Develop Reference

What is the best way to make a clean reinstall of Python on Windows?

I tried to update Python 3.8.5. to 3.8.10 on a Windows 7 machine, but some part of Python's and/or pip's messy installer/path/package management system bricked everything. Nobody I asked knows a canonical solution to this + pretty much everybody is suggesting a complete reinstallation.
Which is why I've now completely removed Python and have to reinstall Python, pip, and all my packages one by one. I've already uninstalled/removed Python and pip and downloaded the official Python 3.8.10 64-bit Windows installer as well as get-pip.py.
But despite spending days and days of reading, I can't see through Python's complicated mess of "user-specific vs. local vs. system-wide" installation schemes, varying package installations paths, the seemingly arbitrary variations introduced by using python vs. python -m, pip install vs. pip install --user etc. during package installations, and the regular whining about some PATH environment variables not being set properly etc. pp. - if you've ever used Python professionally, you'll have an idea of what I'm describing here.
Anyway - what I want to do now is make one clean installation where I stick to one set of rules for everything. All packages installed to one single superdirectory (vs. getting scattered all over the system) and all PATH variables set accordingly to the most universal and complete configuration possible (I don't want to see any complaints from Python ever again in this regard). Note that I'm the administrator of the machine, but working from a normal user account with Windows UAC enabled and want an installation for all users - the most general solution possible, no limiting scenarios that may cause the very problems I'm trying to avoid.
Also, I do not want to use virtual environments for now, but this is different topic I'm already working on independently. So no suggestions regarding venv.
Question: How to procede with the installation?
Possible sub-issues that need to be addressed:
Correct privileges for the Windows installer, e.g. the confusing "for all users (requires elevation)" and subsequent (second!) "Install for all users" options. The latter changes the installation path from C:\Users\<Username>\AppData\Local\Programs\Python\Python38 to C:\Program Files\Python38 and Windows UAC may prevent access of Python and/or pip to C:\Program Files\ without proper exception handling (e.g. user prompt) in place:
Usage of get-pip.py vs. some other methods to install pip, which also concerns the usage of python vs. python -m vs. pip install vs. pip install --user etc. in this context and subsequent installation of user packages.
Prevention of scattering/fragmentation of the Python development framework over the system/different folders/different users, causing e.g. annoying PATH or dependency issues/conflicts.
Defining the correct set of Windows path variables under these requirements and addressing concerns/doubts about Python's and pip's ability of reliably handling this issue on their own.
Note: I'm the owner/only user on this machine and therefore have administrator rights. Managing installations/environments for multiple users is not the subject here and of no interest for me.

Anyway - what I want to do now is make one clean installation where I stick to one set of rules for everything. All packages installed to one single superdirectory (vs. getting scattered all over the system) and all PATH variables set accordingly to the most universal and complete configuration possible (I don't want to see any complaints from Python ever again in this regard).
This is contradictory. A single installation with a common set of rules, every possible installed package, comprehensive PATH etc. is inherently not "clean". The point of maintaining separate installations is so that one user's changes do not unexpectedly impact on the operation of another user's code. It is not possible to do this with a single installation. If you upgrade a library, for example, it affects every user who wrote code that uses that library, who must now check for incompatibilities.
Correct privileges for the Windows installer, e.g. the confusing "for all users (requires elevation)" and subsequent (second!) "Install for all users" options.
The first one means "Install the launcher for all users", which is why that checkbox is on the same line as "py launcher". (If you are not familiar with the Python launcher for Windows, please read the documentation.) it says "(requires elevation)" because the installer requires elevation in order to install this feature for all users. You do not need to do this if you have installed it from a previous version of Python.
and subsequent (second!) "Install for all users" options.
This is the option to install this version of Python for all users. The install directory changes according to the "for all users" setting, in the expected way.
Windows UAC may prevent access of Python and/or pip to C:\Program Files\ without proper exception handling (e.g. user prompt) in place
It will prevent write access without elevation, yes. This is by design, and it is why the option exists for per-user installations.
pip requires write access, because its purpose is to install libraries. I do not know whether it can request elevation from the command prompt; probably not. You can work around this by using the command in an elevated command window. With UAC enabled, you will not be able to install libraries into a Python for-all-users installation (i.e., in Program Files): it is the explicit purpose of UAC to prevent that sort of thing.
Python normally does not require write access to these directories. The standard library does not need write access once the library is installed. There might be a problem if you uncheck "Precompile standard libraries"; I have not tested this and have stopped using Windows. Third-party libraries normally will not require write access for their own installation directories, either. If you encounter a problem, consult the documentation for that library.
Usage of get-pip.py vs. some other methods to install pip, which also concerns the usage of python vs. python -m vs. pip install vs. pip install --user etc. in this context and subsequent installation of user packages.
get-pip etc. are deprecated. They are tools intended to account for the fact that Python didn't always come bundled with pip. It does now. pip works the same way regardless of whether it was bundled with Python or installed to an older Python version separately. There is not a clear question here; there are several specific things that need to be researched and understood about how to use pip.

