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zaneveld / karenina

Simulation and modeling tools for studying Anna Karenina effects in animal microbiomes
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Travis CI Engine and Issue Resolution #23

Closed SLPeoples closed 6 years ago

SLPeoples commented 6 years ago

resolves #21 Updated spatial_ornstein_uhlenbeck.py to provide legible help text when the user provides no output parameter.

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### karenina ```bash Usage: karenina -o ./simulation_results karenina: error: -o --output is required For additional help: karenina -h ``` ### karenina -h ```bash Usage: karenina -o ./simulation_results This script simulates microbiome change over time using Ornstein-Uhlenbeck (OU) models. These are similar to Brownian motion models, with the exception that they include reversion to a mean. Output is a tab-delimited data table and figures. Options: --version show program's version number and exit -h, --help show this help message and exit Required options: -o OUTPUT, --output=OUTPUT the output folder for the simulation results Optional options: --pert_file_path=PERT_FILE_PATH file path to a perturbation file specifying parameters for the simulation results [default: C:\Users\Ripti\Anaconda3\lib\site-packages\karenina-0. 0.1-py3.6.egg\data\perturbations\xyz_lambda_zero.csv] --treatment_names=TREATMENT_NAMES Comma seperated list of treatment named [default:control,destabilizing_treatment] -n N_INDIVIDUALS, --n_individuals=N_INDIVIDUALS Comma-separated number of individuals to simulate per treatment.Note: This value must be enclosed in quotes. Example: "35,35". [default: 35,35] -t N_TIMEPOINTS, --n_timepoints=N_TIMEPOINTS Number of timepoints to simulate. (One number, which is the same for all treatments) [default: 10] -p PERTURBATION_TIMEPOINT, --perturbation_timepoint=PERTURBATION_TIMEPOINT Timepoint at which to apply a perturbation. Must be less than --n_timepoints [default: 5] -d PERTURBATION_DURATION, --perturbation_duration=PERTURBATION_DURATION Duration that the perturbation lasts. [default: 100] --interindividual_variation=INTERINDIVIDUAL_VARIATION Starting variability between individuals. [default: 0.01] --delta=DELTA Starting delta parameter for Brownian motion and Ornstein-Uhlenbeck processes. A higher number indicates more variability over time. [default: 0.25] -l L, --L=L Starting lambda parameter for Ornstein-Uhlenbeck processes. A higher number indicates a greater tendancy to revert to the mean value. [default: 0.2] --fixed_start_pos=FIXED_START_POS Starting x,y,z position for all points, as comma separated floating point values, e.g. 0.0,0.1,0.2. If not supplied, starting positions will be randomized based on the interindividual_variation parameter [default: none] ```

Updated README.md to display status of Travis CI engine, when setup for zaneveld/karenina

Such as the Qiime2 example:

Image

Updated individual import files to accommodate package use.

from individual import Individual

    to -->

from karenina.individual import Individual

This allows the user to use the console command following install:

karenina -o ./current_run

Rather than navigating to the location of spatial_ornstein_uhlenbeck.py and executing:

python spatial_ornstein_uhlenbeck.py -o ./current_run

22

Fixed fit_timeseries.py cogent error, updated to use optparse, could not successfully set up Travis CI without taking care of this at the same time.

Fixed python2 / python3 issue where a function in scipy would provide an error for zip datatypes:

local_min_bounds = zip(xmin.tolist(),xmax.tolist())

    to--> 

local_min_bounds = list(zip(xmin.tolist(),xmax.tolist()))

and

for scale,data in self.BasicNormalData.iteritems():

    to-->

for scale,data in self.BasicNormalData.items():

Travis CI had issues with importing "exists", so this check was temporarily removed, added a #TODO:

if exists(opts.output):
    print("Output saved to: "+str(opts.output))

    to-->

#TODO: Make if not exists output directory
#if exists(opts.output):
#    print("Output saved to: " +str(opts.output))

Temporarily omitted test_fit_timeseries_recovers_OU_params in test_fit_timeseries.py because the 300 iterations would cause TravisCI to time out. Log ouput snippet displays that the timeout occurred after fifty minutes of run time.

n_timepoints:  265

The job exceeded the maximum time limit for jobs, and has been terminated.

