linny-r 2.0.1 → 2.0.4

package/README.md

@@ -1,39 +1,46 @@
-<img src="https://sysmod.tbm.tudelft.nl/linny-r/images/logo.png" height="55px" alt="Linny-R">
+<img src="https://sysmod.tbm.tudelft.nl/linny-r/images/logo.png"
+     height="55px" alt="Linny-R">
 
 Linny-R is an executable graphical specification language for mixed integer 
-<a href="https://en.wikipedia.org/wiki/Linear_programming" target="_blank">linear programming</a>
-(MILP) problems, especially
+<a href="https://en.wikipedia.org/wiki/Linear_programming"
+   target="_blank">linear programming</a> (MILP) problems, especially
 <a href="https://en.wikipedia.org/wiki/Unit_commitment_problem_in_electrical_power_production"
    target="_blank">unit commitment problems</a>
 (UCP) and
 <a href="https://en.wikipedia.org/wiki/Generation_expansion_planning"
    target="_blank">generation expansion planning</a> (GEP).
 
-The graphical language and WYSIWYG model editor are developed by **Pieter Bots** at
-<a href="https://tudelft.nl" target="_blank">Delft University of Technology</a>.
+The graphical language and WYSIWYG model editor are developed by **Pieter Bots**
+at <a href="https://tudelft.nl" target="_blank">Delft University of Technology</a>.
  
-Originally implemented in Delphi Pascal, Linny-R is now developed in HTML+CSS+JavaScript
-so as to be platform-independent and 100% transparent open source (under the MIT license).
-The software comprises a server that runs on **Node.js**,
-and a graphical user interface (GUI) that runs in any modern browser.
-
-These <a href="https://sysmod.tbm.tudelft.nl/linny-r/docs/?68" target="_blank">instruction videos</a>
-published on YouTube give an idea of what Linny-R can do.
-
-User documentation for Linny-R is still scant, but it is growing. You can contribute yourself
-(in "wiki fashion") via the official user documentation site
+Originally implemented in Delphi Pascal, Linny-R is now developed in
+HTML+CSS+JavaScript so as to be platform-independent and 100% transparent
+open source (under the MIT license). The software comprises a server that
+runs on **Node.js**, and a graphical user interface (GUI) that runs in any
+modern browser.
+
+These <a href="https://sysmod.tbm.tudelft.nl/linny-r/docs/?68"
+         target="_blank">instruction videos</a> published on YouTube give
+an idea of what Linny-R can do.
+
+User documentation for Linny-R is still scant. A book "Modeling and
+simulation with Linny-R" will be published by TU Delft OPEN in 2024.
+Meanwhile, you can consult the official user documentation site
 <a href="https://linny-r.info" target="_blank">https://linny-r.info</a>.
-Technical documentation will be developed on GitHub: https://github.com/pwgbots/linny-r/wiki
+Technical documentation will be developed in due time on GitHub:
+https://github.com/pwgbots/linny-r/wiki
 
 ## Installing Node.js
 
-Linny-R is developed as a JavaScript package, and requires that **Node.js** is installed on your computer. 
-This software can be downloaded from <a href="https://nodejs.org" target="_blank">https://nodejs.org</a>. 
+Linny-R is developed as a JavaScript package, and requires that **Node.js**
+is installed on your computer. This software can be downloaded from
+<a href="https://nodejs.org" target="_blank">https://nodejs.org</a>. 
 Make sure that you choose the correct installer for your computer.
-Linny-R is developed using the _current_ release. Presently (April 2024) this is 21.7.3. 
+Linny-R is developed using the _current_ release. Presently (June 2024)
+this is 22.2.0. 
 
 Run the installer and accept the default settings.
-There is **no** need to install the optional _Tools for Native Modules_.
+There is <u>**no**</u> need to install the optional _Tools for Native Modules_.
 
 Open the Command Line Interface (CLI) of your computer. 
 On macOS, this will be `Terminal`, on Windows `Command Prompt`. 
@@ -41,16 +48,19 @@ Verify the installation by typing:
 
 ``node --version``
 
-The response should be the version number of Node.js, for example: v21.7.3.
+The response should be the version number of Node.js, for example: v22.2.0.
 
 ## Installing Linny-R
-It is advisable to install Linny-R in a directory on your computer, not in a cloud. 
+It is advisable to install Linny-R in a directory on your computer, **not**
+in a cloud. 
+
 In this installation guide, the path to this directory is denoted by `Linny-R`,
 so in all commands you should replace this with the actual directory path.
-On a Windows machine the suggested path is `C:\Users\(your user name)\Documents\Linny-R`,
+On a Windows machine the suggested path is `C:\Users\(your user name)\Linny-R`,
 and on a macOS machine `/Users/(your user name)/Linny-R`.
 
-To install Linny-R in this directory, first change to the parent directory like so:
+To install Linny-R in this directory, first change to the parent directory
+like so:
 
 ``cd /Users/(your user name)``
 
@@ -69,7 +79,8 @@ and then type at the command line prompt:
 > [!IMPORTANT]
 > The spacing around the dot is essential. Type the command in lower case.
 
-After installation has completed, `Linny-R` should have this directory tree structure:
+After installation has completed, `Linny-R` should have this directory tree
+structure:
 
 <pre>
 Linny-R
@@ -92,52 +103,73 @@ Linny-R
 </pre>
 
 `Linny-R` should contain two JSON files `package.json` and `package-lock.json`
-that should **not** be removed, or you will have to re-install Linny-R. It should also contain
-a script file to facilitate (single click) launch: on a macOS machine the shell script `linny-r.command`,
-on a Windows machine the batch script `linny-r.bat`. By default, this script file contains
-two commands: first change to the Linny-R directory and then tell Node.js to launch the
-start the Linny-R server.
+that should **not** be removed, or you will have to re-install Linny-R.
+It should also contain the launch script.  On a macOS machine, this will be
+the shell script `linny-r.command`, on a Windows machine the batch script
+`linny-r.bat`.
 
-> [!NOTE]
-> When configuring Linny-R for a network environment where individual users
-> each have their personal work space (e.g., a virtual drive U:), you must edit this script file,
-> adding the argument `workspace=path/to/workspace` to the `node` command.
-> This will instruct Linny-R to create the `user` directory in this workspace directory
-> instead of the Linny-R directory.
+All other software is contained in the `node_modules` directory. It comprises
+two Node.js packages: `@xlmdom` and `linny-r`. 
 
-The `linny-r` directory should contain this file `README.md`,
-the files `server.js` and `console.js` that will be run by Node.js,
-and the sub-directory `static`. This `static` directory should contain three HTML files: 
+The `linny-r` package directory should contain this file `README.md`, the files
+`server.js` and `console.js` that will be run by Node.js, and the sub-directory
+`static`. This `static` directory should contain three HTML files: 
 
 * `index.html` (the browser-based GUI) 
 * `show-png.html` (to render SVG diagrams as PNG images)
-* `show-diff.html` (to display differences betwee two Linny-R models)
+* `show-diff.html` (to display differences between two Linny-R models)
 
 It should also contain the style sheet `linny-r.css` required by the GUI.
 
