arvi 0.1.11__tar.gz → 0.1.12__tar.gz

{arvi-0.1.11 → arvi-0.1.12}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: arvi
-Version: 0.1.11
+Version: 0.1.12
 Summary: The Automated RV Inspector
 Author-email: João Faria <joao.faria@unige.ch>
 License: MIT

{arvi-0.1.11 → arvi-0.1.12}/arvi/__init__.py

@@ -8,6 +8,7 @@ def __getattr__(name: str):
     if name in (
         '_ipython_canary_method_should_not_exist_',
         '_repr_mimebundle_',
+        '__wrapped__'
     ):
         return
 

arvi-0.1.12/arvi/ariadne_wrapper.py

@@ -0,0 +1,70 @@
+import os
+import sys
+from matplotlib import pyplot as plt
+
+try:
+    from astroARIADNE.star import Star
+    from astroARIADNE.fitter import Fitter
+except ImportError:
+    print('This module requires astroARIADNE. Install with `pip install astroARIADNE`')
+    sys.exit(0)
+
+
+def run_ariadne(self, fit=True, plot=True, priors={},
+                models = ('phoenix', 'btsettl', 'btnextgen', 'btcond', 'kurucz', 'ck04'),
+                nlive=300, dlogz=1, threads=6, dynamic=False, **kwargs):
+    if hasattr(self, 'gaia'):
+        s = Star(self.star, self.gaia.ra, self.gaia.dec, g_id=self.gaia.dr3_id,
+                 search_radius=1)
+    else:
+        s = Star(self.star, self.simbad.ra, self.simbad.dec, g_id=self.simbad.gaia_id,
+                 search_radius=1)
+
+    out_folder = f'{self.star}_ariadne'
+
+    setup = dict(engine='dynesty', nlive=nlive, dlogz=dlogz,
+                 bound='multi', sample='auto', threads=threads, dynamic=dynamic)
+    setup = list(setup.values())
+
+    f = Fitter()
+    f.star = s
+    f.setup = setup
+    f.av_law = 'fitzpatrick'
+    f.out_folder = out_folder
+    f.bma = True
+    f.models = models
+    f.n_samples = 10_000
+
+    f.prior_setup = {
+            'teff': priors.get('teff', ('default')),
+            'logg': ('default'),
+            'z': priors.get('feh', ('default')),
+            'dist': ('default'),
+            'rad': ('default'),
+            'Av': ('default')
+    }
+
+    if fit:
+        f.initialize()
+        f.fit_bma()
+
+    if plot:
+        from pkg_resources import resource_filename
+        from astroARIADNE.plotter import SEDPlotter
+        modelsdir = resource_filename('astroARIADNE', 'Datafiles/models')
+        artist = SEDPlotter(os.path.join(out_folder, 'BMA.pkl'), out_folder, models_dir=modelsdir)
+
+        artist.plot_SED_no_model()
+        try:
+            artist.plot_SED()
+        except FileNotFoundError as e:
+            print('No model found:', e)
+        except IndexError as e:
+            print('Error!')
+        artist.plot_bma_hist()
+        artist.plot_bma_HR(10)
+        artist.plot_corner()
+        plt.close('all')
+        return s, f, artist
+
+    return s, f

arvi-0.1.12/arvi/config.py

@@ -0,0 +1,8 @@
+# whether to return self from (some) RV methods
+return_self = False
+
+# whether to check internet connection before querying DACE
+check_internet = False
+
+# make all DACE requests without using a .dacerc file
+request_as_public = False

