Syntax and Basics

Linux, Get Oriented

To login to a linux machine remotely:

ssh username@ipaddress

To see the version of Linux running:

cat /etc/os-release

printenv lists all environment variables

Print working directory:

pwd

Get IP address:

ifconfig or ifconfig | grep inet

See what ports are open:

netstat

List all users:

less /etc/passwd

List groups a user belongs to:

groups username or id username

List groups with their members:

getent group or getent group | grep searchsomething

To get the status, including rules being enforced, of the uncomplicated firewall:

sudo ufw status

To list all processes currently running;

ps aux | grep searchsomething

To find a particular file or directory from among all files:

sudo find / -name "searchsomething"

or for directory name search only:

sudo find / -type d -name "searchsomething"

To search for specific text within the files within the current directory:

grep -nr 'searchsomething*'

• $ is the normal prompt for commands
• # is the system administrator prompt
• in the C shell, the prompt ends with %
• > is used to send the output to a text file. >> is used to append the output to an existing text file without over-writing.
• $VARIABLE_NAME is a variable
• apt combines apt-get and apt-cache and it is newer. Use apt.
• sudo apt update && sudo apt upgrade -y
  • To install Python packages, use apt only if you want to install directly on the machine, otherwise use pip. Pip installs modules slower, but installs the latest versions, and most importantly works within a virtualenv. In the special case of Raspberry Pi, use apt because it knows the unique processor architecture and installs the correct builds of modules.
• script savedcommands.txt
• A .sh file is an executable shell script. # to comment within
• ./ is used to specify the current working directory especially when running something that could be the same as a system command.
• nano is the basic user-friendly text editor.
• To view $PATH, echo "${PATH//:/$'\n'}" or just echo $PATH
• To edit $PATH for the current session, export PATH='/new/directory:$PATH'
• > sends command output to a file. >> appends the output to a file without overwriting existing contents.
• ls -al shows all files in directory including hidden
• whatis is a brief explanation
• man gives a manual
• less is like cat, but one page at a time

Windows PowerShell

• The prompt is PS C:\current\path>
• %VARIABLE_NAME% is a variable

Get the latest version of PowerShell

PS > winget search Microsoft.PowerShell

PS > winget install --id Microsoft.PowerShell --source winget

Scripting with PowerShell ISE

PS > Get-ExecutionPolicy -List

PS > Set-ExecutionPolicy -Scope Process RemoteSigned

Set Up Python from Scratch on Windows

Python is not natively-installed on Windows, unlike on Linux machines. This pretty much covers it: https://learn.microsoft.com/en-us/windows/python/web-frameworks

Develop in Python Using VS Code and WSL

PS > wsl --install

PS > wsl --list --verbose

PS > wsl

# code .

Install a Local Python from Source

sudo apt install -y make build-essential libssl-dev zlib1g-dev libbz2-dev libreadline-dev libsqlite3-dev wget curl llvm libncurses5-dev libncursesw5-dev xz-utils tk-dev

To install dependencies.

What the following does: download source code, unpack it, make directory ~/.localpython to install into, run the configuration file setting install going to install folder, compile, install compilation, create a virtualenv pointing to the install, switch to the virtualenv to use it:

mkdir ~/src

cd ~/src

$ wget http://www.python.org/ftp/python/3.11.0/Python-3.11.0.tgz

$ tar -zxvf Python-3.11.0.tgz

$ cd Python-3.11.0

$ mkdir ~/localpython3110

$ ./configure --prefix=$HOME/localpython3110 --enable-optimizations

https://realpython.com/installing-python/#how-to-build-python-from-source-code

$ make &&make altinstall

Install the Latest Python

sudo apt install software-properties-common -y

sudo add-apt-repository ppa:deadsnakes/ppa

sudo apt update

sudo apt install python3.xx

curl -sS https://bootstrap.pypa.io/get-pip.py | python3.13

Set Up venv

$ ~/localpython3110/bin/python3.11 -m venv py3110_venv

$ source py3110_venv/bin/activate

$ sudo apt install python3-pip -y

$ pip install --upgrade pip

$ pip install tk pillow numpy astropy astroplan pandas pytz matplotlib scikit-learn

$ pip list

$ pip -V

$ which python

$ pip install --upgrade pip

$ pip freeze --local > requirements.txt

$ deactivate

$ rm -rf somename_env

$ pip install -r requirements.txt

Note the venv folder stores neither the Python installation nor your code for your project. It is only used to store version information about the Python installation used for your project.

