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# Analysis from cProfile import label import numpy as np import pandas as pd from scipy.interpolate import griddata # Visualization import seaborn as sns import matplotlib.pyplot as plt from matplotlib.cm import get_cmap from matplotlib.colors import LinearSegmentedColormap, ListedColormap import colour # This comput...
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# Auto generated from ontology_metadata.yaml by pythongen.py version: 0.0.1 # Generation date: 2024-04-14T16:59:12 # Schema: Ontology-Metadata # # id: https://w3id.org/oak/ontology-metadata # description: Schema for ontology metadata # license: https://creativecommons.org/publicdomain/zero/1.0/ import dataclasses impo...
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# Author: Christian Brodbeck <christianbrodbeck@nyu.edu> """Framework for figures embedded in a GUI Implementation ============== Plotting is implemented hierarchically in 3 different types of functions/classes: top-level (public names) Top-level functions or classes have public names create an entire figure. ...
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""" ======================================================================================================================== Analysis Module ======================================================================================================================== Collection of analysis and utility functions that are used...
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import logging import math import re import shutil import typing from collections import defaultdict from dataclasses import dataclass, field from operator import or_ from pathlib import Path from typing import ( Any, Dict, Iterable, Iterator, List, Optional, Set, Tuple, Type, Un...
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# -*- coding: utf-8 -*- """ @author: Michele D'Orazio ——————————————————————————— Michele D'Orazio, PhD Dept. Electronic Engineering Interdisciplinary Center of Advanced Study of Organ-on-Chip and Lab-on-Chip Applications (IC-LOC) University of Rome Tor Vergata Via del politecnico 1, 00133 Roma, Italy co...
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import cv2 import matplotlib.pyplot as plt plt.switch_backend('agg') import matplotlib.colors as mcolors import numpy as np import pandas as pd import sys import math import itertools import scipy import scikit_posthocs import matplotlib as mpl from itertools import groupby from scipy.stats import kde import utils.g...
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import os import types import re import json import logging import itertools import csv import copy import pickle import numpy as np import multiprocessing import matplotlib.pyplot as plt import matplotlib.colors as mcol import slideflow as sf import slideflow.util.neptune_utils from os.path import join, exists, isdir...
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__author__ = 'duarte' """ ======================================================================================================================== Input Architect Module ======================================================================================================================== (this documentation is incomp...
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""" Mask R-CNN The main Mask R-CNN model implementation. Copyright (c) 2017 Matterport, Inc. Licensed under the MIT License (see LICENSE for details) Written by Waleed Abdulla """ import os import random import datetime import re import math import logging from collections import OrderedDict import multiprocessing im...
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__author__ = 'duarte' """ ==================================================================================== Signals Module ==================================================================================== Collection of utilities and functions to create, use and manipulate signals (spike data or analog data) (inco...
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# cython: language_level=3 # Time-stamp: <2025-11-12 22:14:22 Tao Liu> """Input parsers used across MACS3 for reading alignment-like formats. This code is free software; you can redistribute it and/or modify it under the terms of the BSD License (see the file LICENSE included with the distribution). """ # ----------...
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""" ======================================================================================================================== Visualization Module ======================================================================================================================== (incomplete documentation) Provides all the relevant...
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'''Statistical tests for NDVars Common Attributes ----------------- The following attributes are always present. For ANOVA, they are lists with the corresponding items for different effects. t/f/... : NDVar Map of the statistical parameter. p_uncorrected : NDVar Map of uncorrected p values. p : NDVar | None ...
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"""RHINO functions.""" from __future__ import annotations import os import shutil import subprocess import warnings from pathlib import Path import numpy as np import pandas as pd import nibabel as nib import nilearn as nil import matplotlib.pyplot as plt from matplotlib.colors import ListedColormap from matplotlib....
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#!/usr/bin/env python # -*- coding: utf-8 -*- # tifffile.py # Copyright (c) 2008-2014, Christoph Gohlke # Copyright (c) 2008-2014, The Regents of the University of California # Produced at the Laboratory for Fluorescence Dynamics # All rights reserved. # # Redistribution and use in source and binary forms, with or wit...
