arvi 0.2.2__tar.gz → 0.2.3__tar.gz

{arvi-0.2.2/arvi.egg-info → arvi-0.2.3}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: arvi
-Version: 0.2.2
+Version: 0.2.3
 Summary: The Automated RV Inspector
 Author-email: João Faria <joao.faria@unige.ch>
 License: MIT

{arvi-0.2.2 → arvi-0.2.3}/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-0.2.3}/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-0.2.3}/arvi/config.py

@@ -31,6 +31,8 @@ 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,
         # debug
         'debug': False,
     }
@@ -43,10 +45,16 @@ 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 +62,7 @@ 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-0.2.3}/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
@@ -47,6 +49,7 @@ def load_spectroscopy(user=None):
 
 @lru_cache()
 def get_dace_id(star, verbose=True):
+    logger = setup_logger()
     filters = {"obj_id_catname": {"equal": [star]}}
     try:
         with all_logging_disabled():
@@ -58,6 +61,7 @@ def get_dace_id(star, verbose=True):
         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()]
 
@@ -259,6 +263,7 @@ 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 +449,7 @@ 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 +495,7 @@ 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-0.2.3}/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-0.2.3}/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-0.2.3}/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-0.2.3}/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
 
@@ -172,6 +172,7 @@ 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')
@@ -406,6 +407,7 @@ def plot(self, ax=None, show_masked=False, instrument=None, time_offset=0,
 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')
@@ -531,6 +533,7 @@ 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 +695,7 @@ 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 +815,8 @@ 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')

