Merge pull request #26 from zemogle/main

Dev is 24 commits behind main

.github/workflows/publish-to-test-pypi.yml

@@ -0,0 +1,33 @@
+name: Publish 🚀 astrosource distributions 📦 to PyPI and TestPyPI
+
+on: push
+
+jobs:
+  build-n-publish:
+    name: Build and publish astrosource package 📦 to PyPI and TestPyPI
+    runs-on: ubuntu-18.04
+    steps:
+    - uses: actions/checkout@main
+    - name: Set up Python 3.7
+      uses: actions/setup-python@v1
+      with:
+        python-version: 3.7
+    - name: Install pep517
+      run: >-
+        python -m
+        pip install
+        pep517
+        --user
+    - name: Build a binary wheel and a source tarball
+      run: >-
+        python -m
+        pep517.build
+        --source
+        --binary
+        --out-dir dist/
+        .
+    - name: Publish distribution 📦 to PyPI
+      if: startsWith(github.ref, 'refs/tags')
+      uses: pypa/gh-action-pypi-publish@master
+      with:
+        password: ${{ secrets.pypi_password }}

.gitignore

@@ -23,6 +23,7 @@ checkplots/
 outputcats/
 outputplots/
 __pycache__/
+astrosource/test/__pycache__/
 .pytest_cache/
 .cache/
 *.egg-info

README.md

@@ -48,7 +48,7 @@ There are a few input options when running the scripts. You can either run the w
 
 `--indir` [parameter] Path of directory containing LCO data files. If none is given, astrosource assumes the current directory
 
-`--format` [parameter] input file format. If not `fz`, `fits`, or `fit` assumes the input files are photometry files with correct headers. If image files given, code will extra photometry from FITS extension. Defaults to `fz`.
+`--format` [parameter] input file format. If not `fz`, `fits`, or `fit` assumes the input files are photometry files with correct headers. If image files given, code will extract photometry from FITS extension. Defaults to `fz`.
 
 `--stars` [boolean flag] Step 1: Identify and match stars from each data file
 
@@ -83,17 +83,17 @@ There are a few input options when running the scripts. You can either run the w
 
 `--calib` [boolean flag] Perform calibrated
 
-`--lowcounts` [int] Countrate above which to accept a comparison star as a candidate. Defaults to 1000. (Note: This may seem like a low number but realistically stars at this low rate will be highly variable and rejected anyway)
+`--lowcounts` [int] Count rate above which to accept a comparison star as a candidate. Defaults to 1000. (Note: This may seem like a low number but realistically stars at this low rate will be highly variable and rejected anyway)
 
-`--hicounts` [int] Countrate above which to reject a comparison star as a candidate. Defaults to 1000000. (Note: This will vary from camera to camera, but it should be representative of a typical value that would have a peak pixel value significantly below the full range of the ccd, preferably lower rather than higher. )
+`--hicounts` [int] Count rate above which to reject a comparison star as a candidate. Defaults to 1000000. (Note: This will vary from camera to camera, but it should be representative of a typical value that would have a peak pixel value significantly below the full range of the ccd, preferably lower rather than higher. )
 
 `--thresholdcounts` [int] the number of counts at which to stop adding identified comparison stars to the ensemble. Default 1000000.
 
 `--closerejectd` [float] astrosource will reject potential comparison calibration stars if there are nearby stars to it. Closerejectd is the limiting distance in arcseconds. For crowded fields, this value may need to be lowered. Default 5.0. While the primary function here is to identify stars that are not in crowded situations, it also has the side-effect of removing false detections in sky surveys due to image artifacts or diffraction spikes which tend to cluster together.
 
 `--nopanstarrs` [boolean flag] Do not use the PanSTARRS catalogue for calibration. Some regions of the sky in PanSTARRS have poorer quality photometry than SDSS.
 
-`--sdss` [boolean flag] Do not use the SDSS catalogue for calibration. Some regions of the sky in SDSS have poorer quality photometry than PanSTARRS.
+`--nosdss` [boolean flag] Do not use the SDSS catalogue for calibration. Some regions of the sky in SDSS have poorer quality photometry than PanSTARRS.
 
