semvec/pypi-packages huggingface dataset:
sbmlsh 0.0.4
SBML-shorthand conversion tools
Requires Python: >=3.8

# sbmlsh - SBML-shorthand

This page describes a "shorthand" version of [SBML](http://sbml.org/)
that is much easier to read and write by hand than real SBML, together
with a software tool that translates the shorthand model description to
real SBML.

It isn't really meant as a complete alternative to GUI model-building
tools. It is just a useful tool for rapid building of essential model
structure. Once the basics are defined, you can translate to SBML and
load up in the GUI tool of your choice.

### Example

The following is a complete description of a simple enzyme-kinetics
model using the shorthand notation.

    @model:2.3.1=MichaelisMentenKinetics "Michaelis-Menten Kinetics"
    @compartments
     cell=1
    @species
     cell:Substrate=1000
     cell:Enzyme=100
     cell:Complex=0
     cell:Product=0
    @parameters
     k1=1
     k1r=2
    @reactions
    @rr=SubstrateEnzymeBinding "Substrate-enzyme binding"
     Substrate+Enzyme -> Complex
     k1*Substrate*Enzyme-k1r*Complex
    @r=Conversion
     Complex -> Product + Enzyme
     k2*Complex : k2=3

You can download this example: [mm.mod](https://github.com/darrenjw/sbml-sh/blob/master/mm.mod). Using the translation
tool below, this model translates to [this SBML](https://github.com/darrenjw/sbml-sh/blob/master/mm.xml).

### Latest SBML-shorthand specification

-   SBML-shorthand specification, version 3.1.1
    ([PDF](https://github.com/darrenjw/sbml-sh/blob/master/spec/sbml-sh.pdf)) - targeted at SBML Level 3, Version 1.


## Python package containing conversion tools

```bash
pip install sbmlsh
```

### mod2sbml model translation script

-   mod2sbml documentation
    ([PDF](https://github.com/darrenjw/sbml-sh/blob/master/doc/mod2sbml.pdf)) (version 3.1.1.1), which is targeted
    at SBML-shorthand version 3.1.1, *and all previous versions*.

### sbml2mod reverse translation script

-   sbml2mod (version 3.1.1.1) is the reverse
    translation tool for Level 3, version 1 and all previous versions.


Obviously, as the shorthand specification does not contain all SBML
features, there is likely to be loss involved. However, there should be
no semantic loss in the round-trip SBML-sh -\> SBML -\> SBML-sh. ie.
doing a `mod2sbml` conversion followed by a `sbml2mod` conversion
should get back to a shorthand file that is semantically equivalent to
the original.
lectric-sdk 0.0.47
Lectric client
Keywords: lectric, vdb, vector database

# Lectric Software Development Kit (SDK)

Programmatic access to the lectric vector database service.

## Installation

The SDK is exposed as a simple python package. There are two main ways it can be installed.

## Developers

Clone the git repo and install from source:

First clone the repo from [here](https://dev.azure.com/msresearch/WatchFor/_git/lectric), then
```
cd lectric/client
python -m pip install -U -r requirements-dev.txt
python setup.py install
```

### Generating the client

`pipx install openapi-python-client --include-deps`

This will create the `openapi-python-client.exe` executable and its dependencies.

### Running the tests

In order to run the client (SDK) tests a server running on `http://localhost:8000`, with an appropriate `lectric_config.yaml` exported as
an environment variable.

```
cd tests
python -m pytest -s .
```


### Modifying the SDK

The main wrapper to the auto-generated client is located within `lectric/lectric_client.py`.
To refresh/recreate the auto-generated client library. Make sure to run the `uvicorn` fastapi sever from at port `8000`:
```
uvicorn main:app --reload
```

,then generate the client.

```
./generate.sh
```

## General Users

We highly recommend installing Lectric within a virtual environment to avoid package
versioning mismatches. For `Python 3.6+`

### Mac/Linux

```
python -m venv lectric-env
source lectric-env/Scripts/activate
```

### Windows

```
python -m venv lectric-env
./lectric-env/Scripts/Activate.ps1
```


Then install from our WatchFor PyPI registry as follows:

```
pip install --index-url https://pkgs.dev.azure.com/watchfor/WatchForTools/_packaging/w4Tools/pypi/simple/ watchfor-lectric-sdk==<VERSION>
```

Where `<VERSION>` is your desired version (at the time of edit `0.0.3`).


## Checking Installation

Simply run:

```
import lectric
print(lectric.version()) # Should return a string with the version you installed
```

## Documentation

HTML docs are maintained within `docs/build/html`. To review docs open `index.html` within any browser.

## Building the docs

Install the sphinx on the system as per the instructions [here](https://www.sphinx-doc.org/en/master/usage/installation.html).
A few examples are:
**Windows**: `choco install sphinx`
**Ubuntu**: `apt-get install python3-sphinx`
This should put `sphinx-build` on the path.

Then within `docs` run `make html`, for html docs.

## Uploading the new version
Go to https://dev.azure.com/watchfor/WatchForTools/_artifacts/feed/w4Tools/connect and go to the twine section. Copy and paste the .pypirc into ~/.pypirc and make sure to follow the 'Get the tools' instruction (aka downloading twine and key ring)