Felipe S. S. Schneider

Bug in Gaussian parser: len(data.atommasses) != len(data.atomnos)

4

Sometimes Gaussian (09 at least) reports multiple "**Isotopes and Nuclear Properties**". Since the current parser appends from _all_ occurring sections, this leads to more atomic masses being reported than the...

Implement Extend for Vec

1

I would like to implement `Extend

[Bug]: UnboundLocalError: cannot access local variable 'x' where it is not associated with a value

6

### Bug Description `x` below is unbound in a very well defined case: https://github.com/run-llama/llama_index/blob/9859599ecc8d2f61b96c3cde7aa42c733d8c537a/llama-index-core/llama_index/core/llms/callbacks.py#L150-L172 namely, when the `for` body never runs (see reproduction below). ### Version llama-index==0.10.32 ### Steps to...

Imagine what happens when we get ``` $scheme [...] // Harmless, huh? B -> E# -> H -> L# -> M:RNH2 [...] $compounds [...] // Actually eats your brain out...

Complete type hints

2

Support for [type hints](https://docs.python.org/3.9/library/typing.html) is a plus to the future.

The bug was found while working on #416. Possibly related to #68. Failing tests are in place, but they pass since analytical Jacobian usage has been temporarily disabled (see 30a911d8324ad64871508431231c2eda339abc27).

Make [gendocs.sh](https://github.com/geem-lab/overreact/blob/main/gendocs.sh) run @ CI.

Something like using [piccolomo/plotext](https://github.com/piccolomo/plotext).

Often we want to sum concentrations among different conformational structures or solvated ones. Instead of requiring post-processing, one would only need to add some unique IDs shared among some species...

It is a common use case, most of the concentrations in a complex reaction network will be zero. So assume them zero if some are missing. https://github.com/geem-lab/overreact/blob/ae55264300b8d0e13626f8c6fb6000e16f48fa45/overreact/simulate.py#L58-L60