arvi 0.1.25__tar.gz → 0.1.27__tar.gz

arvi-0.1.27/.github/dependabot.yml

@@ -0,0 +1,6 @@
+version: 2
+updates:
+  - package-ecosystem: "github-actions"
+    directory: ".github/workflows/" # Location of the directory containing the GitHub Actions workflows
+    schedule:
+      interval: "weekly" # Check for updates weekly

{arvi-0.1.25 → arvi-0.1.27}/.github/workflows/docs-gh-pages.yml

@@ -26,13 +26,13 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Checkout
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         
       - name: Setup Pages
-        uses: actions/configure-pages@v3
+        uses: actions/configure-pages@v5
 
       - name: Set up Python
-        uses: actions/setup-python@v3
+        uses: actions/setup-python@v5
         with:
           python-version: "3.10"
   
@@ -48,7 +48,7 @@ jobs:
           mkdocs build
 
       - name: Upload artifact
-        uses: actions/upload-pages-artifact@v2
+        uses: actions/upload-pages-artifact@v3
 
   # Deployment job
   deploy:
@@ -60,4 +60,4 @@ jobs:
     steps:
       - name: Deploy to GitHub Pages
         id: deployment
-        uses: actions/deploy-pages@v2
+        uses: actions/deploy-pages@v4

{arvi-0.1.25 → arvi-0.1.27}/.github/workflows/install.yml

@@ -5,9 +5,6 @@ name: Install-Test
 
 on:
   push:
-    #branches: [ "main" ]
-  pull_request:
-    branches: [ "main" ]
 
 jobs:
   build:

{arvi-0.1.25 → arvi-0.1.27}/PKG-INFO

@@ -1,6 +1,6 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.2
 Name: arvi
-Version: 0.1.25
+Version: 0.1.27
 Summary: The Automated RV Inspector
 Author-email: João Faria <joao.faria@unige.ch>
 License: MIT

{arvi-0.1.25 → arvi-0.1.27}/arvi/dace_wrapper.py

@@ -11,16 +11,33 @@ from .setup_logger import logger
 from .utils import create_directory, all_logging_disabled, stdout_disabled, tqdm
 
 
-def load_spectroscopy() -> SpectroscopyClass:
+def load_spectroscopy(user=None) -> SpectroscopyClass:
     from .config import config
+    # requesting as public
     if config.request_as_public:
         with all_logging_disabled():
             dace = DaceClass(dace_rc_config_path='none')
         return SpectroscopyClass(dace_instance=dace)
+    # DACERC environment variable is set, should point to a dacerc file with credentials
     if 'DACERC' in os.environ:
         dace = DaceClass(dace_rc_config_path=os.environ['DACERC'])
         return SpectroscopyClass(dace_instance=dace)
-    # elif os.path.exists(os.path.expanduser('~/.dacerc')):
+    # user provided, should be a section in ~/.dacerc
+    if user is not None:
+        import configparser
+        import tempfile
+        config = configparser.ConfigParser()
+        config.read(os.path.expanduser('~/.dacerc'))
+        if user not in config.sections():
+            raise ValueError(f'Section for user "{user}" not found in ~/.dacerc')
+        with tempfile.NamedTemporaryFile(mode='w', delete=False) as f:
+            new_config = configparser.ConfigParser()
+            new_config['user'] = config[user]
+            new_config.write(f)
+        dace = DaceClass(dace_rc_config_path=f.name)
+        logger.info(f'using credentials for user {user} in ~/.dacerc')
+        return SpectroscopyClass(dace_instance=dace)
+    # default
     return default_Spectroscopy
 
 @lru_cache()
@@ -70,7 +87,6 @@ def get_arrays(result, latest_pipeline=True, ESPRESSO_mode='HR11', NIRPS_mode='H
             if verbose and npipe > 1:
                 logger.info(f'selecting latest pipeline ({pipelines[0]}) for {inst}')
 
-
         for pipe in pipelines:
             modes = [m for m in result[inst][pipe].keys()]
 
@@ -85,24 +101,19 @@ def get_arrays(result, latest_pipeline=True, ESPRESSO_mode='HR11', NIRPS_mode='H
                     if verbose:
                         logger.warning(f'no observations for requested NIRPS mode ({NIRPS_mode})')
 
