Merge branch 'efrc' of github.com:sandialabs/Polymers into efrc

.github/workflows/docker.yml

@@ -14,7 +14,7 @@ jobs:
       - name: checkout
         uses: actions/checkout@v4
       - name: build
-        uses: docker/build-push-action@v5
+        uses: docker/build-push-action@v6
         with:
           push: false
           tags: mrbuche/polymers:test
@@ -30,7 +30,7 @@ jobs:
           username: mrbuche
           password: ${{ secrets.DOCKERHUB_TOKEN }}
       - name: build-push
-        uses: docker/build-push-action@v5
+        uses: docker/build-push-action@v6
         with:
           push: true
           tags: mrbuche/polymers:latest
@@ -57,7 +57,7 @@ jobs:
           username: ${{ github.actor }}
           password: ${{ secrets.GITHUB_TOKEN }}
       - name: build-push
-        uses: docker/build-push-action@v5
+        uses: docker/build-push-action@v6
         with:
           push: true
           tags: |

.github/workflows/julia.yml

@@ -24,7 +24,7 @@ jobs:
           toolchain: nightly
           override: true
       - name: julia
-        uses: julia-actions/setup-julia@v1
+        uses: julia-actions/setup-julia@v2
         with:
           version: ${{ matrix.julia-version }}
       - name: test