{arvi-0.1.11 → arvi-0.1.12}/arvi/dace_wrapper.py

@@ -9,6 +9,11 @@ from .utils import create_directory, all_logging_disabled, stdout_disabled, tqdm
 
 
 def load_spectroscopy() -> SpectroscopyClass:
+    from .config import request_as_public
+    if request_as_public:
+        with all_logging_disabled():
+            dace = DaceClass(dace_rc_config_path='none')
+        return SpectroscopyClass(dace_instance=dace)
     if 'DACERC' in os.environ:
         dace = DaceClass(dace_rc_config_path=os.environ['DACERC'])
         return SpectroscopyClass(dace_instance=dace)
@@ -181,9 +186,9 @@ def check_existing(output_directory, files, type):
 def download(files, type, output_directory):
     """ Download files from DACE """
     Spectroscopy = load_spectroscopy()
-    # with stdout_disabled(), all_logging_disabled():
-    Spectroscopy.download_files(files, file_type=type.lower(),
-                                output_directory=output_directory)
+    with stdout_disabled(), all_logging_disabled():
+        Spectroscopy.download_files(files, file_type=type.lower(),
+                                    output_directory=output_directory)
 
 def extract_fits(output_directory):
     """ Extract fits files from tar.gz file """
@@ -212,21 +217,30 @@ def do_download_filetype(type, raw_files, output_directory, clobber=False,
     if not clobber:
         raw_files = check_existing(output_directory, raw_files, type)
 
+    n = raw_files.size
+
     # any file left to download?
-    if raw_files.size == 0:
+    if n == 0:
         if verbose:
             logger.info('no files to download')
         return
 
-    if verbose:
-        n = raw_files.size
-        logger.info(f"Downloading {n} {type}s into '{output_directory}'...")
-
     # avoid an empty chunk
     if chunk_size > n:
         chunk_size = n
 
-    for files in tqdm(zip(*(iter(raw_files),) * chunk_size), total=n // chunk_size):
+    if verbose:
+        if chunk_size < n:
+            msg = f"Downloading {n} {type}s "
+            msg += f"(in chunks of {chunk_size}) "
+            msg += f"into '{output_directory}'..."
+            logger.info(msg)
+        else:
+            msg = f"Downloading {n} {type}s into '{output_directory}'..."
+            logger.info(msg)
+
+    iterator = [raw_files[i:i + chunk_size] for i in range(0, n, chunk_size)]
+    for files in tqdm(iterator, total=len(iterator)):
         download(files, type, output_directory)
         extract_fits(output_directory)
 