-The sub-directories of `static` contain files that are served to the browser by the script
-`server.js` when it is running in Node.js. 
+The sub-directories of `static` contain files that are served to the browser
+by the script `server.js` when it is running in Node.js.
+
+> [!IMPORTANT]
+> Unless you _really_ know what you are doing, do **not** move or rename
+> your Linny-R directory or change its contents. If for some reason Linny-R
+> does not work, remove _all_ Linny-R software from your machine, and then
+> install it anew, following the procedure described above.
+
+#### Updating to the latest version of Linny-R
+
+When a newer version has beeh released, Linny-R will prompt you to update
+automatically. Click on the link in this prompt to see the release notes
+on GitHub and find out about new features and bug fixes. When you click on
+the _OK_ button, Linny-R will shut down its local server script, and then
+the launch script should perform the `npm update` command and then restart
+the server script. Your browser will prompt you to close its current tab,
+and then Linny-R should reappear in a new browser tab or window.
+
+> [!NOTE]
+> The built-in updating function of Linny-R will _**not**_ automatically
+> upgrade to a new _major_ version. To update from a version like 1.9.x to
+> a version like 2.0.x, you have to open a command line interface
+> (`Command Prompt` or `Terminal`), change to your Linny-R directory, and
+> then type `npm install linny-r@2`. This should perform the upgrade.
+> You can then launch Linny-R as usual by typing `linny-r` (Windows) or
+> `./linny-r.command` (macOS).
 
 #### Installing and using an earlier version of Linny-R
 
 By default, **npm** will install the latest release of the Linny-R software.
-As this software is developed as part of academic research, new features are added 
-without rigorous testing. Although much effort is dedicated to maintaining upward
-and downward compatibility, you may find that the latest version does not work as
-well for you as some earlier version. To re-install an earlier release, for example
-version 1.4.0, open the CLI, change to your `Linny-R` directory, and then type:
+As this software is developed as part of academic research, new features
+are added without rigorous testing. Although much effort is dedicated to
+maintaining upward and downward compatibility, you may find that the latest
+version does not work as well for you as some earlier version. To re-install
+an earlier release, for example version 1.9.3, open the CLI, change to your
+`Linny-R` directory, and then type:
 
-``npm install linny-r@1.4.0``
+``npm install linny-r@1.9.3``
 
 > [!NOTE]
 > This will overwrite the contents of the `node_modules` directory, but
 > it will not affect the files in your user space.
 
-If you prefer to have different versions of Linny-R on your computer, you can
-create a separate directory for a specific version, then change to this
+If you prefer to have different versions of Linny-R on your computer, you
+can create a separate directory for a specific version, then change to this
 directory and type:
 
-``npm install --prefix . linny-r@1.4.0``
+``npm install --prefix . linny-r@1.9.3``
 
 > [!NOTE]
 > To run a specific version in your browser, you must start the server from
@@ -147,10 +179,11 @@ directory and type:
 
 ## Configuring the MILP solver
 
-Linny-R presently supports five MILP solvers: Gurobi, MOSEK, CPLEX, SCIP and LP_solve. 
-Gurobi, MOSEK and CPLEX are _considerably_ more powerful than the open source solvers SCIP and LP_solve,
-but they require a license.
-Academic licenses can be obtained by students and staff of eligible institutions.
+Linny-R presently supports five MILP solvers: Gurobi, MOSEK, CPLEX, SCIP
+and LP_solve. Gurobi, MOSEK and CPLEX are _considerably_ more powerful than
+the open source solvers SCIP and LP_solve, but they require a license.
+Academic licenses can be obtained by students and staff of eligible
+institutions.
 
 > [!IMPORTANT]
 > When installing a solver, it is advisable to accept the default file
@@ -166,8 +199,9 @@ Gurobi on your computer can be obtained via this URL:
 <a href="https://www.gurobi.com/academia/academic-program-and-licenses/"
    target="_blank">https://www.gurobi.com/academia/academic-program-and-licenses/</a>
 
-When running a model, Linny-R will try to execute the command line application `gurobi_cl`.
-It will look for this application in the directory specified in the environment variable PATH on your computer.
+When running a model, Linny-R will try to execute the command line application
+`gurobi_cl`. It will look for this application in the directory specified in
+the environment variable PATH on your computer.
 
 #### Installing CPLEX
 
@@ -177,10 +211,11 @@ CPLEX on your computer can be obtained via this URL:
 <a href="https://www.ibm.com/products/ilog-cplex-optimization-studio"
    target="_blank">https://www.ibm.com/products/ilog-cplex-optimization-studio</a>
 
-When running a model, Linny-R will try to execute the command line application `cplex`.
-It will look for this application in the directory specified in the environment variable PATH
-or more specifically in the environment variable CPLEX_STUDIO_BINARIES<em>nnnn</em>
-(where _nnnn_ denotes the CPLEX version number) on your computer.
+When running a model, Linny-R will try to execute the command line application
+`cplex`. It will look for this application in the directory specified in the
+environment variable PATH or more specifically in the environment variable
+CPLEX_STUDIO_BINARIES<em>nnnn</em> (where _nnnn_ denotes the CPLEX version
+number) on your computer.
 
 #### Installing MOSEK
 
@@ -190,38 +225,46 @@ MOSEK on your computer can be obtained via this URL:
 <a href="https://www.mosek.com/resources/getting-started/"
    target="_blank">https://www.mosek.com/resources/getting-started/</a>
 
-When running a model, Linny-R will try to execute the command line application `mosek`.
-It will look for this application in the directory specified in the environment variable PATH on your computer.
+When running a model, Linny-R will try to execute the command line application
+`mosek`. It will look for this application in the directory specified in the
+environment variable PATH on your computer.
 
 #### Installing SCIP
 
-The SCIP software is open source. Instructions for installation can be found via this URL:
-<a href="https://scipopt.org/doc/html/INSTALL.php" target="_blank">https://scipopt.org/doc/html/INSTALL.php</a>
+The SCIP software is open source. Instructions for installation can be found
+via this URL: <a href="https://scipopt.org/doc/html/INSTALL.php"
+                 target="_blank">https://scipopt.org/doc/html/INSTALL.php</a>
 
-When running a model, Linny-R will try to execute the command line application `scip`.
-It will look for this application in the directory specified in the environment variable PATH on your computer.
+When running a model, Linny-R will try to execute the command line application
+`scip`. It will look for this application in the directory specified in the
+environment variable PATH on your computer.
 
 #### Installing LP_solve
 
 The LP_solve software is open source and can be downloaded via this URL:
-<a href="https://sourceforge.net/projects/lpsolve" target="_blank">https://sourceforge.net/projects/lpsolve</a>
-
-To facilitate installation, the executable files for Windows and macOS can be downloaded from the Linny-R website
-at Delft University of Technology:
-<a href="https://sysmod.tbm.tudelft.nl/linny-r/lp_solve" target="_blank">https://sysmod.tbm.tudelft.nl/linny-r/lp_solve</a>
-
-There you will find links to download LP_solve applications that have been compiled for different platforms.
-If you do not know which platform to choose, run Linny-R as described below, and the platform will be listed in its output.
-If no matching LP_solve version is listed, you can try to compile the software from its source.
-How to do this is explained on the page "Installing LP_solve on a Mac" on the Linny-R documentation site:
+<a href="https://sourceforge.net/projects/lpsolve"
+   target="_blank">https://sourceforge.net/projects/lpsolve</a>
+
+To facilitate installation, the executable files for Windows and macOS can
+be downloaded from the Linny-R website at Delft University of Technology:
+<a href="https://sysmod.tbm.tudelft.nl/linny-r/lp_solve"
+   target="_blank">https://sysmod.tbm.tudelft.nl/linny-r/lp_solve</a>
+
+There you will find links to download LP_solve applications that have been
+compiled for different platforms. If you do not know which platform to choose,
+run Linny-R as described below, and the platform will be listed in its output.
+If no matching LP_solve version is listed, you can try to compile the software
+from its source. How to do this is explained on the page "Installing LP_solve
+on a Mac" on the Linny-R documentation site:
 <a href="https://linny-r.info" target="_blank">https://linny-r.info</a> 
 
-When you have downloaded the file (just `lp_solve` for macOS, `lp_solve.exe` for Windows), 
-you must copy or move this file to your `Linny-R` directory,
-as this is where Linny-R will look for it when it does not find one of the other solvers.
+When you have downloaded the file (just `lp_solve` for macOS, `lp_solve.exe`
+for Windows), you must copy or move this file to your `Linny-R` directory,
+as this is where Linny-R will look for it when it does not find one of the
+other solvers.
 
