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def deploy_services(self, site=None): """ Collects the configurations for all registered services and writes the appropriate supervisord.conf file. """ verbose = self.verbose r = self.local_renderer if not r.env.manage_configs: return # # tar...
def clone(self, remote_url, path=None, use_sudo=False, user=None): """ Clone a remote Git repository into a new directory. :param remote_url: URL of the remote repository to clone. :type remote_url: str :param path: Path of the working copy directory. Must not exist yet. ...
def add_remote(self, path, name, remote_url, use_sudo=False, user=None, fetch=True): """ Add a remote Git repository into a directory. :param path: Path of the working copy directory. This directory must exist and be a Git working copy with a default remote to fetch from. ...
def fetch(self, path, use_sudo=False, user=None, remote=None): """ Fetch changes from the default remote repository. This will fetch new changesets, but will not update the contents of the working tree unless yo do a merge or rebase. :param path: Path of the working copy direct...
def pull(self, path, use_sudo=False, user=None, force=False): """ Fetch changes from the default remote repository and merge them. :param path: Path of the working copy directory. This directory must exist and be a Git working copy with a default remote to pull from. ...
def get_logs_between_commits(self, a, b): """ Retrieves all commit messages for all commits between the given commit numbers on the current branch. """ print('REAL') ret = self.local('git --no-pager log --pretty=oneline %s...%s' % (a, b), capture=True) if self.ver...
def get_current_commit(self): """ Retrieves the git commit number of the current head branch. """ with hide('running', 'stdout', 'stderr', 'warnings'): s = str(self.local('git rev-parse HEAD', capture=True)) self.vprint('current commit:', s) return s
def record_manifest(self): """ Called after a deployment to record any data necessary to detect changes for a future deployment. """ manifest = super(GitTrackerSatchel, self).record_manifest() manifest[CURRENT_COMMIT] = self.get_current_commit() return manifest
def ssh_config(self, name=''): """ Get the SSH parameters for connecting to a vagrant VM. """ r = self.local_renderer with self.settings(hide('running')): output = r.local('vagrant ssh-config %s' % name, capture=True) config = {} for line in output.sp...
def version(self): """ Get the Vagrant version. """ r = self.local_renderer with self.settings(hide('running', 'warnings'), warn_only=True): res = r.local('vagrant --version', capture=True) if res.failed: return None line = res.splitlines()...
def vagrant(self, name=''): """ Run the following tasks on a vagrant box. First, you need to import this task in your ``fabfile.py``:: from fabric.api import * from burlap.vagrant import vagrant @task def some_task(): run('echo h...
def vagrant_settings(self, name='', *args, **kwargs): """ Context manager that sets a vagrant VM as the remote host. Use this context manager inside a task to run commands on your current Vagrant box:: from burlap.vagrant import vagrant_settings with va...
def base_boxes(self): """ Get the list of vagrant base boxes """ return sorted(list(set([name for name, provider in self._box_list()])))
def install_from_upstream(self): """ Installs Vagrant from the most recent package available from their homepage. """ from burlap.system import get_arch, distrib_family r = self.local_renderer content = urlopen(r.env.download_url).read() print(len(content)) ...
def distrib_id(): """ Get the OS distribution ID. Example:: from burlap.system import distrib_id if distrib_id() != 'Debian': abort(u"Distribution is not supported") """ with settings(hide('running', 'stdout')): kernel = (run('uname -s') or '').strip().lower(...
def distrib_release(): """ Get the release number of the distribution. Example:: from burlap.system import distrib_id, distrib_release if distrib_id() == 'CentOS' and distrib_release() == '6.1': print(u"CentOS 6.2 has been released. Please upgrade.") """ with settings...
def distrib_family(): """ Get the distribution family. Returns one of ``debian``, ``redhat``, ``arch``, ``gentoo``, ``sun``, ``other``. """ distrib = (distrib_id() or '').lower() if distrib in ['debian', 'ubuntu', 'linuxmint', 'elementary os']: return DEBIAN elif distrib in ['re...
def supported_locales(): """ Gets the list of supported locales. Each locale is returned as a ``(locale, charset)`` tuple. """ family = distrib_family() if family == 'debian': return _parse_locales('/usr/share/i18n/SUPPORTED') elif family == 'arch': return _parse_locales('/e...
