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What is the step-by-step procedure for installing any npm module with Aurelia CLI?

I wanted to install jquery and found instructions here:
http://aurelia.io/hub.html#/doc/article/aurelia/framework/latest/contact-manager-tutorial/4
I then wanted to install "moment.js" and found instructions here ( I am not using typescript) :
How to import Moment-Timezone with Aurelia/Typescript
To install both of these with the Aurelia CLI the procedure is to install the respective npm module and then to manually modify aurelia.json in some way so the app recognizes it.
In the case of moments the instructions then say to place an import at the top of app.js , but this is not the case for JQuery.
First off , is there any way the changes to aurelia.json can be automated ( like a regular node.js package.json) so I don't need to manually do it and second, how do I know what modifications I am expected to make to aurelia.json ( or app.js or any other file) for the module I want to install?
With a basic node.js app its pretty simple , just npm install. With Aurelia its much more confusing.
Edit: There is also JSPM which I've read is used for front end libraries like the ones I mentioned above. However, the links with instructions for installation that I posted are not using JSPM.
Edit
I found some of the answers here:
http://aurelia.io/hub.html#/doc/article/aurelia/framework/latest/the-aurelia-cli/6

The CLI is still under development. I think the automatic adding of a package might some day be included in the CLI itself, for example with an install command.
The extra registration is required to register the package correctly for usage with RequireJS (http://requirejs.org/). And if the plugin exists of more than just 1 file, this registration is a bit more complex then just adding the name of the plugin.
There is an experimental CLI task here https://github.com/martonsagi/aurelia-cli-pacman that will do the automation for you.
Which can be installed by running:
npm install aurelia-cli-pacman -D
The above will install the package manager and register/ include itself in the tasks in your current project (be sure to run it with install, because npm won't run the post install script if you run it the i shorthand). Next, you can run the following command to install an extension:
npm i aurelia-interactjs -S
au pacman i aurelia-interactjs
The only downside for many might be that currently there aren't that many registry entries, but I think the author of the package would be very happy if you help him out by creating a pull to extend the registry. Would take you some time to figure out what would be the correct install/ import settings, but you will help out someone else and make them happy when they hit the same problem you experience :-).
JSPM has a same sort of issue around this, only is more matured/ the registry is bigger and/ or authors added specific information for JSPM installations to their package.json. For example: To install the above plugin with JSPM it will use the following highlighted section https://github.com/eriklieben/aurelia-interactjs/blob/master/package.json#L72,L86. The same is currently not possible with aurelia-cli, because the installation is done by NPM instead of through JSPM that redirects it to NPM.
If the author of the plugin didn't specify the JSPM section in the package.json, you would most likely and up with the same sort of issues. JSPM has a similar registry (https://github.com/jspm/registry/tree/master/package-overrides/npm) as aurelia-cli-pacman.

Why to use Bower.js if npm works fine?

In the projects prarent directory, if I do,
npm init
a file "package.json" is created,
Now if I want to install dependencies like let's say angular, jQuery and bootstrap I can do
npm install angular --save-dev
npm install jquery --save-dev
npm install bootstrap --save-dev
a folder "node_modules" get created, with the above mentioned dependencies.
and the same entries of dependencies in entered in "package.json" .
Now using any build tool like lets say gulp.js,
I can inject the "node_module" dependencies in my SPA's(Single page application) index.html.
So my question is, why to use Bower ?
Please let me know with some pointers

Short answer: Don't (use bower).
Bower started as a "clone" of npm for the client-side, but meanwhile literally everybody is using npm for this, too.
So there is no need to use bower any more, just rely on npm, and everything is fine. It makes your development workflow simpler, more unified, and you just end up with less friction and complexity (which is a good thing).
My biggest concern with bower is that it introduces unneeded overhead, such as another tool, another configuration file, another way of dealing with versions, another folder where modules go to, … I have hardly seen any benefit of bower that outweighs these drawbacks. Again: Just stick to npm and you're fine.

I myself thought of this just yesterday.
From my experience, you can be well off with just npm, provided the packages you need are registered.
This was not the case a few years ago, but now it nearly mirrors bower's repository.

Is bad practice to run "bower install" when deploying in production?

I am working on an application that uses bower.js; it's the first time I use bower, so please correct me if you see anything evidently wrong in my problem description.
------------------------------------------------
Coming from a Ruby background, I expect a package manager to have a .lock file, tracked under git, that tells me exactly which are the versions currently in use. This doesn't seem to happen with bower (am I right?).
A couple of days ago I deleted and re-cloned my repository, and ran bower install, thinking that such command would just install the required versions of the js components.
Then, today I did a one-line fix in a javascript file, compiled application.js using grunt watch, and realised that application.js was automatically filled up with tons of new code from bower component updates I wasn't aware of.
I found out that our bower components were under .gitignore, and that bower install, that I had run a few days ago, had actually updated two components without me noticing it.
When I realised what was happening, I immediately looked into our deployment procedure, which I paste here:
bundle install --path ${SNAP_CACHE_DIR}/.bundle
npm install -g bower grunt-cli
bower cache clean && bower install && bower list
bundle exec cap [our application name] deploy
Is this dangerous? Will bower install update all the components, that are likely not updated in my local version and are not tracked by git, ending up having completely different js code in production?