arvi-0.1.12/arvi/gaia_wrapper.py

@@ -0,0 +1,94 @@
+import os
+from io import StringIO
+from csv import DictReader
+from dataclasses import dataclass, field
+import requests
+
+from astropy.coordinates import SkyCoord
+import pysweetcat
+
+DATA_PATH = os.path.dirname(__file__)
+DATA_PATH = os.path.join(DATA_PATH, 'data')
+
+QUERY = """
+SELECT TOP 20 gaia_source.designation,gaia_source.source_id,gaia_source.ra,gaia_source.dec,gaia_source.parallax,gaia_source.pmra,gaia_source.pmdec,gaia_source.ruwe,gaia_source.phot_g_mean_mag,gaia_source.bp_rp,gaia_source.radial_velocity,gaia_source.phot_variable_flag,gaia_source.non_single_star,gaia_source.has_xp_continuous,gaia_source.has_xp_sampled,gaia_source.has_rvs,gaia_source.has_epoch_photometry,gaia_source.has_epoch_rv,gaia_source.has_mcmc_gspphot,gaia_source.has_mcmc_msc,gaia_source.teff_gspphot,gaia_source.logg_gspphot,gaia_source.mh_gspphot,gaia_source.distance_gspphot,gaia_source.azero_gspphot,gaia_source.ag_gspphot,gaia_source.ebpminrp_gspphot
+FROM gaiadr3.gaia_source 
+WHERE 
+CONTAINS(
+	POINT('ICRS',gaiadr3.gaia_source.ra,gaiadr3.gaia_source.dec),
+	CIRCLE(
+		'ICRS',
+		COORD1(EPOCH_PROP_POS({ra},{dec},{plx},{pmra},{pmdec},{rv},2000,2016.0)),
+		COORD2(EPOCH_PROP_POS({ra},{dec},{plx},{pmra},{pmdec},{rv},2000,2016.0)),
+		0.001388888888888889)
+)=1
+"""
+
+def run_query(query):
+    url = 'https://gea.esac.esa.int/tap-server/tap/sync'
+    data = dict(query=query, request='doQuery', lang='ADQL', format='csv')
+    try:
+        response = requests.post(url, data=data, timeout=10)
+    except requests.ReadTimeout as err:
+        raise IndexError(err)
+    except requests.ConnectionError as err:
+        raise IndexError(err)
+    return response.content.decode()
+
+def parse_csv(csv):
+    reader = DictReader(StringIO(csv))
+    return list(reader)
+
+
+class gaia:
+    """
+    A very simple wrapper around a TAP query to gaia for a given target. This
+    class simply runs a few TAP queries and stores the result as attributes.
+
+    Attributes:
+        ra (float): right ascension
+        dec (float): declination
+        coords (SkyCoord): coordinates as a SkyCoord object
+        dr3_id (int): Gaia DR3 identifier
+        plx (float): parallax
+        radial_velocity (float): radial velocity
+    """
+    def __init__(self, star:str, simbad=None):
+        """
+        Args:
+            star (str): The name of the star to query simbad
+        """
+        self.star = star
+
+        if simbad is None:
+            from .simbad_wrapper import simbad as Simbad
+            simbad = Simbad(star)
+
+        ra = simbad.ra
+        dec = simbad.dec
+        plx = simbad.plx
+        pmra = simbad.pmra
+        pmdec = simbad.pmdec
+        rv = simbad.rvz_radvel
+        args = dict(ra=ra, dec=dec, plx=plx, pmra=pmra, pmdec=pmdec, rv=rv)          
+
+        try:
+            table1 = run_query(query=QUERY.format(**args))
+            results = parse_csv(table1)[0]
+        except IndexError:
+            raise ValueError(f'Gaia query for {star} failed')
+
+        self.dr3_id = int(results['source_id'])
+
+        self.ra = float(results['ra'])
+        self.dec = float(results['dec'])
+        self.pmra = float(results['pmra'])
+        self.pmdec = float(results['pmdec'])
+        self.coords = SkyCoord(self.ra, self.dec, unit='deg')
+        self.plx = float(results['parallax'])
+        self.radial_velocity = float(results['radial_velocity'])
+
+        return
+
+    def __repr__(self):
+        return f'{self.star} (DR3 id={self.dr3_id})'

{arvi-0.1.11 → arvi-0.1.12}/arvi/programs.py

@@ -1,5 +1,7 @@
 import os
-import concurrent.futures
+import multiprocessing
+from functools import partial
+from itertools import chain
 from collections import namedtuple
 from tqdm import tqdm
 # import numpy as np
@@ -13,7 +15,8 @@ path = os.path.join(os.path.dirname(__file__), 'data')
 
 
 def get_star(star, instrument=None):
-    return RV(star, verbose=False, instrument=instrument, _raise_on_error=False)
+    return RV(star, instrument=instrument,
+              _raise_on_error=False, verbose=False, load_extra_data=False)
 
 
 class LazyRV:
@@ -22,6 +25,7 @@ class LazyRV:
         if isinstance(self.stars, str):
             self.stars = [self.stars]
         self.instrument = instrument
+        self._saved = None
 
