This is how I set up a fresh mac to start working in machine learning and programming. My lab runs under a proxy, so all the settings have that one extra ...sigh... task to work correctly. I keep this tutorial handy in case I do a clean OS install or if I need to check some of my initial settings.
- Basic Settings
- Setup proxy system wise
- Setup proxy settings in bash
- Install Homebrew
- Curl proxy settings
- Install and setup Git
- Check your branches in git log history in a pretty line
- Push with tags: multi-line git alias
- GitHub Markdown math expressions for README.md, etc.
- GitLab Markdown math expressions for README.md, etc.
- Install Git Large File System
- Make a new Git (LFS) repository from local
- Manage multiple GitHub or GitLab accounts
- Install Docker Desktop for Mac
- Install Python versions with pyenv and virtual environments with poetry
- Install and setup Flask for Python Web Development
- Install and setup Ruby, Bundler and Jekyll for websites
- Install MacTeX and latexdiff
- Shell Scripting for convenience
- Install Pandoc to convert/export markdown, HTML, LaTeX, Word
- Accessibility Stuff
Setup root password: https://www.cyberciti.biz/faq/how-to-change-root-password-on-macos-unix-using-terminal/
sudo passwd root
-
Set up the screen lock command so you can do it every time you stand up:
- https://achekulaev.medium.com/lock-screen-with-cmd-l-l-global-hotkey-on-macos-high-sierra-3c596b76026a
- Settings>Keyboard>Keyboard Shortcuts>App Shortcuts
- All Applications
Lock ScreenCMD+L
- All Applications
-
Set up your WiFi connection.
-
For ease of use, make hidden files and file extensions visible.
Hidden files visibility:
I can't work without seeing hidden files, so in the newer versions of MacOSX we can do CMD+Shift+. and the hidden files will appear.
If this doesn't work, open up the terminal and:
defaults write com.apple.finder AppleShowAllFiles YES
- Install SublimeText4 for ease of use (this is my personal favorite, but it's not necessary)
https://www.sublimetext.com/download
- Paste the SublimeText4 preferences (my personal preferences)
{
"ignored_packages":
[
"Vintage",
],
"spell_check": true,
"tab_size": 4,
"translate_tabs_to_spaces": true,
"copy_with_empty_selection": false
}
Also, Sublime Text is all about the plugins. Install Package Control by typing CTRL+Shift+P, then typing "Install Package Control"
Then here's some cool packages to try:
- LaTeXTools
- MarkdownTOC
- MarkdownPreview
- MarkdownEditing
- Alignment
- IncrementSelection
- Selection Evaluator
- Paste as One Line
- Invert Current Color Scheme
- PackageResourceViewer
Now, for the Invert Current Color Scheme, I have my own fork that works with Sublime Text 4, so use the PackageResourceViewer to replace the main python file with my code:
https://github.com/elisa-aleman/sublime-invert-current-color-scheme
In MarkdownTOC.sublime-settings, paste the following for hyperlink markdowns and compatibility with MarkdownPreview:
{
"defaults": {
"autoanchor": true,
"autolink": true,
"markdown_preview": "github",
"uri_encoding": false
},
}
After installing Markdown Editing, add this to the SublimeText4 preferences (my personal preferences)
"mde.auto_fold_link.enabled": false,
I found myself needing paired
Searching for how to do it on macros, I found this post about keybindings which is a way better solution:
https://stackoverflow.com/questions/34115090/sublime-text-2-trying-to-escape-the-dollar-sign
Which, as long as we implement the double escaped dollar sign solution, we can use freely.
- Preferences > Key Bindings:
- Add this inside the brackets:
// Auto-pair dollar signs
{ "keys": ["$"], "command": "insert_snippet", "args": {"contents": "\\$$0\\$"}, "context":
[
{ "key": "setting.auto_match_enabled", "operator": "equal", "operand": true },
{ "key": "selection_empty", "operator": "equal", "operand": true, "match_all": true },
{ "key": "following_text", "operator": "regex_contains", "operand": "^(?:\t| |\\)|]|\\}|>|$)", "match_all": true },
{ "key": "preceding_text", "operator": "not_regex_contains", "operand": "[\\$a-zA-Z0-9_]$", "match_all": true },
{ "key": "eol_selector", "operator": "not_equal", "operand": "string.quoted.double", "match_all": true }
]
},
{ "keys": ["$"], "command": "insert_snippet", "args": {"contents": "\\$${0:$SELECTION}\\$"}, "context":
[
{ "key": "setting.auto_match_enabled", "operator": "equal", "operand": true },
{ "key": "selection_empty", "operator": "equal", "operand": false, "match_all": true }
]
},
{ "keys": ["$"], "command": "move", "args": {"by": "characters", "forward": true}, "context":
[
{ "key": "setting.auto_match_enabled", "operator": "equal", "operand": true },
{ "key": "selection_empty", "operator": "equal", "operand": true, "match_all": true },
{ "key": "following_text", "operator": "regex_contains", "operand": "^\\$", "match_all": true }
]
},
{ "keys": ["backspace"], "command": "run_macro_file", "args": {"file": "Packages/Default/Delete Left Right.sublime-macro"}, "context":
[
{ "key": "setting.auto_match_enabled", "operator": "equal", "operand": true },
{ "key": "selection_empty", "operator": "equal", "operand": true, "match_all": true },
{ "key": "preceding_text", "operator": "regex_contains", "operand": "\\$$", "match_all": true },
{ "key": "following_text", "operator": "regex_contains", "operand": "^\\$", "match_all": true }
]
},
- Sublime text, lower right corner
- Click on Spaces
- Select the current space number
- Click Convert indentation to Tabs
- Select the desired space number
- Click Convert indentation to Spaces
First, know the {PROXY_HOST} url and the {PORT} that you need to access in your specific place of work. Then put those in the system settings as appropriate.
