MultiCSV

Python library multicsv is designed for handling multi-CSV format files. It provides an interface for reading, writing, and manipulating sections of a CSV file as individual text file objects.

Key Features

• Efficient Section Management: Read and write multiple independent sections within a single CSV file.
• TextIO Interface: Sections are treated as TextIO objects, enabling familiar file operations.
• Flexible Operations: Supports reading, writing, iterating, and deleting sections.
• Context Management: Ensures resource safety with with statement compatibility.
• Integrated Testing: Includes comprehensive unit tests, covering 100% of the functionality.

The Multi-CSV Format

The multi-CSV format is an extension of the traditional CSV (Comma-Separated Values) format that supports dividing a single file into multiple independent sections. Each section is demarcated by a header enclosed in square brackets, e.g., [section_name]. This format is commonly known for usage in Illumina-MiSeq sample sheet files.

Conceptually, this file format provides the ability to store a whole SQL database in a single, human readable file.

Example

Here's a simplified example of a multi-CSV file:

[section1]
header1,header2,header3
value1,value2,value3

[section2]
headerA,headerB,headerC
valueA,valueB,valueC

In the example above, the file contains two sections: section1 and section2. Each section has its own headers and rows of data.

Usage

Here's a quick example of how to use the multicsv library:

import csv
import multicsv

with multicsv.open('example.csv', mode='w+') as csv_file:
    # Write the CSV content to the file
    csv_file.section('section1').write("header1,header2,header3\nvalue1,value2,value3\n")
    csv_file.section('section2').write("header4,header5,header6\nvalue4,value5,value6\n")

    # Read a section using the csv module
    csv_reader = csv.reader(csv_file['section1'])
    assert list(csv_reader) == [['header1', 'header2', 'header3'],
                                ['value1', 'value2', 'value3']]

There are only two methods exported in multicsv: open and wrap. This is how the latter one is meant to be used:

import io
import multicsv

# Initialize the MultiCSVFile with a base CSV string
csv_content = io.StringIO("""\
[section1]
a,b,c
1,2,3
[section2]
d,e,f
4,5,6
""")

csv_file = multicsv.wrap(csv_content)

# Accessing a section
section1 = csv_file["section1"]
print(section1.read())  # Outputs: "a,b,c\n1,2,3\n"

# Adding a new section
new_section = io.StringIO("g,h,i\n7,8,9\n")
csv_file["section3"] = new_section
csv_file.flush()

# Verify the new section is added
csv_content.seek(0)
print(csv_content.read())
# Outputs:
# [section1]
# a,b,c
# 1,2,3
# [section2]
# d,e,f
# 4,5,6
# [section3]
# g,h,i
# 7,8,9

Both exported methods return a MultiCSVFile object. Objects of that class are MutableMappings from names of sections (: str) to contents of sections (: TextIO).

So, for instance, this is how to print all sections in a multi-csv file:

import multicsv

for section in multicsv.open("example.csv"):
    print(section)

Installation

Install the library using pip:

pip install multicsv

Development

Setting Up

Set up your environment for development as follows:

1. Clone the repository:

   git clone https://github.com/cfe-lab/multicsv.git
   

2. Navigate to the project directory:

   cd multicsv
   

3. Create a virtual environment:

   python3 -m venv venv
   source venv/bin/activate
   

4. Install dependencies:

   pip install -e .[dev,test]
   

Running Tests

Run the test suite to ensure everything is functioning correctly:

pytest

Contributing

Contributions are welcome! Please follow these steps for contributions:

1. Fork the repository.
2. Create a new branch with a descriptive name.
3. Make your changes and ensure the test suite passes.
4. Open a pull request with a clear description of what you've done.

License

This project is licensed under the GPL-3.0 License - see the LICENSE file for details.