-            # HARPS15 observations should not be separated by 'mode' if some are
-            # done together with NIRPS
-            if 'HARPS15' in inst:
+            # HARPS observations should not be separated by 'mode' if some are
+            # done together with NIRPS, but should be separated by 'EGGS' mode
+            if 'HARPS' in inst:
+                m0 = modes[0]
+                data = {
+                    k: np.concatenate([result[inst][pipe][m][k] for m in modes])
+                    for k in result[inst][pipe][m0].keys()
+                }
                 if 'HARPS+NIRPS' in modes:
-                    m0 = modes[0]
-                    data = {
-                        k: np.concatenate([result[inst][pipe][m][k] for m in modes])
-                        for k in result[inst][pipe][m0].keys()
-                    }
                     arrays.append( ((str(inst), str(pipe), str(m0)), data) )
                     continue
 
-                if 'EGGS+NIRPS' in modes:
-                    m0 = modes[0]
-                    data = {
-                        k: np.concatenate([result[inst][pipe][m][k] for m in modes])
-                        for k in result[inst][pipe][m0].keys()
-                    }
+                if 'EGGS+NIRPS' in modes or 'EGGS' in modes:
                     arrays.append( ((str(inst + '_EGGS'), str(pipe), str(m0)), data) )
                     continue
 
@@ -117,7 +128,7 @@ def get_arrays(result, latest_pipeline=True, ESPRESSO_mode='HR11', NIRPS_mode='H
 
     return arrays
 
-def get_observations_from_instrument(star, instrument, main_id=None, verbose=True):
+def get_observations_from_instrument(star, instrument, user=None, main_id=None, verbose=True):
     """ Query DACE for all observations of a given star and instrument
 
     Args:
@@ -125,6 +136,8 @@ def get_observations_from_instrument(star, instrument, main_id=None, verbose=Tru
             name of the star
         instrument (str):
             instrument name
+        user (str, optional):
+            DACERC user name. Defaults to None.
         main_id (str, optional):
             Simbad main id of target to query DACE id. Defaults to None.
         verbose (bool, optional):
@@ -138,7 +151,7 @@ def get_observations_from_instrument(star, instrument, main_id=None, verbose=Tru
         dict:
             dictionary with data from DACE
     """
-    Spectroscopy = load_spectroscopy()
+    Spectroscopy = load_spectroscopy(user)
     found_dace_id = False
     try:
         dace_id = get_dace_id(star, verbose=verbose)
@@ -239,9 +252,9 @@ def get_observations_from_instrument(star, instrument, main_id=None, verbose=Tru
     # print([r[k1][k2].keys() for k1 in r.keys() for k2 in r[k1].keys()])
     return r
 
-def get_observations(star, instrument=None, main_id=None, verbose=True):
+def get_observations(star, instrument=None, user=None, main_id=None, verbose=True):
     if instrument is None:
-        Spectroscopy = load_spectroscopy()
+        Spectroscopy = load_spectroscopy(user)
         try:
             with stdout_disabled(), all_logging_disabled():
                 result = Spectroscopy.get_timeseries(target=star,
@@ -255,7 +268,7 @@ def get_observations(star, instrument=None, main_id=None, verbose=True):
             raise ValueError(msg) from None
     else:
         try:
-            result = get_observations_from_instrument(star, instrument, main_id, verbose)
+            result = get_observations_from_instrument(star, instrument, user, main_id, verbose)
         except ValueError:
             msg = f'no {instrument} observations for {star}'
             raise ValueError(msg) from None
@@ -339,6 +352,12 @@ def check_existing(output_directory, files, type):
         if type in f
     ]
 
+    if type == 'S2D':
+        existing = [
+            f.partition('.fits')[0] for f in os.listdir(output_directory)
+            if 'e2ds' in f
+        ]   
+
     # also check for lowercase type
     existing += [
         f.partition('.fits')[0] for f in os.listdir(output_directory)
@@ -351,7 +370,8 @@ def check_existing(output_directory, files, type):
     