     @property
     def N(self):
@@ -31,30 +35,49 @@ class LazyRV:
         return f"RV({self.N} stars)"
 
     def _get(self):
-        result = []
-        # use a with statement to ensure threads are cleaned up promptly
-        with concurrent.futures.ThreadPoolExecutor(max_workers=8) as pool:
-            star_to_RV = {
-                pool.submit(get_star, star, self.instrument): star 
-                for star in self.stars
-            }
+        if self.N > 10:
+            # logger.info('Querying DACE...')
+            _get_star = partial(get_star, instrument=self.instrument)
+            with multiprocessing.Pool() as pool:
+                result = list(tqdm(pool.imap(_get_star, self.stars), 
+                                   total=self.N, unit='star', desc='Querying DACE'))
+                # result = pool.map(get_star, self.stars)
+        else:
+            result = []
             logger.info('Querying DACE...')
-            pbar = tqdm(concurrent.futures.as_completed(star_to_RV),
-                        total=self.N, unit='star')
-            for future in pbar:
-                star = star_to_RV[future]
+            pbar = tqdm(self.stars, total=self.N, unit='star')
+            for star in pbar:
                 pbar.set_description(star)
-                try:
-                    result.append(future.result())
-                except Exception:
-                    print(f'{star} generated an exception')
+                result.append(get_star(star, self.instrument))
+
         return result
 
+        # # use a with statement to ensure threads are cleaned up promptly
+        # with concurrent.futures.ThreadPoolExecutor(max_workers=8) as pool:
+        #     star_to_RV = {
+        #         pool.submit(get_star, star, self.instrument): star 
+        #         for star in self.stars
+        #     }
+        #     logger.info('Querying DACE...')
+        #     pbar = tqdm(concurrent.futures.as_completed(star_to_RV),
+        #                 total=self.N, unit='star')
+        #     for future in pbar:
+        #         star = star_to_RV[future]
+        #         pbar.set_description(star)
+        #         try:
+        #             result.append(future.result())
+        #         except ValueError:
+        #             print(f'{star} generated an exception')
+        #             result.append(None)
+        # return result
+
     def __iter__(self):
         return self._get()
 
     def __call__(self):
-        return self._get()
+        if not self._saved:
+            self._saved = self._get()
+        return self._saved
 
 
 # sorted by spectral type

{arvi-0.1.11 → arvi-0.1.12}/arvi/simbad_wrapper.py

@@ -85,7 +85,8 @@ class simbad:
         dec (float): declination
         coords (SkyCoord): coordinates as a SkyCoord object
         main_id (str): main identifier
-        plx_value (float): parallax
+        gaia_id (int): Gaia DR3 identifier
+        plx (float): parallax
         rvz_radvel (float): radial velocity
         sp_type (str): spectral type
         B (float): B magnitude 
@@ -125,6 +126,8 @@ class simbad:
         except IndexError:
             raise ValueError(f'simbad query for {star} failed')
 
+        self.gaia_id = int([i for i in self.ids if 'Gaia DR3' in i][0].split('Gaia DR3')[-1])
+
         for col, val in zip(cols, values):
             if col == 'oid':
                 setattr(self, col, str(val))
@@ -138,6 +141,9 @@ class simbad:
 
         if self.plx_value == '':
             self.plx_value = None
+        
+        self.plx = self._plx_value = self.plx_value
+        del self.plx_value
 
         try:
             swc_data = pysweetcat.get_data()

{arvi-0.1.11 → arvi-0.1.12}/arvi/timeseries.py

@@ -15,6 +15,7 @@ from .config import return_self, check_internet
 from .translations import translate
 from .dace_wrapper import do_download_filetype, get_observations, get_arrays
 from .simbad_wrapper import simbad
+from .gaia_wrapper import gaia
 from .extra_data import get_extra_data
 from .stats import wmean, wrms
 from .binning import bin_ccf_mask, binRV
@@ -49,7 +50,7 @@ class RV:
     do_sigma_clip: bool = field(init=True, repr=False, default=False)
     do_adjust_means: bool = field(init=True, repr=False, default=True)
     only_latest_pipeline: bool = field(init=True, repr=False, default=True)
-    load_extra_data: Union[bool, str] = field(init=True, repr=False, default=True)
+    load_extra_data: Union[bool, str] = field(init=True, repr=False, default=False)
     #
     _child: bool = field(init=True, repr=False, default=False)
     _did_secular_acceleration: bool = field(init=False, repr=False, default=False)
@@ -72,6 +73,7 @@ class RV:
         if not self._child:
             if check_internet and not there_is_internet():
                 raise ConnectionError('There is no internet connection?')
+
             # complicated way to query Simbad with self.__star__ or, if that
             # fails, try after removing a trailing 'A'
             for target in (self.__star__, self.__star__.replace('A', '')):
@@ -84,11 +86,23 @@ class RV:
                 if self.verbose:
                     logger.error(f'simbad query for {self.__star__} failed')
 
