arvi 0.2.3__tar.gz → 0.2.5__tar.gz

{arvi-0.2.3/arvi.egg-info → arvi-0.2.5}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: arvi
-Version: 0.2.3
+Version: 0.2.5
 Summary: The Automated RV Inspector
 Author-email: João Faria <joao.faria@unige.ch>
 License: MIT
@@ -23,7 +23,7 @@ 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"/>
+  <img width = "140" src="https://raw.githubusercontent.com/j-faria/arvi/refs/heads/main/docs/logo/logo.png"/>
 </p>
 
 This package sits alongside [DACE](https://dace.unige.ch/) to help with the

{arvi-0.2.3 → arvi-0.2.5}/README.md

@@ -1,5 +1,5 @@
 <p align="center">
-  <img width = "140" src="https://github.com/j-faria/arvi/blob/main/docs/logo/logo.png?raw=true"/>
+  <img width = "140" src="https://raw.githubusercontent.com/j-faria/arvi/refs/heads/main/docs/logo/logo.png"/>
 </p>
 
 This package sits alongside [DACE](https://dace.unige.ch/) to help with the

{arvi-0.2.3 → arvi-0.2.5}/arvi/config.py

@@ -8,6 +8,7 @@ def get_config_path():
 
 def get_config():
     config = configparser.ConfigParser()
+    config.add_section('config')
     if (path := get_config_path()).exists():
         config.read(path)
     return config
@@ -33,6 +34,8 @@ class config:
         'request_as_public': False,
         # enable from arvi import star_name
         'fancy_import': True,
+        # use the 'dark_background' matplotlib theme
+        'dark_plots': False,
         # debug
         'debug': False,
     }

{arvi-0.2.3 → arvi-0.2.5}/arvi/dace_wrapper.py

@@ -7,7 +7,7 @@ from itertools import islice
 import numpy as np
 
 from .setup_logger import setup_logger
-from .utils import create_directory, all_logging_disabled, stdout_disabled, tqdm
+from .utils import create_directory, all_logging_disabled, stdout_disabled, timer, tqdm
 
 
 def load_spectroscopy(user=None):
@@ -47,8 +47,9 @@ def load_spectroscopy(user=None):
         logger.warning('requesting DACE data as public (no .dacerc file found)')
     return default_Spectroscopy
 
-@lru_cache()
-def get_dace_id(star, verbose=True):
+
+@lru_cache(maxsize=1024)
+def get_dace_id(star, verbose=True, raise_error=False):
     logger = setup_logger()
     filters = {"obj_id_catname": {"equal": [star]}}
     try:
@@ -58,8 +59,11 @@ def get_dace_id(star, verbose=True):
     except KeyError:
         if verbose:
             logger.error(f"Could not find DACE ID for {star}")
+        if not raise_error:
+            return None
         raise ValueError from None
 
+
 def get_arrays(result, latest_pipeline=True, ESPRESSO_mode='HR11', NIRPS_mode='HE', verbose=True):
     logger = setup_logger()
     arrays = []
@@ -70,7 +74,6 @@ def get_arrays(result, latest_pipeline=True, ESPRESSO_mode='HR11', NIRPS_mode='H
 
         # select ESPRESSO mode, which is defined at the level of the pipeline
         if 'ESPRESSO' in inst:
-
             find_mode = [ESPRESSO_mode in pipe for pipe in pipelines]
             # the mode was not found
             if not any(find_mode):
@@ -83,6 +86,11 @@ def get_arrays(result, latest_pipeline=True, ESPRESSO_mode='HR11', NIRPS_mode='H
                 i = [i for i, pipe in enumerate(pipelines) if ESPRESSO_mode in pipe][0]
                 pipelines = [pipelines[i]]
 
