From 4a1fd09308734a3b7d7b71160f1757b128e36ecd Mon Sep 17 00:00:00 2001
From: Andrej Prsa <aprsa09@gmail.com>
Date: Thu, 7 Nov 2024 11:37:51 -0500
Subject: [PATCH 1/3] Improves handling of passband history FITS file format
provides a HISTORY keyword that was not used correctly in previous versions.
This commit fixes that and improves the overall code. WIP!
---
phoebe/atmospheres/passbands.py | 132 +++++++++++++++++++++++---------
1 file changed, 97 insertions(+), 35 deletions(-)
diff --git a/phoebe/atmospheres/passbands.py b/phoebe/atmospheres/passbands.py
index eac4faef6..4a870b073 100644
--- a/phoebe/atmospheres/passbands.py
+++ b/phoebe/atmospheres/passbands.py
@@ -2,7 +2,6 @@
from phoebe import conf, mpi
from phoebe.utils import _bytes
from tqdm import tqdm
-from itertools import product
import ndpolator
@@ -17,14 +16,13 @@
import numpy as np
from scipy import interpolate, integrate
from scipy.optimize import curve_fit as cfit
-from datetime import datetime
+from datetime import datetime as dt
import libphoebe
import os
import sys
import glob
import shutil
import json
-import time
import re
# NOTE: python3 only
@@ -38,7 +36,7 @@
# define the URL to query for online passbands. See tables.phoebe-project.org
# repo for the source-code of the server
-_url_tables_server = 'http://tables.phoebe-project.org'
+_url_tables_server = 'https://tables.phoebe-project.org'
# comment out the following line if testing tables.phoebe-project.org server locally:
# _url_tables_server = 'http://localhost:5555'
@@ -305,11 +303,22 @@ def log(self):
def add_to_history(self, history, max_length=46):
"""
- Adds a history entry to the passband file header.
+ Adds a history entry to the Passband instance.
Parameters
----------
- * `comment` (string, required): comment to be added to the passband header.
+ * `history` (string, required): comment to be added to the passband header.
+ * `max_length` (int, optional, default=46): maximum length of the history entry.
+
+ Raises
+ ------
+ * ValueError: if the history entry is not a string.
+ * ValueError: if the history entry exceeds the maximum length.
+
+ Examples
+ --------
+ >>> pb = phoebe.get_passband('Johnson:V')
+ >>> pb.add_to_history('passband updated.')
"""
if not isinstance(history, str):
@@ -317,21 +326,34 @@ def add_to_history(self, history, max_length=46):
if len(history) > max_length:
raise ValueError(f'comment length should not exceed {max_length} characters.')
- self.history.append(f'{time.ctime()}: {history}')
+ self.history.append(f'{_generate_timestamp()}: {history}')
- def add_comment(self, comment):
+ def add_comment(self, comment, max_length=46):
"""
- Adds a comment to the passband file header.
+ Adds a comment entry to the Passbands instance.
Parameters
----------
* `comment` (string, required): comment to be added to the passband header.
+ * `max_length` (int, optional, default=46): maximum length of the comment entry.
+
+ Raises
+ ------
+ * ValueError: if the comment is not a string.
+ * ValueError: if the comment exceeds the maximum length.
+
+ Examples
+ --------
+ >>> pb = phoebe.get_passband('Johnson:V')
+ >>> pb.add_comment('this is a comment.')
"""
if not isinstance(comment, str):
raise ValueError('passband header comments must be strings.')
+ if len(comment) > max_length:
+ raise ValueError(f'comment length should not exceed {max_length} characters.')
- self.comments.append(comment)
+ self.comments.append(comment)
def on_updated_ptf(self, ptf, wlunits=u.AA, oversampling=1, ptf_order=3):
"""
@@ -380,7 +402,7 @@ def save(self, archive, overwrite=True, update_timestamp=True, export_inorm_tabl
"""
# Timestamp is used for passband versioning.
- timestamp = time.ctime() if update_timestamp else self.timestamp
+ timestamp = _generate_timestamp() if update_timestamp else self.timestamp
header = fits.Header()
header['PHOEBEVN'] = phoebe_version
@@ -1094,13 +1116,12 @@ def export_legacy_ldcoeffs(self, models, atm='ck2004', filename=None, intens_wei
grid = self.ndp[atm].table['ld@photon'][1] if intens_weighting == 'photon' else self.ndp[atm].table['ld@energy'][1]
if filename is not None:
- import time
f = open(filename, 'w')
- f.write('# PASS_SET %s\n' % self.pbset)
- f.write('# PASSBAND %s\n' % self.pbname)
+ f.write(f'# PASS_SET {self.pbset}\n')
+ f.write(f'# PASSBAND {self.pbname}\n')
f.write('# VERSION 1.0\n\n')
- f.write('# Exported from PHOEBE-2 passband on %s\n' % (time.ctime()))
- f.write('# The coefficients are computed for the %s-weighted regime from %s atmospheres.\n\n' % (intens_weighting, atm))
+ f.write(f'# Exported from PHOEBE-2 passband on {_generate_timestamp()}\n')
+ f.write(f'# The coefficients are computed for the {intens_weighting}-weighted regime from {atm} atmospheres.\n\n')
mods = np.loadtxt(models)
for mod in mods:
@@ -1885,12 +1906,51 @@ def bindex(self, teffs=5772., loggs=4.43, abuns=0.0, mus=1.0, atm='ck2004', inte
raise ValueError('Atmosphere parameters out of bounds: Teff=%s, logg=%s, abun=%s' % (Teff[nanmask], logg[nanmask], abun[nanmask]))
return retval
+
+def _generate_timestamp():
+ """
+ Generates a timestamp string in the format 'YYYY-MM-DD HH:MM:SS'.