+            # complicated way to query Gaia with self.__star__ or, if that
+            # fails, try after removing a trailing 'A'
+            for target in (self.__star__, self.__star__.replace('A', '')):
+                try:
+                    self.gaia = gaia(target)
+                    break
+                except ValueError:
+                    continue
+            else:
+                if self.verbose:
+                    logger.error(f'Gaia query for {self.__star__} failed')
+
             # query DACE
             if self.verbose:
                 logger.info(f'querying DACE for {self.__star__}...')
             try:
-                self.dace_result = get_observations(self.__star__, self.instrument, 
+                self.dace_result = get_observations(self.__star__, self.instrument,
                                                     verbose=self.verbose)
             except ValueError as e:
                 # querying DACE failed, should we raise an error?
@@ -248,7 +262,7 @@ class RV:
         """ Masked array of times """
         return self.time[self.mask]
 
-    @property  
+    @property
     def mvrad(self) -> np.ndarray:
         """ Masked array of radial velocities """
         return self.vrad[self.mask]
@@ -374,7 +388,7 @@ class RV:
             star, timestamp = file.replace('.pkl', '').split('_')
         else:
             try:
-                file = sorted(glob(f'{star}_*.pkl'))[-1]
+                file = sorted(glob(f'{star}_*.*.pkl'))[-1]
             except IndexError:
                 raise ValueError(f'cannot find any file matching {star}_*.pkl')
             star, timestamp = file.replace('.pkl', '').split('_')
@@ -409,7 +423,7 @@ class RV:
             if star_.size == 1:
                 logger.info(f'assuming star is {star_[0]}')
                 star = star_[0]
-        
+
         if instrument is None:
             instruments = np.array([os.path.splitext(f)[0].split('_')[1] for f in files])
             logger.info(f'assuming instruments: {instruments}')
@@ -495,7 +509,7 @@ class RV:
             for q in ['drs_qc']:
                 setattr(_s, q, np.full(time.size, True))
                 _quantities.append(q)
-            
+
             #! end hack
 
             _s.mask = np.ones_like(time, dtype=bool)
@@ -522,10 +536,10 @@ class RV:
         except ImportError:
             logger.error('iCCF is not installed. Please install it with `pip install iCCF`')
             return
-        
+
         if isinstance(files, str):
             files = [files]
-    
+
         I = iCCF.from_file(files)
 
         objects = np.unique([i.HDU[0].header['OBJECT'].replace(' ', '') for i in I])
@@ -729,13 +743,13 @@ class RV:
 
     def remove_instrument(self, instrument, strict=False):
         """ Remove all observations from one instrument
-        
+
         Args:
             instrument (str or list):
                 The instrument(s) for which to remove observations.
             strict (bool):
                 Whether to match (each) `instrument` exactly
-        
+
         Note:
             A common name can be used to remove observations for several subsets
             of a given instrument. For example
@@ -788,11 +802,24 @@ class RV:
         if return_self:
             return self
 
+    def remove_condition(self, condition):
+        """ Remove all observations that satisfy a condition
+
+        Args:
+            condition (np.ndarray):
+                Boolean array of the same length as the observations
+        """
+        if self.verbose:
+            inst = np.unique(self.instrument_array[condition])
+            logger.info(f"Removing {condition.sum()} points from instruments {inst}")
+        self.mask = self.mask & ~condition
+        self._propagate_mask_changes()
+
     def remove_point(self, index):
         """
         Remove individual observations at a given index (or indices).
         NOTE: Like Python, the index is 0-based.
-        
+
         Args:
             index (int, list, ndarray):
                 Single index, list, or array of indices to remove.
@@ -899,45 +926,76 @@ class RV:
             n_before = (self.obs < self.obs[m]).sum()
             getattr(self, inst).mask[m - n_before] = False
 
