Merge pull request #3 from GEOS-DEV/feature/sherman/migrateGeosATSPackage

Migrate geos ats package

Author: cssherman

docs/conf.py

@@ -21,6 +21,7 @@
 python_modules = ('geosx_mesh_tools_package',
                   'geosx_xml_tools_package',
                   'geosx_mesh_doctor',
+                  'geos_ats_package',
                   'hdf5_wrapper_package',
                   'pygeosx_tools_package',
                   'timehistory_package')
@@ -61,7 +62,7 @@
 ]
 
 
-autodoc_mock_imports = ["pygeosx", "pylvarray", "meshio", "lxml", "mpi4py", "h5py"]
+autodoc_mock_imports = ["pygeosx", "pylvarray", "meshio", "lxml", "mpi4py", "h5py", "ats", "scipy"]
 
 # The suffix(es) of source filenames.
 # You can specify multiple suffix as a list of string:

docs/geos_ats.rst

@@ -0,0 +1,46 @@
+
+GEOS ATS
+==========
+
+The `geos_ats` python package includes tools for managing integrated tests for GEOS.
+It is built using the `Automated Test System <https://ats.readthedocs.io/en/latest/>`_ (ATS) package.
+The available console scripts for this package and its API are described below.
+
+
+run_geos_ats
+----------------
+
+Primary entry point for running integrated tests.
+
+.. argparse::
+   :module: geos_ats.command_line_parsers
+   :func: build_command_line_parser
+   :prog: run_geos_ats
+
+
+.. note::
+    Arguments can be passed to the underlying ATS system with the `--ats` argument.
+
+
+.. note::
+    Other machine-specific options for ATS can be viewed by running `run_geos_ats --ats help`
+
+
+API
+------
+
+
+Restart Check
+^^^^^^^^^^^^^^^
+
+.. automodule:: geos_ats.helpers.restart_check
+    :members:
+
+
+Curve Check
+^^^^^^^^^^^^^^^
+
+.. automodule:: geos_ats.helpers.curve_check
+    :members:
+
+

docs/index.rst

@@ -43,6 +43,8 @@ Packages
 
     hdf5_wrapper
 
+    geos_ats
+
     geosx_mesh_tools
 
     geosx_xml_tools

geos_ats_package/geos_ats/__init__.py

@@ -0,0 +1,6 @@
+import sys
+from . import machines
+
+# Add the machines module to the ats.atsMachines submodule,
+# So that ats can find our custom definitions at runtime
+sys.modules['ats.atsMachines.machines'] = machines

