Merge pull request #67 from datajoint/stage-external-storage

Add Toolbox packaging

.github/workflows/integration.yml

@@ -0,0 +1,38 @@
+name: Integration Tests
+on:
+  push:
+    branches:
+      - '**' # every branch
+      - '!stage*' # exclude branches beginning with stage
+  pull_request:
+    branches:
+      - '**' # every branch
+      - '!stage*' # exclude branches beginning with stage
+jobs:
+  CI:
+    if: github.event_name == 'push' || github.event_name == 'pull_request'
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        matlab_version: ["R2019a"]
+        mysql_version: ["8.0.18", "5.7", "5.6"]
+        include:
+          - matlab_version: "R2018b"
+            mysql_version: "5.7"
+          - matlab_version: "R2016b"
+            mysql_version: "5.7"
+    steps:
+      - uses: actions/checkout@v2
+      - name: Run primary tests
+        env:
+          MATLAB_UID: "1001"
+          MATLAB_GID: "116"
+          MATLAB_USER: ${{ secrets.matlab_user }}
+          MATLAB_HOSTID: ${{ secrets.matlab_hostid }}
+          MATLAB_VERSION: ${{ matrix.matlab_version }}
+          MYSQL_TAG: ${{ matrix.mysql_version }}
+          MATLAB_LICENSE: ${{ secrets[format('matlab_license_{0}', matrix.matlab_version)] }}
+          DOCKER_CLIENT_TIMEOUT: "120"
+          COMPOSE_HTTP_TIMEOUT: "120"
+        run: |
+          docker-compose -f LNX-docker-compose.yml up --build --exit-code-from app

.gitignore

@@ -6,4 +6,7 @@ notebook
 .vscode
 win.*
 .DS_Store
-macos.*
+macos*
+*.prj
+matlab.prf
+*.mltbx

LNX-docker-compose.yml

@@ -11,7 +11,7 @@ services:
       - MYSQL_ROOT_PASSWORD=simple
   fakeservices.datajoint.io:
     <<: *net
-    image: raphaelguzman/nginx:v0.0.8
+    image: raphaelguzman/nginx:v0.0.10
     environment:
     - ADD_db_TYPE=DATABASE
     - ADD_db_ENDPOINT=db:3306
@@ -21,7 +21,6 @@ services:
   app:
     <<: *net
     environment:
-    - DISPLAY
     - MATLAB_LICENSE
     - MATLAB_USER
     - DJ_HOST=fakeservices.datajoint.io
@@ -35,19 +34,72 @@ services:
       fakeservices.datajoint.io:
         condition: service_healthy
     user: ${MATLAB_UID}:${MATLAB_GID}
-    working_dir: /src
-    command: > 
-      /bin/bash -c "
-        matlab -nodisplay -r \"\
-            feature('DefaultCharacterSet','UTF-8');\
-            res=run(tests.Main);\
+    working_dir: /main
+    command:
+      - /bin/bash
+      - -c
+      - |
+        set -e
+        export ORIG_DIR=$$(pwd)
+        mkdir ~/Documents
+        cd /src
+        # Verify all mex have been updated
+        if [ "distribution/mexa64/mym.mexa64" -nt "distribution/mexmaci64/mym.mexmaci64" ]; then
+          echo "MACOS64 Mex binary appears outdated. Failing check..."
+          exit 1
+        fi
+        if [ "distribution/mexa64/mym.mexa64" -nt "distribution/mexw64/mym.mexw64" ]; then
+          echo "WIN64 Mex binary appears outdated. Failing check..."
+          exit 1
+        fi
+        # Compile mym, package into toolbox, and install
+        matlab -nodisplay -r "
+          try\
+            websave([tempdir 'GHToolbox.mltbx'],\
+                    ['https://github.com/datajoint/GHToolbox' \
+                     '/releases/download/' subsref(webread(['https://api.github.com/repos' \
+                                                            '/datajoint/GHToolbox' \
+                                                            '/releases/latest']),\
+                                                   substruct('.', 'tag_name')) \
+                     '/GHToolbox.mltbx']);\
+            matlab.addons.toolbox.installToolbox([tempdir 'GHToolbox.mltbx']);\
+            origDir = pwd;\
+            cd('distribution/mexa64');\
+            docs = help('mym');\
+            cd(origDir);\
+            ghtb.package('mym',\
+                         'Raphael Guzman',\
+                         '[email protected]',\
+                         ['MySQL API for MATLAB with support for BLOB objects'],\
+                         docs,\
+                         {'.vscode', '.git', '.gitignore', 'build', 'lib', 'maria-plugin',\
+                          'mex_compilation', 'mysql-connector', 'notebook', 'src', 'zlib',\
+                          '*.txt', '*.env', '*.prf', '*.md', '*.yml', 'tests', '.github',\
+                          'distribution/mexa64/libmysqlclient.so.18.4.'},\
+                         @() strjoin(arrayfun(@(x) num2str(x),\
+                                              cell2mat(struct2cell(mym('version'))),\
+                                              'uni', false),\
+                                     '.'),\
+                         {'distribution/mexa64', 'distribution/mexmaci64',\
+                          'distribution/mexw64', 'mym.m'},\
+                         'toolboxVersionDir', 'distribution/mexa64',\
+                         'toolboxRootDir', '.');\
+            matlab.addons.toolbox.installToolbox('mym.mltbx');\
+            cd(getenv('ORIG_DIR'));\
+            addpath('tests');\
+            res=run(Main);\
             disp(res);\
             if all([res.Passed])  exit, else exit(1), end;\
-          \";
-      "
+            ,\
+          catch ME,\
+            disp(getReport(ME, 'extended'));\
+            exit(1);\
+            ,\
+          end;\
+        "
     mac_address: $MATLAB_HOSTID
     volumes:
+      - ./tests:/main/tests
       - .:/src
-      - /tmp/.X11-unix:/tmp/.X11-unix:rw
 networks:
   main:

README.md

@@ -1,5 +1,6 @@
-mym
-===
+[![View mym on File Exchange](https://www.mathworks.com/matlabcentral/images/matlab-file-exchange.svg)](https://www.mathworks.com/matlabcentral/fileexchange/81208-mym)
+
+## mym
 
 MySQL API for MATLAB with support for BLOB objects
 
@@ -11,10 +12,7 @@ work of Robert Almgren from University of Toronto [sourceforge project](http://s
 
 See mym.m for further documentation.
 
-
-Running Tests Locally
-=====================
-
+## Running Tests Locally
 
 * Create an `.env` with desired development environment values e.g.
 ``` sh
@@ -33,28 +31,54 @@ MYSQL_TAG=5.7
 
 | Use Case                     | MATLAB Code                                                                    |
 | ---------------------------- | ------------------------------------------------------------------------------ |
-| Run all tests                | `run(tests.Main)`                                                              |
-| Run one class of tests       | `run(tests.TestTls)`                                                           |
-| Run one specific test        | `runtests('tests.TestTls/TestTls_testInsecureConn')`                                   |
-| Run tests based on test name | `import matlab.unittest.TestSuite;`<br>`import matlab.unittest.selectors.HasName;`<br>`import matlab.unittest.constraints.ContainsSubstring;`<br>`suite = TestSuite.fromClass(?tests.Main, ... `<br><code>&nbsp;&nbsp;&nbsp;&nbsp;</code>`HasName(ContainsSubstring('Conn')));`<br>`run(suite)`|
+| Run all tests                | `run(Main)`                                                              |
+| Run one class of tests       | `run(TestTls)`                                                           |
+| Run one specific test        | `runtests('TestTls/TestTls_testInsecureConn')`                                   |
+| Run tests based on test name | `import matlab.unittest.TestSuite;`<br>`import matlab.unittest.selectors.HasName;`<br>`import matlab.unittest.constraints.ContainsSubstring;`<br>`suite = TestSuite.fromClass(?Main, ... `<br><code>&nbsp;&nbsp;&nbsp;&nbsp;</code>`HasName(ContainsSubstring('Conn')));`<br>`run(suite)`|
 
 
-Launch Jupyter Notebook
------------------------
+### Launch Jupyter Notebook
 * Navigate to `localhost:8888`
 * Input Jupyter password
 * Launch a notebook i.e. `New > MATLAB`
 
 
-Launch MATLAB GUI (supports remote interactive debugger)
---------------------------------------------------------
+### Launch MATLAB GUI (supports remote interactive debugger)
 * Shell into `mym_app_1` i.e. `docker exec -it mym_app_1 bash`
 * Launch Matlab by runnning command `matlab`
 
 
-Launch MATLAB Terminal
-----------------------
+### Launch MATLAB Terminal
 * Shell into `mym_app_1` i.e. `docker exec -it mym_app_1 bash`
 * Launch Matlab with no GUI by runnning command `matlab -nodisplay`
 
 
+## Installation
+
+### (Recommended) Using GHToolbox (FileExchange Community Toolbox)
+
+1. Install *GHToolbox* using using an appropriate method in https://github.com/datajoint/GHToolbox
+2. run: `ghtb.install('datajoint/mym')`
+
+### Greater than R2016b
+
+1. Utilize MATLAB built-in GUI i.e. *Top Ribbon -> Add-Ons -> Get Add-Ons*
+2. Search and Select `mym`
+3. Select *Add from GitHub*
+
+### Less than R2016b
+
+1. Utilize MATLAB built-in GUI i.e. *Top Ribbon -> Add-Ons -> Get Add-Ons*
+2. Search and Select `mym`
+3. Select *Download from GitHub*
+4. Save `mym.mltbx` locally
+5. Navigate in MATLAB tree browser to saved toolbox file
+6. Right-Click and Select *Install*
+7. Select *Install*
+
+### From Source
+
+1. Download `mym.mltbx` locally
+2. Navigate in MATLAB tree browser to saved toolbox file
+3. Right-Click and Select *Install*
+4. Select *Install*