def force_stop(self): """ Forcibly terminates all Celery processes. """ r = self.local_renderer with self.settings(warn_only=True): r.sudo('pkill -9 -f celery') r.sudo('rm -f /tmp/celery*.pid')
def set_permissions(self): """ Sets ownership and permissions for Celery-related files. """ r = self.local_renderer for path in r.env.paths_owned: r.env.path_owned = path r.sudo('chown {celery_daemon_user}:{celery_daemon_user} {celery_path_owned}')
def create_supervisor_services(self, site): """ This is called for each site to render a Celery config file. """ self.vprint('create_supervisor_services:', site) self.set_site_specifics(site=site) r = self.local_renderer if self.verbose: print('r.en...
def check_ok(self): """ Ensures all tests have passed for this branch. This should be called before deployment, to prevent accidental deployment of code that hasn't passed automated testing. """ import requests if not self.env.check_ok: return ...
def is_present(self, host=None): """ Returns true if the given host exists on the network. Returns false otherwise. """ r = self.local_renderer r.env.host = host or self.genv.host_string ret = r._local("getent hosts {host} | awk '{{ print $1 }}'", capture=True) or...
def purge_keys(self): """ Deletes all SSH keys on the localhost associated with the current remote host. """ r = self.local_renderer r.env.default_ip = self.hostname_to_ip(self.env.default_hostname) r.env.home_dir = '/home/%s' % getpass.getuser() r.local('ssh-keyg...
def find_working_password(self, usernames=None, host_strings=None): """ Returns the first working combination of username and password for the current host. """ r = self.local_renderer if host_strings is None: host_strings = [] if not host_strings: ...
def needs_initrole(self, stop_on_error=False): """ Returns true if the host does not exist at the expected location and may need to have its initial configuration set. Returns false if the host exists at the expected location. """ ret = False target_host_present...
def initrole(self, check=True): """ Called to set default password login for systems that do not yet have passwordless login setup. """ if self.env.original_user is None: self.env.original_user = self.genv.user if self.env.original_key_filename is None: ...
def iter_hostnames(self): """ Yields a list of tuples of the form (ip, hostname). """ from burlap.common import get_hosts_retriever if self.env.use_retriever: self.vprint('using retriever') self.vprint('hosts:', self.genv.hosts) retriever = get...
def get_public_ip(self): """ Gets the public IP for a host. """ r = self.local_renderer ret = r.run(r.env.get_public_ip_command) or '' ret = ret.strip() print('ip:', ret) return ret
def configure(self, reboot=1): """ Assigns a name to the server accessible from user space. Note, we add the name to /etc/hosts since not all programs use /etc/hostname to reliably identify the server hostname. """ r = self.local_renderer for ip, hostname in self...
def update_tickets_from_git(self, from_commit=None, to_commit=None): """ Run during a deployment. Looks at all commits between now and the last deployment. Finds all ticket numbers and updates their status in Jira. """ from jira import JIRA, JIRAError #from burlap...
def partitions(device=""): """ Get a partition list for all disk or for selected device only Example:: from burlap.disk import partitions spart = {'Linux': 0x83, 'Swap': 0x82} parts = partitions() # parts = {'/dev/sda1': 131, '/dev/sda2': 130, '/dev/sda3': 131} r ...
def getdevice_by_uuid(uuid): """ Get a HDD device by uuid Example:: from burlap.disk import getdevice_by_uuid device = getdevice_by_uuid("356fafdc-21d5-408e-a3e9-2b3f32cb2a8c") if device: mount(device,'/mountpoint') """ with settings(hide('running', 'warnings',...
def ismounted(device): """ Check if partition is mounted Example:: from burlap.disk import ismounted if ismounted('/dev/sda1'): print ("disk sda1 is mounted") """ # Check filesystem with settings(hide('running', 'stdout')): res = run_as_root('mount') for...
def query(query, use_sudo=True, **kwargs): """ Run a MySQL query. """ func = use_sudo and run_as_root or run user = kwargs.get('mysql_user') or env.get('mysql_user') password = kwargs.get('mysql_password') or env.get('mysql_password') options = [ '--batch', '--raw', ...