Install Packages from Local Folder

pip download package1 package2 -d'~/src/python-packages'

pip install package1 package2 -f ~/src/python-packages --no-index

Deploy Flask App

sudo apt install libapache2-mod-wsgi-py3

sudo a2enmod wsgi

Disable apache2:

sudo update-rc.d apache2 disable

sudo update-rc.d apache2 enable

sudo service apache2 restart

sudo service apache2 start

sudo service apache2 stop

AstroWideImageMapper and Exiv2 with Python

sudo apt install exiv2

From virtual environment:

pip install tk numpy pandas astropy pillow matplotlib pyexiv2

pip install -U scikit-learn

(or pip install -r requirements.txt)

python -c 'import os, sys; print(os.path.dirname(sys.executable))'

to see the path to the current python installation.

PS > $env:path -split ';'

to see the path variable in Windows (readable format)

Astropy on a Raspberry Pi Zero W

This is step-by-step how to install Astropy and Astroplan on a Raspberry Pi Zero W (1st gen, not the ‘2’).

Raspberry Pi OS download here along with imager here.

sudo passwd (change from default as desired for security)

sudo raspi-config

Set up location, time zone, language, keyboard, Wi-Fi, SSH. Turn off Bluetooth? How?

python --version

>> Python 3.9.2

sudo apt install python3-pip – for the Raspberry Pi, it is better to not use pip because it installs software not compiled for the Pi (the Pi Zero ISA is ARMv6l).

sudo apt install python3-numpy

sudo apt install python3-astropy

Note! Astropy installs this one. Not the rc2 or any of the other ones.

sudo apt install python3-pyerfa (installs with Astropy – I think)

sudo apt install python3-pyyaml (installs with Astropy – I think)

sudo apt install python3-packaging (installs with Astropy – I think)

sudo apt install python3-astroplan

sudo apt install python3-pytz (installs with Astroplan)

Other Astroplan options here.

sudo apt install python3-astroquery

sudo apt install python3-scipy

sudo apt install python3-kivy

sudo apt install fim

sudo apt install kivy

sudo apt install libmtdev1

sudo apt autoremove

Notes

Hardware

The Raspberry Pi Zero W is 32-bit and uses ARMv6 instead of the newer ARMv7. The [biggest? only?] difference is in how the processor handles floating point operations.

The Raspberry Pi Zero 2 W is 64-bit.

The Raspberry Pi OS version 11 – the latest version still – is 32-bit. A 64-bit Raspberry Pi OS is in development but not available yet.

To check the version of Raspberry Pi OS installed, cat /etc/os-release.

Python

Python comes already installed with the Raspberry Pi OS. To verify, type python --version. You could install if necessary with sudo apt install python3.8x.

sudo apt update is also a good command to run.

PyCharm on Linux

Pycharm is a the most popular Python editor.

NEVERMIND Develop on Windows, then put the program on the Raspberry Pi after. Or Develop directly on the Pi? Seems like develop on Windows is the best option.

The latest PyCharm is 64-bit and requires a 64-bit OS and 64-bit JDK.

The PyCharm install comes packed as a .tar and compressed as .gz, so .tar.gz. Decompress the file with gzip -d filename.tar.gz, then unpack it with tar -xvf filename.tar. This will create a directory of the same name as the .tar file.

Linux comes with both gzip and tar installed so the commands work right away.

Once unpacked, you can run PyCharm by navigating to the bin folder, in my case /etc/pycharm-community-2018.3/bin and type ./pycharm.sh. You need Java to run it, so …

Ubuntu on a Chromebox

https://mrchromebox.tech/#home

https://cloudbytes.dev/snippets/upgrade-python-to-latest-version-on-ubuntu-linux

https://www.x.org/wiki

On Ubuntu, to get latest python, sudo add-apt-repository ppa:deadsnakes/ppa, then sudo apt update && sudo apt upgrade -y. To see if a version is available, apt list | grep python3.10

2021 Dec – Astropy and Astroplan Notes

Root a Smartphone – Option for an appropriate processor?