-    def secular_acceleration(self, epoch=55500, plot=False):
+    def secular_acceleration(self, epoch=None, just_compute=False, force_simbad=False):
         """
         Remove secular acceleration from RVs
 
         Args:
-            epoch (float):
+            epoch (float, optional):
                 The reference epoch (DACE uses 55500, 31/10/2010)
             instruments (bool or collection of str):
-                Only remove secular acceleration for some instruments, or for all 
+                Only remove secular acceleration for some instruments, or for all
                 if `instruments=True`
-            plot (bool):
-                Show a plot of the RVs with the secular acceleration
         """
-        if self._did_secular_acceleration:  # don't do it twice
+        if self._did_secular_acceleration and not just_compute:  # don't do it twice
             return
-        
+
+        #as_yr = units.arcsec / units.year
+        mas_yr = units.milliarcsecond / units.year
+        mas = units.milliarcsecond
+
         try:
-            self.simbad
-        except AttributeError:
+            if force_simbad:
+                raise AttributeError
+
+            self.gaia
+            self.gaia.plx
+
             if self.verbose:
-                logger.error('no information from simbad, cannot remove secular acceleration')
-            return
+                logger.info('using Gaia information to remove secular acceleration')
+
+            if epoch is None:
+                # Gaia DR3 epoch (astropy.time.Time('J2016.0', format='jyear_str').jd)
+                epoch = 57389.0
+
+            π = self.gaia.plx * mas
+            d = π.to(units.pc, equivalencies=units.parallax())
+            μα = self.gaia.pmra * mas_yr
+            μδ = self.gaia.pmdec * mas_yr
+            μ = μα**2 + μδ**2
+            sa = (μ * d).to(units.m / units.second / units.year,
+                            equivalencies=units.dimensionless_angles())
+
+        except AttributeError:
+            try:
+                self.simbad
+            except AttributeError:
+                if self.verbose:
+                    logger.error('no information from simbad, cannot remove secular acceleration')
+                return
+
+            if self.simbad.plx is None:
+                if self.verbose:
+                    logger.error('no parallax from simbad, cannot remove secular acceleration')
+                return
 
-        if self.simbad.plx_value is None:
             if self.verbose:
-                logger.error('no parallax from simbad, cannot remove secular acceleration')
-            return
+                logger.info('using Simbad information to remove secular acceleration')
 
-        #as_yr = units.arcsec / units.year
-        mas_yr = units.milliarcsecond / units.year
-        mas = units.milliarcsecond
+            if epoch is None:
+                epoch = 55500
+
+            π = self.simbad.plx * mas
+            d = π.to(units.pc, equivalencies=units.parallax())
+            μα = self.simbad.pmra * mas_yr
+            μδ = self.simbad.pmdec * mas_yr
+            μ = μα**2 + μδ**2
+            sa = (μ * d).to(units.m / units.second / units.year,
+                            equivalencies=units.dimensionless_angles())
+
+        if just_compute:
+            return sa
 
-        π = self.simbad.plx_value * mas
-        d = π.to(units.pc, equivalencies=units.parallax())
-        μα = self.simbad.pmra * mas_yr
-        μδ = self.simbad.pmdec * mas_yr
-        μ = μα**2 + μδ**2
-        sa = (μ * d).to(units.m / units.second / units.year,
-                        equivalencies=units.dimensionless_angles())
         sa = sa.value
 
         if self.verbose:
@@ -961,7 +1019,7 @@ class RV:
                     continue
 
                 s.vrad = s.vrad - sa * (s.time - epoch) / 365.25
-            
+
             self._build_arrays()
 
         self._did_secular_acceleration = True
@@ -1012,7 +1070,7 @@ class RV:
 
     def clip_maxerror(self, maxerror:float):
         """ Mask out points with RV error larger than a given value
-        
+
         Args:
             maxerror (float): Maximum error to keep.
         """
@@ -1038,10 +1096,10 @@ class RV:
 