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"""Transforms time domain signals to the frequency domain.""" import warnings from logging import getLogger from typing import TYPE_CHECKING, Any, Literal, Protocol, TypedDict, TypeVar, runtime_checkable import numpy as np from numpy.typing import NDArray from scipy.signal.windows import dpss as scipy_dpss from scipy...
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""" ======================================================================================================================== Signals Module ======================================================================================================================== Collection of utilities and functions to create, use and ma...
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# Built-in import builtins import csv import json import multiprocessing import os import platform import shutil import subprocess import sys import threading import time from datetime import datetime from pathlib import Path from typing import Any # Third-party import brian2 as b2 import brian2cuda # noqa: F401 impo...
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from copy import deepcopy import pickle from typing import Tuple, Union, List import numpy as np import matplotlib from matplotlib import cm, colors import matplotlib.pyplot as plt from matplotlib.colors import LinearSegmentedColormap import statsmodels.api as sm import seaborn as sns from scipy.stats import ttest_ind ...
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""" ======================================================================================================================== Input Architect Module ======================================================================================================================== (this documentation is incomplete) Classes: ------...
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# Analysis import numpy as np import pandas as pd from scipy.signal import resample, coherence, csd, correlate, welch # Visualization from matplotlib import pyplot as plt import seaborn as sns # Statistics from statsmodels.tsa.stattools import grangercausalitytests as gc_test from statsmodels.stats.stattools import d...
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# GoPiGo Connectome # Written by Timothy Busbice, Gabriel Garrett, Geoffrey Churchill (c) 2015 in Python 2.7 # The GoPiGo Connectome uses a Postsynaptic dictionary based on the C Elegans Connectome Model # This application can be ran on the Raspberry Pi GoPiGo robot with a Sonar that represents Nose Touch when activate...
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# GoPiGo Connectome # Written by Timothy Busbice, Gabriel Garrett, Geoffrey Churchill (c) 2015 in Python 2.7 # The GoPiGo Connectome uses a Postsynaptic dictionary based on the C Elegans Connectome Model # This application can be ran on the Raspberry Pi GoPiGo robot with a Sonar that represents Nose Touch when activate...
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import inspect import json import warnings from unittest import mock import numpy as np import pytest import scipy.fft import xarray as xr from spectral_connectivity import MorletWavelet, Multitaper, Welch from spectral_connectivity._input_handling import ( _reject_unmaterialized_backing, _time_axis_from_data...
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# GoPiGo Connectome # Written by Timothy Busbice, Gabriel Garrett, Geoffrey Churchill (c) 2014, in Python 2.7 # The GoPiGo Connectome uses a postSynaptic dictionary based on the C Elegans Connectome Model # This application can be ran on the Raspberry Pi GoPiGo robot with a Sonar that represents Nose Touch when activat...
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# GoPiGo Connectome # Written by Timothy Busbice, Gabriel Garrett, Geoffrey Churchill (c) 2014, in Python 2.7 # The GoPiGo Connectome uses a postSynaptic dictionary based on the C Elegans Connectome Model # This application can be ran on the Raspberry Pi GoPiGo robot with a Sonar that represents Nose Touch when activat...
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# Author: Christian Brodbeck <christianbrodbeck@nyu.edu> """MneExperiment class to manage data from a experiment For testing purposed, set up an experiment class without checking for data: MneExperiment.auto_delete_cache = 'disable' MneExperiment.sessions = ('session',) e = MneExperiment('.', find_subjects=False) ""...
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import matplotlib.pyplot as plt import numpy as np from scipy.signal import butter,filtfilt from sklearn.linear_model import LinearRegression from sklearn.decomposition import PCA from matplotlib.colors import ListedColormap from sklearn.model_selection import train_test_split import matplotlib.colors as colors ...