+        # select NIRPS mode
+        if 'NIRPS' in inst:
+            if any(this_mode := [p for p in pipelines if NIRPS_mode in p]):
+                pipelines = this_mode
+
         if latest_pipeline:
             npipe = len(pipelines)
             if 'NIRPS' in inst and any(['LBL' in p for p in pipelines]):
@@ -161,19 +169,19 @@ def get_observations_from_instrument(star, instrument, user=None, main_id=None,
             dictionary with data from DACE
     """
     Spectroscopy = load_spectroscopy(user)
-
     found_dace_id = False
-    try:
-        dace_id = get_dace_id(star, verbose=verbose)
-        found_dace_id = True
-    except ValueError as e:
-        if main_id is not None:
-            try:
-                dace_id = get_dace_id(main_id, verbose=verbose)
-                found_dace_id = True
-            except ValueError:
-                pass
-    
+    with timer('simbad query'):
+        try:
+            dace_id = get_dace_id(star, verbose=verbose, raise_error=True)
+            found_dace_id = True
+        except ValueError as e:
+            if main_id is not None:
+                try:
+                    dace_id = get_dace_id(main_id, verbose=verbose, raise_error=True)
+                    found_dace_id = True
+                except ValueError:
+                    pass
+
     if not found_dace_id:
         try:
             with all_logging_disabled():
@@ -184,11 +192,16 @@ def get_observations_from_instrument(star, instrument, user=None, main_id=None,
         except TypeError:
             msg = f'no {instrument} observations for {star}'
             raise ValueError(msg) from None
-
-    filters = {
-        "ins_name": {"contains": [instrument]},
-        "obj_id_daceid": {"contains": [dace_id]}
-    }
+    if (isinstance(instrument, str)):
+        filters = {
+            "ins_name": {"contains": [instrument]},
+            "obj_id_daceid": {"contains": [dace_id]}
+        }
+    elif (isinstance(instrument, list)):
+        filters = {
+            "ins_name": {"contains": instrument},
+            "obj_id_daceid": {"contains": [dace_id]}
+        }
     with all_logging_disabled():
         result = Spectroscopy.query_database(filters=filters)
     
@@ -299,12 +312,14 @@ def get_observations(star, instrument=None, user=None, main_id=None, verbose=Tru
             result[inst] = dict(result[inst])
     #
 
-    instruments = list(result.keys())
+    instruments = list(map(str, result.keys()))
 
     if instrument is not None:
         # select only the provided instrument (if it's there)
-        instruments = [inst for inst in instruments if instrument in inst]
-
+        if (isinstance(instrument, str)):
+            instruments = [inst for inst in instruments if instrument in inst]
+        elif (isinstance(instrument, list)):
+            instruments = [inst for inst in instruments if any(i in inst for i in instrument)]
     if len(instruments) == 0:
         if instrument is None:
             msg = f'no observations for {star}'
@@ -328,30 +343,53 @@ def get_observations(star, instrument=None, user=None, main_id=None, verbose=Tru
     #     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 custom_sort_key(s):
-        s = s[0]
-        # Check for version number pattern (e.g., 3.2.5 or 3.2.5-EGGS)
-        version_match = match(r'^(\d+(?:\.\d+)*)(?:[-\s](.*))?$', s)
-        if version_match:
-            version_parts = list(map(int, version_match.group(1).split('.')))
-            if len(version_parts) == 2:
-                version_parts.insert(1, -1)
-            return (0, 1, version_parts)
-        # Check for scientific reference pattern (e.g., 2004A&A...)
-        year_match = match(r'^(\d{4})', s)
-        if year_match:
-            year = int(year_match.group(1))
-            return (1, year)
-        # For all other strings, sort alphabetically
-        return (2, s)
-
-    # from functools import cmp_to_key
+    # # sort pipelines, must be extra careful with HARPS/HARPN pipeline version numbers
+    # # got here with the help of DeepSeek
+    # # from functools import cmp_to_key
+    # from re import match
+    # def custom_sort_key(s):
+    #     s = s[0]
+    #     # Check for version number pattern (e.g., 3.2.5 or 3.2.5-EGGS)
+    #     version_match = match(r'^(\d+(?:\.\d+)*)(?:[-\s](.*))?$', s)
+    #     if version_match:
+    #         version_parts = list(map(int, version_match.group(1).split('.')))
+    #         if len(version_parts) == 2:
+    #             version_parts.insert(1, -1)
+    #         # if version_match.group(2) and 'LBL' in version_match.group(2):
+    #         #     version_parts.append(-1)
+    #         # else:
+    #         #     version_parts.append(0)
+    #         if version_match.group(2) is None:
+    #             version_parts.append('')
+    #         else:
+    #             version_parts.append(version_match.group(2))
+    #         return (0, 1, 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)
+
+    def custom_key(val):
+        key = 0
+        key -= 2 if val == '3.5' else 0
+        key -= 1 if 'EGGS' in val else 0
+        key -= 1 if ('UHR' in val or 'MR' in val) else 0
+        key -= 1 if 'LBL' in val else 0
+        return str(key) if key != 0 else val
+
     new_result = {}
     for inst in instruments:
-        new_result[inst] = dict(sorted(result[inst].items(), key=custom_sort_key, reverse=True))
+        # new_result[inst] = dict(
+        #     sorted(result[inst].items(), key=custom_sort_key, reverse=True)
+        # )
+        # WARNING: not the same as reverse=True (not sure why)
+        sorted_keys = sorted(result[inst].keys(), key=custom_key)[::-1]
+        new_result[inst] = {}
+        for key in sorted_keys:
+            new_result[inst][key] = result[inst][key]
 