Image

Created manifest.in, requirements.txt, setup.cfg as accessory files for build setup.

Created setup.py, configured to download the package data/perturbations file, and scripts.

Usage & Installation: Navigate to the cloned repository, and execute the setup.py script with the parameter install:

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### python setup.py install ```bash running install running bdist_egg running egg_info creating karenina_test.egg-info writing karenina_test.egg-info\PKG-INFO writing dependency_links to karenina_test.egg-info\dependency_links.txt writing entry points to karenina_test.egg-info\entry_points.txt writing top-level names to karenina_test.egg-info\top_level.txt writing manifest file 'karenina_test.egg-info\SOURCES.txt' reading manifest file 'karenina_test.egg-info\SOURCES.txt' reading manifest template 'MANIFEST.in' writing manifest file 'karenina_test.egg-info\SOURCES.txt' installing library code to build\bdist.win-amd64\egg running install_lib running build_py creating build creating build\lib creating build\lib\karenina copying karenina\experiment.py -> build\lib\karenina copying karenina\fit_timeseries.py -> build\lib\karenina copying karenina\individual.py -> build\lib\karenina copying karenina\perturbation.py -> build\lib\karenina copying karenina\process.py -> build\lib\karenina copying karenina\spatial_ornstein_uhlenbeck.py -> build\lib\karenina copying karenina\visualization.py -> build\lib\karenina copying karenina\__init__.py -> build\lib\karenina creating build\bdist.win-amd64 creating build\bdist.win-amd64\egg creating build\bdist.win-amd64\egg\karenina copying build\lib\karenina\experiment.py -> build\bdist.win-amd64\egg\karenina copying build\lib\karenina\fit_timeseries.py -> build\bdist.win-amd64\egg\karenina copying build\lib\karenina\individual.py -> build\bdist.win-amd64\egg\karenina copying build\lib\karenina\perturbation.py -> build\bdist.win-amd64\egg\karenina copying build\lib\karenina\process.py -> build\bdist.win-amd64\egg\karenina copying build\lib\karenina\spatial_ornstein_uhlenbeck.py -> build\bdist.win-amd64\egg\karenina copying build\lib\karenina\visualization.py -> build\bdist.win-amd64\egg\karenina copying build\lib\karenina\__init__.py -> build\bdist.win-amd64\egg\karenina byte-compiling build\bdist.win-amd64\egg\karenina\experiment.py to experiment.cpython-36.pyc byte-compiling build\bdist.win-amd64\egg\karenina\fit_timeseries.py to fit_timeseries.cpython-36.pyc byte-compiling build\bdist.win-amd64\egg\karenina\individual.py to individual.cpython-36.pyc byte-compiling build\bdist.win-amd64\egg\karenina\perturbation.py to perturbation.cpython-36.pyc byte-compiling build\bdist.win-amd64\egg\karenina\process.py to process.cpython-36.pyc byte-compiling build\bdist.win-amd64\egg\karenina\spatial_ornstein_uhlenbeck.py to spatial_ornstein_uhlenbeck.cpython-36.pyc byte-compiling build\bdist.win-amd64\egg\karenina\visualization.py to visualization.cpython-36.pyc byte-compiling build\bdist.win-amd64\egg\karenina\__init__.py to __init__.cpython-36.pyc installing package data to build\bdist.win-amd64\egg running install_data creating build\bdist.win-amd64\egg\data creating build\bdist.win-amd64\egg\data\perturbations copying