pcsv 1.0.8

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Description

This module can be used to handle comma-separated values (CSV) files and do lightweight processing of their data with support for row and column filtering. In addition to basic read, write and data replacement, files can be concatenated, merged, and sorted

Examples

Read/write

# pcsv_example_1.py
import pmisc, pcsv

def main():
    with pmisc.TmpFile() as fname:
        ref_data = [["Item", "Cost"], [1, 9.99], [2, 10000], [3, 0.10]]
        # Write reference data to a file
        pcsv.write(fname, ref_data, append=False)
        # Read the data back
        obj = pcsv.CsvFile(fname)
    # After the object creation the I/O is done,
    # can safely remove file (exit context manager)
    # Check that data read is correct
    assert obj.header() == ref_data[0]
    assert obj.data() == ref_data[1:]
    # Add a simple row filter, only look at rows that have
    # values 1 and 3 in the "Items" column
    obj.rfilter = {"Item": [1, 3]}
    assert obj.data(filtered=True) == [ref_data[1], ref_data[3]]

if __name__ == "__main__":
    main()

Replace data

# pcsv_example_2.py
import pmisc, pcsv

def main():
    ctx = pmisc.TmpFile
    with ctx() as fname1:
        with ctx() as fname2:
            with ctx() as ofname:
                # Create first (input) data file
                input_data = [["Item", "Cost"], [1, 9.99], [2, 10000], [3, 0.10]]
                pcsv.write(fname1, input_data, append=False)
                # Create second (replacement) data file
                replacement_data = [
                    ["Staff", "Rate", "Days"],
                    ["Joe", 10, "Sunday"],
                    ["Sue", 20, "Thursday"],
                    ["Pat", 15, "Tuesday"],
                ]
                pcsv.write(fname2, replacement_data, append=False)
                # Replace "Cost" column of input file with "Rate" column
                # of replacement file for "Items" 2 and 3 with "Staff" data
                # from Joe and Pat. Save resulting data to another file
                pcsv.replace(
                    fname1=fname1,
                    dfilter1=("Cost", {"Item": [1, 3]}),
                    fname2=fname2,
                    dfilter2=("Rate", {"Staff": ["Joe", "Pat"]}),
                    ofname=ofname,
                )
                # Verify that resulting file is correct
                ref_data = [["Item", "Cost"], [1, 10], [2, 10000], [3, 15]]
                obj = pcsv.CsvFile(ofname)
                assert obj.header() == ref_data[0]
                assert obj.data() == ref_data[1:]

if __name__ == "__main__":
    main()

Concatenate two files

# pcsv_example_3.py
import pmisc, pcsv

def main():
    ctx = pmisc.TmpFile
    with ctx() as fname1:
        with ctx() as fname2:
            with ctx() as ofname:
                # Create first data file
                data1 = [[1, 9.99], [2, 10000], [3, 0.10]]
                pcsv.write(fname1, data1, append=False)
                # Create second data file
                data2 = [
                    ["Joe", 10, "Sunday"],
                    ["Sue", 20, "Thursday"],
                    ["Pat", 15, "Tuesday"],
                ]
                pcsv.write(fname2, data2, append=False)
                # Concatenate file1 and file2. Filter out
                # second column of file2
                pcsv.concatenate(
                    fname1=fname1,
                    fname2=fname2,
                    has_header1=False,
                    has_header2=False,
                    dfilter2=[0, 2],
                    ofname=ofname,
                    ocols=["D1", "D2"],
                )
                # Verify that resulting file is correct
                ref_data = [
                    ["D1", "D2"],
                    [1, 9.99],
                    [2, 10000],
                    [3, 0.10],
                    ["Joe", "Sunday"],
                    ["Sue", "Thursday"],
                    ["Pat", "Tuesday"],
                ]
                obj = pcsv.CsvFile(ofname)
                assert obj.header() == ref_data[0]
                assert obj.data() == ref_data[1:]

if __name__ == "__main__":
    main()

Merge two files

# pcsv_example_4.py
import pmisc, pcsv

def main():
    ctx = pmisc.TmpFile
    with ctx() as fname1:
        with ctx() as fname2:
            with ctx() as ofname:
                # Create first data file
                data1 = [[1, 9.99], [2, 10000], [3, 0.10]]
                pcsv.write(fname1, data1, append=False)
                # Create second data file
                data2 = [
                    ["Joe", 10, "Sunday"],
                    ["Sue", 20, "Thursday"],
                    ["Pat", 15, "Tuesday"],
                ]
                pcsv.write(fname2, data2, append=False)
                # Merge file1 and file2
                pcsv.merge(
                    fname1=fname1,
                    has_header1=False,
                    fname2=fname2,
                    has_header2=False,
                    ofname=ofname,
                )
                # Verify that resulting file is correct
                ref_data = [
                    [1, 9.99, "Joe", 10, "Sunday"],
                    [2, 10000, "Sue", 20, "Thursday"],
                    [3, 0.10, "Pat", 15, "Tuesday"],
                ]
                obj = pcsv.CsvFile(ofname, has_header=False)
                assert obj.header() == list(range(0, 5))
                assert obj.data() == ref_data

if __name__ == "__main__":
    main()

