semvec/pypi-packages huggingface dataset:
pycube-parser 0.0.1
Parser for *.cubex files
Requires Python: >=3.5

# Parser for `cubex` files

## `cubex` file format

- `anchor.xml`
    - contains
        - `cnodes`
        - `metrics`
        - `regions`
        - `system_tree_nodes`
            - `locationgroups`
                - `locations`
- `index.0`
    - the `0` stands for the metric ID
    - contains
        - a header
            - "1"
                - a "1" encoded as a 
            - endianness
            - the number of `cnodes` in the `data.0` file
        - a list of `cnode` indices
            - `cnode_indices = [c1, c2, ...]`
- `data.0` 
    - contains
        - a header
        - data for each `cnode_id` in `cnode_indices`
            - contains metric values for all `locations`
            - to retrieve the value of a particular `cnode` with `cnode_id`, and a specific `location_id`
                - get index of `cnode_index` in `cnode_indices`
                    - = the position of the `cnode_id` in `cnode_indices`
                - offset in `data.0`: `cnode_index * num_locations + location_id`
                    - the `locations` all have incrementing `location_ids`
            - Important: the list is sorted!
                - not in the order of the XML 

## Notes

- Requires at least Python version 3.5
    - Contains `typings` as defined in [PEP 484](https://www.python.org/dev/peps/pep-0484/)
- The `cubex` files are `tar` archives
    - :warning:  ... when extracting them and parsing the extracted `0.data` files using the low-level `IndexParser`/`DataParser` directly,
    they will create strange behaviour
        - in the most cases, parsing succeeds but some edge-cases (related to endianness?) create problems
longleding-static-file-service-sdk 0.2.8
Longleding Static File Service SDK
Requires Python: >=3.6

Longleding Static File Service SDK

# Supported Python Versions

Python >= 3.6

# Installation

longleding-static-file-service-sdk is available for Linux, macOS, and Windows.

```shell script
$ pip install longleding-static-file-service-sdk
```

# Basic Usage

```python
# -*- coding: utf-8 -*-
import static_file_service
from staticFileService_pb2 import FileACLEnum

static_file_service_endpoint = "localhost:80"
static_file_service.init_service(endpoint=static_file_service_endpoint)


if __name__ == '__main__':
    test_bytes = b'test file'
    print(static_file_service.get_oss_bucket_info())
    print(static_file_service.get_upload_credentials())
    static_file_service.put_file('upload/t.txt', test_bytes)
    static_file_service.put_file_acl('upload/t.txt', FileACLEnum.PRIVATE)
    print(static_file_service.get_file('upload/t.txt'))
    print(static_file_service.get_file_md5('upload/t.txt'))
    static_file_service.copy_file('upload/t.txt', 'upload/t1.txt')
    print(static_file_service.get_file_md5('upload/t1.txt'))
    static_file_service.move_file('upload/t.txt', 'upload/t2.txt')
    print(static_file_service.get_file_md5('upload/t2.txt'))

```

# Troubleshoot

If you encounter error messages similar to the following:

```shell script
...
TypeError: Couldn't build proto file into descriptor pool!
Invalid proto descriptor for file "common.proto":
  common.proto: A file with this name is already in the pool.
```

Setting an environment variable the following before running:

```shell script
export PROTOCOL_BUFFERS_PYTHON_IMPLEMENTATION='python'
```

See also
- [[Python] A file with this name is already in the pool.](#https://github.com/protocolbuffers/protobuf/issues/3002)
- [Python Generated Code](#https://developers.google.com/protocol-buffers/docs/reference/python-generated)
transcov 1.1.3
A software for mapping coverage around transcription start sites
Requires Python: >=3.6

[![Documentation Status](https://readthedocs.org/projects/transcov/badge/?version=latest)](https://transcov.readthedocs.io/en/latest/?badge=latest) [![Build Status](https://travis-ci.org/Hogfeldt/transcov.svg?branch=master)](https://travis-ci.org/Hogfeldt/transcov)
[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/transcov/README.html)


# transcov
A bioinformatics software for mapping coverage around transcription start sites

For information on how it works and how to install and use. Please refer to the documentation, which can be found on [Read The Docs](https://transcov.readthedocs.io/en/stable/index.html).