Optimise GudPy to Fit Dissolve Data

.github/workflows/get-externals/action.yml

@@ -12,43 +12,21 @@ runs:
     if: runner.os == 'Linux'
     run: |
       curl -L https://github.com/disorderedmaterials/Gudrun/releases/download/${{ env.gudrunTag }}/binaries-${{ env.gudrunTag }}-linux.zip > gudrun-binaries.zip
-      curl -L https://github.com/disorderedmaterials/ModEx/releases/download/${{ env.modexTag }}/binaries-${{ env.modexTag }}-linux.zip > modex-binaries.zip
-  - name: Build Externals (OSX)
-    shell: bash
-    if: runner.os == 'MacOS'
-    run: |
-      # Install Ninja
-      brew update-reset
-      brew install ninja
-      # Retrieve Gudrun source
-      curl -L https://github.com/disorderedmaterials/Gudrun/archive/refs/tags/${{ env.gudrunTag }}.tar.gz > gudrun-source.tar.gz
-      tar -zxvf gudrun-source.tar.gz
-      cd Gudrun-${{ env.gudrunTag }}
-      # Retrieve pre-built HDF5 libs
-      curl -L https://github.com/disorderedmaterials/HDF5/releases/download/${{ env.hdf5tag }}/${{ env.hdf5tag }}-osx.zip > hdf5-osx.zip
-      unzip hdf5-osx.zip
-      # Build Gudrun binaries
-      mkdir build
-      cd build
-      cmake ../ -G Ninja -DCMAKE_Fortran_COMPILER:string="gfortran-11" -DLOCAL_STATIC_HDF5:bool=True -DHDF5_DIR:path=$(pwd)/../${{ env.hdf5tag }} -DCMAKE_Fortran_FLAGS:string="-cpp" -DGUDPY_COMPATIBILITY=1
-      ninja
-      ninja install
-      cd ../
-      # Create binaries zip
-      mkdir binaries-${{ env.gudrunTag }}-linux
-      mv bin/* binaries-${{ env.gudrunTag }}-linux
-      zip -9rv ../gudrun-binaries.zip binaries-${{ env.gudrunTag }}-linux/
+      unzip gudrun-binaries
   - name: Retrieve Externals (OSX)
     shell: bash
     if: runner.os == 'MacOS'
     run: |
-      curl -L https://github.com/disorderedmaterials/ModEx/releases/download/${{ env.modexTag }}/binaries-${{ env.modexTag }}-osx.zip > modex-binaries.zip
+      brew install zlib hdf5 gcc@11
+      curl -L https://github.com/disorderedmaterials/Gudrun/releases/download/${{ env.gudrunTag }}/binaries-${{ env.gudrunTag }}-osx-fat.zip > gudrun-binaries.zip
+      unzip gudrun-binaries
+      chmod +x binaries-${{ env.gudrunTag }}-osx-fat/*
   - name: Retrieve Externals (Windows)
     shell: bash
     if: runner.os == 'Windows'
     run: |
       curl -L https://github.com/disorderedmaterials/Gudrun/releases/download/${{ env.gudrunTag }}/binaries-${{ env.gudrunTag }}-windows.zip > gudrun-binaries.zip
-      curl -L https://github.com/disorderedmaterials/ModEx/releases/download/${{ env.modexTag }}/binaries-${{ env.modexTag }}-windows.zip > modex-binaries.zip
+      unzip gudrun-binaries
   - name: Retrieve StartupFiles
     shell: bash
     run: |
@@ -57,11 +35,7 @@ runs:
     shell: bash
     run: |
       if [ ! -e ${{ inputs.targetDir }} ]; then mkdir ${{ inputs.targetDir }}; fi
-      unzip gudrun-binaries.zip
       mv binaries-${{ env.gudrunTag }}-*/* ${{ inputs.targetDir }}
 
-      unzip modex-binaries.zip
-      mv binaries-${{ env.modexTag }}-*/* ${{ inputs.targetDir }}
-
       unzip startupFiles.zip
       mv StartupFiles ${{ inputs.targetDir }}

.github/workflows/package/action.yml

@@ -14,13 +14,14 @@ runs:
 
   - name: Upload Artifacts (OSX)
     if: runner.os == 'MacOS'
-    uses: actions/upload-artifact@v3
+    uses: actions/upload-artifact@v4
     with:
-      name: Packages
+      name: GudPy-OSX
       path: |
         dist/GudPy-*.dmg
         dist/GudPy-*-OSX
 
+
   - name: Create Zip (Windows)
     if: runner.os == 'Windows'
     shell: bash
@@ -30,9 +31,9 @@ runs:
 
   - name: Upload Artifacts (Windows)
     if: runner.os == 'Windows'
-    uses: actions/upload-artifact@v3
+    uses: actions/upload-artifact@v4
     with:
-      name: Packages
+      name: GudPy-Windows
       path: |
         dist/GudPy-*-Windows.zip
 
@@ -50,9 +51,9 @@ runs:
 
   - name: Upload Artifacts (Linux)
     if: runner.os == 'Linux'
-    uses: actions/upload-artifact@v3
+    uses: actions/upload-artifact@v4
     with:
-      name: Packages
+      name: GudPy-Linux
       path: |
         dist/GudPy-*.sif
         dist/GudPy-*-Linux

.github/workflows/pr.yml

@@ -18,7 +18,6 @@ jobs:
       uses: "./.github/workflows/lint"
 
   Test:
-    needs: Lint
     strategy:
       fail-fast: false
       matrix:

.github/workflows/publish/action.yml

@@ -18,9 +18,9 @@ runs:
       singularity-version: 3.8.3
 
   - name: Download Artifacts
-    uses: actions/download-artifact@v3
+    uses: actions/download-artifact@v4
     with:
-      name: Packages
+      pattern: GudPy-*
       path: ${{ github.workspace }}/packages
 
   - name: Download Prerequisites
@@ -36,7 +36,9 @@ runs:
       echo "Release tag will be: ${{ env.gudPyVersion }}"
       echo "Release name will be: ${{ env.gudPyVersion }}"
       export GITHUB_TOKEN=${{ github.token }}
-      ./update-release -r disorderedmaterials/gudpy -t ${{ env.gudPyVersion }} -e -n "${{ env.gudPyVersion }}" -f ReleaseNotes.md packages/*
+      FILES=( $(find ./packages -mindepth 2 -maxdepth 2 -type f -name "GudPy-${{ env.gudPyVersion }}*") )
+      echo ${FILES[@]}
+      ./update-release -r disorderedmaterials/gudpy -t ${{ env.gudPyVersion }} -e -n "${{ env.gudPyVersion }}" -f ReleaseNotes.md ${FILES[@]}
 
   - name: Publish on GitHub (Continuous)
     if: ${{ inputs.publish == 'true' && inputs.isRelease == 'false' }}
@@ -45,20 +47,22 @@ runs:
       echo "Release tag will be: continuous"
       echo "Release name will be: 'Continuous (${{ env.gudPyVersion }})'"
       export GITHUB_TOKEN=${{ github.token }}
-      ./update-release -r disorderedmaterials/gudpy -t continuous -p -e -u -n "Continuous (${{ env.gudPyVersion }})" -b "Continuous release from \`main\` branch. Built $(date)." packages/*
+      FILES=( $(find ./packages -mindepth 2 -maxdepth 2 -type f -name "GudPy-${{ env.gudPyVersion }}*") )
+      echo ${FILES[@]}
+      ./update-release -r disorderedmaterials/gudpy -t continuous -p -e -u -n "Continuous (${{ env.gudPyVersion }})" -b "Continuous release from \`main\` branch. Built $(date)." ${FILES[@]}
 
   - name: Publish on Harbor (Release)
     if: ${{ inputs.publish == 'true' && inputs.isRelease == 'true' }}
     shell: bash
     run: |
       echo "Release tag will be: latest"
       singularity remote login --username ${HARBOR_USER} --password ${HARBOR_SECRET} docker://harbor.stfc.ac.uk
-      ${SINGULARITY_ROOT}/bin/singularity push packages/GudPy-${{ env.gudPyVersion }}.sif oras://harbor.stfc.ac.uk/isis_disordered_materials/gudpy:latest
+      ${SINGULARITY_ROOT}/bin/singularity push packages/GudPy-Linux/GudPy-${{ env.gudPyVersion }}.sif oras://harbor.stfc.ac.uk/isis_disordered_materials/gudpy:latest
 
   - name: Publish on Harbor (Continuous)
     if: ${{ inputs.publish == 'true' && inputs.isRelease == 'false' }}
     shell: bash
     run: |
       echo "Release tag will be: continuous"
       singularity remote login --username ${HARBOR_USER} --password ${HARBOR_SECRET} docker://harbor.stfc.ac.uk
-      ${SINGULARITY_ROOT}/bin/singularity push packages/GudPy-${{ env.gudPyVersion }}.sif oras://harbor.stfc.ac.uk/isis_disordered_materials/gudpy:continuous
+      ${SINGULARITY_ROOT}/bin/singularity push packages/GudPy-Linux/GudPy-${{ env.gudPyVersion }}.sif oras://harbor.stfc.ac.uk/isis_disordered_materials/gudpy:continuous

.github/workflows/setup/action.yml

@@ -6,7 +6,7 @@ inputs:
     default: 3.9
   gudrunTag:
     type: string
-    default: 2023.1
+    default: 2024.1
   modexTag:
     type: string
     default: 0.1.5

.github/workflows/test/action.yml

@@ -38,9 +38,9 @@ runs:
 
   - name: Upload Test Results
     if: always()
-    uses: actions/upload-artifact@v3
+    uses: actions/upload-artifact@v4
     with:
-      name: testResults
+      name: testResults-${{ runner.os }}
       path: results
 
   - name: Publish Code Coverage

.github/workflows/testresults/action.yml

@@ -5,9 +5,10 @@ runs:
   steps:
 
   - name: Download Test Results
-    uses: actions/download-artifact@v3
+    uses: actions/download-artifact@v4
     with:
-      name: testResults
+      pattern: testResults-*
+      merge-multiple: true
       path: results
 
   - name: Publish Test Results

ci/singularity/ubuntu22.04.def

@@ -8,7 +8,7 @@ From: ubuntu:22.04
 %post
     export DEBIAN_FRONTEND=noninteractive
     apt-get update
-    apt-get install python3.10 python3-distutils curl build-essential libx11-xcb-dev libglu1-mesa-dev libxkbcommon0 libglx0 libfontconfig libglib2.0-0 libdbus-1-3 libxcb-xinerama0 libxkbcommon-x11-0 libxcb-icccm4 libxcb-image0 libxcb-keysyms1 libxcb-render-util0 libxcb-randr0 libxcb-shape0 libgfortran5 libegl-dev libegl-mesa0 -y && rm -rf /var/lib/apt/lists/*
+    apt-get install python3.10 python3-distutils curl build-essential libx11-xcb-dev libglu1-mesa-dev libxkbcommon0 libglx0 libfontconfig libglib2.0-0 libdbus-1-3 libxcb-xinerama0 libxkbcommon-x11-0 libxcb-icccm4 libxcb-image0 libxcb-keysyms1 libxcb-render-util0 libxcb-randr0 libxcb-shape0 libxcb-cursor0 libgfortran5 libegl-dev libegl-mesa0 -y && rm -rf /var/lib/apt/lists/*
     curl https://bootstrap.pypa.io/get-pip.py | python3
     python3 -m pip install -r requirements.txt
     rm requirements.txt
@@ -39,10 +39,10 @@ From: ubuntu:22.04
 
 %runscript
     # If the container is executed, this line will be run.
-    python3.10 /opt/GudPy/gudpy
+    python3.10 /opt/GudPy/gudpy/gudpy_gui.py
 
 %apphelp GudPy
     GudPy GUI version.
 