arvi-0.2.3/arvi/reports.py

@@ -0,0 +1,204 @@
+from functools import partial
+import numpy as np
+from astropy.timeseries import LombScargle
+
+from .setup_logger import setup_logger
+
+
+sine_line = None
+residual_gls = None
+def sine_picker(event, self, fig, ax, ax1):
+    from .timeseries import fit_sine
+    global sine_line, residual_gls
+    if sine_line is not None:
+        sine_line[0].remove()
+    if residual_gls is not None:
+        residual_gls[0].remove()
+    xdata, ydata = event.artist.get_data()
+    ind = event.ind
+    period = xdata[ind][0]
+    p, sine = fit_sine(self.mtime, self.mvrad, self.msvrad, period=period)
+    tt = np.linspace(self.mtime.min(), self.mtime.max(), 100)
+    tt -= 50000
+    sine_line = ax1.plot(tt, sine(tt), 'k')
+    #
+    f, p = LombScargle(self.mtime, self.mvrad - sine(self.mtime), self.msvrad).autopower()
+    residual_gls = ax.semilogx(1/f, p, 'r')
+    fig.canvas.draw_idle()
+
+
+class REPORTS:
+    def summary(self, add_ccf_mask=True, add_prog_id=False, **kwargs):
+        from .utils import pretty_print_table
+        if isinstance(self, list):
+            selfs = self
+        else:
+            selfs = [self]
+        
+        rows = []
+        for self in selfs:
+            rows.append([self.star] + [''] * len(self.instruments) + [''])
+            rows.append([''] + self.instruments + ['full'])
+            rows.append(['N'] + list(self.NN.values()) + [self.N])
+            rows.append(['RV span'] + [np.ptp(s.mvrad).round(3) for s in self] + [np.ptp(self.mvrad).round(3)])
+            rows.append(['RV std'] + [s.mvrad.std().round(3) for s in self] + [self.mvrad.std().round(3)])
+            rows.append(['eRV mean'] + [s.msvrad.mean().round(3) for s in self] + [self.msvrad.mean().round(3)])
+
+            if add_ccf_mask:
+                if hasattr(self, 'ccf_mask'):
+                    row = ['CCF mask']
+                    for inst in self.instruments:
+                        row.append(', '.join(np.unique(getattr(self, inst).ccf_mask)))
+                    row.append('')
+                    rows.append(row)
+
+            if add_prog_id:
+                row = ['prog ID']
+                for inst in self.instruments:
+                    p = ', '.join(np.unique(getattr(self, inst).prog_id))
+                    row.append(p)
+                rows.append(row)
+
+        return pretty_print_table(rows, **kwargs)
+
+
+    def summary_one_instrument(self):
+        from .utils import pretty_print_table
+        if isinstance(self, list):
+            selfs = self
+        else:
+            selfs = [self]
+
+        rows = []
+        rows.append(['', 'N', 'Δt', 'RV std', 'median σRV'])
+        for self in selfs:
+            rows.append([
+                self.star, 
+                self.N, 
+                int(np.ptp(self.mtime).round(0)),
+                np.std(self.mvrad).round(1),
+                np.median(self.msvrad).round(1),
+            ])
+
+        pretty_print_table(rows)
+
+
+    def summary_stellar(self, show_ra_dec=True, show_pm=True, **kwargs):
+        from .utils import pretty_print_table, get_ra_sexagesimal, get_dec_sexagesimal
+        if isinstance(self, list):
+            selfs = self
+        else:
+            selfs = [self]
+        
+
+
+        rows = []
+        rows.append(['star'] + [self.star for self in selfs])
+        if show_ra_dec:
+            rows.append(['RA'] + [get_ra_sexagesimal(self.simbad.ra) for self in selfs])
+            rows.append(['DEC'] + [get_dec_sexagesimal(self.simbad.dec) for self in selfs])
+        
+        if show_pm:
+            rows.append(['pm ra'] + [(self.gaia or self.simbad).pmra for self in selfs])
+            rows.append(['pm dec'] + [(self.gaia or self.simbad).pmdec for self in selfs])
+
+        rows.append(['π (mas)'] + [(self.gaia or self.simbad).plx for self in selfs])
+        # 
+        rows.append(['B (mag)'] + [self.simbad._B for self in selfs])
+        rows.append(['V (mag)'] + [self.simbad._V for self in selfs])
+        rows.append(['B-V'] + [self.simbad._B - self.simbad._V for self in selfs])
+        rows.append(["log R'HK"] + [np.nanmean(self.rhk).round(2) for self in selfs])
+            # rows.append([''] + self.instruments + ['full'])
+            # rows.append(['N'] + list(self.NN.values()) + [self.N])
+            # rows.append(['RV span'] + [np.ptp(s.mvrad).round(3) for s in self] + [np.ptp(self.mvrad).round(3)])
+            # rows.append(['RV std'] + [s.mvrad.std().round(3) for s in self] + [self.mvrad.std().round(3)])
+            # rows.append(['eRV mean'] + [s.msvrad.mean().round(3) for s in self] + [self.msvrad.mean().round(3)])
+
+        return pretty_print_table(rows, **kwargs)
+
+
+
+
+    def report(self, save=None):
+        import matplotlib.pyplot as plt
+        import matplotlib.gridspec as gridspec
+        from matplotlib.backends.backend_pdf import PdfPages
+        logger = setup_logger()
+
+        # size = A4
+        size = 8.27, 11.69
+        fig = plt.figure(figsize=size, constrained_layout=True)
+        gs = gridspec.GridSpec(5, 3, figure=fig, height_ratios=[2, 2, 1, 1, 0.1])
+
+        # first row, all columns
+        ax1 = plt.subplot(gs[0, :])
+
+        title = f'{self.star}'
+        ax1.set_title(title, loc='left', fontsize=14)
+        # ax1.set_title(r"\href{http://www.google.com}{link}", color='blue',
+        #               loc='center')
+
+        if self._did_adjust_means:
+            title = '(instrument means subtracted) '
+        else:
+            title = ''
+        title += f'V={self.simbad.V}, {self.simbad.sp_type}'
+        ax1.set_title(title, loc='right', fontsize=12)
+
+        self.plot(ax=ax1, N_in_label=True, tooltips=False, remove_50000=True)
+
+
+        ax1.legend().remove()
+        legend_ax = plt.subplot(gs[1, -1])
+        legend_ax.axis('off')
+        leg = plt.legend(*ax1.get_legend_handles_labels(),
+                        prop={'family': 'monospace'})
+        legend_ax.add_artist(leg)
+        
+        second_legend = f'rms  : {self.rms:.2f} {self.units}'
+        second_legend += f'\nerror: {self.error:.2f} {self.units}'
+
+        second_legend += f'\n\nCCF masks: {np.unique(self.ccf_mask)}'
+
+        legend_ax.legend([],
+                        title=second_legend,
+                        loc='lower right', frameon=False,
+                        prop={'family': 'monospace'})
+
+        ax2 = plt.subplot(gs[1, :-1])
+        self.gls(ax=ax2, picker=True)
+
+        ax3 = plt.subplot(gs[2, :-1])
+        self.plot_fwhm(ax=ax3, tooltips=False, remove_50000=True)
+        ax3.legend().remove()
+        ax3p = plt.subplot(gs[2, -1])
+        self.gls_fwhm(ax=ax3p, picker=False)
+
+        ax4 = plt.subplot(gs[3, :-1])
+        self.plot_rhk(ax=ax4, tooltips=False, remove_50000=True)
+        ax4.legend().remove()
+        ax4p = plt.subplot(gs[3, -1])
+        self.gls_rhk(ax=ax4p, picker=False)
+
+
+        if save is None:
+            fig.canvas.mpl_connect(
+                'pick_event',
+                partial(sine_picker, self=self, fig=fig, ax=ax2, ax1=ax1))
+
+        if save is not None:
+            if save is True:
+                save = f'report_{"".join(self.star.split())}.pdf'
+
+            if save.endswith('.png'):
+                fig.savefig(save)
+            else:
+                with PdfPages(save) as pdf:
+                    #pdf.attach_note('hello', positionRect=[5, 15, 20, 30])
+
+                    if self.verbose:
+                        logger.info(f'saving to {save}')
+                    pdf.savefig(fig)
+                # os.system(f'evince {save} &')
+
+        return fig

