169 fixed dependency versions

[mschwoer]

Enforce fixed dependency versions, while concurrently supporting also a 'loose' install.
Consolidated and improved the installation docs.

@GeorgWa please check the versions in the requirements.txt .. also, some packages are missing there (like tqdm -> they come from some other alpha package, and maybe other could be removed (or moved to test/development requirements)?

[jalew188]

LGTM

[GeorgWa]

LGTM

[GeorgWa]

What will be the default installation method if somebody types
pip install -e . or pip install alphadia?

I think it's important that this is stable and then we should also simplify the instructions.

[GeorgWa]

Shouldn't this also be pip install -e ".[development,stable]"

[mschwoer]

I did not find a way to support two requirements files (one with fixed, one with loose versions) while concurrently supporting a default. This means that you always need to specify the installation type (stable, loose). If this is omitted, no dependencies are being installed (which should result in errors quite early in the processing ;-))

For the second comment: I deliberately chose to separate the "user" from the "developer" install instructions. The dependencies should be organized as such as that alphaDIA should run without the "development" reqs.

[GeorgWa]

Okay, I see this as quite a problem :/ can't we have a requirements.txt without suffix in the filename as fallback? Even if not perfect.

[mschwoer]

it's not about the file names, it's about this mapping in pyproject.toml

[tool.setuptools.dynamic]
# https://stackoverflow.com/a/73600610
# dependencies = {file = ["requirements/requirements.txt"]}
# no mandatory dependencies: user needs to specify "stable" or "loose" explicitly
optional-dependencies = { 
stable = { file = ["requirements/requirements.txt",] }, 
loose = { file = ["requirements/requirements_loose.txt",] }, 
test = { file = [ "requirements/requirements_test.txt",] }, 
development = { file = ["requirements/requirements_development.txt", "requirements/requirements_test.txt"
] }}

if you make the requirements.txt (with fixed versions) the default (dependencies = {file = ["requirements/requirements.txt"]}), then overriding with pip install -e .[loose] wont work.

We could try to turn it around, i.e. that pip install -e . installs loose, and "stable" must be explicitly stated.
However, I am not in favor of making "loose" the default. Can we not rely upon a user that uses "pip install" can also read off the correct commands from the Readme in case of an error? (we could also introduce a speaking error message: if e.g. alpharaw is not installed we inform about the correct way of installing via pip?)

anyway, I need to try this out first.

[GeorgWa]

LGTM

[GeorgWa]

Let's only cite the alphaRaw instructions here. I don't know why included the other instructions as they are actually not helpfull at all :D