-StaticArrays 0.6
 StatsBase 0.19
-StatsFuns 0.5
 StatsModels 0.2
-StatPlots 0.7
-TaylorSeries 0.7
-TikzGraphs 0.5
 TikzPictures 1.2
 ValueHistories 0.4

deps/build.jl

@@ -0,0 +1,58 @@
+# Originally based on https://github.com/KristofferC/PGFPlotsX.jl/blob/master/deps/build.jl
+
+import Crayons
+
+const OK =  Crayons.Box.GREEN_FG * Crayons.Box.BOLD("OK")
+const X =  Crayons.Box.RED_FG * Crayons.Box.BOLD("X")
+
+print(STDERR, "Looking for lualatex...")
+have_lualatex = try success(`lualatex -v`); catch; false; end
+println(STDERR, "   ", have_lualatex ? OK : X)
+
+print(STDERR, "Looking for pdflatex...")
+have_pdflatex = try success(`pdflatex -v`); catch; false; end
+println(STDERR, "   ", have_pdflatex ? OK : X)
+
+default_engine = ""
+if have_lualatex
+    default_engine = "LUALATEX"
+elseif have_pdflatex
+    default_engine = "PDFLATEX"
+else
+    warn(string("No LaTeX installation found, figures will not be generated. ",
+        "Make sure either pdflatex or lualatex are installed and that ",
+        "the correct paths are set then run Pkg.build(\"PredictMD\")"))
+end
+
+print(STDERR, "Looking for pdftoppm...")
+have_pdftoppm =  try success(`pdftoppm  -v`); catch; false; end
+println(STDERR, "   ", have_pdftoppm ? OK : X)
+if !have_pdftoppm
+    warn(string("Did not find `pdftoppm`, png output will be disabled. Install `pdftoppm` ",
+        "and run Pkg.build(\"PredictMD\") to enable"))
+end
+
+print(STDERR, "Looking for pdf2svg...")
+pdfpath = joinpath(@__DIR__, "pdf2svg.pdf")
+svgpath = joinpath(@__DIR__, "pdf2svg.svg")
+have_pdf2svg = try success(`pdf2svg $pdfpath $svgpath`); catch; false; end
+println(STDERR, "    ", have_pdf2svg ? OK : X)
+if !have_pdf2svg
+    warn(string("Did not find `pdf2svg`, svg output will be disabled. Install `pdf2svg` ",
+        "and run Pkg.build(\"PredictMD\") to enable"))
+end
+
+if !have_pdf2svg && !have_pdftoppm
+    warn(string("Found neither pdf2svg or pdftoppm, figures will not be viewable in Jupyter or Juno"))
+end
+
+open(joinpath(@__DIR__, "deps.jl"), "w") do f
+    println(f, "DEFAULT_ENGINE = \"", default_engine, "\"")
+    println(f, "HAVE_PDFTOPPM = ", have_pdftoppm)
+    println(f, "HAVE_PDFTOSVG = ", have_pdf2svg)
+end
+
+const PREAMBLE_PATH = joinpath(@__DIR__, "custom_preamble.tex")
+if !isfile(PREAMBLE_PATH)
+    touch(PREAMBLE_PATH)
+end