Navigate to About Phone -> Build Number. Tap Build Number 7x for Developer Mode.

Under settings, there will be a new option called Developer Options. Within Developer Options, enable OEM unlocking.

Some useful apps for rooting and installing Linux are

• Linux Deploy
• Busybox
• VNC Viewer

Python

https://www.python.org/downloads

Raspberry Pi OS and Python versions support and description here.

The command pip3 is made for Python 3, so use it, not just pip.

• Python 3.9.2 comes installed on the Raspberry Pi OS. Python 3.9.2 was released in Feb 2021.
• Miniconda 3.5.5 installs Python 2.7.7. Python 2.7.7 was released in Jun 2014 (same month as Miniconda 3.5.5)
• The Miniconda installation instructions specifically say you can leave Python installed do not remove it (see link below under Miniconda).
• Astroplan uses the Python package Numpy. Use either the Linux command pip3 list, or python -c "import numpy; print(numpy.__version__)" to find the Numpy version installed.
  • I have Numpy 1.19.5. Is that because the legacy Miniconda installed it or because of the Python 3.9.2 installed on the Raspberry Pi OS? I think it’s the Python 3.9.2 from the OS.
  • Numpy downloads for Raspberry Pi here.
  • On my first test with Astroplan (and Astropy) I had a Numpy error that sent me to this link. The correction was sudo apt-get install libatlas-base-dev. I also updated Numpy with pip3 install numpy --upgrade and it upgraded to Numpy 1.21.5

Miniconda (a Python Distribution)

Astroplan highly recommends to be installed using Conda rather than by manually installing Python and required packages.

Both Anaconda and Miniconda are Conda and Conda is a Python distro. Miniconda is Python plus data science tools. Anaconda is Minconda plus a GUI and more tools.

Do you have to remove existing Python to install Conda? No, you can leave Python installed. But for a legacy Miniconda install with the latest Python? May be an issue?

https://conda.io/projects/conda/en/latest/user-guide/install/linux.html

Legacy Miniconda downloads here. For the Raspberry Pi Zero W (1st gen, which is an ARMv6 processor), I found just one ARMv6 version from the long list of legacy Miniconda installs: Miniconda-3.5.5-Linux-armv6l.sh.

Miniconda 3.5.5 was released in Jun 2014.

For the conda command to work, an appropriate line has to be added to the .bashrc and .bash_profile files. The install does it automatically, BUT: I installed Miniconda into /etc/miniconda and in order to do this, I installed it as root user and because of that, the conda command only worked if I opened the terminal as the root. Of note, once I switched to root and back to pi in the terminal, the conda command still worked as pi. /home/username/.bashrc is for “non-login” shells. /home/username/.bash_profile is for “login” shells

Astropy

Installation instructions: https://docs.astropy.org/en/stable/install.html

Astropy required Python packages.

Astropy installation files archive with various ISA support. Download the appropriate wheel file, then install with the command pip3 install /home/pi/file_name.whl.

Astropy comes with the full Anaconda install. With Miniconda, the recommended way to install Astropy is using the command conda install astropy.

Astropy Version History

Astropy 0.3.0 is what Miniconda 3.5.5 installs. This is a much earlier version than I would have expected. Astropy 0.3 was released in Nov 2013.

Astropy 0.4 was released in Jul 2014. Therefore Astropy 0.3 was the latest version when Miniconda 3.5.5 was released and is probably why Miniconda 3.5.5 installs with Astropy 0.3.

Astropy v1.2 requires Python v2.7 or later and Numpy 1.7.0 or later.

Astropy v1.3: “vectors and coordinates can be reshaped like arrays.”

Astropy v2.0.0 started to implement Python 3 but specifically says does not change functionality with Python 2. However, from 2.0.0 to 2.0.18, Python 2 was gradually phased out.

