semvec/pypi-packages huggingface dataset:
pyarxiv 1.0.3.1
Python Client Library and CLI client for the ArXiv.org API
License: MIT

See source on GitHub: https://github.com/culshoefer/pyarxiv

|buildstatus|\ |Coverage Status|

pyarxiv
=======

pyarxiv is a wrapper for the API of `Cornell University's famous
repository <http://arxiv.org>`__ for scientific papers.

Supports Python 2.7, 3.3-3.6+

Installation
------------

.. code:: sh

    pip install pyarxiv

Features
--------

-  Query the arXiv API (atom feed) in your code
-  Use enums for arXiv categories
-  Download papers in your code as PDF TODO - Do the above in the
   commandline

Usage
-----

CLI
~~~

.. code:: sh

    pyarxiv-cli download -h
    pyarxiv-cli query -h
    # will download a couple of papers with given ids to folder /home/user, name them according to their titles,
    # append their arxiv ids, and do not give progress feedback when each paper is downloaded
    pyarxiv-cli download 1703.00001 1703.00002v1 ... --target-folder=/home/user --use-title-for-filename --append-id --silent

.. code:: sh

    # Queries for papers with "Lorem" in them, maximally gets 5 papers (default 100), authors Einstein and Zweistein
    # Other potential arguments are --abstract, --journalref and manualmode with --querystring
    pyarxiv-cli query --title="Lorem" --max-results=5 --authors="A Einstein, B Zweistein"

You can also chain commands:

.. code:: sh

    pyarxiv-cli download $(pyarxiv-cli query --title="WaveNet") --use-title-for-filename --append-id

Python
~~~~~~

.. code:: python

    from pyarxiv import query, download_entries
    from pyarxiv.arxiv_categories import ArxivCategory, arxiv_category_map
    #query(max_results=100, ids=[], categories=[],
    #                title='', authors='', abstract='', journal_ref='',
    #                querystring='')
    entries = query(title='WaveNet') 
    titles = map(lambda x: x['title'], entries)
    print(list(titles))


    #download_entries(entries_or_ids_or_uris=[], target_folder='.',
    #                     use_title_for_filename=False, append_id=False,
    #                     progress_callback=(lambda x, y: id))
    download_entries(entries)


    entries_with_category = query([ArxivCategory.cs_AI])
    print(arxiv_category_map(ArxivCategory.cs_AI))

.. |buildstatus| image:: https://travis-ci.org/culshoefer/pyarxiv.svg?branch=master
   :target: https://travis-ci.org/culshoefer/pyarxiv
.. |Coverage Status| image:: https://coveralls.io/repos/github/culshoefer/pyarxiv/badge.svg?branch=master
   :target: https://coveralls.io/github/culshoefer/pyarxiv?branch=master
dcmutils 0.99.3
A collection of DICOM related utilities
License: MIT

##############
pfdcm  v0.99.3
##############

.. image:: https://badge.fury.io/py/pfdcm.svg
    :target: https://badge.fury.io/py/pfdcm

.. image:: https://travis-ci.org/FNNDSC/pfdcm.svg?branch=master
    :target: https://travis-ci.org/FNNDSC/pfdcm

.. image:: https://img.shields.io/badge/python-3.5%2B-blue.svg
    :target: https://badge.fury.io/py/pfdcm

.. contents:: Table of Contents

********
Overview
********

This repository provides ``pfdcm`` -- a controlling service that speaks to a PACS and handles DICOM data management.

pfdcm
=====

Most simply, ``pfdcm`` provides a REST-type interface to querying a PACS as well as managing DICOM data received from a PACS.

************
Installation
************

Installation is relatively straightforward, and we recommend using either python virtual environments or docker.

Python Virtual Environment
==========================

On Ubuntu, install the Python virtual environment creator

.. code-block:: bash

  sudo apt install virtualenv

Then, create a directory for your virtual environments e.g.:

.. code-block:: bash

  mkdir ~/python-envs

You might want to add to your .bashrc file these two lines:

.. code-block:: bash

    export WORKON_HOME=~/python-envs
    source /usr/local/bin/virtualenvwrapper.sh

Then you can source your .bashrc and create a new Python3 virtual environment:

.. code-block:: bash

    source .bashrc
    mkvirtualenv --python=python3 python_env

To activate or "enter" the virtual env:

.. code-block:: bash

    workon python_env

To deactivate virtual env:

.. code-block:: bash

    deactivate

Using the ``fnndsc/ubuntu-python3`` dock
========================================

We provide a slim docker image with python3 based off Ubuntu. If you want to play inside this dock and install ``pman`` manually, do

.. code-block:: bash

    docker pull fnndsc/ubuntu-python3

This docker has an entry point ``python3``. To enter the dock at a different entry and install your own stuff:

.. code-block:: bash

   docker run -ti --entrypoint /bin/bash fnndsc/ubuntu-python3
   
Now, 

.. code-block:: bash

   apt update && \
   apt install -y libssl-dev libcurl4-openssl-dev librtmp-dev && \
   pip install pfdcm
   
**If you do the above, remember to** ``commit`` **your changes to the docker image otherwise they'll be lost when you remove the dock instance!**

.. code-block:: bash

  docker commit <container-ID> local/ubuntu-python3-pfdcm
  
 where ``<container-ID>`` is the ID of the above container.
  

Using the ``fnndsc/pfdcm`` dock
===============================

The easiest option however, is to just use the ``fnndsc/pfdcm`` dock.

.. code-block:: bash

    docker pull fnndsc/pfdcm
    
and then run

.. code-block:: bash

    docker run --name pfdcm -v /home:/Users --rm -ti fnndsc/pfdcm --forever --httpResponse

*****
Usage
*****

For usage of  ``pfdcm``, consult the relevant wiki pages.

``pfdcm`` usage
===============

For ``pfdcm`` detailed information, see the `pfdcm wiki page <https://github.com/FNNDSC/pfdcm/wiki/pfdcm-overview>`_.