From d97b27b6abed6a0e0b0416214cebbfa806c70e61 Mon Sep 17 00:00:00 2001 From: "James P. Fairbanks" Date: Sat, 20 Jul 2024 12:38:06 -0400 Subject: [PATCH 01/11] update profile links for Ben and Luke to match Richard --- members/benbumpus.qmd | 6 ++++-- members/lukemorris.qmd | 8 ++++++-- project/sheaves.qmd | 3 ++- 3 files changed, 12 insertions(+), 5 deletions(-) diff --git a/members/benbumpus.qmd b/members/benbumpus.qmd index 24b0475..b40917c 100644 --- a/members/benbumpus.qmd +++ b/members/benbumpus.qmd @@ -4,8 +4,7 @@ image: images/benbumpus.png start_year: 2022 date: 10/1/2022 role: Research Assistant Professor -degree: -program: +degree: PhD status: Writing href: |- Site @@ -14,6 +13,9 @@ tools: href: members/benbumpus.qmd about: template: solana + links: + - text: Website + href: https://bmbumpus.com/ --- is a faculty research scientist and the lead of algorithms subprojects within the GATAS lab. diff --git a/members/lukemorris.qmd b/members/lukemorris.qmd index cd9eab4..0357d3d 100644 --- a/members/lukemorris.qmd +++ b/members/lukemorris.qmd @@ -13,14 +13,18 @@ tools: href: members/lukemorris.qmd about: template: solana + links: + - text: Website + href: https://www.cise.ufl.edu/~luke.morris + - icon: Github + text: Github + href: https://github.com/lukem12345 --- is leading development on the CombinatorialSpaces.jl and Decapodes.jl projects. ... for representing multiphysics models and automatically generating simulations from those representations. --- -[Personal Website](https://www.cise.ufl.edu/~luke.morris) - I am interested in problems that applied scientists face when they do any computational work. In particular, I mean the problems of developing models faster, and making the models themselves faster and more accurate. I lead a couple of projects on this front: [Decapodes.jl](https://github.com/AlgebraicJulia/Decapodes.jl) and [CombinatorialSpaces.jl](https://github.com/AlgebraicJulia/CombinatorialSpaces.jl). We use techniques from Applied Category Theory (ACT) to represent models (as "Decapodes") and how models compose together. These models are systems of partial differential equations (PDEs). ACT - the "science of composition" - lets us analyze scientific models as mathematical objects in their own right. [Catlab.jl](https://algebraicjulia.github.io/Catlab.jl/stable/) - an ACT programming library - enables us to write a library in an ACT-programming style, without sacrificing performance. We use Catlab's implementation of "C-Sets" by specifying a small Decapode "schema", which produces an efficient in-memory database to store a model. Doing algebra on these models then becomes as efficient as performing database operations. It is quite natural to interpret a system of PDEs as a relational database, adopting the point of view that such systems describe how physical quantities relate to one another. diff --git a/project/sheaves.qmd b/project/sheaves.qmd index 4bbb6b7..4af7e66 100644 --- a/project/sheaves.qmd +++ b/project/sheaves.qmd @@ -26,7 +26,7 @@ listing: - ../members/benbumpus.qmd - ../members/wilmerleal.qmd categories: true - fields: [image, title, start_year, degree, program] + fields: [image, title, start_year, degree, role] sort: none page-size: 10 field-display-names: @@ -34,6 +34,7 @@ listing: start_year: "Member Since" degree: "Degree" program: "Program" + role: "Role" --- [StructuredDecompositions.jl](https://github.com/AlgebraicJulia/StructuredDecompositions.jl) From 614ad320765f28b4176ddebca1239e0ce71e93db Mon Sep 17 00:00:00 2001 From: "James P. Fairbanks" Date: Wed, 31 Jul 2024 21:50:50 -0400 Subject: [PATCH 02/11] add ubuntu upgrade before installing tex dependencies --- .github/workflows/build_quarto.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/build_quarto.yml b/.github/workflows/build_quarto.yml index 4072daf..88b3218 100644 --- a/.github/workflows/build_quarto.yml +++ b/.github/workflows/build_quarto.yml @@ -5,7 +5,7 @@ on: pull_request: jobs: render: - uses: AlgebraicJulia/.github/.github/workflows/render_quarto.yml@main + uses: AlgebraicJulia/GATAS-website/.github/workflows/render_quarto.yml@main with: build_all: false save_build: true From b1ffd9d9cad03d1e09f6d339272d20b0d31b8c1e Mon Sep 17 00:00:00 2001 From: "James P. Fairbanks" Date: Wed, 31 Jul 2024 21:53:10 -0400 Subject: [PATCH 03/11] drop version number from linked yml --- .github/workflows/build_quarto.