 %apprun GudPy
-    python3 /opt/GudPy/gudpy
+    python3.10 /opt/GudPy/gudpy/gudpy_gui.py

gudpy/core/config.py

@@ -12,7 +12,7 @@
 USE_USER_DEFINED_COMPONENTS = False
 NORMALISE_COMPOSITIONS = False
 
-__rootdir__ = os.path.dirname(os.path.abspath(sys.argv[0]))
+__rootdir__ = os.path.dirname(os.path.dirname(os.path.abspath(sys.argv[0])))
 
 __root__ = (
     os.path.join(sys._MEIPASS, "bin", "configs", "containers")

gudpy/core/container.py

@@ -71,7 +71,7 @@ def __init__(self, config=None):
         """
         self.name = ""
         self.periodNumber = 1
-        self.dataFiles = DataFiles([], "CONTAINER")
+        self.dataFiles = DataFiles([], "CONTAINER", True)
         self.composition = Composition("CONTAINER")
         self.geometry = Geometry.SameAsBeam
         self.upstreamThickness = 0.1
@@ -97,6 +97,7 @@ def __init__(self, config=None):
         self.grBroadening = 0.
         self.powerForBroadening = 0.0
         self.stepSize = 0.0
+        self.outputFolder = ""
 
         self.yamlignore = {
             "runAsSample",
@@ -113,6 +114,10 @@ def __init__(self, config=None):
         if config:
             self.parseFromConfig(config)
 
+    @property
+    def gudFile(self):
+        return None
+
     def __str__(self):
         """
         Returns the string representation of the Container object.

gudpy/core/data.py

@@ -0,0 +1,82 @@
+import numpy
+
+
+class Point():
+    def __init__(self, x, y, err=0.0):
+        self.x = x
+        self.y = y
+        self.err = err
+
+
+class DataSet():
+    # mint01 / mdcs01 / mdor01 / mgor01 / dcs
+    def __init__(self, path, exists, lim=None):
+        if not exists:
+            self.dataSet = None
+        else:
+            self.dataSet = self.constructDataSet(path, lim)
+
+    def constructDataSet(self, path, lim=None):
+        dataSet = []
+        with open(path, "r", encoding="utf-8") as fp:
+            for dataLine in fp.readlines():
+
+                # Ignore commented lines.
+                if dataLine[0] == "#":
+                    continue
+
+                splitLine = [float(n) for n in dataLine.split()]
+                if len(splitLine) > 2:
+                    x, y, err, *__ = splitLine
+                    if lim and x > lim:
+                        return dataSet
+                    dataSet.append(Point(x, y, err))
+                else:
+                    x, y = splitLine
+                    if lim and x > lim:
+                        return dataSet
+                    dataSet.append(Point(x, y))
+
+        return dataSet
+
+
+class NpDataSet():
+    # mint01 / mdcs01 / mdor01 / mgor01 / dcs
+    def __init__(self, path, lim=None):
+        self.LIMIT = lim
+        self.x = []
+        self.y = []
+
+        with open(path, "r", encoding="utf-8") as fp:
+            for dataLine in fp.readlines():
+
+                # Ignore commented lines.
+                if dataLine[0] == "#":
+                    continue
+
+                splitLine = [float(n) for n in dataLine.split()]
+                x, y, *__ = splitLine
+                if lim and x > lim:
+                    break
+                self.x.append(x)
+                self.y.append(y)
+
+        if not self.LIMIT:
+            self.LIMIT = self.x[-1]
+
+        self.x = numpy.array(self.x)
+        self.y = numpy.array(self.y)
+
+        self.interpolate()
+
+    def interpolate(self):
+        xnew = numpy.round(numpy.arange(0, self.LIMIT, 0.015), 4)
+        ynew = numpy.interp(xnew, self.x, self.y)
+        self.x = xnew
+        self.y = ynew
+
+
+def meanSquaredError(d1: NpDataSet, d2: NpDataSet) -> float:
+    return sum((y1 - y2)**2
+               for y1, y2 in zip(d1.y, d2.y)
+               ) / len(d1.y)