 `--bjd` [boolean flag] Convert the MJD time into BJD time for LCO images.
 

astrosource/analyse.py

@@ -166,7 +166,6 @@ def find_variable_stars(targets, matchRadius, errorReject=0.05, parentPath=None,
             if diffMagHolder.shape[0] == sizeBefore:
                 break
 
-
         if (diffMagHolder.shape[0] > minimumNoOfObs):
             outputVariableHolder.append( [target[0],target[1],median(diffMagHolder), std(diffMagHolder), diffMagHolder.shape[0]])
 
@@ -446,8 +445,6 @@ def photometric_calculations(targets, paths, targetRadius, errorReject=0.1, file
             logger.error("Rejected Error Measurements: : {}".format(starErrorRejCount))
             logger.error("Rejected Distance Measurements: : {}".format(starDistanceRejCount))
 
-
-
         # Add calibration columns
         outputPhot= np.c_[outputPhot, np.ones(outputPhot.shape[0]),np.ones(outputPhot.shape[0])]
 

astrosource/astrosource.py

@@ -34,7 +34,7 @@ def __init__(self, targets, indir, **kwargs):
         self.format = kwargs.get('format', 'fz')
         self.imgreject = kwargs.get('imgreject', 0.05)
         self.periodupper = kwargs.get('periodupper', -99.9)
-        self.periodlower = kwargs.get('periodlower', -99.9)
+        self.periodlower = kwargs.get('periodlower', 0.05)
         self.periodtests = kwargs.get('periodtests', -99)
 
         self.racut = kwargs.get('racut', -99.9)
@@ -168,6 +168,7 @@ def analyse(self, calib=True, usescreenedcomps=False, usecompsused=False, usecom
             #Check stars are in images
 
         # Check that it is a filter that can actually be calibrated - in the future I am considering calibrating w against V to give a 'rough V' calibration, but not for now.
+
         if usecompletedcalib == False:
             self.calibrated = False
             if calib and self.filtercode in ['B', 'V', 'up', 'gp', 'rp', 'ip', 'zs', 'CV', 'w']:
@@ -201,7 +202,6 @@ def analyse(self, calib=True, usescreenedcomps=False, usecompsused=False, usecom
             self.calibrated = True
         return
 
-
     def find_variables(self):
         find_variable_stars(targets=self.targets, parentPath=self.paths['parent'], matchRadius=self.matchradius, varsearchglobalstdev=self.varsearchglobalstdev, varsearchthresh=self.varsearchthresh, varsearchstdev=self.varsearchstdev, varsearchmagwidth=self.varsearchmagwidth, varsearchminimages=self.varsearchminimages, photCoords=self.photCoords, photFileHolder=self.photFileHolder, fileList=self.usedimages)
 

astrosource/comparison.py

@@ -348,19 +348,18 @@ def calculate_comparison_variation(compFile, photFileArray, fileCount, parentPat
             stdCompDiffMags=std(compDiffMags[:,z])
             medCompDiffMags=np.nanmedian(compDiffMags[:,z])
             medInstrMags=np.nanmedian(instrMags[:,z])
-
             if np.isnan(stdCompDiffMags) :
                 logger.error("Star Variability non rejected")
                 stdCompDiffMags=99
             stdCompStar.append(stdCompDiffMags)
-
             sortStars.append([compFile[z,0],compFile[z,1],stdCompDiffMags,medCompDiffMags,medInstrMags,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0])
 
     return stdCompStar, sortStars
 
 def remove_stars_targets(parentPath, compFile, acceptDistance, targetFile, removeTargets):
     max_sep=acceptDistance * arcsecond
     logger.info("Removing Target Stars from potential Comparisons")
+    tableFound=False
 
     if not (compFile.shape[0] == 2 and compFile.size ==2):
         fileRaDec = SkyCoord(ra=compFile[:,0]*degree, dec=compFile[:,1]*degree)
@@ -398,7 +397,6 @@ def remove_stars_targets(parentPath, compFile, acceptDistance, targetFile, remov
         else:
             avgCoord=SkyCoord(ra=(average(compFile[:,0])*degree), dec=((average(compFile[:,1])*degree)))
 