data\perturbations\add_x_mu_high.csv -> build\bdist.win-amd64\egg\data\perturbations copying data\perturbations\all_perturbations.tsv -> build\bdist.win-amd64\egg\data\perturbations copying data\perturbations\double_xyz_delta.csv -> build\bdist.win-amd64\egg\data\perturbations copying data\perturbations\double_z_delta.csv -> build\bdist.win-amd64\egg\data\perturbations copying data\perturbations\README.txt -> build\bdist.win-amd64\egg\data\perturbations copying data\perturbations\set_x_lambda_high.csv -> build\bdist.win-amd64\egg\data\perturbations copying data\perturbations\set_x_lambda_medium.csv -> build\bdist.win-amd64\egg\data\perturbations copying data\perturbations\set_x_lambda_small.csv -> build\bdist.win-amd64\egg\data\perturbations copying data\perturbations\set_x_mu_high.csv -> build\bdist.win-amd64\egg\data\perturbations copying data\perturbations\set_xyz_mu_high.csv -> build\bdist.win-amd64\egg\data\perturbations copying data\perturbations\set_xyz_mu_low.csv -> build\bdist.win-amd64\egg\data\perturbations copying data\perturbations\set_y_lambda_high.csv -> build\bdist.win-amd64\egg\data\perturbations copying data\perturbations\set_yz_lambda_high.csv -> build\bdist.win-amd64\egg\data\perturbations copying data\perturbations\set_z_lambda_zero.csv -> build\bdist.win-amd64\egg\data\perturbations copying data\perturbations\x_mu_low.csv -> build\bdist.win-amd64\egg\data\perturbations copying data\perturbations\xyz_lambda_low.csv -> build\bdist.win-amd64\egg\data\perturbations copying data\perturbations\xyz_lambda_zero.csv -> build\bdist.win-amd64\egg\data\perturbations copying data\perturbations\xyz_lambda_zero_alt_format.csv -> build\bdist.win-amd64\egg\data\perturbations copying data\perturbations\y_lambda_medium.csv -> build\bdist.win-amd64\egg\data\perturbations copying data\perturbations\yz_lambda_medium.csv -> build\bdist.win-amd64\egg\data\perturbations creating build\bdist.win-amd64\egg\EGG-INFO copying karenina_test.egg-info\PKG-INFO -> build\bdist.win-amd64\egg\EGG-INFO copying karenina_test.egg-info\SOURCES.txt -> build\bdist.win-amd64\egg\EGG-INFO copying karenina_test.egg-info\dependency_links.txt -> build\bdist.win-amd64\egg\EGG-INFO copying karenina_test.egg-info\entry_points.txt -> build\bdist.win-amd64\egg\EGG-INFO copying karenina_test.egg-info\top_level.txt -> build\bdist.win-amd64\egg\EGG-INFO zip_safe flag not set; analyzing archive contents... karenina.__pycache__.spatial_ornstein_uhlenbeck.cpython-36: module references __file__ creating dist creating 'dist\karenina_test-0.0.1-py3.6.egg' and adding 'build\bdist.win-amd64\egg' to it removing 'build\bdist.win-amd64\egg' (and everything under it) Processing karenina_test-0.0.1-py3.6.egg creating c:\users\ripti\anaconda3\lib\site-packages\karenina_test-0.0.1-py3.6.egg Extracting karenina_test-0.0.1-py3.6.egg to c:\users\ripti\anaconda3\lib\site-packages Adding karenina-test 0.0.1 to easy-install.pth file Installing karenina-script.py script to C:\Users\Ripti\Anaconda3\Scripts Installing karenina.exe script to C:\Users\Ripti\Anaconda3\Scripts Installed c:\users\ripti\anaconda3\lib\site-packages\karenina_test-0.0.1-py3.6.egg Processing dependencies for karenina-test==0.0.1 Finished processing dependencies for karenina-test==0.0.1 ```