def user_exists(name, host='localhost', **kwargs): """ Check if a MySQL user exists. """ with settings(hide('running', 'stdout', 'stderr', 'warnings'), warn_only=True): res = query(""" use mysql; SELECT COUNT(*) FROM user WHERE User = '%(name)s' AND Host =...
def create_user(name, password, host='localhost', **kwargs): """ Create a MySQL user. Example:: import burlap # Create DB user if it does not exist if not burlap.mysql.user_exists('dbuser'): burlap.mysql.create_user('dbuser', password='somerandomstring') """ w...
def database_exists(name, **kwargs): """ Check if a MySQL database exists. """ with settings(hide('running', 'stdout', 'stderr', 'warnings'), warn_only=True): res = query("SHOW DATABASES LIKE '%(name)s';" % { 'name': name }, **kwargs) return res.succeeded and (res == nam...
def create_database(name, owner=None, owner_host='localhost', charset='utf8', collate='utf8_general_ci', **kwargs): """ Create a MySQL database. Example:: import burlap # Create DB if it does not exist if not burlap.mysql.database_exists('myapp'): b...
def conf_path(self): """ Retrieves the path to the MySQL configuration file. """ from burlap.system import distrib_id, distrib_release hostname = self.current_hostname if hostname not in self._conf_cache: self.env.conf_specifics[hostname] = self.env.conf_defau...
def prep_root_password(self, password=None, **kwargs): """ Enters the root password prompt entries into the debconf cache so we can set them without user interaction. We keep this process separate from set_root_password() because we also need to do this before installing the bas...
def drop_views(self, name=None, site=None): """ Drops all views. """ r = self.database_renderer result = r.sudo("mysql --batch -v -h {db_host} " #"-u {db_root_username} -p'{db_root_password}' " "-u {db_user} -p'{db_password}' " "--execute=\"SEL...
def exists(self, **kwargs): """ Returns true if a database with the given name exists. False otherwise. """ name = kwargs.pop('name', 'default') site = kwargs.pop('site', None) r = self.database_renderer(name=name, site=site) ret = r.run('mysql -h {db_host} -u {db...
def load(self, dump_fn='', prep_only=0, force_upload=0, from_local=0, name=None, site=None, dest_dir=None, force_host=None): """ Restores a database snapshot onto the target database server. If prep_only=1, commands for preparing the load will be generated, but not the command to finall...
def shell(self, name='default', site=None, use_root=0, **kwargs): """ Opens a SQL shell to the given database, assuming the configured database and user supports this feature. """ r = self.database_renderer(name=name, site=site) if int(use_root): kwargs = dic...
def tic_single_object_crossmatch(ra, dec, radius): '''This does a cross-match against the TIC catalog on MAST. Speed tests: about 10 crossmatches per second. (-> 3 hours for 10^5 objects to crossmatch). Parameters ---------- ra,dec : np.array The coordinates to cross match against, al...
def normalized_flux_to_mag(lcdict, columns=('sap.sap_flux', 'sap.sap_flux_err', 'sap.sap_bkg', 'sap.sap_bkg_err', 'pdc.pdcsap_flux', ...
def get_time_flux_errs_from_Ames_lightcurve(infile, lctype, cadence_min=2): '''Reads TESS Ames-format FITS light curve files. MIT TOI alerts include Ames lightcurve files. This function gets the finite, nonzero times, f...
def read_tess_fitslc(lcfits, headerkeys=LCHEADERKEYS, datakeys=LCDATAKEYS, sapkeys=LCSAPKEYS, pdckeys=LCPDCKEYS, topkeys=LCTOPKEYS, apkeys=LCAPERTUREKEYS, normalize=False, ...
def consolidate_tess_fitslc(lclist, normalize=True, filterqualityflags=False, nanfilter=None, timestoignore=None, headerkeys=LCHEADERKEYS, datakeys=LCDA...
def filter_tess_lcdict(lcdict, filterqualityflags=True, nanfilter='sap,pdc,time', timestoignore=None, quiet=False): '''This filters the provided TESS `lcdict`, removing nans and bad observations. By default, this fu...