-
     # Get search Radius
     radius= 0.5 * pow(  pow(max(compFile[:,0])-min(compFile[:,0]),2) + pow(max((compFile[:,1])-min(compFile[:,1]))*cos((min(compFile[:,1])+max(compFile[:,1]))/2),2) , 0.5)
     if radius > 120:
@@ -435,7 +433,6 @@ def remove_stars_targets(parentPath, compFile, acceptDistance, targetFile, remov
             tableFound=True
 
     except (ConnectionError , requests.exceptions.ConnectionError , http.client.RemoteDisconnected , urllib3.exceptions.ProtocolError) :
-
         connected=False
         logger.info("Connection failed, waiting and trying again")
         cycler=0
@@ -614,6 +611,7 @@ def catalogue_call(avgCoord, radius, opt, cat_name, targets, closerejectd):
         logger.info("Looks like your catalogue has too many sources next to nearby sources. ABORTING.")
 
     # Remove any star that has invalid values for mag or magerror
+
     if len(resp) != 0:
         catReject=[]
 
@@ -771,7 +769,6 @@ def find_comparisons_calibrated(targets, paths, filterCode, nopanstarrs=False, n
                         coords=[]
                         raise AstrosourceException("Empty catalogue produced from catalogue call")
 
-
                     if coords.cat_name == 'PanSTARRS' or coords.cat_name == 'APASS':
                         max_sep=2.5 * arcsecond
                     else:
@@ -1095,7 +1092,6 @@ def find_comparisons_calibrated(targets, paths, filterCode, nopanstarrs=False, n
         colourPath = paths['parent'] / 'colourplots'
         if not colourPath.exists():
             os.makedirs(colourPath)
-
         for qert in range(len(photFileHolder)):
 
 
@@ -1215,11 +1211,6 @@ def find_comparisons_calibrated(targets, paths, filterCode, nopanstarrs=False, n
     else:
         logger.info("Skipping Colour Correction Estimation")
 
-
-
-
-
-
     # Get rid of higher variability stars from calibration list
     varimin=(min(asarray(calibStands)[:,2])) * variabilityMultiplier
     calibStandsReject=[]
@@ -1302,7 +1293,6 @@ def find_comparisons_calibrated(targets, paths, filterCode, nopanstarrs=False, n
         #Replace undetected colours with average colour of the field
         photFile[:,8]=np.nan_to_num(photFile[:,8],nan=np.nanmedian(photFile[:,8]))
         photFile[:,9]=np.nan_to_num(photFile[:,9],nan=np.nanmedian(photFile[:,9]))
-
         # If the colour detection routine was run, this was calculated already
         #if not colourdetect:
         #    photFile[:,5]=1.0857 * (photFile[:,5]/photFile[:,4])
@@ -1365,11 +1355,7 @@ def find_comparisons_calibrated(targets, paths, filterCode, nopanstarrs=False, n
         else:
             calibOut[:,5]=calibOut[:,4]-tempZP # Speedup
             for r in range(len(calibOut[:,0])):
-
                 calibOverlord.append([calibOut[r,0],calibOut[r,1],calibOut[r,2],calibOut[r,3],calibOut[r,4],calibOut[r,5],float(file.split("_")[2].replace("d",".")),tempZP,calibOut[r,6],calibOut[r,7],calibOut[r,8]])
-
-        #breakpoint()
-
         calibOut=asarray(calibOut)
 
         #Save the calibrated photfiles to the calib directory
@@ -1391,6 +1377,7 @@ def find_comparisons_calibrated(targets, paths, filterCode, nopanstarrs=False, n
             weights=1/(calibOut[:,1])
             linA = np.vstack([outplotx,np.ones(len(outplotx))]).T * np.sqrt(weights[:,np.newaxis])
             linB = outploty * np.sqrt(weights)
+
             #breakpoint()
 
 
@@ -1415,17 +1402,10 @@ def find_comparisons_calibrated(targets, paths, filterCode, nopanstarrs=False, n
 
             except:
                 logger.info("\nFailed linear fit on a postcolour plot: ")
-
-
-
+
             z=z+1
 
