arvi 0.1.20__tar.gz → 0.1.22__tar.gz

{arvi-0.1.20 → arvi-0.1.22}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: arvi
-Version: 0.1.20
+Version: 0.1.22
 Summary: The Automated RV Inspector
 Author-email: João Faria <joao.faria@unige.ch>
 License: MIT

arvi-0.1.22/arvi/config.py

@@ -0,0 +1,65 @@
+from pathlib import Path
+import configparser
+from pprint import pprint
+
+
+def get_config_path():
+    return Path.home() / '.config' / 'arvi.ini'
+
+def get_config():
+    config = configparser.ConfigParser()
+    if (path := get_config_path()).exists():
+        config.read(path)
+    return config
+
+def save_config(config):
+    config.write(get_config_path().open('w'))
+
+
+def instancer(cls):
+    return cls()
+
+@instancer
+class config:
+    # configuration values
+    __conf = {
+        # whether to return self from (some) RV methods
+        'return_self': False,
+        # whether to adjust instrument means before gls by default
+        'adjust_means_gls': True,
+        # whether to check internet connection before querying DACE
+        'check_internet': False,
+        # make all DACE requests without using a .dacerc file
+        'request_as_public': False,
+        # debug
+        'debug': False,
+    }
+    __setters = list(__conf.keys())
+
+    __user_config = get_config()
+
+    def __getattr__(self, name):
+        if name in ('__custom_documentations__', ):
+            # return {'return_self': 'help!'}
+            return {}
+
+        if self.__user_config.has_option('config', name):
+            self.__conf[name] = self.__user_config.get('config', name)
+
+        return self.__conf[name]
+
+    def __setattr__(self, name, value):
+        if name in config.__setters:
+            self.__conf[name] = value
+        else:
+            if 'config' not in self.__user_config:
+                self.__user_config.add_section('config')
+            self.__user_config.set('config', name, value)
+            save_config(self.__user_config)
+            # raise NameError(f"unknown configuration name '{name}'")
+
+    def show(self):
+        if 'config' in self.__user_config:
+            pprint(self.__conf | dict(self.__user_config['config']))
+        else:
+            pprint(self.__conf)

{arvi-0.1.20 → arvi-0.1.22}/arvi/simbad_wrapper.py

@@ -45,7 +45,7 @@ def run_query(query):
     url = 'http://simbad.u-strasbg.fr/simbad/sim-tap/sync'
     data = dict(query=query, request='doQuery', lang='ADQL', format='text/plain', phase='run')
     try:
-        response = requests.post(url, data=data, timeout=5)
+        response = requests.post(url, data=data, timeout=2)
     except requests.ReadTimeout as err:
         raise IndexError(err)
     except requests.ConnectionError as err:

{arvi-0.1.20 → arvi-0.1.22}/arvi/timeseries.py

@@ -1,7 +1,7 @@
 import os
 from dataclasses import dataclass, field
 from typing import Union
-from functools import partial, partialmethod
+from functools import lru_cache, partial, partialmethod
 from glob import glob
 import warnings
 from copy import deepcopy
@@ -713,6 +713,89 @@ class RV:
         if instruments == ['ESPRESSO']:
             from .instrument_specific import divide_ESPRESSO
             divide_ESPRESSO(s)
+        elif instruments == ['HARPS']:
+            from .instrument_specific import divide_HARPS
+            divide_HARPS(s)
+
+        if kwargs.get('do_adjust_means', False):
+            s.adjust_means()
+
+        return s
+
+    @classmethod
+    @lru_cache(maxsize=10)
+    def from_KOBE_file(cls, star, **kwargs):
+        assert 'KOBE' in star, f'{star} is not a KOBE star?'
+        import requests
+        from requests.auth import HTTPBasicAuth
+        from io import BytesIO
+        import tarfile
+        from astropy.io import fits
+        from .config import config
+
+        try:
+            config.kobe_password
+        except KeyError:
+            logger.error('please set arvi.config.kobe_password')
+            return
+
+        tar = None
+        fits_file = f'{star}_RVs.fits'
+        resp = requests.get(f'https://kobe.caha.es/internal/fitsfiles/{fits_file}',
+                            auth=HTTPBasicAuth('kobeteam', config.kobe_password))
+        
+        if resp.status_code != 200:
+            # something went wrong, try to extract the file by downloading the
+            # full tar.gz archive
+            
+            logger.warning(f'could not find "{fits_file}" on server, trying to download full archive')
+            resp = requests.get('https://kobe.caha.es/internal/fitsfiles.tar.gz',
+                                auth=HTTPBasicAuth('kobeteam', config.kobe_password))
+
+            if resp.status_code != 200:
+                logger.error(f'KOBE file not found for {star}')
+                return
+
+            tar = tarfile.open(fileobj=BytesIO(resp.content))
+
+            if fits_file not in tar.getnames():
+                logger.error(f'KOBE file not found for {star}')
+                return
+            
+            hdul = fits.open(tar.extractfile(fits_file))
+
+        else:
+            # found the file on the server, read it directly
+            hdul = fits.open(BytesIO(resp.content))
+
+        s = cls(star, _child=True)
+
+        s.time = hdul[1].data['BJD']
+
+        s.vrad = hdul[1].data['RVc']
+        s.svrad = hdul[1].data['eRVc']
+        s.vrad_preNZP = hdul[1].data['RVd']
+        s.vrad_preNZP_err = hdul[1].data['eRVd']
+
+        s.drift = hdul[1].data['drift']
+        s.drift_err = hdul[1].data['e_drift']
+
+        s.nzp = hdul[1].data['NZP']
+        s.nzp_err = hdul[1].data['eNZP']
+
+        s.berv = hdul[1].data['BERV']
+
+        s.mask = np.full_like(s.time, True, dtype=bool)
+        s.instruments = ['CARMENES']
+
+        # so meta!
+        setattr(s, 'CARMENES', s)
+
+        s._kobe_result = hdul[1].data
+
+        if tar is not None:
+            tar.close()
+        hdul.close()
 