     # remove type of file (e.g. _CCF_A)
     existing = [f.partition('_')[0] for f in existing]
-    
+    existing = np.unique(existing)
+
     missing = []
     for file in files:
         if any(other in file for other in existing):
@@ -360,9 +380,9 @@ def check_existing(output_directory, files, type):
 
     return np.array(missing)
 
-def download(files, type, output_directory, output_filename=None, quiet=True, pbar=None):
+def download(files, type, output_directory, output_filename=None, user=None, quiet=True, pbar=None):
     """ Download files from DACE """
-    Spectroscopy = load_spectroscopy()
+    Spectroscopy = load_spectroscopy(user)
     if isinstance(files, str):
         files = [files]
     if quiet:
@@ -439,7 +459,7 @@ def do_symlink_filetype(type, raw_files, output_directory, clobber=False, top_le
             logger.warning(f'file not found: {file}')
 
 
-def do_download_filetype(type, raw_files, output_directory, clobber=False,
+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 """
     raw_files = np.atleast_1d(raw_files)
@@ -475,7 +495,7 @@ def do_download_filetype(type, raw_files, output_directory, clobber=False,
     if n < parallel_limit:
         iterator = [raw_files[i:i + chunk_size] for i in range(0, n, chunk_size)]
         for files in tqdm(iterator, total=len(iterator)):
-            download(files, type, output_directory, quiet=False)
+            download(files, type, output_directory, quiet=False, user=user)
             extract_fits(output_directory)
 
     else:
@@ -487,7 +507,7 @@ def do_download_filetype(type, raw_files, output_directory, clobber=False,
         chunks = list(chunker(raw_files, chunk_size))
         pbar = tqdm(total=len(chunks))
         it1 = [
-            (files, type, output_directory, f'spectroscopy_download{i+1}.tar.gz', True, pbar)
+            (files, type, output_directory, f'spectroscopy_download{i+1}.tar.gz', user, True, pbar)
             for i, files in enumerate(chunks)
         ]
         it2 = [(output_directory, f'spectroscopy_download{i+1}.tar.gz') for i in range(len(chunks))]

{arvi-0.1.25 → arvi-0.1.27}/arvi/extra_data.py

@@ -10,7 +10,8 @@ refs = {
     'HD86226': 'Teske et al. 2020 (AJ, 160, 2)'
 }
 
-def get_extra_data(star, instrument=None, path=None, verbose=True):
+def get_extra_data(star, instrument=None, path=None, verbose=True,
+                   check_for_kms=True):
     if path is None:
         path = os.path.dirname(__file__)
         path = os.path.join(path, 'data', 'extra')
@@ -18,7 +19,7 @@ def get_extra_data(star, instrument=None, path=None, verbose=True):
     metadata = json.load(open(os.path.join(path, 'metadata.json'), 'r'))
     # print(metadata)
 
-    files = glob(os.path.join(path, star + '*'))
+    files = glob(os.path.join(path, star.replace(' ', '') + '*.rdb'))
     files = [f for f in files if os.path.isfile(f)]
     files = [f for f in files if not os.path.basename(f).endswith('.zip')]
 
@@ -57,9 +58,24 @@ def get_extra_data(star, instrument=None, path=None, verbose=True):
             if 'corrected_for_secular_acceleration' in metadata[file_basename]:
                 did_sa[i] = metadata[file_basename]['corrected_for_secular_acceleration']
 
-    s = timeseries.RV.from_rdb(files[0], star=star, instrument=instruments[0], units=units[0])
-    for file, instrument, unit in zip(files[1:], instruments[1:], units[1:]):
-        s = s + timeseries.RV.from_rdb(file, star=star, instrument=instrument, units=unit)
+    with logger.contextualize(indent='  '):
+        s = timeseries.RV.from_rdb(files[0], star=star, instrument=instruments[0], units=units[0])
+        if check_for_kms and s.svrad.min() < 0.01:
+            units[0] = 'kms'
+            s = timeseries.RV.from_rdb(files[0], star=star, instrument=instruments[0], units=units[0])
+        if verbose:
+            logger.info(f'{instruments[0]:>12s} ├ ({s.N} observations)')
+
+        for file, instrument, unit in zip(files[1:], instruments[1:], units[1:]):
+            _s = timeseries.RV.from_rdb(file, star=star, instrument=instrument, units=unit)
+            if check_for_kms and _s.svrad.min() < 0.01:
+                unit = 'kms'
+                _s = timeseries.RV.from_rdb(file, star=star, instrument=instrument, units=unit)
+            if verbose:
+                logger.info(f'{instrument:>12s} ├ ({_s.N} observations)')
+
+            s = s + _s
+
 
     for i, (inst, ref, inst_did_sa) in enumerate(zip(s.instruments, reference, did_sa)):
         _s = getattr(s, inst)

