Move compareVersions to its maintained toolbox, rename setupDJ to +dj…

…/setup, add GHToolbox/mym dependencies, add installation docs, and clean up tests.
guzman-raphael · Sep 22, 2020 · 058227c · 058227c
1 parent b016561
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Showing 10 changed files with 85 additions and 234 deletions.
diff --git a/+dj/+lib/compareVersions.m b/+dj/+lib/compareVersions.m
diff --git a/+dj/Connection.m b/+dj/Connection.m
@@ -27,19 +27,7 @@
             % specify the connection to the database.
             % initQuery is the SQL query to be executed at the start
             % of each new session.
-            if ~any(arrayfun(@(x) strcmp(x.Name, 'mym'), ...
-                             matlab.addons.toolbox.installedToolboxes, 'uni', true))
-                ghtb.install('guzman-raphael/mym');
-            end
-            try
-                mymVersion = mym('version');
-                assert(mymVersion.major > 2 || mymVersion.major==2 && mymVersion.minor>=6)
-            catch
-                error 'Outdated version of mYm.  Please upgrade to version 2.6 or later'
-            end
-            if verLessThan('matlab', '8.6')
-                error 'MATLAB version 8.6 (R2015b) or greater is required'
-            end
+            dj.setup('prompt', ~dj.set('suppressPrompt'));
             self.host = host;
             self.user = username;
             self.password = password;

diff --git a/+dj/conn.m b/+dj/conn.m
@@ -45,7 +45,6 @@
         end
     end
 else
-    % invoke setupDJ
     % optional environment variables specifying the connection.
     env  = struct(...
         'host', 'DJ_HOST', ...

diff --git a/+dj/setup.m b/+dj/setup.m
@@ -0,0 +1,51 @@
+function setup(varargin)
+    p = inputParser;
+    addOptional(p, 'force', false);
+    addOptional(p, 'prompt', true);
+    parse(p, varargin{:});
+    force = p.Results.force;
+    prompt = p.Results.prompt;
+    persistent INVOKED
+    if ~isempty(INVOKED) && ~force
+        return
+    end
+    % check MATLAB
+    if verLessThan('matlab', '9.1')
+        error('DataJoint:System:UnsupportedMatlabVersion', ...
+              'MATLAB version 9.1 (R2016b) or greater is required');
+    end
+    % require certain toolboxes
+    requiredToolboxes = {...
+        struct(...
+            'Name', 'GHToolbox', ...
+            'ResolveTarget', 'datajoint/GHToolbox'...
+        ), ...
+        struct(...
+            'Name', 'mym', ...
+            'ResolveTarget', 'guzman-raphael/mym', ...
+            'Version', '2.7.3'...
+        )...
+    };
+    try
+        ghtb.require(requiredToolboxes, 'prompt', prompt);
+    catch ME
+        if strcmp(ME.identifier, 'MATLAB:undefinedVarOrClass')
+            GHToolboxMsg = {
+                'Toolbox ''GHToolbox'' did not meet the minimum minimum requirements.'
+                'Please install it via instructions in '
+                '''https://github.com/datajoint/GHToolbox'''.'
+            };
+            error('DataJoint:verifyGHToolbox:Failed', ...
+                  sprintf('%s\n', GHToolboxMsg{:}));
+        else
+            rethrow(ME)
+        end
+    end
+    % check mym
+    mymVersion = mym('version');
+    assert(mymVersion.major > 2 || mymVersion.major==2 && mymVersion.minor>=6, ...
+           'DataJoint:System:mYmIncompatible', ...
+           'Outdated version of mYm.  Please upgrade to version 2.6 or later');
+    % set cache
+    INVOKED = true;
+end
diff --git a/DataJoint.mltbx b/DataJoint.mltbx
diff --git a/LNX-docker-compose.yml b/LNX-docker-compose.yml
@@ -40,15 +40,7 @@ services:
       - -c
       - |
         matlab -nodisplay -r "
-          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']);\
-          ghtb.install('DataJoint.mltbx');\
+          matlab.addons.toolbox.installToolbox('DataJoint.mltbx');\
           addpath('tests');\
           res=run(Main);\
           disp(res);\

diff --git a/README.md b/README.md
@@ -2,10 +2,33 @@ DataJoint for MATLAB is a high-level programming interface for relational databa
 
 DataJoint was initially developed in 2009 by Dimitri Yatsenko in [Andreas Tolias' Lab](http://toliaslab.org) for the distributed processing and management of large volumes of data streaming from regular experiments. Starting in 2011, DataJoint has been available as an open-source project adopted by other labs and improved through contributions from several developers.
 
+## Installation
 
-Running Tests Locally
-=====================
+### Greater than R2016b (Recommended)
 
+1. Utilize MATLAB built-in GUI i.e. *Top Ribbon -> Add-Ons -> Get Add-Ons*
+2. Search and Select `DataJoint`
+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 `DataJoint`
+3. Select *Download from GitHub*
+4. Save `DataJoint.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 `DataJoint.mltbx` locally
+2. Navigate in MATLAB tree browser to saved toolbox file
+3. Right-Click and Select *Install*
+4. Select *Install*
+
+
+## Running Tests Locally
 
 * Create an `.env` with desired development environment values e.g.
 ``` sh
@@ -30,20 +53,20 @@ MYSQL_TAG=5.7
 | 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 `datajoint-matlab_app_1` i.e. `docker exec -it datajoint-matlab_app_1 bash`
 * Launch Matlab by runnning command `matlab`
 
 
-Launch MATLAB Terminal
-----------------------
+### Launch MATLAB Terminal
+
 * Shell into `datajoint-matlab_app_1` i.e. `docker exec -it datajoint-matlab_app_1 bash`
 * Launch Matlab with no GUI by runnning command `matlab -nodisplay`
diff --git a/local-docker-compose.yml b/local-docker-compose.yml
@@ -79,8 +79,6 @@ services:
                                             'uni', false),\
                                    '.'),\
                        {'+dj'});\
-          ghtb.install('DataJoint.mltbx');\
-          dj.version;\
         "
         # Copy preferences
         cp /tmp/matlab.prf /home/muser/.matlab/${MATLAB_VERSION}/matlab.prf

diff --git a/tests/+lib/compareVersions.m b/tests/+lib/compareVersions.m
diff --git a/tests/Prep.m b/tests/Prep.m
@@ -35,7 +35,7 @@ function init(testCase)
                 testCase.CONN_INFO_ROOT.user, testCase.CONN_INFO_ROOT.password,'',true);
             % create test users
             ver = curr_conn.query('select @@version as version').version;
-            if lib.compareVersions(ver,'5.8')
+            if compareVersions(ver,'5.8')
                 cmd = {...
                 'CREATE USER IF NOT EXISTS ''datajoint''@''%%'' '
                 'IDENTIFIED BY ''datajoint'';'