Frames White

[Feature] property overload Reaction.lower_bounds/upper_bounds

1

### Checklist - [X] There are [no similar issues or pull requests](https://github.com/opencobra/cobrapy/issues) for this yet. ### Problem I want it to be impossible to set a `Reaction`'s `lower_bound` and `upper_bound`...

Add ability for packages to be "unlisted" in registry

16

Idea: We should add a field in the registry for to mark packages as "unlisted". This can be applied to abandoned packages, or to packages that gave been deprecated or...

Auto block registration of packages pre-1.0

21

From [SemVer 2.0](https://semver.org/) > ### How do I know when to release 1.0.0? > If your software is being used in production, it should probably already be 1.0.0. If you...

Adopt ColPrac

1

I propose we formally adopt ColPrac for this repo we have 3 active maintainers, being myself, @quinnj and @fredrikekre so I think we are in a position to do so....

If I have a file called `foo` which is a gzipped plaintext file (for example), with no extension. And I unpack it, it will yield another file called `foo`, overwriting...

Gene YCR024C should have uniprot identifier P25345 uniprot identifier not P32903

1

I was going through the model in cobrapy and doing some sensibility checked. And I noted their were 1161 unique uniprot identifers, but 1162 unique gene ids. So i went...

Neither `word_tokenize` nor `TreebankWordTokenizer` matchs the original Penn Word Tokenizer

9

Right now, NLTK has 2 tokenizers that are very similar to Robert McIntyre's original treebank tokenizer. Those are: - `nltk.tokenize.treebank.TreebankWordTokenizer()` - a default instance of the type - and `nltk.tokenize._treebank_word_tokenizer`...

Hi, Several bugs around the handling of genes in reactions when not connected to models which were found by @jedforrest. Mostly they boil down to genes with same ID not...

[BUG] Reaction addition/subtraction is unaware of reaction direction

2

### Is there an existing issue for this? - [x] I have searched the existing issues ### Problem description I wanted to test if two reactions we the same at...

[BUG] Setting model.compartments asymmetric with getting

2

### Is there an existing issue for this? - [X] I have searched the existing issues ### Problem description I am programatically manipulating some models I thought I would set...