compass python package (compass v1.0)

LICENSE

@@ -0,0 +1,39 @@
+Copyright (c) 2013-2020,  Los Alamos National Security, LLC (LANS) (Ocean: LA-CC-13-047;
+Land Ice: LA-CC-13-117) and the University Corporation for Atmospheric Research (UCAR).
+
+All rights reserved.
+
+LANS is the operator of the Los Alamos National Laboratory under Contract No.
+DE-AC52-06NA25396 with the U.S. Department of Energy.  UCAR manages the National
+Center for Atmospheric Research under Cooperative Agreement ATM-0753581 with the
+National Science Foundation.  The U.S. Government has rights to use, reproduce,
+and distribute this software.  NO WARRANTY, EXPRESS OR IMPLIED IS OFFERED BY
+LANS, UCAR OR THE GOVERNMENT AND NONE OF THEM ASSUME ANY LIABILITY FOR THE USE
+OF THIS SOFTWARE.  If software is modified to produce derivative works, such
+modified software should be clearly marked, so as not to confuse it with the
+version available from LANS and UCAR.
+
+Additionally, redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+1) Redistributions of source code must retain the above copyright notice, this
+list of conditions and the following disclaimer.
+
+2) Redistributions in binary form must reproduce the above copyright notice,
+this list of conditions and the following disclaimer in the documentation and/or
+other materials provided with the distribution.
+
+3) None of the names of LANS, UCAR or the names of its contributors, if any, may
+be used to endorse or promote products derived from this software without
+specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
+ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
+WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR
+ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
+(INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
+LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON
+ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
+SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

azure-pipelines.yml

@@ -14,13 +14,20 @@ pr:
 
 jobs:
 - job:
-  displayName: docs
+  displayName: linux
   pool:
     vmImage: 'ubuntu-16.04'
   strategy:
     matrix:
-      Python38:
+      nompi:
+        python.version: '3.8'
+        mpi: 'nompi'
+      openmpi:
         python.version: '3.8'
+        mpi: 'openmpi'
+      mpich:
+        python.version: '3.8'
+        mpi: 'mpich'
 
   steps:
   - bash: echo "##vso[task.prependpath]$CONDA/bin"
@@ -31,18 +38,41 @@ jobs:
       eval "$(conda shell.bash hook)"
       conda config --add channels conda-forge
       conda config --set channel_priority strict
-    displayName: Configure conda
+      conda create --yes --quiet --name build python=$PYTHON_VERSION conda conda-build
+    displayName: Create Anaconda build environment
+
+  - bash: |
+      eval "$(conda shell.bash hook)"
+      conda activate build
+      conda build -m ci/mpi_$(mpi).yaml recipe
+    displayName: Build COMPASS metapackage
+
+  - bash: |
+      set -e
+      eval "$(conda shell.bash hook)"
+      conda activate build
+      conda create --yes --quiet --name compass -c ${CONDA_PREFIX}/conda-bld/ \
+          python=$PYTHON_VERSION compass  sphinx mock sphinx_rtd_theme m2r
+    displayName: Create compass conda environment
 
   - bash: |
       set -e
       eval "$(conda shell.bash hook)"
-      conda create -y -n docs python=$PYTHON_VERSION sphinx mock sphinx_rtd_theme m2r
-    displayName: Create docs environment
+      conda activate compass
+
+      compass list
+      compass list --machines
+      compass list --suites
+      compass list --help
+      compass setup --help
+      compass suite --help
+      compass clean --help
+    displayName: Test compass
 
   - bash: |
       set -e
       eval "$(conda shell.bash hook)"
-      conda activate docs
+      conda activate compass
 
       echo "source branch: $(Build.SourceBranch)"
       echo "repository: $(Build.Repository.Name)"
@@ -122,60 +152,9 @@ jobs:
         git push -fq origin $PUBLICATION_BRANCH
       fi
       popd || exit 1
+    condition: eq(variables['mpi'], 'mpich')
     displayName: build and deploy docs
 
-- job:
-  displayName: linux
-  pool:
-    vmImage: 'ubuntu-16.04'
-  strategy:
-    matrix:
-      nompi:
-        python.version: '3.8'
-        mpi: 'nompi'
-      openmpi:
-        python.version: '3.8'
-        mpi: 'openmpi'
-      mpich:
-        python.version: '3.8'
-        mpi: 'mpich'
-
-  steps:
-  - bash: echo "##vso[task.prependpath]$CONDA/bin"
-    displayName: Add conda to PATH
-
-  - bash: |
-      set -e
-      eval "$(conda shell.bash hook)"
-      conda config --add channels conda-forge
-      conda config --set channel_priority strict
-      conda create --yes --quiet --name build python=$PYTHON_VERSION conda conda-build
-    displayName: Create Anaconda build environment
-
-  - bash: |
-      eval "$(conda shell.bash hook)"
-      conda activate build
-      conda build -m ci/mpi_$(mpi).yaml recipe
-    displayName: Build COMPASS metapackage
-
-  - bash: |
-      set -e
-      eval "$(conda shell.bash hook)"
-      conda activate build
-      conda create --yes --quiet --name compass -c ${CONDA_PREFIX}/conda-bld/ \
-          python=$PYTHON_VERSION compass
-    displayName: Create compass conda environment
-
-  - bash: |
-      set -e
-      eval "$(conda shell.bash hook)"
-      conda activate compass
-
-      ./list_testcases.py -h
-      ./setup_testcase.py -h
-      ./clean_testcase.py -h
-      ./manage_regression_suite.py -h
-    displayName: Test compass
 
