Merge branch 'release/v0.13.0'

Author: DilumAluthge

.gitignore

@@ -1,16 +1,23 @@
+# Directories to ignore:
+
+*.ipynb_checkpoints/
+data/
+docs/build/
+docs/site/
+docs/src/examples/
+input/
+output/
+
+# Files to ignore:
+
 .DS_Store
 *.aux
-*.ipynb_checkpoints/
-*.jl.*.cov
 *.jl.cov
+*.jl.*.cov
 *.jl.mem
 *.log
-data/
 deps/custom_preamble.tex
 deps/deps.jl
 deps/pdf2svg.svg
 deps/showed_warning
-docs/build
-input/
-output/
 scratch.jl

.travis.yml

@@ -1,44 +1,49 @@
-## Documentation: http://docs.travis-ci.com/user/languages/julia/
 language: julia
+
 os:
-  - linux
-  - osx
+    - linux
+    - osx
+
 julia:
-  - 0.6
-#  - nightly
+    - 0.6
+    - nightly
+
 notifications:
-  email: false
+    email: false
+
 git:
-  depth: 99999999
+    depth: 99999999
 
-## Allow failures on nightly julia:
 matrix:
-  allow_failures:
-  - julia: nightly
+    allow_failures:
+    - julia: nightly
 
 addons:
-  apt:
-    packages:
-    - gfortran
-    - pdf2svg
-    - pgf
-    - poppler-utils # provides /usr/bin/pdftoppm
-    - texlive-binaries
-    - texlive-latex-base
-    - texlive-latex-extra
-    - texlive-pictures
+    apt:
+        packages:
+        - gfortran
+        - pdf2svg
+        - pgf
+        - poppler-utils
+        - texlive-binaries
+        - texlive-latex-base
+        - texlive-latex-extra
+        - texlive-pictures
 
 before_install:
-  # update homebrew
-  - if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then brew update; fi
-  # install mactex
-  - if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then brew cask install basictex; fi
-  - if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then export PATH=/Library/TeX/texbin:"$PATH"; fi
-  # update tlmgr
-  - if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then sudo tlmgr update --self; fi
-  # install tex packages
-  - if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then sudo tlmgr install luatex85; fi
-  - if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then sudo tlmgr install pgfplots; fi
-  - if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then sudo tlmgr install standalone; fi
-  # install pdf2svg
-  - if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then brew install pdf2svg; fi
+    - if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then brew update; fi
+    - if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then brew cask install basictex; fi
+    - if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then export PATH=/Library/TeX/texbin:"$PATH"; fi
+    - if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then sudo tlmgr update --self; fi
+    - if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then sudo tlmgr install luatex85; fi
+    - if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then sudo tlmgr install pgfplots; fi
+    - if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then sudo tlmgr install standalone; fi
+    - if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then brew install pdf2svg; fi
+
+script:
+    - julia --color=yes -e 'Pkg.clone(pwd())'
+    - julia --color=yes -e 'Pkg.build("PredictMD")'
+    - julia --check-bounds=yes --color=yes -e 'Pkg.test("PredictMD", coverage=true)'
+
+after_success:
+    - julia -e 'cd(Pkg.dir("PredictMD")); include(joinpath("docs", "deploy_docs.jl"))'

