Feature/GitHub actions

.github/workflows/publish.yaml

@@ -0,0 +1,206 @@
+
+name: Publish
+
+on:
+
+  push:
+    branches: [ master, main, develop, feature/github-actions]
+    tags: 'v*.*.*'
+
+  pull_request:
+    branches: '*'
+    types: opened
+
+  release:
+    types: [published]
+
+  workflow_dispatch:
+
+  repository_dispatch:
+    types: [release-event]
+
+jobs:
+
+  init:
+    runs-on: ubuntu-latest
+    outputs:
+      build_type: ${{ steps.setvars.outputs.build_type }}
+      luna_version: ${{ steps.setversion.outputs.luna_version }}
+
+    steps:
+      - name: Cancel previous workflow
+        uses: styfle/[email protected]
+        with:
+          access_token: ${{ github.token }}
+
+      - name: Set variables
+        id: setvars
+        #Only build the tests in a debug build, tests currently don't build in release mode
+        run: |
+          echo ${{github.base_ref}}
+          echo ${{github.ref}}
+          if [[ "${{github.base_ref}}" == "develop" || "${{github.ref}}" == "refs/heads/develop" ]]; then
+            echo "::set-output name=build_type::DEBUG"
+            echo Debug build
+          else
+            echo "::set-output name=build_type::RELEASE"
+          fi
+
+      - name: Set Luna version
+        id: setversion
+        run: |
+          git clone https://github.com/project8/luna_base.git
+          cd luna_base
+          echo "::set-output name=luna_version::$(git describe --abbrev=0 --tags)"
+
+  test_linux:
+    runs-on: ubuntu-latest
+    needs: [init]
+
+    strategy:
+      matrix:
+        build_type: [DEBUG, RELEASE]
+        compiler: [gcc]
+      fail-fast: false
+
+    steps:
+      - name: Checkout the repo 
+        uses: actions/checkout@v2
+        with:
+          submodules: recursive
+
+      - name: Set env
+        run: |
+          if [[ "${{matrix.compiler}}" == "gcc" ]]; then
+            echo "CXX_VAL=g++" >> $GITHUB_ENV
+          else
+            echo "CXX_VAL=clang++" >> $GITHUB_ENV
+          fi
+
+      - name: Print config
+        run: |
+            echo Build type: ${{ matrix.build_type }}
+            echo Compiler: ${{ matrix.compiler }} ${{ env.CXX_VAL }} 
+            echo Luna version: ${{ needs.init.outputs.luna_version }}
+
+      - name: Build with docker
+        run: |
+          cd ${{github.workspace}}
+          docker build \
+            --build-arg IMG_USER=project8 \
+            --build-arg IMG_REPO=p8compute_dependencies \
+            --build-arg IMG_TAG=${{ needs.init.outputs.luna_version }} \
+            --build-arg MERMITHID_TAG=test \
+            --build-arg build_type=${{matrix.build_type}} \
+            --build-arg CC_VAL=${{matrix.compiler}} \
+            --build-arg CXX_VAL=${{env.CXX_VAL}} \
+            --tag project8/mermithid:test \
+            .
+
+  publish:
+    if: github.event_name != 'pull_request'
+    name: Push Docker image to Docker Hub
+    runs-on: ubuntu-latest
+    needs: [init, test_linux]
+    steps:
+
+      - name: Check out the repo
+        uses: actions/checkout@v2
+        with:
+          submodules: recursive
+
+      - name: Docker meta
+        id: docker_meta
+        uses: docker/metadata-action@v3
+        with:
+          images: project8/mermithid
+
+      - name: Set up QEMU
+        uses: docker/setup-qemu-action@v1
+
+      - name: Set up Docker Buildx
+        id: setup_buildx
+        uses: docker/setup-buildx-action@v1
+        with:
+          buildkitd-flags: --debug
+
+      - name: List platforms
+        run: | 
+            echo Platforms: ${{ steps.setup_buildx.outputs.platforms }}
+
+      - name: Log in to Docker Hub
+        uses: docker/login-action@v1
+        with:
+          username: ${{ secrets.DOCKER_USERNAME }}
+          password: ${{ secrets.DOCKER_PASSWORD }}
+
+      - name: Set env
+        run: | 
+            echo "RELEASE_VERSION=${GITHUB_REF#refs/*/}" >> $GITHUB_ENV
+
+      - name: Print config
+        run: |
+            echo Release version: ${{ env.RELEASE_VERSION }}
+            echo Luna version: ${{ needs.init.outputs.luna_version }}
+
+      - name: Push to Docker Hub
+        id: build_push
+        uses: docker/build-push-action@v2
+        with:
+          context: .
+          push: true
+          build-args: |
+            IMG_USER=project8
+            IMG_REPO=p8compute_dependencies
+            IMG_TAG=${{ needs.init.outputs.luna_version }}
+            MERMITHID_TAG=${{ env.RELEASE_VERSION }}
+            build_type=${{needs.init.outputs.build_type}}
+          tags: ${{ steps.docker_meta.outputs.tags }}
+
+# disabled due to error
+#  doc:
+#    name: Build documentation
+#    runs-on: ubuntu-latest
+#    #needs: [init, test_linux]
+#    steps:
+#    
+#      - name: Check out the repo
+#        uses: actions/checkout@v2
+#        with:
+#          submodules: recursive
+#          fetch-depth: 0
+#      
+#      - name: Install dependencies
+#        run: |
+#          sudo apt-get update
+#          DEBIAN_FRONTEND=noninteractive sudo apt-get install -y \
+#            tree \
+#            doxygen \
+#            python3-sphinx \
+#            graphviz
+#          pip install sphinxcontrib-blockdiag
+#          pip install sphinxcontrib-contentui
+#      
+#      - name: Build docs
+#        run: |
+#          cd Documentation
+#          make
+
+  notify-packages:
+
+      if: (github.event_name == 'push' && contains(github.ref, 'refs/tags/') ) 
+            || github.event_name == 'release' 
+            || github.event_name == 'workflow_dispatch'
+            || github.event_name == 'repository_dispatch'
+      name: Trigger new docker P8Compute image
+      runs-on: ubuntu-latest
+      needs: [publish]
+
+      steps:
+
+        - name: Repository dispatch
+          uses: peter-evans/repository-dispatch@v1
+          with:
+            token: ${{ secrets.REPO_ACCESS_TOKEN }}
+            repository: project8/luna
+            event-type: release-event

