arvi 0.2.2__tar.gz → 0.2.4__tar.gz

{arvi-0.2.2/arvi.egg-info → arvi-0.2.4}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: arvi
-Version: 0.2.2
+Version: 0.2.4
 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-0.2.2 → arvi-0.2.4}/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-0.2.2 → arvi-0.2.4}/arvi/__init__.py

@@ -1,4 +1,4 @@
-__all__ = ['RV']
+__all__ = ['RV', 'config', 'simbad', 'gaia']
 
 from importlib.metadata import version, PackageNotFoundError
 try:
@@ -8,17 +8,15 @@ except PackageNotFoundError:
     pass
 
 from .config import config
-from .timeseries import RV
-
 from .simbad_wrapper import simbad
+from .gaia_wrapper import gaia
 
-
-## OLD
-# # the __getattr__ function is always called twice, so we need this
-# # to only build and return the RV object on the second time
-# _ran_once = False
+from .timeseries import RV
 
 def __getattr__(name: str):
+    if not config.fancy_import:
+        raise AttributeError
+    
     if name in (
         '_ipython_canary_method_should_not_exist_',
         '_ipython_display_',
@@ -31,15 +29,5 @@ def __getattr__(name: str):
         globals()[name] = RV(name)
         return globals()[name]
     except ValueError as e:
-        raise ImportError(e) from None
-        # raise AttributeError(f"module {__name__!r} has no attribute {name!r}")
-
-    ## OLD
-    # # can't do it any other way :(
-    # global _ran_once
+        raise AttributeError(e)
 
-    # if _ran_once:
-    #     _ran_once = False
-    #     return RV(name)
-    # else:
-    #     _ran_once = True

{arvi-0.2.2 → arvi-0.2.4}/arvi/binning.py

@@ -1,6 +1,6 @@
 import numpy as np
 
-from .setup_logger import logger
+from .setup_logger import setup_logger
 
 ###############################################################################
 # the following is mostly a copy of the scipy implementation of
@@ -390,6 +390,7 @@ def binRV(time, rv, err=None, stat='wmean', tstat='wmean', estat='addquad',
 
 
 def bin_ccf_mask(time, ccf_mask):
+    logger = setup_logger()
     indices = binRV(time, None, binning_indices=True)
     indices = np.r_[indices, time.size]
     bmask = []

{arvi-0.2.2 → arvi-0.2.4}/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
@@ -31,6 +32,10 @@ class config:
         'check_internet': False,
         # make all DACE requests without using a .dacerc file
         '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,
     }
@@ -43,10 +48,16 @@ class config:
             # return {'return_self': 'help!'}
             return {}
 
-        if self.__user_config.has_option('config', name):
-            self.__conf[name] = self.__user_config.get('config', name)
+        try:
+            if self.__user_config.has_option('config', name):
+                value = self.__user_config.get('config', name)
+                value = True if value == 'True' else value
+                value = False if value == 'False' else value
+                self.__conf[name] = value
 
-        return self.__conf[name]
+            return self.__conf[name]
+        except KeyError:
+            raise KeyError(f"unknown config option '{name}'")
 
     def __setattr__(self, name, value):
         if name in config.__setters:
@@ -54,7 +65,7 @@ class config:
         else:
             if 'config' not in self.__user_config:
                 self.__user_config.add_section('config')
-            self.__user_config.set('config', name, value)
+            self.__user_config.set('config', name, str(value))
             save_config(self.__user_config)
             # raise NameError(f"unknown configuration name '{name}'")
 

{arvi-0.2.2 → arvi-0.2.4}/arvi/dace_wrapper.py

@@ -5,11 +5,13 @@ import collections
 from functools import lru_cache
 from itertools import islice
 import numpy as np
-from .setup_logger import logger
+
+from .setup_logger import setup_logger
 from .utils import create_directory, all_logging_disabled, stdout_disabled, tqdm
 
 
 def load_spectroscopy(user=None):
+    logger = setup_logger()
     with all_logging_disabled():
         from dace_query.spectroscopy import SpectroscopyClass, Spectroscopy as default_Spectroscopy
         from dace_query import DaceClass
@@ -45,8 +47,10 @@ 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:
         with all_logging_disabled():
@@ -55,9 +59,13 @@ 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 = []
     instruments = [str(i) for i in result.keys()]
 
