diff --git a/.github/workflows/ci_tests_nightly.yml b/.github/workflows/ci_tests_nightly.yml index 92bc129c..0203624f 100644 --- a/.github/workflows/ci_tests_nightly.yml +++ b/.github/workflows/ci_tests_nightly.yml @@ -28,10 +28,10 @@ jobs: - name: Run mvesuvio analysis unit tests run: | export MANTIDPROPERTIES=$(pwd)/Mantid.user.properties - python -m unittest discover -s ./EVSVesuvio/vesuvio_analysis/tests + python -m unittest discover -s ./mvesuvio/vesuvio_analysis/tests # Runs System tests - name: Run mvesuvio analysis system tests run: | - export VESUVIOPROPERTIES=$(pwd)/EVSVesuvio/system_tests/test_config/vesuvio.user.properties - python -m unittest discover -s ./EVSVesuvio/system_tests \ No newline at end of file + export VESUVIOPROPERTIES=$(pwd)/mvesuvio/system_tests/test_config/vesuvio.user.properties + python -m unittest discover -s ./mvesuvio/system_tests \ No newline at end of file diff --git a/.github/workflows/pr_workflow.yml b/.github/workflows/pr_workflow.yml index 6a4ef6fe..a15da777 100644 --- a/.github/workflows/pr_workflow.yml +++ b/.github/workflows/pr_workflow.yml @@ -1,4 +1,4 @@ -name: EVSVesuvio pull request workflow +name: mvesuvio pull request workflow on: push @@ -30,18 +30,18 @@ jobs: # Remove `export MANTIDPROPERTIES=$(pwd)/Mantid.user.properties` when updated to mantid > 6.8.0 # Runs Unit tests - - name: Run EVSVesuvio Analysis Unit Tests + - name: Run mvesuvio Analysis Unit Tests run: | export MANTIDPROPERTIES=$(pwd)/Mantid.user.properties - python -m unittest discover -s ./EVSVesuvio/vesuvio_analysis/tests + python -m unittest discover -s ./mvesuvio/vesuvio_analysis/tests # Runs System tests - - name: Run EVSVesuvio Analysis System Tests + - name: Run mvesuvio Analysis System Tests run: | - export VESUVIOPROPERTIES=$(pwd)/EVSVesuvio/system_tests/test_config/vesuvio.user.properties - python -m unittest discover -s ./EVSVesuvio/system_tests + export VESUVIOPROPERTIES=$(pwd)/mvesuvio/system_tests/test_config/vesuvio.user.properties + python -m unittest discover -s ./mvesuvio/system_tests - - name: Run EVSVesuvio Calibration Unit Tests + - name: Run mvesuvio Calibration Unit Tests run: | export MANTIDPROPERTIES=$(pwd)/Mantid.user.properties cd unpackaged/vesuvio_calibration diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index b866a44d..eb898661 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -8,15 +8,15 @@ repos: hooks: - id: trailing-whitespace args: [--markdown-linebreak-ext=md] - exclude: 'EVSVesuvio/vesuvio_analysis/scribles|EVSVesuvio/experiments/original_inputs|EVSVesuvio/original_inputs.py|unpackaged' + exclude: 'mvesuvio/vesuvio_analysis/scribles|mvesuvio/experiments/original_inputs|mvesuvio/original_inputs.py|unpackaged' types: ['python'] - id: check-added-large-files args: ['--maxkb=4096'] - exclude: 'EVSVesuvio/experiments/original_inputs|unpackaged' + exclude: 'mvesuvio/experiments/original_inputs|unpackaged' - repo: https://github.com/PyCQA/flake8.git rev: 6.1.0 hooks: - id: flake8 args: ['--config', 'config.flake8'] - exclude: 'EVSVesuvio/vesuvio_analysis/scribles|EVSVesuvio/experiments/original_inputs|EVSVesuvio/original_inputs.py|unpackaged' + exclude: 'mvesuvio/vesuvio_analysis/scribles|mvesuvio/experiments/original_inputs|mvesuvio/original_inputs.py|unpackaged' diff --git a/EVSVesuvio/system_tests/test_config/vesuvio.user.properties b/EVSVesuvio/system_tests/test_config/vesuvio.user.properties deleted file mode 100644 index 11d27a18..00000000 --- a/EVSVesuvio/system_tests/test_config/vesuvio.user.properties +++ /dev/null @@ -1,4 +0,0 @@ -# properties to be used in CI testing. -caching.location=EVSVesuvio/system_tests/test_config -caching.experiment=test_expr -caching.ipfolder=EVSVesuvio/config/ip_files diff --git a/conda/meta.yaml b/conda/meta.yaml index 15950ccb..e78f2e05 100644 --- a/conda/meta.yaml +++ b/conda/meta.yaml @@ -15,7 +15,7 @@ build: noarch: python script: python -m pip install --ignore-installed . entry_points: - - mvesuvio = EVSVesuvio.scripts:main + - mvesuvio = mvesuvio.scripts:main requirements: build: @@ -32,7 +32,7 @@ requirements: test: imports: - - EVSVesuvio + - mvesuvio about: home: https://github.com/mantidproject/vesuvio diff --git a/EVSVesuvio/__init__.py b/mvesuvio/__init__.py similarity index 97% rename from EVSVesuvio/__init__.py rename to mvesuvio/__init__.py index 0a11c64f..abbaac84 100644 --- a/EVSVesuvio/__init__.py +++ b/mvesuvio/__init__.py @@ -10,7 +10,7 @@ __version__ = ".".join(map(str, version_info)) __project_url__ = "https://github.com/mantidproject/vesuvio" -from EVSVesuvio.scripts import main +from mvesuvio.scripts import main class ArgInputs: def __init__(self, command): diff --git a/EVSVesuvio/analysis_runner.py