arvi-0.2.3/arvi/setup_logger.py

@@ -0,0 +1,24 @@
+import sys
+
+def setup_logger():
+    from loguru import logger
+    try:
+        import marimo as mo
+        if mo.running_in_notebook():
+            raise NotImplementedError
+    except NotImplementedError:
+        pass
+    except (ImportError, ModuleNotFoundError):
+        logger.remove()
+    else:
+        logger.remove()
+
+    logger.configure(extra={"indent": ""})
+    logger.add(
+        sys.stdout,
+        colorize=True,
+        # format="<green>{time:YYYY-MM-DDTHH:mm:ss}</green> <level>{message}</level>",
+        format="{extra[indent]}<level>{message}</level>",
+    )
+
+    return logger

{arvi-0.2.2 → arvi-0.2.3}/arvi/simbad_wrapper.py

@@ -1,9 +1,8 @@
 import os
-import numpy as np
 import requests
 from dataclasses import dataclass
 
-import pysweetcat
+import numpy as np
 
 try:
     from uncertainties import ufloat
@@ -12,7 +11,6 @@ except ImportError:
 
 from .stellar import EFFECTIVE_TEMPERATURES, teff_to_sptype
 from .translations import translate
-from .setup_logger import logger
 
 DATA_PATH = os.path.dirname(__file__)
 DATA_PATH = os.path.join(DATA_PATH, 'data')
@@ -146,6 +144,7 @@ class simbad:
             star (str): The name of the star to query simbad
         """
         from astropy.coordinates import SkyCoord
+        import pysweetcat
 
         self.star = translate(star, ngc=True, ic=True)
 