+
+ Returns
+ ----------
+ * (string) timestamp string
+ """
+
+ return dt.now().strftime("%Y-%m-%d %H:%M:%S")
+
+
def _timestamp_to_dt(timestamp):
+ """
+ Converts a timestamp string to a datetime object.
+
+ Arguments
+ ----------
+ * `timestamp` (string): timestamp string in the format 'YYYY-MM-DD HH:MM:SS' or 'Mon Jan 01 00:00:00 2000'
+
+ Raises
+ ----------
+ * TypeError: if timestamp is not of type string
+ * ValueError: if timestamp is not in the correct format
+
+ Returns
+ ----------
+ * (datetime) datetime object
+ """
+
if timestamp is None:
return None
elif not isinstance(timestamp, str):
raise TypeError("timestamp not of type string")
- return datetime.strptime(timestamp, "%a %b %d %H:%M:%S %Y")
+ try:
+ # if timestamp is in the new format, 'YYYY-MM-DD HH:MM:SS':
+ ts = dt.strptime(timestamp, "%Y-%m-%d %H:%M:%S")
+ except ValueError:
+ # if timestamp is in the old format, 'Mon Jan 01 00:00:00 2000':
+ ts = dt.strptime(timestamp, "%a %b %d %H:%M:%S %Y")
+ else:
+ raise ValueError("timestamp not in the correct format")
+
+ return ts
def _init_passband(fullpath, check_for_update=True):
"""
@@ -2177,34 +2237,36 @@ def list_passband_online_history(passband, since_installed=True):
----------
* (dict): dictionary with timestamps as keys and messages and values.
"""
+
if passband not in list_online_passbands(repeat_errors=False):
- raise ValueError("'{}' passband not available online".format(passband))
+ raise ValueError(f'{passband} passband not available online')
- url = '{}/pbs/history/{}?phoebe_version={}'.format(_url_tables_server, passband, phoebe_version)
+ url = f'{_url_tables_server}/pbs/history/{passband}?phoebe_version={phoebe_version}'
try:
resp = urlopen(url, timeout=3)
except Exception as err:
- msg = "connection to online passbands at {} could not be established. Check your internet connection or try again later. If the problem persists and you're using a Mac, you may need to update openssl (see http://phoebe-project.org/help/faq).".format(_url_tables_server)
- msg += " Original error from urlopen: {} {}".format(err.__class__.__name__, str(err))
+ msg = f"connection to online passbands at {_url_tables_server} could not be established. Check your internet connection or try again later. If the problem persists and you're using a Mac, you may need to update openssl (see http://phoebe-project.org/help/faq)."
+ msg += f" Original error from urlopen: {err.__class__.__name__} {str(err)}"
logger.warning(msg)
- return {str(time.ctime()): "could not retrieve history entries"}
- else:
- try:
- all_history = json.loads(resp.read().decode('utf-8'), object_pairs_hook=parse_json).get('passband_history', {}).get(passband, {})
- except Exception as err:
- msg = "Parsing response from online passbands at {} failed.".format(_url_tables_server)
- msg += " Original error from json.loads: {} {}".format(err.__class__.__name__, str(err))
+ return {_generate_timestamp(): "could not retrieve history entries"}
+
+ try:
+ print(resp.read().decode('utf-8'))
+ all_history = json.loads(resp.read().decode('utf-8'), object_pairs_hook=parse_json).get('passband_history', {}).get(passband, {})
+ except Exception as err:
+ msg = f"Parsing response from online passbands at {_url_tables_server} failed."
+ msg += f" Original error from json.loads: {err.__class__.__name__} {str(err)}"
- logger.warning(msg)
- return {str(time.ctime()): "could not parse history entries"}
+ logger.warning(msg)
+ return {_generate_timestamp(): "could not parse history entries"}
- if since_installed:
- installed_timestamp = _timestamp_to_dt(_pbtable.get(passband, {}).get('timestamp', None))
- return {k:v for k,v in all_history.items() if installed_timestamp < _timestamp_to_dt(k)} if installed_timestamp is not None else all_history
- else:
- return all_history
+ if since_installed:
+ installed_timestamp = _timestamp_to_dt(_pbtable.get(passband, {}).get('timestamp', None))
+ return {k:v for k,v in all_history.items() if installed_timestamp < _timestamp_to_dt(k)} if installed_timestamp is not None else all_history
+ else:
+ return all_history
def update_passband_available(passband, history_dict=False):
"""
From b87c88c3b267d359151d49871d14ee4f6db083fa Mon Sep 17 00:00:00 2001
From: Andrej Prsa <aprsa09@gmail.com>
Date: Thu, 7 Nov 2024 13:41:02 -0500
Subject: [PATCH 2/3] Adds support for both old (ctime-style) and new
(iso-style, locale-independent) timestamps.