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""" Command Line Interface to OAK ---------------------- Executed using "runoak" command """ # TODO: order commands. # See https://stackoverflow.com/questions/47972638/how-can-i-define-the-order-of-click-sub-commands-in-help import json import logging import statistics as stats import sys from collections import defa...
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# Author: Christian Brodbeck <christianbrodbeck@nyu.edu> """Data containers and basic operations Data Representation =================== Data is stored in three main vessels: :class:`Factor`: stores categorical data :class:`Var`: stores numeric data :class:`NDVar`: stores numerical data where each cell c...
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# GoPiGo Connectome # Written by Timothy Busbice, Gabriel Garrett, Geoffrey Churchill (c) 2014, in Python 2.7 # The GoPiGo Connectome uses a Postsynaptic dictionary based on the C Elegans Connectome Model # This application can be ran on the Raspberry Pi GoPiGo robot with a Sonar that represents Nose Touch when activat...
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import os import sys from os.path import dirname, realpath, join from sys import argv, exit import copy import pickle import csv import numpy as np import pandas as pd import math import scipy import scipy.io import scipy.ndimage as ndi from scipy.ndimage import map_coordinates from natsort import natsorted, ns impo...
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#! /usr/bin/python # -*- coding: utf8 -*- import tensorflow as tf import time from . import visualize from . import utils from . import files from . import cost from . import iterate from . import ops import numpy as np from six.moves import xrange import random, warnings import copy import inspect # __all__ = [ # ...
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loadNamespace("future")
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save_rrho_quads <- function(quad_list, )
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# References {.unnumbered} ::: {#refs} :::
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library(testthat) library(RISC) test_check("RISC")
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install.packages('rjson') install.packages('ggplot2')
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library(testthat) library(galamm) test_check("galamm")
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library(testthat) library(SingleR) test_check("SingleR")
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plan(multisession, workers = 2) futureSessionInfo() plan(sequential)
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devtools::install_github("shmohammadi86/ACTIONet", ref = "R-release")
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#' Antoni #' #' The face of an angel, the curls of the sea. #' "antoni"
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## Undo future debug options(future.debug = FALSE) ## Undo future strategy future::plan(oplan)
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plan(multisession) nbrOfWorkers() ## == availableCores() plan(sequential) nbrOfWorkers() ## == 1
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#' @export combineCommonResults <- function(results) { .Defunct(new = "combineRecomputedResults") }
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## Record original state ovars <- ls(envir = globalenv()) oenvs <- oenvs0 <- Sys.getenv() oopts0 <- options()
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#' @importFrom beachmat getExecutor .onLoad <- function(libname, pkgname) { set_executor(getExecutor()) }
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#' @tags sessionDetails library(future) sd <- sessionDetails() print(sd) print(sd, output = "message") rm(list = "sd")
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args = commandArgs(trailingOnly = T) values = as.numeric(args) delta = values - min(values) w = 1/sum(exp(-delta/2)) cat(w)
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load('/share/quonlab/workspaces/ruoxinli/multitask_/data/iPSC_neuronal/FPP/regress_cellcycle_expid_selected_cells_genes.rda')
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counts <- mandelbrot(x = -0.75, y = 0, side = 3) plot(counts) \dontrun{ demo("mandelbrot", package = "future", ask = FALSE) }
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devtools::load_all() data(Orthodont, package = "nlme") x <- galamm(distance ~ age + (age | Subject), data = Orthodont) plot(fm1)
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wgcna_color <- function(module, color) { name_list <- rep(c("color"), nrow(module)) df <- cbind(module, name_list) return(df) }
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testme <- as.environment("testme") if (testme[["debug"]]) { info <- utils::sessionInfo() message("Session information:") print(info) }
