Merge branch 'main' into simplify_low_mass_convective_star

.github/workflows/create_release.yml

@@ -0,0 +1,36 @@
+on:
+  push:
+    # Sequence of patterns matched against refs/tags
+    tags:
+      - '[0-9][0-9].[0-9][0-9]' 
+
+name: Create Release
+
+jobs:
+  build:
+    name: Create Release
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v3
+
+      - name: Get the version
+        id: get_version
+        run: echo "VERSION=${GITHUB_REF/refs\/tags\//}"  >> $GITHUB_ENV
+
+      - name: Set release text
+        id: release_txt
+        run: |
+          python3 .github/workflows/get_release_txt.py ${{ env.VERSION }} >> $GITHUB_ENV
+
+      - name: Create Release
+        id: create_release
+        uses: actions/create-release@v1
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} # This token is provided by Actions, you do not need to create your own token
+        with:
+          tag_name: ${{ github.ref }}
+          release_name: Release ${{ github.ref }}
+          body: ${{ env.RELEASE_TXT }}
+          draft: false
+          prerelease: false

.github/workflows/get_release_txt.py

@@ -0,0 +1,37 @@
+#!/usr/bin/env python3
+
+"""
+Get the text for the release from CHANGES.md
+"""
+
+import re
+import sys
+
+if __name__ == "__main__":
+    if len(sys.argv) < 2:
+        print('No version provided!')
+    else:
+        gen_version_re = re.compile(r'#\s(\d\d\.\d\d)')
+        this_version_re = re.compile(f'#\s{sys.argv[1]}')
+
+        with open('CHANGES.md', 'r') as file:
+            txt = file.read()
+            m = re.search(this_version_re, txt)
+            if m:
+                # find next date
+                m_next = re.search(gen_version_re, txt[m.end():])
+                if m_next:
+                    txt = txt[m.end():m.end()+m_next.start()].strip()
+                else:
+                    txt = txt[m.end():].strip()
+            else:
+                txt = ""
+
+            # we now need to substitute characters in the string so that 
+            # the action can deal with line breaks 
+            txt = txt.replace('%', '%25')
+            txt = txt.replace('\n', '%0A')
+            txt = txt.replace('\r', '%0D')
+            txt = txt.replace('%0A   *', '%0A*')
+
+            print(f'"RELEASE_TXT=${{{txt}}}"')

.github/workflows/sub_chandra.yml

@@ -50,7 +50,7 @@ jobs:
       - name: Compare to stored output
         run: |
           cd sub_chandra
-          diff sub_chandra.M_WD-1.10.M_He-0.050.hse.CO.N14.10.00km ci-benchmarks/sub_chandra.M_WD-1.10.M_He-0.050.hse.CO.N14.10.00km
+          diff sub_chandra.M_WD-1.10.M_He-0.050.delta50.00km.hse.CO.N14.10.00km ci-benchmarks/sub_chandra.M_WD-1.10.M_He-0.050.delta50.00km.hse.CO.N14.10.00km
 
 
 

.github/workflows/urca.yml

@@ -0,0 +1,58 @@
+name: urca
+
+on: [pull_request]
+jobs:
+  urca:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+        with:
+          fetch-depth: 0
+
+      - name: Get AMReX
+        run: |
+          mkdir external
+          cd external
+          git clone https://github.com/AMReX-Codes/amrex.git
+          cd amrex
+          git checkout development
+          echo 'AMREX_HOME=$(GITHUB_WORKSPACE)/external/amrex' >> $GITHUB_ENV
+          echo $AMREX_HOME
+          if [[ -n "${AMREX_HOME}" ]]; then exit 1; fi
+          cd ../..
+
+      - name: Get Microphysics
+        run: |
+          cd external
+          git clone https://github.com/AMReX-Astro/Microphysics.git
+          cd Microphysics
+          git checkout development
+          echo 'MICROPHYSICS_HOME=$(GITHUB_WORKSPACE)/external/Microphysics' >> $GITHUB_ENV
+          echo $MICROPHYSICS_HOME
+          if [[ -n "${MICROPHYSICS_HOME}" ]]; then exit 1; fi
+          cd ../..
+
+      - name: Install dependencies
+        run: |
+          sudo apt-get update -y -qq
+          sudo apt-get -qq -y install curl cmake jq clang g++>=9.3.0
+
+      - name: Compile
+        run: |
+          cd urca/spherical
+          make -j2
+
+      - name: Run with regular grid
+        run: |
+          cd urca/spherical
+          ./initialmodel3d.gnu.ex inputs
+
+      - name: Compare to stored output
+        run: |
+          cd urca/spherical
+          diff WD_urca_nuc_cpp_hot.hse.1024 ci-benchmarks/WD_urca_nuc_cpp_hot.hse.1024
+
+
+
+
+

.zenodo.json

@@ -0,0 +1,29 @@
+{
+    "creators": [
+        {
+            "name": "AMReX-Astro initial_models team"
+        },
+        {   "affiliation": "Department of Physics and Astronomy, Stony Brook University",
+            "name": "Boyd, Brendan",
+            "orcid": "0000-0002-5419-9751"
+        },
+        {
+            "affiliation": "Department of Physics and Astronomy, Stony Brook University",
+            "name": "Smith Clark, Alexander",
+            "orcid": "0000-0001-5961-1680"
+        },
+        {
+            "affiliation": "Center for Computational Sciences and Engineering, Lawrence Berkeley National Laboratory",
+            "name": "Willcox, Donald",
+            "orcid": "0000-0003-2300-5165"
+        },
+        {
+            "affiliation": "Department of Physics and Astronomy, Stony Brook University",
+            "name": "Zingale, Michael",
+            "orcid": "0000-0001-8401-030X"
+        }
+    ],
+    "keywords": [
+        "astrophysics"
+    ]
+}

CHANGES.md

@@ -0,0 +1,3 @@
+# 23.09
+
+Initial release of initial_models.  All code has been converted to C++