Settings > Network > Advanced > Proxies
Web Proxy (HTTP)
{PROXY_HOST}:{PORT}
Secure Proxy (HTTPS)
{PROXY_HOST}:{PORT}
FTP Proxy
{PROXY_HOST}:{PORT}
Bypass proxy settings for these Hosts & Domains:
*.local, 169.254/16, 127.0.0.1, HOST_URL
Depending on your organization, setting a HOST_URL to bypass here might also be necessary. Check with your administrator.
Some proxies need you to set up the time of the computer to match the network in order to work correctly. Mine does at least. So the settings are such:
Settings > Date & Time > Date & Time
Set Date and Time automatically: {TIME_URL}
The {TIME_URL} will depend on your organization, so check with your administrator.
So now that the system settings are out of the way, we need to setup the proxy addresses in bash so that programs we run take those variables, since the system setup doesn't reach deep enough for several tools we use.
So we will add these settings to .zprofile to load each time we login to our user session.
sudo nano .zprofile
This will open a text editor inside the terminal. If the file is new it will be empty. Add the following lines: (copy and paste)
export http_proxy={PROXY_HOST}:{PORT}
export https_proxy={PROXY_HOST}:{PORT}
export all_proxy={PROXY_HOST}:{PORT}
export HTTP_PROXY={PROXY_HOST}:{PORT}
export HTTPS_PROXY={PROXY_HOST}:{PORT}
export ALL_PROXY={PROXY_HOST}:{PORT}
export no_proxy=localhost,127.0.0.1,169.254/16,HOST_URL
export NO_PROXY=localhost,127.0.0.1,169.254/16,HOST_URL
Then these ones for logging in ssh to the servers in the laboratory without typing it every time.
alias lab_server="ssh -p {PORT} {USERNAME}@{HOST_IP_ADDRESS}"
Of course, you'll need your own {PORT} and {USERNAME} and {HOST_IP_ADDRESS} here, depending on where you want to log in.
Press CTRL+O to write, press ENTER to keep the name, then press CTRL+X to close the editor
Relaunch the terminal.
For more info, click here.
First we need to consider the macOS Requirements from their website:
- A 64-bit Intel CPU
- macOS High Sierra (10.13) (or higher)
- Command Line Tools (CLT) for Xcode:
xcode-select --install, developer.apple.com/downloads or Xcode - A Bourne-compatible shell for installation (e.g. bash or zsh)
As it says in the third requirement, we need the Command Line Tools for Xcode.
We have 3 options:
- Install just the tools:
xcode-select --install
- Download them from the official Apple website
Go to developer.apple.com/downloads and sign in with your Apple ID and password.
Agree to the Apple Developer Agreement.
Select the latest non-beta Command Line Tools for Xcode available, download de .dmg file and install.
- Install the full Xcode app
Xcode as an app is really heavy, so if you don't intend to work directly on the IDE of Xcode or on any other uses of the app, I don't recommend it. I also have no experience with setting up the CLT with this path.
For this option, you also need to sign up to be an Apple Developer.
/bin/bash -c "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/HEAD/install.sh)"
Now that we have the CLT, we can proceed.
First configure your git proxy settings:
git config --global http.proxy http://{PROXY_HOST}:{PORT}
Replace your {PROXY_HOST} and your {PORT}.
Then install homebrew using proxy settings as well:
/bin/bash -c "$(curl -x {PROXY_HOST}:{PORT} -fsSL https://raw.githubusercontent.com/Homebrew/install/master/install.sh)"
And finally alias brew so it always uses your proxy settings:
alias brew="https_proxy={PROXY_HOST}:{PORT} brew"
Otherwise, if you're not under a proxy just follow the instructions here: https://docs.brew.sh/Installation
Right there installing Homebrew we used explicit proxy settings on the curl command to avoid any issues, but to avoid doing this every time for future uses of curl, we also need to setup proxy settings.
sudo nano ~/.curlrc
And add the following:
proxy = {PROXY_HOST}:{PORT}
Mac already has git installed (that's how we installed homebrew too), but we can update it and manage it with homebrew.