Sort a file

# pcsv_example_5.py
import pmisc, pcsv

def main():
    ctx = pmisc.TmpFile
    with ctx() as ifname:
        with ctx() as ofname:
            # Create first data file
            data = [
                ["Ctrl", "Ref", "Result"],
                [1, 3, 10],
                [1, 4, 20],
                [2, 4, 30],
                [2, 5, 40],
                [3, 5, 50],
            ]
            pcsv.write(ifname, data, append=False)
            # Sort
            pcsv.dsort(
                fname=ifname,
                order=[{"Ctrl": "D"}, {"Ref": "A"}],
                has_header=True,
                ofname=ofname,
            )
            # Verify that resulting file is correct
            ref_data = [[3, 5, 50], [2, 4, 30], [2, 5, 40], [1, 3, 10], [1, 4, 20]]
            obj = pcsv.CsvFile(ofname, has_header=True)
            assert obj.header() == ["Ctrl", "Ref", "Result"]
            assert obj.data() == ref_data

if __name__ == "__main__":
    main()

Interpreter

The package has been developed and tested with Python 2.7, 3.5, 3.6 and 3.7 under Linux (Debian, Ubuntu), Apple macOS and Microsoft Windows

Installing

$ pip install pcsv

Documentation

Available at Read the Docs

Contributing

1. Abide by the adopted code of conduct

2. Fork the repository from GitHub and then clone personal copy [1]:

   $ github_user=myname
   $ git clone --recurse-submodules \
         https://github.com/"${github_user}"/pcsv.git
   Cloning into 'pcsv'...
   ...
   $ cd pcsv || exit 1
   $ export PCSV_DIR=${PWD}
   $

3. The package uses two sub-modules: a set of custom Pylint plugins to help with some areas of code quality and consistency (under the pylint_plugins directory), and a lightweight package management framework (under the pypkg directory). Additionally, the pre-commit framework is used to perform various pre-commit code quality and consistency checks. To enable the pre-commit hooks:

   $ cd "${PCSV_DIR}" || exit 1
   $ pre-commit install
   pre-commit installed at .../pcsv/.git/hooks/pre-commit
   $

4. Ensure that the Python interpreter can find the package modules (update the $PYTHONPATH environment variable, or use sys.paths(), etc.)

   $ export PYTHONPATH=${PYTHONPATH}:${PCSV_DIR}
   $

5. Install the dependencies (if needed, done automatically by pip):

   • Cog (2.5.1 or newer)

   • Coverage (4.5.3 or newer)

   • Docutils (0.14 or newer)

   • Inline Syntax Highlight Sphinx Extension (0.2 or newer)

   • Mock (Python 2.x only, 2.0.0 or newer)

   • Pexdoc (1.1.4 or newer)

   • Pmisc (1.5.8 or newer)

   • Py.test (4.3.1 or newer)

   • PyContracts (1.8.2 or newer)

   • Pydocstyle (3.0.0 or newer)

   • Pylint (Python 2.x: 1.9.4 or newer, Python 3.x: 2.3.1 or newer)

   • Pytest-coverage (2.6.1 or newer)

   • Pytest-pmisc (1.0.7 or newer)

   • Pytest-xdist (optional, 1.26.1 or newer)

   • ReadTheDocs Sphinx theme (0.4.3 or newer)

   • Shellcheck Linter Sphinx Extension (1.0.8 or newer)

   • Sphinx (1.8.5 or newer)

   • Tox (3.7.0 or newer)

   • Virtualenv (16.4.3 or newer)

6. Implement a new feature or fix a bug

7. Write a unit test which shows that the contributed code works as expected. Run the package tests to ensure that the bug fix or new feature does not have adverse side effects. If possible achieve 100% code and branch coverage of the contribution. Thorough package validation can be done via Tox and Pytest:

   $ PKG_NAME=pcsv tox
   GLOB sdist-make: .../pcsv/setup.py
   py27-pkg create: .../pcsv/.tox/py27
   py27-pkg installdeps: -r.../pcsv/requirements/tests_py27.pip, -r.../pcsv/requirements/docs_py27.pip
   ...
     py27-pkg: commands succeeded
     py35-pkg: commands succeeded
     py36-pkg: commands succeeded
     py37-pkg: commands succeeded
     congratulations :)
   $

   Setuptools can also be used (Tox is configured as its virtual environment manager):

   $ PKG_NAME=pcsv python setup.py tests
   running tests
   running egg_info
   writing pcsv.egg-info/PKG-INFO
   writing dependency_links to pcsv.egg-info/dependency_links.txt
   writing requirements to pcsv.egg-info/requires.txt
   ...
     py27-pkg: commands succeeded
     py35-pkg: commands succeeded
     py36-pkg: commands succeeded
     py37-pkg: commands succeeded
     congratulations :)
   $