Astropy v3.0 is the first version that supports only Python 3.

I think I want Astropy v1.3 – unless it won’t run for some reason. Why does Miniconda 3.5.5 install Astropy 0.3.0? Was it the current Astropy at the release time? Answer: yes, it was. Do the newer Astropy versions require newer ISA? At some point, I got a “need ARMv7” error so probably.

However, also unexpectedly, it updates Python from 2.7.7 to 2.7.8. Python 2.7.8 was released in Jul 2014.

Astroplan

2021 Jun – Set up Linux, Apache, MySQL, PHP Server, LAMP Stack

A Server is a Physical Computer

There are various types of servers, but they all consist of a physical computer somewhere. This tutorial shows how to set up a server first with the simplest of physical devices you can have in your home for less than $20 and side-by-side with how to do it in its more abstract – and more common – form, a VPS (virtual private server) you can rent from a hosting service.

The two procedures are very analogous. Seeing them side-by-side helps make concrete what you are actually doing even though sometimes you can’t physically see it.

Server 1. Raspberry Pi Zero W Running Raspberry Pi OS (Debian, a flavor of Linux)

Can be purchased many places, such as Microcenter or Amazon.

Server 2. VPS (Virtual Private Server) Running Ubuntu 20.04 (a flavor of Linux)

I purchased a VPS from Hostwinds. There are various operating systems available. I used Ubuntu 20.04.

Connect to Your Server over a Network (or the Internet)

Connect Via Secure Shell (SSH)

I SSH login using the MobaXterm SSH Client. The server is usually a remote computer to which you do not have physical access, so instead of plugging in a keyboard, mouse and screen, you establish a connection that gives you access to the server’s command prompt. SSH stands for secure shell, meaning the data you transfer between your computer and the server are encrypted. SSH is enabled by default in Ubuntu, but not all Linux flavors.

Useful Linux Commands: https://vitux.com/40-most-used-ubuntu-commands/

1. Raspberry Pi Zero W

Connect the Raspberry Pi Zero to your LAN. There is a way to do this with command line but the Raspberry Pi OS connects to WiFi on the initial startup, so just do it on initialization. If you want, to view the saved password with the command line to know generally where WiFi passwords are stored, use

sudo grep psk= /etc/wpa_supplicant/*

which searches the appropriate directory for “psk=” and you see the stored WiFi keys.

Enable SSH. SSH is not enabled by default with Raspberry Pi Zero. Many tutorials tell you to add a blank file to the /boot folder called SSH (no extension at all). Use the command touch ssh, then reboot. If you do this, notice once SSH is enabled then the file gets deleted so you will not see any change other than the SSH login should work.

2. VPS

On a VPS, SSH is (should be) enabled by your host to allow the purchaser to access it. You will get a default username and password from the hosting service who established the VPS with its default settings.

In MobaXterm, “Remote host” is where you specify the IP address of your server, available in your Hostwinds account.

The username is “root”

The password is whatever you set in Hostwinds

Useful Linux Commands

At this point, you are using Linux. Either Raspberry Pi OS or Ubuntu are “flavors” of Linux. Having a list of basic commands is helpful:

40+ most used Ubuntu 22.04 Commands

Set up Firewall

sudo ufw allow OpenSSH

sudo ufw allow 22

sudo ufw allow 3306

sudo ufw default deny incoming

sudo ufw default allow outgoing

sudo ufw allow ssh

sudo ufw allow http or sudo ufw allow 80

sudo ufw allow https or sudo ufw allow 443

sudo ufw allow 'apache full'

sudo ufw show added

sudo ufw enable

Create Non-Root Super-User

This step appears complex and does not appear necessary especially this early in the process. Strictly speaking, it is indeed not necessary. You could skip this step and do everything as the root or default user that already exists. However, it is best to do this now because:

• to do things in the right order
• to highlight an important aspect of the Linux OS: that Linux is very user-specific and permissions-based. This makes Linux less intuitive at first but makes it secure enough to be accessed by many different anonymous people as a server without allowing hackers to access sensitive parts of the server.
• to avoid inevitable frustration later. Using Linux you will see “permission denied” errors periodically throughout your experience and you are better off expecting and troubleshooting them than believing that Linux is just annoying. Permissions are built-in to Linux from the ground up and it’s best to work with it rather than try to ignore it.
• Logging in as a non-root user is safer. For example, some installations of Ubuntu default to external root login disabled, which means for a remote server you would be locked out if this were set and you don’t have another user to login as.

sudo adduser new_username

usermod -aG sudo new_username

Change the password for the current user as desired with:

passwd

Grant all privileges to the user with the command

sudo visudo

and add a line in the /etc/sudoers file below the root user line: new_username ALL=(ALL:ALL)ALL

This only allows the user to give itself privileges. The user does not have all read/write privileges like the root itself. Log in as the new user through SSH.

Optional: Update Operating System

1. Raspberry Pi OS

sudo apt update is the Debian update command (Raspberry Pi OS is based on Debian).

2. VPS

Update Ubuntu (only required if there is a new version of Ubuntu).*

*First, be sure you can login as the non-root super-user before updating Ubuntu as the new install will default to not allow root login. This means if you were planning to just use the existing root user with infinite powers you are now infinitely locked out of your own VPS and have to have your host re-initialize it. Your VPS host changed this setting when it set up your VPS so you can login but when you update the Ubuntu OS, the OS returns to the OS default which is to not allow SSH root login! This is a GREAT example of why to do the user basics as the very first step.

sudo do-release-upgrade

Update the advanced package tool:

sudo apt-get update (without the -get is newer, so I use it)

sudo apt update

Install the “L-A-M-P” Programs

L: Linux, already installed. I used 20.04.

A: Apache. The Apache2 default site appears immediately by typing server IP address in browser.

sudo apt install apache2 apache2-utils apache2-dev

P: php

sudo apt install php php-mysql

sudo reboot

php -v

You can test php functionality by making index.php file in the /html/ directory and visiting the file in a browser:

<?phpphpinfo();

M: MySQL. Mariadb forked from MySQL when Oracle bought MySQL, so I use MariaDB. The XAMPP controller that establishes localhost for developing uses MariaDB.

sudo apt install mariadb-server

sudo apt install libmariadb3 libmariadb-dev python3-dev

(I don’t think this was necessary) Enable mysqli in /etc/php/7.2/apache2/php.ini by removing comment ‘;’

extension=mysqli ; nate enabled this

also:

sudo phpenmod mysql

To login to MySQL from the Linux command prompt:

sudo mysql -u root or mysql -u username -p

From the MySQL command prompt, which is “MariaDB” – a version of MySQL, same thing, various self-explanatory commands:

MariaDB [(none)]> CREATE user 'new_username'@'localhost';

SELECT user, host, authentication_string FROM mysql.user;

DROP user 'new_username'@'localhost'

CREATE USER 'new_username'@'localhost' IDENTIFIED BY 'yourpassword';

CREATE database yourdatabasename;

GRANT SELECT, INSERT, UPDATE ON yourdatabasename.* TO 'new_username'@'localhost'; or GRANT ALL ...

SHOW GRANTS FOR new_username;

ALTER USER 'new_username'@'localhost' IDENTIFIED BY 'yournewpassword';

SHOW DATABASES;

USE yourdatabasename;

CREATE table

Connect to MariaDB Remotely

sudo nano /etc/mysql/mariadb.conf.d/50-server.cnf

and change the bind-address line to:

bind-address = 0.0.0.0

Connect to MariaDB with Python

https://mariadb.com/resources/blog/how-to-connect-python-programs-to-mariadb

https://mariadb.com/docs/server/connect/programming-languages/c/install/#Installation_via_Package_Repository_(Linux)

sudo apt install libmariadb3 libmariadb-dev

sudo apt install build-essential libssl-dev libffi-dev python3.13-dev

pip3 install mariadb

https://mariadb.com/resources/blog/how-to-connect-python-programs-to-mariadb

Non-Root Super-User Gives Itself Read/Write Privileges

This sounds convoluted and it is when you are accustomed to dealing with desktop computers designed for convenience. Linux is designed for security.