brew install git
Then setup the configuration. Make an account at GitHub to get a username and email associated with Git. Type the settings on the terminal. My settings are like this:
git config --global http.proxy http://{PROXY_HOST}:{PORT}
git config --global user.name {YOUR_USERNAME}
git config --global user.email {YOUR_EMAIL}
git config --global color.ui auto
git config --global merge.conflictstyle diff3
git config --global core.editor nano
git config --global core.autocrlf input
git config --global core.fileMode false
git config --global pull.ff only
This should make a file ~/.gitconfig with the following text
# ~/.gitconfig
[http]
proxy = http://{PROXY_HOST}:{PORT}
[user]
name = YOUR_USERNAME
email = YOUR_EMAIL
[color]
ui = auto
[merge]
conflictstyle = diff3
[core]
editor = nano
autocrlf = input
fileMode = false
[pull]
ff = only
[alias]
adog = log --all --decorate --oneline --graph
That last one, git adog is very useful as I explain in Check your branches in git log history in a pretty line
Now to make your Mac ignore those pesky Icon? files in git:
The best place for this is in your global gitignore configuration file. You can create this file, access it, and then edit per the following steps (we need to use vim because of a special character in the Icon? files):
git config --global core.excludesfile ~/.gitignore_global
vim ~/.gitignore_global
press i to enter insert mode
type Icon on a new line
while on the same line, ctrl + v, ENTER, ctrl + v, ENTER
Also, let's add .DS_Store to .gitignore_global as well.
press ESC, then type :wq then hit ENTER.
This makes your history tree pretty and easy to understand inside of the terminal. I found this in https://stackoverflow.com/a/35075021
git log --all --decorate --oneline --graph
Not everyone would be doing a git log all the time, but when you need it just remember: "A Dog" = git log --all --decorate --oneline --graph
Actually, let's set an alias:
git config --global alias.adog "log --all --decorate --oneline --graph"
This adds the following to the .gitconfig file:
[alias]
adog = log --all --decorate --oneline --graph
And you run it like:
git adog
To add a multi-line alias, for example, push and then push the tags on one single command, use '!git ... && git ...' as a format:
Push with tags:
git config --global alias.pusht '!git push && git push --tags'
Following this guide, math is different in GitLab markdown than say, GitHub or LaTeX. However, inside of the delimiters, it renders it using KaTeX, which uses LaTeX math syntax!
https://docs.gitlab.com/ee/user/markdown.html#math
Inline:
> $a^2 + b^2 = c^2$
Renders as:
Block:
> $$a^2 + b^2 = c^2$$
Renders as:
But it only supports one line of math, so for multiple lines you have to do this:
> $$a^2 + b^2 = c^2$$
> <!-- (line break is important) -->
> $$c = \sqrt{ a^2 + b^2 }$$
Renders as:
It can even display matrices and the like:
> $$
> l_1 =
> \begin{bmatrix}
> \begin{bmatrix}
> x_1 & y_1
> \end{bmatrix} \\
> \begin{bmatrix}
> x_2 & y_2
> \end{bmatrix} \\
> ... \\
> \begin{bmatrix}
> x_n & y_n
> \end{bmatrix} \\
> \end{bmatrix}
> $$
However, % comments will break the environment.
Math syntax in LaTeX:
https://katex.org/docs/supported.html
Following this guide, math is different in GitLab markdown than say, GitHub or LaTeX. However, inside of the delimiters, it renders it using KaTeX, which uses LaTeX math syntax!
https://docs.gitlab.com/ee/user/markdown.html#math
Inline:
> $`a^2 + b^2 = c^2`$
Renders as:
Block:
> ```math
> a^2 + b^2 = c^2
> ```
Renders as:
But it only supports one line of math, so for multiple lines you have to do this:
> ```math
> a^2 + b^2 = c^2
> ```
> ```math
> c = \sqrt{ a^2 + b^2 }
> ```
Renders as:
It can even display matrices and the like:
> ```math
> l_1 =
> \begin{bmatrix}
> \begin{bmatrix}
> x_1 & y_1
> \end{bmatrix} \\
> \begin{bmatrix}
> x_2 & y_2
> \end{bmatrix} \\
> ... \\
> \begin{bmatrix}
> x_n & y_n
> \end{bmatrix} \\
> \end{bmatrix}
> ```
However, % comments will break the environment.
Math syntax in LaTeX:
https://katex.org/docs/supported.html
This is for files larger than 50 MB to be able to be used in Git. Still, GitLFS has some limitations if you don't buy data packages to increase your usage limit. By default you get 1GB of storage and 1GB of bandwidth (how much you push or pull per month). For 5$USD, you can add a data pack that adds 50GB bandwith and 50GB Git LFS storage.
Now we need to install the git-lfs package to use it:
brew install git-lfs
Now I personally had issues with git-lfs not pushing or pulling because of my proxy.
This was fixed by checking my exported variables in .zprofile.
The problem was it was set up like this:
export https_proxy=http://{PROXY_HOST}:{PORT}
export HTTPS_PROXY=https://{PROXY_HOST}:{PORT}
Where the proxy host at my lab doesn't manage the https:// addresses correctly. So I had to correct them and remove the s like this:
export https_proxy=http://{PROXY_HOST}:{PORT}
export HTTPS_PROXY=http://{PROXY_HOST}:{PORT}
So the https_proxy variables still point to a http:// address. It's not the best but in my network there was no other choice.