{arvi-0.1.25 → arvi-0.1.27}/arvi/gaia_wrapper.py

@@ -9,7 +9,11 @@ DATA_PATH = os.path.dirname(__file__)
 DATA_PATH = os.path.join(DATA_PATH, 'data')
 
 QUERY = """
-SELECT TOP 20 gaia_source.designation,gaia_source.source_id,gaia_source.ra,gaia_source.dec,gaia_source.parallax,gaia_source.pmra,gaia_source.pmdec,gaia_source.ruwe,gaia_source.phot_g_mean_mag,gaia_source.bp_rp,gaia_source.radial_velocity,gaia_source.phot_variable_flag,gaia_source.non_single_star,gaia_source.has_xp_continuous,gaia_source.has_xp_sampled,gaia_source.has_rvs,gaia_source.has_epoch_photometry,gaia_source.has_epoch_rv,gaia_source.has_mcmc_gspphot,gaia_source.has_mcmc_msc,gaia_source.teff_gspphot,gaia_source.logg_gspphot,gaia_source.mh_gspphot,gaia_source.distance_gspphot,gaia_source.azero_gspphot,gaia_source.ag_gspphot,gaia_source.ebpminrp_gspphot
+SELECT TOP 20 gaia_source.designation, gaia_source.source_id,
+              gaia_source.ra, gaia_source.dec, 
+              gaia_source.parallax, gaia_source.pmra, gaia_source.pmdec,
+              gaia_source.ruwe, gaia_source.phot_g_mean_mag, gaia_source.bp_rp, 
+              gaia_source.radial_velocity, gaia_source.radial_velocity_error
 FROM gaiadr3.gaia_source 
 WHERE 
 CONTAINS(
@@ -23,7 +27,11 @@ CONTAINS(
 """
 
 QUERY_ID = """
-SELECT TOP 20 gaia_source.designation,gaia_source.source_id,gaia_source.ra,gaia_source.dec,gaia_source.parallax,gaia_source.pmra,gaia_source.pmdec,gaia_source.ruwe,gaia_source.phot_g_mean_mag,gaia_source.bp_rp,gaia_source.radial_velocity,gaia_source.phot_variable_flag,gaia_source.non_single_star,gaia_source.has_xp_continuous,gaia_source.has_xp_sampled,gaia_source.has_rvs,gaia_source.has_epoch_photometry,gaia_source.has_epoch_rv,gaia_source.has_mcmc_gspphot,gaia_source.has_mcmc_msc,gaia_source.teff_gspphot,gaia_source.logg_gspphot,gaia_source.mh_gspphot,gaia_source.distance_gspphot,gaia_source.azero_gspphot,gaia_source.ag_gspphot,gaia_source.ebpminrp_gspphot
+SELECT TOP 20 gaia_source.designation, gaia_source.source_id,
+              gaia_source.ra, gaia_source.dec, 
+              gaia_source.parallax, gaia_source.pmra, gaia_source.pmdec,
+              gaia_source.ruwe, gaia_source.phot_g_mean_mag, gaia_source.bp_rp, 
+              gaia_source.radial_velocity, gaia_source.radial_velocity_error
 FROM gaiadr3.gaia_source 
 WHERE 
 gaia_source.source_id = {id}
@@ -31,6 +39,7 @@ gaia_source.source_id = {id}
 
 translate = {
     'Proxima': '5853498713190525696',
+    'GJ699': '4472832130942575872',
     'LS II +14 13': '4318465066420528000',
 }
 
