Merge pull request #104 from ska-sa/issue-101

Fixes #101 and #103

Pyxides/im/argo.py

@@ -20,7 +20,6 @@
 
 # register ourselves with Pyxis and define the superglobals
 register_pyxis_module(superglobals="MS LSM")
-register_pyxis_module()
 
 rm_fr = x.rm.args("-fr")
 

Pyxides/imager.py

@@ -1,5 +1,3 @@
-from Pyxides.im import argo
-
 from Pyxis.ModSupport import *
 
 register_pyxis_module(superglobals="MS LSM DESTDIR");

Pyxis/Internals.py

@@ -12,6 +12,7 @@
 import fnmatch
 import shutil
 import shlex
+import six
 
 import Pyxis
 
@@ -725,15 +726,15 @@ def set_logfile (filename,quiet=False):
       sys.stdout,sys.stderr = sys.__stdout__,sys.__stderr__;
       _current_logobj = None;
     else:
-      mode = "wa";
+      mode = "a";
       # append to file if name starts with +, or if file has already been used as a log this session, or if flush is off
       if Pyxis.Context.get("LOG_FLUSH"):
         mode = "w";
         if filename[0] == '+':
           filename = filename[1:];
-          mode = "wa";
+          mode = "a";
         if filename in _visited_logfiles:
-          mode = "wa";
+          mode = "a";
       Pyxis.ModSupport.makedir(os.path.dirname(filename),no_interpolate=True);
       _current_logobj = sys.stdout = sys.stderr = open(filename,mode);
       hdr = Pyxis.Context.get("LOG_HEADER");
@@ -786,7 +787,7 @@ def initconf (force=False,files=[],directory="."):
   if Pyxis.Context.get("PYXIS_AUTO_IMPORT_MODULES",True) and toplevel:
     _verbose(1,"importing top-level modules (%s) for you. Preset PYXIS_AUTO_IMPORT_MODULES=False to disable."%", ".join(toplevel));
     for mod in toplevel:
-      Pyxis.Context[mod] = sys.modules.get(mod,sys.modules.get("Pyxides."+m));
+      Pyxis.Context[mod] = sys.modules.get(mod, sys.modules.get("Pyxides."+mod));
 
 def loadconf (filename,frame=None,chdir=True):
   """Loads config file""";
@@ -822,7 +823,7 @@ def load_package (pkgname,filename,chdir=True,report=True):
     if dirname not in oldpath:
       sys.path.append(dirname);
     try:
-      exec(open(filename),Pyxis.Context);
+      exec(open(filename, "rt").read(), Pyxis.Context, Pyxis.Context)
     finally:
       sys.path = oldpath;
   except SystemExit:

Pyxis/ModSupport.py

@@ -1,6 +1,7 @@
 """Pyxis.ModSupport: functions for programming Pyxides modules"""
 
-import fnmatch    
+import fnmatch
+import inspect, traceback
 
 import Pyxis
 from Pyxis import *
@@ -20,10 +21,10 @@ def register_pyxis_module (superglobals=""):
   module = sys.modules[modname];
   if modname.startswith("Pyxides."):
     modname = modname.split(".",1)[-1];
-  # check for double registration
   if id(globs) in _superglobals:
     if _modules[modname] is not module:
       raise RuntimeError("a different Pyxis module named '%s' is already registered"%modname);
+    return
   _modules[modname] = module;
   # build list of superglobals
   if isinstance(superglobals,str):
@@ -34,7 +35,7 @@ def register_pyxis_module (superglobals=""):
   _verbose(1,"registered module '%s'"%modname);
   _namespaces[modname] = globs;
   _superglobals[id(globs)] = superglobs;
-  Pyxis.Context[modname] = __import__(modname,Pyxis.Context);
+  Pyxis.Context[modname] = module;
   # add superglobals
   for sym in superglobs:
     # if superglobal is already defined, copy its value to the new module

Pyxis/doc/example/pyxis-wsrt21cm.py

@@ -7,7 +7,9 @@
 # import some Pyxides modules.
 # Note that Pyxides is implicitly added to the include path
 # when you import Pyxis above
-import ms,imager,std,lsm,stefcal
+import ms,imager,std,lsm
+
+from Cattery.Pyxides import stefcal
 
 # import some other Python modules that we make use of below
 from astropy.io import fits as pyfits

Pyxis/recipies/imagers-test/basic_imager_test.py → Pyxis/recipes/imagers-test/basic_imager_test.py

@@ -12,7 +12,7 @@
   PYXIS_ROOT_NAMESPACE = True  # must set this before import!
   import Pyxis
   import Pyxides
-  PACKAGE_TEST_DIR = os.path.join(os.path.dirname(Pyxis.__file__), "recipies", "imagers-test")
+  PACKAGE_TEST_DIR = os.path.join(os.path.dirname(Pyxis.__file__), "recipes", "imagers-test")
   if not os.path.exists(PACKAGE_TEST_DIR):
     raise RuntimeError("Installation excludes {}".format(PACKAGE_TEST_DIR))
 except:

Pyxis/recipies/meqtrees-batch-test/batch_test.py → Pyxis/recipes/meqtrees-batch-test/batch_test.py

@@ -12,7 +12,7 @@
   PYXIS_ROOT_NAMESPACE = True  # must set this before import!
   import Pyxis
   import Pyxides
-  PACKAGE_TEST_DIR = os.path.join(os.path.dirname(Pyxis.__file__), "recipies", "meqtrees-batch-test")
+  PACKAGE_TEST_DIR = os.path.join(os.path.dirname(Pyxis.__file__), "recipes", "meqtrees-batch-test")
   if not os.path.exists(PACKAGE_TEST_DIR):
     raise RuntimeError("Installation excludes {}".format(PACKAGE_TEST_DIR))
 except:

setup.py

@@ -10,13 +10,15 @@
       'matplotlib',
       'python_casacore',
       'numpy<=1.16',
+      'scipy',
       'future'
 ] if six.PY2 else [
       'astropy>=3.0',
       # 'timba', not available on pypi
       'matplotlib',
       'python_casacore',
       'numpy>=1.16',
+      'scipy',
       'future'
 ]