def _pkl_finder_objectinfo( objectinfo, varinfo, findercmap, finderconvolve, sigclip, normto, normmingap, deredden_object=True, custom_bandpasses=None, lclistpkl=None, nbrradiusarcsec=30.0, maxnumneighbors=5, plotdpi...
def _pkl_periodogram(lspinfo, plotdpi=100, override_pfmethod=None): '''This returns the periodogram plot PNG as base64, plus info as a dict. Parameters ---------- lspinfo : dict This is an lspinfo dict containing results from a period-finding f...
def _pkl_magseries_plot(stimes, smags, serrs, plotdpi=100, magsarefluxes=False): '''This returns the magseries plot PNG as base64, plus arrays as dict. Parameters ---------- stimes,smags,serrs : np.array The mag/flux time-series arrays along with...
def _pkl_phased_magseries_plot( checkplotdict, lspmethod, periodind, stimes, smags, serrs, varperiod, varepoch, lspmethodind=0, phasewrap=True, phasesort=True, phasebin=0.002, minbinelems=7, plotxlim=(-0.8,0.8), plotdpi=100,...
def prewhiten_magseries(times, mags, errs, whitenperiod, whitenparams, sigclip=3.0, magsarefluxes=False, plotfit=None, plotfitphasedlconly=True, rescale...
def gls_prewhiten(times, mags, errs, fourierorder=3, # 3rd order series to start with initfparams=None, startp_gls=None, endp_gls=None, stepsize=1.0e-4, autofreq=True, sigclip=30.0, ...
def mask_signal(times, mags, errs, signalperiod, signalepoch, magsarefluxes=False, maskphases=(0,0,0.5,1.0), maskphaselength=0.1, plotfit=None, plotfitphasedlconly=True, sigclip=30.0): '''...
def main(): ''' This launches the server. The current script args are shown below:: Usage: checkplotserver [OPTIONS] Options: --help show this help information checkplotserver.py options: --assetpath Sets the asset (server ima...
def find_lc_timegroups(lctimes, mingap=4.0): '''Finds gaps in the provided time-series and indexes them into groups. This finds the gaps in the provided `lctimes` array, so we can figure out which times are for consecutive observations and which represent gaps between seasons or observing eras. Pa...
def normalize_magseries(times, mags, mingap=4.0, normto='globalmedian', magsarefluxes=False, debugmode=False): '''This normalizes the magnitude time-series to a specified value. This is used ...
def sigclip_magseries(times, mags, errs, sigclip=None, iterative=False, niterations=None, meanormedian='median', magsarefluxes=False): '''Sigma-clips a magnitude or flux time-series. Selects the finite...
def sigclip_magseries_with_extparams(times, mags, errs, extparams, sigclip=None, iterative=False, magsarefluxes=False): '''Sigma-clips a magnitude or flux time-series and associated measurement arrays....
def phase_magseries(times, mags, period, epoch, wrap=True, sort=True): '''Phases a magnitude/flux time-series using a given period and epoch. The equation used is:: phase = (times - epoch)/period - floor((times - epoch)/period) This phases the given magnitude timeseries using the given period and...
def time_bin_magseries(times, mags, binsize=540.0, minbinelems=7): '''Bins the given mag/flux time-series in time using the bin size given. Parameters ---------- times,mags : np.array The magnitude/flux time-series to bin in time. Non-finite elemen...
def phase_bin_magseries(phases, mags, binsize=0.005, minbinelems=7): '''Bins a phased magnitude/flux time-series using the bin size provided. Parameters ---------- phases,mags : np.array The phased magnitude/flux time-series to bin in phase. Non-...
def fill_magseries_gaps(times, mags, errs, fillgaps=0.0, sigclip=3.0, magsarefluxes=False, filterwindow=11, forcetimebin=None, verbose=True): '''This fills in gaps in a lig...
def get_snr_of_dip(times, mags, modeltimes, modelmags, atol_normalization=1e-8, indsforrms=None, magsarefluxes=False, verbose=True, transitdepth=None, ...