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relevel_Timepoint <- function(df) { df$Timepoint <- factor(df$Timepoint, levels = c("baseline", "48hrs", "4wks", "endpoint")) return(df) }
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#' @tags prologue-cleanup #' @tags detritus-files message("Test to clean up any detritus files that might originate from R CMD check running examples")
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### script to install R packages # install CRAN packages packs <- c( 'foreach', 'doParallel' ) install.packages(packs) # install Bioconductor packages
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## EXAMPLE: futureCall() and do.call() x <- 1:100 y0 <- do.call(sum, args = list(x)) print(y0) f1 <- futureCall(sum, args = list(x)) y1 <- value(f1) print(y1)
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covr_testing <- ("covr" %in% loadedNamespaces()) on_macos <- grepl("^darwin", R.version$os) on_githubactions <- as.logical(Sys.getenv("GITHUB_ACTIONS", "FALSE"))
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#! /usr/bin/env Rscript ## This runs testme test script inst/testme/test-mpi.R ## Don't edit - it was autogenerated by inst/testme/deploy.R future:::testme("mpi")
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#! /usr/bin/env Rscript ## This runs testme test script inst/testme/test-rng.R ## Don't edit - it was autogenerated by inst/testme/deploy.R future:::testme("rng")
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#! /usr/bin/env Rscript ## This runs testme test script inst/testme/test-000.R ## Don't edit - it was autogenerated by inst/testme/deploy.R future:::testme("000")
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# Session information {.unnumbered} Last, let's reports the version numbers of R and all the packages used. ```{r message=FALSE, warning=FALSE} sessionInfo() ```
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#! /usr/bin/env Rscript ## This runs testme test script inst/testme/test-uuid.R ## Don't edit - it was autogenerated by inst/testme/deploy.R future:::testme("uuid")
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#! /usr/bin/env Rscript ## This runs testme test script inst/testme/test-plan.R ## Don't edit - it was autogenerated by inst/testme/deploy.R future:::testme("plan")
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#! /usr/bin/env Rscript ## This runs testme test script inst/testme/test-tweak.R ## Don't edit - it was autogenerated by inst/testme/deploy.R future:::testme("tweak")
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#! /usr/bin/env Rscript ## This runs testme test script inst/testme/test-value.R ## Don't edit - it was autogenerated by inst/testme/deploy.R future:::testme("value")
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#! /usr/bin/env Rscript ## This runs testme test script inst/testme/test-reset.R ## Don't edit - it was autogenerated by inst/testme/deploy.R future:::testme("reset")
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#! /usr/bin/env Rscript ## This runs testme test script inst/testme/test-utils.R ## Don't edit - it was autogenerated by inst/testme/deploy.R future:::testme("utils")
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#! /usr/bin/env Rscript ## This runs testme test script inst/testme/test-cancel.R ## Don't edit - it was autogenerated by inst/testme/deploy.R future:::testme("cancel")
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#! /usr/bin/env Rscript ## This runs testme test script inst/testme/test-future.R ## Don't edit - it was autogenerated by inst/testme/deploy.R future:::testme("future")
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#! /usr/bin/env Rscript ## This runs testme test script inst/testme/test-bquote.R ## Don't edit - it was autogenerated by inst/testme/deploy.R future:::testme("bquote")
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#! /usr/bin/env Rscript ## This runs testme test script inst/testme/test-result.R ## Don't edit - it was autogenerated by inst/testme/deploy.R future:::testme("result")
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#! /usr/bin/env Rscript ## This runs testme test script inst/testme/test-stdout.R ## Don't edit - it was autogenerated by inst/testme/deploy.R future:::testme("stdout")
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#! /usr/bin/env Rscript ## This runs testme test script inst/testme/test-resolve.R ## Don't edit - it was autogenerated by inst/testme/deploy.R future:::testme("resolve")
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#! /usr/bin/env Rscript ## This runs testme test script inst/testme/test-futures.R ## Don't edit - it was autogenerated by inst/testme/deploy.R future:::testme("futures")
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#! /usr/bin/env Rscript ## This runs testme test script inst/testme/test-futureOf.R ## Don't edit - it was autogenerated by inst/testme/deploy.R future:::testme("futureOf")