Now that we have Git and Python installed, we can make our first project. I like to leave this part of the tutorial in even if it doesn't classify as a setup because using Git and GitLFS was confusing at first.
First make a repository on GitHub with no .gitignore, no README and no license. Then, on local terminal, cd to the directory of your project and initialize git
cd path/to/your/project
git init
If using Git LFS:
git lfs install
It's supposed to be ready, but first, let's make a few hooks executable
chmod +x .git/hooks/*
Make a .gitignore depending on which files you don't want in the repository and add it
git add .gitignore
If using Git LFS, add the tracking settings for this project (For example, heavy csv files in this case)
git lfs track "*.csv"
And then add them to git
git add .gitattributes
Commit these changes first
git commit -m "First commit, add .gitignore and .gitattributes"
Now add all the data from your local repository. git add . adds all the files in the folder.
git add .
Depending on the size of your project, it might be wiser to add it in parts instead of all at once. e.g.
git add *.py
git add *.csv
...
or
git add dir1
git add dir2
...
Check if all the paths are added
git status
Check if all the Git LFS files are tracked correctly
git lfs ls-files
If so, commit.
git commit -m "First data commit"
Set the new remote URL from the repository you created on GitHub. It'll appear with a copy button and everything, and end in .git
git remote add origin remote_repository_URL_here
Verify the new remote URL
git remote -v
Set upstream and then push only the lfs files to remote
git lfs push origin master
Afterwards push normally to upload everything
git push --set-upstream origin master
You only need to write --set-upstream origin master the first time for normal push, after this just write push. For git lfs you always have to write it.
Because I want to update my personal code when I find better ways to program at work, I want to push and pull from my personal GitHub account aside from the work GitLab projects. CAUTION: DON'T UPLOAD COMPANY SECRETS TO YOUR PERSONAL ACCOUNT
To be able to do this, I followed these guides:
https://blog.gitguardian.com/8-easy-steps-to-set-up-multiple-git-accounts/
- Generate an SSH key First, create an SSH key for your personal account:
ssh-keygen -t rsa -b 4096 -C "[email protected]" -f ~/.ssh/<personal_key>
Then for your work account:
ssh-keygen -t rsa -b 4096 -C "[email protected]" -f ~/.ssh/<work_key>
- Add a passphrase
Then add a passphrase and press enter, it will ask for it twice. Press enter again.
To update the passphrase for your SSH keys:
ssh-keygen -p -f ~/.ssh/<personal_key>
You can check your newly created key with:
ls -la ~/.ssh
which should output <personal_key> and <personal_key>.pub.
Do the same steps for the <work_key>.
- Tell ssh-agent
The website has an -K tag that works for macOSX and such but we don't need it.
eval "$(ssh-agent -s)" && \
ssh-add ~/.ssh/<personal_key>
ssh-add ~/.ssh/<work_key>
- Edit your SSH config
nano ~/.ssh/config
-----------nano----------
# Work account - default
Host <some_host_name_work>
HostName <HOST>:<PORT>
User git
IdentityFile ~/.ssh/<work_key>
# Personal account
Host <personal_host_name>
HostName github.com
User git
IdentityFile ~/.ssh/<personal_key>
CTRL+O
CTRL+X
-------------------------
- Copy the SSH public key
cat ~/.ssh/<personal_key>.pub | pbcopy
Then paste on your respective website settings, such as the GitHub SSH settings page. Title it something you'll know it's your work computer.
Same for your <work_key>
- Structure your workspace for different profiles
Now, for each key pair (aka profile or account), we will create a .conf file to make sure that your individual repositories have the user settings overridden accordingly. Let’s suppose your home directory is like that:
/myhome/
|__.gitconfig
|__work/
|__personal/
We are going to create two overriding .gitconfigs for each dir like this:
/myhome/
|__.gitconfig
|__work/
|_.gitconfig.work
|__personal/
|_.gitconfig.pers
Of course the folder and filenames can be whatever you prefer.
- Set up your Git configs
In the personal git projects folder, make .gitconfig.pers
nano ~/personal/.gitconfig.pers
---------------nano-----------------
# ~/personal/.gitconfig.pers
[user]
email = [email protected]
name = Your Name
[github] #or gitlab or whatever
user = "personal-username"
[core]
sshCommand = “ssh -i ~/.ssh/<personal_key>”
# ~/work/.gitconfig.work
[user]
email = [email protected]
name = Your Name
[github] #or gitlab or whatever
user = "work_username"
[core]
sshCommand = “ssh -i ~/.ssh/<work_key>”
And finally add this to the end of your original main .gitconfig file:
[includeIf “gitdir:~/personal/”] # include for all .git projects under personal/
path = ~/personal/.gitconfig.pers
[includeIf “gitdir:~/work/”]
path = ~/work/.gitconfig.work
Now finally to confirm if it worked, go to any work project you have and type the following:
cd ~/work/work-project
git config user.email
It should be your work e-mail.
Now go to a personal project:
cd ~/personal/personal-project
git config user.email
And it should output your personal e-mail.
- To clone new projects, specially private or protected ones, use the username before the website:
git clone https://<username>@github.com/<organization>/<repo>.git
If you have a 2 Factor Authentication, the clone might fail on the first try, because you need to generate a Personal Access Token.