def estimate_achievable_tmid_precision(snr, t_ingress_min=10, t_duration_hr=2.14): '''Using Carter et al. 2009's estimate, calculate the theoretical optimal precision on mid-transit time measurement possible given a transit of a particular SNR. The relation used i...
def get_transit_times( blsd, time, extra_maskfrac, trapd=None, nperiodint=1000 ): '''Given a BLS period, epoch, and transit ingress/egress points (usually from :py:func:`astrobase.periodbase.kbls.bls_stats_singleperiod`), return the times within transit durations + `e...
def given_lc_get_transit_tmids_tstarts_tends( time, flux, err_flux, blsfit_savpath=None, trapfit_savpath=None, magsarefluxes=True, nworkers=1, sigclip=None, extra_maskfrac=0.03 ): '''Gets the transit start, middle, and end times for transits in...
def given_lc_get_out_of_transit_points( time, flux, err_flux, blsfit_savpath=None, trapfit_savpath=None, in_out_transit_savpath=None, sigclip=None, magsarefluxes=True, nworkers=1, extra_maskfrac=0.03 ): '''This gets the out-of-transit light curve point...
def _pycompress_sqlitecurve(sqlitecurve, force=False): '''This just compresses the sqlitecurve. Should be independent of OS. ''' outfile = '%s.gz' % sqlitecurve try: if os.path.exists(outfile) and not force: os.remove(sqlitecurve) return outfile else: ...
def _pyuncompress_sqlitecurve(sqlitecurve, force=False): '''This just uncompresses the sqlitecurve. Should be independent of OS. ''' outfile = sqlitecurve.replace('.gz','') try: if os.path.exists(outfile) and not force: return outfile else: with gzip.open(sq...
def _gzip_sqlitecurve(sqlitecurve, force=False): '''This just compresses the sqlitecurve in gzip format. FIXME: this doesn't work with gzip < 1.6 or non-GNU gzip (probably). ''' # -k to keep the input file just in case something explodes if force: cmd = 'gzip -k -f %s' % sqlitecurve e...
def _gunzip_sqlitecurve(sqlitecurve): '''This just uncompresses the sqlitecurve in gzip format. FIXME: this doesn't work with gzip < 1.6 or non-GNU gzip (probably). ''' # -k to keep the input .gz just in case something explodes cmd = 'gunzip -k %s' % sqlitecurve try: subprocess.check...
def _validate_sqlitecurve_filters(filterstring, lccolumns): '''This validates the sqlitecurve filter string. This MUST be valid SQL but not contain any commands. ''' # first, lowercase, then _squeeze to single spaces stringelems = _squeeze(filterstring).lower() # replace shady characters ...
def read_and_filter_sqlitecurve(lcfile, columns=None, sqlfilters=None, raiseonfail=False, returnarrays=True, forcerecompress=False, ...
def describe(lcdict, returndesc=False, offsetwith=None): '''This describes the light curve object and columns present. Parameters ---------- lcdict : dict The input lcdict to parse for column and metadata info. returndesc : bool If True, returns the description string as an str in...
def _smartcast(castee, caster, subval=None): ''' This just tries to apply the caster function to castee. Returns None on failure. ''' try: return caster(castee) except Exception as e: if caster is float or caster is int: return nan elif caster is str: ...
def _parse_csv_header(header): ''' This parses the CSV header from the CSV HAT sqlitecurve. Returns a dict that can be used to update an existing lcdict with the relevant metadata info needed to form a full LC. ''' # first, break into lines headerlines = header.split('\n') headerlines...
def _parse_csv_header_lcc_csv_v1(headerlines): ''' This parses the header of the LCC CSV V1 LC format. ''' # the first three lines indicate the format name, comment char, separator commentchar = headerlines[1] separator = headerlines[2] headerlines = [x.lstrip('%s ' % commentchar) for x i...
def read_lcc_csvlc(lcfile): '''This reads a CSV LC produced by an `LCC-Server <https://github.com/waqasbhatti/lcc-server>`_ instance. Parameters ---------- lcfile : str The LC file to read. Returns ------- dict Returns an lcdict that's readable by most astrobase funct...
def describe_lcc_csv(lcdict, returndesc=False): ''' This describes the LCC CSV format light curve file. Parameters ---------- lcdict : dict The input lcdict to parse for column and metadata info. returndesc : bool If True, returns the description string as an str instead of ju...