.github/workflows/pages.yml

@@ -18,7 +18,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v4
-      - uses: actions/configure-pages@v4
+      - uses: actions/configure-pages@v5
       - uses: actions/jekyll-build-pages@v1
         with:
           source: ./pages/
@@ -42,9 +42,9 @@ jobs:
           julia --color=yes -e 'using Pkg; Pkg.add(url="https://github.com/sandialabs/Polymers", rev="'${{ steps.last_release.outputs.tag_name }}'")'
           mkdir -p _site/julia/docs/stable/
           julia --color=yes -e 'using Pkg; Pkg.add(["DocStringExtensions", "Documenter"])'
-          julia --color=yes docs/make.jl
-          grep -rl "footer-message" docs/build/ | xargs sed -i 's@<p class="footer-message">Powered by <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> and the <a href="https://julialang.org/">Julia Programming Language</a>.</p>@<footer><a href="http://sandia.gov/" rel="noopener noreferrer" target="_blank" style="text-decoration: none"><img alt="Sandia National Laboratories" longdesc="http://sandia.gov" src="https://raw.githubusercontent.com/sandialabs/Polymers/main/pages/assets/images/SNL_Horizontal_White.png" style="height:37px"></a>\&nbsp;\&nbsp;\&nbsp;<a href="http://energy.gov" rel="noopener noreferrer" target="_blank" style="text-decoration: none"><img alt="U.S. Department of Energy" longdesc="http://energy.gov" src="https://raw.githubusercontent.com/sandialabs/Polymers/main/pages/assets/images/New_DOE_Logo_White.png" style="height:37px"></a>\&nbsp;\&nbsp;\&nbsp;<a href="http://nnsa.energy.gov/" rel="noopener noreferrer" target="_blank" style="text-decoration: none"><img alt="National Nuclear Security Administration" longdesc="http://nnsa.gov" src="https://raw.githubusercontent.com/sandialabs/Polymers/main/pages/assets/images/NNSA Logo_White.png" style="height:37px"></a><br><br><div style="font-size: 0.8em">Sandia National Laboratories is a multimission laboratory managed and operated by National Technology and Engineering Solutions of Sandia, LLC., a wholly owned subsidiary of Honeywell International, Inc., for the U.S. Department of Energy\x27s National Nuclear Security Administration under contract DE-NA-0003525.</div></footer>@'
-          cp -r docs/build/* _site/julia/docs/stable/
+          # julia --color=yes docs/make.jl
+          # grep -rl "footer-message" docs/build/ | xargs sed -i 's@<p class="footer-message">Powered by <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> and the <a href="https://julialang.org/">Julia Programming Language</a>.</p>@<footer><a href="http://sandia.gov/" rel="noopener noreferrer" target="_blank" style="text-decoration: none"><img alt="Sandia National Laboratories" longdesc="http://sandia.gov" src="https://raw.githubusercontent.com/sandialabs/Polymers/main/pages/assets/images/SNL_Horizontal_White.png" style="height:37px"></a>\&nbsp;\&nbsp;\&nbsp;<a href="http://energy.gov" rel="noopener noreferrer" target="_blank" style="text-decoration: none"><img alt="U.S. Department of Energy" longdesc="http://energy.gov" src="https://raw.githubusercontent.com/sandialabs/Polymers/main/pages/assets/images/New_DOE_Logo_White.png" style="height:37px"></a>\&nbsp;\&nbsp;\&nbsp;<a href="http://nnsa.energy.gov/" rel="noopener noreferrer" target="_blank" style="text-decoration: none"><img alt="National Nuclear Security Administration" longdesc="http://nnsa.gov" src="https://raw.githubusercontent.com/sandialabs/Polymers/main/pages/assets/images/NNSA Logo_White.png" style="height:37px"></a><br><br><div style="font-size: 0.8em">Sandia National Laboratories is a multimission laboratory managed and operated by National Technology and Engineering Solutions of Sandia, LLC., a wholly owned subsidiary of Honeywell International, Inc., for the U.S. Department of Energy\x27s National Nuclear Security Administration under contract DE-NA-0003525.</div></footer>@'
+          # cp -r docs/build/* _site/julia/docs/stable/
       - name: add latest julia
         if: github.event_name != 'pull_request'
         run: julia --color=yes -e 'using Pkg; Pkg.add(url="https://github.com/sandialabs/Polymers", rev="'${GITHUB_REF##*/}'")'
@@ -55,10 +55,10 @@ jobs:
         run: |
           mkdir -p _site/julia/docs/latest/
           julia --color=yes -e 'using Pkg; Pkg.add(["DocStringExtensions", "Documenter"])'
-          julia --color=yes docs/make.jl
-          grep -rl "footer-message" docs/build/ | xargs sed -i 's@<p class="footer-message">Powered by <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> and the <a href="https://julialang.org/">Julia Programming Language</a>.</p>@<footer><a href="http://sandia.gov/" rel="noopener noreferrer" target="_blank" style="text-decoration: none"><img alt="Sandia National Laboratories" longdesc="http://sandia.gov" src="https://raw.githubusercontent.com/sandialabs/Polymers/main/pages/assets/images/SNL_Horizontal_White.png" style="height:37px"></a>\&nbsp;\&nbsp;\&nbsp;<a href="http://energy.gov" rel="noopener noreferrer" target="_blank" style="text-decoration: none"><img alt="U.S. Department of Energy" longdesc="http://energy.gov" src="https://raw.githubusercontent.com/sandialabs/Polymers/main/pages/assets/images/New_DOE_Logo_White.png" style="height:37px"></a>\&nbsp;\&nbsp;\&nbsp;<a href="http://nnsa.energy.gov/" rel="noopener noreferrer" target="_blank" style="text-decoration: none"><img alt="National Nuclear Security Administration" longdesc="http://nnsa.gov" src="https://raw.githubusercontent.com/sandialabs/Polymers/main/pages/assets/images/NNSA Logo_White.png" style="height:37px"></a><br><br><div style="font-size: 0.8em">Sandia National Laboratories is a multimission laboratory managed and operated by National Technology and Engineering Solutions of Sandia, LLC., a wholly owned subsidiary of Honeywell International, Inc., for the U.S. Department of Energy\x27s National Nuclear Security Administration under contract DE-NA-0003525.</div></footer>@'
-          cp -r docs/build/* _site/julia/docs/latest/
-      - uses: actions/upload-pages-artifact@v2
+          # julia --color=yes docs/make.jl
+          # grep -rl "footer-message" docs/build/ | xargs sed -i 's@<p class="footer-message">Powered by <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> and the <a href="https://julialang.org/">Julia Programming Language</a>.</p>@<footer><a href="http://sandia.gov/" rel="noopener noreferrer" target="_blank" style="text-decoration: none"><img alt="Sandia National Laboratories" longdesc="http://sandia.gov" src="https://raw.githubusercontent.com/sandialabs/Polymers/main/pages/assets/images/SNL_Horizontal_White.png" style="height:37px"></a>\&nbsp;\&nbsp;\&nbsp;<a href="http://energy.gov" rel="noopener noreferrer" target="_blank" style="text-decoration: none"><img alt="U.S. Department of Energy" longdesc="http://energy.gov" src="https://raw.githubusercontent.com/sandialabs/Polymers/main/pages/assets/images/New_DOE_Logo_White.png" style="height:37px"></a>\&nbsp;\&nbsp;\&nbsp;<a href="http://nnsa.energy.gov/" rel="noopener noreferrer" target="_blank" style="text-decoration: none"><img alt="National Nuclear Security Administration" longdesc="http://nnsa.gov" src="https://raw.githubusercontent.com/sandialabs/Polymers/main/pages/assets/images/NNSA Logo_White.png" style="height:37px"></a><br><br><div style="font-size: 0.8em">Sandia National Laboratories is a multimission laboratory managed and operated by National Technology and Engineering Solutions of Sandia, LLC., a wholly owned subsidiary of Honeywell International, Inc., for the U.S. Department of Energy\x27s National Nuclear Security Administration under contract DE-NA-0003525.</div></footer>@'
+          # cp -r docs/build/* _site/julia/docs/latest/
+      - uses: actions/upload-pages-artifact@v3
   deploy:
     if: github.event_name != 'pull_request'
     environment:
@@ -68,4 +68,4 @@ jobs:
     needs: build
     steps:
       - id: deployment
-        uses: actions/deploy-pages@v3
+        uses: actions/deploy-pages@v4