---
phoebe/atmospheres/passbands.py | 43 +++++++++++++++++++++++++++------
1 file changed, 35 insertions(+), 8 deletions(-)
diff --git a/phoebe/atmospheres/passbands.py b/phoebe/atmospheres/passbands.py
index 4a870b073..9ae18b45a 100644
--- a/phoebe/atmospheres/passbands.py
+++ b/phoebe/atmospheres/passbands.py
@@ -36,7 +36,7 @@
# define the URL to query for online passbands. See tables.phoebe-project.org
# repo for the source-code of the server
-_url_tables_server = 'https://tables.phoebe-project.org'
+_url_tables_server = 'https://staging.phoebe-project.org'
# comment out the following line if testing tables.phoebe-project.org server locally:
# _url_tables_server = 'http://localhost:5555'
@@ -1939,18 +1939,17 @@ def _timestamp_to_dt(timestamp):
if timestamp is None:
return None
- elif not isinstance(timestamp, str):
+ if not isinstance(timestamp, str):
raise TypeError("timestamp not of type string")
+
try:
# if timestamp is in the new format, 'YYYY-MM-DD HH:MM:SS':
- ts = dt.strptime(timestamp, "%Y-%m-%d %H:%M:%S")
+ return dt.strptime(timestamp, "%Y-%m-%d %H:%M:%S")
except ValueError:
# if timestamp is in the old format, 'Mon Jan 01 00:00:00 2000':
- ts = dt.strptime(timestamp, "%a %b %d %H:%M:%S %Y")
+ return dt.strptime(timestamp, "%a %b %d %H:%M:%S %Y")
else:
- raise ValueError("timestamp not in the correct format")
-
- return ts
+ raise ValueError(f'timestamp "{timestamp}" not in the correct format')
def _init_passband(fullpath, check_for_update=True):
"""
@@ -2252,9 +2251,37 @@ def list_passband_online_history(passband, since_installed=True):
logger.warning(msg)
return {_generate_timestamp(): "could not retrieve history entries"}
+ def _parse(entry):
+ # parses the history entry into a timestamp and message
+ parts = entry.split(':')
+
+ # try the new format first: 'YYYY-MM-DD HH:MM:SS'
+ for i in range(len(parts)-1, 0, -1):
+ try:
+ timestamp = ':'.join(parts[:i])
+ dt.strptime(timestamp, "%Y-%m-%d %H:%M:%S")
+ message = ':'.join(parts[i:]).strip()
+ return timestamp, message
+ except ValueError:
+ continue
+
+ # try the old format: 'Mon Jan 01 00:00:00 2000'
+ for i in range(len(parts)-1, 0, -1):
+ try:
+ timestamp = ':'.join(parts[:i])
+ ts = dt.strptime(timestamp, "%a %b %d %H:%M:%S %Y")
+ # if successful, convert to the new format:
+ timestamp = ts.strftime('%Y-%m-%d %H:%M:%S')
+ message = ':'.join(parts[i:]).strip()
+ return timestamp, message
+ except ValueError:
+ continue
+
try:
- print(resp.read().decode('utf-8'))
all_history = json.loads(resp.read().decode('utf-8'), object_pairs_hook=parse_json).get('passband_history', {}).get(passband, {})
+ # convert all_history to dict with timestamps as keys and messages as values:
+ all_history = dict([_parse(entry) for entry in all_history])
+
except Exception as err:
msg = f"Parsing response from online passbands at {_url_tables_server} failed."
msg += f" Original error from json.loads: {err.__class__.__name__} {str(err)}"
From d45c588ef3e799002b8753e00c8c38e0ab7b1402 Mon Sep 17 00:00:00 2001
From: Andrej Prsa <aprsa09@gmail.com>
Date: Thu, 7 Nov 2024 15:34:32 -0500
Subject: [PATCH 3/3] Removes trailing whitespace
Co-authored-by: Kyle Conroy <kyleconroy@gmail.com>
---
phoebe/atmospheres/passbands.py | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/phoebe/atmospheres/passbands.py b/phoebe/atmospheres/passbands.py
index 9ae18b45a..d92d65e1f 100644
--- a/phoebe/atmospheres/passbands.py
+++ b/phoebe/atmospheres/passbands.py
@@ -353,7 +353,7 @@ def add_comment(self, comment, max_length=46):
if len(comment) > max_length:
raise ValueError(f'comment length should not exceed {max_length} characters.')
- self.comments.append(comment)
+ self.comments.append(comment)
def on_updated_ptf(self, ptf, wlunits=u.AA, oversampling=1, ptf_order=3):
"""