b/mvesuvio/analysis_runner.py similarity index 93% rename from EVSVesuvio/analysis_runner.py rename to mvesuvio/analysis_runner.py index 51c79a93..00b58005 100644 --- a/EVSVesuvio/analysis_runner.py +++ b/mvesuvio/analysis_runner.py @@ -2,8 +2,8 @@ from pathlib import Path import importlib import sys -from EVSVesuvio.vesuvio_analysis.run_script import runScript -from EVSVesuvio.scripts import handle_config +from mvesuvio.vesuvio_analysis.run_script import runScript +from mvesuvio.scripts import handle_config def run(yes_to_all=False): diff --git a/EVSVesuvio/config/Mantid.user.properties b/mvesuvio/config/Mantid.user.properties similarity index 100% rename from EVSVesuvio/config/Mantid.user.properties rename to mvesuvio/config/Mantid.user.properties diff --git a/EVSVesuvio/config/__init__.py b/mvesuvio/config/__init__.py similarity index 100% rename from EVSVesuvio/config/__init__.py rename to mvesuvio/config/__init__.py diff --git a/EVSVesuvio/config/analysis_inputs.py b/mvesuvio/config/analysis_inputs.py similarity index 100% rename from EVSVesuvio/config/analysis_inputs.py rename to mvesuvio/config/analysis_inputs.py diff --git a/EVSVesuvio/config/ip_files/__init__.py b/mvesuvio/config/ip_files/__init__.py similarity index 100% rename from EVSVesuvio/config/ip_files/__init__.py rename to mvesuvio/config/ip_files/__init__.py diff --git a/EVSVesuvio/config/ip_files/ip2018.par b/mvesuvio/config/ip_files/ip2018.par similarity index 100% rename from EVSVesuvio/config/ip_files/ip2018.par rename to mvesuvio/config/ip_files/ip2018.par diff --git a/EVSVesuvio/config/ip_files/ip2018_2.par b/mvesuvio/config/ip_files/ip2018_2.par similarity index 100% rename from EVSVesuvio/config/ip_files/ip2018_2.par rename to mvesuvio/config/ip_files/ip2018_2.par diff --git a/EVSVesuvio/config/ip_files/ip2018_3.par b/mvesuvio/config/ip_files/ip2018_3.par similarity index 100% rename from EVSVesuvio/config/ip_files/ip2018_3.par rename to mvesuvio/config/ip_files/ip2018_3.par diff --git a/EVSVesuvio/config/ip_files/ip2019.par b/mvesuvio/config/ip_files/ip2019.par similarity index 100% rename from EVSVesuvio/config/ip_files/ip2019.par rename to mvesuvio/config/ip_files/ip2019.par diff --git a/EVSVesuvio/config/vesuvio.user.properties b/mvesuvio/config/vesuvio.user.properties similarity index 100% rename from EVSVesuvio/config/vesuvio.user.properties rename to mvesuvio/config/vesuvio.user.properties diff --git a/EVSVesuvio/scripts/__init__.py b/mvesuvio/scripts/__init__.py similarity index 97% rename from EVSVesuvio/scripts/__init__.py rename to mvesuvio/scripts/__init__.py index 18ebd86e..7615d88e 100644 --- a/EVSVesuvio/scripts/__init__.py +++ b/mvesuvio/scripts/__init__.py @@ -2,7 +2,7 @@ """ import argparse from os import environ, path -from EVSVesuvio.scripts import handle_config +from mvesuvio.scripts import handle_config def main(manual_args=None): @@ -98,7 +98,7 @@ def __run_analysis(yes_to_all): environ["MANTIDPROPERTIES"] = path.join( handle_config.VESUVIO_CONFIG_PATH, "Mantid.user.properties" ) - from EVSVesuvio import analysis_runner + from mvesuvio import analysis_runner analysis_runner.run(yes_to_all) diff --git a/EVSVesuvio/scripts/handle_config.py b/mvesuvio/scripts/handle_config.py similarity index 100% rename from EVSVesuvio/scripts/handle_config.py rename to mvesuvio/scripts/handle_config.py diff --git a/EVSVesuvio/system_tests/__init__.py b/mvesuvio/system_tests/__init__.py similarity index 100% rename from EVSVesuvio/system_tests/__init__.py rename to mvesuvio/system_tests/__init__.py diff --git a/EVSVesuvio/system_tests/old_new_comparison_inputs.py b/mvesuvio/system_tests/old_new_comparison_inputs.py similarity index 100% rename from EVSVesuvio/system_tests/old_new_comparison_inputs.py rename to mvesuvio/system_tests/old_new_comparison_inputs.py diff --git a/EVSVesuvio/system_tests/stored_analysis.npz b/mvesuvio/system_tests/stored_analysis.npz similarity index 100% rename from EVSVesuvio/system_tests/stored_analysis.npz rename to mvesuvio/system_tests/stored_analysis.npz diff --git a/EVSVesuvio/system_tests/stored_boot_back.npz b/mvesuvio/system_tests/stored_boot_back.npz similarity index 100% rename from EVSVesuvio/system_tests/stored_boot_back.npz rename to mvesuvio/system_tests/stored_boot_back.npz diff --git a/EVSVesuvio/system_tests/stored_boot_front.npz b/mvesuvio/system_tests/stored_boot_front.npz similarity index 100% rename from EVSVesuvio/system_tests/stored_boot_front.npz rename to mvesuvio/system_tests/stored_boot_front.npz diff --git a/EVSVesuvio/system_tests/stored_boot_yfit.npz b/mvesuvio/system_tests/stored_boot_yfit.npz similarity index 100% rename from EVSVesuvio/system_tests/stored_boot_yfit.npz rename