arvi 0.1.28__tar.gz → 0.1.30__tar.gz

{arvi-0.1.28/arvi.egg-info → arvi-0.1.30}/PKG-INFO

@@ -1,6 +1,6 @@
-Metadata-Version: 2.2
+Metadata-Version: 2.4
 Name: arvi
-Version: 0.1.28
+Version: 0.1.30
 Summary: The Automated RV Inspector
 Author-email: João Faria <joao.faria@unige.ch>
 License: MIT
@@ -20,6 +20,7 @@ Requires-Dist: loguru
 Requires-Dist: tqdm
 Requires-Dist: pySWEETCat
 Requires-Dist: kepmodel
+Dynamic: license-file
 
 <p align="center">
   <img width = "140" src="https://github.com/j-faria/arvi/blob/main/docs/logo/logo.png?raw=true"/>
@@ -58,7 +59,7 @@ s = RV('HD1234', instrument='ESPRESSO')
 
 #### Current version
 
-![PyPI - Version](https://img.shields.io/pypi/v/arvi)
+[![PyPI - Version](https://img.shields.io/pypi/v/arvi?color=32c854)](https://pypi.org/project/arvi/)
 
 #### Actions
 

{arvi-0.1.28 → arvi-0.1.30}/README.md

@@ -35,7 +35,7 @@ s = RV('HD1234', instrument='ESPRESSO')
 
 #### Current version
 
-![PyPI - Version](https://img.shields.io/pypi/v/arvi)
+[![PyPI - Version](https://img.shields.io/pypi/v/arvi?color=32c854)](https://pypi.org/project/arvi/)
 
 #### Actions
 

{arvi-0.1.28 → arvi-0.1.30}/arvi/dace_wrapper.py

@@ -15,6 +15,7 @@ def load_spectroscopy(user=None) -> SpectroscopyClass:
     from .config import config
     # requesting as public
     if config.request_as_public:
+        logger.warning('requesting DACE data as public')
         with all_logging_disabled():
             dace = DaceClass(dace_rc_config_path='none')
         return SpectroscopyClass(dace_instance=dace)
@@ -300,26 +301,54 @@ def get_observations(star, instrument=None, user=None, main_id=None, verbose=Tru
             msg = f'no {instrument} observations for {star}'
         raise ValueError(msg)
 
-    # sort pipelines, being extra careful with HARPS pipeline names
-    # (i.e. ensure that 3.x.x > 3.5)
+    # # sort pipelines, being extra careful with HARPS pipeline names
+    # # (i.e. ensure that 3.x.x > 3.5)
+    # from re import match
+    # def cmp(a, b):
+    #     if a[0] in ('3.5', '3.5 EGGS') or 'EGGS' in a[0] and match(r'3.\d.\d', b[0]):
+    #         return -1
+    #     if b[0] in ('3.5', '3.5 EGGS') or 'EGGS' in b[0] and match(r'3.\d.\d', a[0]):
+    #         return 1
+
+    #     if a[0] == b[0]:
+    #         return 0
+    #     elif a[0] > b[0]:
+    #         return 1
+    #     else:
+    #         return -1
+
+    # sort pipelines, must be extra careful with HARPS/HARPN pipeline version numbers
+    # got here with the help of DeepSeek
     from re import match
-    def cmp(a, b):
-        if a[0] in ('3.5', '3.5 EGGS') or 'EGGS' in a[0] and match(r'3.\d.\d', b[0]):
-            return -1
-        if b[0] in ('3.5', '3.5 EGGS') or 'EGGS' in b[0] and match(r'3.\d.\d', a[0]):
-            return 1
-
-        if a[0] == b[0]:
-            return 0
-        elif a[0] > b[0]:
-            return 1
-        else:
-            return -1
-
-    from functools import cmp_to_key
+    def custom_sort_key(s):
+        s = s[0]
+        print(s)
+        # Check for version number pattern (e.g., 3.2.5 or 3.2.5-EGGS)
+        version_match = match(r'^(\d+(?:\.\d+)*)(?:-(.*))?$', s)
+        if version_match:
+            version_parts = tuple(map(int, version_match.group(1).split('.')))
+            suffix = version_match.group(2)
+            
+            if suffix is not None:
+                # Suffixed versions: sort in ascending order (3.2.5-HR11 < 3.3.1-HR11)
+                return (0, 0, version_parts, suffix)
+            else:
+                # Unsuffixed versions: sort in descending order (3.5 > 3.2.5)
+                return (0, 1, tuple(-x for x in version_parts))
+        
+        # Check for scientific reference pattern (e.g., 2004A&A...)
+        year_match = match(r'^(\d{4})', s)
+        if year_match:
+            year = int(year_match.group(1))
+            return (1, year)
+        
+        # For all other strings, sort alphabetically
+        return (2, s)
+
+    # from functools import cmp_to_key
     new_result = {}
     for inst in instruments:
-        new_result[inst] = dict(sorted(result[inst].items(), key=cmp_to_key(cmp), reverse=True))
+        new_result[inst] = dict(sorted(result[inst].items(), key=custom_sort_key, reverse=True))
 