{arvi-0.2.2 → arvi-0.2.3}/arvi/timeseries.py

@@ -1,14 +1,16 @@
 import os
 from dataclasses import dataclass, field
 from typing import Union
-from functools import lru_cache, partial, partialmethod
+from functools import partial, partialmethod
 from glob import glob
 import warnings
 from copy import deepcopy
 from datetime import datetime, timezone
 import numpy as np
 
-from .setup_logger import logger
+from .setup_logger import setup_logger
+logger = setup_logger()
+
 from .config import config
 from .translations import translate
 from .dace_wrapper import do_download_filetype, do_symlink_filetype, get_observations, get_arrays
@@ -19,6 +21,8 @@ from .extra_data import get_extra_data
 from .stats import wmean, wrms
 from .binning import bin_ccf_mask, binRV
 from .HZ import getHZ_period
+from .instrument_specific import ISSUES
+from .reports import REPORTS
 from .utils import sanitize_path, strtobool, there_is_internet, timer, chdir
 from .utils import lazy_import
 
@@ -31,8 +35,8 @@ class ExtraFields:
         return list(self.__dict__.keys())
 
 
-@dataclass
-class RV:
+@dataclass(order=False)
+class RV(ISSUES, REPORTS):
     """
     A class holding RV observations
 
@@ -1245,9 +1249,9 @@ class RV:
 
     from .plots import plot, plot_fwhm, plot_bispan, plot_contrast, plot_rhk, plot_berv, plot_quantity
     from .plots import gls, gls_fwhm, gls_bispan, gls_rhk, gls_quantity, window_function
-    from .reports import report
 
-    from .instrument_specific import known_issues
+    # from .reports import report
+    # from .instrument_specific import known_issues
 
     def change_instrument_name(self, old_name, new_name, strict=False):
         """ Change the name of an instrument

{arvi-0.2.2 → arvi-0.2.3}/arvi/utils.py

@@ -21,7 +21,7 @@ except ImportError:
     tqdm = lambda x, *args, **kwargs: x
     trange = lambda *args, **kwargs: range(*args, **kwargs)
 
-from .setup_logger import logger
+from .setup_logger import setup_logger
 from .config import config
 
 
@@ -70,6 +70,8 @@ def all_logging_disabled():
 @contextmanager
 def timer(name=None):
     """ A simple context manager to time a block of code """
+    logger = setup_logger()
+
     if not config.debug:
         yield
         return

{arvi-0.2.2 → arvi-0.2.3/arvi.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: arvi
-Version: 0.2.2
+Version: 0.2.3
 Summary: The Automated RV Inspector
 Author-email: João Faria <joao.faria@unige.ch>
 License: MIT

{arvi-0.2.2 → arvi-0.2.3}/arvi.egg-info/SOURCES.txt

@@ -54,6 +54,7 @@ docs/logo/logo.png
 docs/stylesheets/extra.css
 tests/HD10700-Bcor_ESPRESSO18.rdb
 tests/test_binning.py
+tests/test_config.py
 tests/test_create_RV.py
 tests/test_import_object.py
 tests/test_simbad.py

{arvi-0.2.2 → arvi-0.2.3}/docs/API.md

@@ -4,13 +4,17 @@ toc: false
 
 # API documentation
 
+## `arvi.timeseries.RV`
+
 ::: arvi.timeseries.RV
     handler: python
     options:
-        show_root_heading: true
+        show_bases: false
+        show_root_heading: false
         show_source: false
         merge_init_into_class: false
         group_by_category: true
+        show_category_heading: true
 
