arvi 0.3.0__tar.gz → 0.3.2__tar.gz

{arvi-0.3.0/arvi.egg-info → arvi-0.3.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: arvi
-Version: 0.3.0
+Version: 0.3.2
 Summary: The Automated RV Inspector
 Author-email: João Faria <joao.faria@unige.ch>
 License: MIT

{arvi-0.3.0 → arvi-0.3.2}/arvi/__init__.py

@@ -17,12 +17,15 @@ def __getattr__(name: str):
     if not config.fancy_import:
         raise AttributeError
     
+    if name.startswith('__'):
+        return
     if name in (
         '_ipython_canary_method_should_not_exist_',
         '_ipython_display_',
-        '__custom_documentations__',
         '_repr_mimebundle_',
-        '__wrapped__'
+        # '__custom_documentations__',
+        # '__wrapped__',
+        # '__dataframe__'
     ):
         return
 

{arvi-0.3.0 → arvi-0.3.2}/arvi/config.py

@@ -36,6 +36,8 @@ class config:
         'fancy_import': True,
         # use the 'dark_background' matplotlib theme
         'dark_plots': False,
+        # specific colors per instrument
+        'colors_per_instrument': False,
         # debug
         'debug': False,
     }
@@ -43,7 +45,7 @@ class config:
 
     __user_config = get_config()
 
-    def __getattr__(self, name):
+    def __getattr__(self, name: str):
         if name in ('__custom_documentations__', ):
             # return {'return_self': 'help!'}
             return {}
@@ -54,7 +56,6 @@ class config:
                 value = True if value == 'True' else value
                 value = False if value == 'False' else value
                 self.__conf[name] = value
-
             return self.__conf[name]
         except KeyError:
             raise KeyError(f"unknown config option '{name}'")

{arvi-0.3.0 → arvi-0.3.2}/arvi/dace_wrapper.py

@@ -310,6 +310,14 @@ def get_observations_from_instrument(star, instrument, user=None, main_id=None,
     # print([r[k1][k2].keys() for k1 in r.keys() for k2 in r[k1].keys()])
     return r
 
+def _warn_harpsn(instrument):
+    if 'HARPSN' in instrument or 'HARPS-N' in instrument:
+        logger = setup_logger()
+        logger.warning(f'Did you mean "HARPN" instead of "{instrument}"?')
+        return True
+    return False
+
+
 def get_observations(star, instrument=None, user=None, main_id=None, verbose=True):
     logger = setup_logger()
     if instrument is None:
@@ -331,6 +339,7 @@ def get_observations(star, instrument=None, user=None, main_id=None, verbose=Tru
             result = get_observations_from_instrument(star, instrument, user, main_id, verbose)
         except ValueError:
             msg = f'no {instrument} observations for {star}'
+            _warn_harpsn(instrument)
             raise ValueError(msg) from None
 
     # defaultdict --> dict
@@ -410,6 +419,8 @@ def get_observations(star, instrument=None, user=None, main_id=None, verbose=Tru
     def custom_key(val, strip_EGGS=False):
         if strip_EGGS:
             val = val.replace('-EGGS', '').replace(' EGGS', '')
+        if val in ('3.3', '3.4', '3.5', '3.6', '3.7', '3.8'):
+            val = '0.' + val
         key = 0
         key -= 1 if '3.5' in val else 0
         key -= 1 if 'EGGS' in val else 0
@@ -434,9 +445,10 @@ def get_observations(star, instrument=None, user=None, main_id=None, verbose=Tru
         logger.info('RVs available from')
         with logger.contextualize(indent='  '):
             _inst = ''
-            for inst in instruments:
+            max_len_inst = max([len(inst) for inst in instruments])
+            for inst in sorted(instruments):
                 pipelines = list(new_result[inst].keys())
-                max_len = max([len(pipe) for pipe in pipelines])
+                max_len_pipe = max([len(pipe) for pipe in pipelines])
                 for pipe in pipelines:
                     last_pipe = pipe == pipelines[-1]
                     modes = list(new_result[inst][pipe].keys())
@@ -444,11 +456,11 @@ def get_observations(star, instrument=None, user=None, main_id=None, verbose=Tru
                         N = len(new_result[inst][pipe][mode]['rjd'])
                         # LOG
                         if inst == _inst and last_pipe:
-                            logger.info(f'{" ":>12s} └ {pipe:{max_len}s} - {mode} ({N} observations)')
+                            logger.info(f'{" ":>{max_len_inst}s} └ {pipe:{max_len_pipe}s} - {mode} ({N} observations)')
                         elif inst == _inst:
-                            logger.info(f'{" ":>12s} ├ {pipe:{max_len}s} - {mode} ({N} observations)')
+                            logger.info(f'{" ":>{max_len_inst}s} ├ {pipe:{max_len_pipe}s} - {mode} ({N} observations)')
                         else:
-                            logger.info(f'{inst:>12s} ├ {pipe:{max_len}s} - {mode} ({N} observations)')
+                            logger.info(f'{inst:>{max_len_inst}s} ├ {pipe:{max_len_pipe}s} - {mode} ({N} observations)')
                             _inst = inst
 