     if verbose:
         logger.info('RVs available from')
@@ -385,7 +423,7 @@ def check_existing(output_directory, files, type):
     ]
 
     if type == 'S2D':
-        existing = [
+        existing += [
             f.partition('.fits')[0] for f in os.listdir(output_directory)
             if 'e2ds' in f
         ]   
@@ -503,7 +541,7 @@ def do_download_filetype(type, raw_files, output_directory, clobber=False, user=
     # check existing files to avoid re-downloading
     if not clobber:
         raw_files = check_existing(output_directory, raw_files, type)
-
+    
     n = raw_files.size
 
     # any file left to download?

{arvi-0.2.3 → arvi-0.2.5}/arvi/instrument_specific.py

@@ -5,7 +5,7 @@ from .setup_logger import setup_logger
 from .utils import ESPRESSO_ADC_issues, ESPRESSO_cryostat_issues
 
 
-# HARPS started operations in October 1st, 2003
+# HARPS started operations on October 1st, 2003
 # https://www.eso.org/sci/facilities/lasilla/instruments/harps/news.html
 HARPS_start = 52913
 
@@ -21,6 +21,11 @@ HARPS_technical_intervention = 57170
 # when the instrument was handed back to Science Operations.
 HARPS_technical_intervention_range = (57161, 57176)
 
+
+# ESPRESSO started operations on October 1st, 2018
+# see Pepe et al. (2021, A&A 645, A96)
+ESPRESSO_start = 58392
+
 # ESPRESSO fiber link upgrade (1 July 2019)
 ESPRESSO_technical_intervention = 58665
 
@@ -113,7 +118,7 @@ def check(self, instrument):
 
 # HARPS commissioning
 def HARPS_commissioning(self, mask=True, plot=True):
-    """ Identify and optionally mask points during HARPS commissioning (HARPS).
+    """ Identify and optionally mask points during HARPS commissioning.
 
     Args:
         mask (bool, optional):
@@ -175,6 +180,38 @@ def HARPS_fiber_commissioning(self, mask=True, plot=True):
     return affected
 
 
+# ESPRESSO commissioning
+def ESPRESSO_commissioning(self, mask=True, plot=True):
+    """ Identify and optionally mask points during ESPRESSO commissioning.
+
+    Args:
+        mask (bool, optional):
+            Whether to mask out the points.
+        plot (bool, optional):
+            Whether to plot the masked points.
+    """
+    logger = setup_logger()
+    if check(self, 'ESPRESSO') is None:
+        return
+
+    affected = self.time < ESPRESSO_start
+    total_affected = affected.sum()
+
+    if self.verbose:
+        n = total_affected
+        logger.info(f"there {'are'[:n^1]}{'is'[n^1:]} {n} frame{'s'[:n^1]} "
+                     "during ESPRESSO commissioning")
+
+    if mask:
+        self.mask[affected] = False
+        self._propagate_mask_changes()
+
+        if plot:
+            self.plot(show_masked=True)
+
+    return affected
+
+
 # ESPRESSO ADC issues
 def ADC_issues(self, mask=True, plot=True, check_headers=False):
     """ Identify and optionally mask points affected by ADC issues (ESPRESSO).
@@ -316,31 +353,25 @@ class ISSUES:
             plot (bool, optional): Whether to plot the masked points.
         """
         logger = setup_logger()
-        try:
-            adc = ADC_issues(self, mask, plot, **kwargs)
-        except IndexError:
-            logger.error('are the data binned? cannot proceed to mask these points...')
-
-        try:
-            cryostat = blue_cryostat_issues(self, mask, plot)
-        except IndexError:
-            logger.error('are the data binned? cannot proceed to mask these points...')
-
-        try:
-            harps_comm = HARPS_commissioning(self, mask, plot)
-        except IndexError:
-            logger.error('are the data binned? cannot proceed to mask these points...')
-
-        try:
-            harps_fibers = HARPS_fiber_commissioning(self, mask, plot)
-        except IndexError:
-            logger.error('are the data binned? cannot proceed to mask these points...')
 
