├── .devcontainer ├── Dockerfile ├── README.md ├── devcontainer.json └── setup.sh ├── .editorconfig ├── .envrc ├── .github └── workflows │ ├── ci.yml │ └── deploy.yml ├── .gitignore ├── .netlify-env ├── package.json ├── pnpm-lock.yaml └── pnpm-workspace.yaml ├── .npmrc ├── .rustfmt.toml ├── Cargo.lock ├── Cargo.nix ├── Cargo.toml ├── LICENSE ├── README.md ├── biome.json ├── dev-docs ├── .envrc ├── .gitignore ├── README.md ├── assets │ └── .gitignore ├── checksums.txt ├── forest.toml ├── forester ├── serve.sh ├── shell.nix ├── theme │ ├── .gitignore │ ├── LICENSES │ │ ├── CC0-1.0.txt │ │ ├── MIT.txt │ │ └── OFL-1.1.txt │ ├── android-chrome-192x192.png │ ├── android-chrome-512x512.png │ ├── apple-touch-icon.png │ ├── bundle-js.sh │ ├── core.xsl │ ├── custom.css │ ├── default.xsl │ ├── favicon-16x16.png │ ├── favicon-32x32.png │ ├── favicon.ico │ ├── fonts │ │ ├── KaTeX_AMS-Regular.ttf │ │ ├── KaTeX_AMS-Regular.woff │ │ ├── KaTeX_AMS-Regular.woff2 │ │ ├── KaTeX_Caligraphic-Bold.ttf │ │ ├── KaTeX_Caligraphic-Bold.woff │ │ ├── KaTeX_Caligraphic-Bold.woff2 │ │ ├── KaTeX_Caligraphic-Regular.ttf │ │ ├── KaTeX_Caligraphic-Regular.woff │ │ ├── KaTeX_Caligraphic-Regular.woff2 │ │ ├── KaTeX_Fraktur-Bold.ttf │ │ ├── KaTeX_Fraktur-Bold.woff │ │ ├── KaTeX_Fraktur-Bold.woff2 │ │ ├── KaTeX_Fraktur-Regular.ttf │ │ ├── KaTeX_Fraktur-Regular.woff │ │ ├── KaTeX_Fraktur-Regular.woff2 │ │ ├── KaTeX_Main-Bold.ttf │ │ ├── KaTeX_Main-Bold.woff │ │ ├── KaTeX_Main-Bold.woff2 │ │ ├── KaTeX_Main-BoldItalic.ttf │ │ ├── KaTeX_Main-BoldItalic.woff │ │ ├── KaTeX_Main-BoldItalic.woff2 │ │ ├── KaTeX_Main-Italic.ttf │ │ ├── KaTeX_Main-Italic.woff │ │ ├── KaTeX_Main-Italic.woff2 │ │ ├── KaTeX_Main-Regular.ttf │ │ ├── KaTeX_Main-Regular.woff │ │ ├── KaTeX_Main-Regular.woff2 │ │ ├── KaTeX_Math-BoldItalic.ttf │ │ ├── KaTeX_Math-BoldItalic.woff │ │ ├── KaTeX_Math-BoldItalic.woff2 │ │ ├── KaTeX_Math-Italic.ttf │ │ ├── KaTeX_Math-Italic.woff │ │ ├── KaTeX_Math-Italic.woff2 │ │ ├── KaTeX_SansSerif-Bold.ttf │ │ ├── KaTeX_SansSerif-Bold.woff │ │ ├── KaTeX_SansSerif-Bold.woff2 │ │ ├── KaTeX_SansSerif-Italic.ttf │ │ ├── KaTeX_SansSerif-Italic.woff │ │ ├── KaTeX_SansSerif-Italic.woff2 │ │ ├── KaTeX_SansSerif-Regular.ttf │ │ ├── KaTeX_SansSerif-Regular.woff │ │ ├── KaTeX_SansSerif-Regular.woff2 │ │ ├── KaTeX_Script-Regular.ttf │ │ ├── KaTeX_Script-Regular.woff │ │ ├── KaTeX_Script-Regular.woff2 │ │ ├── KaTeX_Size1-Regular.ttf │ │ ├── KaTeX_Size1-Regular.woff │ │ ├── KaTeX_Size1-Regular.woff2 │ │ ├── KaTeX_Size2-Regular.ttf │ │ ├── KaTeX_Size2-Regular.woff │ │ ├── KaTeX_Size2-Regular.woff2 │ │ ├── KaTeX_Size3-Regular.ttf │ │ ├── KaTeX_Size3-Regular.woff │ │ ├── KaTeX_Size3-Regular.woff2 │ │ ├── KaTeX_Size4-Regular.ttf │ │ ├── KaTeX_Size4-Regular.woff │ │ ├── KaTeX_Size4-Regular.woff2 │ │ ├── KaTeX_Typewriter-Regular.ttf │ │ ├── KaTeX_Typewriter-Regular.woff │ │ ├── KaTeX_Typewriter-Regular.woff2 │ │ ├── inria-sans-v14-latin_latin-ext-300.woff2 │ │ ├── inria-sans-v14-latin_latin-ext-300italic.woff2 │ │ ├── inria-sans-v14-latin_latin-ext-700.woff2 │ │ ├── inria-sans-v14-latin_latin-ext-700italic.woff2 │ │ ├── inria-sans-v14-latin_latin-ext-italic.woff2 │ │ └── inria-sans-v14-latin_latin-ext-regular.woff2 │ ├── forester.js │ ├── javascript-source │ │ └── forester.js │ ├── katex.min.css │ ├── links.xsl │ ├── metadata.xsl │ ├── package-lock.json │ ├── package.json │ ├── style.css │ └── tree.xsl ├── trees │ ├── bib-0001.tree │ ├── bib-0002.tree │ ├── bib-0003.tree │ ├── dbl-0001.tree │ ├── dbl-0002.tree │ ├── dbl-0003.tree │ ├── dbl-0004.tree │ ├── dbl-0005.tree │ ├── dbl-0006.tree │ ├── dbl-0007.tree │ ├── dbl-0008.tree │ ├── dbl-0009.tree │ ├── dbl-000A.tree │ ├── dbl-000B.tree │ ├── dbl-000C.tree │ ├── dbl-000D.tree │ ├── dbl-000E.tree │ ├── dbl-000F.tree │ ├── dbl-000G.tree │ ├── dbl-000H.tree │ ├── dbl-000I.tree │ ├── dct-0001.tree │ ├── dct-0002.tree │ ├── dct-0003.tree │ ├── dct-0004.tree │ ├── dct-0005.tree │ ├── dct-0006.tree │ ├── dct-0007.tree │ ├── dct-0008.tree │ ├── dct-0009.tree │ ├── dct-000A.tree │ ├── dct-000B.tree │ ├── dev-0001.tree │ ├── dev-0002.tree │ ├── dev-0003.tree │ ├── dev-0004.tree │ ├── dev-0005.tree │ ├── dev-0006.tree │ ├── dev-0007.tree │ ├── dev-0008.tree │ ├── dev-0009.tree │ ├── dev-000A.tree │ ├── dev-000B.tree │ ├── dev-000C.tree │ ├── dev-000D.tree │ ├── macros.tree │ ├── refs │ │ ├── acsets-2022.tree │ │ ├── alg-databases-2017.tree │ │ ├── baez-pollard-2017.tree │ │ ├── barbrook-johnson-2022.tree │ │ ├── cartesian-double-theories-2024.tree │ │ ├── double-products-2024.tree │ │ ├── grandis-2013-homological.tree │ │ ├── grandis-2019.tree │ │ ├── ologs-2012.tree │ │ ├── pisani-2024.tree │ │ ├── reg-nets-2024.tree │ │ ├── shulman-2008.tree │ │ └── stock-flow-2023.tree │ ├── thy-0001.tree │ ├── thy-0002.tree │ ├── thy-0003.tree │ ├── thy-0004.tree │ ├── thy-0005.tree │ ├── thy-0006.tree │ ├── thy-0007.tree │ ├── thy-0008.tree │ ├── thy-0009.tree │ ├── thy-000A.tree │ └── thy-000B.tree └── watch.sh ├── flake.lock ├── flake.nix ├── infrastructure ├── hosts │ ├── catcolab-next │ │ └── default.nix │ └── catcolab │ │ └── default.nix ├── modules │ ├── backend.nix │ ├── backup.nix │ └── host.nix ├── scripts │ ├── db-utils │ └── db-utils-lib.sh └── secrets │ ├── .env.next.age │ ├── .env.prod.age │ ├── rclone.conf.next.age │ ├── rclone.conf.prod.age │ └── secrets.nix ├── package.json ├── packages ├── algjulia-interop │ ├── .gitignore │ ├── Project.toml │ ├── README.md │ ├── jupyter_server.sh │ ├── make_sysimage.jl │ ├── src │ │ ├── CatColabInterop.jl │ │ ├── decapodes-service │ │ │ ├── DecapodesService.jl │ │ │ ├── analysis │ │ │ │ ├── Analysis.jl │ │ │ │ ├── initial_conditions.jl │ │ │ │ ├── ns_helper.jl │ │ │ │ └── simulation.jl │ │ │ ├── diagram.jl │ │ │ ├── geometry.jl │ │ │ └── model.jl │ │ └── kernel_support.jl │ ├── sysimage_precompile.jl │ └── test │ │ ├── Project.toml │ │ ├── runtests.jl │ │ └── test_jsons │ │ ├── diagrams │ │ ├── diffusivity_constant │ │ │ ├── analysis.json │ │ │ └── diagram.json │ │ ├── inverse_laplacian │ │ │ ├── analysis.json │ │ │ └── diagram.json │ │ ├── inverse_laplacian_longtrip │ │ │ ├── analysis.json │ │ │ └── diagram.json │ │ └── ns_vort │ │ │ ├── analysis.json │ │ │ └── diagram.json │ │ ├── diffconst_payload1.json │ │ ├── models │ │ ├── model_dec.json │ │ └── model_dec_scalar.json │ │ └── payload.json ├── automerge-doc-server │ ├── .gitignore │ ├── README.md │ ├── default.nix │ ├── package.json │ ├── pnpm-lock.yaml │ ├── src │ │ ├── main.ts │ │ ├── migrations │ │ │ ├── index.ts │ │ │ └── m20250516154702_automerge_storage.ts │ │ ├── postgres_storage_adapter.test.ts │ │ ├── postgres_storage_adapter.ts │ │ ├── server.ts │ │ ├── socket.ts │ │ └── types.ts │ └── tsconfig.json ├── backend │ ├── .gitignore │ ├── .sqlx │ │ ├── query-05183554f0c9207cdd1e89a948d3da5238ede1773a9507446694e9f7b4d2b16c.json │ │ ├── query-1ddd7b172b0db3b5e7818013b6bb9e2d57dc2e2bc13e1d7faa82e48a77964dcc.json │ │ ├── query-3645a86b3df08de865372b02d588272bb950744a38d46079ca18b11e405058a3.json │ │ ├── query-3e2b3e63a36ffa59ce60f8df19157edc1dfcee0d876d4b0c22c2db24feee6a3c.json │ │ ├── query-3e5c74f41ae9d78fc24ffda059fe9de4cc04f075e43aa9f5ae8237c5cda31726.json │ │ ├── query-3e715aa995094feff20f8254dfd27323844efa31ece5d40ce8778122687cdefc.json │ │ ├── query-4f04b1b2b42a310d659df5700aa47b10a291e6e98d2b989036e8d78ee3b00afd.json │ │ ├── query-513719212b96e260e9c4ce840f716b1b6cb43563371fb35f9677fcf949827363.json │ │ ├── query-6425b7d75c5fd6482701adba8011472860299d4fc872194449e18682cfed5bab.json │ │ ├── query-84f34c3f761dbab809edf2af4104e533a26a50310c90d340fdd90d64683b6b55.json │ │ ├── query-92973a6dc72749d528465057e8bd674427db3a290d6db645dea5ac3c540167ef.json │ │ ├── query-a80368dbf3e74206cdbe08744b1d46924d0731475384201d7f2ddaf51e8e3644.json │ │ ├── query-a8934c50209e48af661186c7d1c2ff8d8f23b4d05f1a7f5783baf74165f464f1.json │ │ ├── query-a8cb9f26893bbf784cf8a71090e64c3603e238ea6786d327f64ae04aef205198.json │ │ ├── query-cca19c531258c9500e4c27e139d15f8bfea54d7fd1b08728debfcacd5de174b4.json │ │ ├── query-cd63d277bd2ae2905790e11cddb4b9bcb5b56e952b854a75dc724e1c253afcf5.json │ │ ├── query-e75b5c0a7da4bc3c0f52a62179d15289fd31d08d48d7a99d37cb1a6414656e7d.json │ │ └── query-eea510d03cc559aa11d46aafe38f57789f5c2e791800f78a751602cc8336c84f.json │ ├── Cargo.toml │ ├── README.md │ ├── default.nix │ ├── pkg │ │ ├── package.json │ │ ├── pnpm-lock.yaml │ │ ├── src │ │ │ ├── NewPermissions.ts │ │ │ ├── Paginated.ts │ │ │ ├── PermissionLevel.ts │ │ │ ├── Permissions.ts │ │ │ ├── RefContent.ts │ │ │ ├── RefDoc.ts │ │ │ ├── RefQueryParams.ts │ │ │ ├── RefStub.ts │ │ │ ├── RpcResult.ts │ │ │ ├── UserPermissions.ts │ │ │ ├── UserProfile.ts │ │ │ ├── UserSummary.ts │ │ │ ├── UsernameStatus.ts │ │ │ ├── index.ts │ │ │ └── serde_json │ │ │ │ └── JsonValue.ts │ │ └── tsconfig.json │ └── src │ │ ├── app.rs │ │ ├── auth.rs │ │ ├── document.rs │ │ ├── main.rs │ │ ├── rpc.rs │ │ ├── socket.rs │ │ └── user.rs ├── catlog-wasm │ ├── .gitignore │ ├── Cargo.toml │ ├── README.md │ ├── src │ │ ├── analyses.rs │ │ ├── lib.rs │ │ ├── model.rs │ │ ├── model_diagram.rs │ │ ├── model_morphism.rs │ │ ├── result.rs │ │ ├── theories.rs │ │ └── theory.rs │ └── tests │ │ └── web.rs ├── catlog │ ├── .gitignore │ ├── Cargo.toml │ └── src │ │ ├── dbl │ │ ├── category.rs │ │ ├── graph.rs │ │ ├── mod.rs │ │ ├── model.rs │ │ ├── model_diagram.rs │ │ ├── model_morphism.rs │ │ ├── theory.rs │ │ └── tree.rs │ │ ├── egglog_util.rs │ │ ├── lib.rs │ │ ├── one │ │ ├── category.rs │ │ ├── fp_category.rs │ │ ├── graph.rs │ │ ├── graph_algorithms.rs │ │ ├── mod.rs │ │ ├── path.rs │ │ ├── tree.rs │ │ └── tree_algorithms.rs │ │ ├── refs.rs │ │ ├── simulate │ │ ├── mod.rs │ │ └── ode │ │ │ ├── lotka_volterra.rs │ │ │ ├── mod.rs │ │ │ └── polynomial.rs │ │ ├── stdlib │ │ ├── analyses │ │ │ ├── mod.rs │ │ │ └── ode │ │ │ │ ├── lotka_volterra.rs │ │ │ │ ├── mass_action.rs │ │ │ │ └── mod.rs │ │ ├── mod.rs │ │ ├── models.rs │ │ └── theories.rs │ │ ├── validate.rs │ │ └── zero │ │ ├── alg.rs │ │ ├── column.rs │ │ ├── mod.rs │ │ ├── rig.rs │ │ └── set.rs ├── frontend │ ├── .env.development │ ├── .env.production │ ├── .env.staging │ ├── .gitignore │ ├── README.md │ ├── index.html │ ├── netlify.toml │ ├── package.json │ ├── pnpm-lock.yaml │ ├── public │ │ └── topos_icon.png │ ├── src │ │ ├── App.tsx │ │ ├── analysis │ │ │ ├── analysis_editor.tsx │ │ │ ├── context.ts │ │ │ ├── document.ts │ │ │ ├── index.ts │ │ │ └── types.ts │ │ ├── api │ │ │ ├── context.ts │ │ │ ├── document.ts │ │ │ ├── document_rpc.test.ts │ │ │ ├── index.ts │ │ │ ├── rpc.ts │ │ │ ├── types.ts │ │ │ └── user_rpc.test.ts │ │ ├── components │ │ │ ├── alert.css │ │ │ ├── alert.tsx │ │ │ ├── completions.css │ │ │ ├── completions.tsx │ │ │ ├── dialog.css │ │ │ ├── dialog.tsx │ │ │ ├── fixed_table_editor.css │ │ │ ├── fixed_table_editor.tsx │ │ │ ├── foldable.css │ │ │ ├── foldable.tsx │ │ │ ├── form.css │ │ │ ├── form.tsx │ │ │ ├── icon_button.css │ │ │ ├── icon_button.tsx │ │ │ ├── id_input.css │ │ │ ├── id_input.tsx │ │ │ ├── index.ts │ │ │ ├── inline_input.css │ │ │ ├── inline_input.tsx │ │ │ ├── json_import.css │ │ │ ├── json_import.tsx │ │ │ ├── name_input.tsx │ │ │ ├── panel.css │ │ │ ├── panel.tsx │ │ │ ├── resizable.css │ │ │ ├── resizable.tsx │ │ │ ├── rich_text_editor.css │ │ │ ├── rich_text_editor.tsx │ │ │ ├── spinner.css │ │ │ └── spinner.tsx │ │ ├── diagram │ │ │ ├── context.ts │ │ │ ├── diagram_editor.css │ │ │ ├── diagram_editor.tsx │ │ │ ├── document.ts │ │ │ ├── index.ts │ │ │ ├── morphism_cell_editor.css │ │ │ ├── morphism_cell_editor.tsx │ │ │ ├── object_cell_editor.css │ │ │ ├── object_cell_editor.tsx │ │ │ ├── object_input.tsx │ │ │ └── types.ts │ │ ├── help │ │ │ ├── credits.mdx │ │ │ ├── help_container.css │ │ │ ├── help_container.tsx │ │ │ ├── index.mdx │ │ │ ├── quick_intro.mdx │ │ │ ├── routes.ts │ │ │ ├── theories.mdx │ │ │ ├── theories.tsx │ │ │ ├── theory.tsx │ │ │ └── theory │ │ │ │ ├── causal-loop-delays.mdx │ │ │ │ ├── causal-loop.mdx │ │ │ │ ├── empty.mdx │ │ │ │ ├── indeterminate-causal-loop.mdx │ │ │ │ ├── olog.mdx │ │ │ │ ├── reg-net.mdx │ │ │ │ ├── schema.mdx │ │ │ │ ├── stock-flow.mdx │ │ │ │ └── unary-dec.mdx │ │ ├── index.css │ │ ├── index.tsx │ │ ├── model │ │ │ ├── context.ts │ │ │ ├── document.ts │ │ │ ├── index.ts │ │ │ ├── model_editor.css │ │ │ ├── model_editor.tsx │ │ │ ├── morphism_cell_editor.css │ │ │ ├── morphism_cell_editor.tsx │ │ │ ├── morphism_input.tsx │ │ │ ├── object_cell_editor.css │ │ │ ├── object_cell_editor.tsx │ │ │ ├── object_input.tsx │ │ │ ├── theory_selector.css │ │ │ ├── theory_selector.tsx │ │ │ └── types.ts │ │ ├── notebook │ │ │ ├── index.ts │ │ │ ├── notebook_cell.css │ │ │ ├── notebook_cell.tsx │ │ │ ├── notebook_editor.css │ │ │ ├── notebook_editor.tsx │ │ │ └── types.ts │ │ ├── page │ │ │ ├── 404_page.tsx │ │ │ ├── context.ts │ │ │ ├── document_breadcrumbs.css │ │ │ ├── document_breadcrumbs.tsx │ │ │ ├── document_loading_screen.tsx │ │ │ ├── document_menu.tsx │ │ │ ├── import_document.tsx │ │ │ ├── index.ts │ │ │ ├── menubar.css │ │ │ ├── menubar.tsx │ │ │ ├── page_container.tsx │ │ │ ├── toolbar.css │ │ │ └── toolbar.tsx │ │ ├── stdlib │ │ │ ├── analyses │ │ │ │ ├── decapodes.css │ │ │ │ ├── decapodes.tsx │ │ │ │ ├── diagram_graph.tsx │ │ │ │ ├── graph_visualization.css │ │ │ │ ├── graph_visualization.tsx │ │ │ │ ├── index.ts │ │ │ │ ├── jupyter.ts │ │ │ │ ├── lotka_volterra.tsx │ │ │ │ ├── mass_action.tsx │ │ │ │ ├── model_graph.tsx │ │ │ │ ├── simulation.css │ │ │ │ ├── simulation.ts │ │ │ │ ├── stock_flow_diagram.tsx │ │ │ │ ├── submodel_graphs.css │ │ │ │ └── submodel_graphs.tsx │ │ │ ├── arrow_styles.module.css │ │ │ ├── arrow_styles.module.css.d.ts │ │ │ ├── context.ts │ │ │ ├── index.ts │ │ │ ├── styles.module.css │ │ │ ├── styles.module.css.d.ts │ │ │ ├── svg_styles.module.css │ │ │ ├── svg_styles.module.css.d.ts │ │ │ ├── text_styles.module.css │ │ │ ├── text_styles.module.css.d.ts │ │ │ ├── theories.tsx │ │ │ └── types.ts │ │ ├── theory │ │ │ ├── index.ts │ │ │ └── types.ts │ │ ├── user │ │ │ ├── documents.css │ │ │ ├── documents.tsx │ │ │ ├── index.ts │ │ │ ├── login.css │ │ │ ├── login.tsx │ │ │ ├── permissions.css │ │ │ ├── permissions.tsx │ │ │ ├── profile.tsx │ │ │ ├── username.css │ │ │ └── username.tsx │ │ ├── util │ │ │ ├── assert_exhaustive.ts │ │ │ ├── deepcopy.ts │ │ │ ├── errors.css │ │ │ ├── errors.tsx │ │ │ ├── focus.ts │ │ │ ├── indexing.ts │ │ │ ├── json_export.ts │ │ │ ├── mdx.tsx │ │ │ ├── test_util.ts │ │ │ └── types.ts │ │ ├── visualization │ │ │ ├── echarts.ts │ │ │ ├── export_svg.ts │ │ │ ├── export_svg_components.tsx │ │ │ ├── graph_layout.ts │ │ │ ├── graph_svg.css │ │ │ ├── graph_svg.tsx │ │ │ ├── graphviz.ts │ │ │ ├── graphviz_json.ts │ │ │ ├── graphviz_svg.tsx │ │ │ ├── index.ts │ │ │ ├── ode_plot.tsx │ │ │ ├── pde_plot.tsx │ │ │ └── types.ts │ │ └── vite-env.d.ts │ ├── tsconfig.json │ └── vite.config.ts ├── migrator │ ├── Cargo.toml │ ├── README.md │ ├── default.nix │ └── src │ │ ├── main.rs │ │ └── migrations │ │ ├── m20241004010448_document_refs.rs │ │ ├── m20241025030906_users.rs │ │ ├── m20250409171833_add_permissions_object_subject_idx.rs │ │ ├── m20250516154702_automerge_storage.rs │ │ └── mod.rs └── notebook-types │ ├── Cargo.toml │ ├── README.md │ ├── examples │ └── v0 │ │ ├── An Example Instance.json │ │ ├── CA Cap-and-trade.json │ │ ├── SEIRV.json │ │ ├── Sustainable Peace.json │ │ └── The Ontology of CatColab.json │ └── src │ ├── lib.rs │ └── v0 │ ├── analysis.rs │ ├── api.rs │ ├── cell.rs │ ├── diagram_judgment.rs │ ├── document.rs │ ├── mod.rs │ ├── model.rs │ ├── model_judgment.rs │ ├── notebook.rs │ ├── path.rs │ └── theory.rs ├── pnpm-lock.yaml ├── pnpm-workspace.yaml └── rust-toolchain.toml /.devcontainer/Dockerfile: -------------------------------------------------------------------------------- 1 | # Use a Debian base image 2 | FROM debian:bullseye-slim AS base 3 | 4 | # Install necessary packages 5 | RUN apt-get update && apt-get install -y \ 6 | curl \ 7 | build-essential \ 8 | && : 9 | 10 | # Install Node.js 18.x 11 | RUN curl -fsSL https://deb.nodesource.com/setup_18.x | bash - \ 12 | && apt-get install -y nodejs 13 | 14 | # Verify Node.js version 15 | #RUN node -v 16 | 17 | # Install Rust 18 | RUN curl https://sh.rustup.rs -sSf | sh -s -- -y \ 19 | && . "$HOME/.cargo/env" \ 20 | && rustup update 21 | 22 | # Ensure the Rust environment is available 23 | ENV PATH="/root/.cargo/bin:${PATH}" 24 | 25 | # Install pnpm globally 26 | RUN npm install -g pnpm 27 | 28 | # Copy project files so that we can install dependencies into the container image. 29 | WORKDIR /app 30 | COPY package.json pnpm-lock.yaml ./ 31 | 32 | # Install project dependencies 33 | RUN pnpm install 34 | 35 | # Pre-build the project (optional) 36 | # RUN pnpm run build 37 | 38 | # # Clean up 39 | # RUN apt-get clean && rm -rf /var/lib/apt/lists/* 40 | 41 | # Debug stage 42 | FROM base AS debug 43 | ARG START_SHELL_ON_FAIL 44 | RUN [ "$START_SHELL_ON_FAIL" = "true" ] && bash || echo "Build continues" 45 | -------------------------------------------------------------------------------- /.devcontainer/README.md: -------------------------------------------------------------------------------- 1 | # CatColab dev container 2 | 3 | CatColab has experimental support for development using a dev container, which 4 | simplifies the setup process by providing a pre-configured environment via a 5 | Dockerfile. This is most useful for developers using [Visual Studio 6 | Code](https://code.visualstudio.com/) or other editors that support the [dev 7 | containers standard](https://containers.dev/). 8 | 9 | To use the dev container: 10 | 11 | 1. Ensure you have a container runtime installed and running on your machine. You can refer to the [Open Container Initiative](https://opencontainers.org/) for more information on container standards and runtimes. For practical guidance, you might consider starting with [Docker's Get Started Guide](https://www.docker.com/get-started). 12 | 2. Open the CatColab repository in VS Code. 13 | 3. Open the VS Code command pallet by pressing `Cmd+Shift+P` on macOS or `Ctrl+Shift+P` on Linux 14 | 4. Issue the command "Dev Containers: Reopen in Container". 15 | 5. Once the container is running, the necessary setup commands will be executed automatically. 16 | 6. VS Code will prompt "Your application running on port 5173 is available. See all forwarded ports". Click the link to open the application in your browser. 17 | -------------------------------------------------------------------------------- /.devcontainer/devcontainer.json: -------------------------------------------------------------------------------- 1 | { 2 | "name": "CatColab Dev Container", 3 | "build": { 4 | "dockerfile": "Dockerfile", 5 | "context": ".." 6 | }, 7 | "customizations": { 8 | "vscode": { 9 | "extensions": [ 10 | "rust-lang.rust-analyzer", 11 | "esbenp.prettier-vscode", 12 | "dbaeumer.vscode-eslint" 13 | ] 14 | } 15 | }, 16 | "postCreateCommand": ".devcontainer/setup.sh", 17 | "remoteUser": "root" 18 | } 19 | -------------------------------------------------------------------------------- /.devcontainer/setup.sh: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | 3 | # Exit immediately if a command exits with a non-zero status 4 | set -e 5 | 6 | # Install dependencies 7 | pnpm install 8 | 9 | # Build the project 10 | pnpm run build 11 | 12 | # Start the development server with the host option 13 | pnpm run dev 14 | -------------------------------------------------------------------------------- /.editorconfig: -------------------------------------------------------------------------------- 1 | [*] 2 | indent_style = space 3 | indent_size = 4 4 | -------------------------------------------------------------------------------- /.envrc: -------------------------------------------------------------------------------- 1 | watch_file flake.nix 2 | 3 | use flake 4 | -------------------------------------------------------------------------------- /.netlify-env/package.json: -------------------------------------------------------------------------------- 1 | { 2 | "dependencies": { 3 | "netlify-cli": "^17.33.4" 4 | } 5 | } 6 | -------------------------------------------------------------------------------- /.netlify-env/pnpm-workspace.yaml: -------------------------------------------------------------------------------- 1 | packages: 2 | - "." 3 | -------------------------------------------------------------------------------- /.npmrc: -------------------------------------------------------------------------------- 1 | shared-workspace-lockfile=false 2 | -------------------------------------------------------------------------------- /.rustfmt.toml: -------------------------------------------------------------------------------- 1 | array_width = 80 2 | chain_width = 80 3 | fn_call_width = 80 4 | -------------------------------------------------------------------------------- /Cargo.toml: -------------------------------------------------------------------------------- 1 | [workspace] 2 | resolver = "2" 3 | 4 | members = [ 5 | "packages/migrator", 6 | "packages/backend", 7 | "packages/catlog", 8 | "packages/catlog-wasm", 9 | "packages/migrator", 10 | "packages/notebook-types", 11 | ] 12 | 13 | [profile.release] 14 | # Tell `rustc` to optimize for small code size. 15 | opt-level = "s" 16 | -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- 1 | MIT License 2 | 3 | Copyright (c) 2024 Evan Patterson 4 | 5 | Permission is hereby granted, free of charge, to any person obtaining a copy 6 | of this software and associated documentation files (the "Software"), to deal 7 | in the Software without restriction, including without limitation the rights 8 | to use, copy, modify, merge, publish, distribute, sublicense, and/or sell 9 | copies of the Software, and to permit persons to whom the Software is 10 | furnished to do so, subject to the following conditions: 11 | 12 | The above copyright notice and this permission notice shall be included in all 13 | copies or substantial portions of the Software. 14 | 15 | THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR 16 | IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, 17 | FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE 18 | AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER 19 | LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, 20 | OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE 21 | SOFTWARE. 22 | -------------------------------------------------------------------------------- /biome.json: -------------------------------------------------------------------------------- 1 | { 2 | "files": { 3 | "ignore": ["dist/**", "docs/**", "catlog-wasm/**", "**/queries.ts"] 4 | }, 5 | "$schema": "https://biomejs.dev/schemas/1.8.3/schema.json", 6 | "organizeImports": { 7 | "enabled": true 8 | }, 9 | "formatter": { 10 | "indentStyle": "space", 11 | "indentWidth": 4, 12 | "lineWidth": 100 13 | }, 14 | "linter": { 15 | "enabled": true, 16 | "rules": { 17 | "a11y": { 18 | "all": false 19 | }, 20 | "recommended": true, 21 | "suspicious": { 22 | "noExplicitAny": "warn", 23 | "noDuplicateTestHooks": { 24 | "level": "off" 25 | } 26 | }, 27 | "complexity": { 28 | "noForEach": "warn", 29 | "useLiteralKeys": { 30 | "level": "off" 31 | } 32 | }, 33 | "style": { 34 | "noParameterAssign": { 35 | "level": "off" 36 | }, 37 | "noUselessElse": { 38 | "level": "off" 39 | } 40 | } 41 | } 42 | }, 43 | "css": { 44 | "formatter": { 45 | "enabled": true 46 | }, 47 | "linter": { 48 | "enabled": true 49 | } 50 | } 51 | } 52 | -------------------------------------------------------------------------------- /dev-docs/.envrc: -------------------------------------------------------------------------------- 1 | use nix 2 | -------------------------------------------------------------------------------- /dev-docs/.gitignore: -------------------------------------------------------------------------------- 1 | build/ 2 | output/ 3 | -------------------------------------------------------------------------------- /dev-docs/README.md: -------------------------------------------------------------------------------- 1 | # CatColab: Design documents 2 | 3 | This folder contains mathematical and technical design documents for CatColab, 4 | written using [forester](https://sr.ht/~jonsterling/forester/). 5 | 6 | ## Building the forest 7 | 8 | *The following instructions are adapted from the upstream [forest template](https://git.sr.ht/~jonsterling/forest-template).* 9 | 10 | To build this forest, you need to have a working installation of the following software: 11 | 12 | - LaTeX, preferably the _full_ [TeXLive distribution](https://tug.org/texlive/) 13 | 14 | To build the forest, then simply run `./forester build`. To view the forest, run `./serve.sh` and go to `http://localhost:8080/index.xml` in your web browser. Note that you will need python installed for `./serve.sh` to work properly. 15 | 16 | You can run `./watch.sh` to watch for changes to the `trees` directory and rebuild accordingly. 17 | -------------------------------------------------------------------------------- /dev-docs/assets/.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ToposInstitute/CatColab/8e6e52655f51b402d22d43a52807a3529e131402/dev-docs/assets/.gitignore -------------------------------------------------------------------------------- /dev-docs/checksums.txt: -------------------------------------------------------------------------------- 1 | 8e03600808a36c35ee70e2522c63566021accff27d6053897d2ca020664e5b57 forester-4.3.1-linux-x86_64.tar.gz 2 | 2d12362094e7c6da31e49a0f2cace7a1f0aff6cdfa8916fc84df84cf147d0055 forester-4.3.1-macos-arm64.tar.gz 3 | e79045ec4571a051a32c5daa531d9df6bfb375c1eb7e351a405e0419c6ef22f9 forester-4.3.1-macos-x86_64.tar.gz 4 | -------------------------------------------------------------------------------- /dev-docs/forest.toml: -------------------------------------------------------------------------------- 1 | [forest] 2 | trees = ["trees"] 3 | assets = ["assets"] 4 | theme = "theme" 5 | root = "dev-0001" 6 | -------------------------------------------------------------------------------- /dev-docs/forester: -------------------------------------------------------------------------------- 1 | #!/usr/bin/env bash 2 | 3 | VERSION=4.3.1 4 | 5 | OS_NAME=$(uname) 6 | 7 | if [[ "$OS_NAME" == "Darwin" ]]; then 8 | OS="macos" 9 | elif [[ "$OS_NAME" == "Linux" ]]; then 10 | OS="linux" 11 | else 12 | echo "Unsupported OS $OS_NAME" 13 | exit 1 14 | fi 15 | 16 | ARCH=$(uname -m) 17 | 18 | SPEC="$VERSION-$OS-$ARCH" 19 | 20 | TARFILE="forester-$SPEC.tar.gz" 21 | 22 | FORESTER_URL="http://forester-builds.s3-website.us-east-2.amazonaws.com/$TARFILE" 23 | 24 | FORESTER_DIR="$HOME/.forester/$VERSION" 25 | FORESTER="$FORESTER_DIR/forester" 26 | 27 | if [[ ! -f "$FORESTER" ]]; then 28 | mkdir -p "$FORESTER_DIR" 29 | PREV=$(pwd) 30 | TMP=$(mktemp -d) 31 | cp checksums.txt $TMP 32 | cd $TMP 33 | curl -O $FORESTER_URL 34 | sha256sum -c checksums.txt --ignore-missing 35 | if [[ $? -ne 0 ]]; then 36 | print "invalid checksum" 37 | exit 1 38 | fi 39 | tar -xf $TARFILE 40 | mv forester "$FORESTER_DIR" 41 | cd $PREV 42 | rm -rf $TMP 43 | fi 44 | 45 | $FORESTER $@ 46 | -------------------------------------------------------------------------------- /dev-docs/serve.sh: -------------------------------------------------------------------------------- 1 | #!/usr/bin/env bash 2 | echo "Open http://localhost:8080/index.xml ..." 