Merge pull request #72 from zwicker-group/templates

Improved job script tempaltes

modelrunner/run/job.py

@@ -219,10 +219,13 @@ def submit_job(
     job_args = []
     if parameters is not None and len(parameters) > 0:
         if isinstance(parameters, dict):
-            parameters = json.dumps(parameters)
-        elif not isinstance(parameters, str):
+            parameters_json = json.dumps(parameters)
+        elif isinstance(parameters, str):
+            parameters_json = parameters
+        else:
             raise TypeError("Parameters need to be given as a string or a dict")
-        job_args.append(f"--json {escape_string(parameters)}")
+        job_args.append(f"--json {escape_string(parameters_json)}")
+        script_args["PARAMETERS"] = parameters  # allow using parameters in job script
 
     logger.debug("Job arguments: `%s`", job_args)
 

scripts/run_tests.py

@@ -1,5 +1,7 @@
 #!/usr/bin/env python3
 
+from __future__ import annotations
+
 import argparse
 import os
 import subprocess as sp
@@ -66,6 +68,7 @@ def run_unit_tests(
     coverage: bool = False,
     no_numba: bool = False,
     pattern: str = None,
+    pytest_args: list[str] = [],
 ) -> int:
     """run the unit tests
 
@@ -74,6 +77,9 @@ def run_unit_tests(
         coverage (bool): Whether to determine the test coverage
         no_numba (bool): Whether to disable numba jit compilation
         pattern (str): A pattern that determines which tests are ran
+        pytest_args (list of str):
+            Additional arguments forwarded to py.test. For instance ["--maxfail=1"]
+            fails tests early.
 
     Returns:
         int: The return code indicating success or failure
@@ -117,6 +123,8 @@ def run_unit_tests(
             ]
         )
 
+    args.extend(pytest_args)
+
     # specify the package to run
     args.append("tests")
 
@@ -191,6 +199,13 @@ def main():
         help="Write a report of the results",
     )
 
+    # set py.test arguments
+    group = parser.add_argument_group(
+        "py.test arguments",
+        description="Additional arguments separated by `--` are forward to py.test",
+    )
+    group.add_argument("pytest_args", nargs="*", help=argparse.SUPPRESS)
+
     # parse the command line arguments
     args = parser.parse_args()
     run_all = not (args.style or args.types or args.unit)
@@ -206,6 +221,7 @@ def main():
             parallel=args.parallel,
             no_numba=args.no_numba,
             pattern=args.pattern,
+            pytest_args=args.pytest_args,
         )
 
 

scripts/tests_debug.sh

@@ -0,0 +1,16 @@
+#!/bin/bash
+
+export PYTHONPATH=../py-modelrunner  # likely path of package, relative to current base path
+
+if [ ! -z $1 ] 
+then 
+    # test pattern was specified 
+    echo 'Run unittests with pattern '$1':'
+    ./run_tests.py --unit --pattern "$1" -- \
+        -o log_cli=true --log-cli-level=debug -vv
+else
+    # test pattern was not specified
+    echo 'Run all unittests:'
+    ./run_tests.py --unit -- \
+        -o log_cli=true --log-cli-level=debug -vv
+fi

tests/run/scripts/custom.jinja

@@ -0,0 +1,19 @@
+#!/bin/bash -l
+
+export PYTHONPATH={{ PACKAGE_PATH }}:$PYTHONPATH
+
+{% if CONFIG.num_threads is number %}
+# set the number of threads to use
+export MKL_NUM_THREADS={{ CONFIG.num_threads }}
+export NUMBA_NUM_THREADS={{ CONFIG.num_threads }}
+export NUMEXPR_NUM_THREADS={{ CONFIG.num_threads }}
+export OMP_NUM_THREADS={{ CONFIG.num_threads }}
+export OPENBLAS_NUM_THREADS={{ CONFIG.num_threads }}
+{% endif %}
+
+{% if OUTPUT_FOLDER is defined and OUTPUT_FOLDER %}
+mkdir -p {{ OUTPUT_FOLDER }}
+{% endif %}
+
+# Run the program
+{{ CONFIG.python_bin }} -m modelrunner {{ MODEL_FILE }} --a {{ PARAMETERS.a }}

tests/run/test_job.py

@@ -57,8 +57,8 @@ def test_submit_job_stdout(tmp_path, method):
         overwrite_strategy="silent_overwrite",
     )
 
-    assert outs == "3.0\n"
     assert errs == ""
+    assert outs == "3.0\n"
     assert Result.from_file(output).result is None
 
 
@@ -69,8 +69,8 @@ def test_submit_job_no_output():
         method="foreground",
         overwrite_strategy="silent_overwrite",
     )
-    assert outs == "3.0\n"
     assert errs == ""
+    assert outs == "3.0\n"
 
 
 def test_submit_jobs(tmp_path):
@@ -137,3 +137,17 @@ def run(**p):
 
     assert run() == ("", "")
     assert run(a=1) == ('--json{"a": 1}', "")
+
+
+def test_submit_job_own_template(tmp_path):
+    """test the submit_job function with a custom template"""
+    outs, errs = submit_job(
+        SCRIPT_PATH / "print.py",
+        method="foreground",
+        parameters={"a": 5, "b": 10},  # b is not used by template
+        template=SCRIPT_PATH / "custom.jinja",
+        overwrite_strategy="silent_overwrite",
+    )
+
+    assert errs == ""
+    assert outs == "7.0\n"  # a + 2 (default value of b)