@@ -66,7 +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):
@@ -160,12 +167,12 @@ def get_observations_from_instrument(star, instrument, user=None, main_id=None,
 
     found_dace_id = False
     try:
-        dace_id = get_dace_id(star, verbose=verbose)
+        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)
+                dace_id = get_dace_id(main_id, verbose=verbose, raise_error=True)
                 found_dace_id = True
             except ValueError:
                 pass
@@ -259,6 +266,7 @@ def get_observations_from_instrument(star, instrument, user=None, main_id=None,
     return r
 
 def get_observations(star, instrument=None, user=None, main_id=None, verbose=True):
+    logger = setup_logger()
     if instrument is None:
         Spectroscopy = load_spectroscopy(user)
 
@@ -444,6 +452,7 @@ def extract_fits(output_directory, filename=None):
 
 
 def do_symlink_filetype(type, raw_files, output_directory, clobber=False, top_level=None, verbose=True):
+    logger = setup_logger()
     terminations = {
         'CCF': '_CCF_A.fits',
         'S1D': '_S1D_A.fits',
@@ -489,6 +498,7 @@ def do_symlink_filetype(type, raw_files, output_directory, clobber=False, top_le
 def do_download_filetype(type, raw_files, output_directory, clobber=False, user=None,
                          verbose=True, chunk_size=20, parallel_limit=30):
     """ Download CCFs / S1Ds / S2Ds from DACE """
+    logger = setup_logger()
     raw_files = np.atleast_1d(raw_files)
 
     create_directory(output_directory)

{arvi-0.2.2 → arvi-0.2.4}/arvi/exofop_wrapper.py

@@ -4,9 +4,10 @@ import time
 import importlib.resources as resources
 import numpy as np
 
-from .setup_logger import logger
+from .setup_logger import setup_logger
 
 def get_toi_list(verbose=True):
+    logger = setup_logger()
     toi_list = resources.files('arvi') / 'data' / 'exofop_toi_list.csv'
     now = time.time()
     download = not toi_list.exists() or toi_list.stat().st_mtime < now - 48 * 60 * 60

{arvi-0.2.2 → arvi-0.2.4}/arvi/extra_data.py

@@ -3,8 +3,7 @@ from glob import glob
 import json
 
 from numpy import full
-from .setup_logger import logger
-from . import timeseries
+from .setup_logger import setup_logger
 
 refs = {
     'HD86226': 'Teske et al. 2020 (AJ, 160, 2)'
@@ -12,7 +11,8 @@ refs = {
 
 def get_extra_data(star, instrument=None, path=None, verbose=True,
                    check_for_kms=True):
-    
+    from . import timeseries
+    logger = setup_logger()
     if path is None:
         path = os.path.dirname(__file__)
         path = os.path.join(path, 'data', 'extra')

{arvi-0.2.2 → arvi-0.2.4}/arvi/instrument_specific.py

@@ -1,7 +1,7 @@
 import os, sys
 import numpy as np
 
-from .setup_logger import logger
+from .setup_logger import setup_logger
 from .utils import ESPRESSO_ADC_issues, ESPRESSO_cryostat_issues
 
 
@@ -27,6 +27,7 @@ ESPRESSO_technical_intervention = 58665
 
 def divide_ESPRESSO(self):
     """ Split ESPRESSO data into separate sub ESP18 and ESP19 subsets """
+    logger = setup_logger()
     if self._check_instrument('ESPRESSO', strict=False) is None:
         return
     if 'ESPRESSO18' in self.instruments and 'ESPRESSO19' in self.instruments:
@@ -64,6 +65,7 @@ def divide_ESPRESSO(self):
 
 def divide_HARPS(self):
     """ Split HARPS data into separate sub HARPS03 and HARPS15 subsets """
+    logger = setup_logger()
     if self._check_instrument('HARPS', strict=False) is None:
         return
     if 'HARPS03' in self.instruments and 'HARPS15' in self.instruments:
@@ -100,6 +102,7 @@ def divide_HARPS(self):
     
 
 def check(self, instrument):
+    logger = setup_logger()
     instruments = self._check_instrument(instrument)
     if instruments is None:
         if self.verbose:
@@ -118,6 +121,7 @@ def HARPS_commissioning(self, mask=True, plot=True):
         plot (bool, optional):
             Whether to plot the masked points.
     """
+    logger = setup_logger()
     if check(self, 'HARPS') is None:
         return
 