3 | echo "" 4 | python3 -m http.server -d output 8080 5 | 6 | -------------------------------------------------------------------------------- /dev-docs/shell.nix: -------------------------------------------------------------------------------- 1 | # shell.nix 2 | { pkgs ? import {} }: 3 | 4 | pkgs.mkShell { 5 | # Swap ‘git’ for whatever you actually need. 6 | buildInputs = [ 7 | pkgs.texlive.combined.scheme-full 8 | pkgs.fswatch 9 | ]; 10 | } 11 | -------------------------------------------------------------------------------- /dev-docs/theme/.gitignore: -------------------------------------------------------------------------------- 1 | node_modules 2 | .DS_Store 3 | -------------------------------------------------------------------------------- /dev-docs/theme/LICENSES/MIT.txt: -------------------------------------------------------------------------------- 1 | The MIT License (MIT) 2 | 3 | Copyright (c) 2013-2020 Khan Academy and other contributors 4 | 5 | Permission is hereby granted, free of charge, to any person obtaining a copy 6 | of this software and associated documentation files (the "Software"), to deal 7 | in the Software without restriction, including without limitation the rights 8 | to use, copy, modify, merge, publish, distribute, sublicense, and/or sell 9 | copies of the Software, and to permit persons to whom the Software is 10 | furnished to do so, subject to the following conditions: 11 | 12 | The above copyright notice and this permission notice shall be included in all 13 | copies or substantial portions of the Software. 14 | 15 | THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR 16 | IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, 17 | FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE 18 | AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER 19 | LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, 20 | OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE 21 | SOFTWARE. 22 | -------------------------------------------------------------------------------- /dev-docs/theme/android-chrome-192x192.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ToposInstitute/CatColab/8e6e52655f51b402d22d43a52807a3529e131402/dev-docs/theme/android-chrome-192x192.png -------------------------------------------------------------------------------- /dev-docs/theme/android-chrome-512x512.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ToposInstitute/CatColab/8e6e52655f51b402d22d43a52807a3529e131402/dev-docs/theme/android-chrome-512x512.png -------------------------------------------------------------------------------- /dev-docs/theme/apple-touch-icon.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ToposInstitute/CatColab/8e6e52655f51b402d22d43a52807a3529e131402/dev-docs/theme/apple-touch-icon.png -------------------------------------------------------------------------------- /dev-docs/theme/bundle-js.sh: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | 3 | npm install 4 | 5 | ./node_modules/.bin/esbuild --minify --bundle javascript-source/forester.js --outfile=forester.js 6 | 7 | 8 | -------------------------------------------------------------------------------- /dev-docs/theme/custom.css: -------------------------------------------------------------------------------- 1 | span.nlab > span > a { 2 | color: #226622; 3 | } 4 | 5 | span.wikipedia > span > a { 6 | color: #3366cc; 7 | } 8 | 9 | .centerfigs { 10 | text-align: center; 11 | 12 | & > img { 13 | vertical-align: middle; 14 | } 15 | } 16 | -------------------------------------------------------------------------------- /dev-docs/theme/default.xsl: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | 11 | 12 | 13 | 14 | 15 | -------------------------------------------------------------------------------- /dev-docs/theme/favicon-16x16.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ToposInstitute/CatColab/8e6e52655f51b402d22d43a52807a3529e131402/dev-docs/theme/favicon-16x16.png -------------------------------------------------------------------------------- /dev-docs/theme/favicon-32x32.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ToposInstitute/CatColab/8e6e52655f51b402d22d43a52807a3529e131402/dev-docs/theme/favicon-32x32.png -------------------------------------------------------------------------------- /dev-docs/theme/favicon.ico: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ToposInstitute/CatColab/8e6e52655f51b402d22d43a52807a3529e131402/dev-docs/theme/favicon.ico -------------------------------------------------------------------------------- /dev-docs/theme/fonts/KaTeX_AMS-Regular.ttf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ToposInstitute/CatColab/8e6e52655f51b402d22d43a52807a3529e131402/dev-docs/theme/fonts/KaTeX_AMS-Regular.ttf -------------------------------------------------------------------------------- /dev-docs/theme/fonts/KaTeX_AMS-Regular.woff: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ToposInstitute/CatColab/8e6e52655f51b402d22d43a52807a3529e131402/dev-docs/theme/fonts/KaTeX_AMS-Regular.woff -------------------------------------------------------------------------------- /dev-docs/theme/fonts/KaTeX_AMS-Regular.woff2: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ToposInstitute/CatColab/8e6e52655f51b402d22d43a52807a3529e131402/dev-docs/theme/fonts/KaTeX_AMS-Regular.woff2 -------------------------------------------------------------------------------- /dev-docs/theme/fonts/KaTeX_Caligraphic-Bold.ttf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ToposInstitute/CatColab/8e6e52655f51b402d22d43a52807a3529e131402/dev-docs/theme/fonts/KaTeX_Caligraphic-Bold.ttf -------------------------------------------------------------------------------- /dev-docs/theme/fonts/KaTeX_Caligraphic-Bold.woff: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ToposInstitute/CatColab/8e6e52655f51b402d22d43a52807a3529e131402/dev-docs/theme/fonts/KaTeX_Caligraphic-Bold.woff -------------------------------------------------------------------------------- /dev-docs/theme/fonts/KaTeX_Caligraphic-Bold.woff2: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ToposInstitute/CatColab/8e6e52655f51b402d22d43a52807a3529e131402/dev-docs/theme/fonts/KaTeX_Caligraphic-Bold.woff2 -------------------------------------------------------------------------------- /dev-docs/theme/fonts/KaTeX_Caligraphic-Regular.ttf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ToposInstitute/CatColab/8e6e52655f51b402d22d43a52807a3529e131402/dev-docs/theme/fonts/KaTeX_Caligraphic-Regular.ttf -------------------------------------------------------------------------------- /dev-docs/theme/fonts/KaTeX_Caligraphic-Regular.woff: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ToposInstitute/CatColab/8e6e52655f51b402d22d43a52807a3529e131402/dev-docs/theme/fonts/KaTeX_Caligraphic-Regular.woff -------------------------------------------------------------------------------- /dev-docs/theme/fonts/KaTeX_Caligraphic-Regular.woff2: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ToposInstitute/CatColab/8e6e52655f51b402d22d43a52807a3529e131402/dev-docs/theme/fonts/KaTeX_Caligraphic-Regular.woff2 -------------------------------------------------------------------------------- /dev-docs/theme/fonts/KaTeX_Fraktur-Bold.ttf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ToposInstitute/CatColab/8e6e52655f51b402d22d43a52807a3529e131402/dev-docs/theme/fonts/KaTeX_Fraktur-Bold.ttf -------------------------------------------------------------------------------- /dev-docs/theme/fonts/KaTeX_Fraktur-Bold.woff: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ToposInstitute/CatColab/8e6e52655f51b402d22d43a52807a3529e131402/dev-docs/theme/fonts/KaTeX_Fraktur-Bold.woff -------------------------------------------------------------------------------- /dev-docs/theme/fonts/KaTeX_Fraktur-Bold.woff2: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ToposInstitute/CatColab/8e6e52655f51b402d22d43a52807a3529e131402/dev-docs/theme/fonts/KaTeX_Fraktur-Bold.woff2 -------------------------------------------------------------------------------- /dev-docs/theme/fonts/KaTeX_Fraktur-Regular.ttf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ToposInstitute/CatColab/8e6e52655f51b402d22d43a52807a3529e131402/dev-docs/theme/fonts/KaTeX_Fraktur-Regular.ttf -------------------------------------------------------------------------------- /dev-docs/theme/fonts/KaTeX_Fraktur-Regular.woff: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ToposInstitute/CatColab/8e6e52655f51b402d22d43a52807a3529e131402/dev-docs/theme/fonts/KaTeX_Fraktur-Regular.woff -------------------------------------------------------------------------------- /dev-docs/theme/fonts/KaTeX_Fraktur-Regular.woff2: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ToposInstitute/CatColab/8e6e52655f51b402d22d43a52807a3529e131402/dev-docs/theme/fonts/KaTeX_Fraktur-Regular.woff2 -------------------------------------------------------------------------------- /dev-docs/theme/fonts/KaTeX_Main-Bold.ttf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ToposInstitute/CatColab/8e6e52655f51b402d22d43a52807a3529e131402/dev-docs/theme/fonts/KaTeX_Main-Bold.ttf -------------------------------------------------------------------------------- /dev-docs/theme/fonts/KaTeX_Main-Bold.woff: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ToposInstitute/CatColab/8e6e52655f51b402d22d43a52807a3529e131402/dev-docs/theme/fonts/KaTeX_Main-Bold.woff -------------------------------------------------------------------------------- /dev-docs/theme/fonts/KaTeX_Main-Bold.woff2: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ToposInstitute/CatColab/8e6e52655f51b402d22d43a52807a3529e131402/dev-docs/theme/fonts/KaTeX_Main-Bold.woff2 -------------------------------------------------------------------------------- /dev-docs/theme/fonts/KaTeX_Main-BoldItalic.ttf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ToposInstitute/CatColab/8e6e52655f51b402d22d43a52807a3529e131402/dev-docs/theme/fonts/KaTeX_Main-BoldItalic.ttf -------------------------------------------------------------------------------- /dev-docs/theme/fonts/KaTeX_Main-BoldItalic.woff: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ToposInstitute/CatColab/8e6e52655f51b402d22d43a52807a3529e131402/dev-docs/theme/fonts/KaTeX_Main-BoldItalic.woff -------------------------------------------------------------------------------- /dev-docs/theme/fonts/KaTeX_Main-BoldItalic.woff2: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ToposInstitute/CatColab/8e6e52655f51b402d22d43a52807a3529e131402/dev-docs/theme/fonts/KaTeX_Main-BoldItalic.woff2 -------------------------------------------------------------------------------- /dev-docs/theme/fonts/KaTeX_Main-Italic.ttf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ToposInstitute/CatColab/8e6e52655f51b402d22d43a52807a3529e131402/dev-docs/theme/fonts/KaTeX_Main-Italic.ttf -------------------------------------------------------------------------------- /dev-docs/theme/fonts/KaTeX_Main-Italic.woff: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ToposInstitute/CatColab/8e6e52655f51b402d22d43a52807a3529e131402/dev-docs/theme/fonts/KaTeX_Main-Italic.woff -------------------------------------------------------------------------------- /dev-docs/theme/fonts/KaTeX_Main-Italic.woff2: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ToposInstitute/CatColab/8e6e52655f51b402d22d43a52807a3529e131402/dev-docs/theme/fonts/KaTeX_Main-Italic.woff2 -------------------------------------------------------------------------------- /dev-docs/theme/fonts/KaTeX_Main-Regular.ttf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ToposInstitute/CatColab/8e6e52655f51b402d22d43a52807a3529e131402/dev-docs/theme/fonts/KaTeX_Main-Regular.ttf -------------------------------------------------------------------------------- /dev-docs/theme/fonts/KaTeX_Main-Regular.woff: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ToposInstitute/CatColab/8e6e52655f51b402d22d43a52807a3529e131402/dev-docs/theme/fonts/KaTeX_Main-Regular.woff -------------------------------------------------------------------------------- /dev-docs/theme/fonts/KaTeX_Main-Regular.woff2: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ToposInstitute/CatColab/8e6e52655f51b402d22d43a52807a3529e131402/dev-docs/theme/fonts/KaTeX_Main-Regular.woff2 -------------------------------------------------------------------------------- /dev-docs/theme/fonts/KaTeX_Math-BoldItalic.ttf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ToposInstitute/CatColab/8e6e52655f51b402d22d43a52807a3529e131402/dev-docs/theme/fonts/KaTeX_Math-BoldItalic.ttf -------------------------------------------------------------------------------- /dev-docs/theme/fonts/KaTeX_Math-BoldItalic.woff: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ToposInstitute/CatColab/8e6e52655f51b402d22d43a52807a3529e131402/dev-docs/theme/fonts/KaTeX_Math-BoldItalic.woff -------------------------------------------------------------------------------- /dev-docs/theme/fonts/KaTeX_Math-BoldItalic.woff2: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ToposInstitute/CatColab/8e6e52655f51b402d22d43a52807a3529e131402/dev-docs/theme/fonts/KaTeX_Math-BoldItalic.woff2 -------------------------------------------------------------------------------- /dev-docs/theme/fonts/KaTeX_Math-Italic.ttf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ToposInstitute/CatColab/8e6e52655f51b402d22d43a52807a3529e131402/dev-docs/theme/fonts/KaTeX_Math-Italic.ttf -------------------------------------------------------------------------------- /dev-docs/theme/fonts/KaTeX_Math-Italic.woff: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ToposInstitute/CatColab/8e6e52655f51b402d22d43a52807a3529e131402/dev-docs/theme/fonts/KaTeX_Math-Italic.woff -------------------------------------------------------------------------------- /dev-docs/theme/fonts/KaTeX_Math-Italic.woff2: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ToposInstitute/CatColab/8e6e52655f51b402d22d43a52807a3529e131402/dev-docs/theme/fonts/KaTeX_Math-Italic.woff2 -------------------------------------------------------------------------------- /dev-docs/theme/fonts/KaTeX_SansSerif-Bold.ttf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ToposInstitute/CatColab/8e6e52655f51b402d22d43a52807a3529e131402/dev-docs/theme/fonts/KaTeX_SansSerif-Bold.ttf -------------------------------------------------------------------------------- /dev-docs/theme/fonts/KaTeX_SansSerif-Bold.woff: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ToposInstitute/CatColab/8e6e52655f51b402d22d43a52807a3529e131402/dev-docs/theme/fonts/KaTeX_SansSerif-Bold.woff -------------------------------------------------------------------------------- /dev-docs/theme/fonts/KaTeX_SansSerif-Bold.woff2: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ToposInstitute/CatColab/8e6e52655f51b402d22d43a52807a3529e131402/dev-docs/theme/fonts/KaTeX_SansSerif-Bold.woff2 -------------------------------------------------------------------------------- /dev-docs/theme/fonts/KaTeX_SansSerif-Italic.ttf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ToposInstitute/CatColab/8e6e52655f51b402d22d43a52807a3529e131402/dev-docs/theme/fonts/KaTeX_SansSerif-Italic.ttf -------------------------------------------------------------------------------- /dev-docs/theme/fonts/KaTeX_SansSerif-Italic.woff: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ToposInstitute/CatColab/8e6e52655f51b402d22d43a52807a3529e131402/dev-docs/theme/fonts/KaTeX_SansSerif-Italic.woff -------------------------------------------------------------------------------- /dev-docs/theme/fonts/KaTeX_SansSerif-Italic.woff2: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ToposInstitute/CatColab/8e6e52655f51b402d22d43a52807a3529e131402/dev-docs/theme/fonts/KaTeX_SansSerif-Italic.woff2 -------------------------------------------------------------------------------- /dev-docs/theme/fonts/KaTeX_SansSerif-Regular.ttf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ToposInstitute/CatColab/8e6e52655f51b402d22d43a52807a3529e131402/dev-docs/theme/fonts/KaTeX_SansSerif-Regular.ttf -------------------------------------------------------------------------------- /dev-docs/theme/fonts/KaTeX_SansSerif-Regular.woff: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ToposInstitute/CatColab/8e6e52655f51b402d22d43a52807a3529e131402/dev-docs/theme/fonts/KaTeX_SansSerif-Regular.woff -------------------------------------------------------------------------------- /dev-docs/theme/fonts/KaTeX_SansSerif-Regular.woff2: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ToposInstitute/CatColab/8e6e52655f51b402d22d43a52807a3529e131402/dev-docs/theme/fonts/KaTeX_SansSerif-Regular.woff2 -------------------------------------------------------------------------------- /dev-docs/theme/fonts/KaTeX_Script-Regular.ttf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ToposInstitute/CatColab/8e6e52655f51b402d22d43a52807a3529e131402/dev-docs/theme/fonts/KaTeX_Script-Regular.ttf -------------------------------------------------------------------------------- /dev-docs/theme/fonts/KaTeX_Script-Regular.woff: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ToposInstitute/CatColab/8e6e52655f51b402d22d43a52807a3529e131402/dev-docs/theme/fonts/KaTeX_Script-Regular.woff -------------------------------------------------------------------------------- /dev-docs/theme/fonts/KaTeX_Script-Regular.woff2: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ToposInstitute/CatColab/8e6e52655f51b402d22d43a52807a3529e131402/dev-docs/theme/fonts/KaTeX_Script-Regular.woff2 -------------------------------------------------------------------------------- /dev-docs/theme/fonts/KaTeX_Size1-Regular.ttf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ToposInstitute/CatColab/8e6e52655f51b402d22d43a52807a3529e131402/dev-docs/theme/fonts/KaTeX_Size1-Regular.ttf -------------------------------------------------------------------------------- /dev-docs/theme/fonts/KaTeX_Size1-Regular.woff: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ToposInstitute/CatColab/8e6e52655f51b402d22d43a52807a3529e131402/dev-docs/theme/fonts/KaTeX_Size1-Regular.woff -------------------------------------------------------------------------------- /dev-docs/theme/fonts/KaTeX_Size1-Regular.woff2: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ToposInstitute/CatColab/8e6e52655f51b402d22d43a52807a3529e131402/dev-docs/theme/fonts/KaTeX_Size1-Regular.woff2 -------------------------------------------------------------------------------- /dev-docs/theme/fonts/KaTeX_Size2-Regular.ttf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ToposInstitute/CatColab/8e6e52655f51b402d22d43a52807a3529e131402/dev-docs/theme/fonts/KaTeX_Size2-Regular.ttf -------------------------------------------------------------------------------- /dev-docs/theme/fonts/KaTeX_Size2-Regular.woff: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ToposInstitute/CatColab/8e6e52655f51b402d22d43a52807a3529e131402/dev-docs/theme/fonts/KaTeX_Size2-Regular.woff -------------------------------------------------------------------------------- /dev-docs/theme/fonts/KaTeX_Size2-Regular.woff2: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ToposInstitute/CatColab/8e6e52655f51b402d22d43a52807a3529e131402/dev-docs/theme/fonts/KaTeX_Size2-Regular.woff2 -------------------------------------------------------------------------------- /dev-docs/theme/fonts/KaTeX_Size3-Regular.ttf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ToposInstitute/CatColab/8e6e52655f51b402d22d43a52807a3529e131402/dev-docs/theme/fonts/KaTeX_Size3-Regular.ttf -------------------------------------------------------------------------------- /dev-docs/theme/fonts/KaTeX_Size3-Regular.woff: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ToposInstitute/CatColab/8e6e52655f51b402d22d43a52807a3529e131402/dev-docs/theme/fonts/KaTeX_Size3-Regular.woff -------------------------------------------------------------------------------- /dev-docs/theme/fonts/KaTeX_Size3-Regular.woff2: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ToposInstitute/CatColab/8e6e52655f51b402d22d43a52807a3529e131402/dev-docs/theme/fonts/KaTeX_Size3-Regular.woff2 -------------------------------------------------------------------------------- /dev-docs/theme/fonts/KaTeX_Size4-Regular.ttf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ToposInstitute/CatColab/8e6e52655f51b402d22d43a52807a3529e131402/dev-docs/theme/fonts/KaTeX_Size4-Regular.ttf -------------------------------------------------------------------------------- /dev-docs/theme/fonts/KaTeX_Size4-Regular.woff: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ToposInstitute/CatColab/8e6e52655f51b402d22d43a52807a3529e131402/dev-docs/theme/fonts/KaTeX_Size4-Regular.woff -------------------------------------------------------------------------------- /dev-docs/theme/fonts/KaTeX_Size4-Regular.woff2: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ToposInstitute/CatColab/8e6e52655f51b402d22d43a52807a3529e131402/dev-docs/theme/fonts/KaTeX_Size4-Regular.woff2 -------------------------------------------------------------------------------- /dev-docs/theme/fonts/KaTeX_Typewriter-Regular.ttf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ToposInstitute/CatColab/8e6e52655f51b402d22d43a52807a3529e131402/dev-docs/theme/fonts/KaTeX_Typewriter-Regular.ttf -------------------------------------------------------------------------------- /dev-docs/theme/fonts/KaTeX_Typewriter-Regular.woff: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ToposInstitute/CatColab/8e6e52655f51b402d22d43a52807a3529e131402/dev-docs/theme/fonts/KaTeX_Typewriter-Regular.woff -------------------------------------------------------------------------------- /dev-docs/theme/fonts/KaTeX_Typewriter-Regular.woff2: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ToposInstitute/CatColab/8e6e52655f51b402d22d43a52807a3529e131402/dev-docs/theme/fonts/KaTeX_Typewriter-Regular.woff2 -------------------------------------------------------------------------------- /dev-docs/theme/fonts/inria-sans-v14-latin_latin-ext-300.woff2: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ToposInstitute/CatColab/8e6e52655f51b402d22d43a52807a3529e131402/dev-docs/theme/fonts/inria-sans-v14-latin_latin-ext-300.woff2 -------------------------------------------------------------------------------- /dev-docs/theme/fonts/inria-sans-v14-latin_latin-ext-300italic.woff2: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ToposInstitute/CatColab/8e6e52655f51b402d22d43a52807a3529e131402/dev-docs/theme/fonts/inria-sans-v14-latin_latin-ext-300italic.woff2 -------------------------------------------------------------------------------- /dev-docs/theme/fonts/inria-sans-v14-latin_latin-ext-700.woff2: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ToposInstitute/CatColab/8e6e52655f51b402d22d43a52807a3529e131402/dev-docs/theme/fonts/inria-sans-v14-latin_latin-ext-700.woff2 -------------------------------------------------------------------------------- /dev-docs/theme/fonts/inria-sans-v14-latin_latin-ext-700italic.woff2: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ToposInstitute/CatColab/8e6e52655f51b402d22d43a52807a3529e131402/dev-docs/theme/fonts/inria-sans-v14-latin_latin-ext-700italic.woff2 -------------------------------------------------------------------------------- /dev-docs/theme/fonts/inria-sans-v14-latin_latin-ext-italic.woff2: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ToposInstitute/CatColab/8e6e52655f51b402d22d43a52807a3529e131402/dev-docs/theme/fonts/inria-sans-v14-latin_latin-ext-italic.woff2 -------------------------------------------------------------------------------- /dev-docs/theme/fonts/inria-sans-v14-latin_latin-ext-regular.woff2: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ToposInstitute/CatColab/8e6e52655f51b402d22d43a52807a3529e131402/dev-docs/theme/fonts/inria-sans-v14-latin_latin-ext-regular.woff2 -------------------------------------------------------------------------------- /dev-docs/theme/links.xsl: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | 11 | 12 | 13 | 14 | 15 | 16 | 17 | 18 | [ 19 | 21 | ] 22 | 23 | 24 | 25 | 26 | 27 | 28 | 29 | 30 | 31 | 32 | 33 | 34 | 35 | -------------------------------------------------------------------------------- /dev-docs/theme/package.json: -------------------------------------------------------------------------------- 1 | { 2 | "dependencies": { 3 | "esbuild": "^0.18.15", 4 | "katex": "^0.16.8", 5 | "ninja-keys": "^1.2.2" 6 | } 7 | } 8 | -------------------------------------------------------------------------------- /dev-docs/trees/bib-0001.tree: -------------------------------------------------------------------------------- 1 | \title{Mathematical bibliography} 2 | \taxon{bibliography} 3 | 4 | \transclude{bib-0002} 5 | \transclude{bib-0003} 6 | -------------------------------------------------------------------------------- /dev-docs/trees/bib-0002.tree: -------------------------------------------------------------------------------- 1 | \title{Double categories} 2 | \taxon{bibliography} 3 | 4 | \ul{ 5 | \li{General reference: [[grandis-2019]]} 6 | \li{[[cartesian-double-theories-2024]]} 7 | \li{[[double-products-2024]]} 8 | } 9 | -------------------------------------------------------------------------------- /dev-docs/trees/bib-0003.tree: -------------------------------------------------------------------------------- 1 | \title{Modeling frameworks} 2 | \taxon{bibliography} 3 | 4 | \subtree{ 5 | \title{Knowledge and data} 6 | \ul{ 7 | \li{[[ologs-2012]]} 8 | \li{[[alg-databases-2017]]; see also [[acsets-2022]]} 9 | } 10 | } 11 | 12 | \subtree{ 13 | \title{Dynamical systems} 14 | \ul{ 15 | \li{Regulatory networks and causal loop diagrams: [[reg-nets-2024]]} 16 | \li{Stock-flow diagrams: [[stock-flow-2023]]} 17 | } 18 | } 19 | -------------------------------------------------------------------------------- /dev-docs/trees/dbl-0001.tree: -------------------------------------------------------------------------------- 1 | \title{Background on double categories} 2 | 3 | \p{General double category theory: 4 | \ul{ 5 | \li{[[dbl-0002]]} 6 | } 7 | } 8 | 9 | \p{Double theories and models: 10 | \ul{ 11 | \li{[[dbl-0008]]} 12 | \li{[Discrete models](dbl-0005)} 13 | \li{[Free models](dbl-000D)} 14 | \li{[[dbl-000C]]} 15 | } 16 | } 17 | -------------------------------------------------------------------------------- /dev-docs/trees/dbl-0003.tree: -------------------------------------------------------------------------------- 1 | \title{Tabulator of span} 2 | \taxon{example} 3 | 4 | \p{The tabulator of a span is the apex of the span. Its two projection arrows 5 | are the legs of the span, and its projection cell is the evident one with 6 | identity map between apexes.} 7 | -------------------------------------------------------------------------------- /dev-docs/trees/dbl-0004.tree: -------------------------------------------------------------------------------- 1 | \title{Tabulator of profunctor} 2 | \taxon{example} 3 | \import{macros} 4 | 5 | \p{The tabulator #{\top P} of a profunctor #{P: \cat{C} \proto \cat{D}} is its 6 | \nlab{category of elements}, defined such that there are \em{covariant} 7 | projection functors #{\top P \to \cat{C}} and #{\top P \to \cat{D}}. Spelling 8 | this out, an object of #{\top P} is a triple #{(c,d,p)} such that #{c \in 9 | \cat{C}}, #{d \in \cat{D}}, and #{p \in P(c,d)}, and a morphism #{(c,d,p) \to 10 | (c',d',p')} in #{\top P} consists of morphisms #{f: c \to c'} and #{g: d \to d'} 11 | such that the square commutes: 12 | 13 | \quiver{ 14 | % https://q.uiver.app/#q=WzAsNCxbMCwwLCJjIl0sWzEsMCwiZCJdLFsxLDEsImQnIl0sWzAsMSwiYyciXSxbMCwxLCJwIiwwLHsic3R5bGUiOnsiYm9keSI6eyJuYW1lIjoiZGFzaGVkIn19fV0sWzEsMiwiZyJdLFswLDMsImYiLDJdLFszLDIsInAnIiwyLHsic3R5bGUiOnsiYm9keSI6eyJuYW1lIjoiZGFzaGVkIn19fV1d 15 | \begin{tikzcd} 16 | c & d \\ 17 | {c'} & {d'} 18 | \arrow["p", dashed, from=1-1, to=1-2] 19 | \arrow["f"', from=1-1, to=2-1] 20 | \arrow["g", from=1-2, to=2-2] 21 | \arrow["{p'}"', dashed, from=2-1, to=2-2] 22 | \end{tikzcd} 23 | }} 24 | 25 | \p{Be warned that this is only one of four possible ways to define the 26 | \nlab{graph of a profunctor}, as discussed on nLab.} 27 | -------------------------------------------------------------------------------- /dev-docs/trees/dbl-0005.tree: -------------------------------------------------------------------------------- 1 | \title{Discrete models of double theories} 2 | \import{macros} 3 | 4 | \p{A model of a double theory is \em{discrete} if it is freely generated by a 5 | set of objects.} 6 | 7 | \subtree{ 8 | \title{Object set} 9 | \taxon{Notation} 10 | 11 | \p{If \dbl{D} is a double category, then #{\dbl{D}_0} is its underlying category 12 | of objects and arrows and #{\dbl{D}_{00} \coloneqq \Ob(\dbl{D}_0)} is its 13 | underlying set of objects ([Grandis 2019](grandis-2019), Sec. 3.2.3).