@@ -81,7 +90,7 @@ class gaia:
         pmra = simbad.pmra
         pmdec = simbad.pmdec
         rv = simbad.rvz_radvel
-        args = dict(ra=ra, dec=dec, plx=plx, pmra=pmra, pmdec=pmdec, rv=rv)          
+        args = dict(ra=ra, dec=dec, plx=plx, pmra=pmra, pmdec=pmdec, rv=rv) 
 
         try:
             if star in translate:
@@ -109,6 +118,10 @@ class gaia:
             self.radial_velocity = float(results['radial_velocity'])
         except ValueError:
             self.radial_velocity = None
+        try:
+            self.radial_velocity_error = float(results['radial_velocity_error'])
+        except ValueError:
+            self.radial_velocity_error = None
 
         return
 

{arvi-0.1.25 → arvi-0.1.27}/arvi/plots.py

@@ -6,7 +6,7 @@ import numpy as np
 from astropy.timeseries import LombScargle
 
 from .setup_logger import logger
-from . import config
+from .config import config
 from .stats import wmean
 
 from .utils import lazy_import
@@ -123,8 +123,12 @@ def clickable_legend(fig, ax, leg):
                 h = handles[labels.index(artist.get_text())]
                 alpha_text = {None:0.2, 1.0: 0.2, 0.2:1.0}[artist.get_alpha()]
                 alpha_point = {None: 0.0, 1.0: 0.0, 0.2: 1.0}[artist.get_alpha()]
-                h[0].set_alpha(alpha_point)
-                h[2][0].set_alpha(alpha_point)
+                try:
+                    h[0].set_alpha(alpha_point)
+                    h[2][0].set_alpha(alpha_point)
+                except TypeError:
+                    h.set_alpha(alpha_point)
+
                 artist.set_alpha(alpha_text)
                 fig.canvas.draw()
             except ValueError:
@@ -488,14 +492,15 @@ def plot_quantity(self, quantity, ax=None, show_masked=False, instrument=None,
 
 
 plot_fwhm = partialmethod(plot_quantity, quantity='fwhm')
-plot_bis = partialmethod(plot_quantity, quantity='bispan')
+plot_bispan = partialmethod(plot_quantity, quantity='bispan')
 plot_contrast = partialmethod(plot_quantity, quantity='contrast')
 plot_rhk = partialmethod(plot_quantity, quantity='rhk')
 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, fap=True, instrument=None, 
+        adjust_means=config.adjust_means_gls,
         picker=True, **kwargs):
     """
     Calculate and plot the Generalised Lomb-Scargle periodogram of the radial
@@ -711,7 +716,7 @@ def gls_quantity(self, quantity, ax=None, fap=True, instrument=None,
 
 
 gls_fwhm = partialmethod(gls_quantity, quantity='fwhm')
-gls_bis = partialmethod(gls_quantity, quantity='bispan')
+gls_bispan = partialmethod(gls_quantity, quantity='bispan')
 gls_rhk = partialmethod(gls_quantity, quantity='rhk')
 
 

{arvi-0.1.25 → arvi-0.1.27}/arvi/simbad_wrapper.py

@@ -1,8 +1,15 @@
 import os
+import numpy as np
 import requests
+from dataclasses import dataclass
 
 import pysweetcat
 
+try:
+    from uncertainties import ufloat
+except ImportError:
+    ufloat = lambda x, y: x
+
 from .translations import translate
 
 DATA_PATH = os.path.dirname(__file__)
@@ -15,19 +22,35 @@ SELECT basic.OID,
        main_id,
        pmra,
        pmdec,
-       plx_value,
+       plx_value, plx_err,
        rvz_radvel,
        sp_type
 FROM basic JOIN ident ON oidref = oid
 WHERE id = '{star}';
 """
 
+# SELECT filter, flux, flux_err
+# FROM basic JOIN ident ON oid = ident.oidref JOIN flux ON oid = flux.oidref
+# WHERE id = 'HD23079';
+
 BV_QUERY = """
 SELECT B, V FROM allfluxes
 JOIN ident USING(oidref)
 WHERE id = '{star}';
 """
 