 On a macOS machine, you must then make the file `lp_solve` executable.
-Open Terminal and change to your Linny-R directory, and then type:
+Open `Terminal` and change to your Linny-R directory, and then type:
 
 ``chmod +x lp_solve``
 
@@ -230,35 +273,36 @@ When you then type:
 ``./lp_solve -h``
 
 a window may appear that warns you that the software may be malicious.
-To allow running LP_solve, you must then go to Security & Privacy (via System Preferences)
-and there click the Open Anyway button in the General pane to confirm that you wish to use LP_solve.
-Then return to Terminal and once more type `./lp_solve -h`.
-The response should then be a listing of all the command line options of LP_solve.
-If you reach this stage, Linny-R will be able to run LP_solve.
+To allow running LP_solve, you must then go to _Security & Privacy_ (via
+_System Preferences_) and there click the _Open Anyway_ button in the _General_
+pane to confirm that you wish to use LP_solve. Then return to `Terminal`
+and once more type `./lp_solve -h`. The response should then be a listing
+of all the command line options of LP_solve. If you reach this stage,
+Linny-R will be able to run LP_solve.
 
 ## Running Linny-R
 
-Open the Command Line Interface (CLI) of your computer, change to your Linny-R directory and type:
+On a Windows machine, open `Command Prompt`, change to your Linny-R
+directory and type:
 
-``node node_modules/linny-r/server launch``
+``linny-r``
 
-This response should be something similar to:
+On a macOS machine, open `Terminal`, change to your Linny-R directory
+and type:
 
-<pre>
-Node.js server for Linny-R version 1.9.3
-Node.js version: v21.7.3
-... etc.
-</pre>
+``./linny-r.command``
 
-Meanwhile, your default web browser should have opened a tab for the local server URL,
-which by default will be http://127.0.0.1:5050.
-The Linny-R GUI should show in your browser window, 
-while in the CLI you should see a long series of server log messages like:
+This should run the launch script for Linny-R, which will start the
+local server script that connects your browser with the solver. 
+Meanwhile, your default web browser should have opened a tab for the local
+server URL, which by default will be http://127.0.0.1:5050.
+The Linny-R GUI should show in your browser window, while in the CLI you
+should see a long series of server log messages like:
 
 <pre>
-[2023-11-19 22:55:17] Static file: /index.html
-[2023-11-19 22:55:17] Static file: /scripts/iro.min.js
-[2023-11-19 22:55:17] Static file: /images/open.png
+[2024-06-11 22:55:17] Static file: /index.html
+[2024-06-11 22:55:17] Static file: /scripts/iro.min.js
+[2024-06-11 22:55:17] Static file: /images/open.png
 ... etc.
 </pre>
 
@@ -266,16 +310,16 @@ while in the CLI you should see a long series of server log messages like:
 > Do **not** close the CLI. If you do, the Linny-R GUI may still be
 > visible in your browser, but you will be warned that it cannot connect
 > to the server (at 127.0.0.1:5050). This means that you have to restart
-> Linny-R from a new CLI.
+> Linny-R as described above.
 
 After loading into the browser, Linny-R will try to connect to the solver.
-If successful, a notification (blue background) will appear on the status bar
-at the bottom of the window, stating the name of the solver.
+If successful, a notification (blue background) will appear on the status
+bar at the bottom of the window, stating the name of the solver.
 
 You can then test the GUI by creating a simple model.
 Make one that has at least one process that outputs a product, 
-and this product must have a price or a set lower bound, otherwise the model
-will have no objective function.
+and this product must have a price or a set lower bound, otherwise the
+model will have no objective function.
 Then click on the _Solve_ button at the bottom of the left-hand tool bar.
 The Linny-R icon in the upper left corner should start rotating, while the
 status bar at the bottom should display:
@@ -298,9 +342,41 @@ confirming that you want to leave, and then closing your browser (tab).
 If you do not shut down the server from the browser, you can also stop the
 server by repeatedly pressing ``Ctrl+C`` in the CLI.
 
+## Click-start for Linny-R
+
+When `npm` installs the Linny-R package, it creates a script file in your
+Linny-R directory that launches Linny-R. On a macOS machine, this will be
+the shell script `linny-r.command`, on a Windows machine the batch script
+`linny-r.bat`. When you create a desktop shortcut to this script, this will
+allow you to click-start Linny-R. 
+
+How you can create a shortcut icon for Linny-R on your desktop depends on
+the type of computer you use.
+
+On a Windows machine, open the `File Explorer`, select your Linny-R folder,
+right-click on the batch file `linny-r.bat`, and select the _Create shortcut_
+option. Then right-click on the shortcut file to edit its properties, and
+click the _Change Icon_ button. The dialog that then appears will allow
+you to go to the sub-folder `node_modules\linny-r\static\images`, where
+you should select the file `linny-r.ico`. Finally, rename the shortcut to
+`Linny-R` and move or copy it to your desktop.
+
+On a macOS machine, open `Terminal` and change to your Linny-R directory,
+and then type:
+
+``chmod +x linny-r.command``
+
+to make the script file executable. To set the icon, use `Finder` to open
+the folder that contains the file `linny-r.command`, click on its icon
+(which still is plain) and open the _Info dialog_ by pressing ``Cmd+I``.
+Then open your Linny-R folder in `Finder`, change to the sub-folder
+`node_modules/linny-r/static/images`, and from there drag/drop the file
+`linny-r.icns` on the icon shown in the top left corner of the _Info dialog_.
+
 ## Command line options
 
-Optionally, you can add more arguments to the `node` command:
+You can customize Linny-R by adding more arguments to the `node` command
+in the launch script:
 
 <pre>
 dpi=[number]       to overrule the default resolution (300 dpi) for Inkscape 
@@ -310,26 +386,12 @@ solver=[name]      to overrule the default sequence (Gurobi, MOSEK, CPLEX, SCIP,
 workspace=[path]   to overrule the default path for the user directory
 </pre>
 