-        # if None in (adc, cryostat, harps_comm, harps_fibers):
-        #     return
+        functions = (
+            ESPRESSO_commissioning,
+            ADC_issues,
+            blue_cryostat_issues,
+            HARPS_commissioning,
+            HARPS_fiber_commissioning
+        )
+        results = []
+
+        for fun in functions:
+            try:
+                results.append(fun(self, mask, plot, **kwargs))
+            except IndexError:
+                logger.error('are the data binned? cannot proceed to mask these points...')
+        
+        results = list(filter(lambda x: x is not None, results))
 
         try:
-            # return adc | cryostat
-            return np.logical_or.reduce((adc, cryostat, harps_comm, harps_fibers))
+            return np.logical_or.reduce(results)
         except UnboundLocalError:
             return

{arvi-0.2.3 → arvi-0.2.5}/arvi/plots.py

@@ -13,10 +13,12 @@ from .utils import lazy_import
 plt = lazy_import('matplotlib.pyplot')
 
 
-def plot_fast(func):
+def plot_settings(func):
     @wraps(func)
     def wrapper(*args, **kwargs):
-        with plt.style.context('fast'):
+        # with plt.style.context('fast'):
+        theme = 'dark_background' if config.dark_plots else 'fast'
+        with plt.style.context(theme):
             return func(*args, **kwargs)
     return wrapper
 
@@ -135,7 +137,7 @@ def clickable_legend(fig, ax, leg):
                 pass
     return on_pick_legend
 
-# @plot_fast
+@plot_settings
 def plot(self, ax=None, show_masked=False, instrument=None, time_offset=0,
          remove_50000=False, tooltips=True, show_title=False, show_legend=True, label=None, 
          jitter=None, N_in_label=False, versus_n=False, show_histogram=False, bw=False, **kwargs):
@@ -403,7 +405,7 @@ def plot(self, ax=None, show_masked=False, instrument=None, time_offset=0,
     return fig, ax
 
 
-@plot_fast
+# @plot_fast
 def plot_quantity(self, quantity, ax=None, show_masked=False, instrument=None,
                   time_offset=0, remove_50000=False, tooltips=False, show_legend=True,
                   N_in_label=False, **kwargs):
@@ -506,7 +508,88 @@ plot_rhk = partialmethod(plot_quantity, quantity='rhk')
 plot_berv = partialmethod(plot_quantity, quantity='berv')
 
