updated SIROCCO env in Python scripts

py_progs/autogenerate_parameter_docs.py

@@ -18,16 +18,16 @@
         Print the full text of all .yaml files that would be created to the screen.
 
     -w / --write
-        Move any deprecated parameters to `$PYTHON/parameters/old/`,
-        then write any new parameters to in `$PYTHON/parameters/`
+        Move any deprecated parameters to `$SIROCCO/parameters/old/`,
+        then write any new parameters to in `$SIROCCO/parameters/`
 
         Note, this will not over-write any parameters that have changed types
         but not names e.g. `rdflo('thing')` to `rdint('thing')`.
 
     -h / --help
         Prints this documentation.
 
-After the program has been run $PYTHON/parameters should contain a yaml file
+After the program has been run $SIROCCO/parameters should contain a yaml file
 for every possible input, and any input that has changed significantly should
 be in $PYHON/parameters.old  One should normally be sure to add the new yaml
 files to the repository.
@@ -58,7 +58,7 @@
 
     The recommendation is to:
 
-    * to clean both $PYTHON/parameters/, and $PYTHON/parameters/old/ from your
+    * to clean both $SIROCCO/parameters/, and $SIROCCO/parameters/old/ from your
       local directories before using writing files using this routine, and then
     * to add and comit  all of the files that are produced before going on to other
       stages of activities associated with documentation.
@@ -464,9 +464,9 @@ def autogenerate_parameter_docs():
     """
     Function to autogenerate parameter documentation.
     """
-    input_folder = os.path.join(os.environ["PYTHON"], "source")
-    output_folder = os.path.join(os.environ["PYTHON"], "docs", "parameters")
-    output_old_folder = os.path.join(os.environ["PYTHON"], "docs", "parameters", "old")
+    input_folder = os.path.join(os.environ["SIROCCO"], "source")
+    output_folder = os.path.join(os.environ["SIROCCO"], "docs", "parameters")
+    output_old_folder = os.path.join(os.environ["SIROCCO"], "docs", "parameters", "old")
 
     input_files = list_input_files(input_folder)
     existing_documentation = list_existing_documentation(output_folder)

py_progs/autogenerate_rtd_pages.py

@@ -228,11 +228,11 @@ def autogenerate_rtd_pages(output_folder):
     """
     Write the RTD files to disk and add them to git, then run sphinx-build to generate the docs.
     """
-    # html_folder = os.path.join(os.environ["PYTHON"], "docs", "html")
-    docs_folder = os.path.join(os.environ["PYTHON"], "docs")
+    # html_folder = os.path.join(os.environ["SIROCCO"], "docs", "html")
+    docs_folder = os.path.join(os.environ["SIROCCO"], "docs")
     dox_all = {}
 
-    par_folder=  os.path.join(os.environ["PYTHON"], "docs", "parameters")
+    par_folder=  os.path.join(os.environ["SIROCCO"], "docs", "parameters")
     print('Par folder',par_folder)
 
     dox_all = read_yaml(
@@ -296,8 +296,8 @@ def steer(argv):
     This is just a steering routine to enable better control of the program
     '''
 
-    outdir= os.path.join(os.environ["PYTHON"], "docs", "rst", "parameters")
-    xdir= os.path.join(os.environ["PYTHON"], "docs","sphinx")
+    outdir= os.path.join(os.environ["SIROCCO"], "docs", "rst", "parameters")
+    xdir= os.path.join(os.environ["SIROCCO"], "docs","sphinx")
 
     i=1
     while i< len(argv):

py_progs/balmer_decrement.py

@@ -1,8 +1,8 @@
 #!/usr/bin/env python
 '''
-Runs tests of the Balmer decrement for a one zone  thin shell Python model.
+Runs tests of the Balmer decrement for a one zone  thin shell Sirocco model.
 
-Involves running py_wind on a wind_save file and reading some output files.
+Involves running swind on a wind_save file and reading some output files.
 Compares to Osterbrock values.
 