-## Click-start for Linny-R
-
-To facilitate start-up, you can create a shortcut icon for Linny-R on your desktop. 
-
-On a Windows machine, open the _File Explorer_, select your Linny-R folder,
-right-click on the batch file `linny-r.bat`, and select the _Create shortcut_ option. 
-Then right-click on the shortcut file to edit its properties, and click the _Change Icon_ button.
-The dialog that then appears will allow you to go to the sub-folder
-`node_modules\linny-r\static\images`, where you should select the file `linny-r.ico`.
-Finally, rename the shortcut to `Linny-R` and move or copy it to your desktop.
-
-On a macOS machine, open Terminal and change to your Linny-R directory, and then type:
-
-``chmod +x linny-r.command``
-
-to make the script file executable.
-To set the icon, use Finder to open the folder that contains the file `linny-r.command`,
-click on its icon (which still is plain) and open the _Info dialog_ by pressing ``Cmd+I``.
-Then open your Linny-R folder in Finder, change to the sub-folder `node_modules/linny-r/static/images`, 
-and from there drag/drop the file `linny-r.icns` on the icon shown in the top left corner of the _Info dialog_.
+> [!NOTE]
+> When configuring Linny-R for a network environment where individual users
+> each have their personal work space (e.g., a virtual drive U:), you **must**
+> edit the launch script file, adding the argument `workspace=path/to/workspace`
+> to the `node` command. This will instruct Linny-R to create the `user`
+> directory in this workspace directory instead of the Linny-R directory.
 
 ## User workspace
 
@@ -338,20 +400,23 @@ The sub-directories of this directory `user` are used by Linny-R to store files.
 
 * `autosave` will contain models that have been _auto-saved_ 
 * `channel` and `callback` will be used to interact with Linny-R via its _Receiver_ 
-* `data` will be used by the _Dataset Manager_ to locate datasets for which a path
-  has been specified
+* `data` will be used by the _Dataset Manager_ to locate datasets for which
+  a path has been specified
 * `diagrams` will be used to render Scalable Vector Graphics (SVG) files as
   Portable Network Graphics (PNG) using Inkscape (if installed)
+* `models` will contain models that you saved by Shift-clicking on the
+  _Save_ button, or using the keyboard shortcut Ctrl-Shift-S
 * `modules` will contain models stored in the `local host` _repository_
-* `reports` will contain text files with time series data and statistics in tab-separated
-  format that can be imported or copy/pasted into Excel
-* `solver` will contain the files that are exchanged with the Mixed Integer Linear Programming (MILP) solver
-  (the names of the files that will appear in this directory may vary, depending on the MILP-solver you use)
+* `reports` will contain text files with time series data and statistics in
+  tab-separated format that can be imported or copy/pasted into Excel
+* `solver` will contain the files that are exchanged with the Mixed Integer
+  Linear Programming (MILP) solver (the names of the files that will appear
+  in this directory may vary, depending on the MILP-solver you use)
 
 > [!NOTE]
 > By default, the `user` directory is created in your `Linny-R` directory.
-> You can overrule this by starting the server with the `workspace=[path]` option.
-> This will create a new, empty workspace (the directories listed above) in the specified path.
+> You can overrule this by starting the server with the `workspace=[path]`
+> option. This will create a new, empty workspace in the specified path.
 > It will **not** affect or duplicate information from existing workspaces.
 
 ## Installing Inkscape
@@ -362,8 +427,8 @@ These files can be viewed and edited using Inkscape, an open source
 vector graphics editor. 
 
 As it may be tedious to first save a diagram as SVG and then render it
-manually as a bitmap image, Linny-R features a *Render diagram as bitmap* button
-on the top toolbar, and on the bottom toolbar of the _Chart manager_.
+manually as a bitmap image, Linny-R features a *Render diagram as bitmap*
+button on the top toolbar, and on the bottom toolbar of the _Chart manager_.
 When you click it, Linny-R will send the image as SVG to the server. 
 The server script will save the SVG in the `user/diagrams` sub-directory, 
 and then try to execute an Inkscape command that will convert this SVG to
@@ -375,7 +440,8 @@ If rendering was successful, the image will appear in this browser tab;
 if rendering failed, the original SVG image will be shown.
 
 To install Inkscape, please look here:
-<a href="https://inkscape.org/release" target="_blank">https://inkscape.org/release</a>
+<a href="https://inkscape.org/release"
+   target="_blank">https://inkscape.org/release</a>
 
 Linny-R will automatically detect whether Inkscape is installed by searching
 for it in the environment variable PATH on your computer. On a macOS computer,
@@ -388,21 +454,25 @@ Linny-R will look for Inkscape in `/Applications/Inkscape.app/Contents/MacOS`.
 
 ## Using Linny-R console
 
-The console-only version of Linny-R allows you to run a Linny-R model without a web browser.
-This may be useful when you want run models from a script (shell script, Python, ...). 
-If you open a CLI box, change to your `Linny-R` directory, and then type:
+The console-only version of Linny-R allows you to run a Linny-R model without
+a web browser. This may be useful when you want run models from a script
+(shell script, Python, ...). If you open a CLI box, change to your `Linny-R`
+directory, and then type:
 
 ``node node_modules/linny-r/console``  _(on Windows, use backslashes)_
 
-you will see the command line options that allow you to run models in various ways.
+you will see the command line options that allow you to run models in various
+ways.
 
 > [!NOTE]
-> The console-only version is still in development, and does not provide all functions yet.
+> The console-only version is still in development, and does not provide
+> all functions yet.
 
 ## Troubleshooting problems
 
-If during any of the steps above you encounter problems, please try to diagnose them and resolve them yourself.
-You can find a lot of useful information on the Linny-R user documentation website:
+If during any of the steps above you encounter problems, please try to
+diagnose them and resolve them yourself. You can find a lot of useful
+information on the Linny-R user documentation website:
 <a href="https://linny-r.info" target="_blank">https://linny-r.info</a>.
 
 > [!IMPORTANT]
@@ -411,6 +481,8 @@ You can find a lot of useful information on the Linny-R user documentation websi
 
 Then also look at the console window of your browser. 
 Most browsers offer a _Web Developer Tools_ option via their application menu.
-This will allow you to view the browser console, which will display JavaScript errors in red font.
+This will allow you to view the browser console, which will display JavaScript
+errors in red font.
 
-If you've tried hard, but failed, you can try to contact Pieter Bots at ``p.w.g.bots@tudelft.nl``
+If you've tried hard, but failed, you can try to contact Pieter Bots at
+``p.w.g.bots@tudelft.nl``

package/console.js

@@ -16,7 +16,7 @@ NOTE: For browser-based Linny-R, this file should NOT be loaded, as it
 */
 
 /*
-Copyright (c) 2017-2022 Delft University of Technology
+Copyright (c) 2017-2024 Delft University of Technology
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal
@@ -953,6 +953,7 @@ function createWorkspace() {
       callback: path.join(SETTINGS.user_dir, 'callback'),
       data: path.join(SETTINGS.user_dir, 'data'),
       diagrams: path.join(SETTINGS.user_dir, 'diagrams'),
+      models: path.join(SETTINGS.user_dir, 'models'),
       modules: path.join(SETTINGS.user_dir, 'modules'),
       reports: path.join(SETTINGS.user_dir, 'reports'),
       solver_output: path.join(SETTINGS.user_dir, 'solver'),

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "linny-r",
-  "version": "2.0.1",
+  "version": "2.0.4",
   "description": "Executable graphical language with WYSIWYG editor for MILP models",
   "main": "server.js",
   "scripts": {

package/post-install.js

@@ -5,28 +5,30 @@ The Linny-R language and tool have been developed by Pieter Bots at Delft
 University of Technology, starting in 2009. The project to develop a browser-
 based version started in 2017. See https://linny-r.org for more information.
 
