How to build Atmosphere 1.9.3

Putting this up for Archival purposes. Credit for guide will be listed.

Sometimes you need to build the binaries for Atmosphère, or you want to change something on the source code, for building your starting point should be: https://github.com/Atmosphere-NX/Atmosphere/blob/master/docs/building.md
On that document you can read:

BUILDING ATMOSPHERE

Building Atmosphère is a very straightforward process that relies almost exclusively on tools provided by the devkitPro organization.​
Dependencies:​
devkitA64
devkitARM
Python 2 (Python 3 may work as well, but this is not guaranteed)
LZ4
PyCryptodome (optional)
Hactool
Setup a DevKitPro environment: (https://devkitpro.org/wiki/Getting_Started)​
Install the following packages via (dkp-)pacman:​
switch-dev
switch-glm
switch-libjpeg-turbo
devkitARM
devkitarm-rules
hactool
Install the following library via python's package manager pip, required by exosphere:​
lz4
Finally, clone the Atmosphère repository and run make under its root directory.​

Now lets break it down to get it everytime.

First you need Install a MSYS environment:
The latest instructions for install the MSYS environment are on https://gbatemp.net/threads/install-msys-environment.652234/ if you don't have one working, use them. (for building and installing dependencies please use Mingw64)

After you have the MSYS environment working you need to install DevKitPro
For that you can follow the instructions on the tutorial https://gbatemp.net/threads/setup-a-devkitpro-environment-on-windows.652238/

Now you can install DevKitPro packages:

You Need base DevKitPro packages:
in mingw64
bash

pacman -S --noconfirm switch-dev devkitA64 dkp-toolchain-vars libnx switch-tools switch-mesa switch-libdrm_nouveau switch-sdl2

And the Atmosphère prerequisites
Pacman -Sy --noconfirm devkitA64 devkitARM devkitarm-rules hactool mingw-w64-x86_64-python mingw-w64-x86_64-python-lz4 mingw-w64-x86_64-python-pycryptodome switch-dev switch-glm switch-libjpeg-turbo mingw-w64-x86_64-python-pip

I had to add zip package because even if wasn't explicit indicated on the build page, the code needs it.

You also will need the packages git make lz4 for all to work, use the command:
Pacman -Sy --noconfirm zip git make lz4


All packages on a combined command:​
pacman -S --noconfirm switch-dev devkitA64 dkp-toolchain-vars libnx switch-tools switch-mesa switch-libdrm_nouveau switch-sdl2 devkitA64 devkitARM devkitarm-rules hactool mingw-w64-x86_64-python mingw-w64-x86_64-python-lz4 mingw-w64-x86_64-python-pycryptodome switch-dev switch-glm switch-libjpeg-turbo mingw-w64-x86_64-python-pip zip git make lz4

The package hactool need you to copy your own prod.keys file on $HOME/.switch folder. (c:\msys64\home\USERNAME\.switch if you use the default installation folder)

LibNX Dependency
Atmosphère depends heavily on LibNX, generally when a major version of firmware is released or great changes on the code are made, changes to LibNX are also made.
The Atmosphère team works on their own repo of LibNX (https://github.com/Atmosphere-NX/libnx) and forward Pull Request to official SwitchBrew LibNX repo (https://github.com/switchbrew/libnx).


So ONLY if there are changes on LibNX repository, no yet committed to DevKitPro release, you need to build it and install on your setup.

Libnx Build and Install
If you haven't done already, setup the environment variables
You can test it running the command
export
You should have this:
Bash:
export DEVKITPRO=/opt/devkitpro
export DEVKITARM=${DEVKITPRO}/devkitARM
export DEVKITPPC=${DEVKITPRO}/devkitPPC
export PATH=${DEVKITPRO}/tools/bin:$PATH

Then go to the Atmosphere-NX/LibNX repo and look what is the new branch for the current firmware, by example, for Firmware 20.3.0 the branch name is "20_Support"

(Click the little branch button that says master to select the new branch)
Then go to your MSYS MinGW64 window and clone the Atmosphere-NX/LibNX repo

cd ~
git clone --recursive https://github.com/Atmosphere-NX/libnx.git
cd libnx

And checkout the needed branch:
git checkout 20_support

Then build and install the new LibNX libraries
make install -j$(nproc)

Now you can build Atmosphère with latest LibNX code; remember if you update the pacman LibNX package the changes get reversed and you need to build LibNX again.

Now is time to build the binaries
Clone the repository:

cd ~
git clone --recursive https://github.com/Atmosphere-NX/Atmosphere

now
cd Atmosphere

Copy prod.keys file on $HOME/.switch
mkdir ~/.switch
cp YOURCURRENTPATHTOKEYS ~/.switch/prod.keys
(use the path for where you placed your keys in place here)

Atmosphère is a Python 2 project, even when python 2 has been deprecated by almost 5 years now. some * insist on never update it so as far as that is going, you need to change some files in order to work on python 3, on the files:
Atmosphere\fusee\program\update_mtc_tables.py
Atmosphere\fusee\program\update_sdram_params.py
The function XRANGE must to be changed to RANGE, edit the files and change xrange(  to range( save the files and continue.

And now you are ready to start the building process:

make -j$(nproc)

I do use the "-j$(nproc)" parameter to "bleed" all the available CPU to run the compiler, without that the whole process could take up to 1 hour. Otherwise you can also just use make

I want to thank a lot to @binkinator and @godreborn for all the help and inspiration to make this guide, and want to ask you for help improving this guide.

Also special thanks to @godreborn for been a support of the users replies and suggestions to the OP.

Remember, as you are getting a new set of binaries, you need new set of sigpatches if you use it. So the great tool from @mrdude comes in hand, the latest release can be downloaded from: https://github.com/mrdude2478/IPS_Patch_Creator/releases/; you use the program to generate a new set of patches for your recently build package3 file.


Latest IPS Patch Creator:
https://gbatemp.net/download/ips-patch-creator-1-5-9.38850/
Original guide by Impeeza