Suggested Improvements to PackMan

.gitignore

@@ -32,3 +32,5 @@ slprj/
 
 # Session info
 octave-workspace
+
+package.json

.travis.yml

@@ -0,0 +1,170 @@
+os: linux
+dist: xenial
+language: general
+
+###############################################################################
+cache:
+  # Downloading octave takes a while, so let's cache apt
+  apt: true
+  directories:
+    # Cache octave packages
+    - $HOME/octave
+    # Cache other packages
+    - $HOME/external_cache
+
+###############################################################################
+env:
+    jobs:
+        - COVERAGE="false"
+        - COVERAGE="true"    
+    jobs:
+        allow_failures: '[{ env: COVERAGE=true }]'
+        fast_finish: true
+
+###############################################################################
+# Command to install dependencies
+before_install:
+    - echo '<?xml version="1.0" encoding="UTF-8" standalone="no"?><project basedir="." default="build" name="PackMan"><target name="test"/></project>' > build.xml
+    # Remember the directory where our repository to test is located
+    - REPOPATH="$(pwd)" && pwd
+    # ---------------------------------------------------------------------------
+    # Check whether we need to upgrade the gcc and g++ versions. We do need to if
+    # the version is less the 4.8 and we need to install the image package from
+    # Octave Forge (possibly for other packages as well).
+    # For now, lets just always say we do need to do this.
+    - UPGRADE_GCC="true"
+    # ---------------------------------------------------------------------------
+    # Add repository for octave
+    - travis_retry sudo add-apt-repository -y ppa:octave/stable
+    # Add repository for installing g++-4.8 on Ubuntu 12.04
+    - if [ "$UPGRADE_GCC" = "true" ]; then
+        sudo add-apt-repository -y ppa:ubuntu-toolchain-r/test;
+      fi
+    # Update apt-get to include the contents from the new locations
+    - travis_retry sudo apt-get update -qq
+    # Install octave with apt-get
+    - travis_retry sudo apt-get install -y octave liboctave-dev
+    # Add a C++11 compiler so we can install image package
+    - if [ "$UPGRADE_GCC" = "true" ]; then
+        travis_retry sudo apt-get install -y gcc-4.8 g++-4.8;
+        sudo update-alternatives --install /usr/bin/gcc gcc /usr/bin/gcc-4.8 50;
+        sudo update-alternatives --install /usr/bin/g++ g++ /usr/bin/g++-4.8 50;
+      fi;
+    # Check which versions of g++ and gcc we are using
+    - which g++;
+      g++ --version;
+      which gcc;
+      gcc --version;
+    # ---------------------------------------------------------------------------
+    # Go up one level and retrieve MOxUnit from its repository
+    - cd ..;
+      ls -alh;
+    # Remove directory if it is already there from previous build
+    - rm -rf MOxUnit;
+    - git clone https://github.com/MOxUnit/MOxUnit.git
+    # Install MOxUnit, which adds itself to the startup path
+    - make -C MOxUnit install
+    # Install MOcov, which adds itself to the startup path
+    - if [ "$COVERAGE" = "true" ]; then
+          rm -rf MOcov;
+          git clone https://github.com/MOcov/MOcov.git;
+          make -C MOcov install;
+      fi;
+    # Go back to the repository directory
+    - cd ${REPOPATH}
+
+###############################################################################
+install:
+    # Ensure external packages folder exists and is empty
+    - EXTPATH="source/external";
+      echo ${EXTPATH};
+      rm -rf ${EXTPATH};
+      mkdir -p ${EXTPATH};
+    # Install required packages for Octave
+    - if [ -f requirements-octave.txt ]; then
+        mopi/mopi.sh requirements-octave.txt ${EXTPATH} "$HOME/external_cache";
+      fi;
+    # Install other required packages
+    - if [ -f requirements.txt ]; then
+        mopi/mopi.sh requirements.txt ${EXTPATH} "$HOME/external_cache";
+      fi;
+    # Install developmental requirements
+    - if [ -f requirements-dev.txt ]; then
+        mopi/mopi.sh requirements-dev.txt ${EXTPATH} "$HOME/external_cache";
+      fi;
+    # Before running the tests, we will have to add our package and our
+    # external dependencies to the octave path
+    - PACKAGE_FOLDER="source";
+      ADDPATH_COMMAND="addpath(genpath(fullfile(pwd, '$PACKAGE_FOLDER')));";
+      ADDPATH_COMMAND+=" addpath(genpath(fullfile(pwd, '${EXTPATH}')));";
+      echo "ADDPATH_COMMAND| $ADDPATH_COMMAND";
+
+###############################################################################
+before_script:
+    - testFolder="source/tests"
+    - TEST_ARGS="'-recursive', '-verbose', '-junit_xml_file', 'testresults.xml'";
+      if [ "$COVERAGE" = "true" ]; then
+          TEST_ARGS+=", '-with_coverage', '-cover', '$PACKAGE_FOLDER'";
+          TEST_ARGS+=", '-cover_exclude', ${testFolder}";
+          TEST_ARGS+=", '-cover_xml_file', 'coverage.xml'";
+          TEST_ARGS+=", '-cover_json_file', 'coveralls.json'";
+      fi;
+      TEST_COMMAND="exit(~moxunit_runtests('${testFolder}', $TEST_ARGS));";
+      echo "TEST_COMMAND| $TEST_COMMAND";
+    # Double-check we are still in the right directory
+    - pwd
+    # Check what octave packages we have installed
+    # - octave -q --eval "ver"
+    # - octave -q --eval "2+3"
+    # ---------------------------------------------------------------------------
+    # Remove any cached results files from previous build, if present
+    - rm -f testresults.xml;
+      rm -f coverage.xml;
+      rm -f .coverage;
+      rm -f coveralls.json;
+    # ---------------------------------------------------------------------------
+    # Set up folders for test results on Shippable
+    - if [ "$SHIPPABLE" = "true" ]; then
+        rm -fr shippable;
+        mkdir -p shippable/testresults;
+        mkdir -p shippable/codecoverage;
+      fi;
+###############################################################################
+script:
+    - octave -v --eval "moxunit_runtests('${testFolder}')"
+    # - octave -v --eval "$ADDPATH_COMMAND $TEST_COMMAND";
+
+###############################################################################
+after_script:
+    # Check where we ended up and what's going on where we are
+    - pwd
+    - ls -alh
+    # ---------------------------------------------------------------------------
+    # Move results and coverage files into appropriate places
+    - if [ "$SHIPPABLE" = "true" ] && [ -f testresults.xml ]; then
+        mv testresults.xml shippable/testresults/;
+      fi;
+      if [ "$SHIPPABLE" = "true" ] && [ -f coverage.xml ]; then
+        cp coverage.xml shippable/codecoverage/;
+      fi;
+
+###############################################################################
+after_success:
+    # Only run coveralls on Travis. When running on a public Travis-CI, the
+    # repo token is automatically inferred, but to run coveralls on Shippable
+    # the repo token needs to be specified in a .coveralls.yml or as an
+    # environment variable COVERALLS_REPO_TOKEN. This should be kept hidden
+    # from public viewing, either by encrypting the token or running on a
+    # private build.
+    # We ignore coverage push failures because the servers are not 100%
+    # reliable and we don't want the CI to report a failure just because the
+    # coverage report wasn't published.
+    # For Codecov, we use this https://github.com/codecov/codecov-bash
+    - if [ "$COVERAGE" = "true" ] && [ "$TRAVIS" = "true" ] && [ "$SHIPPABLE" != "true" ]; then
+        curl --verbose -F json_file=`pwd`/coveralls.json https://coveralls.io/api/v1/jobs  || echo "Coveralls push failed";
+        bash <(curl -s https://codecov.io/bash) || echo "Codecov push failed";
+      fi;
+
+###############################################################################
+# Enable archiving of artifacts on Shippable (does nothing on Travis)
+archive: true      