} 14 | } 15 | 16 | \transclude{dbl-0006} 17 | 18 | \p{Discrete models of a cartesian or finite-product double theory can be defined 19 | in much the same way, but since our double theories are usually presented by 20 | generators and relations, we prefer that a discrete model of such a theory be 21 | specified by a set of elements for each \em{generating} object in the theory.} 22 | 23 | \transclude{dbl-0007} 24 | -------------------------------------------------------------------------------- /dev-docs/trees/dbl-0006.tree: -------------------------------------------------------------------------------- 1 | \title{Discrete model of a simple double theory} 2 | \taxon{definition} 3 | \import{macros} 4 | 5 | \p{Let \dbl{T} be a simple double theory. 6 | 7 | The \define{discrete model functor} 8 | 9 | ##{ 10 | \Disc: \cat{Fun}(\dbl{T}_{00}, \Set) \to \cat{Lax}(\dbl{T}, \Span) 11 | } 12 | is the left adjoint to the forgetful functor 13 | 14 | ##{ 15 | \cat{Lax}(\dbl{T}, \Span) \xto{(-)_0} 16 | \cat{Fun}(\dbl{T}_0, \Set) \xto{\varepsilon_{\dbl{T_0}}^*} 17 | \cat{Fun}(\dbl{T}_{00}, \Set), 18 | } 19 | 20 | where #{\varepsilon_{\dbl{T_0}}: \dbl{T}_{00} \hookrightarrow \dbl{T}_0} is the 21 | counit of the adjunction #{\Disc: \Set \rightleftarrows \cat{Cat}: \Ob}.} 22 | 23 | \p{A \define{discrete model} of a simple double theory \dbl{T} is a model of 24 | \dbl{T} in the image of the discrete model functor.} 25 | -------------------------------------------------------------------------------- /dev-docs/trees/dbl-0007.tree: -------------------------------------------------------------------------------- 1 | \title{Discrete model of a double Lawvere theory} 2 | \taxon{definition} 3 | \import{macros} 4 | 5 | \p{Let \dbl{T} be a [double Lawvere theory](dbl-0008) with object sorts 6 | #{\Lambda_0}. 7 | 8 | The \define{discrete model functor} 9 | 10 | ##{ 11 | \Disc: \cat{Fun}(\Lambda_0, \Set) \to \cat{fpLax}(\dbl{T}, \Span) 12 | } 13 | 14 | is the left adjoint to the forgetful functor 15 | 16 | ##{ 17 | \cat{fpLax}(\dbl{T}, \Span) \xto{(-)_0} 18 | \cat{fpFun}(\dbl{T}_0, \Set) \to 19 | \cat{Fun}(\Lambda_0, \Set). 20 | } 21 | 22 | } 23 | 24 | \p{A \define{discrete model} of a double Lawvere theory \dbl{T} is a model of 25 | \dbl{T} in the image of the discrete model functor.} 26 | -------------------------------------------------------------------------------- /dev-docs/trees/dbl-0008.tree: -------------------------------------------------------------------------------- 1 | \title{Double Lawvere theories} 2 | \import{macros} 3 | 4 | \p{A multisorted \nlab{Lawvere theory} is a finite-product theory with a 5 | distinguished set of generating objects/types. This idea can be formulated 6 | precisely in a couple of ways; here is [Todd Trimble's 7 | definition](https://ncatlab.org/toddtrimble/published/multisorted+Lawvere+theories).} 8 | 9 | \transclude{dbl-0009} 10 | 11 | \p{Just as a [finite-product double theory](double-products-2024) is a 12 | categorification of a finite-product theory, so should a "double Lawvere theory" 13 | be a categorification of a Lawvere theory. Since we think of a double theory as 14 | having both object types (its objects) and morphism types (its proarrows), a 15 | multisorted double Lawvere theory ought to have both \em{object sorts} and 16 | \em{morphism sorts}. But stating this definition is more complicated than simply 17 | replacing the family construction with the double family construction, because 18 | the source or target of a morphism sort must be a finite family of object sorts 19 | rather than a single sort. For now we make the following incomplete definition.} 20 | 21 | \transclude{dbl-000A} 22 | -------------------------------------------------------------------------------- /dev-docs/trees/dbl-0009.tree: -------------------------------------------------------------------------------- 1 | \title{Multisorted Lawvere theory} 2 | \taxon{definition} 3 | \import{macros} 4 | 5 | \p{Given a set #{\Lambda}, a \define{Lawvere theory with sorts #{\Lambda}} is a 6 | category #{\cat{T}} with finite products equipped with an identity-on-objects, 7 | finite-product preserving functor 8 | 9 | ##{ 10 | i: \FinFam^*(\Lambda) \to \cat{T}. 11 | } 12 | 13 | } 14 | -------------------------------------------------------------------------------- /dev-docs/trees/dbl-000A.tree: -------------------------------------------------------------------------------- 1 | \title{Multisorted double Lawvere theory} 2 | \taxon{definition} 3 | \import{macros} 4 | 5 | \p{Given a set #{\Lambda_0}, a \define{double Lawvere theory with object sorts 6 | #{\Lambda_0}} is a finite-product double theory \dbl{T} equipped with an 7 | identity-on-objects, finite-product preserving functor 8 | 9 | ##{ 10 | i_0: \FinFam^*(\Lambda_0) \to \dbl{T}_0. 11 | } 12 | 13 | } 14 | -------------------------------------------------------------------------------- /dev-docs/trees/dbl-000E.tree: -------------------------------------------------------------------------------- 1 | \title{Double graph} 2 | \taxon{definition} 3 | \import{macros} 4 | 5 | \p{A \define{double graph} is a graph object \dbl{G} in \Cat, i.e., an endospan 6 | #{\dbl{G}_0 \xfrom{s} \dbl{G}_1 \xto{t} \dbl{G}_0} of categories.} 7 | -------------------------------------------------------------------------------- /dev-docs/trees/dbl-000F.tree: -------------------------------------------------------------------------------- 1 | \title{Graphs in a 2-category} 2 | \taxon{definition} 3 | \import{macros} 4 | 5 | \p{Let \twocat{K} be a 2-category. In the \define{2-category of graphs in 6 | \twocat{K},} 7 | 8 | \ul{ 9 | 10 | \li{an object \dbl{G} is a graph object #{s,t: \dbl{G}_1 \rightrightarrows 11 | \dbl{G}_0} in \twocat{K}, where #{s} is called the \define{source} map and #{t} 12 | is called the \define{target} map;} 13 | 14 | \li{a morphism #{F: \dbl{G} \to \dbl{H}} is a pair of morphisms #{F_i: \dbl{G}_i 15 | \to \dbl{H}_i}, for #{i = 0,1}, in \twocat{K} that commute with the source and 16 | target maps; and} 17 | 18 | \li{a cell #{\alpha: F \To G} is a pair of cells #{\alpha_i: F_i \To G_i}, for 19 | #{i = 0,1}, in \twocat{K} that commute with whiskering by the source and target 20 | maps.} 21 | 22 | } 23 | 24 | Composition in this 2-category is inherited componentwise from \twocat{K}.} 25 | -------------------------------------------------------------------------------- /dev-docs/trees/dbl-000G.tree: -------------------------------------------------------------------------------- 1 | \title{Cartesian double graph} 2 | \taxon{definition} 3 | \import{macros} 4 | 5 | \p{A [double graph](dbl-000E) \dbl{G} is \define{cartesian} when either of the 6 | following equivalent conditions hold: 7 | 8 | \ul{ 9 | 10 | \li{\dbl{G} is a \nlab{cartesian object} in the [2-category of double 11 | graphs](dbl-000F).} 12 | 13 | \li{The underlying categories #{\dbl{G}_0} and #{\dbl{G}_1} have finite 14 | products, which are preserved by the source and target functors #{s,t: \dbl{G}_1 15 | \rightrightarrows \dbl{G}_0}.} 16 | 17 | } 18 | } 19 | -------------------------------------------------------------------------------- /dev-docs/trees/dbl-000H.tree: -------------------------------------------------------------------------------- 1 | \title{Network over a double theory} 2 | \taxon{definition} 3 | \import{macros} 4 | 5 | \p{Let #{\dbl{T}} be a simple or cartesian double theory. A \define{network over 6 | \dbl{T}}, or \define{\dbl{T}-network}, is a morphism of (cartesian) double 7 | graphs 8 | 9 | ##{N: U(\dbl{T}) \to \Span,} 10 | 11 | where #{U} is the forgetful 2-functor and, by a harmless abuse of notation, 12 | \Span also denotes the (cartesian) double graph of spans. 13 | 14 | } 15 | -------------------------------------------------------------------------------- /dev-docs/trees/dbl-000I.tree: -------------------------------------------------------------------------------- 1 | \title{Free model functor} 2 | \taxon{definition} 3 | \import{macros} 4 | 5 | \p{The \define{free model functor} for a simple double theory \dbl{T}, denoted 6 | 7 | ##{F: \cat{Net}_{\dbl{T}} \to \cat{Mod}_{\dbl{T}},} 8 | 9 | is the left adjoint to the forgetful functor 10 | 11 | ##{ 12 | \cat{Mod}_{\dbl{T}} \coloneqq 13 | \twocat{Dbl}_{\mathrm{lax}}(\dbl{T}, \Span) \xto{U} 14 | \twocat{DblGraph}(U(\dbl{T}), \Span) 15 | \eqqcolon \cat{Net}_{\dbl{T}} 16 | } 17 | 18 | given by applying the forgetful 2-functor #{U: \twocat{Dbl}_{\mathrm{lax}} \to 19 | \twocat{DblGph}}. The \define{free model functor} for a cartesian double theory 20 | is defined similarly, inserting the modifier "cartesian" where appropriate.} 21 | -------------------------------------------------------------------------------- /dev-docs/trees/dct-0001.tree: -------------------------------------------------------------------------------- 1 | \title{Categories} 2 | \taxon{doctrine} 3 | \import{macros} 4 | 5 | \p{Categories are the simplest of all doctrines. In the formalism of double 6 | theories, a category is precisely a model of the trivial double theory.} 7 | 8 | \transclude{thy-0001} 9 | -------------------------------------------------------------------------------- /dev-docs/trees/dct-0002.tree: -------------------------------------------------------------------------------- 1 | \title{Signed categories} 2 | \taxon{doctrine} 3 | \import{macros} 4 | 5 | \def\Sgn{#{\operatorname{Sgn}}} 6 | 7 | \p{A [signed category](reg-nets-2024) is a category graded by signs. To be more 8 | precise, let #{\Sgn \coloneqq \{\pm 1\} \cong \Z_2} be the group of nonzero 9 | signs under their usual multiplication.} 10 | 11 | \definition{Signed category}{ 12 | \p{A \define{signed category} a category \cat{A} along 13 | with a functor #{\cat{A} \to \Sgn}, viewing \Sgn as a one-object category.} 14 | \p{These are the objects of the slice category #{\cat{Cat}/\Sgn}, 15 | the \define{category of signed categories}.} 16 | } 17 | 18 | \transclude{thy-0002} 19 | 20 | \proposition{Characterization of signed categories}{The following are equivalent: 21 | \ol{ 22 | \li{a signed category;} 23 | \li{a category \cat{C} equipped with a profunctor #{N: \cat{C} \proto \cat{C}} 24 | and a composition operation ##{\mu: N \odot N \To \Hom_{\cat{C}},} which is 25 | a natural transformation;} 26 | \li{a model of the theory of signed categories.} 27 | } 28 | } 29 | -------------------------------------------------------------------------------- /dev-docs/trees/dct-0004.tree: -------------------------------------------------------------------------------- 1 | \title{Monoids} 2 | \taxon{doctrine} 3 | \import{macros} 4 | 5 | \p{In the formalism of double theories, it is [categories](dct-0001), not 6 | monoids, that are the primitive concept. Nevertheless, monoids can be obtained 7 | as models of a double theory, requiring only a terminal object.} 8 | 9 | \transclude{thy-0004} 10 | -------------------------------------------------------------------------------- /dev-docs/trees/dct-0005.tree: -------------------------------------------------------------------------------- 1 | \title{Monoid actions} 2 | \taxon{doctrine} 3 | \import{macros} 4 | 5 | \p{As categories are more primitive than [monoids](dct-0004) in the formalism of 6 | double theories, so are category actions (presheaves and copresheaves) 7 | more primitive than monoid actions. Nevertheless, monoid actions are models 8 | of a double theory.} 9 | 10 | \transclude{thy-0005} 11 | 12 | \example{Dynamical systems}{ 13 | On one definition, a \nlab{dynamical system} is a monoid action in a concrete 14 | category. Common choice of monoids are the nonnegative natural or real numbers 15 | under addition. 16 | } 17 | 18 | \example{Transition systems}{ 19 | \p{Actions of free monoids can be identified with deterministic, labelled 20 | transition systems, also known as \wikipedia{semiautomata}.} 21 | 22 | \p{When such transition systems are equipped with an output function, one 23 | obtains \nlab{Moore machines} or, more generally, \nlab{Mealy machines}.} 24 | } -------------------------------------------------------------------------------- /dev-docs/trees/dct-0006.tree: -------------------------------------------------------------------------------- 1 | \title{Profunctors} 2 | \taxon{doctrine} 3 | 4 | \p{Profunctors form a doctrine, being the models of the following simple double 5 | theory. Note that profunctors are viewed here as objects rather than morphisms.} 6 | 7 | \transclude{thy-0006} 8 | 9 | \p{Finitely presented profunctors are a simplified version of the database 10 | schemas in Schultz et al's [[alg-databases-2017]], disallowing products on the 11 | type side. Alternatively, they are a slight extension of [acset](acsets-2022) 12 | schemas, allowing unary operations on types.} 13 | -------------------------------------------------------------------------------- /dev-docs/trees/dct-0007.tree: -------------------------------------------------------------------------------- 1 | \title{Nullable signed categories} 2 | \taxon{doctrine} 3 | \import{macros} 4 | 5 | \p{ 6 | A nullable signed category is a category graded by possibly vanishing signs. 7 | 8 | To be more precise: 9 | } 10 | 11 | \subtree{ 12 | \title{Nullable signed category} 13 | \taxon{definition} 14 | 15 | \p{A \define{nullable signed category} is a category sliced over the monoid 16 | #{\{+1,-1,0\}} of signs, including zero, under their usual multiplication.} 17 | 18 | } 19 | 20 | \transclude{thy-0007} 21 | 22 | \p{ 23 | Nullable signed category generalize [signed categories](dct-0002). 24 | 25 | They are examples of "categories with null morphisms" in the sense of 26 | [Grandis](grandis-2013-homological). 27 | } 28 | 29 | \p{From a systems perspective, null morphisms appear in certain flavors of 30 | system map, such as the Participatory System Maps of [Barbrook-Johnson and 31 | Penn](barbrook-johnson-2022). In this context, the null morphisms do not mean 32 | "no effect" but rather an effect with a complex or unknown direction. It then 33 | makes sense that the composite of a null morphism with any other morphism 34 | (positive, negative, or null) is again null.