to mvesuvio/system_tests/stored_boot_yfit.npz diff --git a/EVSVesuvio/system_tests/stored_joint_jack_back.npz b/mvesuvio/system_tests/stored_joint_jack_back.npz similarity index 100% rename from EVSVesuvio/system_tests/stored_joint_jack_back.npz rename to mvesuvio/system_tests/stored_joint_jack_back.npz diff --git a/EVSVesuvio/system_tests/stored_joint_jack_front.npz b/mvesuvio/system_tests/stored_joint_jack_front.npz similarity index 100% rename from EVSVesuvio/system_tests/stored_joint_jack_front.npz rename to mvesuvio/system_tests/stored_joint_jack_front.npz diff --git a/EVSVesuvio/system_tests/stored_single_boot_back.npz b/mvesuvio/system_tests/stored_single_boot_back.npz similarity index 100% rename from EVSVesuvio/system_tests/stored_single_boot_back.npz rename to mvesuvio/system_tests/stored_single_boot_back.npz diff --git a/EVSVesuvio/system_tests/stored_single_boot_back_yfit.npz b/mvesuvio/system_tests/stored_single_boot_back_yfit.npz similarity index 100% rename from EVSVesuvio/system_tests/stored_single_boot_back_yfit.npz rename to mvesuvio/system_tests/stored_single_boot_back_yfit.npz diff --git a/EVSVesuvio/system_tests/stored_spec_144-182_iter_3_GC_MS.npz b/mvesuvio/system_tests/stored_spec_144-182_iter_3_GC_MS.npz similarity index 100% rename from EVSVesuvio/system_tests/stored_spec_144-182_iter_3_GC_MS.npz rename to mvesuvio/system_tests/stored_spec_144-182_iter_3_GC_MS.npz diff --git a/EVSVesuvio/system_tests/stored_yspace_fit.npz b/mvesuvio/system_tests/stored_yspace_fit.npz similarity index 100% rename from EVSVesuvio/system_tests/stored_yspace_fit.npz rename to mvesuvio/system_tests/stored_yspace_fit.npz diff --git a/EVSVesuvio/system_tests/stored_yspace_fit_GC.npz b/mvesuvio/system_tests/stored_yspace_fit_GC.npz similarity index 100% rename from EVSVesuvio/system_tests/stored_yspace_fit_GC.npz rename to mvesuvio/system_tests/stored_yspace_fit_GC.npz diff --git a/EVSVesuvio/system_tests/test_analysis.py b/mvesuvio/system_tests/test_analysis.py similarity index 98% rename from EVSVesuvio/system_tests/test_analysis.py rename to mvesuvio/system_tests/test_analysis.py index b93415b2..eef97e20 100644 --- a/EVSVesuvio/system_tests/test_analysis.py +++ b/mvesuvio/system_tests/test_analysis.py @@ -1,9 +1,9 @@ -from EVSVesuvio.vesuvio_analysis.run_script import runScript +from mvesuvio.vesuvio_analysis.run_script import runScript import unittest import numpy as np import numpy.testing as nptest from pathlib import Path -from EVSVesuvio.system_tests.tests_IC import ( +from mvesuvio.system_tests.tests_IC import ( scriptName, wsBackIC, wsFrontIC, diff --git a/EVSVesuvio/system_tests/test_bootstrap.py b/mvesuvio/system_tests/test_bootstrap.py similarity index 97% rename from EVSVesuvio/system_tests/test_bootstrap.py rename to mvesuvio/system_tests/test_bootstrap.py index 6f2f4072..d61f09bc 100644 --- a/EVSVesuvio/system_tests/test_bootstrap.py +++ b/mvesuvio/system_tests/test_bootstrap.py @@ -1,9 +1,9 @@ -from EVSVesuvio.vesuvio_analysis.run_script import runScript +from mvesuvio.vesuvio_analysis.run_script import runScript import unittest import numpy as np import numpy.testing as nptest from pathlib import Path -from EVSVesuvio.system_tests.tests_IC import ( +from mvesuvio.system_tests.tests_IC import ( scriptName, wsBackIC, wsFrontIC, diff --git a/mvesuvio/system_tests/test_config/experiments/test_expr/bootstrap_data/with_MS_corrections/data_files_log.txt b/mvesuvio/system_tests/test_config/experiments/test_expr/bootstrap_data/with_MS_corrections/data_files_log.txt new file mode 100644 index 00000000..34595752 --- /dev/null +++ b/mvesuvio/system_tests/test_config/experiments/test_expr/bootstrap_data/with_MS_corrections/data_files_log.txt @@ -0,0 +1,26 @@ + + This file contains some information about each data file in the folder. + ncp data file: boot type | procedure | tof binning | masked tof range. + yspace fit data file: boot type | procedure | symmetrisation | rebin pars | fit model | mask type + +spec_3-13_iter_0_nsampl_3.npz : BOOT_RESIDUALS | JOINT | 275.,1.,420 | None +spec_164-175_iter_1_MS_GC_nsampl_3.npz : BOOT_RESIDUALS | JOINT | 110,1.,430 | None +spec_164-175_iter_1_MS_GC_ySpaceFit_nsampl_3.npz : BOOT_RESIDUALS | FORWARD | True | -20, 0.5, 20 | SINGLE_GAUSSIAN | None +spec_3-13_iter_0_nsampl_3.npz : BOOT_RESIDUALS | JOINT | 275.,1.,420 | None +spec_164-175_iter_1_MS_GC_nsampl_3.npz : BOOT_RESIDUALS | JOINT | 110,1.,430 | None +spec_164-175_iter_1_MS_GC_ySpaceFit_nsampl_3.npz : BOOT_RESIDUALS | FORWARD | True | -20, 0.5, 20 | SINGLE_GAUSSIAN | None +spec_3-13_iter_0_nsampl_3.npz : BOOT_RESIDUALS | JOINT | 275.,1.,420 | None +spec_164-175_iter_1_MS_GC_nsampl_3.npz : BOOT_RESIDUALS | JOINT | 