And then copy and paste that as the password when the terminal asks you for user and password.s
And done! When you push or pull from the personal account you might encounter some 2 factor authorizations at login, but otherwise it's ready to work on both personal and work projects.
Docker allows us to run server apps that share an internal environment separate from the OS.
Follow the following guide for docker. https://docs.docker.com/desktop/install/mac-install/
- Use Apple menu >About this Mac.
- Confirm the Chip to determine the installation method
The desktop app needs to be running before being able to run commands on the terminal.
Test:docker container --list
Mac already has a system used python but it is better to avoid using it as it interacts with the system, so we install a local version with Pyenv. Pyenv also makes it so that pip and python are always matched for each other in the correct version.
This is specially useful if you need different versions for different projects (Maybe caused by tensorflow updates vs other libraries updates...), you should follow these tutorials:
https://opensource.com/article/19/5/python-3-default-mac https://opensource.com/article/20/4/pyenv
brew install pyenv
Recent versions of MacOS have a dependency error when installing python via pyenv sometimes. Let's install that dependency first.
brew install xz
Now let's install and set the latest version as the global python:
pyenv install --list
pyenv install 3.11.5
pyenv global 3.11.5
And then we can add it to our PATH so that every time we open python it's the pyenv one and not the system one:
nano ~/.zprofile
---- add in nano interface---
export PATH=$PATH:~/.pyenv/shims
export PYENV=~/.pyenv
export PYENV_ROOT=~/.pyenv
export PYENV_HOME=~/.pyenv
eval "$(pyenv init -)"
CTRL+O
CTRL+X
--------------------
source ~/.zprofile
That eval line I found out thanks to this StackOverflow post
We can confirm we are using the correct one:
pyenv versions
which python
python -V
which pip
pip -V
Poetry is a tool to manage python project dependencies and environments in a version controlled (e.g. git) and group accessible syntax. It allows to use a virtual environment to locally install all dependencies, remove or update them as needed while having access to previous instances of the environment at a given time via the commit history
pip install poetry
Usage guide: https://python-poetry.org/
Making a new project can be as easy as:
poetry new project-name-here
cd project-name-here
Then, instead of using pip install or pip uninstall we use poetry add
poetry add pathlib
This updates the dependency control files poetry.toml, poetry.lock, and pyproject.toml, which can be committed to version control.
And finally, when cloning a repository, you can use poetry install to easily install all the dependencies controlled by poetry in one command.
This is my generic fresh start install so I can work. Usually I'd install all of them in general, but recently I only install the necessary libraries under venv. There's more libraries with complicated installations in other repositories of mine, and you might not wanna run this particular piece of code without checking what I'm doing first. For example, you might have a specific version of Tensorflow that you want, or some of these you won't use. But I'll leave it here as reference.
pip install numpy scipy jupyter statsmodels \
pandas pathlib tqdm retry openpyxl
pip install matplotlib adjustText plotly kaleido
pip install sklearn sympy pyclustering
pip install beautifulsoup4 requests selenium
pip install gensim nltk langdetect
For Japanese NLP tools see: https://github.com/elisa-aleman/MeCab-python
For Chinese NLP tools see: https://github.com/elisa-aleman/StanfordCoreNLP_Chinese
pip install tensorflow tflearn keras \
torch torchaudio torchvision \
optuna
To Install with CPU:
pip install xgboost
Install with CPU:
pip install lightgbm
For Minepy / Maximal Information Coefficient, we need the Visual Studio C++ Build Tools as a dependency, so install it first:
https://visualstudio.microsoft.com/visual-cpp-build-tools/
pip install minepy
Note to self: re-write with poetry project use instead of venv
with CPU and no extra options:
python -m pip install -U opencv-python opencv-contrib-python
Note to self: re-write with poetry project use instead of venv
I'm using this guide: https://flask.palletsprojects.com/en/2.1.x/installation/#install-flask
For Web Development, it's apparently better to make a Virtual Environment to install flask project-wise instead of system or user level.
First we go to our project and make the virtual environment.
cd my-project
python -m venv venv
. venv/scripts/activate
it might also be
. venv/bin/activate
so if one fails try the other.
Activate results in the python and pip versions to be internal to the project now and active in the bash:
which python
>>> .... my-project\venv/Scripts/python
pip --version
pip 22.1 from c:\users\...\my-project\venv\lib\site-packages\pip (python 3.9)
So since this pip is empty, let's install ONLY what we need for the project:
pip install --upgrade pip
pip install selenium beautifulsoup4 pandas pathlib retry
pip install flask
Now let's test it:
I'm using this guide here:
https://flask.palletsprojects.com/en/2.1.x/quickstart/
Under: my-project/python/hello.py
from flask import Flask
app = Flask(__name__)
@app.route("/")
def hello_world():
return "<p>Hello, World!</p>"
Then in bash:
cd my-project/python
export FLASK_APP=hello
flask run
and it should return:
* Serving Flask app 'hello' (lazy loading)
* Environment: production
WARNING: This is a development server. Do not use it in a production deployment.