} 35 | -------------------------------------------------------------------------------- /dev-docs/trees/dct-000A.tree: -------------------------------------------------------------------------------- 1 | \title{Multicategories} 2 | \taxon{doctrine} 3 | \import{macros} 4 | 5 | \p{A \nlab{multicategory}, also known as a \em{colored} or \em{typed operad}, is 6 | a model of the following double theory.} 7 | 8 | \transclude{thy-000A} 9 | 10 | \p{A model #{M} of the theory of promonoids maps the object #{x} to the object 11 | set #{M_0 \coloneqq M(x)} of the multicategory and maps the proarrow #{\mu_n} to 12 | the span #{M_0^n\proto M_0} whose preimage at #{((x_i)_1^n,y)} is the set of 13 | multimorphisms #{(x_i)_1^n \to y}.} 14 | -------------------------------------------------------------------------------- /dev-docs/trees/dct-000B.tree: -------------------------------------------------------------------------------- 1 | \title{Delayable signed categories} 2 | \taxon{doctrine} 3 | \import{macros} 4 | 5 | \p{Informally, a delayable signed category is a category graded by signs (plus 6 | or minus) and, independently, by speed (fast or slow).} 7 | 8 | \subtree{ 9 | \title{Delayable signed category} 10 | \taxon{definition} 11 | 12 | \p{A \define{delayable signed category} is a category sliced over the product 13 | monoid #{M \coloneqq\{+1,-1\} \times \{1,0\}}, where both component monoids are 14 | equipped with their usual multiplications.} 15 | 16 | } 17 | 18 | \p{In the second component of #{M}, we interpret the identity element #{1} as 19 | "fast" and the absorbing element #{0} as "slow" or "delayed".} 20 | 21 | \transclude{thy-000B} 22 | 23 | \p{A free model of this double theory a causal loop diagram in which edges can 24 | be optionally marked as delayed. An example is this causal loop diagram for the 25 | [temperature control of a 26 | shower](https://sustainabilitymethods.org/index.php/File:Causal_Loop_Delays.png).} 27 | -------------------------------------------------------------------------------- /dev-docs/trees/dev-0002.tree: -------------------------------------------------------------------------------- 1 | \title{Frontend technology survey} 2 | 3 | \p{A survey of relevant frontend technology for building a structure editor.} 4 | 5 | \transclude{dev-0003} 6 | \transclude{dev-0004} 7 | \transclude{dev-0006} 8 | \transclude{dev-0007} 9 | -------------------------------------------------------------------------------- /dev-docs/trees/dev-0003.tree: -------------------------------------------------------------------------------- 1 | \title{Frontend base} 2 | 3 | \subtree{ 4 | \title{Language} 5 | 6 | \p{The obvious choice is \strong{[TypeScript](https://www.typescriptlang.org/)}. 7 | It is a saner JavaScript and the new industry standard.} 8 | 9 | \p{OCaml, Scala, and Kotlin stand out as modern, statically typed programming 10 | languages with reasonable stories about compiling to JavaScript, but will have 11 | less refined ecosystems and toolchains. [Hazel](https://hazel.org/), a 12 | proof-of-concept structure editor for a functional programming language, is 13 | written in OCaml ([GitHub](https://github.com/hazelgrove/hazel)). Since we do 14 | not aim to innovate in frontend programming, we should stick to the mainstream, 15 | hence JavaScript/TypeScript.} } 16 | 17 | \subtree{ 18 | \title{UI framework} 19 | 20 | \p{The proliferation of web 21 | [UI frameworks](https://bestofjs.org/projects?tags=framework) is notorious. 22 | \strong{React} remains the industry standard and would be a safe choice, 23 | although in past experience it felt a bit clunky and boilerplate-y.} 24 | 25 | \p{\strong{[Solid](https://www.solidjs.com/)} is an appealing newer framework 26 | that is clearly inspired by React but has learned some lessons 27 | ([HN](https://news.ycombinator.com/item?id=30508524)). It ditches the virtual 28 | DOM and has a better story about component updates ("reactivity"), being one 29 | of few frameworks to have proper support for 30 | [nested reactivity](https://www.solidjs.com/tutorial/stores_nested_reactivity).} 31 | } 32 | -------------------------------------------------------------------------------- /dev-docs/trees/dev-0008.tree: -------------------------------------------------------------------------------- 1 | \title{Rust ecosystem survey} 2 | 3 | \transclude{dev-0009} -------------------------------------------------------------------------------- /dev-docs/trees/dev-000B.tree: -------------------------------------------------------------------------------- 1 | \title{Database design} 2 | 3 | \p{The database contains the following tables.} 4 | 5 | \transclude{dev-000C} 6 | 7 | \transclude{dev-000D} 8 | -------------------------------------------------------------------------------- /dev-docs/trees/dev-000C.tree: -------------------------------------------------------------------------------- 1 | \taxon{table} 2 | \title{Snapshots} 3 | 4 | \p{A document snapshot is an arbitrary JSON object stored in binary format. 5 | Every snapshot has a timestamp and is associated with a single [ref](dev-000D).} 6 | 7 | \p{Snapshots are retained for all time unless their associated ref is deleted.} 8 | -------------------------------------------------------------------------------- /dev-docs/trees/dev-000D.tree: -------------------------------------------------------------------------------- 1 | \taxon{table} 2 | \title{Refs} 3 | 4 | \p{A "ref" is a persistent reference to a document. A running CatColab server 5 | maintains an in-memory hash map from refs to Automerge documents; there can be 6 | at most one Automerge document that is "controlling" a ref at a given time.} 7 | 8 | \p{Refs are identified by UUIDs. In the future, they will also have editable 9 | metadata such as taxon, title, author(s), tags, and so on.} 10 | 11 | \p{Additionally, a ref has a \code{head} field that points to a particular 12 | [snapshot](dev-000C) for the ref. The "autosave" mechanism updates the content 13 | of this snapshot every time the Automerge document connected to the ref is 14 | mutated. "Saving" a ref just means creating a new snapshot and making it the 15 | head. The previous head will continue to exist as a snapshot, and can be used to 16 | revert the ref to its state at a previous point in time.} 17 | -------------------------------------------------------------------------------- /dev-docs/trees/refs/acsets-2022.tree: -------------------------------------------------------------------------------- 1 | \title{Categorical data structures for technical computing} 2 | \author{Evan Patterson} 3 | \author{Owen Lynch} 4 | \author{James Fairbanks} 5 | \date{2022} 6 | \taxon{reference} 7 | \meta{external}{https://github.com/AlgebraicJulia/ACSets.jl} 8 | \meta{doi}{10.32408/compositionality-4-5} 9 | \meta{arxiv}{2106.04703} 10 | -------------------------------------------------------------------------------- /dev-docs/trees/refs/alg-databases-2017.tree: -------------------------------------------------------------------------------- 1 | \title{Algebraic databases} 2 | \author{Patrick Schultz} 3 | \author{David I. Spivak} 4 | \author{Christina Vasilakopoulou} 5 | \author{Ryan Wisnesky} 6 | \date{2017} 7 | \taxon{reference} 8 | \meta{external}{http://www.tac.mta.ca/tac/volumes/32/16/32-16abs.html} 9 | \meta{arxiv}{1602.03501} 10 | -------------------------------------------------------------------------------- /dev-docs/trees/refs/baez-pollard-2017.tree: -------------------------------------------------------------------------------- 1 | \title{A compositional framework for reaction networks} 2 | \author{John Baez} 3 | \author{Blake Pollard} 4 | \date{2017} 5 | \taxon{reference} 6 | \meta{arxiv}{1704.02051} 7 | \meta{doi}{10.1142/S0129055X17500283} 8 | -------------------------------------------------------------------------------- /dev-docs/trees/refs/barbrook-johnson-2022.tree: -------------------------------------------------------------------------------- 1 | \title{Systems mapping: How to build use and causal models of systems} 2 | \author{Pete Barbrook-Johnson} 3 | \author{Alexandra S. Penn} 4 | \date{2022} 5 | \taxon{reference} 6 | \meta{doi}{10.1007/978-3-031-01919-7} 7 | -------------------------------------------------------------------------------- /dev-docs/trees/refs/cartesian-double-theories-2024.tree: -------------------------------------------------------------------------------- 1 | \title{Cartesian double theories: A double-categorical framework for categorical doctrines} 2 | \author{Michael Lambert} 3 | \author{Evan Patterson} 4 | \date{2024} 5 | \taxon{reference} 6 | \meta{doi}{10.1016/j.aim.2024.109630} 7 | \meta{arxiv}{2310.05384} 8 | -------------------------------------------------------------------------------- /dev-docs/trees/refs/double-products-2024.tree: -------------------------------------------------------------------------------- 1 | \title{Products in double categories, revisited} 2 | \author{Evan Patterson} 3 | \date{2024} 4 | \taxon{reference} 5 | \meta{arxiv}{2401.08990} 6 | -------------------------------------------------------------------------------- /dev-docs/trees/refs/grandis-2013-homological.tree: -------------------------------------------------------------------------------- 1 | \title{Homological algebra in strongly non-abelian settings} 2 | \author{Marco Grandis} 3 | \date{2013} 4 | \taxon{reference} 5 | -------------------------------------------------------------------------------- /dev-docs/trees/refs/grandis-2019.tree: -------------------------------------------------------------------------------- 1 | \title{Higher dimensional categories: From double to multiple categories} 2 | \author{Marco Grandis} 3 | \date{2019} 4 | \taxon{reference} 5 | \meta{doi}{10.1142/11406} 6 | -------------------------------------------------------------------------------- /dev-docs/trees/refs/ologs-2012.tree: -------------------------------------------------------------------------------- 1 | \title{Ologs: A categorical framework for knowledge representation} 2 | \author{David I. Spivak} 3 | \author{Robert E. Kent} 4 | \date{2012} 5 | \taxon{reference} 6 | \meta{doi}{10.1371/journal.pone.0024274} 7 | \meta{arxiv}{1102.1889} 8 | -------------------------------------------------------------------------------- /dev-docs/trees/refs/pisani-2024.tree: -------------------------------------------------------------------------------- 1 | \title{Unbiased multicategory theory} 2 | \author{Claudio Pisani} 3 | \date{2024} 4 | \taxon{reference} 5 | \meta{doi}{10.48550/arXiv.2409.10150} 6 | \meta{arxiv}{2409.10150} 7 | -------------------------------------------------------------------------------- /dev-docs/trees/refs/reg-nets-2024.tree: -------------------------------------------------------------------------------- 1 | \title{A compositional account of motifs, mechanisms, and dynamics in biochemical regulatory networks} 2 | \author{Rebekah Aduddell} 3 | \author{James Fairbanks} 4 | \author{Amit Kumar} 5 | \author{Pablo S. Ocal} 6 | \author{Evan Patterson} 7 | \author{Brandon T. Shapiro} 8 | \date{2024} 9 | \taxon{reference} 10 | \meta{arxiv}{2301.01445} 11 | \meta{doi}{10.32408/compositionality-6-2} 12 | -------------------------------------------------------------------------------- /dev-docs/trees/refs/shulman-2008.tree: -------------------------------------------------------------------------------- 1 | \title{Framed bicategories and monoidal fibrations} 2 | \author{Michael Shulman} 3 | \date{2008} 4 | \taxon{reference} 5 | \meta{arxiv}{0706.1286} 6 | \meta{external}{http://www.tac.mta.ca/tac/volumes/20/18/20-18abs.html} 7 | -------------------------------------------------------------------------------- /dev-docs/trees/refs/stock-flow-2023.tree: -------------------------------------------------------------------------------- 1 | \title{Compositional modeling with stock and flow diagrams} 2 | \author{John Baez} 3 | \author{Xiaoyan Li} 4 | \author{Sophie Libkind} 5 | \author{Nathaniel Osgood} 6 | \author{Evan Patterson} 7 | \date{2023} 8 | \taxon{reference} 9 | \meta{doi}{10.4204/EPTCS.380.5} 10 | \meta{arxiv}{2205.08373} 11 | -------------------------------------------------------------------------------- /dev-docs/trees/thy-0001.tree: -------------------------------------------------------------------------------- 1 | \title{Categories} 2 | \taxon{theory} 3 | \import{macros} 4 | 5 | \p{The \define{trivial double theory} or \define{theory of categories} is the 6 | terminal double category \dbl{1}.} 7 | 8 | \p{The trivial double theory is a simple double theory, but it can also be 9 | regarded as a finite-product double theory that trivially has products.} 10 | -------------------------------------------------------------------------------- /dev-docs/trees/thy-0002.tree: -------------------------------------------------------------------------------- 1 | \title{Signed categories} 2 | \taxon{theory} 3 | \import{macros} 4 | 5 | \p{The \define{theory of signed categories} is the simple double theory generated by 6 | \ul{ 7 | \li{an object #{c}} 8 | \li{a proarrow #{n: c \proto c}} 9 | } 10 | subject to the equation 11 | ##{n \odot n = \id_c.} 12 | } 13 | -------------------------------------------------------------------------------- /dev-docs/trees/thy-0003.tree: -------------------------------------------------------------------------------- 1 | \title{Categories with links} 2 | \taxon{theory} 3 | \import{macros} 4 | 5 | \p{The \define{theory of categories with links} is the double theory freely generated by 6 | \ul{ 7 | \li{an object #{c}} 8 | \li{a proarrow #{\ell: c \proto \tabulator{\id_c}}.} 9 | }} 10 | 11 | \p{The theory of categories with links is an example of a "simple tabulator 12 | theory," i.e., a small double category with [tabulators](dbl-0002).