Dockerfile

@@ -7,9 +7,15 @@ FROM ${IMG_USER}/${IMG_REPO}:${IMG_TAG} as mermithid_common
 ARG build_type=Release
 ENV MERMITHID_BUILD_TYPE=$build_type
 
-ENV MERMITHID_TAG=v1.2.2
+ARG MERMITHID_TAG=beta
+ENV MERMITHID_TAG=${MERMITHID_TAG}
 ENV MERMITHID_BUILD_PREFIX=/usr/local/p8/mermithid/$MERMITHID_TAG
 
+ARG CC_VAL=gcc
+ENV CC=${CC_VAL}
+ARG CXX_VAL=g++
+ENV CXX=${CXX_VAL}
+
 RUN mkdir -p $MERMITHID_BUILD_PREFIX &&\
     chmod -R 777 $MERMITHID_BUILD_PREFIX/.. &&\
     cd $MERMITHID_BUILD_PREFIX &&\
@@ -22,6 +28,10 @@ RUN mkdir -p $MERMITHID_BUILD_PREFIX &&\
     echo 'export PYTHONPATH=$MERMITHID_BUILD_PREFIX/$(python3 -m site --user-site | sed "s%$(python3 -m site --user-base)%%"):$PYTHONPATH' >> setup.sh &&\
     /bin/true
 