Use a production WSGI server instead.
* Debug mode: off
* Running on http://127.0.0.1:5000 (Press CTRL+C to quit)
Unlike Jekyll, it won't update as you edit, unless you set up a development environment variable:
export FLASK_APP=hello
export FLASK_ENV=development
flask run
It will update, but you still have to click refresh on the screen.
from flask import Flask
app = Flask(__name__)
@app.route("/")
def hello_world():
return "<h1>Hello, World!</h1>"
Now to make the project a package and keep running under the same structure as before, now I use this structure: (which by the way you can output with tree -a -N -n --charset ascii | pbcopy on the terminal if you install it with Homebrew with brew install tree).
my-project
|-- .gitignore
|-- README.md
|-- logs
| `-- tasklog.md
|-- python
| |-- ProjectPaths.py
| |-- __pycache__
| |-- package
| | |-- __init__.py
| | |-- __pycache__
| | `-- module.py
| `-- tests
| |-- 0_test.py
| `-- __pycache__
|-- requirements.txt
`-- venv
ProjectPaths.py is just a bunch of methods I like to call to make directories without much hassle.
To run the tests and the files in the package, now the command is like this:
cd my-project/python
python -m tests.0_test
Notice that it's a . instead of a / and also there's no .py
It should now run and import as if from the parent directory python
I also make websites on my free time, and lots of researchers have their projects on a github pages website. For this, I like to use Jekyll in combination with github pages. First lets install all our dependencies.
brew install ruby
Then, we have to add to the $PATH so that ruby gems are found:
echo 'export PATH="/usr/local/bin:$PATH"' >> ~/.zprofile
echo 'export PATH="/usr/local/opt/ruby/bin:$PATH"' >> ~/.zprofile
echo 'export PATH="~/.local/share/gem/ruby/X.X.X/bin:$PATH"' >> ~/.zprofile
source ~/.zprofile
Where X.X.X is the version you have installed.
In my case it was:
echo 'export PATH="/usr/local/bin:$PATH"' >> ~/.zprofile
echo 'export PATH="/usr/local/opt/ruby/bin:$PATH"' >> ~/.zprofile
echo 'export PATH="~/.local/share/gem/ruby/3.0.0/bin:$PATH"' >> ~/.zprofile
source ~/.zprofile
Check that we're indeed using the Homebrew version of ruby:
which ruby
Which should output this:
/usr/local/opt/ruby/bin/ruby
gem install --user-install bundler jekyll jekyll-sitemap
This should install both of them as user-install, but if errors occur just install separately instead of together.
Now it's installed! Well, to make a Jekyll Github Page I followed this tutorial, so go ahead and do it:
https://docs.github.com/en/pages/setting-up-a-github-pages-site-with-jekyll
Now, once you have your webiste repository and you're ready to test the jekyll serve, do the following:
cd (your_repository_here)
bundle init
bundle add jekyll
bundle add jekyll-sitemap
bundle add webrick
And then all that's left to do is to serve the website with jekyll! Also for the sitemaps make sure to check this tutorial:
https://github.com/jekyll/jekyll-sitemap
And add this to your _config.yml
url: "https://example.com" # the base hostname & protocol for your site
plugins:
- jekyll-sitemap
bundle exec jekyll serve
If you get an error like:
Could not find webrick-1.7.0 in any of the sources
Run `bundle install` to install missing gems.
Do as it says and just run:
bundle install
Now you can work on the website and look at how it changes on screen.
By the way, if you are hosting on GitHub Pages and have a custom domain, you need to add these to the DNS
Type Name Points to TTL
a @ 185.199.108.153 600 seconds
a @ 185.199.109.153 600 seconds
a @ 185.199.110.153 600 seconds
a @ 185.199.111.153 600 seconds
cname www your-username.github.io 600 seconds
Download the .pkg file and install it manually.
https://www.tug.org/mactex/downloading.html
This installs a few packages along with it, including latexdiff which I use a lot as a PhD student.
It is installed under /Library/TeX/texbin, but if you have any terminal sessions open it will probably not load, so you should open a new session, and then confirm that it also installed latexdiff with:
which latexdiff
https://github.com/elisa-aleman/latex_helpers
I made these shell scripts to help in compiling faster when using bibliographies and to delete cumbersome files when not necessary every time I compile. Since they are .sh scripts, they run normally with git bash.
- Install Package Control.
- Install LaTeXTools plugin.
https://tex.stackexchange.com/a/85487
If you have the LaTeXTools plugin, it already does that except that it is mapped on Shift+Enter instead of Enter.