         WARNING: This creates and returns a new object and does not modify self.
         """
-        
+
         # create copy of self to be returned
         snew = deepcopy(self)
-        
+
         all_bad_quantities = []
 
         for inst in snew.instruments:
@@ -1050,7 +1108,7 @@ class RV:
             # only one observation?
             if s.N == 1:
                 continue
-        
+
             # are all observations masked?
             if s.mtime.size == 0:
                 continue
@@ -1101,7 +1159,7 @@ class RV:
                     with warnings.catch_warnings():
                         warnings.filterwarnings('ignore', category=RuntimeWarning)
                         try:
-                            _, yb = binRV(s.mtime, Q[s.mask], 
+                            _, yb = binRV(s.mtime, Q[s.mask],
                                         stat=np.nanmean, tstat=np.nanmean)
                             setattr(s, q, yb)
                         except TypeError:
@@ -1116,7 +1174,7 @@ class RV:
 
             s.time = tb
             s.mask = np.full(tb.shape, True)
-        
+
         if snew.verbose and len(all_bad_quantities) > 0:
             logger.warning('\nnew object will not have these non-float quantities')
 
@@ -1186,7 +1244,7 @@ class RV:
                 # log_msg += other
                 # if i < len(others) - 1:
                 #     log_msg += ', '
-            
+
             # if self.verbose:
             #     logger.info(log_msg)
 
@@ -1237,7 +1295,7 @@ class RV:
             self._build_arrays()
 
 
-    def save(self, directory=None, instrument=None, full=False,
+    def save(self, directory=None, instrument=None, full=False, postfix=None,
              save_masked=False, save_nans=True):
         """ Save the observations in .rdb files.
 
@@ -1246,9 +1304,10 @@ class RV:
                 Directory where to save the .rdb files.
             instrument (str, optional):
                 Instrument for which to save observations.
-            full (bool, optional): 
-                Whether to save just RVs and errors (False) or more indicators
-                (True).
+            full (bool, optional):
+                Save just RVs and errors (False) or more indicators (True).
+            postfix (str, optional):
+                Postfix to add to the filenames ([star]_[instrument]_[postfix].rdb).
             save_nans (bool, optional)
                 Whether to save NaN values in the indicators, if they exist. If
                 False, the full observation is not saved.
@@ -1301,8 +1360,11 @@ class RV:
                 else:
                     d = np.c_[_s.mtime, _s.mvrad, _s.msvrad]
                 header = 'bjd\tvrad\tsvrad\n---\t----\t-----'
-            
+
             file = f'{star_name}_{inst}.rdb'
+            if postfix is not None:
+                file = f'{star_name}_{inst}_{postfix}.rdb'
+
             files.append(file)
             file = os.path.join(directory, file)
 
@@ -1310,7 +1372,7 @@ class RV:
 
             if self.verbose:
                 logger.info(f'saving to {file}')
-        
+
         return files
 
     def checksum(self, write_to=None):
@@ -1325,7 +1387,7 @@ class RV:
 
 
     #
-    def run_lbl(self, instrument=None, data_dir=None, 
+    def run_lbl(self, instrument=None, data_dir=None,
                 skysub=False, tell=False, limit=None, **kwargs):
         from .lbl_wrapper import run_lbl, NIRPS_create_telluric_corrected_S2D
 
