arvi 0.2.8__py3-none-any.whl → 0.2.11__py3-none-any.whl

arvi/utils.py

@@ -2,6 +2,9 @@ import os
 import sys
 import time
 from contextlib import contextmanager
+from functools import partial
+from collections import defaultdict
+
 try:
     from unittest.mock import patch
 except ImportError:
@@ -67,6 +70,50 @@ def all_logging_disabled():
         logging.disable(previous_level)
 
 
+class record_removals:
+    def __init__(self, s, storage=None):
+        """
+        A simple context manager to record removed files
+
+        Args:
+            s (RV):
+                An `RV` object
+            storage (dict): 
+                A dictionary to store the removed files, with keys 'raw_file'
+                and 'reason' as lists.
+        
+        Examples:
+            >>> with record_removals(s) as rec:
+              :    s.remove_instrument('HARPS')
+              :    rec.store('removed HARPS')
+            >>> rec.storage
+        """
+        self.s = s
+        if storage is None:
+            self.storage = defaultdict(list)
+        else:
+            if 'raw_file' not in storage:
+                storage['raw_file'] = []
+            if 'reason' not in storage:
+                storage['reason'] = []
+            self.storage = storage
+        self.raw_file_start = self.s.raw_file.copy()
+
+    def store(self, reason):
+        missing = ~ np.isin(self.raw_file_start, self.s.raw_file[self.s.mask])
+        if missing.any():
+            lost = self.raw_file_start[missing]
+            self.storage['raw_file'].extend(lost)
+            self.storage['reason'].extend(len(lost) * [reason])
+            self.raw_file_start = self.s.raw_file[self.s.mask].copy()
+
+    def __enter__(self):
+        return self
+
+    def __exit__(self, exc_type, exc_value, traceback):
+        pass
+
+
 @contextmanager
 def timer(name=None):
     """ A simple context manager to time a block of code """
@@ -98,8 +145,9 @@ def sanitize_path(path):
     path = path.replace('*', '_')
     return path
 
-def pretty_print_table(rows, line_between_rows=True, logger=None):
-    """
+def pretty_print_table(rows, line_between_rows=True, string=False, 
+                       markdown=False, latex=False, logger=None):
+    r"""
     Example Output
     ┌──────┬─────────────┬────┬───────┐
     │ True │ short       │ 77 │ catty │
@@ -110,25 +158,76 @@ def pretty_print_table(rows, line_between_rows=True, logger=None):
     └──────┴─────────────┴────┴───────┘
     """
     _print = logger.info if logger else print
+    if string:
+        def _print(x, s):
+            s += x + '\n'
+            return s
+    else:
+        if logger:
+            def _print(x, _):
+                logger.info(x)
+        else:
+            def _print(x, _):
+                print(x)
+
+    if latex or markdown:
+        line_between_rows = False
+
+    s = ''
 
     # find the max length of each column
     max_col_lens = list(map(max, zip(*[(len(str(cell)) for cell in row) for row in rows])))
 
+    if markdown:
+        bar_char = '|'
+    else:
+        bar_char = r'│'
+
     # print the table's top border
-    _print('┌' + '┬'.join('─' * (n + 2) for n in max_col_lens) + '┐')
+    if markdown:
+        pass
+    elif latex:
+        s = _print(r'\begin{table*}', s)
+        # s = _print(r'\centering', s)
+        s = _print(r'\begin{tabular}' + '{' + ' c ' * len(rows[0]) + '}', s)
+    else:
+        s = _print(r'┌' + r'┬'.join(r'─' * (n + 2) for n in max_col_lens) + r'┐', s)
 
-    rows_separator = '├' + '┼'.join('─' * (n + 2) for n in max_col_lens) + '┤'
+    if markdown:
+        header_separator = bar_char + bar_char.join('-' * (n + 2) for n in max_col_lens) + bar_char
 
-    row_fstring = ' │ '.join("{: <%s}" % n for n in max_col_lens)
+    rows_separator = r'├' + r'┼'.join(r'─' * (n + 2) for n in max_col_lens) + r'┤'
+
+    if latex:
+        row_fstring = ' & '.join("{: <%s}" % n for n in max_col_lens)
+    else:
+        row_fstring = bar_char.center(3).join("{: <%s}" % n for n in max_col_lens)
 
     for i, row in enumerate(rows):
-        _print('│ ' + row_fstring.format(*map(str, row)) + ' │')
+        if markdown and i == 1:
+            s = _print(header_separator, s)
+
+        if latex:
+            s = _print(row_fstring.format(*map(str, row)) + r' \\', s)
+        else:
+            s = _print(bar_char + ' ' + row_fstring.format(*map(str, row)) + ' ' + bar_char, s)
         
+
         if line_between_rows and i < len(rows) - 1:
-            _print(rows_separator)
+            s = _print(rows_separator, s)
+
 