For Japanese UTF-8 text in XeLaTeX:
\usepackage{xeCJK}
Set the fonts: these are the default, but they have no bold
\setCJKmainfont{IPAMincho} % No bold, serif
\setCJKsansfont{IPAGothic} % No bold, sans-serif
\setCJKmonofont{IPAGothic} % No bold, sans-serif
Installing fonts, for example, Aozora mincho has guaranteed bold
https://web.archive.org/web/20200321102301/http://blueskis.wktk.so/AozoraMincho/download.html
Make sure to install for all users:
https://stackoverflow.com/questions/55264642/how-to-force-win10-to-install-fonts-in-c-windows-fonts
Set the installed font:
\setCJKmainfont[BoldFont=AozoraMincho-bold,AutoFakeSlant=0.15]{Aozora Mincho}
Japanse document style:
\usepackage[english,japanese]{babel} % For Japanese date format
\usepackage{indentfirst} % For Japanese style indentation
\setlength\parindent{11pt}
Japanese babel messes itemize up inside tables, so:
\usepackage{enumitem}
\newlist{jpcompactitemize}{itemize}{1} % defined new list
\setlist[jpcompactitemize]{topsep=0em, itemsep=-0.5em, label=\textbullet} % new list setup
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\usepackage[lighttt]{lmodern}
\usepackage{listings} % to display code
\usepackage{lstautogobble} % to indent inside latex without affecting the code, keeping the indent the code has inside
\usepackage{anyfontsize} % for code font size
\usepackage[os=win]{menukeys} % to display keystrokes
% For the color behind the code sections:
\usepackage{xcolor} %custom colours
\definecolor{light-gray}{gray}{0.95} %the shade of grey that stack exchange uses
\definecolor{editorGreen}{rgb}{0, 0.5, 0} % #007C00 -> rgb(0, 124, 0)
% Make a more defined languages for nice colors
\include{lststyle-css.sty}
\include{lststyle-html5.sty}
% Set up the code display lst options
\lstset{
% for the code font and size:
% basicstyle=\ttfamily\small,
basicstyle=\ttfamily\fontsize{10}{12}\selectfont,
% to avoid spaces showing as brackets in strings
showstringspaces=false,
% for straight quotes in code
upquote=true,
% for the middle tildes in the code
literate={~}{{\fontfamily{ptm}\selectfont \textasciitilde}}1,
% for the line break in long texts
breaklines=true,
postbreak=\mbox{\textcolor{red}{$\hookrightarrow$}\space},
% for the keyword colors in the code
keywordstyle=\color{blue}\bfseries\ttfamily,
stringstyle=\color{purple},
commentstyle=\color{darkgray}\ttfamily,
keywordstyle={[2]{\color{editorGreen}\bfseries\ttfamily}},
autogobble=true % to ignore latex indents but keep code indent
}
% unnecessary in XeLaTeX
% % For this specific document with lots of degree signs inside listings
% \lstset{
% literate={°}{\textdegree}1
% }
% for straight double quotes in code
\usepackage[T1]{fontenc}
% frame set up
\usepackage[framemethod=TikZ]{mdframed} %nice frames
\mdfsetup{
backgroundcolor=light-gray,
roundcorner=7pt,
leftmargin=1,
rightmargin=1,
innerleftmargin=1em,
innertopmargin=0.5em,
innerbottommargin=0,
outerlinewidth=1,
linecolor=light-gray,
}
% Make it affect all lstlistings
\BeforeBeginEnvironment{lstlisting}{\begin{mdframed}\vskip-.5\baselineskip}
\AfterEndEnvironment{lstlisting}{\end{mdframed}}
% Make colored box around inline code
\usepackage{realboxes}
\usepackage{xpatch}
\makeatletter
\xpretocmd\lstinline{\Colorbox{light-gray}\bgroup\appto\lst@DeInit{\egroup}}{}{}
\makeatother
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
When it comes down to it, specially when working with LaTeX or git, you find yourself making the same commands over and over again. That takes time and frustration, so I find that making scripts from time to time saves me a lot of time in the future.
Once in a while those scripts will need some input to be more useful in as many cases as possible instead of a one time thing.
Looking for how to do this I ran across a simple StackOverflow question, which led me to the getopts package and its tutorial:
This is a working example:
while getopts ":a:" opt; do
case $opt in
a)
echo "-a was triggered, Parameter: $OPTARG" >&2
;;
\?)
echo "Invalid option: -$OPTARG" >&2
exit 1
;;
:)
echo "Option -$OPTARG requires an argument." >&2
exit 1
;;
esac
done
Now sometimes you'll want to have fancy arguments with both a shortcut name (-) and a long name (--), for example -a and --doall both pointing to the same command. In that case I recommend using nhoffman's implementation of Python's argparse in bash:
argparse.bash by nhoffman on GitHub
Personally, I find it tiring to try to compile a LaTeX document, only to have to run the bibliography, and then compile the document twice again so all the references are well put where they need to be, rather tiring. Also, I find that the output files are cluttering my space and I only need to see them when I run into certain errors.
Also, for academic papers, I used latexdiff commands quite a lot, and while customizable, I noticed I needed a certain configuration for most journals and that was it.
So I made LaTeX helpers, a couple of bash scripts that make that process faster.
So instead of typing
pdflatex paper.tex
bibtex paper
pdflatex paper.tex
pdflatex paper.tex
open paper.tex
rm paper.log paper.out paper.aux paper.... and so on
Every. Single. Time.
I just need to type:
./latexcompile.sh paper.tex --view --clean
and if I needed to make a latexdiff I just:
./my_latexdiff.sh paper_V1-1.tex paper.tex --newversion="2" --compile --view --clean
And there it is, a latexdiff PDF right on my screen.