} 13 | -------------------------------------------------------------------------------- /dev-docs/trees/thy-0004.tree: -------------------------------------------------------------------------------- 1 | \title{Monoids} 2 | \taxon{theory} 3 | \import{macros} 4 | 5 | \p{The \define{theory of semigroups} is the double theory generated by a single 6 | proarrow #{m: 1 \proto 1} subject to the equation ##{m \odot m = m.}} 7 | 8 | \p{The \define{theory of monoids} augments the theory of semigroups with a cell 9 | 10 | \quiver{ 11 | % https://q.uiver.app/#q=WzAsNCxbMCwwLCIxIl0sWzEsMCwiMSJdLFswLDEsIjEiXSxbMSwxLCIxIl0sWzIsMywibSIsMix7InN0eWxlIjp7ImJvZHkiOnsibmFtZSI6ImJhcnJlZCJ9fX1dLFswLDIsIiIsMix7ImxldmVsIjoyLCJzdHlsZSI6eyJoZWFkIjp7Im5hbWUiOiJub25lIn19fV0sWzEsMywiIiwwLHsibGV2ZWwiOjIsInN0eWxlIjp7ImhlYWQiOnsibmFtZSI6Im5vbmUifX19XSxbMCwxLCJcXGlkXzEiLDAseyJzdHlsZSI6eyJib2R5Ijp7Im5hbWUiOiJiYXJyZWQifX19XSxbNyw0LCJcXGV0YSIsMSx7InNob3J0ZW4iOnsic291cmNlIjoyMCwidGFyZ2V0IjoyMH0sInN0eWxlIjp7ImJvZHkiOnsibmFtZSI6Im5vbmUifSwiaGVhZCI6eyJuYW1lIjoibm9uZSJ9fX1dXQ== 12 | \begin{tikzcd}[row sep=scriptsize] 13 | 1 & 1 \\ 14 | 1 & 1 15 | \arrow[""{name=0, anchor=center, inner sep=0}, "{\id_1}", "\shortmid"{marking}, from=1-1, to=1-2] 16 | \arrow[Rightarrow, no head, from=1-1, to=2-1] 17 | \arrow[Rightarrow, no head, from=1-2, to=2-2] 18 | \arrow[""{name=1, anchor=center, inner sep=0}, "m"', "\shortmid"{marking}, from=2-1, to=2-2] 19 | \arrow["\eta"{description}, draw=none, from=0, to=1] 20 | \end{tikzcd} 21 | } 22 | 23 | subject to the equations 24 | 25 | ##{ 26 | %\eta \odot \eta = \eta 27 | %\qquad\text{and}\qquad 28 | 1_m \odot \eta = 1_m = \eta \odot 1_m. 29 | }} 30 | -------------------------------------------------------------------------------- /dev-docs/trees/thy-0005.tree: -------------------------------------------------------------------------------- 1 | \title{Monoid actions} 2 | \taxon{theory} 3 | \import{macros} 4 | 5 | \p{The \define{theory of monoid actions} extends the [theory of monoids](thy-0004) 6 | with another proarrow #{s: 1 \proto 1}, subject to the equations 7 | 8 | ##{ 9 | m \odot s = s \qquad\text{and}\qquad \eta \odot 1_s = 1_s, 10 | } 11 | 12 | endowing with #{s} with a (left) action by #{m}, along with the side equations 13 | 14 | ##{ 15 | s \odot s = \id_1 = s \odot m, 16 | } 17 | 18 | trivializing the implicit self-multiplication on #{s} and right action by #{m}.} 19 | -------------------------------------------------------------------------------- /dev-docs/trees/thy-0006.tree: -------------------------------------------------------------------------------- 1 | \title{Profunctors} 2 | \taxon{theory} 3 | \import{macros} 4 | 5 | \p{The \define{theory of profunctors}, also known as the \define{walking 6 | proarrow} and the \define{theory of simple schemas}, is the double category 7 | freely generated by two distinct objects, say #{0} and #{1}, and a proarrow 8 | #{0 \proto 1}.} 9 | -------------------------------------------------------------------------------- /dev-docs/trees/thy-0007.tree: -------------------------------------------------------------------------------- 1 | \title{Nullable signed categories} 2 | \taxon{theory} 3 | \import{macros} 4 | 5 | \p{ 6 | The \define{theory of nullable signed categories} is the simple double theory 7 | generated by 8 | 9 | \ul{ 10 | \li{an object #{c}} 11 | \li{proarrows #{n: c \proto c} and #{z: c \proto c}} 12 | } 13 | 14 | subject to the equations 15 | ##{ 16 | n \odot n = \id_c, \qquad 17 | z \odot z = n \odot z = z \odot n = z. 18 | } 19 | } 20 | -------------------------------------------------------------------------------- /dev-docs/trees/thy-0008.tree: -------------------------------------------------------------------------------- 1 | \title{Companions} 2 | \taxon{theory} 3 | \import{macros} 4 | 5 | \p{The \define{theory of companion pairs} or \define{walking companion pair} is 6 | the simple double theory generated by 7 | 8 | \ul{ 9 | \li{a pair of objects #{x} and #{y}} 10 | \li{an arrow #{f: x \to y}} 11 | \li{a proarrow #{f_!: x \proto y}} 12 | \li{a pair of cells #{\eta} and #{\varepsilon} shaped as usual} 13 | } 14 | 15 | subject to the equations #{\eta \cdot \varepsilon = \id_f} and #{\eta \odot 16 | \varepsilon = 1_{f_!}}. 17 | 18 | } 19 | -------------------------------------------------------------------------------- /dev-docs/trees/thy-0009.tree: -------------------------------------------------------------------------------- 1 | \title{Conjoints} 2 | \taxon{theory} 3 | \import{macros} 4 | 5 | \p{The \define{theory of conjoint pairs} or \define{walking conjoint pair} is 6 | the simple double theory generated by 7 | 8 | \ul{ 9 | \li{a pair of objects #{x} and #{y}} 10 | \li{an arrow #{f: x \to y}} 11 | \li{a proarrow #{f^*: y \proto x}} 12 | \li{a pair of cells #{\eta} and #{\varepsilon} shaped as usual} 13 | } 14 | 15 | subject to the equations #{\eta \cdot \varepsilon = \id_f} and #{\varepsilon 16 | \odot \eta = 1_{f^*}}. 17 | 18 | } 19 | -------------------------------------------------------------------------------- /dev-docs/trees/thy-000A.tree: -------------------------------------------------------------------------------- 1 | \title{Promonoids} 2 | \taxon{theory} 3 | \import{macros} 4 | 5 | \p{The \define{theory of promonoids} #{\mathbb{T}_{\mathrm{pm}}} is the cartesian double theory generated by an object #{x} 6 | equipped with proarrows #{\mu_2:x^2 \proto x,\mu_0:x^0\proto x}, subject to associativity and unitality conditions. In other words, there is a unique counary proarrow #{\mu_n:x^n \proto x} for every #{n \geq 0}. See ([Lambert & 7 | Patterson 2024](cartesian-double-theories-2024), Theory 6.9).} 8 | 9 | \p{Arbitrary proarrows #{p:x^m\proto x^n} must then be a product of #{n} proarrows 10 | #{\mu_{m_i}:x^{m_i}\proto x} for some partition #{m=m_1+\cdots +m_n} of #{m}. Thus the loose 11 | category of #{\mathbb{T}_{\mathrm{pm}}} is the \nlab{augmented simplex category}, the category 12 | of totally-ordered, possibly-empty finite sets and order-preserving maps between them. This 13 | phenomenon is familiar from the fact that the augmented simplicial category is itself the 14 | strict monoidal category freely generated by a monoid object. Compare [Pisani 2024](pisani-2024) for a theory of multicategories in which the proarrows are instead maps of sets with orders 15 | on the fibers only, for better comparison with symmetric multicategories.} 16 | -------------------------------------------------------------------------------- /dev-docs/trees/thy-000B.tree: -------------------------------------------------------------------------------- 1 | \title{Theory of delayable signed categories} 2 | \taxon{theory} 3 | \import{macros} 4 | 5 | \p{The \define{theory of delayable signed categories} is the simple double 6 | theory with a single object and with proarrows given by the elements of the 7 | monoid #{M} [defined previously](dct-000B).} 8 | -------------------------------------------------------------------------------- /dev-docs/watch.sh: -------------------------------------------------------------------------------- 1 | #!/usr/bin/env bash 2 | 3 | watch_directory="trees" 4 | build_command="./forester build" 5 | 6 | # Function to use fswatch 7 | use_fswatch() { 8 | echo "Using fswatch to monitor changes..." 9 | fswatch -o -e ".*" -i "\\.tree$" --event Created --event Updated --event Removed --event MovedFrom --event MovedTo "$watch_directory" | while read num; do 10 | $build_command 11 | done 12 | } 13 | 14 | # Function to use inotifywait 15 | use_inotifywait() { 16 | echo "Using inotifywait to monitor changes..." 17 | while inotifywait -e modify,create,delete,move -r "$watch_directory"; do 18 | $build_command 19 | done 20 | } 21 | 22 | # Function to use find/stat method 23 | use_find_stat() { 24 | echo "Using find/stat method to monitor changes..." 25 | last_update=$(date +%s) 26 | while true; do 27 | current_update=$(find "$watch_directory" -type f -newer "$watch_directory" -print -quit | wc -l) 28 | if [ "$current_update" != "0" ]; then 29 | $build_command 30 | last_update=$(date +%s) 31 | fi 32 | sleep 2 33 | done 34 | } 35 | 36 | # Check for available tools and use the appropriate method 37 | $build_command 38 | if command -v fswatch >/dev/null 2>&1; then 39 | use_fswatch 40 | elif command -v inotifywait >/dev/null 2>&1; then 41 | use_inotifywait 42 | else 43 | echo "Neither fswatch nor inotifywait found. Falling back to find/stat method." 44 | use_find_stat 45 | fi 46 | -------------------------------------------------------------------------------- /infrastructure/secrets/.env.next.age: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ToposInstitute/CatColab/8e6e52655f51b402d22d43a52807a3529e131402/infrastructure/secrets/.env.next.age -------------------------------------------------------------------------------- /infrastructure/secrets/.env.prod.age: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ToposInstitute/CatColab/8e6e52655f51b402d22d43a52807a3529e131402/infrastructure/secrets/.env.prod.age -------------------------------------------------------------------------------- /infrastructure/secrets/rclone.conf.next.age: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ToposInstitute/CatColab/8e6e52655f51b402d22d43a52807a3529e131402/infrastructure/secrets/rclone.conf.next.age -------------------------------------------------------------------------------- /infrastructure/secrets/rclone.conf.prod.age: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ToposInstitute/CatColab/8e6e52655f51b402d22d43a52807a3529e131402/infrastructure/secrets/rclone.conf.prod.age -------------------------------------------------------------------------------- /infrastructure/secrets/secrets.nix: -------------------------------------------------------------------------------- 1 | let 2 | catcolab = "ssh-ed25519 AAAAC3NzaC1lZDI1NTE5AAAAIPyxORhhfO+9F2hQZ3I/EiSpfg+caWpG6c8AuG5u1XtK root@ip-172-31-14-38.us-east-2.compute.internal"; 3 | catcolab-next = "ssh-ed25519 AAAAC3NzaC1lZDI1NTE5AAAAIBZaycYjvaZ5XhxVIvFr8zXvcy1GrViCKLIZCalZuk1l root@ip-172-31-9-45.us-east-2.compute.internal"; 4 | owen = "ssh-ed25519 AAAAC3NzaC1lZDI1NTE5AAAAIF2sBTuqGoEXRWpBRqTBwZZPDdLGGJ0GQcuX5dfIZKb4 o@red-special"; 5 | epatters = "ssh-ed25519 AAAAC3NzaC1lZDI1NTE5AAAAIAKXx6wMJSeYKCHNmbyR803RQ72uto9uYsHhAPPWNl2D evan@epatters.org"; 6 | jmoggr = "ssh-ed25519 AAAAC3NzaC1lZDI1NTE5AAAAIMiaHaeJ5PQL0mka/lY1yGXIs/bDK85uY1O3mLySnwHd j@jmoggr.com"; 7 | catcolab-next-deployuser = "ssh-ed25519 AAAAC3NzaC1lZDI1NTE5AAAAIM7AYg1fZM0zMxb/BuZTSwK4O3ycUIHruApr1tKoO8nJ deployuser@next.catcolab.org"; 8 | in 9 | builtins.mapAttrs (_: publicKeys: { inherit publicKeys; }) ({ 10 | ".env.next.age" = [ 11 | catcolab-next 12 | owen 13 | epatters 14 | jmoggr 15 | catcolab-next-deployuser 16 | ]; 17 | ".env.prod.age" = [ 18 | catcolab 19 | owen 20 | epatters 21 | ]; 22 | "rclone.conf.next.age" = [ 23 | catcolab-next 24 | owen 25 | epatters 26 | jmoggr 27 | catcolab-next-deployuser 28 | ]; 29 | "rclone.conf.prod.age" = [ 30 | catcolab 31 | owen 32 | epatters 33 | ]; 34 | }) 35 | -------------------------------------------------------------------------------- /package.json: -------------------------------------------------------------------------------- 1 | { 2 | "name": "catcolab-monorepo", 3 | "version": "0.0.1", 4 | "description": "The catcolab monorepo", 5 | "scripts": { 6 | "test": "echo \"Error: no test specified\" && exit 1", 7 | "build": "pnpm --filter ./packages/frontend run build", 8 | "dev": "pnpm --filter ./packages/frontend run dev" 9 | }, 10 | "repository": { 11 | "type": "git", 12 | "url": "git+https://github.com/ToposInstitute/CatColab.git" 13 | }, 14 | "author": "The CatColab Developers", 15 | "license": "MIT", 16 | "bugs": { 17 | "url": "https://github.com/ToposInstitute/CatColab/issues" 18 | }, 19 | "homepage": "https://next.catcolab.org", 20 | "devDependencies": { 21 | "@biomejs/biome": "^1.8.3", 22 | "biome": "^0.3.3", 23 | "depcheck": "^1.4.7", 24 | "tsx": "^4.16.5", 25 | "typedoc": "^0.26.5" 26 | }, 27 | "packageManager": "pnpm@9.12.3" 28 | } 29 | -------------------------------------------------------------------------------- /packages/algjulia-interop/.gitignore: -------------------------------------------------------------------------------- 1 | # Files generated by invoking Julia with --code-coverage 2 | *.jl.cov 3 | *.jl.*.cov 4 | 5 | # Files generated by invoking Julia with --track-allocation 6 | *.jl.mem 7 | 8 | # System-specific files and directories generated by the BinaryProvider and BinDeps packages 9 | # They contain absolute paths specific to the host computer, and so should not be committed 10 | deps/deps.jl 11 | deps/build.log 12 | deps/downloads/ 13 | deps/usr/ 14 | deps/src/ 15 | 16 | # Build artifacts for creating documentation generated by the Documenter package 17 | docs/build/ 18 | docs/site/ 19 | 20 | # File generated by Pkg, the package manager, based on a corresponding Project.toml 21 | # It records a fixed state of all packages used by the project. As such, it should not be 22 | # committed for packages, but should be committed for applications that require a static 23 | # environment. 24 | Manifest.toml 25 | 26 | # Julia sys images 27 | *.so 28 | -------------------------------------------------------------------------------- /packages/algjulia-interop/Project.toml: -------------------------------------------------------------------------------- 1 | name = "CatColabInterop" 2 | uuid = "9ecda8fb-39ab-46a2-a496-7285fa6368c1" 3 | license = "MIT" 4 | authors = ["CatColab team"] 5 | version = "0.1.0" 6 | 7 | [deps] 8 | ACSets = "227ef7b5-1206-438b-ac65-934d6da304b8" 9 | Catlab = "134e5e36-593f-5add-ad60-77f754baafbe" 10 | CombinatorialSpaces = "b1c52339-7909-45ad-8b6a-6e388f7c67f2" 11 | ComponentArrays = "b0b7db55-cfe3-40fc-9ded-d10e2dbeff66" 12 | CoordRefSystems = "b46f11dc-f210-4604-bfba-323c1ec968cb" 13 | Decapodes = "679ab3ea-c928-4fe6-8d59-fd451142d391" 14 | DiagrammaticEquations = "6f00c28b-6bed-4403-80fa-30e0dc12f317" 15 | Distributions = "31c24e10-a181-5473-b8eb-7969acd0382f" 16 | GeometryBasics = "5c1252a2-5f33-56bf-86c9-59e7332b4326" 17 | IJulia = "7073ff75-c697-5162-941a-fcdaad2a7d2a" 18 | JSON3 = "0f8b85d8-7281-11e9-16c2-39a750bddbf1" 19 | LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e" 20 | MLStyle = "d8e11817-5142-5d16-987a-aa16d5891078" 21 | OrdinaryDiffEq = "1dea7af3-3e70-54e6-95c3-0bf5283fa5ed" 22 | Reexport = "189a3867-3050-52da-a836-e630ba90ab69" 23 | StaticArrays = "90137ffa-7385-5640-81b9-e52037218182" 24 | 25 | [compat] 26 | ACSets = "0.2.21" 27 | Catlab = "0.16.19" 28 | CombinatorialSpaces = "0.7.4" 29 | ComponentArrays = "0.15" 30 | CoordRefSystems = "0.17.2" 31 | Decapodes = "0.6" 32 | DiagrammaticEquations = "0.1.7" 33 | Distributions = "0.25" 34 | GeometryBasics = "0.5.7" 35 | IJulia = "1.26.0" 36 | JSON3 = "1" 37 | LinearAlgebra = "1" 38 | MLStyle = "0.4" 39 | OrdinaryDiffEq = "6" 40 | Reexport = "1.2.2" 41 | StaticArrays = "1" 42 | -------------------------------------------------------------------------------- /packages/algjulia-interop/jupyter_server.sh: -------------------------------------------------------------------------------- 1 | #!