     return new_result

{arvi-0.3.0 → arvi-0.3.2}/arvi/plots.py

@@ -587,6 +587,32 @@ def plot_xy(self, x, y, ax=None, instrument=None, show_legend=True, **kwargs):
         return fig, ax
 
 
+def plot_several(obj, axs=None, **kwargs):
+    try:
+        from grid_strategy.strategies import SquareStrategy
+    except ImportError:
+        raise ImportError("Please install 'grid-strategy' to use this function")
+    if axs is None:
+        if isinstance(obj, (list, tuple)):
+            n = len(obj)
+            GS = SquareStrategy().get_grid(n)
+            fig = plt.gcf()
+            fig.set_size_inches(8, 6)
+            axs = [fig.add_subplot(gs) for gs in GS]
+        else:
+            raise NotImplementedError('`obj` should be a list or tuple')
+    else:
+        assert isinstance(axs, (list, tuple))
+        assert len(axs) == len(obj), 'Number of axes does not match number of objects'
+
+    kwargs.setdefault('show_legend', False)
+    kwargs.setdefault('show_title', True)
+
+    for ax, s in zip(axs, obj):
+        s.plot(ax=ax, **kwargs)
+        ax.set(xlabel='', ylabel='')
+
+
 # @plot_fast
 def gls(self, ax=None, label=None, instrument=None, 
         fap=True, fap_method='baluev', adjust_means=config.adjust_means_gls,

{arvi-0.3.0 → arvi-0.3.2}/arvi/programs.py

@@ -23,6 +23,7 @@ def get_star(star, instrument=None, verbose=False, **kwargs):
 
 
 class LazyRV:
+    """ A lazy wrapper around `RV` """
     def __init__(self, stars: list, instrument: str = None,
                  _parallel_limit=10, _parallel_workers=8):
         self.stars = stars
@@ -60,25 +61,6 @@ class LazyRV:
 
         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 reload(self, **kwargs):
         self._saved = self._get(**kwargs)
         return self._saved
@@ -92,12 +74,24 @@ class LazyRV:
         return self._saved
 
     @lru_cache(maxsize=10)
-    def __getitem__(self, index):
-        star = self.stars[index]
+    def __getitem__(self, index_or_name):
+        if isinstance(index_or_name, str):
+            index = self.stars.index(index_or_name)
+        else:
+            index = index_or_name
+
         if self._saved is not None:
             return self._saved[index]
+
+        star = self.stars[index]
         return get_star(star, self.instrument, verbose=True)
 
+    def plot(self, split=20, **kwargs):
+        from .plots import plot_several
+        from itertools import batched
+        S = list(batched(self.__call__(), split))
+        for s in S:
+            plot_several(s, **kwargs)
 
 # sorted by spectral type
 WG1_stars = [

{arvi-0.3.0 → arvi-0.3.2}/arvi/setup_logger.py

@@ -2,17 +2,17 @@ import sys
 
 def setup_logger():
     from loguru import logger
-    try:
-        import marimo as mo
-        if mo.running_in_notebook():
-            raise NotImplementedError
-    except (NotImplementedError, AttributeError):
-        pass
-    except (ImportError, ModuleNotFoundError):
-        logger.remove()
-    else:
-        logger.remove()
-
+    # try:
+    #     import marimo as mo
+    #     if mo.running_in_notebook():
+    #         return logger
+    #         raise NotImplementedError
+    # except (NotImplementedError, AttributeError):
+    #     pass
+    # except (ImportError, ModuleNotFoundError):
+    #     logger.remove()
+    # else:
+    logger.remove()
     logger.configure(extra={"indent": ""})
     logger.add(
         sys.stdout,