README.md

@@ -1,27 +1,57 @@
 # PackMan
-PackMan aims to bring dependency management, similar to what [npm](https://www.npmjs.com) does for [Node.js](https://nodejs.org), to [MATLAB](https://www.mathworks.com/products/matlab.html). It is a fork of and improves on [DepMat](https://github.com/tomdoel/depmat).
 
-# Usage guide
+## Table of Contents
+
+1. [Acknowledgements](#acknowledgements)
+2. [Description](#description)
+3. [Usage Guide](#usage-guide)
+4. [Examples](#examples)
+5. [Test](#test)
+6. [ToDo](#todo)
+7. [Limitations](#limitations)
+8. [References](#references)
+
+## Acknowledgements
+
+- This PackMan was forked from [OmidS's Packman](https://github.com/OmidS/PackMan).
+- OmidS's Packman was forked from a great repository called [DepMat](https://github.com/tomdoel/depmat), by [Tom Doel](http://www.tomdoel.com).
+
+## Description
+
+PackMan aims to bring dependency management, similar to what [npm](https://www.npmjs.com) does for [Node.js](https://nodejs.org), to [MATLAB](https://www.mathworks.com/products/matlab.html). It is a fork of and improves on [OmidS's Packman](https://github.com/OmidS/PackMan).
+
+### Additional Features
+
+- Adds the possibility to source from private repositories.
+- Adds the possibility to write git native commands directly from matlab.
+
+## Usage guide
+
 Let's say you have a MATLAB project and you want to be able to use external packages in your code. An external package can be any git repository for which you have read access (e.g. any public repository on GitHub).
 