 
 ## Sub-packages

{arvi-0.2.2 → arvi-0.2.3}/docs/detailed.ipynb

@@ -2,7 +2,7 @@
  "cells": [
   {
    "cell_type": "code",
-   "execution_count": 79,
+   "execution_count": 1,
    "metadata": {
     "tags": [
      "hide_code"
@@ -36,7 +36,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 80,
+   "execution_count": 2,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -45,7 +45,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 81,
+   "execution_count": 3,
    "metadata": {},
    "outputs": [
     {
@@ -53,13 +53,7 @@
      "output_type": "stream",
      "text": [
       "\u001b[1mquerying Simbad...\u001b[0m\n",
-      "\u001b[1mquerying Gaia...\u001b[0m\n"
-     ]
-    },
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
+      "\u001b[1mquerying Gaia...\u001b[0m\n",
       "\u001b[1mquerying DACE for HD69830...\u001b[0m\n",
       "\u001b[33m\u001b[1mrequesting DACE data as public\u001b[0m\n",
       "\u001b[1mRVs available from\u001b[0m\n",
@@ -181,8 +175,8 @@
    "metadata": {},
    "source": [
     "<div class=\"admonition note\">\n",
-    "    <p class=\"admonition-title\">Note</p>\n",
-    "    <p>\n",
+    "    <div class=\"admonition-title\">Note</div>\n",
+    "    <p style=\"margin-top: 1em\">\n",
     "        We used the <code>strict=True</code> option above to select only HIRES and HARPS. By default, the match with the instrument names is done recursively as 'HIRES*', so without <code>strict=True</code> we would have removed both HIRES and HIRES_post04 as well as HARPS and HARPS03.\n",
     "    </p>\n",
     "</div>"
@@ -379,8 +373,8 @@
    "metadata": {},
    "source": [
     "<div class=\"admonition note\">\n",
-    "    <p class=\"admonition-title\">Note</p>\n",
-    "    <p>\n",
+    "    <div class=\"admonition-title\">Note</div>\n",
+    "    <p style=\"margin-top: 1em\">\n",
     "        The names <code>vrad</code> and <code>svrad</code> have become somewhat standard in the community to refer to the radial velocities and their uncertainties.\n",
     "    </p>\n",
     "</div>"
@@ -555,8 +549,8 @@
    "metadata": {},
    "source": [
     "<div class=\"admonition warning\">\n",
-    "    <p class=\"admonition-title\">Warning</p>\n",
-    "    <p>\n",
+    "    <div class=\"admonition-title\">Warning</div>\n",
+    "    <p style=\"margin-top: 1em\">\n",
     "        The <code>remove_instrument</code> method we used above does not modify <code>s.mask</code> but instead completely removes the data from that instrument.\n",
     "    </p>\n",
     "</div>"
@@ -634,8 +628,8 @@
    "metadata": {},
    "source": [
     "<div class=\"admonition note\">\n",
-    "    <p class=\"admonition-title\">Note</p>\n",
-    "    <p>\n",
+    "    <div class=\"admonition-title\">Note</div>\n",
+    "    <p style=\"margin-top: 1em\">\n",
     "        Only the HARPS03 data has log R'HK values, which is why the function warns us about NaN values for the other instruments.\n",
     "    </p>\n",
     "</div>"
@@ -644,7 +638,7 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 3",
+   "display_name": "Python 3 (ipykernel)",
    "language": "python",
    "name": "python3"
   },

{arvi-0.2.2 → arvi-0.2.3}/mkdocs.yml

@@ -1,13 +1,33 @@
 site_name: arvi
-
 site_dir: _site
 
+repo_url: https://github.com/j-faria/arvi
+# repo_name: j-faria/arvi
+
 theme:
   name: "material"
   logo: logo/detective.png
   favicon: logo/detective.png
+  # palette:
+  #   primary: amber
   palette:
-    primary: amber
+    # Palette toggle for light mode
+    - media: "(prefers-color-scheme: light)"
+      scheme: default
+      primary: amber
+      accent: indigo
+      toggle:
+        icon: material/weather-night
+        name: Switch to dark mode
+    # Palette toggle for dark mode
+    - media: "(prefers-color-scheme: dark)"
+      scheme: slate
+      primary: black
+      accent: light blue
+      toggle:
+        icon: material/weather-sunny
+        name: Switch to light mode
+
   features:
     - content.code.copy
     - navigation.instant