Usage following installation:

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### karenina -o ./test_run ```bash {'output': './test_run', 'pert_file_path': 'C:\\Users\\Ripti\\Anaconda3\\lib\\site-packages\\karenina_test-0.0.1-py3.6.egg\\data\\perturbations\\xyz_lambda_zero.csv', 'treatment_names': 'control,destabilizing_treatment', 'n_individuals': '35,35', 'n_timepoints': 10, 'perturbation_timepoint': 5, 'perturbation_duration': 100, 'interindividual_variation': 0.01, 'delta': 0.25, 'L': 0.2, 'fixed_start_pos': None} params lambda 0 update_mode replace axes x y z Raw number of individuals from user: 35,35 n_individuals.split(',') ['35', '35'] **Experiment Design** treatments: ['control', 'destabilizing_treatment'] n_individuals: [35, 35] interindividual_variation 0.01 treatment_effects: [[], [{'start': 5, 'end': 105, 'params': {'lambda': 0.0}, 'update_mode': 'replace', 'axes': ['x', 'y', 'z']}]] individual_base_params: {'lambda': 0.2, 'delta': 0.25, 'interindividual_variation': 0.01} treatment_names: ['control', 'destabilizing_treatment'] n_individuals: [35, 35] treatment_params: [[], [{'start': 5, 'end': 105, 'params': {'lambda': 0.0}, 'update_mode': 'replace', 'axes': ['x', 'y', 'z']}]] [35, 35] ['control', 'destabilizing_treatment'] [[], [{'start': 5, 'end': 105, 'params': {'lambda': 0.0}, 'update_mode': 'replace', 'axes': ['x', 'y', 'z']}]] ['control', 'destabilizing_treatment'] {'treatment_name': 'control', 'n_individuals': 35} start_coord: -0.004348116398810584 curr_params['mu'] -0.004348116398810584 start_coord: 0.006009581228813295 curr_params['mu'] 0.006009581228813295 start_coord: 0.006792901950451617 curr_params['mu'] 0.006792901950451617 start_coord: -0.009725834226746865 curr_params['mu'] -0.009725834226746865 start_coord: -0.0006283269483692888 curr_params['mu'] -0.0006283269483692888 start_coord: 0.009010605774671606 curr_params['mu'] 0.009010605774671606 start_coord: 0.009180989056326184 curr_params['mu'] 0.009180989056326184 start_coord: 0.004140893064358304 curr_params['mu'] 0.004140893064358304 start_coord: 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curr_params['mu'] 0.004422553664122646 start_coord: 0.008900240764048804 curr_params['mu'] 0.008900240764048804 start_coord: -0.00883393915075497 curr_params['mu'] -0.00883393915075497 start_coord: -0.005688164989323048 curr_params['mu'] -0.005688164989323048 start_coord: -0.005527361247882263 curr_params['mu'] -0.005527361247882263 start_coord: 0.000376441979205 curr_params['mu'] 0.000376441979205 start_coord: -0.003388181561660195 curr_params['mu'] -0.003388181561660195 start_coord: 0.009223645041869068 curr_params['mu'] 0.009223645041869068 start_coord: 0.008348673228703717 curr_params['mu'] 0.008348673228703717 start_coord: 0.009216630892606213 curr_params['mu'] 0.009216630892606213 start_coord: -0.004358615086233673 curr_params['mu'] -0.004358615086233673 start_coord: -0.006839329229480431 curr_params['mu'] -0.006839329229480431 start_coord: 0.008354247601959098 curr_params['mu'] 0.008354247601959098 start_coord: -0.00535894335421675 curr_params['mu'] -0.00535894335421675 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4.30011480e-05, -3.54239822e-02, 2.11871414e-02, -5.81087460e-02, 1.75249114e-02, -3.53236585e-02, 3.10378759e-02, 1.05932984e-02, 6.59477647e-03, -1.46389690e-01], [-9.24673647e-03, -9.24673647e-03, 2.79583347e-03, 9.75030009e-04, -2.53885986e-02, -1.59819269e-02, -1.62485504e-02, -1.19229719e-02, 1.15624104e-02, 2.44841351e-02, -2.23556908e-02]])] {'color': (0.5, 0, 0, 1), 'linewidth': 1.0, 'linestyle': '-'} ```

Uninstall (in the linked example, karenina-test is used, rather than karenina):

Expand

### pip uninstall karenina-test ```bash Uninstalling karenina-test-0.0.1: Would remove: c:\users\ripti\anaconda3\lib\site-packages\karenina_test-0.0.1-py3.6.egg c:\users\ripti\anaconda3\scripts\karenina-script.py c:\users\ripti\anaconda3\scripts\karenina.exe Proceed (y/n)? y Successfully uninstalled karenina-test-0.0.1 ```

To set up Travis CI:

  1. Log into github at the following address https://travis-ci.org/auth

  2. Navigate to your Travis CI profile and use the switch on karenina to enable Travis CI for this repository.

Note: Currently, Travis CI will install both scipy and ffmpeg, and does pass for python 2.7, 3.4, and 3.6.

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