geos_ats_package/geos_ats/command_line_parsers.py

@@ -0,0 +1,151 @@
+import logging
+import argparse
+import os
+import shutil
+from pydoc import locate
+
+action_options = {
+    "run": "execute the test cases that previously did not pass.",
+    "rerun": "ignore the status from previous runs, and rerun the tests.",
+    "continue": "continue running, ignoring tests that have either passed or failed",
+    "list": "list the test cases.",
+    "commands": "display the command line of each test step.",
+    "reset": "Removes Failed status from any test case.",
+    "clean": "remove files generated by the test cases.",
+    "veryclean": "does a clean plus removes non testcase created files (TestLog, results, ...)",
+    "check": "skip the action steps and just run the check steps.",
+    "rebaseline": "rebaseline the testcases from a previous run.",
+    "rebaselinefailed": "rebaseline only failed testcases from a previous run.",
+    "report": "generate a text or html report, see config for the reporting options.",
+}
+
+check_options = {
+    "all": "run all checks",
+    "none": "no additional checking",
+    "stopcheck": "check the stop time and stop cycle",
+    "curvecheck": "check the ultra curves",
+    "restartcheck": "check the restart file",
+}
+
+verbose_options = {
+    "debug": "Show detailed log information",
+    "info": "Show typical log information",
+    "warnings": "Show warnings only",
+    "errors": "Show errors only",
+}
+
+
+def build_command_line_parser():
+    parser = argparse.ArgumentParser(description="Runs GEOS integrated tests")
+
+    parser.add_argument("geos_bin_dir", type=str, help="GEOS binary directory.")
+
+    parser.add_argument("-w", "--workingDir", type=str, help="Initial working directory")
+
+    action_names = ','.join(action_options.keys())
+    parser.add_argument("-a", "--action", type=str, default="run", help=f"Test actions options ({action_names})")
+
+    check_names = ','.join(check_options.keys())
+    parser.add_argument("-c", "--check", type=str, default="all", help=f"Test check options ({check_names})")
+
+    verbosity_names = ','.join(verbose_options.keys())
+    parser.add_argument("-v", "--verbose", type=str, default="info", help=f"Log verbosity options ({verbosity_names})")
+
+    parser.add_argument("-d", "--detail", action="store_true", default=False, help="Show detailed action/check options")
+
+    parser.add_argument("-i", "--info", action="store_true", default=False, help="Info on various topics")
+
+    parser.add_argument("-r",
+                        "--restartCheckOverrides",
+                        nargs='+',
+                        action='append',
+                        help='Restart check parameter override (name value)',
+                        default=[])
+
+    parser.add_argument("--salloc",
+                        default=True,
+                        help="Used by the chaosM machine to first allocate nodes with salloc, before running the tests")
+
+    parser.add_argument(
+        "--sallocoptions",
+        type=str,
+        default="",
+        help="Used to override all command-line options for salloc. No other options with be used or added.")
+
+    parser.add_argument("--ats", nargs='+', default=[], action="append", help="pass arguments to ats")
+
+    parser.add_argument("--machine", default=None, help="name of the machine")
+
+    parser.add_argument("--machine-dir", default=None, help="Search path for machine definitions")
+
+    parser.add_argument("-l", "--logs", type=str, default=None)
+
+    parser.add_argument(
+        "--failIfTestsFail",
+        action="store_true",
+        default=False,
+        help="geos_ats normally exits with 0. This will cause it to exit with an error code if there was a failed test."
+    )
+
+    parser.add_argument("-n", "-N", "--numNodes", type=int, default="2")
+
+    parser.add_argument("ats_targets", type=str, nargs='*', help="ats files or directories.")
+
+    return parser
+
+
+def parse_command_line_arguments(args):
+    parser = build_command_line_parser()
+    options, unkown_args = parser.parse_known_args()
+    exit_flag = False
+
+    # Check action, check, verbosity items
+    check = options.check
+    if check not in check_options:
+        print(
+            f"Selected check option ({check}) not recognized.  Try running with --help/--details for more information")
+        exit_flag = True
+
+    action = options.action
+    if action not in action_options:
+        print(
+            f"Selected action option ({action}) not recognized.  Try running with --help/--details for more information"
+        )
+        exit_flag = True
+
+    verbose = options.verbose
+    if verbose not in verbose_options:
+        print(f"Selected verbose option ({verbose}) not recognized")
+        exit_flag = True
+
+    # Print detailed information
+    if options.detail:
+        for option_type, details in zip(['action', 'check'], [action_options, check_options]):
+            print(f'\nAvailable {option_type} options:')
+            for k, v in details.items():
+                print(f'    {k}:  {v}')
+        exit_flag = True
+
+    if exit_flag:
+        quit()
+
+    return options
+
+
+def patch_parser(parser):
+
+    def add_option_patch(*xargs, **kwargs):
+        """
+        Convert type string to actual type instance
+        """
+        tmp = kwargs.get('type', str)
+        type_map = {'string': str}
+        if isinstance(tmp, str):
+            if tmp in type_map:
+                tmp = type_map[tmp]
+            else:
+                tmp = locate(tmp)
+        kwargs['type'] = tmp
+        parser.add_argument(*xargs, **kwargs)
+
+    parser.add_option = add_option_patch