intorduce amend_config context manager

Signed-off-by: Jose Borreguero <[email protected]>

.github/workflows/actions.yml

@@ -24,9 +24,6 @@ jobs:
     - name: Test with pytest
       working-directory: ./reduction
       run: |
-        #echo datasearch.directories=${{ github.workspace }}/reduction/tests/data/liquidsreflectometer-data/nexus/ >> ${{ runner.home }}/.mantid/Mantid.user.properties
-        #echo ${{ runner.home }}/.mantid/Mantid.user.properties
-        #cat ${{ runner.home }}/.mantid/Mantid.user.properties
         git submodule add --force https://code.ornl.gov/sns-hfir-scse/infrastructure/test-data/liquidsreflectometer-data.git tests/data/liquidsreflectometer-data
         git submodule update --init
         python -m pytest -vv --cov=. --cov-report=xml --cov-report=term test

reduction/lr_reduction/utils.py

@@ -0,0 +1,63 @@
+# standard imports
+from contextlib import contextmanager
+from copy import deepcopy
+from typing import Union
+
+# third-party libraries
+from mantid.kernel import ConfigService
+
+
+@contextmanager
+def amend_config(
+    new_config: dict = None, data_dir: Union[str, list] = None, data_dir_insert_mode: str = "prepend"
+) -> None:
+    r"""
+    Context manager to safely modify Mantid Configuration Service while
+    the function is executed.
+
+    Parameters
+    ----------
+    new_config
+        (key, value) pairs to substitute in the configuration service
+    data_dir
+        prepend one (when passing a string) or more (when passing a list)
+        directories to the list of data search directories. Alternatively, replace instead of prepend.
+    data_dir_insert_mode
+        How to insert the data directories. Options are: "prepend" (default) and "replace".
+    """
+    modified_keys = list()
+    backup = dict()
+    config = ConfigService.Instance()
+    if new_config is not None:
+        SEARCH_ARCHIVE = "datasearch.searcharchive"
+        if SEARCH_ARCHIVE not in new_config:
+            new_config[SEARCH_ARCHIVE] = "hfir, sns"
+        DEFAULT_FACILITY = "default.facility"
+        if DEFAULT_FACILITY not in new_config:
+            new_config[DEFAULT_FACILITY] = "SNS"
+        for key, val in new_config.items():
+            backup[key] = config[key]
+            config[key] = val  # config does not have an 'update' method
+            modified_keys.append(key)
+    if data_dir is not None:
+        data_dirs = (
+            [
+                data_dir,
+            ]
+            if isinstance(data_dir, str)
+            else data_dir
+        )
+        key = "datasearch.directories"
+        backup[key] = deepcopy(config[key])
+        # prepend or replace our custom data directories to the list of data search directories
+        if data_dir_insert_mode == "prepend":
+            config.setDataSearchDirs(data_dirs + list(config.getDataSearchDirs()))
+        elif data_dir_insert_mode == "replace":
+            config.setDataSearchDirs(data_dirs)
+        else:
+            raise ValueError(f"Invalid data_dir_insert_mode: {data_dir_insert_mode}")
+    try:
+        yield
+    finally:
+        for key in modified_keys:
+            config[key] = backup[key]

reduction/test/conftest.py

@@ -1,18 +1,11 @@
 # standard imports
-import logging
 from pathlib import Path
-import os
 
+# third-party imports
+import pytest
 
-def pytest_sessionstart(session):
-    r"""invoked by pytest at the very beginning"""
-    logger = logging.getLogger()
-    # Insert data directory in Mantid config file
-    mantid_config_dir = Path(os.environ["HOME"]) / ".mantid"
-    os.makedirs(str(mantid_config_dir), exist_ok=True)  # create directory if it doesn't exists
-    mantid_config_file = mantid_config_dir / "Mantid.user.properties"
-    write_mode = "a" if mantid_config_file.exists() else "w"  # append or create-then-write
-    with open(mantid_config_file, write_mode) as file_handle:
-        data_path = str(Path(__file__).parent.parent / "tests/data/liquidsreflectometer-data/nexus")
-        file_handle.write(f"datasearch.directories={data_path}")
-        logger.info(f"Appending data directory {data_path} to mantid config file {str(mantid_config_file)}")
+
+@pytest.fixture(scope="session")
+def nexus_dir() -> str:
+    r"""Absolute path to the event nexus files"""
+    return str(Path(__file__).parent.parent / "tests/data/liquidsreflectometer-data/nexus")

reduction/test/test_reduction.py

@@ -1,15 +1,20 @@
+# standard imports
 import os
 
+# third-party imports
 import mantid
 import mantid.simpleapi as mtd_api
 import numpy as np
+
+# lr_reduction imports
+from lr_reduction import event_reduction, template, workflow
+from lr_reduction.utils import amend_config
+
+
 mtd_api.config["default.facility"] = "SNS"
 mtd_api.config["default.instrument"] = "REF_L"
-
 mantid.kernel.config.setLogLevel(3)
 