arvi-0.2.3/tests/test_config.py

@@ -0,0 +1,22 @@
+# import pytest
+
+def test_config_keys():
+    from arvi import config
+    assert hasattr(config, 'return_self'), 'config.return_self not found'
+    assert hasattr(config, 'adjust_means_gls'), 'config.adjust_means_gls not found'
+    assert hasattr(config, 'check_internet'), 'config.check_internet not found'
+    assert hasattr(config, 'request_as_public'), 'config.request_as_public not found'
+    assert hasattr(config, 'fancy_import'), 'config.fancy_import not found'
+    assert hasattr(config, 'debug'), 'config.debug not found'
+
+
+def test_config_set():
+    from arvi import config
+    config.return_self = True
+    assert config.return_self
+
+    config.new_option = False
+    assert not config.new_option
+
+    config.new_option_str = 'hello'
+    assert config.new_option_str == 'hello'

arvi-0.2.3/tests/test_import_object.py

@@ -0,0 +1,33 @@
+import pytest
+import os
+
+def test_import():
+    import arvi
+    from arvi import RV
+
+
+def test_import_object():
+    from arvi import _51Peg
+    from arvi import HD10180
+
+def test_import_object_public():
+    from arvi import config
+
+    config.request_as_public = True
+    
+    from arvi import _51Peg
+    from arvi import HD10180
+
+    config.request_as_public = False
+
+
+def test_fancy_import_off():
+    from arvi import config
+
+    from arvi import HD10180
+
+    config.fancy_import = False
+
+    with pytest.raises(ImportError):
+        from arvi import HD69830
+

