Merge pull request #631 from galacticusorg/featMangleBuild

Build `mangle` from our forked repo

.github/workflows/cicd.yml

@@ -372,12 +372,14 @@ jobs:
           forutilsVersion=`awk '{if ($1 == "forutils:") print $2}' ${GALACTICUS_EXEC_PATH}/aux/dependencies.yml`
           fspsVersion=`awk '{if ($1 == "fsps:") print $2}' ${GALACTICUS_EXEC_PATH}/aux/dependencies.yml`
           cloudyVersion=`awk '{if ($1 == "cloudy:") print $2}' ${GALACTICUS_EXEC_PATH}/aux/dependencies.yml`
+          mangleVersion=`awk '{if ($1 == "mangle:") print $2}' ${GALACTICUS_EXEC_PATH}/aux/dependencies.yml`
           # Check that executables were statically linked
           ! ldd dynamic/CAMB-${cambVersion}/fortran/camb
           ! ldd dynamic/AxionCAMB/camb
           ! ldd dynamic/class_public-${classVersion}/class
           ! ldd dynamic/RecFast/recfast.exe
           ! ldd dynamic/fsps-${fspsVersion}/src/autosps.exe
+          ! ldd dynamic/mangle-${mangleVersion}/bin/ransack
           tar cfj tools.tar.bz2 \
             dynamic/CAMB-${cambVersion}/fortran/camb \
             dynamic/AxionCAMB/camb \
@@ -392,7 +394,8 @@ jobs:
             dynamic/fsps-${fspsVersion}/nebular \
             dynamic/fsps-${fspsVersion}/SPECTRA \
             dynamic/fsps-${fspsVersion}/OUTPUTS \
-            dynamic/fsps-${fspsVersion}/ISOCHRONES
+            dynamic/fsps-${fspsVersion}/ISOCHRONES \
+            dynamic/mangle-${mangleVersion}/bin/harmonize
       - name: Upload tools
         uses: actions/upload-artifact@v4
         with:
@@ -532,6 +535,7 @@ jobs:
           forutilsVersion=`awk '{if ($1 == "forutils:") print $2}' ${GALACTICUS_EXEC_PATH}/aux/dependencies.yml`
           fspsVersion=`awk '{if ($1 == "fsps:") print $2}' ${GALACTICUS_EXEC_PATH}/aux/dependencies.yml`
           cloudyVersion=`awk '{if ($1 == "cloudy:") print $2}' ${GALACTICUS_EXEC_PATH}/aux/dependencies.yml`
+          mangleVersion=`awk '{if ($1 == "mangle:") print $2}' ${GALACTICUS_EXEC_PATH}/aux/dependencies.yml`
           cd $GALACTICUS_EXEC_PATH
           git config --global --add safe.directory $GALACTICUS_EXEC_PATH
           mkdir -p $GALACTICUS_DATA_PATH/dynamic
@@ -549,6 +553,8 @@ jobs:
           $GALACTICUS_EXEC_PATH/scripts/build/staticRelinker.pl `grep -E '\-o cloudy.exe' $GALACTICUS_EXEC_PATH/build.log`
           cd $GALACTICUS_DATA_PATH/dynamic/fsps-${fspsVersion}/src
           $GALACTICUS_EXEC_PATH/scripts/build/staticRelinker.pl `grep -E '\-o autosps.exe' $GALACTICUS_EXEC_PATH/build.log`
+          cd $GALACTICUS_DATA_PATH/dynamic/mangle-${mangleVersion}/bin/
+          $GALACTICUS_EXEC_PATH/scripts/build/staticRelinker.pl `grep -E '\-o harmonize' $GALACTICUS_EXEC_PATH/build.log`
           cd $GALACTICUS_DATA_PATH
           zip -r toolsMacOS.zip \
             dynamic/CAMB-${cambVersion}/fortran/camb \
@@ -564,7 +570,8 @@ jobs:
             dynamic/fsps-${fspsVersion}/nebular \
             dynamic/fsps-${fspsVersion}/SPECTRA \
             dynamic/fsps-${fspsVersion}/OUTPUTS \
-            dynamic/fsps-${fspsVersion}/ISOCHRONES
+            dynamic/fsps-${fspsVersion}/ISOCHRONES \
+            dynamic/mangle-${mangleVersion}/bin/harmonize
       - name: Upload Galacticus executable
         uses: actions/upload-artifact@v4
         with:
@@ -605,6 +612,7 @@ jobs:
           forutilsVersion=`awk '{if ($1 == "forutils:") print $2}' ${GALACTICUS_EXEC_PATH}/aux/dependencies.yml`
           fspsVersion=`awk '{if ($1 == "fsps:") print $2}' ${GALACTICUS_EXEC_PATH}/aux/dependencies.yml`
           cloudyVersion=`awk '{if ($1 == "cloudy:") print $2}' ${GALACTICUS_EXEC_PATH}/aux/dependencies.yml`
+          mangleVersion=`awk '{if ($1 == "mangle:") print $2}' ${GALACTICUS_EXEC_PATH}/aux/dependencies.yml`
           cd $GALACTICUS_EXEC_PATH
           git config --global --add safe.directory $GALACTICUS_EXEC_PATH
           mkdir -p $GALACTICUS_DATA_PATH/dynamic
@@ -622,6 +630,8 @@ jobs:
           $GALACTICUS_EXEC_PATH/scripts/build/staticRelinker.pl `grep -E '\-o cloudy.exe' $GALACTICUS_EXEC_PATH/build.log`
           cd $GALACTICUS_DATA_PATH/dynamic/fsps-${fspsVersion}/src
           $GALACTICUS_EXEC_PATH/scripts/build/staticRelinker.pl `grep -E '\-o autosps.exe' $GALACTICUS_EXEC_PATH/build.log`
+          cd $GALACTICUS_DATA_PATH/dynamic/mangle-${mangleVersion}/bin/
+          $GALACTICUS_EXEC_PATH/scripts/build/staticRelinker.pl `grep -E '\-o harmonize' $GALACTICUS_EXEC_PATH/build.log`
           cd $GALACTICUS_DATA_PATH
           zip -r toolsMacOSM1.zip \
             dynamic/CAMB-${cambVersion}/fortran/camb \
@@ -637,7 +647,8 @@ jobs:
             dynamic/fsps-${fspsVersion}/nebular \
             dynamic/fsps-${fspsVersion}/SPECTRA \
             dynamic/fsps-${fspsVersion}/OUTPUTS \
-            dynamic/fsps-${fspsVersion}/ISOCHRONES
+            dynamic/fsps-${fspsVersion}/ISOCHRONES \
+            dynamic/mangle-${mangleVersion}/bin/harmonize
       - name: Upload Galacticus executable
         uses: actions/upload-artifact@v4
         with:

.github/workflows/dependencyBot.yml

@@ -148,3 +148,30 @@ jobs:
           branch: depup/${{ steps.depup.outputs.branch }}
           assignees: abensonca
           token: ${{ steps.generate-token.outputs.token }}
+  mangle:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: tibdex/github-app-token@v2
+        id: generate-token
+        with:
+          app_id: ${{ secrets.DEPLOY_APP_ID }}
+          private_key: ${{ secrets.DEPLOY_APP_PRIVATE_KEY }}
+      - uses: reviewdog/action-depup@v1
+        id: depup
+        with:
+          file: aux/dependencies.yml
+          version_name: mangle
+          repo: galacticusorg/mangle
+      - name: Create Pull Request
+        uses: peter-evans/create-pull-request@v6
+        with:
+          title: "fix(deps): update ${{ steps.depup.outputs.repo }} to ${{ steps.depup.outputs.latest }}"
+          commit-message: "fix(deps): update ${{ steps.depup.outputs.repo }} to ${{ steps.depup.outputs.latest }}"
+          body: |
+            Update ${{ steps.depup.outputs.repo }} to [${{ steps.depup.outputs.latest }}](https://github.com/${{ steps.depup.outputs.repo }}/releases/tag/v${{ steps.depup.outputs.latest }})
+
+            This PR is auto generated by [dependencyBot](https://github.com/${{ github.repository }}/actions?query=workflow%3A${{ github.workflow }}).
+          branch: depup/${{ steps.depup.outputs.repo }}
+          assignees: abensonca
+          token: ${{ steps.generate-token.outputs.token }}

.github/workflows/profile.yml

@@ -94,8 +94,9 @@ jobs:
           forutilsVersion=`awk '{if ($1 == "forutils:") print $2}' ${GALACTICUS_EXEC_PATH}/aux/dependencies.yml`
           fspsVersion=`awk '{if ($1 == "fsps:") print $2}' ${GALACTICUS_EXEC_PATH}/aux/dependencies.yml`
           cloudyVersion=`awk '{if ($1 == "cloudy:") print $2}' ${GALACTICUS_EXEC_PATH}/aux/dependencies.yml`
+          mangleVersion=`awk '{if ($1 == "mangle:") print $2}' ${GALACTICUS_EXEC_PATH}/aux/dependencies.yml`
           find $GALACTICUS_DATA_PATH/dynamic/ -type d \( -path $GALACTICUS_DATA_PATH/dynamic/fsps-${fspsVersion} -o -path $GALACTICUS_DATA_PATH/dynamic/AxionCAMB -o -path $GALACTICUS_DATA_PATH/dynamic/CAMB-${cambVersion} -o -path $GALACTICUS_DATA_PATH/dynamic/RecFast -o -path $GALACTICUS_DATA_PATH/dynamic/class_public-${classVersion} \) -prune -o -type f -anewer mark.time -print
-          find $GALACTICUS_DATA_PATH/dynamic/ -type d \( -path $GALACTICUS_DATA_PATH/dynamic/fsps-${fspsVersion} -o -path $GALACTICUS_DATA_PATH/dynamic/AxionCAMB -o -path $GALACTICUS_DATA_PATH/dynamic/CAMB-${cambVersion} -o -path $GALACTICUS_DATA_PATH/dynamic/RecFast -o -path $GALACTICUS_DATA_PATH/dynamic/class_public-${classVersion} \) -prune -o -type f -not -anewer mark.time -print0 | xargs --no-run-if-empty -0 rm
+          find $GALACTICUS_DATA_PATH/dynamic/ -type d \( -path $GALACTICUS_DATA_PATH/dynamic/fsps-${fspsVersion} -o -path $GALACTICUS_DATA_PATH/dynamic/AxionCAMB -o -path $GALACTICUS_DATA_PATH/dynamic/CAMB-${cambVersion} -o -path $GALACTICUS_DATA_PATH/dynamic/RecFast -o -path $GALACTICUS_DATA_PATH/dynamic/class_public-${classVersion} -o -path $GALACTICUS_DATA_PATH/dynamic/mangle-${mangleVersion} \) -prune -o -type f -not -anewer mark.time -print0 | xargs --no-run-if-empty -0 rm
       - name: Upload profile
         uses: actions/upload-artifact@v4
         with:

.github/workflows/testModel.yml

@@ -167,8 +167,9 @@ jobs:
           forutilsVersion=`awk '{if ($1 == "forutils:") print $2}' ${GALACTICUS_EXEC_PATH}/aux/dependencies.yml`
           fspsVersion=`awk '{if ($1 == "fsps:") print $2}' ${GALACTICUS_EXEC_PATH}/aux/dependencies.yml`
           cloudyVersion=`awk '{if ($1 == "cloudy:") print $2}' ${GALACTICUS_EXEC_PATH}/aux/dependencies.yml`
-          find $GALACTICUS_DATA_PATH/dynamic/ -type d \( -path $GALACTICUS_DATA_PATH/dynamic/fsps-${fspsVersion} -o -path $GALACTICUS_DATA_PATH/dynamic/AxionCAMB -o -path $GALACTICUS_DATA_PATH/dynamic/CAMB-${cambVersion} -o -path $GALACTICUS_DATA_PATH/dynamic/RecFast -o -path $GALACTICUS_DATA_PATH/dynamic/class_public-${classVersion} \) -prune -o -type f -anewer mark.time -print
-          find $GALACTICUS_DATA_PATH/dynamic/ -type d \( -path $GALACTICUS_DATA_PATH/dynamic/fsps-${fspsVersion} -o -path $GALACTICUS_DATA_PATH/dynamic/AxionCAMB -o -path $GALACTICUS_DATA_PATH/dynamic/CAMB-${cambVersion} -o -path $GALACTICUS_DATA_PATH/dynamic/RecFast -o -path $GALACTICUS_DATA_PATH/dynamic/class_public-${classVersion} \) -prune -o -type f -not -anewer mark.time -print0 | xargs --no-run-if-empty -0 rm
+          mangleVersion=`awk '{if ($1 == "mangle:") print $2}' ${GALACTICUS_EXEC_PATH}/aux/dependencies.yml`
+          find $GALACTICUS_DATA_PATH/dynamic/ -type d \( -path $GALACTICUS_DATA_PATH/dynamic/fsps-${fspsVersion} -o -path $GALACTICUS_DATA_PATH/dynamic/AxionCAMB -o -path $GALACTICUS_DATA_PATH/dynamic/CAMB-${cambVersion} -o -path $GALACTICUS_DATA_PATH/dynamic/RecFast -o -path $GALACTICUS_DATA_PATH/dynamic/class_public-${classVersion} -o -path $GALACTICUS_DATA_PATH/dynamic/mangle-${mangleVersion} \) -prune -o -type f -anewer mark.time -print
+          find $GALACTICUS_DATA_PATH/dynamic/ -type d \( -path $GALACTICUS_DATA_PATH/dynamic/fsps-${fspsVersion} -o -path $GALACTICUS_DATA_PATH/dynamic/AxionCAMB -o -path $GALACTICUS_DATA_PATH/dynamic/CAMB-${cambVersion} -o -path $GALACTICUS_DATA_PATH/dynamic/RecFast -o -path $GALACTICUS_DATA_PATH/dynamic/class_public-${classVersion} -o -path $GALACTICUS_DATA_PATH/dynamic/mangle-${mangleVersion} \) -prune -o -type f -not -anewer mark.time -print0 | xargs --no-run-if-empty -0 rm
       - name: Upload result
         if: inputs.uploadName != '' && inputs.uploadFile != ''
         uses: actions/upload-artifact@v4

aux/dependencies.yml

@@ -3,3 +3,4 @@ camb: 1.5.5
 forutils: 1.0
 fsps: 3.2
 cloudy: 23.01
+mangle: 2.3.2

parameters/buildTools.xml

@@ -11,6 +11,7 @@
     <task value="buildToolCLASS"/>
     <task value="buildToolRecFast"/>
     <task value="buildToolCloudy"/>
+    <task value="buildToolMangle"/>
   </task>
 
 </parameters>