Updates

src/sunbather/__init__.py

@@ -9,72 +9,104 @@
 from sunbather.install_cloudy import GetCloudy
 
 
-def check_cloudy():
+def check_cloudy(quiet=False, cloudy_version="23.01"):
     """
     Checks if Cloudy executable exists, and if not, prompts to download and build it.
+    :quiet: bool, if True, does not ask for input
+    :cloudy_version: str, Cloudy version (default: "23.01", environment variable
+    CLOUDY_VERSION overrides this)
     """
     try:
-        cloudyversion = os.environ["CLOUDY_VERSION"]
+        cloudy_version = os.environ["CLOUDY_VERSION"]
     except KeyError:
-        cloudyversion = "23.01"
+        pass
     sunbatherpath = os.path.dirname(
         os.path.abspath(__file__)
     )  # the absolute path where this code lives
     try:
         # the path where Cloudy is installed
         cloudypath = os.environ["cloudy_path"]
     except KeyError:
-        cloudypath = f"{sunbatherpath}/cloudy/c{cloudyversion}"
+        cloudypath = f"{sunbatherpath}/cloudy/c{cloudy_version}"
     if not os.path.exists(f"{cloudypath}/source/cloudy.exe"):
-        q = input(
-            f"Cloudy not found and CLOUDY_PATH is not set. "
-            f"Do you want to install Cloudy {cloudyversion} now in the sunbather path? "
-            f"(y/n) "
-        )
-        while q.lower() not in ["y", "n"]:
-            q = input("Please enter 'y' or 'n'")
-        if q == "n":
-            raise KeyError(
-                "Cloudy not found, and the environment variable 'CLOUDY_PATH' is not "
-                "set. Please set this variable in your .bashrc/.zshrc file "
-                "to the path where the Cloudy installation is located. "
-                "Do not point it to the /source/ subfolder, but to the main folder."
+        if not quiet:
+            q = input(
+                f"Cloudy not found and CLOUDY_PATH is not set. Do you want to install "
+                f"Cloudy {cloudy_version} now in the sunbather path? (y/n) "
             )
-        installer = GetCloudy(version=cloudyversion)
+            while q.lower() not in ["y", "n"]:
+                q = input("Please enter 'y' or 'n'")
+            if q == "n":
+                raise KeyError(
+                    "Cloudy not found, and the environment variable 'CLOUDY_PATH' is "
+                    "not set. Please set this variable in your .bashrc/.zshrc file "
+                    "to the path where the Cloudy installation is located. "
+                    "Do not point it to the /source/ subfolder, but to the main folder."
+                )
+        installer = GetCloudy(version=cloudy_version)
         installer.download()
         installer.extract()
         installer.compile()
         installer.test()
         installer.copy_data()
 
 
-def make_workingdir():
+def make_workingdir(workingdir=None, quiet=False):
     """
     Checks if the SUNBATHER_PROJECT_PATH environment variable has been set and
     asks for input if not. Also asks to copy the default files to the working dir.
+
+    :workingdir: str, path to the working dir. If None, checks the
+    SUNBATHER_PROJECT_PATH environment variable, and asks for input if this is
+    not set. (default: None)
+    :quiet: bool, if True, does not ask for input (default: False)
     """
-    try:
-        workingdir = os.environ["SUNBATHER_PROJECT_PATH"]
-    except KeyError:
-        workingdir = input("Enter the working dir for Sunbather: ")
-    q = input(f"Copy default files to the working dir ({workingdir})? (y/n) ")
-    while q.lower() not in ["y", "n"]:
-        q = input("Please enter 'y' or 'n': ")
-    if q == "n":
-        return
+    if workingdir is None:
+        try:
+            workingdir = os.environ["SUNBATHER_PROJECT_PATH"]
+        except KeyError:
+            if not quiet:
+                workingdir = input("Enter the working dir for Sunbather: ")
+            else:
+                # if quiet, use the current dir
+                workingdir = "./"
+    if not quiet:
+        q = input(f"Copy default files to the working dir ({workingdir})? (y/n) ")
+        while q.lower() not in ["y", "n"]:
+            q = input("Please enter 'y' or 'n': ")
+        if q == "n":
+            return
 
     sunbatherpath = f"{pathlib.Path(__file__).parent.resolve()}"
-    shutil.copytree(
-        f"{sunbatherpath}/data/workingdir",
-        workingdir,
-    )
+    for file in os.listdir(f"{sunbatherpath}/data/workingdir"):
+        if not os.path.exists(f"{workingdir}/{file}"):
+            shutil.copyfile(
+                f"{sunbatherpath}/data/workingdir/{file}",
+                f"{workingdir}/{file}",
+            )
+        else:
+            if not quiet:
+                print("File already exists! Overwrite?")
+                q = input("(y/n) ")
+                while q.lower() not in ["y", "n"]:
+                    q = input("Please enter 'y' or 'n': ")
+                if q == "n":
+                    continue
+            else:
+                continue
+            shutil.copyfile(
+                f"{sunbatherpath}/data/workingdir/{file}",
+                f"{workingdir}/{file}",
+            )
+
+    return
 
