semvec/pypi-packages huggingface dataset:
pbalancing 3.0.0a1
Parameter balancing of metabolic models in systems biology
License: MIT
Requires Python: >=3.8
Keywords: parameter balancing,bayesian inference,multivariate Gaussian distribution

# Parameter Balancing: Standalone Version

Parameter balancing is a tool for metabolic modeling in systems biology. It is implemented in Python and its code underlies the PEP8 guidelines. It can either be downloaded and used from command-line as is or embedded in your own Python3 projects. In both cases, you will be required to install Python packages to make the scripts work.

## Parameter balancing on the command-line

Parameter balancing can be employed on the command-line by
```bash
python -m scripts.parameter_balancing.py model.xml
```

where `model.xml` corresponds to the path of your SBML model. It is also possible to provide further input files, such as
an SBtab parameter files (`.tsv`), an SBtab prior information file (`.tsv`), and an SBtab options file (`.tsv`) for the
configuration of parameter balancing. Providing complete file information would look like this:

```bash
python -m scripts.parameter_balancing.py model.xml --sbtab_data data_file.tsv --sbtab_prior prior_file.tsv --sbtab_options options_file.tsv
```

You can create a log file by setting the flag -l, you can use pseudo values to account for a lack of data by setting the flag -p, you can watch program outputs on your command-line by setting the flag -v. Information on the SBtab format can be found on `www.sbtab.net`, more information on the mentioned file types can be found in the parameter balancing manual in this repository's `examples/pb_manual.pdf`, and example files can be found in `examples/example_files/`.

## Embedding parameter balancing in your Python package

You can also embed the modules of parameter balancing in your own Python workflow.

```python
from pbalancing import parameter_balancing_wrapper

balanced_sbml, balanced_sbtab = parameter_balancing_wrapper(
  sbml,
  sbtab_data,
  sbtab_prior,
  sbtab_options,
  verbose,
  no_pseudo_values,
  output_name,
  pb_log
)
```

### Input arguments
  - `sbml` - path to SBML file, REQUIRED)
  - `sbtab_data` - path to SBtab data file (OPTIONAL)
  - `sbtab_prior` - path to SBtab prior file (OPTIONAL)
  - `sbtab_options` - path to SBtab options file (OPTIONAL)
  - `verbose` - Boolean, enable messages on command-line (OPTIONAL)
  - `no_pseudo_values` - Boolean, disable usage of pseudo values (OPTIONAL)
  - `output_name` - name for the output files (OPTIONAL)
  - `pb_log` - Boolean, enable writing of a log file (OPTIONAL)

### Output parameters
  - `balanced_sbml` - SBML file object with balanced content
  - `balanced_sbtab` - SBtab object with balanced content

## Citation and Contact

If you use parameter balancing, please cite http://pubs.acs.org/doi/abs/10.1021/jp108764b for details.

If you are encountering trouble with any of the above, please file a bug report in GitLab. You can also feel free to file feature requests in the same manner.
gitflic 1.1
GitflicApi wrapper
License: MIT
Requires Python: >=3.7

# gitflic

<p align="center">
    <a href="https://github.com/SantaSpeen/gitflic/blob/master/LICENSE"><img alt="GitHub license" src="https://img.shields.io/github/license/SantaSpeen/gitflic?style=for-the-badge"></a>    
    <a href="https://github.com/SantaSpeen/gitflic/stargazers"><img alt="GitHub stars" src="https://img.shields.io/github/stars/SantaSpeen/gitflic?style=for-the-badge"></a>    
    <a href="https://github.com/SantaSpeen"><img src="https://img.santaspeen.ru/github/magic.svg" alt="magic"></a>
    <br/>
    <a href="examples/reg_call.py">
        <img src="https://img.santaspeen.ru/github/gitflic/preview.png" alt="preview">
    </a>
    <br/>
</p>

### About 

[![PyPI download month](https://img.shields.io/pypi/dm/gitflic.svg)](https://pypi.python.org/pypi/gitflic/)
[![PyPI download week](https://img.shields.io/pypi/dd/gitflic.svg)](https://pypi.python.org/pypi/gitflic/)

This is wrapper of gitflic API.\
All API documentation is here: https://gitflic.ru/help/api/intro

### Installation

Install via pip:

`pip install gitflic`

### Example:

All examples in [examples](./examples) dir.

```python
from gitflic import Gitflic, GitflicAuth

# Your authentication token.
# See: https://gitflic.ru/settings/oauth/token/create
token = "token_here"  

# Creating authorized session with our token.
gf_session = GitflicAuth(token)
gf = Gitflic(gf_session)


# Call method to get authorized user from API.
user_me = gf.call("/user/me")
print(user_me)
```