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#! /usr/bin/env Rscript ## This runs testme test script inst/testme/test-timeouts.R ## Don't edit - it was autogenerated by inst/testme/deploy.R future:::testme("timeouts")
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#! /usr/bin/env Rscript ## This runs testme test script inst/testme/test-relaying.R ## Don't edit - it was autogenerated by inst/testme/deploy.R future:::testme("relaying")
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#! /usr/bin/env Rscript ## This runs testme test script inst/testme/test-backtrace.R ## Don't edit - it was autogenerated by inst/testme/deploy.R future:::testme("backtrace")
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#! /usr/bin/env Rscript ## This runs testme test script inst/testme/test-tweakable.R ## Don't edit - it was autogenerated by inst/testme/deploy.R future:::testme("tweakable")
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#! /usr/bin/env Rscript ## This runs testme test script inst/testme/test-rng_utils.R ## Don't edit - it was autogenerated by inst/testme/deploy.R future:::testme("rng_utils")
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#! /usr/bin/env Rscript ## This runs testme test script inst/testme/test-dotdotdot.R ## Don't edit - it was autogenerated by inst/testme/deploy.R future:::testme("dotdotdot")
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#! /usr/bin/env Rscript ## This runs testme test script inst/testme/test-futureCall.R ## Don't edit - it was autogenerated by inst/testme/deploy.R future:::testme("futureCall")
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#! /usr/bin/env Rscript ## This runs testme test script inst/testme/test-sequential.R ## Don't edit - it was autogenerated by inst/testme/deploy.R future:::testme("sequential")
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#! /usr/bin/env Rscript ## This runs testme test script inst/testme/test-whichIndex.R ## Don't edit - it was autogenerated by inst/testme/deploy.R future:::testme("whichIndex")
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#! /usr/bin/env Rscript ## This runs testme test script inst/testme/test-mandelbrot.R ## Don't edit - it was autogenerated by inst/testme/deploy.R future:::testme("mandelbrot")
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#! /usr/bin/env Rscript ## This runs testme test script inst/testme/test-objectSize.R ## Don't edit - it was autogenerated by inst/testme/deploy.R future:::testme("objectSize")
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#! /usr/bin/env Rscript ## This runs testme test script inst/testme/test-minifuture.R ## Don't edit - it was autogenerated by inst/testme/deploy.R future:::testme("minifuture")
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#! /usr/bin/env Rscript ## This runs testme test script inst/testme/test-signalEarly.R ## Don't edit - it was autogenerated by inst/testme/deploy.R future:::testme("signalEarly")
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#! /usr/bin/env Rscript ## This runs testme test script inst/testme/test-globals,NSE.R ## Don't edit - it was autogenerated by inst/testme/deploy.R future:::testme("globals,NSE")
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#! /usr/bin/env Rscript ## This runs testme test script inst/testme/test-import_from.R ## Don't edit - it was autogenerated by inst/testme/deploy.R future:::testme("import_from")
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#! /usr/bin/env Rscript ## This runs testme test script inst/testme/test-requestCore.R ## Don't edit - it was autogenerated by inst/testme/deploy.R future:::testme("requestCore")
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#! /usr/bin/env Rscript ## This runs testme test script inst/testme/test-marshalling.R ## Don't edit - it was autogenerated by inst/testme/deploy.R future:::testme("marshalling")
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#! /usr/bin/env Rscript ## This runs testme test script inst/testme/test-deprecation.R ## Don't edit - it was autogenerated by inst/testme/deploy.R future:::testme("deprecation")
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#! /usr/bin/env Rscript ## This runs testme test script inst/testme/test-FutureError.R ## Don't edit - it was autogenerated by inst/testme/deploy.R future:::testme("FutureError")
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#! /usr/bin/env Rscript ## This runs testme test script inst/testme/test-requestNode.R ## Don't edit - it was autogenerated by inst/testme/deploy.R future:::testme("requestNode")
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#! /usr/bin/env Rscript ## This runs testme test script inst/testme/test-utils-basic.R ## Don't edit - it was autogenerated by inst/testme/deploy.R future:::testme("utils-basic")