 
-def firstrun():
+def firstrun(quiet=False, workingdir=None, cloudy_version="23.01"):
     """
     Runs 'check_cloudy()' and 'make_workingdir()'.
     """
-    check_cloudy()
-    make_workingdir()
+    check_cloudy(quiet=quiet, cloudy_version=cloudy_version)
+    make_workingdir(quiet=quiet, workingdir=workingdir)
 
     print("Sunbather is ready to go!")

src/sunbather/construct_parker.py

@@ -990,7 +990,7 @@ def run_g(
     p.join()
 
 
-def new_argument_parser(args, **kwargs):
+def new_argument_parser():
     parser = argparse.ArgumentParser(
         description="Creates 1D Parker profile(s) using the p_winds code and Cloudy.",
         formatter_class=argparse.ArgumentDefaultsHelpFormatter,
@@ -1141,15 +1141,22 @@ def __call__(self, parser, namespace, values, option_string=None):
         action="store_true",
         help="neglect the stellar tidal gravity term",
     )
-    args = parser.parse_args(args, **kwargs)
+    return parser
 
-    return args
 
-
-def main(args, **kwargs):
+def main(**kwargs):
+    """
+    Main function to construct a Parker profile.
+    """
     t0 = time.time()
-
-    args = new_argument_parser(args, **kwargs)
+    parser = new_argument_parser()
+    if not kwargs:
+        args = parser.parse_args(sys.argv[1:])
+    else:
+        # This is a bit ugly, but it allows us to either call main directly or
+        # to call the script with command line arguments
+        print(f"-{key}={value}" for key, value in kwargs.items())
+        args = parser.parse_args([f'-{key}={value}' for key, value in kwargs.items()])
 
     if args.z is not None:
         zdict = tools.get_zdict(z=args.z, zelem=args.zelem)
@@ -1174,18 +1181,18 @@ def main(args, **kwargs):
     if not os.path.isdir(projectpath + "/parker_profiles/" + args.plname + "/"):
         os.mkdir(projectpath + "/parker_profiles/" + args.plname)
     if not os.path.isdir(
-        projectpath + "/parker_profiles/" + args.plname + "/" + args.pdir + "/"
+        f"{projectpath}/parker_profiles/{args.plname}/{args.pdir}/"
     ):
         os.mkdir(
-            projectpath + "/parker_profiles/" + args.plname + "/" + args.pdir + "/"
+            f"{projectpath}/parker_profiles/{args.plname}/{args.pdir}/"
         )
     if (args.fH is None) and (
         not os.path.isdir(
-            projectpath + "/parker_profiles/" + args.plname + "/" + args.pdir + "/temp/"
+            f"{projectpath}/parker_profiles/{args.plname}/{args.pdir}/temp/"
         )
     ):
         os.mkdir(
-            projectpath + "/parker_profiles/" + args.plname + "/" + args.pdir + "/temp"
+            f"{projectpath}/parker_profiles/{args.plname}/{args.pdir}/temp"
         )
 
     if len(args.T) == 1 and len(args.Mdot) == 1:  # then we run a single model

src/sunbather/install_cloudy.py

@@ -73,16 +73,22 @@ def test(self):
         exited OK" at the end.
         """
         os.chdir(f"{self.cloudypath}/c{self.version}/source/")
-        print(
-            'Type "test" and hit return twice. '
-            'It should print "Cloudy exited OK" at the end.'
-        )
         with subprocess.Popen(
             [
                 "./cloudy.exe",
-            ]
+            ],
+            stdin=subprocess.PIPE,
+            stdout=subprocess.PIPE,
+            stderr=subprocess.STDOUT,
         ) as p:
+            cloudy_output = p.communicate(input=b"test\n\n")[0]
             p.wait()
+            try:
+                assert b"Cloudy exited OK" in cloudy_output
+            except AssertionError:
+                print("Cloudy did not test OK...")
+            else:
+                print("Cloudy tested OK.")
 
     def copy_data(self):
         """