def read_csvlc(lcfile): '''This reads a HAT data server or LCC-Server produced CSV light curve into an lcdict. This will automatically figure out the format of the file provided. Currently, it can read: - legacy HAT data server CSV LCs (e.g. from https://hatsouth.org/planets/lightcurves.html...
def find_lc_timegroups(lctimes, mingap=4.0): '''This finds the time gaps in the light curve, so we can figure out which times are for consecutive observations and which represent gaps between seasons. Parameters ---------- lctimes : np.array This is the input array of times, assumed to...
def normalize_lcdict(lcdict, timecol='rjd', magcols='all', mingap=4.0, normto='sdssr', debugmode=False, quiet=False): '''This normalizes magcols in `lcdict` using `timecol` to find timegroup...
def normalize_lcdict_byinst( lcdict, magcols='all', normto='sdssr', normkeylist=('stf','ccd','flt','fld','prj','exp'), debugmode=False, quiet=False ): '''This is a function to normalize light curves across all instrument combinations present. Use this to norm...
def main(): ''' This is called when we're executed from the commandline. The current usage from the command-line is described below:: usage: hatlc [-h] [--describe] hatlcfile read a HAT LC of any format and output to stdout positional arguments: hatlcfile path to the ...
def coord_features(objectinfo): '''Calculates object coordinates features, including: - galactic coordinates - total proper motion from pmra, pmdecl - reduced J proper motion from propermotion and Jmag Parameters ---------- objectinfo : dict This is an objectinfo dict from a ligh...
def color_features(in_objectinfo, deredden=True, custom_bandpasses=None, dust_timeout=10.0): '''Stellar colors and dereddened stellar colors using 2MASS DUST API: http://irsa.ipac.caltech.edu/applications/DUST/docs/dustProgramInterface.html Paramete...
def mdwarf_subtype_from_sdsscolor(ri_color, iz_color): '''This calculates the M-dwarf subtype given SDSS `r-i` and `i-z` colors. Parameters ---------- ri_color : float The SDSS `r-i` color of the object. iz_color : float The SDSS `i-z` color of the object. Returns -------...
def color_classification(colorfeatures, pmfeatures): '''This calculates rough star type classifications based on star colors in the ugrizJHK bands. Uses the output from `color_features` and `coord_features`. By default, `color_features` will use dereddened colors, as are expected by most relations ...
def neighbor_gaia_features(objectinfo, lclist_kdtree, neighbor_radius_arcsec, gaia_matchdist_arcsec=3.0, verbose=True, gaia_submit_timeout=10.0, gaia_submit_t...
def apply_epd_magseries(lcfile, timecol, magcol, errcol, externalparams, lcformat='hat-sql', lcformatdir=None, epdsmooth_sigclip=3.0, ...
def parallel_epd_worker(task): '''This is a parallel worker for the function below. Parameters ---------- task : tuple - task[0] = lcfile - task[1] = timecol - task[2] = magcol - task[3] = errcol - task[4] = externalparams - task[5] = lcformat - ...
def parallel_epd_lclist(lclist, externalparams, timecols=None, magcols=None, errcols=None, lcformat='hat-sql', lcformatdir=None, epdsmooth_sigclip=3.0, ...
def parallel_epd_lcdir( lcdir, externalparams, lcfileglob=None, timecols=None, magcols=None, errcols=None, lcformat='hat-sql', lcformatdir=None, epdsmooth_sigclip=3.0, epdsmooth_windowsize=21, epdsmooth_func=smooth_magseries_savgol,...
def bls_serial_pfind(times, mags, errs, magsarefluxes=False, startp=0.1, # search from 0.1 d to... endp=100.0, # ... 100.0 d -- don't search full timebase stepsize=5.0e-4, mintransitduration=0.01, # minimum trans...
def _parallel_bls_worker(task): ''' This wraps Astropy's BoxLeastSquares for use with bls_parallel_pfind below. `task` is a tuple:: task[0] = times task[1] = mags task[2] = errs task[3] = magsarefluxes task[4] = minfreq task[5] = nfreq task[6] = ste...