     # print the table's bottom border
-    _print('└' + '┴'.join('─' * (n + 2) for n in max_col_lens) + '┘')
+    if markdown:
+        pass
+    elif latex:
+        s = _print(r'\end{tabular}', s)
+        s = _print(r'\end{table*}', s)
+    else:
+        s = _print(r'└' + r'┴'.join(r'─' * (n + 2) for n in max_col_lens) + r'┘', s)
+
+    if string:
+        return s
 
 
 def strtobool(val):
@@ -238,3 +337,28 @@ def get_object_fast(file):
         value = f.read(20)
     return value.decode().split("'")[1].strip()
 
+
+def get_simbad_oid(self):
+    import requests
+    if isinstance(self, str):
+        star = self
+    else:
+        star = self.star
+    oid = requests.post('https://simbad.cds.unistra.fr/simbad/sim-tap/sync', 
+                        data=dict(format='text', request='doQuery', lang='adql', phase='run', 
+                                  query=f"SELECT basic.OID FROM basic JOIN ident ON oidref = oid WHERE id = '{star}';"))
+    oid = oid.text.split()[-1]
+    return oid
+
+
+
+# from https://stackoverflow.com/questions/37765197/darken-or-lighten-a-color-in-matplotlib
+def adjust_lightness(color, amount=0.5):
+    import matplotlib.colors as mc
+    import colorsys
+    try:
+        c = mc.cnames[color]
+    except KeyError:
+        c = color
+    c = colorsys.rgb_to_hls(*mc.to_rgb(c))
+    return colorsys.hls_to_rgb(c[0], max(0, min(1, amount * c[1])), c[2])

{arvi-0.2.8.dist-info → arvi-0.2.11.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: arvi
-Version: 0.2.8
+Version: 0.2.11
 Summary: The Automated RV Inspector
 Author-email: João Faria <joao.faria@unige.ch>
 License: MIT