How to manage python project that depends on multiple versions of a shared library?

I am on macOS, using brew, pyenv, and virtualenv.
I have a Python project that depends on bokeh and gdal (both python packages were installed with pip inside a virtual environment). Both bokeh and gdal depend on a system version of libopenssl, but they depend on different versions (1.0 and 1.1).
I have had this project working at various points in the past, with some combination of libraries (using pip for all python packages and brew for system packages) but when I change python versions and environments (using pyenv) to work on other projects, and then come back to this project, it no longer works. Usually something along these lines with a problem finding a shared library for openssl:
$ ./my_python_program.py
...
ImportError: dlopen(/Users/userBob/.pyenv/versions/3.7.0/lib/python3.7/lib-dynload/_ssl.cpython-37m-darwin.so, 2):
Library not loaded: /usr/local/opt/openssl#1.1/lib/libssl.1.1.dylib
Referenced from: /Users/userBob/.pyenv/versions/3.7.0/lib/python3.7/lib-dynload/_ssl.cpython-37m-darwin.so
Reason: image not found
I feel like I am eventually able to get things to work by trying random combinations of installing and uninstalling various package versions using pip and brew. But this is a fragile and inefficient way to maintain my projects.
In general what is the best way to handle this kind of situation? Do I need to simply record the exact brew and pip install/uninstall commands to get it working? Am I missing the concept of version "pinning"? Are there additional options with brew and pyenv that I am missing that might make this process easier?

I'm not sure this is the best way to do it, but I can tell you what I do usually.
First of all, I'm using Anaconda.
When I'm on a project, I switch to the relevant virtual environment.
Before switching out, when I commit/push my modifications, I also create an export file of my environment like you can find it there.
I also track this file with git, this way, if I make any modification when working on the environment, it's stored in the .yml file.
This way, I can reinstall all dependencies needed for the project if I format my machine or get a new one, etc. And the reference for every dependency I need is stored in the cloud with my sources. So in case I start getting weird behaviour, I just restore my environment with this reference file from the time when it was working.
I'm not switching between projects fast enough for me to justify automatizing this process, but I'm sure that's feasible if you want to.

How do I replace my Homebrew based Python configuration with Conda

I currently have a rather complex Python configuration that has evolved over the years, and I'd like to clean it up and "modernize" it.
The existing configuration has a the default macOS Python, and Homebrew's Python 3 and Python 2 all existing side-by-side, along with their associated Pips. I also have some python command line tools that these Pythons or their associated installed packages have created, and which I use more or less frequently.
What I'd like to do is:
Leave macOS Python untouched
Eliminate all Homebrew Python's
Remove non-macOS Python 2 entirely
Switch to Conda Python as my Python 3
Have access to mkvirtualenv (as an alternative to creating environments) with virtualenvwrapper
Have access to Jupyter
I'm not sure how to do this without creating problems, and want to confirm that the obvious thing is the safe thing:
use Homebrew to uninstall its Pythons,
install Conada, and then
use (Conda's) pip to install mkvirtualenv, virtualenvwrapper, and Jupyter (and any other tools I subsequently need)
Is that the correct procedure? Is so are there particular forms of the commands I should use or options I should chose for them?

The biggest and/or first issue is how to not break existing functionality that relies on Python. There are two broad camps here:
1) tools and other scripts that hard-code the Python executable's location, and
2) tools and other scripts that rely on the/a system PATH variable.
#1 is the easier one. If you aren't going to remove any Python versions, then these are no work at all...these will keep working. If you do want to uninstall some Python versions, then you have to work to switch any tools relying on those versions you want to remove to another version that also works for that tool. The path in question is commonly in a shebang ('#! xxx') line at the top of each main Python binary, but there are other ways that the path to the Python binary can be formed. In short, why uninstall anything? Disk space is cheap. Maybe instead just make sure that these unwanted versions are not referenced by any PATH variables.
#2 is the hard one. It isn't necessarily the case that all of the tools in this category are using the version of Python you get when you just type "python" at a command prompt for your primary account. There can be other modes of operation that initialize the execution environment (the PATH variable) in different ways, and so may be running different Python versions despite depending on the value of PATH.
Part of #2 is worrying about not just "python" references, but "python2", "python3", and possibly other variants as well.
Only once you've got a plan for dealing with the above so you don't break things can you worry about possibly getting rid of Python versions and installing new ones. Hopefully, Brew does a good job of uninstalling the versions it's installed, so if you can remove dependencies on one or more of them, they can potentially be easily removed. If you've got self-installed Python versions, those should be easy to uninstall as well by just removing references to them in PATH variables (or not...shouldn't be a big problem if you miss some) and then deleting the install directory.
Then there's adding the new version(s) of Python. This can only affect #2 above. You have to think about that one and know what affect you're going to have if the new install(s) manipulate any PATH variables. If it only manipulates your own user's PATH, or it leaves it to you to do so, this is a much easier to understand task, but any change to the environment is a chance to break existing functionality.
Finally, there's the mechanisms for choosing different Python versions for new development, including the use of virtual envs. This is probably the easiest part, as you can do research, try things, and test that you can do whatever you want to do. This part of the problem is the best bounded.
I don't know anything about Jupyter, other than knowing vaguely what it is, so I don't know how that complicates all this.
UPDATE: A final note. As you may already know, Python does a good job of isolating itself in terms of each version keeping its unique identity. If you use the right 'pip' and 'easy_install' that are sitting right next to the 'python' binary you're going to run with, you should be cleanly affecting just that one environment. I can't know that it's this easy for all Python versions, but I've never seen this convention broken by a version of Python that I've used. The complications here, of course, involve which versions of these tools you're getting in various situations when they are found via a PATH variable.

