Rework Initial Infections and Support Exponential Growth Initializations

[damonbayer]

Closes #116.

Requesting early feedback on my very WIP changes, since this is my first contribution, and I'm pretty inexperienced at Python, object-oriented programming, and Numpyro/JAX.

Eventually, this PR will achieve several objectives:

1. Implementation of InfectionSeedMethod of which the current only behavior (padding with 0's) will be one method, and an exponential grown initialization will be another. Must meet all specifications documented in Exponential growth model for initial infections #116.
2. Rewrite of the Infections0 class to correspond to all of the "seed" infections, rather than just the initial infections (see here). This work is currently being done in model/src/pyrenew/latent/infection_seeding_method.py.
3. Update all existing tutorials to work with the new methods.
4. Maybe: write a new tutorial relating to the seeding methods.

Much of the current PR was implemented by pattern matching existing classes and not fully understanding what I was doing. I have littered the code with questions throughout and will self-review to ask more questions.

[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 94.81%. Comparing base (f28ad47) to head (0854aee).
Report is 1 commits behind head on main.

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #124      +/-   ##
==========================================
+ Coverage   94.29%   94.81%   +0.51%     
==========================================
  Files          37       39       +2     
  Lines         771      848      +77     
==========================================
+ Hits          727      804      +77     
  Misses         44       44              

Flag	Coverage Δ
unittests	94.81% <100.00%> (+0.51%)	⬆️

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[damonbayer]

Self-reviewing to ask questions for other reviewers (or future me) to answer.

[damonbayer]

@gvegayon and I discussed all my questions over Teams. No need review the current state.

[gvegayon]

To regenerate the image, I did the following:

cd model
poetry shell
make test_images

Which runs:

poetry run pytest --mpl-generate-path=src/test/baseline

This is the "session info"

>>> import sys
>>> import platform
on version")
print(sys.version)
print("Version info.")
print(sys.version_info)

print("\nOperating s>>> import pip
ystem")
print(platform.system(), platform.release())

print("\nInstalled packages")
pip.main(['list'])>>> 
>>> print("Python version")
Python version
>>> print(sys.version)
3.10.12 (main, Nov 20 2023, 15:14:05) [GCC 11.4.0]
>>> print("Version info.")
Version info.
>>> print(sys.version_info)
sys.version_info(major=3, minor=10, micro=12, releaselevel='final', serial=0)
>>> 
>>> print("\nOperating system")

Operating system
>>> print(platform.system(), platform.release())
Linux 6.5.0-35-generic
>>> 
>>> print("\nInstalled packages")

Installed packages
>>> pip.main(['list'])
WARNING: pip is being invoked by an old script wrapper. This will fail in a future version of pip.
Please see https://github.com/pypa/pip/issues/5599 for advice on fixing the underlying issue.
To avoid this problem you can invoke Python with '-m pip' instead of running pip directly.
Package                       Version     Editable project location
----------------------------- ----------- --------------------------------------------
alabaster                     0.7.16
asttokens                     2.4.1
attrs                         23.2.0
Babel                         2.15.0
certifi                       2024.2.2
charset-normalizer            3.3.2
comm                          0.2.2
contourpy                     1.2.1
coverage                      7.5.1
cycler                        0.12.1
debugpy                       1.8.1
decorator                     5.1.1
docutils                      0.21.2
exceptiongroup                1.2.1
executing                     2.0.1
fastjsonschema                2.19.1
fonttools                     4.51.0
idna                          3.7
imagesize                     1.4.1
iniconfig                     2.0.0
ipykernel                     6.29.4
ipython                       8.24.0
jax                           0.4.27
jaxlib                        0.4.27
jedi                          0.19.1
Jinja2                        3.1.4
jsonschema                    4.22.0
jsonschema-specifications     2023.12.1
jupyter_client                8.6.1
jupyter_core                  5.7.2
kiwisolver                    1.4.5
MarkupSafe                    2.1.5
matplotlib                    3.8.4
matplotlib-inline             0.1.7
ml-dtypes                     0.4.0
multipledispatch              1.0.0
nbclient                      0.10.0
nbformat                      5.10.4
nest-asyncio                  1.6.0
numpy                         1.26.4
numpydoc                      1.7.0
numpyro                       0.13.2
opt-einsum                    3.3.0
packaging                     24.0
parso                         0.8.4
pexpect                       4.9.0
pillow                        10.3.0
pip                           24.0
platformdirs                  4.2.1
pluggy                        1.5.0
polars                        0.20.25
prompt-toolkit                3.0.43
psutil                        5.9.8
ptyprocess                    0.7.0
pure-eval                     0.2.2
Pygments                      2.18.0
pyparsing                     3.1.2
pyrenew                       0.1.0       /home/george/Documents/development/msr/model
pytest                        8.2.0
pytest-cov                    5.0.0
pytest-mpl                    0.17.0
python-dateutil               2.9.0.post0
PyYAML                        6.0.1
pyzmq                         26.0.3
referencing                   0.35.1
requests                      2.32.2
rpds-py                       0.18.1
scipy                         1.13.0
setuptools                    69.1.0
six                           1.16.0
snowballstemmer               2.2.0
Sphinx                        7.3.7
sphinxcontrib-applehelp       1.0.8
sphinxcontrib-devhelp         1.0.6
sphinxcontrib-htmlhelp        2.0.5
sphinxcontrib-jsmath          1.0.1
sphinxcontrib-qthelp          1.0.7
sphinxcontrib-serializinghtml 1.1.10
stack-data                    0.6.3
tabulate                      0.9.0
tomli                         2.0.1
tornado                       6.4
tqdm                          4.66.4
traitlets                     5.14.3
typing_extensions             4.11.0
urllib3                       2.2.1
wcwidth                       0.2.13
0
>>> 

Here is the clean code:

import sys
import platform
import pip

print("Python version")
print(sys.version)
print("Version info.")
print(sys.version_info)

print("\nOperating system")
print(platform.system(), platform.release())

print("\nInstalled packages")
pip.main(['list'])

resolved all comments