{arvi-0.2.8.dist-info → arvi-0.2.11.dist-info}/RECORD

@@ -4,35 +4,36 @@ arvi/ariadne_wrapper.py,sha256=YvilopJa9T4NwPcj3Nah_U8smSeSAU5-HYZMb_GJ-BQ,2232
 arvi/berv.py,sha256=eKnpuPC1w45UrUEyFRbs9F9j3bXz3kxYzNXbnRgvFQM,17596
 arvi/binning.py,sha256=NK9y9bUrdyWCbh79LkcRABHG-n5MtlETMHMvLj1z-OM,15437
 arvi/config.py,sha256=JkHSwF-EEqwwbcc8thGgbFc9udDZPjQH-9XFjqDepBY,2337
-arvi/dace_wrapper.py,sha256=zgA8cT5eqYvHVMBfBO8aqua24FDfDilnDdPA3AajVew,25896
+arvi/dace_wrapper.py,sha256=i3aIRKSc2MylEzM5WbbU-BnuLbz8JlG1ez6sK_vvQH0,26125
 arvi/exofop_wrapper.py,sha256=8S7UEcrBAgANIweMV0-CvaWaVTPgGVo8vQQk_KRa0nU,2414
 arvi/extra_data.py,sha256=Xi65pI5kkzqlMmHGl9xFoumtH699611pJJ5PV-a_IfU,3397
 arvi/gaia_wrapper.py,sha256=HTuigIduin3raWfSC7QYuQxDk2dEXYH_4egRkzzg7Xw,4379
 arvi/headers.py,sha256=uvdJebw1M5YkGjE3vJJwYBOnLikib75uuZE9FXB5JJM,1673
-arvi/instrument_specific.py,sha256=ycLhtT3oeNtSREm9bmWICaT8uureYcl3NFzbdDYRMVY,11624
+arvi/instrument_specific.py,sha256=94oMb6UeH6tp7H8YXnXHpxEhIz2evz0iYsT_HrNOCTo,12105
+arvi/kepmodel_wrapper.py,sha256=mmHudetAZ4cBxKDwzQzgUydzkjhomCWw5VVuyiKfXq8,10288
 arvi/kima_wrapper.py,sha256=GrAZWkDCg8ukhW41M1VTadSbab0GBa6BIzjtAtvjk58,3891
 arvi/lbl_wrapper.py,sha256=_ViGVkpakvuBR_xhu9XJRV5EKHpj5Go6jBZGJZMIS2Y,11850
-arvi/nasaexo_wrapper.py,sha256=mWt7eHgSZe4MBKCmUvMPTyUPGuiwGTqKugNBvmjOg9s,7306
-arvi/plots.py,sha256=fHc6ScATCzvM4KQ77TYfHYmY6HSZ4N4oMYsLEUvxJpU,35279
+arvi/nasaexo_wrapper.py,sha256=ZKY3IUClqsJuysxDv0Gu51EnzMX7101zQb7UQy_urhI,7431
+arvi/plots.py,sha256=U4VUNyIx4h_rEFd7ZWgBcawUcIGcURES0A4VXIBKp3U,35240
 arvi/programs.py,sha256=M8o8hXr6W22dMiIX3Nxz4pgb8lsJXApDlq7HStyTfqs,9047
-arvi/reports.py,sha256=CKmtg5rewMyT26gbWeoZDYrL0z5Sbb6cTJry0HWk_rs,7445
+arvi/reports.py,sha256=a38EZNhyGoSSzJh63wBQCAt3_xhqbpVGcDOXaZWTLXs,11127
 arvi/setup_logger.py,sha256=dHzO2gPjw6CaKWpYZd2f83z09tmxgi--qpp7k1jROjI,615
 arvi/simbad_wrapper.py,sha256=uZc8mcfNijXsQi29LReRTabZb2hRPhYdLsDLMgq1OEI,9927
 arvi/sophie_wrapper.py,sha256=KUeWccXud5_Lrx72S1HSemHIZRdjd2oLvqyofwsL0QQ,3440
 arvi/spectra.py,sha256=ebF1ocodTastLx0CyqLSpE8EZNDXBF8riyfxMr3L6H0,7491
-arvi/stats.py,sha256=ilzzGL9ew-SyVa9eEdrYCpD3DliOAwhoNUg9LIlHjzU,2583
+arvi/stats.py,sha256=gvMkKzP83AV8_Oi71JHmA8QH8Y1z1viYykV9ELVDqZI,3547
 arvi/stellar.py,sha256=GQ7yweuBRnfkJ0M5eWjvLd8uvGq_by81PbXfidBvWis,4918
-arvi/timeseries.py,sha256=HUsJE5F6-urGNjt5Q-SX0IeREM_vo9M8WdXZ2WR24b8,97260
+arvi/timeseries.py,sha256=suXPLmFlNbnFbfixXufNMwqwZWz-FwKdckJ1x2PtrXQ,104664
 arvi/translations.py,sha256=PUSrn4zvYO2MqGzUxlFGwev_tBkgJaJrIYs6NKHzbWo,951
-arvi/utils.py,sha256=EY4hdwGcTUZg_tPT3yQ7ShLIVm9dAfmJC0c7toAVSKI,7221
+arvi/utils.py,sha256=MuAgjyXr297Sm_T6QmB1riVUktyT9ud1qngGMgKlXMc,10863
 arvi/data/info.svg,sha256=0IMI6W-eFoTD8acnury79WJJakpBwLa4qKS4JWpsXiI,489
 arvi/data/obs_affected_ADC_issues.dat,sha256=tn93uOL0eCTYhireqp1wG-_c3CbxPA7C-Rf-pejVY8M,10853
 arvi/data/obs_affected_blue_cryostat_issues.dat,sha256=z4AK17xfz8tGTDv1FjRvQFnio4XA6PNNfDXuicewHk4,1771
 arvi/data/extra/HD86226_PFS1.rdb,sha256=vfAozbrKHM_j8dYkCBJsuHyD01KEM1asghe2KInwVao,3475
 arvi/data/extra/HD86226_PFS2.rdb,sha256=F2P7dB6gVyzCglUjNheB0hIHVClC5RmARrGwbrY1cfo,4114
 arvi/data/extra/metadata.json,sha256=C69hIw6CohyES6BI9vDWjxwSz7N4VOYX0PCgjXtYFmU,178
-arvi-0.2.8.dist-info/licenses/LICENSE,sha256=6JfQgl7SpM55t0EHMFNMnNh-AdkpGW25MwMiTnhdWQg,1068
-arvi-0.2.8.dist-info/METADATA,sha256=f3ma5e17xovCE6ImErgCAkYANL6wRvaXbqN65xVZExw,1932
-arvi-0.2.8.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
-arvi-0.2.8.dist-info/top_level.txt,sha256=4EeiKDVLD45ztuflTGfQ3TU8GVjJg5Y95xS5XjI-utU,5
-arvi-0.2.8.dist-info/RECORD,,
+arvi-0.2.11.dist-info/licenses/LICENSE,sha256=6JfQgl7SpM55t0EHMFNMnNh-AdkpGW25MwMiTnhdWQg,1068
+arvi-0.2.11.dist-info/METADATA,sha256=G2yojj2vhNVuEPtoY81O3aWPvgMMxNw5ax4_40zVhb8,1933
+arvi-0.2.11.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
+arvi-0.2.11.dist-info/top_level.txt,sha256=4EeiKDVLD45ztuflTGfQ3TU8GVjJg5Y95xS5XjI-utU,5
+arvi-0.2.11.dist-info/RECORD,,