-## One time setup
+### One time setup
+
 You will need to do the following once, to enable package management with PackMan for your project:
+
 - Make sure there is no directory called 'external' at the root directory of your project
-- Copy "[installDeps.m](https://github.com/OmidS/PackMan/blob/master/source/installDeps.m)" to the root directory of your project
-- (Optional) Copy "[getDepList.m](https://github.com/OmidS/PackMan/blob/master/source/getDepList.m)" to the root directory of your project.
+- Copy "[installDeps.m](https://raw.githubusercontent.com/DanielAtKrypton/PackMan/master/source/installDeps.m)" to the root directory of your project
+- Copy "[getDepList.m](https://raw.githubusercontent.com/DanielAtKrypton/PackMan/master/source/getDepList.m)" to the root directory of your project.
 
 Done! Your project is now equipped with dependency management.
 
-## Add/remove dependencies
+### Add/remove dependencies
+
 You will need to do the following any time you want to add/remove a dependency
+
 - (Option 1) Update the list of dependencies in a file called package.json (for R2016b and later). PackMan will create a package.json file the first time you call "installDeps.m". Each dependency can have the fields listed in the following sample "package.json":
-```
+
+```json
 {
  "dependencies":{
   "PackMan":{
    "Name":"PackMan",
    "Branch":"master",
-   "Url":"https://github.com/OmidS/PackMan.git",
+   "Url":"https://github.com/DanielAtKrypton/PackMan.git",
    "FolderName":"PackMan",
    "Commit":"",
    "GetLatest":true
@@ -34,31 +64,52 @@ You will need to do the following any time you want to add/remove a dependency
 
 Note: when removing any repositories, it is best to delete the 'external' directory completely so that PackMan starts fresh.
 
-## Install/update dependencies
+### Install/update dependencies
+
 You will need to do the following to install or update dependencies
+
 - Run the following command (this will install/update all dependencies)
-```
+
+```matlab
 >> installDeps;
 ```
 
+### Add dependencies to the path
+
+You will need to run the following to add the dependencies to the MATLAB path before running your code
 
-## Add dependencies to the path
-You will need to run the following to add the dependencies to the MATALAB path before running your code
 - Now before running you code, add dependencies to the path by calling:
-```
+
+```matlab
 >> pm = installDeps;
->> addpath(pm.genPath());
+>> addpath(pm.genPath(:));
 ```
 
 You can also gracefully remove all dependencies from the path by calling:
+
+```matlab
+>> rmpath(pm.genPath(:));
 ```
->> rmpath(pm.genPath());
+
+## Examples
+
+- [PackManRecursiveSample](https://github.com/DanielAtKrypton/PackManRecursiveSample.git)
+
+## Test
+
+```matlab
+testsResults = runtests('testPackMan')
 ```
 
-## Complete example:
-See the following sample repository for a complete usage example for PackMan:
-https://github.com/OmidS/matlabPackManSample
+## ToDo
+
+- Add and successfully pass continuous integration.
+- Make sure it works for Mac and Linux operating systems.
+
+## Limitations
+
+- It was tested for Windows only because git.m uses a batch file workaround (RunCommand.cmd) to allow private repositories to be used within Packman.
 
+## References
 
-# Credits
-PackMan was forked from a great repository called [DepMat](https://github.com/tomdoel/depmat), by [Tom Doel](http://www.tomdoel.com).
+- [matlab-continuous-integration](https://github.com/scottclowe/matlab-continuous-integration)

source/DepMat.m

@@ -84,16 +84,19 @@ function setDispHandler(obj, funcHandle)
             [return_value, output] = system(command);
             success = return_value == 0;
             if ~success
-                if strfind(output, 'Protocol https not supported or disabled in libcurl')
+                if contains(output, 'Protocol https not supported or disabled in libcurl')
                     obj.dispHandler('! You need to modify the the DYLD_LIBRARY_PATH environment variable to point to a newer version of libcurl. The version installed with Matlab does not support using https with git.');
                 end
             end
         end
 
         function installed = isGitInstalled
-            command = 'git --help';
-
-            installed = DepMat.execute(command);
+            installed = true;
+            try
+                git('--help');
+            catch
+                installed = false;
+            end
         end
 
         function fixCurlPath

source/DepMatAddPaths.m

@@ -21,7 +21,7 @@ function DepMatAddPaths(baseFolderList, repoNameList, forceUpdate)
 
     full_path = mfilename('fullpath');
     [path_root, ~, ~] = fileparts(full_path);
-    myPaths = genpath(path_root);
+    myPaths = genNonGitPath(path_root);
     allPathsToAdd = [allPathsToAdd, myPaths];
 
     for repoIndex = 1 : numel(baseFolderList)
@@ -32,7 +32,7 @@ function DepMatAddPaths(baseFolderList, repoNameList, forceUpdate)
             DepMat_PathsHaveBeenSet{end + 1} = repoName;
         end
         if doAddPaths
-            repoPaths = genpath(baseFolderList{repoIndex});
+            repoPaths = genNonGitPath(baseFolderList{repoIndex});
             allPathsToAdd = [allPathsToAdd, repoPaths];
         end