 Usage:
@@ -14,7 +14,7 @@
 	py_wind
 	numpy 
 	matplotlib 
-	py_plot_util, py_read_output from $PYTHON/py_progs in the python path
+	py_plot_util, py_read_output from $SIROCCO/py_progs in the python path
 
 Notes:
 	This routine is a routine to check the results of running a one zone
@@ -26,8 +26,8 @@
 
 # Do not call this when we're on ReadTheDocs
 if not os.environ.get('READTHEDOCS'):
-	PYTHON = os.environ["PYTHON"]
-	sys.path.append("$PYTHON/py_progs/")
+	SIROCCO = os.environ["SIROCCO"]
+	sys.path.append("$SIROCCO/py_progs/")
 
 import py_plot_util as util 
 import py_read_output as rd 
@@ -48,7 +48,7 @@ def BalmerTest(root, plotit=True):
 
 	print ("Running Balmer Test for run {}...".format(root))
 
-	# create the list of commands to run in py wind
+	# create the list of commands to run in swind
 	nlevels = 8
 	cmds = ["1","s","n","i","1","1","1","1","2","0","M","2"]
 	for i in range(nlevels):
@@ -57,8 +57,8 @@ def BalmerTest(root, plotit=True):
 	cmds.append("q")
 
 	# run py wind. pass the command to run for situations in CI where we can't get the path working
-	py_wind_cmd = "{}/bin/py_wind".format(PYTHON)
-	isys, logfile_contents = util.run_py_wind(root, cmds=cmds, py_wind_cmd = py_wind_cmd, return_output = True)
+	swind_cmd = "{}/bin/swind".format(SIROCCO)
+	isys, logfile_contents = util.run_py_wind(root, cmds=cmds, py_wind_cmd = swind_cmd, return_output = True)
 	print (isys)
 
 	# these could be in principle be used to check absolute emissivity values 
@@ -74,7 +74,7 @@ def BalmerTest(root, plotit=True):
 		for i in range(nlevels):
 			ratios[i] = rd.read_pywind("{}.lev{}_emiss.dat".format(root,i+3), mode="1d")[2][1]
 	except FileNotFoundError:
-		print("Error reading py_wind output. Logfile follows...")
+		print("Error reading swind output. Logfile follows...")
 		print (logfile_contents)
 
 

py_progs/pf_check.py

@@ -29,12 +29,12 @@
 
         pf_check_directory_date
 
-    The full path names to directories in the `$PYTHON/examples`
+    The full path names to directories in the `$SIROCCO/examples`
     do not need to be given, so for example::
 
         pf_check.py beta
 
-    will test the parameter files in `$PYTHON/examples/beta`.
+    will test the parameter files in `$SIROCCO/examples/beta`.
 
     After running Python in -i mode for each of the files, 
     the routine diffs the .out.pf file with the original.pf
@@ -95,9 +95,9 @@ def travis():
     Return a special set of commands when dealing with the travis directory
     '''
 
-    PYTHON=os.environ['PYTHON']
+    SIROCCO=os.environ['SIROCCO']
 
-    x=open('%s/.travis.yml' % (PYTHON))
+    x=open('%s/.travis.yml' % (SIROCCO))
     z=yaml.load(x)
     print(z['script'])
     commands=[]
@@ -132,9 +132,9 @@ def doit(directory):
     if os.path.isdir(directory):
         xdir=directory
     else:
-        # Get the PYTHON environment variable
-        PYTHON=os.environ['PYTHON']
-        ydir='%s/examples/%s' % (PYTHON,directory)
+        # Get the SIROCCO environment variable
+        SIROCCO=os.environ['SIROCCO']
+        ydir='%s/examples/%s' % (SIROCCO,directory)
         if os.path.isdir(ydir):
             xdir=ydir
         else:

py_progs/py_error.py

@@ -4,7 +4,7 @@
 Post-run parser for error logs from parallel simulation runs.
     
 This is the post-processing code to deal with the error logs in 
-PYTHON's parallel mode. It basically sums the number of errors
+SIROCCO's parallel mode. It basically sums the number of errors
 in the various diagnostic files
 
 usage and arguments:

py_progs/py_plot_output.py

@@ -98,7 +98,7 @@ def make_spec_plot(s, fname, smooth_factor = 10, angles = True, components = Fal
         print ("Making a {} by {} plot, {} spectra".format(nx, ny, nspecs))
 
         if with_composite:
-            lambda_composite, f_composite, errors = np.loadtxt("%s/examples/telfer_qso_composite_hst.asc" % (os.environ["PYTHON"]), unpack=True, comments="#")
+            lambda_composite, f_composite, errors = np.loadtxt("%s/examples/telfer_qso_composite_hst.asc" % (os.environ["SIROCCO"]), unpack=True, comments="#")
 
         for i in range(nspecs):
 

py_progs/py_plot_util.py

@@ -134,7 +134,7 @@ def read_pywind_smart(filename, return_inwind=False):
 
     values = d[2].reshape(xshape, zshape)
 
-    # these are the values of inwind PYTHON spits out
+    # these are the values of inwind SIROCCO spits out
     inwind = d[3].reshape(xshape, zshape)
 
     # create an inwind boolean to use to create mask
@@ -211,7 +211,7 @@ def wind_to_masked(d, value_string, return_inwind=False, mode="2d", ignore_parti
 
         values = d[value_string].reshape(xshape, zshape)
 