-This NodeJS script (post-install.js) creates a launch script for Linny-R
-that facilitates start-up: the user can then type `linny-r` at the command
-line prompt, and also create a clickable icon as desktop shortcut.
+This NodeJS script (post-install.js) checks whether the Linny-R directory
+contains a launch script for Linny-R. For macOS, the script file is
+`linny-r.command`, for Windows `linny-r.bat`.
+If such a file already exists, this script will try to rename it, adding
+the prefix `OLD-` to the name. Doing this will make that the the Linny-R
+server script will create the newest version of the launch script the
+first time it is run.
 
-For macOS, the script file is `linny-r.command`, for Windows `linny-r.bat`.
-The script comprises two commands:
+The launch script has two intended functions:
+(1) to facilitate start-up: the user can type `linny-r` at the command
+    line prompt,and (more importantly) create a clickable icon as desktop
+    shortcut.
+(2) to facilitate automatic software updates: when (after lauch in a browser)
+    Linny-R detects a newer version, it will prompt the user whether this
+    update should be installed. When the user confirms, the server script
+    is terminated, and then launch script executes the commands to update
+    and then restart the Linny-R server.
 
-  cd path/to/linny-r/directory
-  node node_modules/linny-r/server launch
-  
-since Windows also supports the slash as path separator. The "launch"
-command tells the script `server.js` to start Linny-R in the default
-web browser. 
-
-Comments are added to the script file to facilitate customization of the
-scripts by the user. The README.md file explains how the script file can be
-used for single-click launch of Linny-R, and how the "workspace" parameter
-can be used in a multi-user network environment to provide individual
-workspaces for users.
+The README.md file explains how the script file can be used for single-click
+launch of Linny-R, and how the "workspace" parameter can be used in a
+multi-user network environment to provide individual workspaces for users.
 */
 /*
-Copyright (c) 2020-2022 Delft University of Technology
+Copyright (c) 2020-2024 Delft University of Technology
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal
@@ -56,32 +58,86 @@ const
     // NOTE: working directory for this script is the *module* directory,
     // which is two levels deeper than the actual working directory
     WORKING_DIRECTORY = process.cwd().replace(path.sep + mod_dir, ''),
-    lines = [
+    ext = (PLATFORM.startsWith('win') ? 'bat' : 'command'),
+    sp = path.join(WORKING_DIRECTORY, 'linny-r.' + ext);
+
+// NOTE: Function `createLaunchScript` is a copy of this function as
+// defined in script file `server.js`.
+
+function createLaunchScript() {
+  // Creates platform-specific script with Linny-R start-up command
+  const
+      lines = [
         '# The first line (without the comment symbol #) should be like this:',
-        '# cd ',
         '',
+        'cd ' + WORKING_DIRECTORY,
         '# Then this command to launch the Linny-R server should work:',
-        `node ${mod_dir}${path.sep}server launch`
-      ];
-let sp;
-if(PLATFORM.startsWith('win')) {
-  sp = path.join(WORKING_DIRECTORY, 'linny-r.bat');
-  lines[1] += 'C:\\path\\to\\\\your\\Linny-R\\directory';
-} else {
-  sp = path.join(WORKING_DIRECTORY, 'linny-r.command'); 
-  lines[1] += '/path/to/your/Linny-R/directory';
+        '',
+        '# After shut-down, check whether new version should be installed:'
+      ],
+    windows = PLATFORM.startsWith('win'),
+    sp = path.join(WORKING_DIRECTORY, 'linny-r.' + (windows ? 'bat' : 'command'));
+  if(windows) {
+    lines.push(
+      ':loop',
+      'if exist newer_version (',
+      '    del newer_version',
+      '    npm update linny-r',
+      '    node node_modules\\linny-r\\server',
+      '    goto loop',
+      ')');
+    lines[1] = '# cd C:\\path\\to\\main\\Linny-R\\directory';
+    lines[4] = 'node node_modules\\linny-r\\server launch';
+  } else {
+    lines.push(
+      'while test -f newer_version; do',
+      '    unlink newer_version',
+      '    npm update linny-r',
+      '    node node_modules/linny-r/server',
+      'done');
+    lines[1] = '# cd /path/to/main/Linny-R/directory';
+    lines[4] = 'node node_modules/linny-r/server launch';
+  }
+  try {
+    let code = lines.join(os.EOL);
+    if(windows) code = code.replaceAll('#', '::');
+    try {
+      fs.accessSync(sp);
+      // Do not overwrite existing script, as it may have been customized
+      // by the user. When istalling/updating Linny-R, the post-install
+      // script should have renamed it, so typically it is created the
+      // first time Linny-R is run after install/update.
+    } catch(err) {
+      console.log('Creating launch script:', sp);
+      fs.writeFileSync(sp, code, 'utf8');
+      // On macOS machines, try to make the script executable.
+      if(!windows) try {
+        fs.chmodSync(sp, '+x');
+      } catch(err) {
+        console.log('WARNING: Failed to make script executable -- please check');
+      }
+    }
+  } catch(err) {
+    console.log('WARNING: Failed to create launch script');
+  }
 }
-lines[2] = 'cd ' + WORKING_DIRECTORY;
+
+// First rename the existing script (if any) as this may have been changed
+// by the user, and the idea of the changes would be lost by overwriting it.
 try {
+  fs.accessSync(sp);
   try {
-    fs.accessSync(sp);
+    // Only rename the script content if the file it does not yet exist
+    console.log('Renaming existing launch script:', sp);
+    fs.renameSync(sp, path.join(WORKING_DIRECTORY, 'OLD-linny-r.' + ext));
   } catch(err) {
-    // Only write the script content if the file it does not yet exist
-    console.log('Creating launch script:', sp);
-    let code = lines.join(os.EOL);
-    if(PLATFORM.startsWith('win')) code = code.replaceAll('#', '::');
-    fs.writeFileSync(sp, code, 'utf8');
+    console.log('WARNING: Failed to rename existing launch script');
   }
 } catch(err) {
-  console.log('WARNING: Failed to create launch script');
+  // No existing script => action needed.
 }
+
+// Then create new launch script. This way, after update or clean install,
+// the user can
+createLaunchScript();
+