     if verbose:
         logger.info('RVs available from')

{arvi-0.1.28 → arvi-0.1.30}/arvi/plots.py

@@ -502,8 +502,8 @@ plot_berv = partialmethod(plot_quantity, quantity='berv')
 
 
 @plot_fast
-def gls(self, ax=None, label=None, fap=True, instrument=None, 
-        adjust_means=config.adjust_means_gls,
+def gls(self, ax=None, label=None, instrument=None, 
+        fap=True, fap_method='baluev', adjust_means=config.adjust_means_gls,
         picker=True, **kwargs):
     """
     Calculate and plot the Generalised Lomb-Scargle periodogram of the radial
@@ -515,11 +515,15 @@ def gls(self, ax=None, label=None, fap=True, instrument=None,
             created.
         label (str):
             The label to use for the plot.
-        fap (bool):
-            Whether to show the false alarm probability. Default is True.
         instrument (str or list):
             Which instruments' data to include in the periodogram. Default is
             all instruments.
+        fap (bool or float):
+            Whether to show the false alarm probability. A value (not a
+            percentage) can be provided to display a given FAP. Default is True.
+        fap_method (str):
+            Method used to estimate the FAP, passed directly to
+            `astropy.timeseries.LombScargle`. Default is 'baluev'.
         adjust_means (bool):
             Whether to adjust (subtract) the weighted means of each instrument.
             Default is `config.adjust_means_gls`.
@@ -597,8 +601,14 @@ def gls(self, ax=None, label=None, fap=True, instrument=None,
         fap_level = 0.01
         if isinstance(fap, float):
             fap_level = fap
-        ax.axhline(gls.false_alarm_level(fap_level),
-                   color='k', alpha=0.2, zorder=-1)
+
+        fap = gls.false_alarm_level(fap_level, method=fap_method)
+
+        if fap > 0.05 and fap_method == 'baluev':
+            logger.warning('FAP is high (>5%), the analytical estimate may be underestimated. Using the bootstrap method instead.')
+            fap = gls.false_alarm_level(fap_level, method='bootstrap')
+
+        ax.axhline(fap, color='k', alpha=0.2, zorder=-1)
 
     ax.set(xlabel='Period [days]', ylabel='Normalized power', ylim=(0, None))
     ax.minorticks_on()
@@ -640,8 +650,32 @@ def gls(self, ax=None, label=None, fap=True, instrument=None,
 
 
 # @plot_fast
-def gls_quantity(self, quantity, ax=None, fap=True, instrument=None,
+def gls_quantity(self, quantity, ax=None, instrument=None,
+                 fap=True, fap_method='baluev',
                  adjust_means=True, picker=True, **kwargs):
+    """
+    Calculate and plot the Generalised Lomb-Scargle periodogram of the given
+    quantity (e.g. fwhm, rhk, etc.)
+
+    Args:
+        quantity (str):
+            The quantity to calculate for which to compute the periodogram.
+        ax (matplotlib.axes.Axes):
+            The matplotlib axes to plot on. If None, a new figure will be
+            created.
+        instrument (str or list):
+            Which instruments' data to include in the periodogram. Default is
+            all instruments.
+        fap (bool or float):
+            Whether to show the false alarm probability. A value (not a
+            percentage) can be provided to display a given FAP. Default is True.
+        fap_method (str):
+            Method used to estimate the FAP, passed directly to
+            `astropy.timeseries.LombScargle`. Default is 'baluev'.
+        adjust_means (bool):
+            Whether to adjust (subtract) the weighted means of each instrument.
+            Default is `config.adjust_means_gls`.
+    """
 
