workflow fix (hopefully)

.github/workflows/main.yaml

@@ -6,10 +6,7 @@ on:
 
 jobs:
   build:
-
     runs-on: ubuntu-latest
-
-
     steps:
       - uses: actions/checkout@v4
       - name: Set up Python
@@ -30,4 +27,6 @@ jobs:
       - name: Test with pytest
         run: |
           pip install pytest pytest-cov
-          pytest --doctest-modules --junitxml=junit/test-results.xml --cov=com --cov-report=xml --cov-report=html
+          pytest --junitxml=junit/test-results.xml
+        # pip install pytest-cov
+        # pytest --doctest-modules --junitxml=junit/test-results.xml --cov=com --cov-report=xml --cov-report=html

.gitignore

@@ -61,3 +61,4 @@ target/
 .DS_Store
 **/.idea/*
 pyhdust/.*
+junit/*

docs/index.rst

@@ -4,7 +4,7 @@ Welcome to **pyhdust** documentation!
 =============================================================
 **Analysis tools for multi-technique astronomical data and** *hdust* **models**. About the *hdust* code, see Carciofi & Bjorkman (`2006 <http://adsabs.harvard.edu/abs/2006ApJ...639.1081C>`_, `2008 <http://adsabs.harvard.edu/abs/2008ApJ...684.1374C>`_).
 
-Pyhdust is currently at **version 1.5.12**.
+Pyhdust is currently at **version 1.5.12-1**.
 
 **pyhdust** should be independent of plataform (Linux, Mac, Windows) and compatible with any version of Python (3.6+).
 

scripts/extract3Dfits.py

@@ -7,28 +7,30 @@
 import sys
 from argparse import ArgumentParser
 import os
-import pyfits as pf
+import astropy.io.fits as pf
 
-__version__ = "0.91"
+__version__ = "0.92"
 __author__ = "Daniel Moser"
 __email__ = "[email protected]"
 
 
-class MyParser(ArgumentParser): 
+class MyParser(ArgumentParser):
     def error(self, message):
-        sys.stderr.write('# ERROR! %s\n' % message)
+        sys.stderr.write("# ERROR! %s\n" % message)
         self.print_help()
         sys.exit(2)
 
+
 parser = MyParser(description=__doc__)
-parser.add_argument('--version', action='version', 
-    version='%(prog)s {0}'.format(__version__))
+parser.add_argument(
+    "--version", action="version", version="%(prog)s {0}".format(__version__)
+)
 parser.add_argument("INPUT", help=("Filename of the 3D FITS cube"), type=str)
 
 args = parser.parse_args()
 
 
-if __name__ == '__main__':
+if __name__ == "__main__":
 
     fname = args.INPUT
     fits = pf.open(fname)
@@ -39,6 +41,7 @@ def error(self, message):
         hdulist[0].header = fits[0].header
         path, oname = os.path.split(fname)
         pref, ext = os.path.splitext(oname)
-        hdu.writeto(os.path.join(path, pref+"_{0:04d}".format(i)+ext), 
-            overwrite=True)
-    print('# Saved {0} 2D images from {1}'.format(nimgs, oname))
+        hdu.writeto(
+            os.path.join(path, pref + "_{0:04d}".format(i) + ext), overwrite=True
+        )
+    print("# Saved {0} 2D images from {1}".format(nimgs, oname))

scripts/extract_ms_opera.py

@@ -13,12 +13,12 @@
 import matplotlib.pyplot as plt
 from scipy.signal import savgol_filter
 
-__version__ = "0.9"
+__version__ = "0.91"
 __author__ = "Daniel Moser"
 __email__ = "[email protected]"
 