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/build_quarto.yml b/.github/workflows/build_quarto.yml index 88b3218..1fa0e07 100644 --- a/.github/workflows/build_quarto.yml +++ b/.github/workflows/build_quarto.yml @@ -5,7 +5,7 @@ on: pull_request: jobs: render: - uses: AlgebraicJulia/GATAS-website/.github/workflows/render_quarto.yml@main + uses: AlgebraicJulia/GATAS-website/.github/workflows/render_quarto.yml with: build_all: false save_build: true From 36c8539f8a3ae459700b6ff44c3b7493ecf911c1 Mon Sep 17 00:00:00 2001 From: "James P. Fairbanks" Date: Wed, 31 Jul 2024 21:53:55 -0400 Subject: [PATCH 04/11] use branch name as version in linked yml --- .github/workflows/build_quarto.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/build_quarto.yml b/.github/workflows/build_quarto.yml index 1fa0e07..c8360ac 100644 --- a/.github/workflows/build_quarto.yml +++ b/.github/workflows/build_quarto.yml @@ -5,7 +5,7 @@ on: pull_request: jobs: render: - uses: AlgebraicJulia/GATAS-website/.github/workflows/render_quarto.yml + uses: AlgebraicJulia/GATAS-website/.github/workflows/render_quarto.yml@jpf/fix-actions with: build_all: false save_build: true From 299e86b2f878215ec7c8ace15400d14c74f532de Mon Sep 17 00:00:00 2001 From: "James P. Fairbanks" Date: Wed, 31 Jul 2024 21:55:30 -0400 Subject: [PATCH 05/11] use local path in linked yml --- .github/workflows/build_quarto.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/build_quarto.yml b/.github/workflows/build_quarto.yml index c8360ac..b5df3f5 100644 --- a/.github/workflows/build_quarto.yml +++ b/.github/workflows/build_quarto.yml @@ -5,7 +5,7 @@ on: pull_request: jobs: render: - uses: AlgebraicJulia/GATAS-website/.github/workflows/render_quarto.yml@jpf/fix-actions + uses: ./.github/workflows/render_quarto.yml with: build_all: false save_build: true From 526350ae6535208c5a6e8568a04d833008aca454 Mon Sep 17 00:00:00 2001 From: "James P. Fairbanks" Date: Wed, 31 Jul 2024 21:56:28 -0400 Subject: [PATCH 06/11] add linked yml file to git --- .github/workflows/render_quarto.yml | 57 +++++++++++++++++++++++++++++ 1 file changed, 57 insertions(+) create mode 100644 .github/workflows/render_quarto.yml diff --git a/.github/workflows/render_quarto.yml b/.github/workflows/render_quarto.yml new file mode 100644 index 0000000..e05b43d --- /dev/null +++ b/.github/workflows/render_quarto.yml @@ -0,0 +1,57 @@ +name: Render Quarto Website +on: + workflow_call: + inputs: + build_all: + description: "Whether or not to delete the _freeze directory before rendering" + required: true + type: boolean + save_build: + description: "Whether or not to upload _site and _freeze artifacts" + required: true + type: boolean +jobs: + render: + runs-on: ubuntu-latest + env: + # Work around GR segfault: https://github.com/jheinen/GR.jl/issues/422 + GKSwstype: nul + steps: + - name: Checkout + uses: actions/checkout@v4 + with: + persist-credentials: false + - name: Install Quarto + uses: quarto-dev/quarto-actions/setup@v2 + - name: Intall LaTeX dependencies + run: | + sudo apt-get update + sudo apt-get install graphviz pdf2svg dvisvgm + quarto install tinytex --update-path + tlmgr update --self + tlmgr install tikz-cd luatex85 + - name: Install Julia + uses: julia-actions/setup-julia@v1 + with: + version: 1.8 + - name: Setup up Julia Project + run: | + python3 -m pip install jupyter + julia -e 'using Pkg; Pkg.activate("."); Pkg.instantiate();' + - name: Remove frozen posts + if: ${{ inputs.build_all }} + run: | + rm -rf _freeze _site + # TODO: IF RENDER FAILS, OPEN NEW ISSUE OF BROKEN POSTS + - name: Render Quarto Project + uses: quarto-dev/quarto-actions/render@v2 + - uses: actions/upload-artifact@v3 + if: ${{ inputs.save_build }} + with: + name: _site + path: _site + - uses: actions/upload-artifact@v3 + if: ${{ inputs.save_build }} + with: + name: _freeze + path: _freeze From f121a13e9f9f55dfb3263bd0d9530704c5407782 Mon Sep 17 00:00:00 2001 From: "James P. Fairbanks" Date: Wed, 31 Jul 2024 21:50:50 -0400 Subject: [PATCH 07/11] add ubuntu upgrade before installing tex dependencies --- .github/workflows/build_quarto.