Merge pull request #105 from mantidproject/simplifying-directories

Changing user experience

.github/workflows/ci_tests_nightly.yml

@@ -33,5 +33,4 @@ jobs:
       # Runs System tests
       - name: Run mvesuvio analysis system tests
         run: |
-          export VESUVIOPROPERTIES=$(pwd)/mvesuvio/system_tests/test_config/vesuvio.user.properties
-          python -m unittest discover -s ./mvesuvio/system_tests
+          python -m unittest discover -s ./mvesuvio/system_tests

.github/workflows/pr_workflow.yml

@@ -38,7 +38,6 @@ jobs:
       # Runs System tests
       - name: Run mvesuvio Analysis System Tests
         run: |
-          export VESUVIOPROPERTIES=$(pwd)/mvesuvio/system_tests/test_config/vesuvio.user.properties
           python -m unittest discover -s ./mvesuvio/system_tests
 
       - name: Run mvesuvio Calibration Unit Tests
@@ -54,4 +53,4 @@ jobs:
 
       # Report coverage
       #- name: Report Coverage
-      #  run: coverage report
+      #  run: coverage report

.gitignore

@@ -7,3 +7,4 @@ output_npz_for_testing
 vesuvio_analysis/core_functions/bootstrap_ws/
 running_times.txt
 figures/
+mvesuvio/system_tests/test_config/expr_for_tests/output_files

mvesuvio/__init__.py

@@ -6,8 +6,7 @@
 nuclear kinetic energies and moment distributions.
 """
 
-version_info = (0, 0, 0)
-__version__ = ".".join(map(str, version_info))
+from mvesuvio._version import __version__
 __project_url__ = "https://github.com/mantidproject/vesuvio"
 
 from mvesuvio.scripts import main
@@ -21,19 +20,14 @@ def command(self):
         return self.__command
 
 class ConfigArgInputs(ArgInputs):
-    def __init__(self, set_cache, set_experiment, set_ipfolder):
+    def __init__(self, set_inputs, set_ipfolder):
         super().__init__("config")
-        self.__set_cache = set_cache
-        self.__set_experiment = set_experiment
+        self.__set_inputs = set_inputs
         self.__set_ipfolder = set_ipfolder
 
     @property
-    def set_cache(self):
-        return self.__set_cache
-
-    @property
-    def set_experiment(self):
-        return self.__set_experiment
+    def set_inputs(self):
+        return self.__set_inputs
 
     @property
     def set_ipfolder(self):
@@ -50,8 +44,8 @@ def yes(self):
         return self.__yes
 
 
-def set_config(cache_directory="", experiment_id="", ip_folder=""):
-    config_args = ConfigArgInputs(cache_directory, experiment_id, ip_folder)
+def set_config(inputs_file="", ip_folder=""):
+    config_args = ConfigArgInputs(inputs_file, ip_folder)
     main(config_args)
 
 def run(yes_to_all=False):

mvesuvio/_version.py

@@ -0,0 +1 @@
+__version__ = "0.0.0"

mvesuvio/analysis_runner.py

@@ -7,14 +7,9 @@
 
 
 def run(yes_to_all=False):
-    scriptName = handle_config.read_config_var("caching.experiment")
-    experimentsPath = (
-        Path(handle_config.read_config_var("caching.location"))
-        / "experiments"
-        / scriptName
-    )  # Path to the repository
-    inputs_path = experimentsPath / "analysis_inputs.py"
+    inputs_path = Path(handle_config.read_config_var("caching.inputs"))
     ipFilesPath = Path(handle_config.read_config_var("caching.ipfolder"))
+
     ai = import_from_path(inputs_path, "analysis_inputs")
 
     start_time = time.time()
@@ -29,7 +24,6 @@ def run(yes_to_all=False):
 
     runScript(
         userCtr,
-        scriptName,
         wsBackIC,
         wsFrontIC,
         bckwdIC,

mvesuvio/config/analysis_inputs.py

@@ -141,7 +141,7 @@ class YSpaceFitInitialConditions:
     showPlots = True
     symmetrisationFlag = True
     rebinParametersForYSpaceFit = "-25, 0.5, 25"  # Needs to be symetric
-    fitModel = "Gaussian3D"  # Options: 'SINGLE_GAUSSIAN', 'GC_C4', 'GC_C6', 'GC_C4_C6', 'DOUBLE_WELL', 'ANSIO_GAUSSIAN', 'Gaussian3D'
+    fitModel = "SINGLE_GAUSSIAN"  # Options: 'SINGLE_GAUSSIAN', 'GC_C4', 'GC_C6', 'GC_C4_C6', 'DOUBLE_WELL', 'ANSIO_GAUSSIAN', 'Gaussian3D'
     runMinos = True
     globalFit = True  # Performs global fit with Minuit by default
     nGlobalFitGroups = 4  # Number or string "ALL"
@@ -160,3 +160,14 @@ class UserScriptControls:
 
 class BootstrapInitialConditions:
     runBootstrap = False
+
+
+####################
+### RUN ANALYSIS ###
+####################
+
+if (__name__ == "__main__") or (__name__ == "mantidqt.widgets.codeeditor.execution"):
+    import mvesuvio
+    from pathlib import Path
+    mvesuvio.set_config(inputs_file=Path(__file__))
+    mvesuvio.run()

mvesuvio/config/vesuvio.user.properties

@@ -1,4 +1,3 @@
 # properties that suit your particular installation.
-caching.location=
-caching.experiment=
+caching.inputs=
 caching.ipfolder=

mvesuvio/scripts/__init__.py

@@ -15,19 +15,21 @@ def main(manual_args=None):
             __setup_config(None)
         __run_analysis(args.yes)
 