-from lr_reduction import event_reduction, template, workflow
-
 
 def cleanup_partial_files(output_dir, runs):
     """
@@ -21,17 +26,18 @@ def cleanup_partial_files(output_dir, runs):
             os.remove(reduced_path)
 
 
-def test_info():
+def test_info(nexus_dir):
     """
         Test utility functions to get basic info
     """
-    ws_sc = mtd_api.Load("REF_L_198409")
+    with amend_config(data_dir=nexus_dir):
+        ws_sc = mtd_api.Load("REF_L_198409")
     wl_min, wl_max = event_reduction.get_wl_range(ws_sc)
     assert(wl_min == 13.7)
     assert(wl_max == 16.3)
 
 
-def test_full_reduction():
+def test_full_reduction(nexus_dir):
     """
         Test the fill reduction chain
     """
@@ -41,7 +47,8 @@ def test_full_reduction():
     d_refl_all = []
     first_run = None
     for run_number in range(198409, 198417):
-        ws_sc = mtd_api.Load("REF_L_%s" % run_number)
+        with amend_config(data_dir=nexus_dir):
+            ws_sc = mtd_api.Load("REF_L_%s" % run_number)
         qz_mid, refl, d_refl = template.process_from_template_ws(ws_sc, template_path)
 
         if first_run is None:
@@ -72,15 +79,16 @@ def test_full_reduction():
     cleanup_partial_files(output_dir, range(198409, 198417))
 
 
-def test_reduce_workflow():
+def test_reduce_workflow(nexus_dir):
     template_path = 'data/template.xml'
     output_dir = 'data/'
     reduced_path = os.path.join(output_dir, 'REFL_198409_combined_data_auto.txt')
     if os.path.isfile(reduced_path):
         os.remove(reduced_path)
 
     for i in range(198409, 198417):
-        ws = mtd_api.Load("REF_L_%s" % i)
+        with amend_config(data_dir=nexus_dir):
+            ws = mtd_api.Load("REF_L_%s" % i)
         workflow.reduce(ws, template_path, output_dir=output_dir,
                         average_overlap=False)
 
@@ -102,15 +110,16 @@ def test_reduce_workflow():
     cleanup_partial_files(output_dir, range(198409, 198417))
 
 
-def test_reduce_functional_bck():
+def test_reduce_functional_bck(nexus_dir):
     template_path = 'data/template_fbck.xml'
     output_dir = 'data/'
     reduced_path = os.path.join(output_dir, 'REFL_198409_combined_data_auto.txt')
     if os.path.isfile(reduced_path):
         os.remove(reduced_path)
 
     for i in range(198409, 198417):
-        ws = mtd_api.Load("REF_L_%s" % i)
+        with amend_config(data_dir=nexus_dir):
+            ws = mtd_api.Load("REF_L_%s" % i)
         workflow.reduce(ws, template_path, output_dir=output_dir,
                         average_overlap=False,
                         functional_background=True)
@@ -136,7 +145,7 @@ def test_reduce_functional_bck():
     cleanup_partial_files(output_dir, range(198409, 198417))
 
 
-def test_reduce_bck_option_mismatch():
+def test_reduce_bck_option_mismatch(nexus_dir):
     """
         Ask for functional background but pass by a background range with
         only a single region. This will revert to simple averaging over the range.
@@ -148,7 +157,8 @@ def test_reduce_bck_option_mismatch():
         os.remove(reduced_path)
 
     for i in range(198409, 198417):
-        ws = mtd_api.Load("REF_L_%s" % i)
+        with amend_config(data_dir=nexus_dir):
+            ws = mtd_api.Load("REF_L_%s" % i)
         sequence_number = ws.getRun().getProperty("sequence_number").value[0]
         template_data = template.read_template(template_path, sequence_number)
         template_data.background_roi = template_data.background_roi[:2]
@@ -174,7 +184,7 @@ def test_reduce_bck_option_mismatch():
     cleanup_partial_files(output_dir, range(198409, 198417))
 