110,1.,430 | None +spec_164-175_iter_1_MS_GC_ySpaceFit_nsampl_3.npz : BOOT_RESIDUALS | FORWARD | True | -20, 0.5, 20 | SINGLE_GAUSSIAN | None +spec_3-13_iter_0_nsampl_3.npz : BOOT_RESIDUALS | JOINT | 275.,1.,420 | None +spec_164-175_iter_1_MS_GC_nsampl_3.npz : BOOT_RESIDUALS | JOINT | 110,1.,430 | None +spec_164-175_iter_1_MS_GC_ySpaceFit_nsampl_3.npz : BOOT_RESIDUALS | FORWARD | True | -20, 0.5, 20 | SINGLE_GAUSSIAN | None +spec_3-13_iter_0_nsampl_3.npz : BOOT_RESIDUALS | JOINT | 275.,1.,420 | None +spec_164-175_iter_1_MS_GC_nsampl_3.npz : BOOT_RESIDUALS | JOINT | 110,1.,430 | None +spec_164-175_iter_1_MS_GC_ySpaceFit_nsampl_3.npz : BOOT_RESIDUALS | FORWARD | True | -20, 0.5, 20 | SINGLE_GAUSSIAN | None +spec_3-13_iter_0_nsampl_3.npz : BOOT_RESIDUALS | JOINT | 275.,1.,420 | None +spec_164-175_iter_1_MS_GC_nsampl_3.npz : BOOT_RESIDUALS | JOINT | 110,1.,430 | None +spec_164-175_iter_1_MS_GC_ySpaceFit_nsampl_3.npz : BOOT_RESIDUALS | FORWARD | True | -20, 0.5, 20 | SINGLE_GAUSSIAN | None +spec_3-13_iter_0_nsampl_3.npz : BOOT_RESIDUALS | JOINT | 275.,1.,420 | None +spec_164-175_iter_1_MS_GC_nsampl_3.npz : BOOT_RESIDUALS | JOINT | 110,1.,430 | None +spec_164-175_iter_1_MS_GC_ySpaceFit_nsampl_3.npz : BOOT_RESIDUALS | FORWARD | True | -20, 0.5, 20 | SINGLE_GAUSSIAN | None \ No newline at end of file diff --git a/mvesuvio/system_tests/test_config/experiments/test_expr/bootstrap_data/with_MS_corrections/spec_164-175_iter_1_MS_GC_nsampl_3.npz b/mvesuvio/system_tests/test_config/experiments/test_expr/bootstrap_data/with_MS_corrections/spec_164-175_iter_1_MS_GC_nsampl_3.npz new file mode 100644 index 00000000..24a1d9b2 Binary files /dev/null and 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differ diff --git a/mvesuvio/system_tests/test_config/experiments/test_expr/jackknife_data/with_MS_corrections/data_files_log.txt b/mvesuvio/system_tests/test_config/experiments/test_expr/jackknife_data/with_MS_corrections/data_files_log.txt new file mode 100644 index 00000000..50604c64 --- /dev/null +++ b/mvesuvio/system_tests/test_config/experiments/test_expr/jackknife_data/with_MS_corrections/data_files_log.txt @@ -0,0 +1,33 @@ + + This file contains some information about each data file in the folder. + ncp data file: boot type | procedure | tof binning | masked tof range. + yspace fit data file: boot type | procedure | symmetrisation | rebin pars | fit model | mask type + +spec_3-13_iter_0_nsampl_3.npz : JACKKNIFE | JOINT | 275.,1.,420 | None +spec_3-13_iter_0_ySpaceFit_nsampl_3.npz : JACKKNIFE | None | True | -20, 0.5, 20 | SINGLE_GAUSSIAN | None +spec_164-175_iter_1_MS_GC_nsampl_3.npz : JACKKNIFE | JOINT | 110,1.,430 | None +spec_164-175_iter_1_MS_GC_ySpaceFit_nsampl_3.npz : JACKKNIFE | None | True | -20, 0.5, 20 | SINGLE_GAUSSIAN | None +spec_3-13_iter_0_nsampl_3.npz : JACKKNIFE | JOINT | 275.,1.,420 | None +spec_3-13_iter_0_ySpaceFit_nsampl_3.npz : JACKKNIFE | None | True | -20, 0.5, 20 | SINGLE_GAUSSIAN | None +spec_164-175_iter_1_MS_GC_nsampl_3.npz : JACKKNIFE | JOINT | 110,1.,430 | None +spec_164-175_iter_1_MS_GC_ySpaceFit_nsampl_3.npz : JACKKNIFE | None | True | -20, 0.5, 20 | SINGLE_GAUSSIAN | None +spec_3-13_iter_0_nsampl_3.npz : JACKKNIFE | JOINT | 275.,1.,420 | None +spec_3-13_iter_0_ySpaceFit_nsampl_3.npz : JACKKNIFE | None | True | -20, 0.5, 20 | SINGLE_GAUSSIAN | None +spec_164-175_iter_1_MS_GC_nsampl_3.npz : JACKKNIFE | JOINT | 110,1.,430 | None +spec_164-175_iter_1_MS_GC_ySpaceFit_nsampl_3.npz : JACKKNIFE | None | True | -20, 0.5, 20 | SINGLE_GAUSSIAN | None +spec_3-13_iter_0_nsampl_3.npz : JACKKNIFE | JOINT | 275.,1.,420 | None +spec_3-13_iter_0_ySpaceFit_nsampl_3.npz : JACKKNIFE | None | True | -20, 0.5, 20 | SINGLE_GAUSSIAN | None +spec_164-175_iter_1_MS_GC_nsampl_3.npz : JACKKNIFE | JOINT | 110,1.,430 | None +spec_164-175_iter_1_MS_GC_ySpaceFit_nsampl_3.npz : JACKKNIFE | None | True | -20, 0.5, 20 | SINGLE_GAUSSIAN | None +spec_3-13_iter_0_nsampl_3.npz : JACKKNIFE | JOINT | 275.,1.,420 | None +spec_3-13_iter_0_ySpaceFit_nsampl_3.npz : JACKKNIFE | None | True | -20, 0.5, 20 | SINGLE_GAUSSIAN | None +spec_164-175_iter_1_MS_GC_nsampl_3.npz : JACKKNIFE | JOINT | 110,1.,430 | None +spec_164-175_iter_1_MS_GC_ySpaceFit_nsampl_3.npz : JACKKNIFE | None | True | -20, 0.5, 20 | SINGLE_GAUSSIAN | None +spec_3-13_iter_0_nsampl_3.npz : JACKKNIFE | JOINT | 275.,1.,420 | None +spec_3-13_iter_0_ySpaceFit_nsampl_3.npz : JACKKNIFE | None | True | -20, 0.5, 20 | SINGLE_GAUSSIAN | None +spec_164-175_iter_1_MS_GC_nsampl_3.npz : JACKKNIFE | JOINT | 110,1.,430 | None +spec_164-175_iter_1_MS_GC_ySpaceFit_nsampl_3.npz : JACKKNIFE | None | True | -20, 0.5, 20 | SINGLE_GAUSSIAN | None +spec_3-13_iter_0_nsampl_3.npz : JACKKNIFE | JOINT | 