@@ -149,6 +153,7 @@ def HARPS_fiber_commissioning(self, mask=True, plot=True):
         plot (bool, optional):
             Whether to plot the masked points.
     """
+    logger = setup_logger()
     if check(self, 'HARPS') is None:
         return
 
@@ -182,6 +187,7 @@ def ADC_issues(self, mask=True, plot=True, check_headers=False):
         check_headers (bool, optional):
             Whether to (double-)check the headers for missing/zero keywords.
     """
+    logger = setup_logger()
     instruments = self._check_instrument('ESPRESSO')
     
     if instruments is None:
@@ -225,6 +231,7 @@ def blue_cryostat_issues(self, mask=True, plot=True):
         mask (bool, optional): Whether to mask out the points.
         plot (bool, optional): Whether to plot the masked points.
     """
+    logger = setup_logger()
     instruments = self._check_instrument('ESPRESSO')
     
     if instruments is None:
@@ -259,6 +266,7 @@ def qc_scired_issues(self, plot=False, **kwargs):
     Args:
         plot (bool, optional): Whether to plot the masked points.
     """
+    logger = setup_logger()
     from .headers import get_headers
 
     instruments = self._check_instrument('ESPRESSO')
@@ -299,38 +307,40 @@ def qc_scired_issues(self, plot=False, **kwargs):
     return affected
 
 
-def known_issues(self, mask=True, plot=False, **kwargs):
-    """ Identify and optionally mask known instrumental issues.
-
-    Args:
-        mask (bool, optional): Whether to mask out the points.
-        plot (bool, optional): Whether to plot the masked points.
-    """
-    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
-
-    try:
-        # return adc | cryostat
-        return np.logical_or.reduce((adc, cryostat, harps_comm, harps_fibers))
-    except UnboundLocalError:
-        return
+class ISSUES:
+    def known_issues(self, mask=True, plot=False, **kwargs):
+        """ Identify and optionally mask known instrumental issues.
+
+        Args:
+            mask (bool, optional): Whether to mask out the points.
+            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
+
+        try:
+            # return adc | cryostat
+            return np.logical_or.reduce((adc, cryostat, harps_comm, harps_fibers))
+        except UnboundLocalError:
+            return

{arvi-0.2.2 → arvi-0.2.4}/arvi/plots.py

@@ -5,7 +5,7 @@ import numpy as np
 
 from astropy.timeseries import LombScargle
 
-from .setup_logger import logger
+from .setup_logger import setup_logger
 from .config import config
 from .stats import wmean
 
@@ -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):
@@ -172,6 +174,7 @@ def plot(self, ax=None, show_masked=False, instrument=None, time_offset=0,
         Figure: the figure
         Axes: the axis
     """
+    logger = setup_logger()
     if self.N == 0:
         if self.verbose:
             logger.error('no data to plot')
@@ -402,10 +405,11 @@ 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):
+    logger = setup_logger()
     if self.N == 0:
         if self.verbose:
             logger.error('no data to plot')
@@ -504,7 +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):
@@ -531,6 +616,7 @@ def gls(self, ax=None, label=None, instrument=None,
             Whether to adjust (subtract) the weighted means of each instrument.
             Default is `config.adjust_means_gls`.
     """
+    logger = setup_logger()
     if self.N == 0:
         if self.verbose:
             logger.error('no data to compute gls')
@@ -692,7 +778,7 @@ def gls_quantity(self, quantity, ax=None, instrument=None,
             Whether to adjust (subtract) the weighted means of each instrument.
             Default is `config.adjust_means_gls`.
     """
-
+    logger = setup_logger()
     if not hasattr(self, quantity):
         if self.verbose:
             logger.error(f"cannot find '{quantity}' attribute")
@@ -812,6 +898,8 @@ def window_function(self, ax1=None, ax2=None, instrument=None, crosshair=False,
         crosshair (bool):
             If True, a crosshair will be drawn on the plot.
     """
+    logger = setup_logger()
+
     if self.N == 0:
         if self.verbose:
             logger.error('no data to compute window function')