 
 - job:
@@ -225,9 +204,12 @@ jobs:
       eval "$(conda shell.bash hook)"
       conda activate compass
 
-      ./list_testcases.py -h
-      ./setup_testcase.py -h
-      ./clean_testcase.py -h
-      ./manage_regression_suite.py -h
+      compass list
+      compass list --machines
+      compass list --suites
+      compass list --help
+      compass setup --help
+      compass suite --help
+      compass clean --help
     displayName: Test compass
 

compass/__init__.py

@@ -0,0 +1,7 @@
+from compass.mpas_core import MpasCore
+from compass.testgroup import TestGroup
+from compass.testcase import TestCase
+from compass.step import Step
+
+__version_info__ = (1, 0, 0)
+__version__ = '.'.join(str(vi) for vi in __version_info__)

compass/__main__.py

@@ -0,0 +1,56 @@
+#!/usr/bin/env python
+
+import sys
+import argparse
+
+import compass
+from compass import list, setup, clean, suite
+
+
+def main():
+    """
+    Entry point for the main script ``compass``
+    """
+
+    parser = argparse.ArgumentParser(
+        description="Perform compass operations",
+        usage='''
+compass <command> [<args>]
+
+The available compass commands are:
+    list    List the available test cases
+    setup   Set up a test case
+    clean   Clean up a test case
+    suite   Manage a regression test suite
+
+ To get help on an individual command, run:
+
+    compass <command> --help
+    ''')
+
+    parser.add_argument('command', help='command to run')
+    parser.add_argument('-v', '--version',
+                        action='version',
+                        version='compass {}'.format(compass.__version__),
+                        help="Show version number and exit")
+    if len(sys.argv) == 1:
+        parser.print_help()
+        sys.exit(0)
+
+    args = parser.parse_args(sys.argv[1:2])
+
+    commands = {'list': list.main,
+                'setup': setup.main,
+                'clean': clean.main,
+                'suite': suite.main}
+    if args.command not in commands:
+        print('Unrecognized command {}'.format(args.command))
+        parser.print_help()
+        exit(1)
+
+    # call the function associated with the requested command
+    commands[args.command]()
+
+
+if __name__ == "__main__":
+    main()

compass/clean.py

@@ -0,0 +1,90 @@
+import argparse
+import sys
+import os
+import shutil
+
+from compass.mpas_cores import get_mpas_cores
+from compass import provenance
+
+
+def clean_cases(tests=None, numbers=None, work_dir=None):
+    """
+    Set up one or more test cases
+
+    Parameters
+    ----------
+    tests : list of str, optional
+        Relative paths for a test cases to set up
+
+    numbers : list of int, optional
+        Case numbers to setup, as listed from ``compass list``
+
+    work_dir : str, optional
+        A directory that will serve as the base for creating case directories
+    """
+
+    if tests is None and numbers is None:
+        raise ValueError('At least one of tests or numbers is needed.')
+
+    if work_dir is None:
+        work_dir = os.getcwd()
+
+    mpas_cores = get_mpas_cores()
+    all_test_cases = dict()
+    for mpas_core in mpas_cores:
+        for test_group in mpas_core.test_groups.values():
+            for test_case in test_group.test_cases.values():
+                all_test_cases[test_case.path] = test_case
+
+    test_cases = dict()
+    if numbers is not None:
+        keys = list(all_test_cases)
+        for number in numbers:
+            if number >= len(keys):
+                raise ValueError('test number {} is out of range.  There are '
+                                 'only {} tests.'.format(number, len(keys)))
+            path = keys[number]
+            test_cases[path] = all_test_cases[path]
+
+    if tests is not None:
+        for path in tests:
+            if path not in all_test_cases:
+                raise ValueError('Test case with path {} is not in '
+                                 'the list of test cases'.format(path))
+            test_cases[path] = all_test_cases[path]
+
+    provenance.write(work_dir, test_cases)
+
+    print('Cleaning test cases:')
+    for path in test_cases.keys():
+        print('  {}'.format(path))
+
+        test_case_dir = os.path.join(work_dir, path)
+        try:
+            shutil.rmtree(test_case_dir)
+        except OSError:
+            pass
+
+
+def main():
+    parser = argparse.ArgumentParser(
+        description='Clean up one or more test cases', prog='compass clean')
+
+    parser.add_argument("-t", "--test", dest="test",
+                        help="Relative path for a test case to set up",
+                        metavar="PATH")
+    parser.add_argument("-n", "--case_number", nargs='+', dest="case_num",
+                        type=int,
+                        help="Case number(s) to setup, as listed from "
+                             "'compass list'. Can be a space-separated"
+                             "list of case numbers.", metavar="NUM")
+    parser.add_argument("-w", "--work_dir", dest="work_dir",
+                        help="If set, case directories are created in "
+                             "work_dir rather than the current directory.",
+                        metavar="PATH")
+    args = parser.parse_args(sys.argv[2:])
+    if args.test is None:
+        tests = None
+    else:
+        tests = [args.test]
+    clean_cases(tests=tests, numbers=args.case_num, work_dir=args.work_dir)