@@ -1339,7 +1401,7 @@ class RV:
                     logger.error(f"No data from instrument '{instrument}'")
                     logger.info(f'available: {self.instruments}')
                     return
-            
+
             if isinstance(instrument, str):
                 instruments = [instrument]
             else:
@@ -1394,7 +1456,7 @@ class RV:
                     logger.error(f"No data from instrument '{instrument}'")
                     logger.info(f'available: {self.instruments}')
                     return
-            
+
             if isinstance(instrument, str):
                 instruments = [instrument]
             else:
@@ -1448,4 +1510,4 @@ def fit_sine(t, y, yerr, period='gls', fix_period=False):
     p0 = [y.ptp(), period, 0.0, 0.0]
     xbest, _ = leastsq(lambda p, t, y, ye: (sine(t, p) - y) / ye,
                        p0, args=(t, y, yerr))
-    return xbest, partial(sine, p=xbest)
+    return xbest, partial(sine, p=xbest)

arvi-0.1.12/arvi/translations.py

@@ -0,0 +1,21 @@
+import re
+
+STARS = {
+    'Barnard': 'GJ699',
+    "Barnard's": 'GJ699',
+}
+
+
+def translate(star):
+    # known translations
+    if star in STARS:
+        return STARS[star]
+
+    # regex translations
+    NGC_match = re.match(r'NGC([\s\d]+)No([\s\d]+)', star)
+    if NGC_match:
+        cluster = NGC_match.group(1).replace(' ', '')
+        target = NGC_match.group(2).replace(' ', '')
+        return f'Cl* NGC {cluster} MMU {target}'
+
+    return star

{arvi-0.1.11 → arvi-0.1.12}/arvi.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: arvi
-Version: 0.1.11
+Version: 0.1.12
 Summary: The Automated RV Inspector
 Author-email: João Faria <joao.faria@unige.ch>
 License: MIT

{arvi-0.1.11 → arvi-0.1.12}/arvi.egg-info/SOURCES.txt

@@ -9,10 +9,12 @@ setup.py
 .github/workflows/python-publish.yml
 arvi/HZ.py
 arvi/__init__.py
+arvi/ariadne_wrapper.py
 arvi/binning.py
 arvi/config.py
 arvi/dace_wrapper.py
 arvi/extra_data.py
+arvi/gaia_wrapper.py
 arvi/instrument_specific.py
 arvi/lbl_wrapper.py
 arvi/nasaexo_wrapper.py
@@ -43,4 +45,5 @@ docs/logo/detective.png
 docs/logo/logo.png
 tests/test_binning.py
 tests/test_import_object.py
+tests/test_simbad.py
 tests/test_stats.py

{arvi-0.1.11 → arvi-0.1.12}/pyproject.toml

@@ -8,7 +8,7 @@ authors = [
     {name = "João Faria", email = "joao.faria@unige.ch"},
 ]
 description = "The Automated RV Inspector"
-version = "0.1.11"
+version = "0.1.12"
 readme = {file = "README.md", content-type = "text/markdown"}
 requires-python = ">=3.8"
 keywords = ["RV", "exoplanets"]

arvi-0.1.12/tests/test_simbad.py

@@ -0,0 +1,20 @@
+import pytest
+
+def test_import():
+    from arvi.simbad_wrapper import simbad
+
+def test_star():
+    from arvi.simbad_wrapper import simbad
+    s = simbad('HD69830')
+    assert hasattr(s, 'ra')
+    assert hasattr(s, 'dec')
+    assert hasattr(s, 'coords')
+    assert hasattr(s, 'plx')
+    assert hasattr(s, 'sp_type')
+    assert hasattr(s, 'B')
+    assert hasattr(s, 'V')
+    assert hasattr(s, 'ids')
+    assert s.V == 5.95
+    assert s.sp_type == 'G8:V'
+
+

arvi-0.1.11/arvi/config.py

@@ -1,2 +0,0 @@
-return_self = False
-check_internet = False

arvi-0.1.11/arvi/translations.py

@@ -1,10 +0,0 @@
-STARS = {
-    'Barnard': 'GJ699',
-    "Barnard's": 'GJ699',
-}
-
-
-def translate(star):
-    if star in STARS:
-        return STARS[star]
-    return star