 
-def plot_orders(ax, fwl, fflx, mode='o'):
+def plot_orders(ax, fwl, fflx, mode="o"):
     for i in range(len(fwl)):
         ax.plot(fwl[i], fflx[i], mode, ms=1)
     return ax
@@ -28,22 +28,22 @@ def do_norm(wl, flx):
     xout, yout = spt.max_func_pts(wl, flx, ws=0.01, avgbox=5)
     tck = interpolate.splrep(xout, yout)
     ynew = interpolate.splev(xout, tck, der=1)
-    dmed = np.median( np.abs(ynew) )
+    dmed = np.median(np.abs(ynew))
     l = len(wl)
-    # ConditionA: small derivative 
-    conda = ( np.abs(ynew) < dmed )  
+    # ConditionA: small derivative
+    conda = np.abs(ynew) < dmed
     # ConditionB: in the limits
-    condb = ( wl[int(l*0.15)] > xout ) | ( xout > wl[int(l*(1-.15))] )
+    condb = (wl[int(l * 0.15)] > xout) | (xout > wl[int(l * (1 - 0.15))])
     # xmax = phc.find_nearest(yout, np.max(yout), idx=True)
     # xmax = xout[xmax]
     # xmax = wl[l/2]
     # ConditionC: xout < max(flx) AND ynew > 0
     # condc = ( xout <= xmax ) & ( ynew >= 0 )
     # ConditionD: xout > max(flx) AND ynew < 0
     # condd = ( xout >= xmax ) & ( ynew <= 0 )
-    conde = ( ( xout > 658.45 ) | ( xout < 654.1 ) )
-    # idx = np.where( (( conda & (condd | condc) ) | condb) & (conde) )  
-    idx = np.where( (conda | condb) & (conde) )  
+    conde = (xout > 658.45) | (xout < 654.1)
+    # idx = np.where( (( conda & (condd | condc) ) | condb) & (conde) )
+    idx = np.where((conda | condb) & (conde))
     # & (condd | condc))
     xout = xout[idx]
     yout = yout[idx]
@@ -54,20 +54,20 @@ def do_norm(wl, flx):
     return wl, flx, ynew
 
 
-path = '.'
-opsps = glob('*.spc.gz')
-print opsps
+path = "."
+opsps = glob("*.spc.gz")
+print(opsps)
 
 avgspecs = []
 for sp in opsps:
-    os.system('gunzip -c {0} > tmp.txt'.format(sp))
-    spec = np.loadtxt('tmp.txt', skiprows=11)
+    os.system("gunzip -c {0} > tmp.txt".format(sp))
+    spec = np.loadtxt("tmp.txt", skiprows=11)
 
     fig, ax = plt.subplots()
-    ax.plot(spec[:, 5], spec[:, 10], label='Leg.')
+    ax.plot(spec[:, 5], spec[:, 10], label="Leg.")
     # ax.set_title('Title')
     # ax.legend()
-    plt.savefig(sp.replace('.spc.gz', '_ori'))
+    plt.savefig(sp.replace(".spc.gz", "_ori"))
     plt.close(fig)
 
     # i = 0
@@ -83,46 +83,50 @@ def do_norm(wl, flx):
         try:
             wl, flx, ynew = do_norm(wl, flx)
             fwl.append(wl)
-            onorm.append(flx/ynew)
+            onorm.append(flx / ynew)
             ocont.append(ynew)
-            oflx.append(flx)        
+            oflx.append(flx)
         except:
-            print('# Error in order {0}'.format(o))
+            print("# Error in order {0}".format(o))
 
     fig, ax = plt.subplots()
-    ax = plot_orders(ax, fwl, oflx, 'o')
-    ax = plot_orders(ax, fwl, ocont, '-')
-    plt.savefig(sp.replace('.spc.gz', '.orders'))
+    ax = plot_orders(ax, fwl, oflx, "o")
+    ax = plot_orders(ax, fwl, ocont, "-")
+    plt.savefig(sp.replace(".spc.gz", ".orders"))
     plt.close(fig)
 
     swl, sflx = spt.sum_ec(fwl, oflx)
     swl, scont = spt.sum_ec(fwl, ocont)
     swl, snorm = spt.sum_ec(fwl, onorm)
 
-    avgspecs.append(sp.replace('.spc.gz', '.rv.fits'))
+    avgspecs.append(sp.replace(".spc.gz", ".rv.fits"))
     nans, x = (np.isnan(scont), lambda z: z.nonzero()[0])
-    sflx[nans] = 1.
-    scont[nans] = 1.
+    sflx[nans] = 1.0
+    scont[nans] = 1.0
     idx = np.where(scont <= 1e-3)
-    scont[idx] = 1.
-    sflx[idx] = 1.
-    final = sflx/scont
+    scont[idx] = 1.0
+    sflx[idx] = 1.0
+    final = sflx / scont
     idx = np.where((final > 0.986) & (final < 1.014))
     pflx = final[idx]
     pwl = swl[idx]
-    pflx = np.interp(swl, pwl, savgol_filter(pflx, 3, 1, mode='nearest'))
-    final = final/pflx
-    spt.writeFits(final, swl*10, 
-        savename=sp.replace('.spc.gz', '.rv.fits'), quiet=False, 
-        externhd='../../{0}'.format(sp.replace('.spc.gz', '.fits')) )
+    pflx = np.interp(swl, pwl, savgol_filter(pflx, 3, 1, mode="nearest"))
+    final = final / pflx
+    spt.writeFits(
+        final,
+        swl * 10,
+        savename=sp.replace(".spc.gz", ".rv.fits"),
+        quiet=False,
+        externhd="../../{0}".format(sp.replace(".spc.gz", ".fits")),
+    )
 