-
-
-
-
-
-        #Look within photfile for ACTUAL usedcomps.csv and pull them out
+    #Look within photfile for ACTUAL usedcomps.csv and pull them out
         lineCompUsed=[]
         if compUsedFile.shape[0] ==3 and compUsedFile.size == 3:
             lenloop=1
@@ -1629,7 +1609,6 @@ def find_comparisons_calibrated(targets, paths, filterCode, nopanstarrs=False, n
         nonlinearZero=c
         nonlinearError=residuals[0] / pow(len(fileList), 0.5)
 
-
         with open(parentPath / "results/CalibrationSanityPlotCoefficients.txt", "a+") as f:
             f.write("Corrected Magnitude slope     : " + str(m)+"\n")
             f.write("Corrected Magnitude zeropoint : " + str(c) +"\n")

astrosource/main.py

@@ -20,6 +20,7 @@
 @click.option('--phot', is_flag=True, help='Step 4: Photometry calculations for either differential or calibrated')
 @click.option('--plot', is_flag=True, help='Step 5: Produce lightcurve plots')
 
+
 @click.option('--indir', default=None, type=str, required=True, help='Path of directory containing LCO data files. If none is given, astrosource assumes the current directory')
 @click.option('--ra', type=str, help='Right Ascension of the target (in decimal or H:M:S)')
 @click.option('--dec', type=str, help='Declination of the target (in decimal or D:M:S)')

astrosource/plots.py

@@ -32,8 +32,6 @@ def output_files(paths, photometrydata, mode='diff'):
             magColumn=outputPhot[:,10]
             magerrColumn=outputPhot[:,11]
 
-        #breakpoint()
-
         outputPeransoCalib = [x for x in zip(outputPhot[:,6],magColumn,magerrColumn)]
         outputPeransoCalib = asarray(outputPeransoCalib)
 

astrosource/test/test_comparison.py

@@ -71,7 +71,7 @@ def test_remove_targets_calibrated(setup):
 @patch('astrosource.comparison.Vizier',mock_vizier_apass_b)
 def test_find_comparisons_calibrated_b(setup):
     compFile = find_comparisons_calibrated(filterCode='B', paths=TEST_PATHS, targets=setup.targets)
-    
+
     assert asarray(compFile).shape == (3,)
 
 @patch('astrosource.comparison.Vizier',mock_vizier_apass_v)

astrosource/utils.py

@@ -1,7 +1,6 @@
 from os import getcwd, makedirs, remove
 import shutil
 import logging
-import sys
 import time
 
 from numpy import asarray, genfromtxt, load, isnan, delete

docs/source/api_usage.rst

@@ -1,10 +1,10 @@
 Library Usage
 =============
-To take advantage of some of the more advance options in AstroSource, you want to import the library as part of a larger code base.
+To take advantage of some of the more advance options in ``astrosource``, you want to import the library as part of a larger code base.
 
 Getting Started
 ---------------
-The fundamental role of AstroSource is the analysis of time-series data. So, the basic class in AstroSource is called `TimeSeries`.
+The fundamental role of ``astrosource`` is the analysis of time-series data. So, the basic class in ``astrosource`` is called `TimeSeries`.
 
 There are only *2* required inputs: a list of targets and a directory where the input files can be found.
 
@@ -34,7 +34,7 @@ Optional Inputs
 **format** `str`
   A file extension for the files in `indir` which contain the photometry data.
 **imgreject** `float`
-  Image fraction rejection allowance. Defaults to `0.0`. Increasing this will allow AstroSource to reject some of your data files if there are not enough comparison stars.
+  Image fraction rejection allowance. Defaults to `0.0`. Increasing this will allow ``astrosource`` to reject some of your data files if there are not enough comparison stars.
 
 
 Analysis
@@ -55,5 +55,5 @@ This is an example of the full analysis code using the input directory `indir` a
 The `plot` stage has 3 optional inputs:
 
 * detrend: detrend exoplanet data
-* period: recursively attempt to find a period (for periodic sources like variable stars or binaries)
-* eebls: Edge Enhanced Box-fitting Least Squares analysis for an exoplanet transit curve  
+* :ref:`period<Period Folding>`: recursively attempt to find a period (for periodic sources like variable stars or binaries)
+* eebls: Edge Enhanced Box-fitting Least Squares analysis for an exoplanet transit curve