Merge branch 'master' into debug

.github/workflows/build_wheels.yml

@@ -0,0 +1,52 @@
+name: swiftest
+
+on: 
+  release:
+    types: [published]
+
+jobs:
+  build_wheels:
+    name: Build wheels on ${{ matrix.os }}
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        os: [ubuntu-latest, macos-11, macos-12, macos-13]
+        cibw_archs: [x86_64]
+        include:
+          - os: ubuntu-latest
+            cibw_archs: "aarch64"
+    env:
+      SYSTEM_VERSION_COMPAT: 0
+
+    steps:
+      - name: Set up QEMU
+        if: matrix.cibw_archs == 'aarch64'
+        uses: docker/setup-qemu-action@v2
+        with:
+          platforms: arm64        
+      - uses: actions/checkout@v3
+      - name: Build wheels
+        uses: pypa/cibuildwheel@v2.15.0
+        env:
+          CIBW_ARCHS: ${{ matrix.cibw_archs }}
+        with:
+          package-dir: .
+          output-dir: wheelhouse
+          config-file: "{package}/pyproject.toml"
+
+      - uses: actions/upload-artifact@v3
+        with:
+          path: ./wheelhouse/*.whl
+
+  build_sdist:
+    name: Build source distribution
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Build sdist
+        run: pipx run build --sdist
+
+      - uses: actions/upload-artifact@v3
+        with:
+          path: dist/*.tar.gz

.github/workflows/draft-pdf.yml

@@ -0,0 +1,23 @@
+on: [push]
+
+jobs:
+  paper:
+    runs-on: ubuntu-latest
+    name: Paper Draft
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v3
+      - name: Build draft PDF
+        uses: openjournals/openjournals-draft-action@master
+        with:
+          journal: joss
+          # This should be the path to the paper within your repo.
+          paper-path: paper/paper.md
+      - name: Upload
+        uses: actions/upload-artifact@v1
+        with:
+          name: paper
+          # This is the output path where Pandoc will write the compiled
+          # PDF. Note, this should be the same directory as the input
+          # paper.md
+          path: paper/paper.pdf

.gitignore

@@ -7,7 +7,8 @@
 swiftest_driver.sh
 !CMakeLists.txt
 !*.cmake
-!COPYING.txt
+!COPYING
+!LICENSE
 !CHANGELOG 
 !README.md
 !README_figs/**
@@ -18,10 +19,13 @@ swiftest_driver.sh
 !README.swifter 
 dump*
 !**/.gitignore
+!.github/workflows/*.yml
 !setup.py
 !examples/**
 !swiftest/**
 !tests/**
+!.zenodo.json
+!CITATION.cff
 *ipynb_checkpoints
 **/.DS_Store
 !version.txt
@@ -36,6 +40,7 @@ _dependencies
 
 
 #Documentation
+!mkdocs.yml
 !docs/*
 !docs/*/*
 !docs/*/*/*
@@ -55,4 +60,7 @@ netcdf-c-*
 netcdf-fortran-*
 zlib-*
 
+actions-runner*
 
+env/**
+venv/**

.zenodo.json

@@ -0,0 +1,58 @@
+{
+    "description": "Official release for the Journal of Open Source Software.", 
+    "license" : "GPLv3+", 
+    "title": "profminton/swiftest: v2023.10.2", 
+    "version": "v2023.10.2", 
+    "upload_type": "software", 
+    "publication_date": "2023-10-07", 
+    "creators": [
+      {
+        "name": "Carlisle Wishard",
+        "affiliation": [
+            "Department of Earth, Atmospheric, and Planetary Sciences, Purdue University, USA",
+            "Evansville Museum of Arts, History & Science, USA"
+          ],
+        "orcid": "0009-0001-0733-3268"
+      },
+      {
+        "name": "Jennifer Pouplin",
+        "affiliation": [
+          "Department of Earth, Atmospheric, and Planetary Sciences, Purdue University, USA",
+          "School of Aeronautics and Astronautics, Purdue University, USA"
+        ]
+      },
+      {
+        "name": "Jacob Elliott",
+        "affiliation": "Department of Earth, Atmospheric, and Planetary Sciences, Purdue University, USA"
+      },
+      {
+        "name": "Dana Singh",
+        "affiliation": "SAIC, Princeton, NJ, USA"
+      },
+      {
+        "name": "Kaustub Anand",
+        "affiliation": [
+          "Department of Earth, Atmospheric, and Planetary Sciences, Purdue University, USA",
+          "Department of Physics and Astronomy, Purdue University, USA"
+        ]
+      },
+      {
+        "name": "David Minton",
+        "affiliation": "Department of Earth, Atmospheric, and Planetary Sciences, Purdue University, USA",
+        "orcid": "0000-0003-1656-9704"
+      }
+    ],
+    "access_right": "open",
+    "related_identifiers": [
+        {
+            "scheme": "url", 
+            "identifier": "https://github.com/profminton/swiftest/tree/v2023.10.2", 
+            "relation": "isSupplementTo"
+        }, 
+        {
+            "scheme": "doi", 
+            "identifier": "10.5281/zenodo.8417147", 
+            "relation": "isVersionOf"
+        }
+    ]
+}

CITATION.cff

@@ -0,0 +1,22 @@
+cff-version: 1.1.0
+message: "If you use this software, please cite it as below."
+authors:
+  - name: Wishard
+    given-names: Carlislse
+    orcid: https://orcid.org/0009-0001-0733-3268
+  - family-names: Pouplin
+    given-names: Jennifer 
+  - family-names: Elliott
+    given-names: Jacob
+  - family-names: Dana
+    given-names: Singh
+  - family-names: Anand
+    given-names: Kaustub
+  - family-names: Minton
+    given-names: David
+    affiliation: "1"
+    orcid: https://orcid.org/0000-0003-1656-9704
+title: profminton/swiftest: v2023.10.2
+version: v2023.10.2
+date-released: 2023-10-07
+

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