     fig, ax = plt.subplots()
     ax.plot(swl, final)
     ax.set_ylim([0, 3])
-    plt.savefig(figname=sp.replace('.spc.gz', ''))
+    plt.savefig(figname=sp.replace(".spc.gz", ""))
     plt.close(fig)
 
-if os.path.exists('tmp.txt'):
-    os.system('rm tmp.txt')
+if os.path.exists("tmp.txt"):
+    os.system("rm tmp.txt")
 
 spt.averagespecs(avgspecs)

scripts/hdcompact.py

@@ -18,49 +18,63 @@
 __email__ = "[email protected]"
 
 
-class MyParser(ArgumentParser): 
+class MyParser(ArgumentParser):
     def error(self, message):
-        sys.stderr.write('# ERROR! %s\n' % message)
+        sys.stderr.write("# ERROR! %s\n" % message)
         self.print_help()
         sys.exit(2)
 
 
 parser = MyParser(description=__doc__)
-parser.add_argument('--version', action='version', 
-    version='%(prog)s {0}'.format(__version__))
-parser.add_argument("-n", action="store", dest="n", 
-    help=("Number of cores to be used [default: %(default)s]"), 
-    type=int, default=2)
-
-group2 = parser.add_argument_group('other arguments')
-group2.add_argument("-c", "--check", action="store_true", dest="chk", 
-    help=("If this flag is enabled, it does not make new compressed files. It "
+parser.add_argument(
+    "--version", action="version", version="%(prog)s {0}".format(__version__)
+)
+parser.add_argument(
+    "-n",
+    action="store",
+    dest="n",
+    help=("Number of cores to be used [default: %(default)s]"),
+    type=int,
+    default=2,
+)
+
+group2 = parser.add_argument_group("other arguments")
+group2.add_argument(
+    "-c",
+    "--check",
+    action="store_true",
+    dest="chk",
+    help=(
+        "If this flag is enabled, it does not make new compressed files. It "
         "will only removed the *.map* file if the "
-        "*.map.bz2 file exists"), default=False)
+        "*.map.bz2 file exists"
+    ),
+    default=False,
+)
 
 args = parser.parse_args()
 
 
 def compact(fp):
     if os.path.exists(fp):
         # print('# Creating '+fpnew)
-        fpnew = fp+'.bz2'
+        fpnew = fp + ".bz2"
         # fpnew = fp+'.gz'
         # with gzip.open(fpnew, 'wb') as fout:
-        with bz2.BZ2File(fpnew, 'wb', compresslevel=1) as fout:
-            fout.write(open(fp, 'rb').read())
+        with bz2.BZ2File(fpnew, "wb", compresslevel=1) as fout:
+            fout.write(open(fp, "rb").read())
         if os.path.exists(fpnew):
             if os.path.getsize(fpnew) > 40000:
                 os.remove(fp)
-        print('# Processed '+fp)
+        print("# Processed " + fp)
         return 0
     else:
-        print('# {0} was not found!'.format(fp))
+        print("# {0} was not found!".format(fp))
         return 1
 
 
-if __name__ == '__main__':
-    extensions = ['.tau', '.map']
+if __name__ == "__main__":
+    extensions = [".tau", ".map"]
 
     path = "."
     if len(sys.argv) == 2:
@@ -75,18 +89,18 @@ def compact(fp):
                 if not args.chk:
                     clist.append(fp)
                 else:
-                    fpnew = fp+'.bz2'
+                    fpnew = fp + ".bz2"
                     if os.path.exists(fpnew):
                         if os.path.getsize(fpnew) > 40000:
                             os.remove(fp)
-                            print('# Removing '+fp)
+                            print("# Removing " + fp)
 
     if not args.chk and args.n > 1:
         pool = Pool(processes=args.n)
         # for result in pool.imap_unordered(compact, clist):
         result = pool.map(compact, clist)
-        print('# DONE!')
+        print("# DONE!")
     if not args.chk and args.n == 1:
         for c in clist:
             compact(c)
-        print('# DONE!')
+        print("# DONE!")