mantidproject · robertapplin · May 10, 2024 · May 10, 2024 · May 10, 2024 · May 10, 2024
diff --git a/Framework/WorkflowAlgorithms/src/AlignAndFocusPowder.cpp b/Framework/WorkflowAlgorithms/src/AlignAndFocusPowder.cpp
@@ -22,6 +22,7 @@
 #include "MantidKernel/ConfigService.h"
 #include "MantidKernel/DateTimeValidator.h"
 #include "MantidKernel/EnabledWhenProperty.h"
+#include "MantidKernel/EnumeratedString.h"
 #include "MantidKernel/InstrumentInfo.h"
 #include "MantidKernel/ListValidator.h"
 #include "MantidKernel/PropertyManager.h"
@@ -70,6 +71,7 @@ const std::string RESONANCE_UPPER_LIMITS("ResonanceFilterUpperLimits");
 const std::string COMPRESS_TOF_TOL("CompressTolerance");
 const std::string COMPRESS_WALL_TOL("CompressWallClockTolerance");
 const std::string COMPRESS_WALL_START("CompressStartTime");
+const std::string COMPRESS_MODE("CompressBinningMode");
 const std::string L1("PrimaryFlightPath");
 const std::string SPEC_IDS("SpectrumIDs");
 const std::string L2("L2");
@@ -89,6 +91,11 @@ void getTofRange(const MatrixWorkspace_const_sptr &wksp, double &tmin, double &t
     wksp->getXMinMax(tmin, tmax);
   }
 }
+
+const std::vector<std::string> binningModeNames{"Default", "Linear", "Logarithmic"};
+enum class BinningMode { DEFAULT, LINEAR, LOGARITHMIC, enum_count };
+typedef Mantid::Kernel::EnumeratedString<BinningMode, &binningModeNames> BINMODE;
+
 } // anonymous namespace
 
 // Register the class into the algorithm factory
@@ -186,24 +193,25 @@ void AlignAndFocusPowder::init() {
                   "Maximum values to filter absorption resonance. This must have same number of values as "
                   "ResonanceFilterLowerLimits. Default behavior is to not filter.");
 
-  declareProperty(std::make_unique<PropertyWithValue<double>>(PropertyNames::COMPRESS_TOF_TOL, 1e-5, mustBePositive,
-                                                              Direction::Input),
-                  "Compress events (in "
-                  "microseconds) within this "
-                  "tolerance. (Default 1e-5)");
+  declareProperty(std::make_unique<PropertyWithValue<double>>(PropertyNames::COMPRESS_TOF_TOL, 1e-5, Direction::Input),
+                  "Compress events (in microseconds) within this tolerance. (Default 1e-5). If negative then do "
+                  "logorithmic compression.");
   declareProperty(std::make_unique<PropertyWithValue<double>>(PropertyNames::COMPRESS_WALL_TOL, EMPTY_DBL(),
                                                               mustBePositive, Direction::Input),
                   "The tolerance (in seconds) on the wall-clock time for comparison. Unset "
                   "means compressing all wall-clock times together disabling pulsetime "
                   "resolution.");
-
   auto dateValidator = std::make_shared<DateTimeValidator>();
   dateValidator->allowEmpty(true);
   declareProperty(PropertyNames::COMPRESS_WALL_START, "", dateValidator,
                   "An ISO formatted date/time string specifying the timestamp for "
                   "starting filtering. Ignored if WallClockTolerance is not specified. "
                   "Default is start of run",
                   Direction::Input);
+  declareProperty(PropertyNames::COMPRESS_MODE, binningModeNames[size_t(BinningMode::DEFAULT)],
+                  std::make_shared<Mantid::Kernel::StringListValidator>(binningModeNames),
+                  "Optional.  Binning behavior can be specified in the usual way through sign of tolerance "
+                  "('Default'); or can be set to one of the allowed binning modes. ");
   declareProperty(PropertyNames::LORENTZ, false,
                   "Multiply each spectrum by "
                   "sin(theta) where theta is "
@@ -382,8 +390,14 @@ void AlignAndFocusPowder::exec() {
   tmax = getProperty(PropertyNames::TOF_MAX);
   m_preserveEvents = getProperty(PropertyNames::PRESERVE_EVENTS);
   m_resampleX = getProperty(PropertyNames::RESAMPLEX);
-  const double compressEventsTolerance = getProperty(PropertyNames::COMPRESS_TOF_TOL);
+  double compressEventsTolerance = getProperty(PropertyNames::COMPRESS_TOF_TOL);
   const double wallClockTolerance = getProperty(PropertyNames::COMPRESS_WALL_TOL);
+  const BINMODE mode = getPropertyValue(PropertyNames::COMPRESS_MODE);
+  if (mode == BinningMode::LINEAR)
+    compressEventsTolerance = std::fabs(compressEventsTolerance);
+  else if (mode == BinningMode::LOGARITHMIC)
+    compressEventsTolerance = -1. * std::fabs(compressEventsTolerance);
+
   // determine some bits about d-space and binning
   if (m_resampleX != 0) {
     // ignore the normal rebin parameters
@@ -1223,7 +1237,7 @@ bool AlignAndFocusPowder::shouldCompressUnfocused(const double compressTolerance
   if (hasWallClockTolerance)
     return false;
   // compressing isn't an option
-  if (compressTolerance <= 0)
+  if (compressTolerance == 0)
     return false;
 
   if (const auto eventWS = std::dynamic_pointer_cast<const EventWorkspace>(m_outputW)) {
@@ -1242,7 +1256,19 @@ bool AlignAndFocusPowder::shouldCompressUnfocused(const double compressTolerance
 
     // assume one frame although this is generically wrong
     // there are 3 fields in weighted events no time
-    const double sizeWeightedEventsEstimate = WEIGHTED_NOTIME_EVENT_BYTE_SIZE * tofRange / compressTolerance;
+    double sizeWeightedEventsEstimate;
+    if (compressTolerance > 0) // linear
+      sizeWeightedEventsEstimate = WEIGHTED_NOTIME_EVENT_BYTE_SIZE * tofRange / compressTolerance;
+    else { // log
+      if (tofmin_wksp < 0)
+        return false; // log compression cannot have negative TOF values
+
+      if (tofmin_wksp == 0)
+        tofmin_wksp = compressTolerance;
+
+      sizeWeightedEventsEstimate =
+          WEIGHTED_NOTIME_EVENT_BYTE_SIZE * log(tofmax_wksp / tofmin_wksp) / log1p(abs(compressTolerance));
+    }
 
     double numEvents = static_cast<double>(eventWS->getNumberEvents());
     const auto eventType = eventWS->getEventType();

diff --git a/Framework/WorkflowAlgorithms/test/AlignAndFocusPowderTest.h b/Framework/WorkflowAlgorithms/test/AlignAndFocusPowderTest.h
@@ -93,6 +93,8 @@ class AlignAndFocusPowderTest : public CxxTest::TestSuite {
     AnalysisDataService::Instance().remove(m_inputWS);
 
     // Test the output
+    auto eventWS = std::dynamic_pointer_cast<EventWorkspace>(m_outWS);
+    TS_ASSERT_EQUALS(eventWS->getNumberEvents(), 870622);
     // [99] 1920.2339999999983, 41
     TS_ASSERT_DELTA(m_outWS->x(0)[99], 1920.23400, 0.0001);
     TS_ASSERT_EQUALS(m_outWS->y(0)[99], 41.);
@@ -421,6 +423,38 @@ class AlignAndFocusPowderTest : public CxxTest::TestSuite {
     AnalysisDataService::Instance().remove(m_outputWS);
   }
 
+  void testEventWksp_preserveEvents_logCompressTolerance() {
+    // Setup the event workspace
+    setUp_EventWorkspace("EventWksp_preserveEvents_logCompressTolerance");
+
+    // Set the inputs for doTestEventWksp
+    m_preserveEvents = true;
+    m_useGroupAll = false;
+    m_useResamplex = true;
+    m_compressTolerance = "-1e-5";
+
+    // Run the main test function
+    doTestEventWksp();
+
+    // Reset inputs to default values
+    m_compressTolerance = "0";
+
+    // Test the input
+    docheckEventInputWksp();
+    AnalysisDataService::Instance().remove(m_inputWS);
+
+    // Test the output: expected result shall be same as testEventWksp_preserveEvents but have fewer events
+    auto eventWS = std::dynamic_pointer_cast<EventWorkspace>(m_outWS);
+    TS_ASSERT_EQUALS(eventWS->getNumberEvents(), 451436);
+    // [99] 1920.2339999999983, 41
+    TS_ASSERT_DELTA(m_outWS->x(0)[99], 1920.23400, 0.0001);
+    TS_ASSERT_EQUALS(m_outWS->y(0)[99], 41.);
+    // [899] 673.0, 15013.033999999987
+    TS_ASSERT_DELTA(m_outWS->x(0)[899], 15013.03400, 0.0001);
+    TS_ASSERT_EQUALS(m_outWS->y(0)[899], 673.0);
+    AnalysisDataService::Instance().remove(m_outputWS);
+  }
+
   void testEventWksp_preserveEvents_removePromptPulse() {
     // Setup the event workspace
     setUp_EventWorkspace("EventWksp_preserveEvents_removePromptPulse");

diff --git a/buildconfig/Jenkins/Conda/conda-buildscript b/buildconfig/Jenkins/Conda/conda-buildscript
@@ -117,10 +117,15 @@ create_and_activate_mantid_developer_env
 
 # Check whether this is an incremental build that only changes rst files
 if [ -d $BUILD_DIR ]; then
-    if ${SCRIPT_DIR}/../check_for_changes dev-docs-only || ${SCRIPT_DIR}/../check_for_changes user-docs-only; then
+    if ${SCRIPT_DIR}/../check_for_changes user-docs-only; then
       ENABLE_BUILD_CODE=false
       ENABLE_UNIT_TESTS=false
       ENABLE_SYSTEM_TESTS=false
+    elif ${SCRIPT_DIR}/../check_for_changes dev-docs-only; then
+      ENABLE_BUILD_CODE=false
+      ENABLE_UNIT_TESTS=false
+      ENABLE_SYSTEM_TESTS=false
+      ENABLE_DOC_TESTS=false
     fi
     rm -rf ${BUILD_DIR}/bin ${BUILD_DIR}/ExternalData ${BUILD_DIR}/Testing
     find $WORKSPACE \( -iname 'TEST-*.xml' -o -name 'Test.xml' \) -delete

diff --git a/dev-docs/source/Packaging.rst b/dev-docs/source/Packaging.rst
@@ -118,6 +118,59 @@ The ``--package-suffix`` argument is an optional string to append to the name
 of the final package. We generally pick ``Unstable`` for installers not built
 by the CI pipeline to indicate it has been built outside of the standard process.
 
+.. _build_packages_from_branch:
+
+Build packages from branch using Jenkins
+----------------------------------------
+
+Developers can build packages to test branches using the ``build_packages_from_branch`` `Jenkins job <build_packages_from_branch_job_>`_. This job provides the ability to,
+
+- Run system tests on Windows, Mac, Linux, or all three.
+- Build a packages on Windows, Mac, Linux, or all three.
+- Publish the package(s) to a given Anaconda channel and label.
+- Publish the package(s) to a given Github repository under a specified tag.
+
+for a given branch of mantid. The branch can be from the main mantid repo or from a remote.
+
+Options
+#######
+
+- ``BUILD_DEVEL`` [``none``, ``all``, ``linux-64``, ``win-64``, ``osx-64``]: Run the system tests for this OS.
+- ``BUILD_PACKAGE`` [``none``, ``all``, ``linux-64``, ``win-64``, ``osx-64``]: Build a package on this OS.
+- ``PACKAGE_SUFFIX``: String to append onto the standalone package name, useful for distinguishing builds. By default this is ``Unstable``.
+- ``PUBLISH_TO_ANACONDA``: Set true to publish to the given Anaconda channel and label.
+- ``PUBLISH_TO_GITHUB``: Set true to publish to the Github repository using the specified tag.
+- ``ANACONDA_CHANNEL``: Anaconda channel to upload the package to. By default this is ``mantid``.
+- ``ANACONDA_CHANNEL_LABEL``: Label attached to the uploaded package. By default this is ``unstable``.
+- ``GITHUB_RELEASES_REPO``: Repository to store the release. By Default this is ``mantidproject/mantid``.
+- ``GITHUB_RELEASES_TAG``: Name of the tag for the release; only to be used for release candidate builds.
+- ``ANACONDA_TOKEN_CREDENTIAL_ID`` [``anaconda-cloud-token``, ``anaconda-token-ornl``]: One of two credentials to use for publishing to Anaconda.
+- ``GH_ORGANIZATION_OR_USERNAME``: Name of the organisation or Github user name who owns the repository with the code to build. By default this is ``mantidproject``, if you are building from a fork this will need to change to your username.
+- ``BRANCH_NAME``: Name of the branch to build the packages from.
+
+Example
+#######
+
+Say I've implemented a new file searching method on a branch ``1234_new_file_search`` and I want to test this on IDAaaS, one of the easiest ways to do this would be to build the packages and upload them to Anaconda using the pipeline. These are the steps I'd take to do this.
+
+1. Go to the ``build_packages_from_branch`` `Jenkins job <build_packages_from_branch_job_>`_.
+2. If needed click ``login`` in the top right of the window.
+3. Go to ``Build with parameters`` in the side bar.
+4. Fill out the following options:
+
+   - ``BUILD_DEVEL`` = ``none``
+   - ``BUILD_PACKAGE`` = ``linux-64``
+   - ``PUBLISH_TO_ANACONDA`` = true
+   - ``ANACONDA_CHANNEL_LABEL`` = ``new_file_system_test``
+   - ``ANACONDA_TOKEN_CREDENTIAL_ID`` = ``anaconda-cloud-token``
+   - ``BRANCH_NAME`` = ``1234_new_file_search``
+
+5. Click ``Build``. This will take you back to the main job page, the build just set off will be the most recent (highest number) build on the left hand side. It is a good idea to make note of the build number / copy the link somewhere safe. If the build is for testing a pr, make sure to add the link to the testing instructions.
+6. Once the job has successfully completed, check `the Mantid Anaconda page <mantid-conda-org_>`_ to make sure it has uploaded.
+7. Head to IDAaaS (or any linux system) and run ``mamba install -c mantid/label/new_file_system_test mantidworkbench`` in a new environment to install the test package.
+
+Most often, you won't need to upload the packages to Anaconda, this is most useful in cases where installing standalone packages is inconvenient. Standalone package builds created by the jenkins job can be found under the jenkins job build artifacts, this is near the top of the page. Say you built a package for Windows using the jenkins job, you should find a ``mantidworkbench`` exe file in the build artifacts.
+
 
 .. _conda: https://conda.io
 .. _mantid-conda-recipes: https://github.com/mantidproject/mantid/tree/main/conda
@@ -130,4 +183,4 @@ by the CI pipeline to indicate it has been built outside of the standard process
 .. _download-page: https://download.mantidproject.org
 .. _nsis: https://sourceforge.net/projects/nsis/
 .. _dmg: https://en.wikipedia.org/wiki/Apple_Disk_Image
-.. _standalone-scripts: https://github.com/mantidproject/mantid/blob/main/installers/conda
+.. _build_packages_from_branch_job: https://builds.mantidproject.org/job/build_packages_from_branch/
diff --git a/dev-docs/source/Testing/Indirect/DataReductionTests.rst b/dev-docs/source/Testing/Indirect/DataReductionTests.rst
@@ -28,7 +28,7 @@ Data reduction
 #. Enter ``Input Runs`` 26173
 #. Click ``Run``
 #. This should generate a workspace with ``_calib`` at the end, delete this workspace
-#. Change the ``Scale by factor`` value to 0.5
+#. Check the ``Scale by factor`` checkbox and change the value of the scale to 0.5.
 #. Click ``Run``
 #. This should generate a workspace with ``_calib`` at the end
 #. Check the ``Create RES`` box
@@ -41,6 +41,7 @@ Data reduction
 #. Make sure that you keep the ``_calib`` workspace, it is needed for the next test
 #. Enter ``Input Runs`` 59057-59059 and check ``Sum Files``
 #. Set ``Reflection`` to 004
+#. Click ``Run``
 #. This should produce a new ``_calib`` workspace, with ``004`` in the name.
 #. Before moving on, set ``Reflection`` to 002
 
@@ -57,13 +58,13 @@ Data reduction
 #. Check the ``Use Calib File`` box
 #. Change ``File`` to ``Workspace`` and choose the ``_calib`` workspace previously created (55878 from the previous test)
 #. Click ``Run``
-#. In the main GUI right-click on the ``iris26184_multi_graphite002_red`` workspace
+#. In the main GUI right-click on the ``iris26184-26185_multi_graphite002_red`` workspace
 #. Choose ``Plot spectrum``, note the number of spectra, should be 51
 #. Click ``Cancel``
 #. In the ``Data reduction`` GUI, change the ``Detector Grouping`` to Groups
 #. Set ``Groups`` to 5
 #. Click ``Run``
-#. In the main GUI right-click on the ``iris26184_multi_graphite002_red`` workspace
+#. In the main GUI right-click on the ``iris26184-26185_multi_graphite002_red`` workspace
 #. Choose ``Plot spectrum``, note the number of spectra, should be 6
 #. Choose ``Plot All``, this should result in a plot of all 6 spectra
 #. Open ``Interfaces`` > ``Inelastic`` > ``Data Manipulation`` and go to the ``S(Q, W)`` tab

diff --git a/dev-docs/source/Testing/Inelastic/DataManipulationTests.rst b/dev-docs/source/Testing/Inelastic/DataManipulationTests.rst
@@ -31,7 +31,7 @@ Elwin tab
 #. Add the loaded workspaces
 #. Click ``Run``
 #. This should result in three new workspaces again, this time with file ranges as their name
-#. In the main GUI right-click on ``MAR27691-27698_graphite002_red_elwin_eq2`` and choose ``Plot Spectrum``, choose ``Plot All``
+#. In the main GUI right-click on ``MAR27691-27698_red_elwin_eq2`` and choose ``Plot Spectrum``, choose ``Plot All``
 #. This should plot two lines of :math:`ln(Counts(microAmp.hour))^{-1}` vs :math:`Q2`
 
 .. _elwin_inelastic_test:

diff --git a/...rce/Testing/MuonAnalysis_test_guides/Muon Analysis Unscripted Testing Guide.rst b/...rce/Testing/MuonAnalysis_test_guides/Muon Analysis Unscripted Testing Guide.rst
@@ -39,9 +39,9 @@ Group 2: PSI data
 
 This group tests bin data from the PSI facility and introduces background corrections.
 Test instructions can be found at :ref:`Muon_Analysis_PSI-ref`.
-You will need the following run:
+You will need the following file from the unit test data:
 
-- dolly 1529
+- deltat_tdc_dolly_1529.bin
 
 Group 3: HIFI data
 ^^^^^^^^^^^^^^^^^^

diff --git a/dev-docs/source/Testing/MuonAnalysis_test_guides/Muon_Analysis_PSI.rst b/dev-docs/source/Testing/MuonAnalysis_test_guides/Muon_Analysis_PSI.rst
@@ -23,7 +23,7 @@ Loading Data Test
 - Open Muon Analysis
 - On the **Home** tab set the instrument to **PSI**
 - The load current run button should be greyed out
-- Load **dolly 1529** using the **Browse** button
+- Load **deltat_tdc_dolly_1529.bin** from the unit test data using the **Browse** button
 - Set `Rebin` to `Fixed` and enter a value of `5`
 - You will get 4 lines that all curve upwards
 - If you tick the `Plot raw` option the data will change

diff --git a/dev-docs/source/Testing/MuonAnalysis_test_guides/Muon_FDA.rst b/dev-docs/source/Testing/MuonAnalysis_test_guides/Muon_FDA.rst
@@ -23,7 +23,7 @@ FFT Test
 - Change *Instrument* to **MUSR**, found in the *Home* tab
 - In the loading bar enter ``62260``
 - Go to the **Transform** tab
-    - Set the workspace to "MUSR00062260; Group; bkwd; Asym; FD"
+    - Set the workspace to "MUSR00062260; Group; bkwd; Asymmetry; FD"
     - Click the calculate FFT button and a plot will appear
     - The plot window will show a broad peak
 - In the **Fitting** tab it will contain 3 workspace ending in `Re_unit_MHz` (real), `Im_unit_MHz` (imaginary) and `mod_unit_MHz` (modulus)
@@ -36,7 +36,7 @@ FFT Test
     - The "padding" adds zeros to the end of the time domain data set, to improve the sampling of the FFT
     - Set the xrange for the plot to be from ``0`` to ``2`` by changing the x min and x max values below the plot
     - Set the "padding" to zero and press calculate
-    - The plots should be a nice peak, but it will have lots of straight lines
+    - The plot should still have a peak, but it will be less smooth
     - Set the "padding" to ``50`` and press calculate
     - The plot will now be nice and smooth
 - At the top of the plotting window change the unit from "Frequency" to "Field", the data will have different x axis

diff --git a/dev-docs/source/Testing/MuonAnalysis_test_guides/Muon_HIFI.rst b/dev-docs/source/Testing/MuonAnalysis_test_guides/Muon_HIFI.rst
@@ -54,8 +54,8 @@ HIFI Transverse Field Simultaneous Fitting
 	- Click **Undo Fits**
 	- Click the value for the **Frequency** parameter; A ``...`` should appear
 	  next to it, click it. A new window should appear
-	- Enter values for each run in the table as from ``0.0`` to ``1.1`` in
-	  steps of ``0.1``
+	- Enter a value of ``0.01`` for the first run in the table
+	- For each of the other runs in the table, enter values from ``0.1`` to ``1.1`` in steps of ``0.1``
 	- Click **Ok**
 	- Click **Fit**
 	- This time the fit should work with a significantly lower value for **Chi-squared** (``<10``)
@@ -83,6 +83,7 @@ HIFI MultiPeriod Data
 - Go to the **Sequential Fitting** tab
 	- Press ``Sequentially fit all``
 	- When its complete the table should update
+	- It is ok if some of the rows say "Failed". This happens because these rows need more iterations to converge. However, if you go to the Fitting tab and cycle through the datasets, you can see that the fits are still reasonably good.
 	- Selecting rows will show you the data and fit for those rows
 - Go to the **Grouping** tab
 	- The ``Period`` column in the group table will show a series of numbers (1, 2, 3 or 4)

diff --git a/dev-docs/source/Testing/SANSGUI/ISISSANSGUITests.rst b/dev-docs/source/Testing/SANSGUI/ISISSANSGUITests.rst
@@ -124,8 +124,10 @@ Processing
 #. In the workspaces list, there should be a series of new workspaces; four
    group workspaces and four 1D workspaces.
 #. Check your default save directory. For each reduction two banks (HAB/main) should
-   be saved. In total there should be 12 workspaces (6 CanSAS ``.xml`` and 6 NXcanSAS ``.h5``) saved. For each row and
-   file type there should be a reduced file (with no suffix), a sample, and a can workspace.
+   be saved. In total, there should be 20 workspaces saved. For each row, file type, and bank, there should be a
+   reduced file (with no suffix) and a ``sample`` file. The ``first_time`` line should also produce a ``can`` workspace
+   for each file type and bank. This is because both workspaces have the same ``can`` input run numbers and so the
+   reduction only calculates it once.
 #. Double-click the 1D workspaces and you should get a single line plot.
 #. Clear the newly created files and workspaces to make the next test easier
 #. Change the contents of the first cell in the first row to ``74045`` and click
@@ -263,3 +265,5 @@ Display
    have clear tooltips.
 #. In the settings, hover over a random selection of buttons and text boxes to check tooltips are still there.
    Users rely on the tooltips a lot and really do notice each missing one.
+   *Note: The* ``Wavelength`` *section of the settings is missing its tooltips. We and the users are aware of this so an
+   issue should not be made when it is discovered.*