275.,1.,420 | None +spec_3-13_iter_0_ySpaceFit_nsampl_3.npz : JACKKNIFE | None | True | -20, 0.5, 20 | SINGLE_GAUSSIAN | None +spec_164-175_iter_1_MS_GC_nsampl_3.npz : JACKKNIFE | JOINT | 110,1.,430 | None +spec_164-175_iter_1_MS_GC_ySpaceFit_nsampl_3.npz : JACKKNIFE | None | True | -20, 0.5, 20 | SINGLE_GAUSSIAN | None \ No newline at end of file diff --git a/mvesuvio/system_tests/test_config/experiments/test_expr/jackknife_data/with_MS_corrections/spec_164-175_iter_1_MS_GC_nsampl_3.npz b/mvesuvio/system_tests/test_config/experiments/test_expr/jackknife_data/with_MS_corrections/spec_164-175_iter_1_MS_GC_nsampl_3.npz new file mode 100644 index 00000000..72b15900 Binary files /dev/null and b/mvesuvio/system_tests/test_config/experiments/test_expr/jackknife_data/with_MS_corrections/spec_164-175_iter_1_MS_GC_nsampl_3.npz differ diff --git a/mvesuvio/system_tests/test_config/experiments/test_expr/jackknife_data/with_MS_corrections/spec_164-175_iter_1_MS_GC_ySpaceFit_nsampl_3.npz 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b/mvesuvio/system_tests/test_config/vesuvio.user.properties new file mode 100644 index 00000000..7bf33e58 --- /dev/null +++ b/mvesuvio/system_tests/test_config/vesuvio.user.properties @@ -0,0 +1,4 @@ +# properties to be used in CI testing. +caching.location=mvesuvio/system_tests/test_config +caching.experiment=test_expr +caching.ipfolder=mvesuvio/config/ip_files diff --git a/EVSVesuvio/system_tests/test_jackknife.py b/mvesuvio/system_tests/test_jackknife.py similarity index 94% rename from EVSVesuvio/system_tests/test_jackknife.py rename to mvesuvio/system_tests/test_jackknife.py index d93cf2f0..06eb2a61 100644 --- a/EVSVesuvio/system_tests/test_jackknife.py +++ b/mvesuvio/system_tests/test_jackknife.py @@ -1,9 +1,9 @@ -from EVSVesuvio.vesuvio_analysis.run_script import runScript +from mvesuvio.vesuvio_analysis.run_script import runScript import unittest import numpy as np import numpy.testing as nptest from pathlib import Path -from EVSVesuvio.system_tests.tests_IC import ( +from mvesuvio.system_tests.tests_IC import ( scriptName, wsBackIC, wsFrontIC, diff --git a/EVSVesuvio/system_tests/test_old_new_comparison.py b/mvesuvio/system_tests/test_old_new_comparison.py similarity index 97% rename from EVSVesuvio/system_tests/test_old_new_comparison.py rename to mvesuvio/system_tests/test_old_new_comparison.py index 0aaadf3c..2923f92f 100644 --- a/EVSVesuvio/system_tests/test_old_new_comparison.py +++ b/mvesuvio/system_tests/test_old_new_comparison.py @@ -1,10 +1,10 @@ -from EVSVesuvio.vesuvio_analysis.run_script import runScript +from mvesuvio.vesuvio_analysis.run_script import runScript import unittest import numpy as np import numpy.testing as nptest from pathlib import Path -from EVSVesuvio.scripts import handle_config -from EVSVesuvio.system_tests.old_new_comparison_inputs import ( +from mvesuvio.scripts import handle_config +from mvesuvio.system_tests.old_new_comparison_inputs import ( LoadVesuvioBackParameters, LoadVesuvioFrontParameters, BackwardInitialConditions, diff --git a/EVSVesuvio/system_tests/test_yspace_fit.py b/mvesuvio/system_tests/test_yspace_fit.py similarity index 98% rename from EVSVesuvio/system_tests/test_yspace_fit.py rename to mvesuvio/system_tests/test_yspace_fit.py index 2e36a483..10b3a83f 100644 --- a/EVSVesuvio/system_tests/test_yspace_fit.py +++ b/mvesuvio/system_tests/test_yspace_fit.py @@ -1,11 +1,11 @@ -from EVSVesuvio.vesuvio_analysis.run_script import runScript +from mvesuvio.vesuvio_analysis.run_script import runScript from mantid.simpleapi import Load from mantid.api import AnalysisDataService from pathlib import Path import numpy as np import unittest import numpy.testing as nptest -from EVSVesuvio.system_tests.tests_IC import ( +from mvesuvio.system_tests.tests_IC import ( scriptName, wsBackIC, wsFrontIC, diff --git a/EVSVesuvio/system_tests/test_yspace_fit_GC.py b/mvesuvio/system_tests/test_yspace_fit_GC.py similarity index 98% rename from EVSVesuvio/system_tests/test_yspace_fit_GC.py rename to mvesuvio/system_tests/test_yspace_fit_GC.py index b03b290b..a13a6dad 100644 --- a/EVSVesuvio/system_tests/test_yspace_fit_GC.py +++ b/mvesuvio/system_tests/test_yspace_fit_GC.py @@ -1,11 +1,11 @@ -from EVSVesuvio.vesuvio_analysis.run_script import runScript +from mvesuvio.vesuvio_analysis.run_script import runScript from mantid.simpleapi import Load from mantid.api import AnalysisDataService from pathlib import Path import numpy as np import unittest import numpy.testing as nptest -from EVSVesuvio.system_tests.tests_IC import ( +from mvesuvio.system_tests.tests_IC import ( scriptName, wsBackIC, wsFrontIC, diff --git a/EVSVesuvio/system_tests/tests_IC.py