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Table of Contents

• 1 MacPorts
• 4 Networking
• 5 SSH
• 8 Safari
• 9 Emacs
• 10 iPhone/iPad
• 11 Useful Applications
  • 11.4 Docker/AWS-CLI
  • 11.6 Graphics

Here are some notes about how I configure Mac OS X.

MacPorts brings to Mac OS X many programs available on Linux. The programs are conpiled from source, which means it can take a while to install everything and that they need the Xcode command line tools installed:

These are installed in /opt/local/ and to use them, you should add /opt/local/bin to your initialization scripts. (I do this with various configuration files in my configurations project: see for example my ~/.environment_site file.)

I do not like running these commands as root, so once I install MacPorts, the first thing I do is make everything owned by an unprivledged user (me).

This has a couple of complications (see rsync below) but works well for the most part. If you do this, be sure to run portwithout sudo which will be counter to the usual instructions found on the internet. If there is a permissions issue, then check where and deal with it on a case-by-case basis.

See Common Tasks for more details.

• Information:

• Marking ports as requested (so they don't appear as leaves)

• Updating and Cleaning

Here is what I typically install:

The rsync package needs access to /Library/LaunchDaemons.

To clean your installation you might want to do the following:

According to this answer, you might also be able to delete the following:

After installation, my typical setup consumes about 1.6GB of disk space:

Physiced Mac Os X

Sometimes one might like to use another shell instead of /bin/bash. For example, one might like to use the version /opt/local/bin/bash provided by MacPorts so that one can use the bash-completion package. To do this, we first install the shell, then enable it, finally we change the user shell:

The for completions, I do things like:

Finally, in my ~/.bashrc file, I have:

XCode is huge (~10GB), so I remove it (just drag XCode.app to the trash) and just keep the command line tools installed:

After agreeing to the licence, you should see

Note: after you do this you will likely see the following warning from MacPorts:

If you need to change it, then you can spoof it with

Note: make sure that en0 is the correct device. You might want to check the ouput of ifconfig first to see that this is indeed the active device.

To connect to various services at WSU, I downloaded their Global Protect client. This is needed for some reason. In particular, without using the VPN, the following does not work:

then on my Mac:

Without VPN, I can only send about 4 messages in either direction, then the connection hangs. Not sure why.

Wireshark is a full-featured debugging tool for networks. I install it and add it to the PATH so I can use it in a terminal.

To tell KeyChain to remember your SSH keys do the following:

You can use SSH to mount remote file systems locally with sshfs. On Mac OS X, do this by installing FUSE and the associated SSHFS package from that site. Once it is installed, you can mount a filesystem as follows:

To unmount:

This will forward all traffic through the specified host. See https://superuser.com/a/757974. sshuttle can be installed with pip or macports.

Related to SCP is bbcp which can be downloaded for OS X here. This is a fast tool for transferring files. I just copy it to /usr/local/bin/bbcp.

I install the MacTeX which puts most things in /usr/local/texlive and also includes BibDesk, Skim etc. When you upgrade from one year to the next (say 2017 to 2018), the new installation will be placed in /usr/local/texlive/2018 leaving the old version in /usr/local/texlive/2017. These can be big (~5.4GB) so you might want to move the old version off your hard-drive (but keep it for a bit in case things go wrong.)

Once you upgrade, you may need to make a few changes to keep things working, setting the path for the LaTeX programs. These should be set to

but might need to be updated. Check in the preferences of the following packages if things do not work as expected:

• BibDesk: (Seems okay with symlink above.)
• TeX Live: (Needed path refreshed as it seems to use the absolute path, but can refresh this for you if you confirm.)
• LaTeXiT: (Seems okay with symlinks.)

Extensions¶

• Ad Blocking: There are several extensions that block ads.

  • AdBlock: I have been using this and am reasonably happy with it. The blocking of ads in YouTube is especially valuable.
  • AdBlock Plus: Another alternative that is almost the same (small UI differences).
  • AdGuard for Safari: Was recommended in an uBlock issue about Safari. Does not block YouTube ads, but I have not tried the full AdGuard (just the browser extension).

  For a comparison of the first two, see AdBlock vs AdBlock Plus.

• StopTheMadness: Some websites disable useful features such as copy and paste. This extension claims to restore this functionality.

  I used a different approach - temporarily disable JavaScript. This can be done under the Safari Develop/Disable JavaScript menu item, but I also enabled a shortcut ⌘J to Disable JavaScript.

There are several options for using Emacs on Mac OS X:

• GNU Emacs for Mac OS X: I use this. It is a fairly generic version of emacs with traditional key bindings. The only annoyance is that one must use Esc for the Meta key. (M-x is achieved by 'pressing and releasingEsc, then pressing x.)
• Aquamacs: This more tightly integrates with the OS X interface, but is significantly slower.