arvi-0.2.2/arvi/reports.py

@@ -1,130 +0,0 @@
-from functools import partial
-import numpy as np
-from astropy.timeseries import LombScargle
-
-from .setup_logger import logger
-
-
-sine_line = None
-residual_gls = None
-def sine_picker(event, self, fig, ax, ax1):
-    from .timeseries import fit_sine
-    global sine_line, residual_gls
-    if sine_line is not None:
-        sine_line[0].remove()
-    if residual_gls is not None:
-        residual_gls[0].remove()
-    xdata, ydata = event.artist.get_data()
-    ind = event.ind
-    period = xdata[ind][0]
-    p, sine = fit_sine(self.mtime, self.mvrad, self.msvrad, period=period)
-    tt = np.linspace(self.mtime.min(), self.mtime.max(), 100)
-    tt -= 50000
-    sine_line = ax1.plot(tt, sine(tt), 'k')
-    #
-    f, p = LombScargle(self.mtime, self.mvrad - sine(self.mtime), self.msvrad).autopower()
-    residual_gls = ax.semilogx(1/f, p, 'r')
-    fig.canvas.draw_idle()
-
-
-def summary(self, add_ccf_mask=True, add_prog_id=False):
-    from .utils import pretty_print_table
-    rows = []
-    rows.append([self.star] + [''] * len(self.instruments))
-    rows.append([''] + self.instruments)
-    rows.append(['N'] + list(self.NN.values()))
-
-    if add_ccf_mask:
-        row = ['CCF mask']
-        for inst in self.instruments:
-            row.append(', '.join(np.unique(getattr(self, inst).ccf_mask)))
-        rows.append(row)
-
-    if add_prog_id:
-        row = ['prog ID']
-        for inst in self.instruments:
-            p = ', '.join(np.unique(getattr(self, inst).prog_id))
-            row.append(p)
-        rows.append(row)
-
-    pretty_print_table(rows)
-
-
-def report(self, save=None):
-    import matplotlib.pyplot as plt
-    import matplotlib.gridspec as gridspec
-    from matplotlib.backends.backend_pdf import PdfPages
-
-    # size = A4
-    size = 8.27, 11.69
-    fig = plt.figure(figsize=size, constrained_layout=True)
-    gs = gridspec.GridSpec(5, 3, figure=fig, height_ratios=[2, 2, 1, 1, 0.1])
-
-    # first row, all columns
-    ax1 = plt.subplot(gs[0, :])
-
-    title = f'{self.star}'
-    ax1.set_title(title, loc='left', fontsize=14)
-    # ax1.set_title(r"\href{http://www.google.com}{link}", color='blue',
-    #               loc='center')
-
-    if self._did_adjust_means:
-        title = '(instrument means subtracted) '
-    else:
-        title = ''
-    title += f'V={self.simbad.V}, {self.simbad.sp_type}'
-    ax1.set_title(title, loc='right', fontsize=12)
-
-    self.plot(ax=ax1, N_in_label=True, tooltips=False, remove_50000=True)
-
-
-    ax1.legend().remove()
-    legend_ax = plt.subplot(gs[1, -1])
-    legend_ax.axis('off')
-    leg = plt.legend(*ax1.get_legend_handles_labels(),
-                     prop={'family': 'monospace'})
-    legend_ax.add_artist(leg)
-    second_legend = f'rms  : {self.rms:.2f} {self.units}\n'
-    second_legend += f'error: {self.error:.2f} {self.units}'
-    legend_ax.legend([],
-                     title=second_legend,
-                     loc='lower right', frameon=False,
-                     prop={'family': 'monospace'})
-
-    ax2 = plt.subplot(gs[1, :-1])
-    self.gls(ax=ax2, picker=True)
-
-    ax3 = plt.subplot(gs[2, :-1])
-    self.plot_fwhm(ax=ax3, tooltips=False, remove_50000=True)
-    ax3.legend().remove()
-    ax3p = plt.subplot(gs[2, -1])
-    self.gls_fwhm(ax=ax3p, picker=False)
-
-    ax4 = plt.subplot(gs[3, :-1])
-    self.plot_bis(ax=ax4, tooltips=False, remove_50000=True)
-    ax4.legend().remove()
-    ax4p = plt.subplot(gs[3, -1])
-    self.gls_bis(ax=ax4p, picker=False)
-
-
-    if save is None:
-        fig.canvas.mpl_connect(
-            'pick_event',
-            partial(sine_picker, self=self, fig=fig, ax=ax2, ax1=ax1))
-
-    if save is not None:
-        if save is True:
-            save = f'report_{"".join(self.star.split())}.pdf'
-
-        if save.endswith('.png'):
-            fig.savefig(save)
-        else:
-            with PdfPages(save) as pdf:
-                #pdf.attach_note('hello', positionRect=[5, 15, 20, 30])
-
-                if self.verbose:
-                    logger.info(f'saving to {save}')
-                pdf.savefig(fig)
-            # os.system(f'evince {save} &')
-
-    return fig

arvi-0.2.2/arvi/setup_logger.py

@@ -1,20 +0,0 @@
-import sys
-from loguru import logger
-
-try:
-    import marimo as mo
-    if mo.running_in_notebook():
-        raise ImportError
-except (ImportError, ModuleNotFoundError):
-    pass
-else:
-    logger.remove()
-
-
-logger.configure(extra={"indent": ""})
-logger.add(
-    sys.stdout,
-    colorize=True,
-    # format="<green>{time:YYYY-MM-DDTHH:mm:ss}</green> <level>{message}</level>",
-    format="{extra[indent]}<level>{message}</level>",
-)

arvi-0.2.2/tests/test_import_object.py

@@ -1,17 +0,0 @@
-import pytest
-import os
-
-def test_import():
-    import arvi
-    from arvi import RV
-
-
-def test_import_object():
-    from arvi import _51Peg
-
-    from arvi import HD10180
-    # if os.path.exists(os.path.expanduser('~/.dacerc')):
-    # else:
-    #     with pytest.raises(ImportError):
-    #         from arvi import HD10180
-