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Change Log

Fix/rtd dependencies (#108) by Evan Berkowitz at 2023-08-08 20:16:33

* Bump meta tag.
* requirements.txt
* readthedocs needs requirements.txt as they are deprecating the "use system packages" option.

Harmonize gases –> gasses by Evan Berkowitz at 2023-07-27 11:33:15

gitignore for readthedocs by Evan Berkowitz at 2023-07-27 10:48:45

I had my own user-wide .gitignore which was hiding all the .h5 and .pdfs
generated.  Hopefully that fixes the docs shwoing uncommited changes and
untracked files!

Feature/readthedocs (#102) by Evan Berkowitz at 2023-07-27 10:39:41
```
* readthedocs
```
Fix a few minor annoyances with the free-theory limit notebooks (#101) by Evan Berkowitz at 2023-07-26 21:36:11

Bootstrapping can compute ensemble intermediates (#100) by Evan Berkowitz at 2023-07-26 21:30:38

I tried running

docs/sanity-checks/free-theory-{continuum,infinite-volume}-limit.ipynb

and found that I couldn't compute pairing observables because the
bootstrap no longer had access to G.

G was marked @intermediate in #84, but in my trial production I was
manually storing the propagator and therefore wasn't noticing this
issue.

Intermediate quantities (typically) are not needed at the bootstrap
level, but the propagator is an exception if you try to compute pairing
matrix observables.  There's no reason I can think of, though, to make
it *disallowed* for the bootstrap to compute the intermediate if it
knows what it's doing.

Feature/first production (#97) by Evan Berkowitz at 2023-07-23 15:46:02

USABILITY
=========
* Autotuner plotting shows target.
* More readable str(Action), str(ERE)
* Log formatting is better for actual production
* Add _top argument to {to,from}_h5 to keep logs shorter.
    The issue was that the logs were very very high % i/o, even at the INFO
    level.  By adding the _top argument and setting it to False in the
    H5ableStrategy we only emit info lines when the user themselves call the
    {to,from}_h5.
* One can .measure() an ensemble's intermediates
* Detaching configurations after generator step
    That allows pytorch to free a bunch of the generator.step internals.
    In other words, don't store the whole computational graph of all of
    molecular dynamics!
* Log # when amortizing Timing
* Track down dependencies

BOOTSTRAP
=========
* Feature/better bootstrap (#96)
* @derived more closely mirrors @observable
* Bootstrap stores all computed means #95
    Because the observables were forwarded via __getattr__ and 
    was cached, the stored observables were being stored in the function cache rather
    than the object dictionary.
* Bootstrap.measure()

PHYSICS
=======
* log_kFa observable
* Squash extra dimension of condensate fractions
* Use derived_intermediate for some pairing quantities.

Forward colors in History, Scatter{Matrix,Triangle} (#92) by Evan Berkowitz at 2023-07-18 09:11:52
Derived pairing quantities cannot be intermediate. (#88) by Evan Berkowitz at 2023-07-17 14:11:01

Feature/clean up (#87) by Evan Berkowitz at 2023-07-17 14:05:38

* Substantially simplify example notebooks
* Many-body contact comparison update
 - Run on GPU if possible.
 - Use the contact_comparison from tdg.references.
 - Use autotuning.
 - Store measurements.