PyND

Python module for calculating neighborhood density

Getting Started

1. Be sure you have Python installed. From a shell session, run python --version. The output should look something like what is shown below. This package was developed against Python 3.6, though it may work with newer versions of python.

   $ python --version
   Python 3.6.6

2. Check that pip is installed for the version of Python you intend on using. From a shell session, run pip --version. The output should look something like what is shown below. It's critical that the python version shown at the end of the line matches the one above.

   $ pip --version
   pip 18.1 from c:\...python\python36\lib\site-packages\pip (python 3.6)

3. Install prun, a tool that makes running shell commands from your python virtual environment easy.

   $ pip install prun

4. Clone this repository.

5. From the root directory of the repository, create a python virtual environment for the project in the PyND/venv/ directory

   $ cd PyND
   $ python -m venv venv

6. Install the pynd package into your newly created virtual environment. From the PyND directory, run:

   $ prun pip install -e .

   Note: to support automated unit tests with pytest run instead prun pip install -e .[dev]

7. Install the R packages reticulate, which allows you to run python from within an R session and pass objects back and forth between the two, and here which makes using relative paths within an R project structure easier.

   install.packages("reticulate")
   install.packages("here")

8. From R, source() the file PyND\test.R, using chdir=TRUE

   source("PyND\test.R", chdir=TRUE)

   You should get some output like:

pynd.neighbors - 10-01 21:41:33 INFO : starting word 1 of 100, "B_01_061" pynd.neighbors - 10-01 21:41:35 INFO : .. 9.0% complete, 5.63 words/sec. Est. 0:00:16.16 (H:MM:SS.ms) remaining. pynd.neighbors - 10-01 21:41:35 INFO : starting word 10 of 100, "G_02_26" pynd.neighbors - 10-01 21:41:36 INFO : .. 19.0% complete, 6.19 words/sec. Est. 0:00:13.08 (H:MM:SS.ms) remaining. pynd.neighbors - 10-01 21:41:36 INFO : starting word 20 of 100, "E_02_92" pynd.neighbors - 10-01 21:41:38 INFO : .. 29.0% complete, 6.91 words/sec. Est. 0:00:10.27 (H:MM:SS.ms) remaining. pynd.neighbors - 10-01 21:41:38 INFO : starting word 30 of 100, "H_02_20" pynd.neighbors - 10-01 21:41:39 INFO : .. 39.0% complete, 7.45 words/sec. Est. 0:00:08.19 (H:MM:SS.ms) remaining. pynd.neighbors - 10-01 21:41:39 INFO : starting word 40 of 100, "C_01_080" pynd.neighbors - 10-01 21:41:40 INFO : .. 49.0% complete, 8.84 words/sec. Est. 0:00:05.77 (H:MM:SS.ms) remaining. pynd.neighbors - 10-01 21:41:40 INFO : starting word 50 of 100, "A_01_003" pynd.neighbors - 10-01 21:41:41 INFO : .. 59.0% complete, 10.76 words/sec. Est. 0:00:03.81 (H:MM:SS.ms) remaining. pynd.neighbors - 10-01 21:41:41 INFO : starting word 60 of 100, "B_01_034" pynd.neighbors - 10-01 21:41:42 INFO : .. 69.0% complete, 14.09 words/sec. Est. 0:00:02.20 (H:MM:SS.ms) remaining. pynd.neighbors - 10-01 21:41:42 INFO : starting word 70 of 100, "J_02_071" pynd.neighbors - 10-01 21:41:42 INFO : .. 79.0% complete, 20.41 words/sec. Est. 0:00:01.03 (H:MM:SS.ms) remaining. pynd.neighbors - 10-01 21:41:42 INFO : starting word 80 of 100, "C_02_044" pynd.neighbors - 10-01 21:41:43 INFO : .. 89.0% complete, 34.74 words/sec. Est. 0:00:00.32 (H:MM:SS.ms) remaining. pynd.neighbors - 10-01 21:41:43 INFO : starting word 90 of 100, "D_02_021" pynd.neighbors - 10-01 21:41:43 INFO : .. 99.0% complete, 89.79 words/sec. Est. 0:00:00.01 (H:MM:SS.ms) remaining. pynd.neighbors - 10-01 21:41:43 INFO : starting word 100 of 100, "B_03_061" pynd.neighbors - 10-01 21:41:43 INFO : completed 100 words in 0:00:09.67 (H:MM:SS.ms) (10.35 word/sec) pynd.neighbors - 10-01 21:41:43 INFO : Wrote file /Users/nkc/PyND/output/foo-neighbors.csv pynd.neighbors - 10-01 21:41:43 INFO : wrote file /Users/nkc/PyND/output/foo-nd.csv