Make a new group, sudo addgroup servermanager, and add the new user to the group, sudo adduser new_username servermanager, groups new_username

make the new group the owner of the required directories:

sudo chown -vR :servermanager /var/www/

sudo chown -vR :servermanager /etc/apache2/sites-available/

sudo chown -vR :servermanager /etc/apache2/sites-enabled

then modify the directory permission to be written by the owner group:

sudo chmod -vR g+w /var/www/ (add +x if you want to be able to develop in this directory)

sudo chmod -vR g+w /etc/apache2/sites-available

sudo chmod -vR g+w /etc/apache2/sites-enabled

(Useful Users and Permissions Commands)

Linux has a group and user structure to manage permissions and it is very useful to be able to view the current state:

List all users in the system:

cat /etc/passwd

List all groups on the system:

cat etc/group or less etc/group

or

getent group

for all members of a single group:

getent group group_name

check ownership of a directory, for example:

ls -ld /var/www/

check ownership of a file:

ls -l /var/www/

Find all the files owned by a particular user (may take some time):

sudo find / -user username

Change the active group for the session, possibly not:

newgrp servermanager

delete a group:

sudo groupdel group_name

delete a user (-r removes the user’s directory and mail spool):

sudo userdel -r username

search “linux octal permissions” to understand the numbering system.

Show all currently logged in users on a system:

w

Upload and Enable a Site

With the commands above, you gave the non-root super-user sufficient permission to set up sites.

Upload any site directory to /var/www/html/your_site/

Go to /etc/apache2/sites-available/ and copy the default .conf file:

cp 000-default.conf your_site.conf

and modify with the following information:

ServerName your_site.com

ServerAlias www.your_site.com

ServerAdmin you@email.com

DocumentRoot /var/www/html/your_site

Use the following command to enable the site. What it actually does is copy the .conf file from /sites-available/ to /sites-enabled/:

sudo a2ensite your_site opposite is sudo a2dissite your_site

sudo systemctl reload apache2

to show some server information:

ps aux | grep apache2 | less

#q

to get out of this command.

Make Website Available Outside Your LAN

1. Raspberry Pi Zero W

Once the Pi server is serving a site on its IP within the LAN, making the site available outside the LAN (on the internet) is as simple as directing site requests that arrive to your internet IP to the Pi server. Sounds complicated, but when a browser looks for a website on the internet, it looks on port 80. Most routers have an option to direct all traffic arriving on a specific port to a specific IP within the LAN. Connect to your network’s router to configure it, usually by entering its IP (often 192.168.1.1) into a browser and logging in with a password you set. You should see an option like this under the advanced settings.

To Do: Establish an SSH Connection with SSH Keys for the Non-Root User

Normally, you generate a public and private key on your local computer then copy the public key to the server along with some settings. Hostwinds has an option in server management to generate the key, download the private key, and install the public key on the server. Reboot required.

WordPress from Scratch

On a fresh Debian VPN. Per WordPress.org’s own list:

sudo apt install apache2

sudo apt install php

sudo apt install php-curl

sudo apt install php-[the rest of the recommended extensions]

php -m to see a list of the php extensions installed.

sudo apt install mariadb-server

sudo systemctl start apache2

sudo systemctl start mariadb

sudo mysql_secure_installation

mysql -u root -p

sudo apt install httpd mariadb mariadb-server php php-common php-mysql php-gd php-xml php-mbstring php-mcrypt php-xmlrpc unzip wget -y

Backup the Server

To make a backup file, sudo su root then navigate to root directory, and:

tar cvpzf backup.tgz --exclude=/proc --exclude=/lost+found --exclude=/backup.tgz --exclude=/mnt --exclude=/sys /

Download the resulting file.

To restore:

tar -xvpfz backup.tgz -C /

then, mkdir /proc, mkdir /lost+found, mkdir /mnt, mkdir /sys

reboot

Serve a Flask App from Ubuntu Apache Server with WSGI

sudo apt-get install libapache2-mod-wsgi-py3

Put the files you have been using to dev in

/var/www/app_name