b/mvesuvio/system_tests/tests_IC.py similarity index 99% rename from EVSVesuvio/system_tests/tests_IC.py rename to mvesuvio/system_tests/tests_IC.py index 077a00cf..79bf4880 100644 --- a/EVSVesuvio/system_tests/tests_IC.py +++ b/mvesuvio/system_tests/tests_IC.py @@ -1,6 +1,6 @@ import numpy as np from pathlib import Path -from EVSVesuvio.scripts import handle_config +from mvesuvio.scripts import handle_config ipFilesPath = Path(handle_config.read_config_var("caching.ipfolder")) ipFilePath = ipFilesPath / "ip2018_3.par" diff --git a/EVSVesuvio/system_tests/wsFinal.nxs b/mvesuvio/system_tests/wsFinal.nxs similarity index 100% rename from EVSVesuvio/system_tests/wsFinal.nxs rename to mvesuvio/system_tests/wsFinal.nxs diff --git a/EVSVesuvio/system_tests/wsFinal_ncp_0.nxs b/mvesuvio/system_tests/wsFinal_ncp_0.nxs similarity index 100% rename from EVSVesuvio/system_tests/wsFinal_ncp_0.nxs rename to mvesuvio/system_tests/wsFinal_ncp_0.nxs diff --git a/EVSVesuvio/system_tests/wsFinal_ncp_1.nxs b/mvesuvio/system_tests/wsFinal_ncp_1.nxs similarity index 100% rename from EVSVesuvio/system_tests/wsFinal_ncp_1.nxs rename to mvesuvio/system_tests/wsFinal_ncp_1.nxs diff --git a/EVSVesuvio/system_tests/wsFinal_ncp_2.nxs b/mvesuvio/system_tests/wsFinal_ncp_2.nxs similarity index 100% rename from EVSVesuvio/system_tests/wsFinal_ncp_2.nxs rename to mvesuvio/system_tests/wsFinal_ncp_2.nxs diff --git a/EVSVesuvio/system_tests/wsFinal_ncp_3.nxs b/mvesuvio/system_tests/wsFinal_ncp_3.nxs similarity index 100% rename from EVSVesuvio/system_tests/wsFinal_ncp_3.nxs rename to mvesuvio/system_tests/wsFinal_ncp_3.nxs diff --git a/EVSVesuvio/vesuvio_analysis/ICHelpers.py b/mvesuvio/vesuvio_analysis/ICHelpers.py similarity index 99% rename from EVSVesuvio/vesuvio_analysis/ICHelpers.py rename to mvesuvio/vesuvio_analysis/ICHelpers.py index 7459fef0..19d2cfb9 100644 --- a/EVSVesuvio/vesuvio_analysis/ICHelpers.py +++ b/mvesuvio/vesuvio_analysis/ICHelpers.py @@ -1,6 +1,6 @@ from mantid.simpleapi import Load, LoadVesuvio, SaveNexus from pathlib import Path -from EVSVesuvio.scripts import handle_config +from mvesuvio.scripts import handle_config from mantid.kernel import logger import ntpath diff --git a/EVSVesuvio/vesuvio_analysis/__init__.py b/mvesuvio/vesuvio_analysis/__init__.py similarity index 100% rename from EVSVesuvio/vesuvio_analysis/__init__.py rename to mvesuvio/vesuvio_analysis/__init__.py diff --git a/EVSVesuvio/vesuvio_analysis/analysis_functions.py b/mvesuvio/vesuvio_analysis/analysis_functions.py similarity index 100% rename from EVSVesuvio/vesuvio_analysis/analysis_functions.py rename to mvesuvio/vesuvio_analysis/analysis_functions.py diff --git a/EVSVesuvio/vesuvio_analysis/bootstrap.py b/mvesuvio/vesuvio_analysis/bootstrap.py similarity index 99% rename from EVSVesuvio/vesuvio_analysis/bootstrap.py rename to mvesuvio/vesuvio_analysis/bootstrap.py index f64465d1..0467ff57 100644 --- a/EVSVesuvio/vesuvio_analysis/bootstrap.py +++ b/mvesuvio/vesuvio_analysis/bootstrap.py @@ -1,9 +1,9 @@ -from EVSVesuvio.vesuvio_analysis.fit_in_yspace import fitInYSpaceProcedure -from EVSVesuvio.vesuvio_analysis.procedures import ( +from mvesuvio.vesuvio_analysis.fit_in_yspace import fitInYSpaceProcedure +from mvesuvio.vesuvio_analysis.procedures import ( runJointBackAndForwardProcedure, runIndependentIterativeProcedure, ) -from EVSVesuvio.vesuvio_analysis.ICHelpers import ( +from mvesuvio.vesuvio_analysis.ICHelpers import ( buildFinalWSName, noOfHistsFromTOFBinning, ) diff --git a/EVSVesuvio/vesuvio_analysis/bootstrap_analysis.py b/mvesuvio/vesuvio_analysis/bootstrap_analysis.py similarity index 99% rename from EVSVesuvio/vesuvio_analysis/bootstrap_analysis.py rename to mvesuvio/vesuvio_analysis/bootstrap_analysis.py index c39d07f3..d5319362 100644 --- a/EVSVesuvio/vesuvio_analysis/bootstrap_analysis.py +++ b/mvesuvio/vesuvio_analysis/bootstrap_analysis.py @@ -1,10 +1,10 @@ from xml.dom import NotFoundErr -from EVSVesuvio.vesuvio_analysis.analysis_functions import ( +from mvesuvio.vesuvio_analysis.analysis_functions import ( calculateMeansAndStds, filterWidthsAndIntensities, ) -from EVSVesuvio.vesuvio_analysis.ICHelpers import setBootstrapDirs -from EVSVesuvio.vesuvio_analysis.fit_in_yspace import selectModelAndPars +from mvesuvio.vesuvio_analysis.ICHelpers import setBootstrapDirs +from mvesuvio.vesuvio_analysis.fit_in_yspace import selectModelAndPars import numpy as np import matplotlib.pyplot as plt from scipy import stats diff --git a/mvesuvio/vesuvio_analysis/bootstrap_ws/Parent_Back.nxs b/mvesuvio/vesuvio_analysis/bootstrap_ws/Parent_Back.nxs new file mode 100644 index 00000000..b208407d Binary files /dev/null and b/mvesuvio/vesuvio_analysis/bootstrap_ws/Parent_Back.nxs