Is this dangerous? Will bower install update all the components, that are likely not updated in my local version and are not tracked by git, ending up having completely different js code in production?
Yes, this may happen and can cause problems. Although the impact will be limited as long as your dependency versions are specified as e.g. "~1.2.3", which will lock the major/minor version and only allow patch level updates.
In contrast to bower, the package manager normally used in node.js environments - npm - has a feature/command called npm shrinkwrap, which creates an npm-shrinkwrap.json file which locks down your dependency versions so that it is safe to run npm install afterwards.
This is probably what you would want.
However, bower as it stands does not have this feature yet - there is a discussion about it going on on Github e.g. here.
I think there currently are the following options to solve this problem in your situation:
Un-ignore and commit your bower_components (very ugly because of the huge amount of noise this produces in git).
Specify your dependency versions down to the patch level, e.g. "1.2.3" instead of "~1.2.3".
Culprit: If your dependencies have sub-dependencies, they might still be specified on the minor-version level, which means that even if your direct dependencies have a predictable version, your transitive dependencies may not.
Stop using bower and use npm instead (interface-/usability-wise, they are almost identical imho) and use npm shrinkwrap to lock down your dependencies.
Cheers, Alex

Sails.js 0.10 generators

The upcoming Sails.js 0.10 features custom generators. (at the time of writing it is currently # rc4)
There's a migration page on Sails github describing how wonderful generators are, but not so much how to go about installing them into your own application.
A few really interesting custom generators start to pop up:
sails-generate-auth
sails-generate-gulp-bower
The first one is available on npm. So it was a matter of npm install and generator was available in my app right away.
I wanted to try out the second one to replace Grunt with Gulp, but I couldn't install the generator.
Can anyone explain how to install custom generator and hook it up with Sails.js app?

You can install a sails-generator just like any other npm package:
npm install sails-generate-auth
The problem with sails-generate-gulp-bower is that it hasn't been released to npm yet.
You can trick npm by using the following url to install the latest version of it anyway.
npm install https://github.com/PaulAvery/sails-generate-gulp-bower/archive/master.tar.gz --save
But keep in mind that the author probably has his reason why he didn't release it.

I created generaters to use gulp with sails. https://github.com/Karnith/sails-generate-new-gulp
There are 4 in total that need to be used together with a .sailsrc file. They should be installed globally and then sails new can be used to create the app. Sails lift works also.

package.json generation / npm unused packages

I'm introducing unit testing in my project and for this, I need to make myself a package.json file.
First question is, which unit testing suite are you using? I'm looking forward mocha which seem to be pretty much standard for Node.js projects.
Second question is: Is there any magical way of generating a package.json file? (for dependencies and versions)
Third question is: I've been testing a lot of npm packages while developing my project and now I'm stuck with a lot of probably unused packages. Is there any way to tell which one are useless? (I saw npm list installed which is useful though)

I am using Mocha.
npm init
npm ls will list "extraneous" next to ones that are not in your package.json. But, it sounds like you don't have a package.json yet.
Basically, your workflow is very backward. Here is how it is intended to work:
Start a new project with npm init. It has no dependencies.
Oh, I want to start using a package, say express? Add it to package.json under dependencies, then run npm install.
Oh, I want to start using a package for development, say mocha? Add it to package.json under devDependencies, then run npm install.
You seem to have some existing code with manually-installed packages (via npm install <packageName>), which is a mess. I suggest starting over and following the above workflow.

To answer the third question:
npm prune
will remove all installed modules that are no longer mentioned in your package.json.
And you should really have asked 3 separate questions.

I am also using Mocha. It has code coverage, BDD, TDD, runs in browser. It is pretty complete and also heavily maintained by I think one of the most brilliant javascript/node.js programmers named TJ.
It is almost impossible to guess which version(s) to use. Because npm does not know which version breaks which dependencies. You could probably install all dependencies using something like node-detective. Then you can just install them using npm.js from within javascript. Maybe I would like to tackle this in the future.
I would also probably delete all dependencies , next install needed dependencies back using step(2). But also disc-space is not such a big case anymore with the current HDs.
P.S: I think I also agree with Domenic

I am using vows. It's pretty good, but not perfect. I have found unit testing in node to often be challenging because of async callbacks to dbs & such, and have mostly been testing top level functionality.
Here's your magic: Managing Node.js Dependencies with Shrinkwrap.
The only way to know what packages you are using is to know. You can't generate this programmatically. My advice would be to remove packages aggressively, then retest all functionality - if it breaks, you'll know you need to reinstall one of your packages.

Answering your third question, you can use Sweeper to list unused dependencies, and them remove them from your package.json. Just npm install -g sweeper then on your project directory call sweeper on the command line.