+RUN source $COMMON_BUILD_PREFIX/setup.sh &&\
+    pip install iminuit &&\
+    /bin/true
+
 ########################
 FROM mermithid_common as mermithid_done
 

mermithid/misc/ComplexLineShapeUtilities.py

@@ -58,6 +58,10 @@ def aseev_func_tail(energy_loss_array, gas_type):
         A2, omeg2, eps2 = 0.195, 14.13, 10.60
     elif gas_type=="Kr":
         A2, omeg2, eps2 = 0.4019, 22.31, 16.725
+    elif gas_type=="He":
+        A2, omeg2, eps2 = 0.1187, 33.40, 10.43
+    elif gas_type=="Ar":
+        A2, omeg2, eps2 = 0.3344, 21.91, 21.14
     return A2*omeg2**2./(omeg2**2.+4*(energy_loss_array-eps2)**2.)
 
 #convert oscillator strength into energy loss spectrum

mermithid/misc/FakeTritiumDataFunctions.py

@@ -7,6 +7,7 @@
 from __future__ import absolute_import
 
 import numpy as np
+import json
 
 from scipy.special import gamma
 from scipy import integrate
@@ -18,7 +19,6 @@
 
 from mermithid.misc.Constants import *
 from mermithid.misc.ConversionFunctions import *
-from mermithid.misc.KrLineshapeFunctions import *
 
 """
 Constants and functions used by processors/TritiumSpectrum/FakeDataGenerator.py
@@ -147,13 +147,42 @@ def spectral_rate_in_window(K, Q, mnu, Kmin):
     else:
         return 0.
 
+
+def beta_rates(K, Q, mnu, index):
+    beta_rates = np.zeros(len(K))
+    nu_mass_shape = ((Q - K[index])**2 -mnu**2)**0.5
+    beta_rates[index] = GF**2.*Vud**2*Mnuc2/(2.*np.pi**3)*ephasespace(K[index], Q)*(Q - K[index])*nu_mass_shape
+    return beta_rates
+
+
+
 # Unsmeared eta spectrum without a lower energy bound
-def spectral_rate(K, Q, mnu):
-    if Q-mnu > K > 0:
-        return GF**2.*Vud**2*Mnuc2/(2.*np.pi**3)*ephasespace(K, Q)*(Q - K)*np.sqrt((Q - K)**2 - (mnu)**2)
+def spectral_rate(K, Q, mnu, final_state_array):
+
+    if isinstance(K, list) or isinstance(K, np.ndarray):
+        N_states = len(final_state_array[0])
+        beta_rates_array = np.zeros([N_states, len(K)])
+
+        Q_states = Q+final_state_array[0]-np.max(final_state_array[0])
+
+        index = [np.where(K < Q_states[i]-mnu) for i in range(N_states)]
+
+        beta_rates_array = [beta_rates(K, Q_states[i], mnu, index[i])*final_state_array[1][i] for i in range(N_states)]
+        to_return = np.nansum(beta_rates_array, axis=0)/np.nansum(final_state_array[1])
+
+        return to_return
+
     else:
-            return 0.
-    #np.heaviside(Q-mnu-K, 0.5)*np.heaviside(K-V0, 0.5)
+
+        return_value = 0.
+
+        for i, e_binding in enumerate(final_state_array[0]):
+            # binding energies are negative
+            Q_state = Q+e_binding
+            if Q_state-mnu > K > 0:
+                return_value += final_state_array[1][i] *(GF**2.*Vud**2*Mnuc2/(2.*np.pi**3)*ephasespace(K, Q_state)*(Q_state - K)*np.sqrt((Q_state - K)**2 - (mnu)**2))
+
+        return return_value/np.sum(final_state_array[1])
 
 
 #Flat background with lower and upper bounds Kmin and Kmax
@@ -169,12 +198,12 @@ def bkgd_rate():
     return 1.
 