I would also commonly have several documents of different languages, or save my latexdiff command in another script, called cur_compile_all.sh or cur_latexdiff.sh so I didn't have to remember version numbers and stuff when working across several weeks or months.
Usually with code such as:
cd en
./latexcompile.sh paper.tex --view --clean --xelatex
cd ../es
./latexcompile.sh paper.tex --view --clean --xelatex
cd ../jp
./latexcompile.sh paper.tex --view --clean --xelatex
And so on, to save time.
I discovered this tool recently when I was asked to share a PDF of my private GitLab MarkDown notes. Of course I wouldn't share the whole repository so that it can be displayed in GitLab for them, so I searched for an alternative.
It can be installed in Windows, macOS, Linux, ChromeOS, BSD, Docker, ... it's really portable
Pandoc Install:
https://pandoc.org/installing.html
Pandoc Manual:
https://pandoc.org/MANUAL.html
Export to PDF syntax
pandoc test1.md -s -o test1.pdf
Note that it uses LaTeX to convert to PDF, so UTF-8 languages (japanese, etc.) might return errors.
pandoc test1.md -s -o test1.pdf --pdf-engine=xelatex
But it doesn't load the Font for Japanese... Also, the default margins are way too wide.
So, in the original markdown file preamble we need to add Variables for LaTeX:
---
title: "Title"
author: "Name"
date: YYYY-MM-DD
<!-- add the following -->
geometry: margin=1.5cm
output: pdf_document
<!-- CJKmainfont: IPAMincho #default font but no bold -->
<!-- install this one for bold japanese: https://web.archive.org/web/20200321102301/http://blueskis.wktk.so/AozoraMincho/download.html -->
<!-- https://stackoverflow.com/questions/55264642/how-to-force-win10-to-install-fonts-in-c-windows-fonts (install for all users) -->
CJKmainfont: Aozora Mincho
CJKoptions:
- BoldFont=AozoraMincho-bold
- AutoFakeSlant=0.15
---
And voilà, the markdown is now a PDF.
I'm still unsure if it will process the GitHub or GitLab math environments, since the syntax is different.
Upon confirmation with the User's Guide: Math section, it uses the GitHub math syntax.
Inline: $x=3$
Renders as:
Block: $$x=3$$
Renders as:
When designing new things it's important to keep in mind color theory, as well as accessibility for the visually impaired and color blind people, etc. But that's so much time one could spend doing so much else, so here's a tool that can help with that and also visualizing how other people with different ranges of color vision would perceive it. It's called Paletton.
There was a new tool developed called "Bionic Reading", which bolds the beginnings of words so that our eyes glide over them more easily, basically making a tool for speed reading without having to train specifically for that. Lots of neurodivergent people such as myself (I have ADHD and am autistic), have a hard time following long texts or focusing when there is too much information at the same time (say, with very small line spacing). This new tool has been praised by the ND (neurodivergent) community, since making it available for businesses or companies to use would mean more accessibility in everyday services... or at least it was until they decided to charge an OUTRAGEOUS amount of money to implement it, making it obviously not attractive for companies to implement and therefore ruining it for everyone.
That is why someone decided to make "Not Bionic Reading" which is, legally speaking, not the same thing as Bionic Reading and therefore can be made available for everyone as Open Source.
Here's the usable link: https://not-br.neocities.org/
Have fun reading!
https://pncnmnp.github.io/blogs/firefox-dark-mode.html
After hunting on the web for about 30 minutes, I found this thread on Bugzilla. It turns out starting with Firefox 60, extensions are no longer allowed to interact with the native pdf viewer. Determined, I decided to locally modify the CSS rendered by Firefox's PDF viewer. The steps for the same are:
- Open Firefox and press Alt to show the top menu, then click on Help → Troubleshooting Information
- Click the Open Directory button beside the Profile Directory entry
- Create a folder named chrome in the directory that opens
- In the chrome folder, create a CSS file with the name userContent.css
- Open the userContent.css file and insert -
#viewerContainer > #viewer > .page > .canvasWrapper > canvas {
filter: grayscale(100%);
filter: invert(100%);
}
- On Firefox's URL bar, type about:config.
- Search for toolkit.legacyUserProfileCustomizations.stylesheets and set it to true.
- Restart Firefox and fire up a PDF file to see the change!
I found a solution in this post:
https://superuser.com/a/1527417
The following snippet adds a div overlay to any browser tab currently displaying a PDF document.
- Open up your browser's Dev tools then browser console.
- Paste this JavaScript code in your browser console:
const overlay = document.createElement("div");
const css = `
position: fixed;
pointer-events: none;
top: 0;
left: 0;
width: 100vw;
height: 100vh;
background-color: white;
mix-blend-mode: difference;
z-index: 1;
`
overlay.setAttribute("style", css);
document.body.appendChild(overlay);
- Hit Enter
Special thanks: https://www.reddit.com/r/chrome/comments/e3txhi/comment/fem1cto
That is all for now. This is my initial setup for the lab environment under a proxy. If I have any projects that need further tinkering, that goes on another repository / tutorial.