package/server.js

@@ -255,22 +255,24 @@ function clearNewerVersion() {
 }
 
 // HTML page to show when the server is shut down by the user.
-// NOTE: on a macOS machine, this is slightly more work
-const OS_TEXT = {close: '', reopen: ''};
-if(PLATFORM === 'darwin') {
-  OS_TEXT.close =
-`<p>You can close the <em>Terminal</em> window that shows
-  <tt>[Process Terminated]</tt> at the bottom.
-</p>`;
-  OS_TEXT.reopen =
-`open <em>Terminal</em> again, change to your Linny-R directory by typing:
+// Parts of the text are platform-specific.
+const
+    macOS = (PLATFORM === 'darwin'),
+    close = (macOS ?
+        `<p>You can now close the <em>Terminal</em> window that shows
+         <tt>[Process Terminated]</tt> at the bottom.</p>` :
+        `<p>The <em>Command Prompt</em> window where the server was
+         running will be closed automatically.</p>`),
+    cli = (macOS ? 'Terminal' : 'Command Prompt'),
+    ext = (macOS ? '.command' : ''),
+    chmod = (!macOS ? '' : `
+<p>If launch fails, you may still need to make the script executable.</p>
+<p>
+  You can do this by typing <code>chmod +x linny-r.command</code>
+  at the command prompt.
 </p>
-<p><code>cd ${WORKING_DIRECTORY}</code></p>
-<p>`;
-} else {
-  OS_TEXT.reopen = 'switch to your <em>Command Prompt</em> window ';
-}
-const SHUTDOWN_MESSAGE = `<!DOCTYPE html>
+<p>Then retype <code>linny-r.command</code> to launch Linny-R.</p>`),
+    SHUTDOWN_MESSAGE = `<!DOCTYPE html>
 <html lang="en-US">
 <head>
   <meta http-equiv="content-type" content="text/html; charset=UTF-8">
@@ -290,16 +292,18 @@ const SHUTDOWN_MESSAGE = `<!DOCTYPE html>
   </style>
 </head>
 <body>
-  <h3>Linny-R server (127.0.0.1) is shutting down</h3>${OS_TEXT.close}
-  <p>To restart Linny-R, ${OS_TEXT.reopen} and then at the prompt type:</p>
-  <p><code>node node_modules${path.sep}linny-r${path.sep}server</code></p>
+  <h3>Linny-R server (127.0.0.1) is shutting down</h3>${close}
   <p>
-    Then switch back to this window, and click this
-    <button type="button"
-      onclick="window.location.href = 'http://127.0.0.1:${SETTINGS.port}';">
-      Restart
-    </button> button.
+    To restart Linny-R, open <em>${cli}</em> again, change to
+    your Linny-R directory by typing:
   </p>
+  <p><code>cd ${WORKING_DIRECTORY}</code></p>
+  <p>and then type:</p>
+  <p><code>linny-r${ext}</code></p>
+  <p>
+    This should launch Linny-R in a new browser window or tab, so you
+    can close this one.
+  </p>${chmod}
 </body>
 </html>`;
 
@@ -416,9 +420,21 @@ function autoSaveLoad(res, sp) {
 function autoSaveStore(res, sp) {
   // Stores XML data under specified file name in the auto-save directory
   let data = 'OK';
-  const fn = sp.get('file');
+  const
+      fn = sp.get('file'),
+      wsd = sp.get('wsd'),
+      ws = (wsd ? WORKSPACE.models : WORKSPACE.autosave),
+      msg = (wsd === 'models' ? 'save to user workspace' : 'auto-save'),
+      exists = (path) => {
+          try {
+            fs.accessSync(path);
+            return true;
+          } catch(err) {
+            return false;
+          }
+        };
   if(!fn) {
-    data = 'WARNING: No name for file to auto-save';
+    data = 'WARNING: No name for file to ' + msg;
   } else {
     const xml = sp.get('xml');
     // Validate XML as a Linny-R model
@@ -429,10 +445,41 @@ function autoSaveStore(res, sp) {
           root = doc.documentElement;
       // Linny-R models have a model element as root
       if(root.nodeName !== 'model') throw 'XML document has no model element';
-      fs.writeFileSync(path.join(WORKSPACE.autosave, fn + '.lnr'), xml);
+      let fp = path.join(ws, fn + '.lnr');
+      if(wsd) {
+        // Append a version number to the file name if named file exists.
+        const re = /\(\d+\).lnr$/;
+        if(exists(fp)) {
+          const m = fp.match(re);
+          let n = 1;
+          if(m) {
+            // Replace version number (n) by (n+1).
+            n = parseInt(m[0].substring(1, m[0].length - 1)) + 1;
+            fp = fp.replace(re, `(${n}).lnr`);
+          } else {
+            // Add (1) as version number.
+            fp = fp.substring(0, fp.length - 4) + ' (1).lnr';
+          }
+          while(exists(fp)) {
+            // Iterate to find the first available version number.
+            n++;
+            fp = fp.replace(re, `(${n}).lnr`);
+          }
+        }
+      }
+      try {
+        fs.writeFileSync(fp, xml);
+        const d = `Model ${ws ? '' : 'auto-'}saved as ${fp}`;
+        console.log(d);
+        // No message (other than OK) when auto-saving.
+        if(ws) data = d;
+      } catch(err) {
+        console.log(err);
+        data = `ERROR: Failed to ${msg} to ${fp}`;
+      }
     } catch(err) {
       console.log(err);
-      data = 'ERROR: Not a Linny-R model to auto-save';
+      data = 'ERROR: Not a Linny-R model to ' + msg;
     }
   }
   servePlainText(res, data);
@@ -1687,6 +1734,7 @@ function createWorkspace() {
       callback: path.join(SETTINGS.user_dir, 'callback'),
       data: path.join(SETTINGS.user_dir, 'data'),
       diagrams: path.join(SETTINGS.user_dir, 'diagrams'),
+      models: path.join(SETTINGS.user_dir, 'models'),
       modules: path.join(SETTINGS.user_dir, 'modules'),
       reports: path.join(SETTINGS.user_dir, 'reports'),
       solver_output: path.join(SETTINGS.user_dir, 'solver')
@@ -1715,18 +1763,18 @@ function createWorkspace() {
 
 function createLaunchScript() {
   // Creates platform-specific script with Linny-R start-up command
-  const lines = [
-      '# The first line (without the comment symbol #) should be like this:',
-      '',
-      '',
-      '# Then this command to launch the Linny-R server should work:',
-      '',
-      '# After shut-down, check whether new version should be installed:'
-    ];
-  lines[2] = 'cd ' + WORKING_DIRECTORY;
-  let sp;
-  if(PLATFORM.startsWith('win')) {
-    sp = path.join(WORKING_DIRECTORY, 'linny-r.bat');
+  const
+      lines = [
+        '# The first line (without the comment symbol #) should be like this:',
+        '',
+        'cd ' + WORKING_DIRECTORY,
+        '# Then this command to launch the Linny-R server should work:',
+        '',
+        '# After shut-down, check whether new version should be installed:'
+      ],
+    windows = PLATFORM.startsWith('win'),
+    sp = path.join(WORKING_DIRECTORY, 'linny-r.' + (windows ? 'bat' : 'command'));
+  if(windows) {
     lines.push(
       ':loop',
       'if exist newer_version (',
@@ -1738,7 +1786,6 @@ function createLaunchScript() {
     lines[1] = '# cd C:\\path\\to\\main\\Linny-R\\directory';
     lines[4] = 'node node_modules\\linny-r\\server launch';
   } else {
-    sp = path.join(WORKING_DIRECTORY, 'linny-r.command'); 
     lines.push(
       'while test -f newer_version; do',
       '    unlink newer_version',
@@ -1749,22 +1796,23 @@ function createLaunchScript() {
     lines[4] = 'node node_modules/linny-r/server launch';
   }
   try {
-    let make_script = false,
-        code = lines.join(os.EOL);
-    if(PLATFORM.startsWith('win')) code = code.replaceAll('#', '::');
+    let code = lines.join(os.EOL);
+    if(windows) code = code.replaceAll('#', '::');
     try {
       fs.accessSync(sp);
-      // Only write the script content if the file has not been customized
-      // by the user...
-      const data = fs.readFileSync(sp, 'utf-8');
-      make_script = code.indexOf(data) >= 0;
+      // Do not overwrite existing script, as it may have been customized
+      // by the user. When istalling/updating Linny-R, the post-install
+      // script should have renamed it, so typically it is created the
+      // first time Linny-R is run after install/update.
     } catch(err) {
-      // ... or if it does not exist yet.
-      make_script = true;
-    }
-    if(make_script) {
       console.log('Creating launch script:', sp);
       fs.writeFileSync(sp, code, 'utf8');
+      // On macOS machines, try to make the script executable.
+      if(!windows) try {
+        fs.chmodSync(sp, '+x');
+      } catch(err) {
+        console.log('WARNING: Failed to make script executable -- please check');
+      }
     }
   } catch(err) {
     console.log('WARNING: Failed to create launch script');