differ diff --git a/mvesuvio/vesuvio_analysis/bootstrap_ws/Parent_Back_NCP.nxs b/mvesuvio/vesuvio_analysis/bootstrap_ws/Parent_Back_NCP.nxs new file mode 100644 index 00000000..3f489612 Binary files /dev/null and b/mvesuvio/vesuvio_analysis/bootstrap_ws/Parent_Back_NCP.nxs differ diff --git a/mvesuvio/vesuvio_analysis/bootstrap_ws/Parent_Front.nxs b/mvesuvio/vesuvio_analysis/bootstrap_ws/Parent_Front.nxs new file mode 100644 index 00000000..372e77a4 Binary files /dev/null and b/mvesuvio/vesuvio_analysis/bootstrap_ws/Parent_Front.nxs differ diff --git a/mvesuvio/vesuvio_analysis/bootstrap_ws/Parent_Front_NCP.nxs b/mvesuvio/vesuvio_analysis/bootstrap_ws/Parent_Front_NCP.nxs new file mode 100644 index 00000000..4e5580a9 Binary files /dev/null and b/mvesuvio/vesuvio_analysis/bootstrap_ws/Parent_Front_NCP.nxs differ diff --git a/EVSVesuvio/vesuvio_analysis/deprecated_mantid_global_fit.py b/mvesuvio/vesuvio_analysis/deprecated_mantid_global_fit.py similarity index 100% rename from EVSVesuvio/vesuvio_analysis/deprecated_mantid_global_fit.py rename to mvesuvio/vesuvio_analysis/deprecated_mantid_global_fit.py diff --git a/EVSVesuvio/vesuvio_analysis/fit_in_yspace.py b/mvesuvio/vesuvio_analysis/fit_in_yspace.py similarity index 100% rename from EVSVesuvio/vesuvio_analysis/fit_in_yspace.py rename to mvesuvio/vesuvio_analysis/fit_in_yspace.py diff --git a/EVSVesuvio/vesuvio_analysis/procedures.py b/mvesuvio/vesuvio_analysis/procedures.py similarity index 100% rename from EVSVesuvio/vesuvio_analysis/procedures.py rename to mvesuvio/vesuvio_analysis/procedures.py diff --git a/EVSVesuvio/vesuvio_analysis/run_script.py b/mvesuvio/vesuvio_analysis/run_script.py similarity index 94% rename from EVSVesuvio/vesuvio_analysis/run_script.py rename to mvesuvio/vesuvio_analysis/run_script.py index e62a8761..00ac7f9c 100644 --- a/EVSVesuvio/vesuvio_analysis/run_script.py +++ b/mvesuvio/vesuvio_analysis/run_script.py @@ -1,12 +1,12 @@ -from EVSVesuvio.vesuvio_analysis.ICHelpers import ( +from mvesuvio.vesuvio_analysis.ICHelpers import ( buildFinalWSName, completeICFromInputs, completeBootIC, completeYFitIC, ) -from EVSVesuvio.vesuvio_analysis.bootstrap import runBootstrap -from EVSVesuvio.vesuvio_analysis.fit_in_yspace import fitInYSpaceProcedure -from EVSVesuvio.vesuvio_analysis.procedures import ( +from mvesuvio.vesuvio_analysis.bootstrap import runBootstrap +from mvesuvio.vesuvio_analysis.fit_in_yspace import fitInYSpaceProcedure +from mvesuvio.vesuvio_analysis.procedures import ( runIndependentIterativeProcedure, runJointBackAndForwardProcedure, runPreProcToEstHRatio, diff --git a/EVSVesuvio/vesuvio_analysis/tests/__init__.py b/mvesuvio/vesuvio_analysis/tests/__init__.py similarity index 100% rename from EVSVesuvio/vesuvio_analysis/tests/__init__.py rename to mvesuvio/vesuvio_analysis/tests/__init__.py diff --git a/EVSVesuvio/vesuvio_analysis/tests/test_analysis_functions.py b/mvesuvio/vesuvio_analysis/tests/test_analysis_functions.py similarity index 90% rename from EVSVesuvio/vesuvio_analysis/tests/test_analysis_functions.py rename to mvesuvio/vesuvio_analysis/tests/test_analysis_functions.py index b59bbdd8..78e5f54e 100644 --- a/EVSVesuvio/vesuvio_analysis/tests/test_analysis_functions.py +++ b/mvesuvio/vesuvio_analysis/tests/test_analysis_functions.py @@ -1,6 +1,6 @@ import unittest from mock import MagicMock -from EVSVesuvio.vesuvio_analysis.analysis_functions import extractWS +from mvesuvio.vesuvio_analysis.analysis_functions import extractWS class TestAnalysisFunctions(unittest.TestCase): diff --git a/pyproject.toml b/pyproject.toml index 86e8d3a6..0f5f80aa 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -40,24 +40,24 @@ tests_require = [ "Bug Tracker" = "https://github.com/mantidproject/vesuvio/issues" [project.entry-points] -console_scripts = { mvesuvio = "EVSVesuvio.scripts:main" } +console_scripts = { mvesuvio = "mvesuvio.scripts:main" } [tool.setuptools.packages.find] -include = ["EVSVesuvio*"] +include = ["mvesuvio*"] namespaces = false [tool.setuptools.package-data] -"EVSVesuvio.config.ip_files" = ["*.par"] -"EVSVesuvio.config" = ["*.properties"] +"mvesuvio.config.ip_files" = ["*.par"] +"mvesuvio.config" = ["*.properties"] [tool.pytest.ini_options] pythonpath = ["."] -testpaths = ["EVSVesuvio/system_tests"] +testpaths = ["mvesuvio/system_tests"] filterwarnings = ["error"] [tool.coverage.report] include = [ - "*/EVSVesuvio/vesuvio_analysis/*", + "*/mvesuvio/vesuvio_analysis/*", ] omit = [ @@ -82,4 +82,4 @@ dirty = "{version}+uncommitted" distance-dirty = "{version}.dev{distance}+uncommitted" [tool.versioningit.write] -file = "EVSVesuvio/__init__.py" +file = "mvesuvio/__init__.py" diff --git a/unpackaged/examples/BaH2_500C.py b/unpackaged/examples/BaH2_500C.py index 30ec4863..ac83c134 100644 --- a/unpackaged/examples/BaH2_500C.py +++ b/unpackaged/examples/BaH2_500C.py @@ -1,8 +1,8 @@ import time import numpy as np from pathlib import Path -from EVSVesuvio.vesuvio_analysis.bootstrap_analysis import runAnalysisOfStoredBootstrap -from EVSVesuvio.vesuvio_analysis.run_script import runScript +from mvesuvio.vesuvio_analysis.bootstrap_analysis import runAnalysisOfStoredBootstrap +from mvesuvio.vesuvio_analysis.run_script import runScript scriptName = Path(__file__).name.split(".")