{arvi-0.3.0 → arvi-0.3.2}/arvi/simbad_wrapper.py

@@ -1,4 +1,5 @@
 import os
+from urllib.error import URLError
 import requests
 from dataclasses import dataclass
 from functools import partial
@@ -64,6 +65,12 @@ JOIN ident ON oidref = oid
 WHERE id = '{star}';
 """
 
+OTYPE_QUERY = """
+SELECT otype FROM basic 
+JOIN ident ON oidref = oid 
+WHERE id = '{star}';
+"""
+
 HD_GJ_HIP_QUERY = """
 SELECT id2.id
 FROM ident AS id1 JOIN ident AS id2 USING(oidref)
@@ -209,6 +216,14 @@ class simbad:
         except IndexError:
             self.B = self.V = np.nan
 
+        try:
+            table21 = run_query(query=OTYPE_QUERY.format(star=self.star))
+            if _debug:
+                print('table21:\n', table21)
+            cols, values = parse_table1(table21, cols, values)
+        except IndexError:
+            self.otype = None
+
         try:
             table3 = run_query(query=IDS_QUERY.format(star=self.star))
             if _debug:
@@ -266,6 +281,8 @@ class simbad:
             try:
                 setattr(self, col, float(val))
             except ValueError:
+                if val == '':
+                    val = None
                 setattr(self, col, val)
 
         self.coords = SkyCoord(self.ra, self.dec, unit='deg')
@@ -289,9 +306,10 @@ class simbad:
             else:
                 self.teff = data['teff']
                 self.sweetcat = data
-
+        except URLError:
+            pass
         except IndexError:
-            if self.sp_type == '':
+            if self.sp_type in (None, ''):
                 if len(self.measurements.teff) > 0:
                     try:
                         self.teff = int(np.mean(self.measurements.teff))

{arvi-0.3.0 → arvi-0.3.2}/arvi/sophie_wrapper.py

@@ -13,7 +13,7 @@ URL_HEADER = "http://atlas.obs-hp.fr/sophie/sophie.cgi?n=sophiecc&c=i&z=fd&a=t&o
 def extract_keyword(keyword, text, raise_error=True):
     for line in text.splitlines():
         if keyword in line:
-            value = re.findall(fr'{keyword}\s+([\'\w\d.]+)', line)[0]
+            value = re.findall(fr'{keyword}\s+([-\'\w\d.]+)', line)[0]
             value = value.replace("'", "")
             try:
                 return float(value)

{arvi-0.3.0 → arvi-0.3.2}/arvi/stats.py

@@ -1,6 +1,6 @@
 from functools import partial
 import numpy as np
-from scipy.stats import norm
+
 
 def wmean(a, e):
     """Weighted mean of array `a`, with uncertainties given by `e`.
@@ -69,7 +69,7 @@ weighted_median = partial(weighted_quantiles_interpolate, quantiles=0.5)
 
 
 
-def sigmaclip_median(a, low=4.0, high=4.0, k=1/norm.ppf(3/4)):
+def sigmaclip_median(a, low=4.0, high=4.0, k=None):
     """
     Same as scipy.stats.sigmaclip but using the median and median absolute
     deviation instead of the mean and standard deviation.
@@ -91,8 +91,12 @@ def sigmaclip_median(a, low=4.0, high=4.0, k=1/norm.ppf(3/4)):
             - `lower`: Lower clipping limit
             - `upper`: Upper clipping limit
     """
-    from scipy.stats import median_abs_deviation
+    from scipy.stats import median_abs_deviation, norm
     from scipy.stats._stats_py import SigmaclipResult
+
+    if k is None:
+        k = 1 / norm.ppf(3 / 4)
+
     c = np.asarray(a).ravel()
     delta = 1
     while delta:

{arvi-0.3.0 → arvi-0.3.2/arvi.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: arvi
-Version: 0.3.0
+Version: 0.3.2
 Summary: The Automated RV Inspector
 Author-email: João Faria <joao.faria@unige.ch>
 License: MIT