         return s
 
@@ -1699,15 +1782,19 @@ class RV:
                     d = np.c_[
                         _s.time, _s.vrad, _s.svrad,
                         _s.fwhm, _s.fwhm_err,
-                        _s.rhk, _s.rhk_err,
                         _s.bispan, _s.bispan_err,
+                        _s.contrast, _s.contrast_err,
+                        _s.rhk, _s.rhk_err,
+                        _s.berv,
                     ]
                 else:
                     d = np.c_[
                         _s.mtime, _s.mvrad, _s.msvrad,
                         _s.fwhm[_s.mask], _s.fwhm_err[_s.mask],
-                        _s.rhk[_s.mask], _s.rhk_err[_s.mask],
                         _s.bispan[_s.mask], _s.bispan_err[_s.mask],
+                        _s.contrast[_s.mask], _s.contrast_err[_s.mask],
+                        _s.rhk[_s.mask], _s.rhk_err[_s.mask],
+                        _s.berv[_s.mask],
                     ]
                 if not save_nans:
                     if np.isnan(d).any():
@@ -1718,9 +1805,11 @@ class RV:
                             logger.warning(f'masking {nan_mask.sum()} observations with NaN in indicators')
 
                 header = '\t'.join(['bjd', 'vrad', 'svrad', 
-                                    'fwhm', 'sfwhm',
-                                    'rhk', 'srhk',
-                                    'bispan', 'sbispan'
+                                    'fwhm', 'sig_fwhm',
+                                    'bispan', 'sig_bispan',
+                                    'contrast', 'sig_contrast',
+                                    'rhk', 'sig_rhk',
+                                    'berv',
                                     ]) 
                 header += '\n'
                 header += '\t'.join(['-' * len(c) for c in header.strip().split('\t')])

{arvi-0.1.20 → arvi-0.1.22}/arvi.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: arvi
-Version: 0.1.20
+Version: 0.1.22
 Summary: The Automated RV Inspector
 Author-email: João Faria <joao.faria@unige.ch>
 License: MIT

arvi-0.1.20/arvi/config.py

@@ -1,36 +0,0 @@
-
-def instancer(cls):
-    return cls()
-
-@instancer
-class config:
-    # configuration values
-    __conf = {
-        # whether to return self from (some) RV methods
-        'return_self': False,
-        # whether to adjust instrument means before gls by default
-        'adjust_means_gls': True,
-        # whether to check internet connection before querying DACE
-        'check_internet': False,
-        # make all DACE requests without using a .dacerc file
-        'request_as_public': False,
-        # username for DACE servers
-        'username': 'desousaj',
-        # debug
-        'debug': False,
-    }
-    # all, for now
-    __setters = list(__conf.keys())
-
-    def __getattr__(self, name):
-        if name in ('__custom_documentations__', ):
-            # return {'return_self': 'help!'}
-            return {}
-
-        return self.__conf[name]
-
-    def __setattr__(self, name, value):
-        if name in config.__setters:
-            self.__conf[name] = value
-        else:
-            raise NameError(f"unknown configuration name '{name}'")