+
 def __setup_and_parse_args():
     parser = __set_up_parser()
     args = parser.parse_args()
     return args
 
+
 def __set_up_parser():
     parser = argparse.ArgumentParser(
         description="Package to analyse Vesuvio instrument data"
     )
     subparsers = parser.add_subparsers(dest="command", required=True)
     config_parser = subparsers.add_parser("config", help="set mvesuvio configuration")
     config_parser.add_argument(
-        "--set-cache", "-c", help="set the cache directory", default="", type=str
+        "--set-inputs", "-i", help="set the inputs python file", default="", type=str
     )
     config_parser.add_argument(
         "--set-ipfolder",
@@ -36,13 +38,6 @@ def __set_up_parser():
         default="",
         type=str,
     )
-    config_parser.add_argument(
-        "--set-experiment",
-        "-e",
-        help="set the current experiment",
-        default="",
-        type=str,
-    )
 
     run_parser = subparsers.add_parser("run", help="run mvesuvio analysis")
     run_parser.add_argument(
@@ -55,42 +50,36 @@ def __setup_config(args):
     config_dir = handle_config.VESUVIO_CONFIG_PATH
     handle_config.setup_config_dir(config_dir)
     ipfolder_dir = handle_config.VESUVIO_IPFOLDER_PATH
+    inputs = handle_config.VESUVIO_INPUTS_PATH
 
     if handle_config.config_set():
-        cache_dir = (
-            handle_config.read_config_var("caching.location")
-            if not args or not args.set_cache
-            else args.set_cache
-        )
-        experiment = (
-            handle_config.read_config_var("caching.experiment")
-            if not args or not args.set_experiment
-            else args.set_experiment
+        inputs = (
+            handle_config.read_config_var("caching.inputs")
+            if not args or not args.set_inputs
+            else args.set_inputs
         )
         ipfolder_dir = (
             handle_config.read_config_var("caching.ipfolder")
             if not args or not args.set_ipfolder
             else args.set_ipfolder
         )
     else:
-        cache_dir = config_dir if not args or not args.set_cache else args.set_cache
-        experiment = (
-            "default" if not args or not args.set_experiment else args.set_experiment
+        inputs = (
+            inputs if not args or not args.set_inputs else args.set_inputs
         )
         ipfolder_dir = (
             ipfolder_dir if not args or not args.set_ipfolder else args.set_ipfolder
         )
 
         handle_config.setup_default_ipfile_dir()
+        handle_config.setup_default_inputs()
 
     handle_config.set_config_vars(
         {
-            "caching.location": cache_dir,
-            "caching.experiment": experiment,
+            "caching.inputs": inputs,
             "caching.ipfolder": ipfolder_dir,
         }
     )
-    handle_config.setup_expr_dir(cache_dir, experiment)
     handle_config.check_dir_exists("IP folder", ipfolder_dir)
 
 

mvesuvio/scripts/handle_config.py

@@ -15,6 +15,7 @@ def __parse_config_env_var():
 ### PATH CONSTANTS ###
 VESUVIO_CONFIG_PATH, VESUVIO_CONFIG_FILE = __parse_config_env_var()
 VESUVIO_INPUTS_FILE = "analysis_inputs.py"
+VESUVIO_INPUTS_PATH = os.path.join(VESUVIO_CONFIG_PATH, VESUVIO_INPUTS_FILE)
 VESUVIO_PACKAGE_PATH = os.path.dirname(os.path.dirname(os.path.abspath(__file__)))
 MANTID_CONFIG_FILE = "Mantid.user.properties"
 VESUVIO_IPFOLDER_PATH = os.path.join(VESUVIO_CONFIG_PATH, "ip_files")
@@ -70,6 +71,12 @@ def read_config_var(var, throw_on_not_found=True):
     return result
 
 
+def get_script_name():
+    filename = os.path.basename(read_config_var("caching.inputs"))
+    scriptName = filename.removesuffix(".py")
+    return scriptName
+
+
 def setup_config_dir(config_dir):
     success = __mk_dir("config", config_dir)
     if success:
@@ -83,13 +90,11 @@ def setup_config_dir(config_dir):
         )
 