[0] # Take out .py experimentPath = Path(__file__).absolute().parent.parent / "experiments" / scriptName # Path to the repository diff --git a/unpackaged/examples/D_HMT.py b/unpackaged/examples/D_HMT.py index 75457faf..e804be2e 100644 --- a/unpackaged/examples/D_HMT.py +++ b/unpackaged/examples/D_HMT.py @@ -2,8 +2,8 @@ import time import numpy as np from pathlib import Path -from EVSVesuvio.vesuvio_analysis.bootstrap_analysis import runAnalysisOfStoredBootstrap -from EVSVesuvio.vesuvio_analysis.run_script import runScript +from mvesuvio.vesuvio_analysis.bootstrap_analysis import runAnalysisOfStoredBootstrap +from mvesuvio.vesuvio_analysis.run_script import runScript scriptName = Path(__file__).name.split(".")[0] # Take out .py experimentPath = Path(__file__).absolute().parent.parent / "experiments" / scriptName # Path to experiments/sample diff --git a/unpackaged/examples/starch_80_RD.py b/unpackaged/examples/starch_80_RD.py index 3e6fb810..09f1de80 100644 --- a/unpackaged/examples/starch_80_RD.py +++ b/unpackaged/examples/starch_80_RD.py @@ -2,8 +2,8 @@ import time import numpy as np from pathlib import Path -from EVSVesuvio.vesuvio_analysis.bootstrap_analysis import runAnalysisOfStoredBootstrap -from EVSVesuvio.vesuvio_analysis.run_script import runScript +from mvesuvio.vesuvio_analysis.bootstrap_analysis import runAnalysisOfStoredBootstrap +from mvesuvio.vesuvio_analysis.run_script import runScript scriptName = Path(__file__).name.split(".")[0] # Take out .py experimentPath = Path(__file__).absolute().parent.parent / "experiments" / scriptName # Path to the repository diff --git a/unpackaged/original_analysis/Original_adapted_bckwd_script.py b/unpackaged/original_analysis/Original_adapted_bckwd_script.py index 30deb4ef..0f8c1c0b 100644 --- a/unpackaged/original_analysis/Original_adapted_bckwd_script.py +++ b/unpackaged/original_analysis/Original_adapted_bckwd_script.py @@ -28,8 +28,8 @@ from pathlib import Path # ------------ sort out paths -from EVSVesuvio.scripts import handle_config -from EVSVesuvio.analysis_runner import import_from_path +from mvesuvio.scripts import handle_config +from mvesuvio.analysis_runner import import_from_path from pathlib import Path from os import path diff --git a/unpackaged/original_analysis/Original_adapted_fwrd_script.py b/unpackaged/original_analysis/Original_adapted_fwrd_script.py index 0c2baf4f..708973a8 100644 --- a/unpackaged/original_analysis/Original_adapted_fwrd_script.py +++ b/unpackaged/original_analysis/Original_adapted_fwrd_script.py @@ -29,8 +29,8 @@ start_time = time.time() # ------------ sort out paths -from EVSVesuvio.scripts import handle_config -from EVSVesuvio.analysis_runner import import_from_path +from mvesuvio.scripts import handle_config +from mvesuvio.analysis_runner import import_from_path from pathlib import Path from os import path diff --git a/unpackaged/original_analysis/compare_current_with_original_results.py b/unpackaged/original_analysis/compare_current_with_original_results.py index fa3c0d05..695f2783 100644 --- a/unpackaged/original_analysis/compare_current_with_original_results.py +++ b/unpackaged/original_analysis/compare_current_with_original_results.py @@ -13,8 +13,8 @@ np.set_printoptions(suppress=True, precision=8, linewidth=150) # plt.style.use('dark_background') -from EVSVesuvio.scripts import handle_config -from EVSVesuvio.analysis_runner import import_from_path +from mvesuvio.scripts import handle_config +from mvesuvio.analysis_runner import import_from_path from pathlib import Path from os import path diff --git a/unpackaged/vesuvio_calibration/README.md b/unpackaged/vesuvio_calibration/README.md index ca7c711c..13e6a617 100644 --- a/unpackaged/vesuvio_calibration/README.md +++ b/unpackaged/vesuvio_calibration/README.md @@ -1,6 +1,6 @@ # Vesuvio Calibration Scripts -In this subdirectory of the EVSVesuvio repository the following is provided: +In this subdirectory of the mvesuvio repository the following is provided: - Vesuvio calibration scripts, composed of 3 python modules: 1. `calibration_scripts.calibrate_vesuvio_fit` 2. `calibration_scripts.calibrate_vesuvio_analysis`