+FILTERS_QUERY = """
+SELECT filter, flux, flux_err, bibcode FROM flux 
+JOIN ident USING(oidref)
+WHERE id = '{star}';
+"""
+
+MEAS_QUERY = """
+SELECT teff, log_g, log_g_prec, fe_h, fe_h_prec, bibcode FROM mesFe_H 
+JOIN ident USING(oidref)
+WHERE id = '{star}';
+"""
+
 IDS_QUERY = """
 SELECT ids FROM ids
 JOIN ident USING(oidref)
@@ -40,6 +63,13 @@ JOIN ident ON oidref = oid
 WHERE id = '{star}';
 """
 
+@dataclass
+class Measurements:
+    teff: list
+    logg: list
+    feh: list
+    bibcode: list
+
 
 def run_query(query):
     url = 'http://simbad.u-strasbg.fr/simbad/sim-tap/sync'
@@ -52,7 +82,7 @@ def run_query(query):
         raise IndexError(err)
     return response.content.decode()
 
-def parse_table(table, cols=None, values=None):
+def parse_table1(table, cols=None, values=None):
     header = table.splitlines()[0].split('|')
     if cols is None:
         cols = list(map(str.strip, header))
@@ -66,6 +96,29 @@ def parse_table(table, cols=None, values=None):
     values = [value.replace('"', '') for value in values]
     return cols, values
 
+def parse_tablen(table, cols=None, values=None):
+    header = table.splitlines()[0].split('|')
+    cols = list(map(str.strip, header))
+    values = [list(map(str.strip, row.split('|'))) for row in table.splitlines()[2:]]
+    return cols, values
+
+def parse_value(value, err=None, prec=None):
+    try:
+        v = float(value)
+        if err:
+            try:
+                v = ufloat(float(value), float(err))
+            except ValueError:
+                pass
+        if prec:
+            try:
+                v = ufloat(float(value), 10**-int(prec))
+            except ValueError:
+                pass
+    except ValueError:
+        v = np.nan
+    return v
+
 
 effective_temperatures = {
     'F0': 7350, 'F2': 7050, 'F3': 6850, 'F5': 6700, 'F6': 6550, 'F7': 6400, 'F8': 6300, 
@@ -120,14 +173,37 @@ class simbad:
 
         try:
             table1 = run_query(query=QUERY.format(star=self.star))
-            cols, values = parse_table(table1)
+            cols, values = parse_table1(table1)
 
             table2 = run_query(query=BV_QUERY.format(star=self.star))
-            cols, values = parse_table(table2, cols, values)
+            cols, values = parse_table1(table2, cols, values)
 
             table3 = run_query(query=IDS_QUERY.format(star=self.star))
             line = table3.splitlines()[2]
             self.ids = line.replace('"', '').replace('    ', ' ').replace('   ', ' ').replace('  ', ' ').split('|')
+
+            table4 = run_query(query=FILTERS_QUERY.format(star=self.star))
+            for row in table4.splitlines()[2:]:
+                filter_name, mag, mag_err, bibcode = row.replace('"', '').split('|')
+                filter_name = filter_name.strip()
+                try:
+                    setattr(self, '_' + filter_name, ufloat(float(mag), float(mag_err)))
+                except ValueError:
+                    setattr(self, '_' + filter_name, float(mag))
+
+            # measurements table
+            table5 = run_query(query=MEAS_QUERY.format(star=self.star))
+            _teff, _logg, _feh, _bibcode = [], [], [], []
+            for row in table5.splitlines()[2:]:
+                teff, log_g, log_g_prec, fe_h, fe_h_prec, bibcode = row.replace('"', '').split('|')
+                _bibcode.append(bibcode)
+                _teff.append(parse_value(teff))
+                _logg.append(parse_value(log_g, prec=log_g_prec))
+                _feh.append(parse_value(fe_h, prec=fe_h_prec))
+
+            self.measurements = Measurements(_teff, _logg, _feh, _bibcode)
+
+
         except IndexError:
             raise ValueError(f'simbad query for {star} failed')
 
@@ -176,6 +252,9 @@ class simbad:
         sp_type = self.sp_type
         return f'{self.star} ({V=}, {sp_type=})'
 
+    @property
+    def bmv(self):
+        return self.B - self.V
 
 
 def argsort_by_spectral_type(sptypes):