 
-def setup_expr_dir(cache_dir, experiment):
-    expr_path = os.path.join(cache_dir, "experiments", experiment)
-    success = __mk_dir("experiment", expr_path)
-    if success:
+def setup_default_inputs():
+    if not os.path.isfile(VESUVIO_INPUTS_PATH):
         copyfile(
             os.path.join(VESUVIO_PACKAGE_PATH, "config", VESUVIO_INPUTS_FILE),
-            input_file_path(cache_dir, experiment),
+            os.path.join(VESUVIO_INPUTS_PATH),
         )
 
 
@@ -114,16 +119,12 @@ def __mk_dir(type, path):
 
 
 def config_set():
-    if read_config_var("caching.location", False):
+    if read_config_var("caching.inputs", False):
         return True
     else:
         return False
 
 
-def input_file_path(cache_dir, experiment):
-    return os.path.join(cache_dir, "experiments", experiment, VESUVIO_INPUTS_FILE)
-
-
 def check_dir_exists(type, path):
     if not os.path.isdir(path):
         print(f"Directory of {type} could not be found at location: {path}")

mvesuvio/system_tests/test_analysis.py

@@ -4,7 +4,7 @@
 import numpy.testing as nptest
 from pathlib import Path
 from mvesuvio.scripts import handle_config
-from mvesuvio.system_tests.analysis_inputs import (
+from mvesuvio.system_tests.test_config.expr_for_tests import (
     LoadVesuvioBackParameters,
     LoadVesuvioFrontParameters,
     BackwardInitialConditions,
@@ -13,7 +13,11 @@
     BootstrapInitialConditions,
     UserScriptControls,
 )
-
+import mvesuvio
+mvesuvio.set_config(
+    ip_folder=str(Path(handle_config.VESUVIO_PACKAGE_PATH).joinpath("config", "ip_files")),
+    inputs_file=str(Path(handle_config.VESUVIO_PACKAGE_PATH).joinpath("system_tests", "test_config", "expr_for_tests.py"))
+)
 
 ipFilesPath = Path(handle_config.read_config_var("caching.ipfolder"))
 
@@ -38,7 +42,6 @@ def get_current_result(cls):
     def _run(cls):
         scattRes, yfitRes = runScript(
             UserScriptControls(),
-            "test_expr",
             LoadVesuvioBackParameters(ipFilesPath),
             LoadVesuvioFrontParameters(ipFilesPath),
             BackwardInitialConditions(ipFilesPath),

mvesuvio/system_tests/test_bootstrap.py

@@ -1,18 +1,20 @@
+
+# This file needs updating once the bootstrap functunality is properly
+# implemented in the mvesuvio package
+
 from mvesuvio.vesuvio_analysis.run_script import runScript
 import unittest
 import numpy as np
 import numpy.testing as nptest
 from pathlib import Path
 from mvesuvio.system_tests.tests_IC import (
-    scriptName,
     wsBackIC,
     wsFrontIC,
     bckwdIC,
     fwdIC,
     yFitIC,
 )
 
-
 class BootstrapInitialConditions:
     runBootstrap = True
 
@@ -45,7 +47,7 @@ def _run_analysis(cls):
         yFitIC.symmetrisationFlag = True
 
         bootRes, noneRes = runScript(
-            userCtr, scriptName, wsBackIC, wsFrontIC, bckwdIC, fwdIC, yFitIC, bootIC, True
+            userCtr, wsBackIC, wsFrontIC, bckwdIC, fwdIC, yFitIC, bootIC, True
         )
 
         # TODO: Figure out why doing the two tests simultaneously fails the testing

mvesuvio/system_tests/analysis_inputs.py → mvesuvio/system_tests/test_config/expr_for_tests.py

@@ -107,7 +107,14 @@ def __init__(self, ipFilesPath):
 
 
 class YSpaceFitInitialConditions:
-    anything = True
+    showPlots = False
+    symmetrisationFlag = True
+    rebinParametersForYSpaceFit = "-20, 0.5, 20"  # Needs to be symetric
+    fitModel = "SINGLE_GAUSSIAN"
+    runMinos = True
+    globalFit = None
+    nGlobalFitGroups = 4
+    maskTypeProcedure = None
 
 
 class UserScriptControls:

mvesuvio/system_tests/test_jackknife.py

@@ -1,10 +1,13 @@
+
+# This file needs updating once the bootstrap functunality is properly
+# implemented in the mvesuvio package
+
 from mvesuvio.vesuvio_analysis.run_script import runScript
 import unittest
 import numpy as np
 import numpy.testing as nptest
 from pathlib import Path
 from mvesuvio.system_tests.tests_IC import (
-    scriptName,
     wsBackIC,
     wsFrontIC,
     bckwdIC,
@@ -42,7 +45,7 @@ def _run_analysis(cls):
         userCtr = UserScriptControls
 
         bootRes, noneRes = runScript(
-            userCtr, scriptName, wsBackIC, wsFrontIC, bckwdIC, fwdIC, yFitIC, bootIC, True
+            userCtr, wsBackIC, wsFrontIC, bckwdIC, fwdIC, yFitIC, bootIC, True
         )
 
         cls._jackBackSamples = bootRes["bckwdScat"].bootSamples