First, install anaconda or miniconda. The installation is non-destructive and does not conflict with your other Python installations. Check that it works before you consider removing homebrew installed Pythons.
The conda command is used both as a package manager and as an environment manager. You cannot avoid creating conda environments: the default installation is already part of an environment named base. I'm not sure why you would want to, either.
You can use pip to install any package you choose into a conda environment, but since you can use conda install for any package available on any conda channel (e.g. 'defaults', 'conda-forge'), using pip often is redundant.
You could use non-conda virtual environments, but again: why? conda create -n foo python=x.x jupyter #etc and then conda activate foo is all you need to get one up and running.

/usr/bin/python vs /usr/local/bin/python

On Linux, specifically Debian Jessie, should I use /usr/bin/python or should I install another copy in /usr/local/bin?
I understand that the former is the system version and that it can change when the operating system is updated. This would mean that I can update the version in the latter independently of the OS. As I am already using python 3, I don't see what significant practical difference that would make.
Are there other reasons to use a local version?
(I know there are ~42 SO questions about how to change between version, but I can't find any about why)

I don't think I'd recommend either of these approaches, and simply would stick to a virtualenv to further isolate Python instances.
The biggest reason that you'd use a specific Python environment - be it the system, a local one, or a virtualenv - would be control. The more control you have over the environment and what gets installed in it, the less surface area you have to find or encounter bugs due to libraries which you didn't realize you introduced. If it's a virtualenv, that also makes cleanup easier; just delete the virtualenv when you no longer need it as opposed to trying to uninstall libraries installed at the system level.
Not just that, but more and more distros are converting their scripts to use Python 3. The less stomping around you do in that environment, the better.
Finally - just as a generic Shell scripting tip - I'd also encourage the use of /usr/bin/env python to ensure that you're using the version of Python that's most prominent on your PATH.

1) You should not modify the system's binaries yourself directly
2) If your $PATH variable doesn't contain /usr/local/bin, the naming of that secondary directory isn't really important. You can install / upgrade independently wherever you have installed your extra binaries.
3) For Python specifically, you could also just use conda / virtualenv invoked by your system's python to manage your versions & projects.

Is there a way to "version" my python distribution?

I'm working by myself right now, but am looking at ways to scale my operation.
I'd like to find an easy way to version my Python distribution, so that I can recreate it very easily. Is there a tool to do this? Or can I add /usr/local/lib/python2.7/site-packages/ (or whatever) to an svn repo? This doesn't solve the problems with PATHs, but I can always write a script to alter the path. Ideally, the solution would be to build my Python env in a VM, and then hand copies of the VM out.
How have other people solved this?

virtualenv + requirements.txt are your friend.
You can create several virtual python installs for your projects, everything containing exactly those library versions you need (Tip: pip freeze spits out a requirements.txt with the exact library versions).
Find a good reference to virtualenv here: http://simononsoftware.com/virtualenv-tutorial/ (it's from this question Comprehensive beginner's virtualenv tutorial?).
Alternatively, if you just want to distribute your code together with libraries, PyInstaller is worth a try. You can package everything together in a static executable - you don't even have to install the software afterwards.

You want to use virtualenv. It lets you create an application(s) specific directory for installed packages. You can also use pip to generate and build a requirements.txt

For the same goal, i.e. having the exact same Python distribution as my colleagues, I tried to create a virtual environment in a network drive, so that everybody of us would be able to use it, without anybody making his local copy.
The idea was to share the same packages installed in a shared folder.
Outcome: Python run so unbearably slow that it could not be used. Also installing a package was very very sluggish.
So it looks there is no other way than using virtualenv and a requirements file. (Even if unfortunately often it does not always work smoothly on Windows and it requires manual installation of some packages and dependencies, at least at this time of writing.)