 
-##Lineshape option: In this case, simply a Gaussian
-#def gaussian(x,a):
-#    return 1/((2.*np.pi)**0.5*a[0])*(np.exp(-0.5*((x-a[1])/a[0])**2))
+#Lineshape option: In this case, simply a Gaussian
+def gaussian(x,a):
+    return 1/((2.*np.pi)**0.5*a[0])*(np.exp(-0.5*((x-a[1])/a[0])**2))
 
 
-#Normalized simplified linesahape with scattering
+#Normalized simplified lineshape with scattering
 def simplified_ls(K, Kcenter, FWHM, prob, p0, p1, p2, p3):
     sig0 = FWHM/float(2*np.sqrt(2*np.log(2)))
     shape = gaussian(K, [sig0, Kcenter])
@@ -245,7 +274,8 @@ def convolved_bkgd_rate(K, Kmin, Kmax, lineshape, ls_params, min_energy, max_ene
 
 #Convolution of signal and lineshape using scipy.signal.convolve
 def convolved_spectral_rate_arrays(K, Q, mnu, Kmin,
-                                   lineshape, ls_params, min_energy, max_energy):
+                                   lineshape, ls_params, min_energy, max_energy,
+                                   complexLineShape, final_state_array):
     """K is an array-like object
     """
     logger.info('Using scipy convolve')
@@ -263,11 +293,12 @@ def convolved_spectral_rate_arrays(K, Q, mnu, Kmin,
     elif lineshape=='simplified_scattering' or lineshape=='simplified':
         lineshape_rates = simplified_ls(K_lineshape, 0, ls_params[0], ls_params[1], ls_params[2], ls_params[3], ls_params[4], ls_params[5])
     elif lineshape=='detailed_scattering' or lineshape=='detailed':
-        lineshape_rates = spectrum_func(K_lineshape/1000., ls_params[0], 0, ls_params[1], 1)
 
-    beta_rates = np.zeros(len(K))
-    for i,ke in enumerate(K):
-        beta_rates[i] = spectral_rate(ke, Q, mnu)
+        lineshape_rates = complexLineShape.spectrum_func_1(K_lineshape/1000., ls_params[0], 0, 1, ls_params[1])
+
+    beta_rates = spectral_rate(K, Q, mnu, final_state_array) #np.zeros(len(K))
+    #for i,ke in enumerate(K):
+    #    beta_rates[i] = spectral_rate(ke, Q, mnu, final_state_array)
 
     #Convolving
     convolved = convolve(beta_rates, lineshape_rates, mode='same')
@@ -278,7 +309,7 @@ def convolved_spectral_rate_arrays(K, Q, mnu, Kmin,
 
 
 #Convolution of background and lineshape using scipy.signal.convolve
-def convolved_bkgd_rate_arrays(K, Kmin, Kmax, lineshape, ls_params, min_energy, max_energy):
+def convolved_bkgd_rate_arrays(K, Kmin, Kmax, lineshape, ls_params, min_energy, max_energy, complexLineShape):
     """K is an array-like object
     """
     energy_half_range = max(max_energy, abs(min_energy))
@@ -294,7 +325,7 @@ def convolved_bkgd_rate_arrays(K, Kmin, Kmax, lineshape, ls_params, min_energy,
     elif lineshape=='simplified_scattering' or lineshape=='simplified':
         lineshape_rates = simplified_ls(K_lineshape, 0, ls_params[0], ls_params[1], ls_params[2], ls_params[3], ls_params[4], ls_params[5])
     elif lineshape=='detailed_scattering' or lineshape=='detailed':
-        lineshape_rates = spectrum_func(K_lineshape/1000., ls_params[0], 0, ls_params[1], 1)
+        lineshape_rates = complexLineShape.spectrum_func_1(K_lineshape/1000., ls_params[0], 0, 1, ls_params[1])
 
     bkgd_rates = np.full(len(K), bkgd_rate())
     if len(K) < len(K_lineshape):