-        # these are the values of inwind PYTHON spits out
+        # these are the values of inwind SIROCCO spits out
         inwind = d["inwind"].reshape(xshape, zshape)
 
         # create an inwind boolean to use to create mask

py_progs/regression.py

@@ -17,10 +17,10 @@
         the number of processors with which to run (default 3)
     `-pf_dir test`
         the directory containing all of the .pf files which will be run
-        The defaults is `$PYTHON/examples/regress`.  One does not need
+        The defaults is `$SIROCCO/examples/regress`.  One does not need
         to provide the full path name to the directory.  The routine doit
         first searches the current workind directory for the directory and then
-        looks in `$PYTHON/examples/`
+        looks in `$SIROCCO/examples/`
     `-x  '-v/c'`
         Extra switches to be applied to the run, such as using linear Doppler
         shifts.  Note that these will be applied to everything except the
@@ -207,7 +207,7 @@ def doit(version='py',pf_dir='',out_dir='',np=3,switches='',outputfile='Summary.
     Notes:
 
         The routine looks for the input directory first as a subdirectory
-        of the directory from which regression is run, and then in $PYTHON/examples/
+        of the directory from which regression is run, and then in $SIROCCO/examples/
 
     History:
 
@@ -235,22 +235,22 @@ def doit(version='py',pf_dir='',out_dir='',np=3,switches='',outputfile='Summary.
 
     print(date)
 
-    # Get the PYTHON environment variable
+    # Get the SIROCCO environment variable
 
-    PYTHON=os.environ['PYTHON']
-    print(PYTHON)
+    SIROCCO=os.environ['SIROCCO']
+    print(SIROCCO)
 
     if pf_dir=='':
-        pf_dir=PYTHON+'/examples/regress'
+        pf_dir=SIROCCO+'/examples/regress'
 
     if os.path.isdir(pf_dir):
         pf_files=glob(pf_dir+'/*pf')
         txt_files=glob(pf_dir+'/*.txt')
         dat_files=glob(pf_dir+'/*.dat')
         wind_save=glob(pf_dir+'/*.wind_save')
-    elif os.path.isdir('%s/examples/%s' % (PYTHON,pf_dir)):
-        pf_files=glob('%s/examples/%s/*pf' % (PYTHON,pf_dir))
-        txt_files=glob('%s/examples/%s/*.txt' % (PYTHON,pf_dir))
+    elif os.path.isdir('%s/examples/%s' % (SIROCCO,pf_dir)):
+        pf_files=glob('%s/examples/%s/*pf' % (SIROCCO,pf_dir))
+        txt_files=glob('%s/examples/%s/*.txt' % (SIROCCO,pf_dir))
         dat_files=glob(pf_dir+'/*.dat')
         wind_save=glob(pf_dir+'/*.wind_save')
     else:

py_progs/regression_nsh.py

@@ -17,10 +17,10 @@
         the number of processors with which to run (default 3)
     -pf_dir test
         the directory containing all of the .pf files which will be run
-        The defaults is $PYTHON/examples/regress.  One does not need
+        The defaults is $SIROCCO/examples/regress.  One does not need
         to provide the full path name to the directory.  The routine doit
         first searches the current workind directory for the directory and then
-        looks in $PYTHON/examples/
+        looks in $SIROCCO/examples/
     -out_dir foo
         The directory (below the current working directory) where the
         tests will run.  The defauld is constructed for the version and the data
@@ -162,7 +162,7 @@ def doit(version='py',pf_dir='',out_dir='',np=3,outputfile='Summary.txt'):
     Notes:
 
         The routine looks for the input directory first as a subdirectory
-        of the directory from which regression is run, and then in $PYTHON/examples/
+        of the directory from which regression is run, and then in $SIROCCO/examples/
 
     History:
 
@@ -183,18 +183,18 @@ def doit(version='py',pf_dir='',out_dir='',np=3,outputfile='Summary.txt'):
 
     print(date)
 
-    # Get the PYTHON environment variable
+    # Get the SIROCCO environment variable
 