   Tox (or Setuptools via Tox) runs with the following default environments: py27-pkg, py35-pkg, py36-pkg and py37-pkg [3]. These use the 2.7, 3.5, 3.6 and 3.7 interpreters, respectively, to test all code in the documentation (both in Sphinx *.rst source files and in docstrings), run all unit tests, measure test coverage and re-build the exceptions documentation. To pass arguments to Pytest (the test runner) use a double dash (--) after all the Tox arguments, for example:

   $ PKG_NAME=pcsv tox -e py27-pkg -- -n 4
   GLOB sdist-make: .../pcsv/setup.py
   py27-pkg inst-nodeps: .../pcsv/.tox/.tmp/package/1/pcsv-1.0.8.zip
   ...
     py27-pkg: commands succeeded
     congratulations :)
   $

   Or use the -a Setuptools optional argument followed by a quoted string with the arguments for Pytest. For example:

   $ PKG_NAME=pcsv python setup.py tests -a "-e py27-pkg -- -n 4"
   running tests
   ...
     py27-pkg: commands succeeded
     congratulations :)
   $

   There are other convenience environments defined for Tox [3]:

   • py27-repl, py35-repl, py36-repl and py37-repl run the Python 2.7, 3.5, 3.6 and 3.7 REPL, respectively, in the appropriate virtual environment. The pcsv package is pip-installed by Tox when the environments are created. Arguments to the interpreter can be passed in the command line after a double dash (--).

   • py27-test, py35-test, py36-test and py37-test run Pytest using the Python 2.7, 3.5, 3.6 and 3.7 interpreter, respectively, in the appropriate virtual environment. Arguments to pytest can be passed in the command line after a double dash (--) , for example:

     $ PKG_NAME=pcsv tox -e py27-test -- -x test_pcsv.py
     GLOB sdist-make: .../pcsv/setup.py
     py27-pkg inst-nodeps: .../pcsv/.tox/.tmp/package/1/pcsv-1.0.8.zip
     ...
       py27-pkg: commands succeeded
       congratulations :)
     $

   • py27-test, py35-test, py36-test and py37-test test code and branch coverage using the 2.7, 3.5, 3.6 and 3.7 interpreter, respectively, in the appropriate virtual environment. Arguments to pytest can be passed in the command line after a double dash (--). The report can be found in ${PCSV_DIR}/.tox/py[PV]/usr/share/pcsv/tests/htmlcov/index.html where [PV] stands for 2.7, 3.5, 3.6 or 3.7 depending on the interpreter used.

8. Verify that continuous integration tests pass. The package has continuous integration configured for Linux, Apple macOS and Microsoft Windows (all via Azure DevOps).

9. Document the new feature or bug fix (if needed). The script ${PCSV_DIR}/pypkg/build_docs.py re-builds the whole package documentation (re-generates images, cogs source files, etc.):

   $ "${PCSV_DIR}"/pypkg/build_docs.py -h
   usage: build_docs.py [-h] [-d DIRECTORY] [-r]
                        [-n NUM_CPUS] [-t]
   
   Build pcsv package documentation
   
   optional arguments:
     -h, --help            show this help message and exit
     -d DIRECTORY, --directory DIRECTORY
                           specify source file directory
                           (default ../pcsv)
     -r, --rebuild         rebuild exceptions documentation.
                           If no module name is given all
                           modules with auto-generated
                           exceptions documentation are
                           rebuilt
     -n NUM_CPUS, --num-cpus NUM_CPUS
                           number of CPUs to use (default: 1)
     -t, --test            diff original and rebuilt file(s)
                           (exit code 0 indicates file(s) are
                           identical, exit code 1 indicates
                           file(s) are different)

Footnotes

[1]

All examples are for the bash shell

[2]

It is assumed that all the Python interpreters are in the executables path. Source code for the interpreters can be downloaded from Python’s main site

[3] (1,2)

Tox configuration largely inspired by Ionel’s codelog

License

The MIT License (MIT)

Copyright (c) 2013-2019 Pablo Acosta-Serafini

Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the “Software”), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED “AS IS”, WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. .. CHANGELOG.rst .. Copyright (c) 2013-2019 Pablo Acosta-Serafini .. See LICENSE for details

Changelog

• 1.0.8 [2019-03-22]: Documentation and dependency update

• 1.0.7 [2019-03-09]: Dropped support for Python 2.6, 3.3 and 3.4. Updates to support newest versions of dependencies. Adopted lightweight package management framework

• 1.0.6 [2017-09-10]: Fixed bug while filtering rows that have empty column specified in filter. Fixed broken multi-line links in documentation

• 1.0.5 [2017-02-10]: Package build enhancements and fixes

• 1.0.4 [2017-02-07]: Python 3.6 support

• 1.0.3 [2016-06-10]: Minor documentation build bug fix

• 1.0.2 [2016-05-12]: Minor documentation updates

• 1.0.1 [2016-05-12]: Minor documentation updates

• 1.0.0 [2016-05-12]: Final release of 1.0.0 branch

• 1.0.0rc1 [2016-05-11]: Initial commit, forked a subset from putil PyPI package