Merge pull request #158 from cgat-developers/AC-paramoutput

The pipeline outputs the global params before they are updated. The p…

cgatcore/experiment.py

@@ -1049,9 +1049,6 @@ def start(parser=None,
         else:
             logger = logging.getLogger("cgatcore")
 
-        logger.info(get_header())
-        logger.info(get_params(global_options))
-
         if global_options.tracing == "function":
             sys.settrace(trace_calls)
 

cgatcore/pipeline/control.py

@@ -24,6 +24,7 @@
 import math
 import os
 import re
+import inspect
 import shutil
 import subprocess
 import sys
@@ -46,6 +47,7 @@
 import cgatcore.experiment as E
 import cgatcore.iotools as iotools
 from cgatcore.pipeline.parameters import input_validation, get_params, get_parameters
+from cgatcore.experiment import get_header, MultiLineFormatter
 from cgatcore.pipeline.utils import get_caller, get_caller_locals, is_test
 from cgatcore.pipeline.execution import execute, start_session,\
     close_session
@@ -106,6 +108,28 @@ def get_logger():
     return logging.getLogger("cgatcore.pipeline")
 
 
+def get_param_output(options=None):
+    """return a string containing script parameters.
+
+    Parameters are all variables that start with ``param_``.
+    """
+    result = []
+    if options:
+        members = options
+        for k, v in sorted(members.items()):
+            result.append("%-40s: %s" % (k, str(v)))
+    else:
+        vars = inspect.currentframe().f_back.f_locals
+        for var in [x for x in list(vars.keys()) if re.match("param_", x)]:
+            result.append("%-40s: %s" %
+                          (var, str(vars[var])))
+
+    if result:
+        return "\n".join(result)
+    else:
+        return "# no parameters."
+
+
 def write_config_files(pipeline_path, general_path):
     '''create default configuration files in `path`.
     '''
@@ -1209,6 +1233,10 @@ def initialize(argv=None, caller=None, defaults=None, optparse=True, **kwargs):
     # configuration files.
     update_params_with_commandline_options(get_params(), args)
 
+    logger.info(get_header())
+
+    logger.info(get_param_output(get_params()))
+
     code_location, version = get_version()
     logger.info("code location: {}".format(code_location))
     logger.info("code version: {}".format(version))

cgatcore/version.py

@@ -1 +1 @@
-__version__ = "0.6.10"
+__version__ = "0.6.11"