-    PYTHON=os.environ['PYTHON']
-    print(PYTHON)
+    SIROCCO=os.environ['SIROCCO']
+    print(SIROCCO)
 
     if pf_dir=='':
-        pf_dir=PYTHON+'/examples/regress'
+        pf_dir=SIROCCO+'/examples/regress'
 
     if os.path.isdir(pf_dir):
         pf_files=glob(pf_dir+'/*pf')
-    elif os.path('%s/%s' % (PYTHON,pf_dir)):
-        pf_files=glob('%s/%s' % (PYTHON,pf_dir))
+    elif os.path('%s/%s' % (SIROCCO,pf_dir)):
+        pf_files=glob('%s/%s' % (SIROCCO,pf_dir))
     else:
         print('Error: The pf directory %s does not appear to exist' % pf_dir)
         return

py_progs/retro.py

@@ -191,20 +191,20 @@ def log2table(logfile='commits.txt',masterfile='retro_master.txt'):
 
     return SUCCESS
 
-PYTHON_SOURCE_DIRECTORY=''
+SIROCCO_SOURCE_DIRECTORY=''
 
 def get_python_source_directory():
-    global PYTHON_SOURCE_DIRECTORY
+    global SIROCCO_SOURCE_DIRECTORY
 
     result=subprocess.run(['which','py'],capture_output=True,text=True)
     location=str(result.stdout)
     x=location.strip()
     xx=x.replace('bin/py','source/')
 
-    PYTHON_SOURCE_DIRECTORY=xx
-    print('Set Python source directory to :',PYTHON_SOURCE_DIRECTORY)
+    SIROCCO_SOURCE_DIRECTORY=xx
+    print('Set Python source directory to :',SIROCCO_SOURCE_DIRECTORY)
 
-    return  PYTHON_SOURCE_DIRECTORY 
+    return  SIROCCO_SOURCE_DIRECTORY 
 
 
 def compile_one(commit='a77ec180c017244cb56f41b50178daf81541748a',number=35,print_output=False):
@@ -215,9 +215,9 @@ def compile_one(commit='a77ec180c017244cb56f41b50178daf81541748a',number=35,prin
 
     # cwd=os.getcwd()
 
-    if PYTHON_SOURCE_DIRECTORY=='':
+    if SIROCCO_SOURCE_DIRECTORY=='':
         get_python_source_directory()
-    os.chdir(PYTHON_SOURCE_DIRECTORY)
+    os.chdir(SIROCCO_SOURCE_DIRECTORY)
 
     result=subprocess.run(['git', 'checkout', commit],capture_output=True,text=True)
     if result.returncode:

py_progs/test_masterfiles.py

@@ -5,15 +5,15 @@
 needs python to be compiled.
 
 Usage:
-	test_masterfiles.py [PYTHON VERSION]
+	test_masterfiles.py [SIROCCO VERSION]
 '''
 import py_read_output as rd 
 import subprocess, os, sys
 
 # set env variable
 # Do not call this when we're on ReadTheDocs
 if not os.environ.get('READTHEDOCS'):
-	PYTHON = os.environ["PYTHON"]
+	SIROCCO = os.environ["SIROCCO"]
 
 # change these if you want to test different files. These are all in data/ as of October 2019
 macro_files = ['h20', 'h10_hetop_lohe1_standard80', 'h10_standard80', 'h10_hetop_standard80', 'h20_hetop_standard80']
@@ -33,7 +33,7 @@ def run_file(pf_template, masterfile, version=""):
 	rd.write_pf("_tmp.pf", pf)
 
 	# run process
-	process = subprocess.run("{}/bin/py{} -i _tmp.pf".format(PYTHON, version), shell=True, stdout=subprocess.PIPE)
+	process = subprocess.run("{}/bin/py{} -i _tmp.pf".format(SIROCCO, version), shell=True, stdout=subprocess.PIPE)
 
 	subprocess.run("/bin/rm -f _tmp.sig _tmp.out.pf logfile _tmp.out.pf.old _tmp.pf", shell=True, stdout=subprocess.PIPE)
 	subprocess.run("/bin/rm -rf diag__tmp", shell=True, stdout=subprocess.PIPE)
@@ -60,8 +60,8 @@ def run_test(VERSION):
 	run the test. 
 	'''
 
-	macro_template = rd.read_pf("{}/examples/extended/cv_macro_benchmark.pf".format(PYTHON))
-	std_template = rd.read_pf("{}/examples/basic/cv_standard.pf".format(PYTHON))
+	macro_template = rd.read_pf("{}/examples/extended/cv_macro_benchmark.pf".format(SIROCCO))
+	std_template = rd.read_pf("{}/examples/basic/cv_standard.pf".format(SIROCCO))
 
 	subprocess.run("Setup_Py_Dir")
 

py_progs/watchdog.py

@@ -4,7 +4,7 @@
 During-run parser for error logs from parallel simulation runs.
 	
 This is the during-processing watchdog code to deal with the error logs in 
-PYTHON's parallel mode. Very similar to py_error.py
+SIROCCO's parallel mode. Very similar to py_error.py
 
 usage and arguments: