Merge pull request #52 from KrisThielemans/merge_master_at_v5.2.0_to_TOF

Merge master at v5.2.0 to TOF

.appveyor.yml

@@ -3,6 +3,7 @@ shallow_clone: true
 skip_commits:
   files:
     - .github/**/*
+    - 'CITATION.cff'
     - '**/*.md'
     - '**/*.html'
     - '**/*.htm'

.gitattributes

@@ -12,6 +12,8 @@
 *.v     -text -diff
 *.s     -text -diff
 *.scn     -text -diff
+*.l     -text -diff
+*.root  -text -diff
 *.gz     -text -diff
 *.nii     -text -diff
 *.sh    eol=lf

.github/PULL_REQUEST_TEMPLATE.md

@@ -0,0 +1,22 @@
+<!-- Fill in most of this text, and delete what is not appropriate.
+Please read and adhere to the [contribution guidelines](https://github.com/UCL/STIR/blob/master/CONTRIBUTING.md).
+Did you sign the STIR Contribution License Agreement?
+-->
+
+## Changes in this pull request
+
+
+## Testing performed
+
+
+## Related issues
+<!-- Use keywords such as "fixes", "closes", see https://docs.github.com/en/issues/tracking-your-work-with-issues/linking-a-pull-request-to-an-issue -->
+
+
+## Checklist before requesting a review
+<!--Put an x between the [] when completed. Delete a line if not applicable. -->
+  - [] I have performed a self-review of my code
+  - [] I have added docstrings/doxygen in line with the guidance in the developer guide
+  - [] I have implemented unit tests that cover any new or modified functionality (if applicable)
+  - [] The code builds and runs on my machine
+  - [] `documentation/release_XXX.md` has been updated with any functionality change (if applicable)

.github/workflows/build-test.yml

@@ -7,6 +7,7 @@ on:
       - tof_sino_UCL
     paths-ignore:
       - '.appveyor.yml'
+      - 'CITATION.cff'
       - '**/*.md'
       - '**/*.html'
       - '**/*.htm'
@@ -18,6 +19,7 @@ on:
       - tof_sino_UCL
     paths-ignore:
       - '.appveyor.yml'
+      - 'CITATION.cff'
       - '**/*.md'
       - '**/*.html'
       - '**/*.htm'
@@ -334,7 +336,7 @@ jobs:
             ./run_scatter_tests.sh
             ./run_test_zoom_image.sh
             ./run_ML_norm_tests.sh
-            if [[ $BUILD_FLAGS == *"DDISABLE_CERN_ROOT=0"* ]]; then ./run_root_GATE.sh; fi
+            if test "${{matrix.ROOT}}XX" == "ONXX"; then ./run_root_GATE.sh; fi
             ./run_tests_modelling.sh
             cd ${GITHUB_WORKSPACE}/recon_test_pack/SPECT
             ./run_SPECT_tests.sh
@@ -345,14 +347,17 @@ jobs:
       if: failure()
       with:
         name: recon_test_pack_log_files-${{ matrix.os }}-${{ matrix.compiler }}${{ matrix.compiler_version }}-${{ matrix.BUILD_TYPE }}-pp=${{ matrix.parallelproj }}-ROOT=${{ matrix.ROOT }}
-        path: ${{ github.workspace }}/recon_test_pack/**/*.log
+        path: |
+          ${{ github.workspace }}/recon_test_pack/**/*.log
+          ${{ github.workspace }}/recon_test_pack/**/my_*v
+          ${{ github.workspace }}/recon_test_pack/**/my_*s
         retention-days: 7
 
     # Enable tmate debugging of manually-triggered workflows if the input option was provided
     - name: Setup tmate session if triggered
       uses: mxschmitt/action-tmate@v3
       timeout-minutes: 15
-      if: ${{ github.event_name == 'workflow_dispatch' && github.event.inputs.debug_enabled }}
+      if: ${{ github.event_name == 'workflow_dispatch' && inputs.debug_enabled == 'true' }}
 
     - name: examples
       shell: bash

.github/workflows/cffconvert.yml

@@ -0,0 +1,19 @@
+name: cffconvert
+
+on:
+  push:
+    paths:
+      - CITATION.cff
+
+jobs:
+  validate:
+    name: "validate"
+    runs-on: ubuntu-latest
+    steps:
+      - name: Check out a copy of the repository
+        uses: actions/checkout@v2
+
+      - name: Check whether the citation metadata from CITATION.cff is valid
+        uses: citation-file-format/[email protected]
+        with:
+          args: "--validate"

.mailmap

@@ -45,8 +45,10 @@ Palak Wadhwa <[email protected]> <[email protected]>
 Rebecca Gillen <[email protected]> <[email protected]>
 Richard Brown <[email protected]> <[email protected]>
 Richard Brown <[email protected]>  <[email protected]>
-Robert Twyman <[email protected]> <[email protected]>
-Robert Twyman <[email protected]> <[email protected]>
+Robert Twyman Skelly <[email protected]> <[email protected]>
+Robert Twyman Skelly <[email protected]> <[email protected]>
+Robert Twyman Skelly <[email protected]> <[email protected]>
+Robert Twyman Skelly <[email protected]> <[email protected]>
 Yu-jung Tsai <[email protected]> <[email protected]>
 Gemma Fardell <[email protected]> <[email protected]>
 Gemma Fardell <[email protected]> <[email protected]>
@@ -62,5 +64,6 @@ Nicole Jurjew <[email protected]>
 Tahereh Niknejad <[email protected]>
 Tahereh Niknejad <[email protected]> <[email protected]>
 Sam D Porter <[email protected]>
+Sam D Porter <[email protected]>  <[email protected]>
 Matthew Strugari <[email protected]>
 Matthew Strugari <[email protected]> <[email protected]>