     if not hasattr(self, quantity):
         if self.verbose:
@@ -715,8 +749,14 @@ def gls_quantity(self, quantity, ax=None, fap=True, instrument=None,
         fap_level = 0.01
         if isinstance(fap, float):
             fap_level = fap
-        ax.axhline(gls.false_alarm_level(fap_level),
-                   color='k', alpha=0.2, zorder=-1)
+
+        fap = gls.false_alarm_level(fap_level, method=fap_method)
+
+        if fap > 0.05 and fap_method == 'baluev':
+            logger.warning('FAP is high (>5%), the analytical estimate may be underestimated. Using the bootstrap method instead.')
+            fap = gls.false_alarm_level(fap_level, method='bootstrap')
+
+        ax.axhline(fap, color='k', alpha=0.2, zorder=-1)
 
     ax.set(xlabel='Period [days]', ylabel='Normalized power', ylim=(0, None))
     ax.minorticks_on()

{arvi-0.1.28 → arvi-0.1.30}/arvi/timeseries.py

@@ -765,13 +765,19 @@ class RV:
         if isinstance(files, str):
             files = [files]
 
-        CCFs = iCCF.from_file(files)
+        hdu_number = kwargs.pop('hdu_number', 1)
+        data_index = kwargs.pop('data_index', -1)
+        CCFs = iCCF.from_file(files, hdu_number=hdu_number, data_index=data_index)
 
         if not isinstance(CCFs, list):
             CCFs = [CCFs]
 
-        objects = np.unique([i.HDU[0].header['OBJECT'].replace(' ', '') for i in CCFs])
-        if objects.size != 1:
+        try:
+            objects = [i.OBJECT for i in CCFs]
+        except AttributeError:
+            objects = np.unique([i.HDU[0].header['OBJECT'].replace(' ', '') for i in CCFs])
+
+        if len(objects) != 1:
             logger.warning(f'found {objects.size} different stars in the CCF files, '
                            'choosing the first one')
         star = objects[0]
@@ -808,7 +814,7 @@ class RV:
 
             _s.mask = np.full_like(_s.time, True, dtype=bool)
 
-            _s.drs_qc = np.array([i.HDU[0].header['HIERARCH ESO QC SCIRED CHECK'] for i in CCFs], dtype=bool)
+            _s.drs_qc = np.array([i.HDU[0].header['*QC SCIRED CHECK'][0] for i in CCFs], dtype=bool)
             # mask out drs_qc = False
             if not _s.drs_qc.all():
                 n = (~ _s.drs_qc).sum()
@@ -859,7 +865,7 @@ class RV:
         fits_file = f'{star}_RVs.fits'
 
         local_exists = os.path.exists(local_targz_file)
-        local_recent = os.path.getmtime(local_targz_file) > pytime() - 60*60*2
+        local_recent = local_exists and os.path.getmtime(local_targz_file) > pytime() - 60*60*2
 
         if os.path.exists(os.path.join(directory, fits_file)):
             logger.info(f'found file "{fits_file}" in "{directory}"')

{arvi-0.1.28 → arvi-0.1.30/arvi.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
-Metadata-Version: 2.2
+Metadata-Version: 2.4
 Name: arvi
-Version: 0.1.28
+Version: 0.1.30
 Summary: The Automated RV Inspector
 Author-email: João Faria <joao.faria@unige.ch>
 License: MIT
@@ -20,6 +20,7 @@ Requires-Dist: loguru
 Requires-Dist: tqdm
 Requires-Dist: pySWEETCat
 Requires-Dist: kepmodel
+Dynamic: license-file
 
 <p align="center">
   <img width = "140" src="https://github.com/j-faria/arvi/blob/main/docs/logo/logo.png?raw=true"/>
@@ -58,7 +59,7 @@ s = RV('HD1234', instrument='ESPRESSO')
 
 #### Current version
 
-![PyPI - Version](https://img.shields.io/pypi/v/arvi)
+[![PyPI - Version](https://img.shields.io/pypi/v/arvi?color=32c854)](https://pypi.org/project/arvi/)
 
 #### Actions