 
-def test_reduce_workflow_with_overlap_avg():
+def test_reduce_workflow_with_overlap_avg(nexus_dir):
     """
         Test the complete working, but this time we average the point in the
         overlap regions.
@@ -186,7 +196,8 @@ def test_reduce_workflow_with_overlap_avg():
         os.remove(reduced_path)
 
     for i in range(198409, 198417):
-        ws = mtd_api.Load("REF_L_%s" % i)
+        with amend_config(data_dir=nexus_dir):
+            ws = mtd_api.Load("REF_L_%s" % i)
         workflow.reduce(ws, template_path, output_dir=output_dir,
                         average_overlap=True)
 
@@ -208,12 +219,13 @@ def test_reduce_workflow_with_overlap_avg():
     cleanup_partial_files(output_dir, range(198409, 198417))
 
 
-def test_quick_reduce():
+def test_quick_reduce(nexus_dir):
     """
         Test the quick reduction workflow
     """
-    ws = mtd_api.Load("REF_L_201284")
-    ws_db = mtd_api.Load("REF_L_201045")
+    with amend_config(data_dir=nexus_dir):
+        ws = mtd_api.Load("REF_L_201284")
+        ws_db = mtd_api.Load("REF_L_201045")
 
     _refl = workflow.reduce_explorer(ws, ws_db, center_pixel=145, db_center_pixel=145)
     reference_path = 'data/reference_r201284_quick.txt'
@@ -224,7 +236,7 @@ def test_quick_reduce():
         assert(np.fabs(np.sum(_data[i] - _refl[i])) < 1e-10)
 
 
-def test_reduce_workflow_201282():
+def test_reduce_workflow_201282(nexus_dir):
     """
         Test to reproduce autoreduction output
     """
@@ -235,7 +247,8 @@ def test_reduce_workflow_201282():
         os.remove(reduced_path)
 
     for i in range(201282, 201289):
-        ws = mtd_api.Load("REF_L_%s" % i)
+        with amend_config(data_dir=nexus_dir):
+            ws = mtd_api.Load("REF_L_%s" % i)
         workflow.reduce(ws, template_path, output_dir=output_dir,
                         average_overlap=False)
 
@@ -254,7 +267,7 @@ def test_reduce_workflow_201282():
     assert(np.sum((_data[3]-_refl[3])/_refl[3])/len(_refl[3]) < 0.01)
 
 
-def test_background_subtraction():
+def test_background_subtraction(nexus_dir):
     """
         Test with background subtraction off for the data and on for the normalization
     """
@@ -265,7 +278,8 @@ def test_background_subtraction():
         os.remove(reduced_path)
 
     for i in range(198388, 198390):
-        ws = mtd_api.Load("REF_L_%s" % i)
+        with amend_config(data_dir=nexus_dir):
+            ws = mtd_api.Load("REF_L_%s" % i)
         workflow.reduce(ws, template_path, output_dir=output_dir,
                         average_overlap=False)
 

reduction/test/test_time_resolved.py

@@ -1,9 +1,15 @@
+# standard imports
 import os
+
+# third-party imports
 import numpy as np
+
+# lr_reduction imports
 from lr_reduction import time_resolved
+from lr_reduction.utils import amend_config
 
 
-def test_reduce_workflow():
+def test_reduce_workflow(nexus_dir):
     """
         Test the time-resolved reduction that uses a measured reference.
         It is generally used at 30 Hz but it also works at 60 Hz.
@@ -12,11 +18,11 @@ def test_reduce_workflow():
     output_dir = 'data/'
     reduced_path = 'data/reference_rq_avg_overlap.txt'
     ref_data = np.loadtxt(reduced_path).T
-
-    reduced = time_resolved.reduce_30Hz_slices(198413, 198413, ref_data_60Hz=reduced_path,
-                                               template_30Hz=template_path,
-                                               time_interval=300, output_dir=output_dir,
-                                               scan_index=5, create_plot=False)
+    with amend_config(data_dir=nexus_dir):
+        reduced = time_resolved.reduce_30Hz_slices(198413, 198413, ref_data_60Hz=reduced_path,
+                                                   template_30Hz=template_path,
+                                                   time_interval=300, output_dir=output_dir,
+                                                   scan_index=5, create_plot=False)
 
     q_long = len(ref_data[0])
     q_short = len(reduced[0][0])