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/build_quarto.yml b/.github/workflows/build_quarto.yml index 4072daf..88b3218 100644 --- a/.github/workflows/build_quarto.yml +++ b/.github/workflows/build_quarto.yml @@ -5,7 +5,7 @@ on: pull_request: jobs: render: - uses: AlgebraicJulia/.github/.github/workflows/render_quarto.yml@main + uses: AlgebraicJulia/GATAS-website/.github/workflows/render_quarto.yml@main with: build_all: false save_build: true From 3404c56022691f3f196395547bbd55331bda0047 Mon Sep 17 00:00:00 2001 From: "James P. Fairbanks" Date: Wed, 31 Jul 2024 21:53:10 -0400 Subject: [PATCH 08/11] drop version number from linked yml --- .github/workflows/build_quarto.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/build_quarto.yml b/.github/workflows/build_quarto.yml index 88b3218..1fa0e07 100644 --- a/.github/workflows/build_quarto.yml +++ b/.github/workflows/build_quarto.yml @@ -5,7 +5,7 @@ on: pull_request: jobs: render: - uses: AlgebraicJulia/GATAS-website/.github/workflows/render_quarto.yml@main + uses: AlgebraicJulia/GATAS-website/.github/workflows/render_quarto.yml with: build_all: false save_build: true From 6a6e4f00c65a1ffaee9861df5769c9a95c739d3d Mon Sep 17 00:00:00 2001 From: "James P. Fairbanks" Date: Wed, 31 Jul 2024 21:53:55 -0400 Subject: [PATCH 09/11] use branch name as version in linked yml --- .github/workflows/build_quarto.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/build_quarto.yml b/.github/workflows/build_quarto.yml index 1fa0e07..c8360ac 100644 --- a/.github/workflows/build_quarto.yml +++ b/.github/workflows/build_quarto.yml @@ -5,7 +5,7 @@ on: pull_request: jobs: render: - uses: AlgebraicJulia/GATAS-website/.github/workflows/render_quarto.yml + uses: AlgebraicJulia/GATAS-website/.github/workflows/render_quarto.yml@jpf/fix-actions with: build_all: false save_build: true From 93993ae6152b15b93ee22a27480598a9a4e47bd2 Mon Sep 17 00:00:00 2001 From: "James P. Fairbanks" Date: Wed, 31 Jul 2024 21:55:30 -0400 Subject: [PATCH 10/11] use local path in linked yml --- .github/workflows/build_quarto.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/build_quarto.yml b/.github/workflows/build_quarto.yml index c8360ac..b5df3f5 100644 --- a/.github/workflows/build_quarto.yml +++ b/.github/workflows/build_quarto.yml @@ -5,7 +5,7 @@ on: pull_request: jobs: render: - uses: AlgebraicJulia/GATAS-website/.github/workflows/render_quarto.yml@jpf/fix-actions + uses: ./.github/workflows/render_quarto.yml with: build_all: false save_build: true From 3fc3b8be60ebcc0078f34148dc02cd0fb452c894 Mon Sep 17 00:00:00 2001 From: "James P. Fairbanks" Date: Wed, 31 Jul 2024 21:56:28 -0400 Subject: [PATCH 11/11] add linked yml file to git --- .github/workflows/render_quarto.yml | 57 +++++++++++++++++++++++++++++ 1 file changed, 57 insertions(+) create mode 100644 .github/workflows/render_quarto.yml diff --git a/.github/workflows/render_quarto.yml b/.github/workflows/render_quarto.yml new file mode 100644 index 0000000..e05b43d --- /dev/null +++ b/.github/workflows/render_quarto.yml @@ -0,0 +1,57 @@ +name: Render Quarto Website +on: + workflow_call: + inputs: + build_all: + description: "Whether or not to delete the _freeze directory before rendering" + required: true + type: boolean + save_build: + description: "Whether or not to upload _site and _freeze artifacts" + required: true + type: boolean +jobs: + render: + runs-on: ubuntu-latest + env: + # Work around GR segfault: https://github.com/jheinen/GR.jl/issues/422 + GKSwstype: nul + steps: + - name: Checkout + uses: actions/checkout@v4 + with: + persist-credentials: false + - name: Install Quarto + uses: quarto-dev/quarto-actions/setup@v2 + - name: Intall LaTeX dependencies + run: | + sudo apt-get update + sudo apt-get install graphviz pdf2svg dvisvgm + quarto install tinytex --update-path + tlmgr update --self + tlmgr install tikz-cd luatex85 + - name: Install Julia + uses: julia-actions/setup-julia@v1 + with: + version: 1.8 + - name: Setup up Julia Project + run: | + python3 -m pip install jupyter + julia -e 'using Pkg; Pkg.activate("."); Pkg.instantiate();' + - name: Remove frozen posts + if: ${{ inputs.build_all }} + run: | + rm -rf _freeze _site + # TODO: IF RENDER FAILS, OPEN NEW ISSUE OF BROKEN POSTS + - name: Render Quarto Project + uses: quarto-dev/quarto-actions/render@v2 + - uses: actions/upload-artifact@v3 + if: ${{ inputs.save_build }} + with: + name: _site + path: _site + - uses: actions/upload-artifact@v3 + if: ${{ inputs.save_build }} + with: + name: _freeze + path: _freeze