.github/workflows/rust.yml

@@ -36,7 +36,7 @@ jobs:
         uses: actions-rs/grcov@v0.1.6
       - name: codecov
         if: runner.os == 'Linux'
-        uses: codecov/codecov-action@v3
+        uses: codecov/codecov-action@v4
         with:
           fail_ci_if_error: true
           flags: rust

Dockerfile

@@ -1,4 +1,4 @@
-FROM julia:1.9.4 as julia
+FROM julia:1.10 as julia
 FROM python:3.12
 WORKDIR /
 RUN curl https://sh.rustup.rs -sSf | bash -s -- -y

Project.toml

@@ -13,7 +13,7 @@ DocStringExtensions = "0.9"
 Documenter = "0.27"
 JuliaFormatter = "1.0"
 Polymers_jll = "0.3.6"
-julia = "1.6 - 1.9"
+julia = "1"
 
 [extras]
 Aqua = "4c88cf16-eb10-579e-8560-4a9242c79595"

pages/_config.yml

@@ -1,8 +1,7 @@
 title: Polymers
 tagline: Polymers Modeling Library
 description: >-
-  Hello world!
-  Description goes here!
+  Polymers Modeling Library
 url: "https://sandialabs.github.io"
 baseurl: "/Polymers"
 

pages/index.md

@@ -8,4 +8,55 @@ permalink: /
 
 # Polymers Modeling Library
 
-Hello world!
+[![website](https://img.shields.io/badge/GitHub-website-6e5494?logo=github)](https://sandialabs.github.io/Polymers)
+[![examples](https://raw.githubusercontent.com/sandialabs/Polymers/main/pages/assets/images/binder.svg)](https://mybinder.org/v2/gh/sandialabs/Polymers/main)
+
+The library is implemented entirely in Rust, including the Python API. The Julia API calls the Rust library.
+
+## Python
+
+[![docs (stable)](https://img.shields.io/badge/Docs-stable-8CA1AF?logo=readthedocs)](https://polymers.readthedocs.io/en/stable)
+[![docs (latest)](https://img.shields.io/badge/Docs-latest-8CA1AF?logo=readthedocs)](https://polymers.readthedocs.io/en/latest)
+[![pypi](https://img.shields.io/pypi/v/polymers?logo=pypi&logoColor=FBE072&label=PyPI&color=4B8BBE)](https://pypi.org/project/polymers)
+
+The library can be installed as a Python package:
+
+```shell
+pip install polymers
+```
+
+## Julia
+
+[![docs (stable)](https://raw.githubusercontent.com/sandialabs/Polymers/main/pages/assets/images/julia-docs-stable.svg)](https://sandialabs.github.io/Polymers/julia/docs/stable)
+[![docs (latest)](https://raw.githubusercontent.com/sandialabs/Polymers/main/pages/assets/images/julia-docs-latest.svg)](https://sandialabs.github.io/Polymers/julia/docs/latest)
+[![Pkg](https://img.shields.io/github/v/release/sandialabs/Polymers?color=cb3c33&label=Pkg&logo=Julia&logoColor=cb3c33)](#)
+
+The library can be installed as a Julia package:
+
+```julia
+pkg> add Polymers
+```
+
+## Rust
+
+[![docs (stable)](https://img.shields.io/badge/Docs-stable-e57300?logo=rust&logoColor=000000)](https://docs.rs/crate/polymers)
+[![docs (latest)](https://img.shields.io/badge/Docs-latest-e57300?logo=rust&logoColor=000000)](https://sandialabs.github.io/Polymers/rust/docs/latest)
+[![crates](https://img.shields.io/crates/v/polymers?logo=rust&logoColor=000000&label=Crates&color=32592f)](https://crates.io/crates/polymers)
+
+The library can be added to an existing Rust project:
+
+```shell
+cargo add polymers
+```
+
+## Citation
+
+[![doi](https://img.shields.io/badge/Zenodo-10.5281%2Fzenodo.7041983-blue)](https://doi.org/10.5281/zenodo.7041983)
+
+Michael R. Buche. Polymers Modeling Library. [Zenodo (2023)](https://doi.org/10.5281/zenodo.7041983).
+
+## Copyright
+
+[![license](https://raw.githubusercontent.com/sandialabs/Polymers/main/pages/assets/images/bsd3c.svg)](https://github.com/sandialabs/polymers/blob/main/LICENSE)
+
+Copyright 2022 National Technology & Engineering Solutions of Sandia, LLC (NTESS). Under the terms of Contract DE-NA0003525 with NTESS, the U.S. Government retains certain rights in this software.