package/static/index.html

@@ -262,7 +262,7 @@ SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
       <img id="settings-btn" class="btn enab" src="images/settings.png"
            title="Change model settings (Alt-M)">
       <img id="save-btn" class="btn enab" src="images/save.png"
-           title="Save model (Ctrl-S)">
+           title="Save model (Ctrl-S) &ndash; Shift-click to save to user workspace (Ctrl-Shift-S)">
       <img id="repository-btn" class="btn enab" src="images/repository.png"
            title="Browse repositories (Ctrl-B)">
       <img id="actors-btn" class="btn enab" src="images/actors.png"

package/static/scripts/linny-r-gui-controller.js

@@ -549,7 +549,7 @@ class GUIController extends Controller {
     this.buttons.settings.addEventListener('click',
         () => UI.showSettingsDialog(MODEL));
     this.buttons.save.addEventListener('click',
-        () => FILE_MANAGER.saveModel());
+        () => FILE_MANAGER.saveModel(event.shiftKey));
     this.buttons.actors.addEventListener('click',
         () => ACTOR_MANAGER.showDialog());
     this.buttons.diagram.addEventListener('click',
@@ -1099,10 +1099,10 @@ class GUIController extends Controller {
     // Only then try to restart.
     if(SOLVER.user_id) return;
     UI.updating_modal.show();
-    setTimeout(() => UI.tryToRestart(0), 5000);
+    setTimeout(() => UI.tryToRestart(), 5000);
   }
 
-  tryToRestart(trials) {
+  tryToRestart() {
     // Fetch the current version number from the server. This may take
     // a wile, as the server was shut down and restarts only after npm
     // has updated the Linny-R software. Typically, this takes only a few
@@ -1132,6 +1132,7 @@ class GUIController extends Controller {
                 'confirm when prompted by your browser.');
               // Hide "update" button in server dialog.
               UI.modals.server.element('update').style.display = 'none';
+              return;
             } else {
               // Inform user that install appears to have failed.
               msg.push(
@@ -1145,11 +1146,7 @@ class GUIController extends Controller {
           }
         })
       .catch((err) => {
-          if(trials < 10) {
-            setTimeout(() => UI.tryToRestart(trials + 1), 5000);
-          } else {
-            UI.warn(UI.WARNING.NO_CONNECTION, err);
-          }
+          UI.warn(UI.WARNING.NO_CONNECTION, err);
         });    
   }
 
@@ -2310,9 +2307,14 @@ class GUIController extends Controller {
       } else if(code === 'ArrowRight') {
         e.preventDefault();
         this.stepForward(e);
+      } else if(e.ctrlKey && code === 'KeyS') {
+        // Ctrl-S means: save model. Treat separately because Shift-key
+        // alters the way in which the model file is saved.
+        e.preventDefault();
+        FILE_MANAGER.saveModel(e.shiftKey);
       } else if(alt && code === 'KeyR') {
         // Alt-R means: run to diagnose infeasible/unbounded problem.
-          VM.solveModel(true);
+        VM.solveModel(true);
       } else if(alt && ['KeyC', 'KeyM'].indexOf(code) >= 0) {
         // Special shortcut keys for "clone selection" and "model settings".
         const be = new Event('click');

package/static/scripts/linny-r-gui-file-manager.js

@@ -253,7 +253,12 @@ class GUIFileManager {
     code.focus();
   }
   
-  saveModel() {
+  saveModel(ws=false) {
+    // Save the current model either as a download (directly from the browser),
+    // or in the user workspace (via the server) when the Save button is
+    // Shift-clicked.
+    // NOTE: The File manager keeps track of which option to use.
+    this.save_to_workspace = ws;
     MODEL.clearSelection();
     if(MODEL.encrypt) {
       const md = UI.modals.password;
@@ -270,7 +275,17 @@ class GUIFileManager {
   }
   
   pushModelToBrowser(xml) {
+    // Save model as .lnr file.
     UI.setMessage('Model file size: ' + UI.sizeInBytes(xml.length));
+    // NOTE: Since version 2.0.2, Shift-click on the Save button means
+    // that the model should be saved in the user workspace.
+    if(this.save_to_workspace) {
+      // Immediately reset the flag...
+      this.save_to_workspace = false;
+      // ... but pass is on to the auto-save routine.
+      this.storeAutoSavedModel(true);
+      return;
+    }
     const el = document.getElementById('xml-saver');
     el.href = 'data:attachment/text,' + encodeURI(xml);
     console.log('Encoded file size:', el.href.length);
@@ -281,6 +296,9 @@ class GUIFileManager {
           'If it does not download, store it in a repository');
     }
     el.click();
+    // Clear the HREF after 3 seconds or it may use a lot of memory.
+    setTimeout(
+        () => { document.getElementById('xml-saver').href = ''; }, 3000);
     UI.normalCursor();
   }
   
@@ -289,7 +307,7 @@ class GUIFileManager {
         md = UI.modals.password,
         code = md.element('code'),
         pwd = code.value;
-    // NOTE: immediately clear password field
+    // NOTE: Immediately clear password field.
     code.value = '';
     md.hide();
     if(pwd !== md.encryption_code) {
@@ -298,7 +316,7 @@ class GUIFileManager {
     }
     UI.setMessage('Encrypting...');
     UI.waitingCursor();
-    // Wait for key (NOTE: asynchronous functions defined in linny-r.js)
+    // Wait for key (NOTE: asynchronous functions defined in linny-r.js).
     encryptionKey(pwd)
       .then((key) => encryptMessage(MODEL.asXML.replace(/#/g, '%23'), key)
           .then((enc) => this.pushModelToBrowser(MODEL.asEncryptedXML(enc)))
@@ -329,8 +347,12 @@ class GUIFileManager {
       .catch((err) => UI.warn(UI.WARNING.NO_CONNECTION, err));
   }
 
