arvi 0.1.20__py3-none-any.whl → 0.1.22__py3-none-any.whl

arvi/config.py

@@ -1,3 +1,20 @@
+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()
@@ -14,23 +31,35 @@ class config:
         '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())
 
+    __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:
-            raise NameError(f"unknown configuration name '{name}'")
+            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/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/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.dist-info → arvi-0.1.22.dist-info}/METADATA

@@ -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.dist-info → arvi-0.1.22.dist-info}/RECORD

@@ -3,7 +3,7 @@ arvi/__init__.py,sha256=r3oaMVwQCjNTd6odg-ga9IRncn54i7tawZrIrvSRQOo,1012
 arvi/ariadne_wrapper.py,sha256=YvilopJa9T4NwPcj3Nah_U8smSeSAU5-HYZMb_GJ-BQ,2232
 arvi/berv.py,sha256=eKnpuPC1w45UrUEyFRbs9F9j3bXz3kxYzNXbnRgvFQM,17596
 arvi/binning.py,sha256=jbemJ-bM3aqoOsqMo_OhWt_co-JAQ0nhdG_GpTsrRsw,15403
-arvi/config.py,sha256=ftqR38bV-zohTynPguiKSp4kSHPjiqJwEi-u6dFrFwk,1047
+arvi/config.py,sha256=W-v8NNhRd_PROu0wCMilXmOhYcju4xbUalugd5u7SRU,1881
 arvi/dace_wrapper.py,sha256=ml0xC_KR-oXwEo6ysODzfpx-eP7VNbxURZSns31WbK4,18196
 arvi/extra_data.py,sha256=WEEaYeLh52Zdv0uyHO72Ys5MWS3naTAP4wJV2BJ1mbk,2551
 arvi/gaia_wrapper.py,sha256=icm3LJjG9pjP47_bM30NFyocUQO3X3SHS5yQ-Dwcr5w,4653
@@ -16,11 +16,11 @@ arvi/plots.py,sha256=WUm-sqN0aZTNXvE1kYpvmHTW9QPWqSCpKhNjwaqxjEk,29628
 arvi/programs.py,sha256=C0Fbldjf-QEZYYJp5wBKP3h7zraD0O2mJC7Su967STg,4607
 arvi/reports.py,sha256=ayPdZ4HZO9iCDdnADQ18gQPJh79o-1UYG7TYkvm9Lrc,4051
 arvi/setup_logger.py,sha256=pBzaRTn0hntozjbaRVx0JIbWGuENkvYUApa6uB-FsRo,279
-arvi/simbad_wrapper.py,sha256=f6QYrMN0KzBH9KhdrUR5w6ZK00EoRIYr3Z9jS4CzP_s,5791
+arvi/simbad_wrapper.py,sha256=iAAwEMcr1Hgu6lnDctmaCC1TLPCB8yAfHG0wxh9K9C8,5791
 arvi/spectra.py,sha256=pTAWSW4vk96DWRQ-6l5mNJHUhiAyaPR-QDjZdOT6Ak0,7489
 arvi/stats.py,sha256=ilzzGL9ew-SyVa9eEdrYCpD3DliOAwhoNUg9LIlHjzU,2583
 arvi/stellar.py,sha256=veuL_y9kJvvApU_jqYQqP3EkcRnQffTc8Us6iT5UrFI,3790
-arvi/timeseries.py,sha256=OVxzJSopPNmE47HRn7hQO_2SQdEpVU1OvR1VV8C1DM0,71307
+arvi/timeseries.py,sha256=IYv_9qTuvxMQWK8As1xRM1_X-ZAxisz1FRCydG2-900,74264
 arvi/translations.py,sha256=FBF_2OrpMQBG4GtV4_UOspiaxetiGCY7TQFcwZMMVuQ,838
 arvi/utils.py,sha256=ihQcYvk_ix52CW8fVP16CKTVEamGU5gPNRneVcgDrWc,6534
 arvi/data/info.svg,sha256=0IMI6W-eFoTD8acnury79WJJakpBwLa4qKS4JWpsXiI,489
@@ -29,8 +29,8 @@ arvi/data/obs_affected_blue_cryostat_issues.dat,sha256=z4AK17xfz8tGTDv1FjRvQFnio
 arvi/data/extra/HD86226_PFS1.rdb,sha256=vfAozbrKHM_j8dYkCBJsuHyD01KEM1asghe2KInwVao,3475
 arvi/data/extra/HD86226_PFS2.rdb,sha256=F2P7dB6gVyzCglUjNheB0hIHVClC5RmARrGwbrY1cfo,4114
 arvi/data/extra/metadata.json,sha256=C69hIw6CohyES6BI9vDWjxwSz7N4VOYX0PCgjXtYFmU,178
-arvi-0.1.20.dist-info/LICENSE,sha256=6JfQgl7SpM55t0EHMFNMnNh-AdkpGW25MwMiTnhdWQg,1068
-arvi-0.1.20.dist-info/METADATA,sha256=wScAhfEK59QQD1OdPPhv-NHAdYjQznKOPebHA5XVmRQ,1852
-arvi-0.1.20.dist-info/WHEEL,sha256=P9jw-gEje8ByB7_hXoICnHtVCrEwMQh-630tKvQWehc,91
-arvi-0.1.20.dist-info/top_level.txt,sha256=4EeiKDVLD45ztuflTGfQ3TU8GVjJg5Y95xS5XjI-utU,5
-arvi-0.1.20.dist-info/RECORD,,
+arvi-0.1.22.dist-info/LICENSE,sha256=6JfQgl7SpM55t0EHMFNMnNh-AdkpGW25MwMiTnhdWQg,1068
+arvi-0.1.22.dist-info/METADATA,sha256=J__w4ZE5d8POUPhA7vd_zoLkyxY-62ddCGZ0r3bJXf8,1852
+arvi-0.1.22.dist-info/WHEEL,sha256=P9jw-gEje8ByB7_hXoICnHtVCrEwMQh-630tKvQWehc,91
+arvi-0.1.22.dist-info/top_level.txt,sha256=4EeiKDVLD45ztuflTGfQ3TU8GVjJg5Y95xS5XjI-utU,5
+arvi-0.1.22.dist-info/RECORD,,