CONTRIBUTING.md

@@ -14,9 +14,6 @@ This document provides information on contributing to the PredictMD source code.
         </tr>
         <tr>
             <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>
@@ -156,41 +153,3 @@ cd ~/.julia/v0.6/PredictMD
 ```bash
 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

@@ -3,15 +3,22 @@
 <table>
     <thead>
         <tr>
+            <th>branch</th>
             <th>master</th>
             <th>develop</th>
         </tr>
     </thead>
     <tbody>
         <tr>
+            <td>travis</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>
+        <tr>
+            <td>docs</td>
+            <td><a href="https://bcbi.github.io/PredictMD.jl/stable"><img alt="Documentation (stable)" title="Documentation (stable)" src="https://img.shields.io/badge/docs-stable-blue.svg"></a></td>
+            <td><a href="https://bcbi.github.io/PredictMD.jl/latest"><img alt="Documentation (latest)" title="Documentation (latest)" src="https://img.shields.io/badge/docs-latest-blue.svg"></a></td>
+        </tr>
     </tbody>
 </table>
 
@@ -28,16 +35,13 @@ PredictMD is a [Julia](https://julialang.org/) package that provides a uniform i
             <td align="left"><a href="#1-prerequisites">1. Prerequisites</a></td>
         </tr>
         <tr>
-            <td align="left"><a href="#2-installation-recommended-method">2. Installation (recommended method)</a></td>
-        </tr>
-        <tr>
-            <td align="left"><a href="#3-installation-alternate-method-with-conda">3. Installation (alternate method with Conda)</a></td>
+            <td align="left"><a href="#2-installation">2. Installation</a></td>
         </tr>
         <tr>
-            <td align="left"><a href="#4-examples">4. Examples</a></td>
+            <td align="left"><a href="#3-examples">3. Examples</a></td>
         </tr>
         <tr>
-            <td align="left"><a href="#5-contributing">5. Contributing</a></td>
+            <td align="left"><a href="#4-contributing">4. Contributing</a></td>
         </tr>
     </tbody>
 </table>
@@ -107,7 +111,7 @@ If you receive an error (e.g. "command not found"), download and install pdf2svg
 * macOS: [http://brewinstall.org/Install-pdf2svg-on-Mac-with-Brew/](http://brewinstall.org/Install-pdf2svg-on-Mac-with-Brew/)
 * GNU/Linux: [https://github.com/dawbarton/pdf2svg](https://github.com/dawbarton/pdf2svg)
 
-## 2. Installation (recommended method)
+## 2. Installation
 
 **Step 1:** Make sure that you have followed all of the instructions in [Section 1 (Prerequisites)](#1-prerequisites).
 
@@ -126,11 +130,7 @@ If you receive the message "INFO: PredictMD tests passed", then you have success
 
 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. Installation (alternate method with Conda)
-
-Alternatively, you can install PredictMD using the Conda package manager. Just follow the instructions here: [https://github.com/dilumaluthge/conda-predictmd-cpu](https://github.com/dilumaluthge/conda-predictmd-cpu)
-
-## 4. Examples
+## 3. Examples
 The `examples/` folder contains several files that illustrate the usage of PredictMD:
 
 <table>
@@ -158,6 +158,6 @@ The `examples/` folder contains several files that illustrate the usage of Predi
     <tbody>
 </table>
 
-## 5. Contributing
+## 4. Contributing
 
 If you would like to contribute to the PredictMD source code, please see [CONTRIBUTING.md](CONTRIBUTING.md).

REQUIRE

@@ -6,6 +6,7 @@ BSON 0.1
 CSV 0.2
 ClassImbalance 0.2
 Combinatorics 0.6
+Compat
 Crayons 0.4
 DataFrames 0.11
 DecisionTree 0.6
@@ -27,7 +28,6 @@ NNlib 0.2
 NumericalIntegration 0.0.3
 PGFPlots 2.2
 PGFPlotsX 0.2
-PackageCompiler 0.3
 ProgressMeter 0.5
 RDatasets 0.3
 ROCAnalysis 0.2

docs/deploy_docs.jl

@@ -0,0 +1,20 @@
+import Documenter
+import PredictMD
+
+ENV["PREDICTMD_IS_DEPLOY_DOCS"] = "true"
+
+Documenter.deploydocs(
+    branch = "gh-pages",
+    deps = Documenter.Deps.pip(
+        "mkdocs",
+        "pygments",
+        "python-markdown-math",
+        ),
+    julia = "0.6",
+    latest = "develop",
+    osname = "linux",
+    repo = "github.com/bcbi/PredictMD.jl.git",
+    target = "site",
+    )
+
+ENV["PREDICTMD_IS_DEPLOY_DOCS"] = "false"