 
-@plot_fast
+def plot_xy(self, x, y, ax=None, instrument=None, show_legend=True, **kwargs):
+    logger = setup_logger()
+    if self.N == 0:
+        if self.verbose:
+            logger.error('no data to plot')
+        return
+
+    if ax is None:
+        fig, ax = plt.subplots(1, 1, constrained_layout=True)
+    else:
+        fig = ax.figure
+
+    kwargs.setdefault('marker', 'o')
+    kwargs.setdefault('ls', '')
+    kwargs.setdefault('capsize', 0)
+    kwargs.setdefault('ms', 4)
+
+    instruments = self._check_instrument(instrument)
+
+    for inst in instruments:
+        s = self if self._child else getattr(self, inst)
+        label = inst
+
+        missing = False
+        try:
+            xdata = getattr(s, x).copy()
+        except AttributeError:
+            missing = True
+        try:
+            e_xdata = getattr(s, x + '_err').copy()
+        except AttributeError:
+            e_xdata = np.zeros_like(xdata)
+
+        try:
+            ydata = getattr(s, y).copy()
+        except AttributeError:
+            missing = True
+        try:
+            e_ydata = getattr(s, y + '_err').copy()
+        except AttributeError:
+            e_ydata = np.zeros_like(ydata)
+
+        if missing:
+            lines, *_ = ax.errorbar([], [], [],
+                                    label=label, picker=True, **kwargs)
+            continue
+
+        ax.errorbar(xdata[s.mask], ydata[s.mask], e_xdata[s.mask], e_ydata[s.mask],
+                    label=label, **kwargs)
+
+    # if show_masked:
+    #     ax.errorbar(self.time[~self.mask] - time_offset,
+    #                 getattr(self, quantity)[~self.mask],
+    #                 getattr(self, quantity + '_err')[~self.mask],
+    #                 label='masked', fmt='x', ms=10, color='k', zorder=-2)
+
+    if show_legend:
+        leg = ax.legend()
+        on_pick_legend = clickable_legend(fig, ax, leg)
+        plt.connect('pick_event', on_pick_legend)
+
+    ax.minorticks_on()
+
+    delta = 'Δ' if self._did_adjust_means else ''
+
+    # ylabel = {
+    #     quantity.lower(): quantity,
+    #     'fwhm': f'{delta}FWHM [{self.units}]',
+    #     'bispan': f'{delta}BIS [{self.units}]',
+    #     'rhk': r"$\log$ R'$_{HK}$",
+    #     'berv': 'BERV [km/s]',
+    # }
+
+    # ax.set_ylabel(ylabel[quantity.lower()])
+
+    if config.return_self:
+        return self
+    else:
+        return fig, ax
+
+
+# @plot_fast
 def gls(self, ax=None, label=None, instrument=None, 
         fap=True, fap_method='baluev', adjust_means=config.adjust_means_gls,
         picker=True, **kwargs):

{arvi-0.2.3 → arvi-0.2.5}/arvi/setup_logger.py

@@ -6,7 +6,7 @@ def setup_logger():
         import marimo as mo
         if mo.running_in_notebook():
             raise NotImplementedError
-    except NotImplementedError:
+    except (NotImplementedError, AttributeError):
         pass
     except (ImportError, ModuleNotFoundError):
         logger.remove()

{arvi-0.2.3 → arvi-0.2.5}/arvi/timeseries.py

@@ -55,7 +55,7 @@ class RV(ISSUES, REPORTS):
             Information on the target from Simbad
     """
     star: str
-    instrument: str = field(init=True, repr=False, default=None)
+    instrument: Union[str, list] = field(init=True, repr=False, default=None)
     verbose: bool = field(init=True, repr=False, default=True)
     do_maxerror: Union[bool, float] = field(init=True, repr=False, default=False)
     do_secular_acceleration: bool = field(init=True, repr=False, default=True)

{arvi-0.2.3 → arvi-0.2.5/arvi.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: arvi
-Version: 0.2.3
+Version: 0.2.5
 Summary: The Automated RV Inspector
 Author-email: João Faria <joao.faria@unige.ch>
 License: MIT
@@ -23,7 +23,7 @@ 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"/>
+  <img width = "140" src="https://raw.githubusercontent.com/j-faria/arvi/refs/heads/main/docs/logo/logo.png"/>
 </p>
 
 This package sits alongside [DACE](https://dace.unige.ch/) to help with the

{arvi-0.2.3 → arvi-0.2.5}/tests/test_create_RV.py

@@ -19,3 +19,10 @@ def test_from_rdb(change_test_dir):
     assert (s.bispan == 0).all()
     assert isnan(s.rhk).all()
 
+
+def test_list_instruments():
+    from arvi import RV, config
+    config.request_as_public = True
+    _ = RV('HD28185', instrument='CORALIE')
+    _ = RV('HD28185', instrument=['CORALIE'])
+    _ = RV('HD28185', instrument=['CORALIE', 'HRS'])