JSON update (#122)

* JSON update

* fix requirements

* expected files

* Expected files

* tests rework

* improved tests

.github/workflows/test-run.yml

@@ -9,11 +9,41 @@ on:
   workflow_dispatch:
 
 jobs:
-  build-and-test:
+
+  smoke-test-on-linux:
     runs-on: ubuntu-latest
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v3
+
+      - name: Setup Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: '3.11'
+
+      - name: Install dependencies
+        run: |
+          python3 -m pip install --upgrade pip
+          pip3 install -r requirements.txt
+          pip3 install -r test_requirements.txt
+
+      - name: Run main tests
+        run: python -m pytest tests/
+
+
+  build-and-test:
+    runs-on: ${{ matrix.platform }}
+    needs: smoke-test-on-linux
     strategy:
-       matrix:
-         python-version: ['3.9', '3.10', '3.11']
+      matrix:
+        python-version: ['3.11']
+        platform: ['windows-latest', 'macos-latest']
+        include:
+          - python-version: '3.9'
+            platform: 'ubuntu-latest'
+          - python-version: '3.10'
+            platform: 'ubuntu-latest'
+
     steps:
       - name: Checkout
         uses: actions/checkout@v3

.gitignore

@@ -264,7 +264,6 @@ cython_debug/
 .ionide
 
 # End of https://www.toptal.com/developers/gitignore/api/python,visualstudiocode,pycharm
-beam.dat
-detect.dat
-geo.dat
-mat.dat
+
+**/*.dat
+!input_examples/expected_shieldhit_output/*.dat

README.md

@@ -1,6 +1,8 @@
 # Yet Another Particle Transport IDE - converter
 
-The Converter of the project file (JSON file generated by frontend part) into a set of input files for SHIELD-HIT12A (beam.dat, mat.dat, geo.dat and detect.dat).
+The Converter of the project file (JSON file generated by frontend part) into a set of input files for particle transport simulators:
+ - SHIELD-HIT12A (beam.dat, mat.dat, geo.dat and detect.dat).
+ - TOPAS
 
 ## Requirements
 - Python 3.9+

input_examples/README.md

@@ -0,0 +1,2 @@
+An input file generated with yaptide UI (https://yaptide.github.io/web_dev/).
+Open first example, then save it as JSON file under `sh_parser_test.json` name.

input_examples/expected_shieldhit_output/README.md

@@ -0,0 +1 @@
+Output files generated using the UI ("Input files" / "Generate from editor").

input_examples/expected_shieldhit_output/beam.dat

@@ -0,0 +1,14 @@
+
+RNDSEED      	89736501     ! Random seed
+JPART0       	2            ! Incident particle type
+TMAX0      	150.0 1.5       ! Incident energy and energy spread; both in (MeV/nucl)
+TCUT0 0 1000  ! energy cutoffs [MeV]
+NSTAT       10000    0       ! NSTAT, Step of saving
+STRAGG          2            ! Straggling: 0-Off 1-Gauss, 2-Vavilov
+MSCAT           2            ! Mult. scatt 0-Off 1-Gauss, 2-Moliere
+NUCRE           1            ! Nucl.Reac. switcher: 1-ON, 0-OFF
+BEAMPOS 0 0 0 ! Position of the beam
+BEAMDIR 0.0 0.0 ! Direction of the beam
+BEAMSIGMA  0 0  ! Beam extension
+! no BEAMSAD value
+DELTAE   0.03   ! relative mean energy loss per transportation step

input_examples/expected_shieldhit_output/detect.dat

@@ -0,0 +1,75 @@
+Geometry Cyl
+    Name CylZ_Mesh
+    R 0 5 1
+    Z 0 20 400
+
+Geometry Mesh
+    Name YZ_Mesh
+    X -0.25 0.25 1
+    Y -2 2 80
+    Z 0 20 400
+
+Geometry Cyl
+    Name EntrySlab
+    R 0 5 1
+    Z 0 0.1 1
+
+Geometry Cyl
+    Name PeakSlab
+    R 0 5 1
+    Z 15.3 15.4 1
+
+Filter
+    Name Protons
+    Z == 1
+    A == 1
+Filter
+    Name Primaries
+    Z == 1
+    A == 1
+    GEN == 0
+Filter
+    Name Secondary_protons
+    Z == 1
+    A == 1
+    GEN >= 1
+Output
+    Filename z_profile.bdo
+    Geo CylZ_Mesh
+    Quantity Dose 
+    Quantity Fluence Protons
+    Quantity Fluence Primaries
+    Quantity Fluence Secondary_protons
+
+Output
+    Filename yz_profile.bdo
+    Geo YZ_Mesh
+    Quantity Dose 
+    Quantity Fluence Protons
+    Quantity Fluence Secondary_protons
+
+Output
+    Filename entrance.bdo
+    Geo EntrySlab
+    Quantity Dose 
+    Quantity AvgEnergy Primaries
+    Quantity AvgEnergy Protons
+    Quantity AvgEnergy Secondary_protons
+    Quantity dLET Protons
+    Quantity tLET Protons
+    Quantity Fluence Protons
+    Diff1 0 160 640 
+    Diff1Type E
+
+Output
+    Filename peak.bdo
+    Geo PeakSlab
+    Quantity Dose 
+    Quantity AvgEnergy Primaries
+    Quantity AvgEnergy Protons
+    Quantity AvgEnergy Secondary_protons
+    Quantity dLET Protons
+    Quantity tLET Protons
+    Quantity Fluence Protons
+    Diff1 0 160 640 
+    Diff1Type E

input_examples/expected_shieldhit_output/geo.dat

@@ -0,0 +1,15 @@
+
+    0    0          Proton pencil beam in water
+  RCC    1       0.0       0.0       0.0       0.0       0.0      20.0
+                 5.0
+  RCC    2       0.0       0.0      -0.5       0.0       0.0      22.0
+                 5.5
+  RCC    3       0.0       0.0      -1.5       0.0       0.0      24.0
+                 6.0
+  END
+  001          +1
+  002          +2     -1
+  003          -2     +3     -1
+  END
+    1    2    3
+    1 1000    0

input_examples/expected_shieldhit_output/mat.dat

@@ -0,0 +1,3 @@
+MEDIUM 1
+ICRU 276
+END