Configuration¶

I install the following packages using the Options/Manage Emacs Packages menu option. Note, there are three main package archives. I use these with the following preference: 1) gnu, 2) marmalade, 3) melpa (see this discussion for more details.

Itube studio 7 2 1 5 download free. Editing Features

• autopair: Automagically pair braces and quotes like TextMate.
• org: Outline-based notes management and organizer.

Modes:

• auctex-latexmk: Add LatexMk support to AUCTeX.
• haskell-mode: A Haskell editing mode.
• lua-mode: A major-mode for editing Lua scripts.
• markdown-mode+: Extra functions for markdown-mode.
• markdown-preview-mode: Markdown realtime preview minor mode.
• markdown-toc: A simple TOC generator for markdown file.
• yaml-mode: Major mode for editing YAML files

Elisp Debugging (init files)

• benchmark-init: Benchmarks Emacs require and load calls.
• bug-hunter: Hunt down errors by bisecting elisp files.
• use-package: A configuration macro for simplifying your .emacs.

Git: (I don't really use these, but they were recommended at some point.)

• git-commit-mode: Major mode for editing git commit messages [github].
• git-rebase-mode: Major mode for editing git rebase files [github].
• magit: A Git porcelain inside Emacs.

Python: Modes for working with python.

• conda: Work with your conda environments
• python-mode: Python major mode. This has some major problems when using Tramp for remote editing, so I do not use it any more.
• elpy: Emacs Python Development Environment

Web/Blog:

• sass-mode: Major mode for editing Sass files.
• scss-mode: Major mode for editing SCSS files.
• json-mode: Major mode for editing JSON files.
• jinja2-mode: A major mode for jinja2.
• tidy: Interface to the HTML Tidy program.

I load these in my .emacs file with the following code

Physiced Mac Os Download

If you make backups of your iPhone or iPad with iTunes, you can locate these with

• iTunes/Preferences/Devices/Device Backups and right-click to Reveal in Finder.

These files, however, are not organized and obfuscated. To interpret this data you seem to need to use a third party application. Most of these have a demo mode that will allow you to view the files, but put severe limitations on how much data you can actually extract without paying.

• iPhoneBackupViewer: View photos, but must save them one at a time.

GPG¶

This is useful for encryption and signing files. I use the vi plugin which allows you to edit encrypted files. Play for fun poker.

• Simply move the gnugpg.vim script into ~.vim/plugin:

• Choosy: A 'browser' that redirects websites to specific browsers. I am just trying this, but hope to use it to open CoCalc websites exclusively in Chrome for example even though I generally prefer Safari.

Vagrant provides a platform for running code in isolated virtual environments. If you need more fine-grained control and provisioning, [Docker] is another option, but I use Vagrant for developing websites for example.

I don't really use Docker on my Mac, but install it so I can provision images on AWS. To do this I did the following:

1. Make a directory for installing the aws-cli without sudo:

2. Download and install the aws-cli as a local user ('Install for Me Only').

3. Install the Docker App for OS X. Note: I though I could use port install docker docker-machine and save on some disk space, but this needs Vagrant, so no clear savings there. There are some relevant discussions in this direction though:

   • Building containers without Docker (Alex Ellis's Blog Jan 2020).

Disk Space:¶

Docker uses lots of space. Some can be reclaimed with:

To maintain some coherence with HPC environments, we install some version of the Environment Modules package. Here we use the Lmod variant as this is used on our local cluster.

Physiced Mac Os Catalina

I then added the following (from Environment Modules):

To use these, I add the following to my ~/.environment_site file: Gemini 1 5 10 – locate and eliminate duplicate files.

For details about what these do, see my modules configurations folder.

Needed by some applications (I needed it to build VisIt plugins. I simply added this line to my environment_site file:

Some tools - in particular the diffeq library - use Julia, but it is not so easy to install via Conda. I install the native application. After installing I had to link it:

Then, using julia:

Note: If this fails, you might need to manually clone the registry:

Then, in python, I needed to:

This installed everything needed into ~/.julia.

References¶

Physiced Mac Os 11

• R and Julia Kernels not available in Jupyter notebook.

Sound: Black Hole¶

I used to use SoundFlower to route audio on my Mac. https://os-my-work-gr-mac-doesnt-game-torrent-level.peatix.com. This is no longer supported, but they recommend Loopback. Another option is BlackHole as discussed in this article. JACK is another option (this is used by Audacity – a great open-source tool for editing audio.)

Simple program for capturing activity on your screen and turning it into an animated GIF. Useful for demonstrating how to use an interface.

Color-blind simulator. Useful for checking graphs, posters, etc.