-  storeAutoSavedModel() {
-    // Stores the current model in the local auto-save directory
+  storeAutoSavedModel(workspace=false) {
+    // Store the current model in the local auto-save directory, or in
+    // the local models directory when `workspace` = TRUE.
+    // NOTE: Always reset the "save to workspace" flag, because it may
+    // have not been cleared when the user canceled encryption.
+    this.save_to_workspace = false;
     const bcl = document.getElementById('autosave-btn').classList;
     if(MODEL.running_experiment) {
       console.log('No autosaving while running an experiment');
@@ -342,7 +364,8 @@ class GUIFileManager {
           file: REPOSITORY_BROWSER.asFileName(
               (MODEL.name || 'no-name') + '_by_' +
                   (MODEL.author || 'no-author')),
-          xml: MODEL.asXML
+          xml: MODEL.asXML,
+          wsd: workspace
         }))
       .then((response) => {
           if(!response.ok) {
@@ -356,6 +379,9 @@ class GUIFileManager {
             AUTO_SAVE.interval = 0;
             AUTO_SAVE.not_implemented = true;
             console.log('Auto-save disabled');
+          } else if(workspace) {
+            // Notify user where the model file has been stored.
+            UI.notify(data);
           }
           bcl.remove('stay-activ');
         })

package/static/scripts/linny-r-model.js

@@ -5710,6 +5710,12 @@ class NodeBox extends ObjectWithXYWH {
       UI.warningInvalidName(name);
       return false;
     }
+    // Check whether a non-node entity has this name.
+    const nne = MODEL.namedObjectByID(UI.nameToID(name));
+    if(nne && nne !== this) {
+      UI.warningEntityExists(nne);
+      return false;
+    }
     // Compose the full name.
     if(actor_name === '') actor_name = UI.NO_ACTOR;
     let fn = name;
@@ -8747,8 +8753,8 @@ class Product extends Node {
         NL = '\\\\\n',
         tex = [NL],
         x = (this.level_to_zero ? '\\hat{x}' : 'x'),
-        sub = (MODEL.start_period !== MODEL.end_period ?
-            '_{' + this.TEX_id + ',t}' : '_' + this.TEX_id),
+        dyn = (MODEL.start_period !== MODEL.end_period),
+        sub = (dyn ? '_{' + this.TEX_id + ',t}' : '_' + this.TEX_id),
         param = (x, p) => {
             if(!x.defined) return '';
             const v = safeStrToFloat(x.text, p + sub);
@@ -8780,8 +8786,7 @@ class Product extends Node {
     tex.push(x + sub, '=');
     if(this.is_buffer) {
       // Insert X[t-1]
-      tex.push(x + '_{' + this.code +
-            (MODEL.start_period !== MODEL.end_period ? ',t-1}' : ',0}'));
+      tex.push(x + '_{' + this.code + (dyn ? ',t-1}' : ',0}'));
     }
     let first = true;
     for(let i = 0; i < this.inputs.length; i++) {
@@ -8793,11 +8798,13 @@ class Product extends Node {
     for(let i = 0; i < this.outputs.length; i++) {
       let ltex = this.outputs[i].TEXcode.trim();
       if(ltex.trim().startsWith('-')) {
-        ltex = ltex.substring(1);
         if(!first) {
-          ltex = '+ ' + ltex;
+          ltex = ltex.substring(1);
+          ltex = '- ' + ltex;
           first = false;
         }
+      } else {
+        ltex = '- ' + ltex;        
       }
       tex.push(ltex);
     }
@@ -9059,15 +9066,13 @@ class Link {
     // products will take care of the sign of this term.
     const
         dyn = MODEL.start_period !== MODEL.end_period,
-        x = (this.from_node.level_to_zero ? '\\hat(x)' : 'x'),
-        fsub = (dyn ?
-            '_{' + this.from_node.TEX_id + ',t}' :
-            '_' + this.from_node.TEX_id),
+        n1 = (this.to_node instanceof Process ? this.to_node : this.from_node),
+        n2 = (n1 === this.to_node ? this.from_node: this.to_node),
+        x = (n1.level_to_zero ? '\\hat(x)' : 'x'),
+        fsub = (dyn ? '_{' + n1.TEX_id + ',t}' : '_' + n1.TEX_id),
         fsub_i = fsub.replace(',t}', ',i}'),
-        rsub = (dyn ?
-            '_{' + this.from_node.TEX_id +
-            ' \\rightarrow ' + this.to_node.TEX_id + ',t}' :
-            '_' + this.from_node.TEX_id),
+        rs = n1.TEX_id + ' \\rightarrow ' + n2.TEX_id,
+        rsub = (dyn ? '_{' + rs + ',t}' : '_' + rs),
         param = (x, p, sub) => {
             if(!x.defined) return '';
             const v = safeStrToFloat(x.text, p + sub);
@@ -10052,7 +10057,8 @@ class ChartVariable {
   }
   
   tallyVector() {
-    // Use local constants to save some time within the FOR loop
+    // Compute the histogram bin tallies for this chart variable.
+    // Use local constants to save some time within the FOR loop.
     const
         bins = this.chart.bins,
         bin1 = this.chart.first_bin,
@@ -10061,7 +10067,7 @@ class ChartVariable {
     this.bin_tallies = Array(bins).fill(0);
     for(let i = 1; i < l; i++) {
       let v = this.vector[i];
-      // NOTE: ignore exceptional values in histogram
+      // NOTE: Ignore exceptional values in histogram.
       if(v >= VM.MINUS_INFINITY && v <= VM.PLUS_INFINITY) {
         const bi = Math.min(bins,
           Math.floor((v - bin1 - VM.NEAR_ZERO) / binsize + 1));
@@ -11922,7 +11928,7 @@ class Experiment {
   }
   
   matchingCombinationIndex(sl) {
-    // Returns index of combination with most selectors in common wilt `sl`
+    // Returns index of combination with most selectors in common with `sl`
     let high = 0,
         index = false;
     // NOTE: results of current run are not available yet, hence length-1

package/static/scripts/linny-r-vm.js

@@ -663,10 +663,23 @@ class ExpressionParser {
       this.context_number = owner.numberContext;
       // NOTE: The owner prefix includes the trailing colon+space.
       if(owner instanceof Link || owner instanceof Constraint) {
-        // For links and constraints, use the longest prefix that
-        // their nodes have in common.
-        this.owner_prefix = UI.sharedPrefix(owner.from_node.displayName,
-            owner.to_node.displayName) + UI.PREFIXER;
+        // For links and constraints, it depends:
+        const
+            fn = owner.from_node.displayName,
+            tn = owner.to_node.displayName;
+        if(fn.indexOf(UI.PREFIXER) >= 0) {
+          if(tn.indexOf(UI.PREFIXER) >= 0) {
+            // If both nodes are prefixed, use the longest prefix that these
+            // nodes have in common.
+            this.owner_prefix = UI.sharedPrefix(fn, tn) + UI.PREFIXER;
+          } else {
+            // Use the FROM node prefix.
+            this.owner_prefix = UI.completePrefix(fn);
+          }
+        } else if(tn.indexOf(UI.PREFIXER) >= 0) {
+          // Use the TO node prefix.
+          this.owner_prefix = UI.completePrefix(tn);
+        }
       } else if(owner === MODEL.equations_dataset) {
         this.owner_prefix = UI.completePrefix(attribute);
       } else {
@@ -8993,13 +9006,15 @@ function VMI_add_bound_line_constraint(args) {
       vy = VM.variables[viy - 1],
       objy= vy[1],
       uby = args[5].result(VM.t),
-      bl = args[6],
+      bl = args[6];
+  // Set bound line point coordinates for current run and time step.
+  bl.setDynamicPoints(VM.t);
+  // Then use the actualized points.
+  const
       n = bl.points.length,
       x = new Array(n),
       y = new Array(n),
       w = new Array(n);
-  // Set bound line point coordinates for current run and time step.
-  bl.setDynamicPoints(VM.t);
   if(DEBUGGING) {
     console.log('add_bound_line_constraint:', bl.displayName);
   }