/usr/bin/env bash 2 | 3 | USAGE=$(cat <<-END 4 | \033[1mUsage:\033[0m 5 | 6 | -k|--kernel: specify the kernel. Defaults to the value of julia-\$(VERSION.major).\$(VERSION.minor). 7 | 8 | -m|--mode: a keyword which specifies the domain/port the Jupyter server is accessible. Valid arguments are 'dev', 'staging', and 'production' (default). 9 | END 10 | ) 11 | 12 | KERNEL=$(julia -e 'print("julia-$(VERSION.major).$(VERSION.minor)")') 13 | ORIGIN="https://catcolab.org" 14 | 15 | while [[ $# -gt 0 ]]; do 16 | case $1 in 17 | -k|--kernel) 18 | KERNEL=$2 19 | shift 20 | shift 21 | ;; 22 | -m|--mode) 23 | case "$2" in 24 | production) 25 | ;; 26 | staging) 27 | ORIGIN="https://next.catcolab.org" 28 | ;; 29 | dev) 30 | ORIGIN="http://localhost:5173" 31 | ;; 32 | *) 33 | echo "$2 is not an eligible mode. Please provide 'production', 'staging', or 'dev'" 34 | exit 1 35 | esac 36 | shift 37 | shift 38 | ;; 39 | -h|--help) 40 | echo -e "$USAGE" 41 | ;; 42 | *) 43 | echo " Unknown option: $1 44 | " 45 | echo -e "$USAGE" 46 | exit 1 47 | ;; 48 | esac 49 | done 50 | 51 | jupyter server \ 52 | --IdentityProvider.token="" \ 53 | --ServerApp.disable_check_xsrf=True \ 54 | --ServerApp.allow_origin="$ORIGIN" \ 55 | --ServerApp.allow_credentials=True \ 56 | --MultiKernelManager.default_kernel_name="$KERNEL" 57 | -------------------------------------------------------------------------------- /packages/algjulia-interop/make_sysimage.jl: -------------------------------------------------------------------------------- 1 | #!/usr/bin/env julia 2 | 3 | @info "Verifying PackageCompiler is installed globally" 4 | using Pkg; Pkg.activate(); Pkg.add("PackageCompiler") 5 | using PackageCompiler 6 | 7 | @info "Activating sysimage environment" 8 | Pkg.activate(@__DIR__) 9 | 10 | @info "Creating the sysimage. This may take a while..." 11 | sysimg="CatColabInterop.so" 12 | create_sysimage(["CatColabInterop"], sysimage_path=sysimg, 13 | precompile_execution_file="sysimage_precompile.jl") 14 | sysimg_path=joinpath(@__DIR__, sysimg); 15 | 16 | @info "Adding $sysimg_path to IJulia kernel" 17 | Pkg.activate(); Pkg.add("IJulia") 18 | using IJulia 19 | Pkg.build("IJulia") 20 | 21 | installkernel("Julia CatColab Interop", "--project=@.", "--sysimage=$sysimg_path") 22 | 23 | @info "Done!" 24 | exit() 25 | -------------------------------------------------------------------------------- /packages/algjulia-interop/src/decapodes-service/DecapodesService.jl: -------------------------------------------------------------------------------- 1 | module DecapodesService 2 | 3 | # algebraicjulia dependencies 4 | using ACSets 5 | using DiagrammaticEquations 6 | using Decapodes 7 | using CombinatorialSpaces 8 | 9 | # dependencies 10 | import JSON3 11 | using StaticArrays 12 | using MLStyle 13 | using LinearAlgebra 14 | using ComponentArrays 15 | using Distributions # for initial conditions 16 | 17 | # meshing 18 | using CoordRefSystems 19 | using GeometryBasics: Point2, Point3 20 | Point3D = Point3{Float64}; 21 | 22 | # simulation 23 | using OrdinaryDiffEq 24 | 25 | using ..CatColabInterop 26 | using ..CatColabInterop: AlgebraicJuliaIntegration, AbstractDiagram, AbstractAnalysis 27 | import ..CatColabInterop: Model, to_model 28 | 29 | # necessary to export 30 | export infer_types!, evalsim, default_dec_generate, default_dec_matrix_generate, 31 | DiagonalHodge, ComponentArray 32 | 33 | struct ThDecapode <: AlgebraicJuliaIntegration end 34 | export ThDecapode 35 | 36 | # funcitons for geometry and initial conditions 37 | include("geometry.jl") 38 | include("model.jl") ## model-building 39 | include("diagram.jl") ## diagram-building 40 | include("analysis/Analysis.jl") 41 | 42 | end 43 | -------------------------------------------------------------------------------- /packages/algjulia-interop/src/decapodes-service/analysis/Analysis.jl: -------------------------------------------------------------------------------- 1 | include("ns_helper.jl") 2 | include("initial_conditions.jl") 3 | include("simulation.jl") 4 | -------------------------------------------------------------------------------- /packages/algjulia-interop/src/kernel_support.jl: -------------------------------------------------------------------------------- 1 | import JSON3 2 | 3 | export JsonValue 4 | 5 | """ Container for an arbitrary JSON value. """ 6 | struct JsonValue 7 | value::Any 8 | end 9 | 10 | function Base.show(io::IO, ::MIME"text/plain", json::JsonValue) 11 | print(io, "JsonValue(") 12 | show(IOContext(io, :compact => true), json.value) 13 | print(io, ")") 14 | end 15 | 16 | function Base.show(io::IO, ::MIME"application/json", json::JsonValue) 17 | JSON3.write(io, json.value) 18 | end 19 | -------------------------------------------------------------------------------- /packages/algjulia-interop/sysimage_precompile.jl: -------------------------------------------------------------------------------- 1 | import CatColabInterop 2 | include(joinpath(pkgdir(CatColabInterop), "test", "runtests.jl")) 3 | -------------------------------------------------------------------------------- /packages/algjulia-interop/test/Project.toml: -------------------------------------------------------------------------------- 1 | [deps] 2 | ACSets = "227ef7b5-1206-438b-ac65-934d6da304b8" 3 | CatColabInterop = "9ecda8fb-39ab-46a2-a496-7285fa6368c1" 4 | CombinatorialSpaces = "b1c52339-7909-45ad-8b6a-6e388f7c67f2" 5 | ComponentArrays = "b0b7db55-cfe3-40fc-9ded-d10e2dbeff66" 6 | Decapodes = "679ab3ea-c928-4fe6-8d59-fd451142d391" 7 | DiagrammaticEquations = "6f00c28b-6bed-4403-80fa-30e0dc12f317" 8 | JSON3 = "0f8b85d8-7281-11e9-16c2-39a750bddbf1" 9 | LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e" 10 | MLStyle = "d8e11817-5142-5d16-987a-aa16d5891078" 11 | OrdinaryDiffEq = "1dea7af3-3e70-54e6-95c3-0bf5283fa5ed" 12 | StaticArrays = "90137ffa-7385-5640-81b9-e52037218182" 13 | Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40" 14 | -------------------------------------------------------------------------------- /packages/algjulia-interop/test/test_jsons/diagrams/diffusivity_constant/analysis.json: -------------------------------------------------------------------------------- 1 | { 2 | "analysisOf": { 3 | "_id": "0196021c-dee3-75b3-bb79-2f940651a1a1", 4 | "_server": "backend.catcolab.org", 5 | "_version": null, 6 | "type": "analysis-of" 7 | }, 8 | "analysisType": "diagram", 9 | "name": "", 10 | "notebook": { 11 | "cells": [ 12 | { 13 | "content": { 14 | "content": { 15 | "domain": "Plane", 16 | "duration": 10, 17 | "initialConditions": { 18 | "0196021c-f5fe-70f3-ac68-89ae212970ea": "Gaussian", 19 | "0196021d-1aa4-776d-b4fb-05d24d0c6de4": "Gaussian" 20 | }, 21 | "mesh": "Rectangle", 22 | "plotVariables": { 23 | "0196021c-f5fe-70f3-ac68-89ae212970ea": true 24 | }, 25 | "scalars": { 26 | "01960dde-1193-7132-b662-9bf24ed05264": 1 27 | } 28 | }, 29 | "id": "decapodes" 30 | }, 31 | "id": "0196021f-beef-74b0-9103-9ab1982255cf", 32 | "tag": "formal" 33 | }, 34 | { 35 | "content": { 36 | "content": { 37 | "layout": "graphviz-directed" 38 | }, 39 | "id": "graph" 40 | }, 41 | "id": "01960ddd-8fc3-7482-a2c8-a0a59ee85709", 42 | "tag": "formal" 43 | } 44 | ] 45 | }, 46 | "type": "analysis" 47 | } 48 | -------------------------------------------------------------------------------- /packages/algjulia-interop/test/test_jsons/diagrams/inverse_laplacian_longtrip/analysis.json: -------------------------------------------------------------------------------- 1 | {"analysisOf":{"_id":"0195ecdc-cf21-7091-94a3-7644d5103743","_server":"backend.catcolab.org","_version":null,"type":"analysis-of"},"analysisType":"diagram","name":"","notebook":{"cells":[{"id":"0195ed44-aa9e-730d-807d-57cf94417236","tag":"stem"},{"content":{"content":{"domain":"Plane","duration":10,"initialConditions":{"0195ecdc-d7e1-768a-8862-76a47f2f4e06":"Gaussian","0195ecdc-f625-71c8-a044-a6ce2fb3dd31":"Gaussian"},"mesh":"Rectangle","plotVariables":{"0195ecdc-d7e1-768a-8862-76a47f2f4e06":true},"scalars":{}},"id":"decapodes"},"id":"0195ed44-c260-755f-9c1f-80c13253e575","tag":"formal"}]},"type":"analysis"} 2 | -------------------------------------------------------------------------------- /packages/algjulia-interop/test/test_jsons/diagrams/ns_vort/analysis.json: -------------------------------------------------------------------------------- 1 | {"analysisOf":{"_id":"0195ecc4-4c4d-70e2-bee7-18221e6c42e7","_server":"backend.catcolab.org","_version":null,"type":"analysis-of"},"analysisType":"diagram","name":"","notebook":{"cells":[{"content":{"content":{"domain":"Sphere","duration":1,"initialConditions":{"0195ecc5-9eaf-71dd-a9c8-621d888e2add":"TaylorVortex","0195ecc5-b1b0-746e-8a04-ebd359da2bfd":"TaylorVortex","0195ecc5-d39a-72bf-8cd3-236d5211e122":"TaylorVortex"},"mesh":"Icosphere6","plotVariables":{"0195ecc5-9eaf-71dd-a9c8-621d888e2add":true},"scalars":{}},"id":"decapodes"},"id":"0195ecca-f11e-74c8-8fa4-fb8b03a93274","tag":"formal"}]},"type":"analysis"} 2 | -------------------------------------------------------------------------------- /packages/automerge-doc-server/.gitignore: -------------------------------------------------------------------------------- 1 | dist/ 2 | -------------------------------------------------------------------------------- /packages/automerge-doc-server/package.json: -------------------------------------------------------------------------------- 1 | { 2 | "name": "automerge-doc-server", 3 | "version": "0.1.0", 4 | "type": "module", 5 | "main": "dist/main.js", 6 | "scripts": { 7 | "main": "tsx src/main.ts", 8 | "format": "biome format --write", 9 | "lint": "biome lint --write && biome check --write" 10 | }, 11 | "author": "CatColab developer team", 12 | "license": "MIT", 13 | "dependencies": { 14 | "@automerge/automerge-repo": "^1.2.1", 15 | "@automerge/automerge-repo-network-websocket": "^1.2.1", 16 | "dotenv": "^16.5.0", 17 | "express": "^4.19.2", 18 | "pg": "^8.16.0", 19 | "socket.io-client": "^4.8.0", 20 | "ws": "^8.18.0" 21 | }, 22 | "devDependencies": { 23 | "@biomejs/biome": "^1.8.3", 24 | "@types/express": "^4.17.21", 25 | "@types/node": "^22.7.4", 26 | "@types/ws": "^8.5.12", 27 | "tsx": "^4.19.1", 28 | "typescript": "^5.6.2" 29 | } 30 | } 31 | -------------------------------------------------------------------------------- /packages/automerge-doc-server/src/main.ts: -------------------------------------------------------------------------------- 1 | import { runMigration } from "./migrations/index.js"; 2 | import { AutomergeServer } from "./server.js"; 3 | import { SocketServer } from "./socket.js"; 4 | 5 | async function main() { 6 | const args = process.argv.slice(2); 7 | 8 | if (args[0] === "--migrate") { 9 | const migrationName = args[1]; 10 | if (!migrationName) { 11 | console.error("Missing migration name after --migrate"); 12 | process.exit(1); 13 | } 14 | 15 | await runMigration(migrationName); 16 | process.exit(0); 17 | } 18 | 19 | const internal_port = process.env.AUTOMERGE_INTERNAL_PORT || 3000; 20 | const port = process.env.AUTOMERGE_PORT || 8010; 21 | 22 | const server = new AutomergeServer(port); 23 | const socket_server = new SocketServer(internal_port, server); 24 | 25 | server.handleChange = (refId, content) => socket_server.autosave(refId, content); 26 | 27 | process.once("SIGINT", () => { 28 | socket_server.close(); 29 | server.close(); 30 | }); 31 | 32 | process.once("SIGTERM", () => { 33 | socket_server.close(); 34 | server.close(); 35 | }); 36 | } 37 | 38 | main(); 39 | -------------------------------------------------------------------------------- /packages/automerge-doc-server/src/migrations/index.ts: -------------------------------------------------------------------------------- 1 | import { automergeStorage } from "./m20250516154702_automerge_storage.js"; 2 | 3 | export async function runMigration(name: string) { 4 | switch (name) { 5 | case "automerge_storage": { 6 | await automergeStorage(); 7 | break; 8 | } 9 | default: 10 | console.error(`Unknown migration: ${name}`); 11 | process.exit(1); 12 | } 13 | } 14 | -------------------------------------------------------------------------------- /packages/automerge-doc-server/src/migrations/m20250516154702_automerge_storage.ts: -------------------------------------------------------------------------------- 1 | import { Repo, type RepoConfig } from "@automerge/automerge-repo"; 2 | import dotenv from "dotenv"; 3 | import pgPkg from "pg"; 4 | import { PostgresStorageAdapter } from "../postgres_storage_adapter.js"; 5 | 6 | const { Pool } = pgPkg; 7 | 8 | dotenv.config(); 9 | 10 | export async function automergeStorage() { 11 | const pool = new Pool({ 12 | connectionString: process.env.DATABASE_URL, 13 | }); 14 | 15 | const storageAdapter = new PostgresStorageAdapter(pool); 16 | 17 | const config: RepoConfig = { 18 | sharePolicy: async () => false, 19 | storage: storageAdapter, 20 | }; 21 | 22 | const repo = new Repo(config); 23 | 24 | const result = await pool.query("SELECT id, content, doc_id FROM snapshots"); 25 | 26 | for (const { id, content, doc_id } of result.rows) { 27 | if (doc_id) { 28 | continue; 29 | } 30 | 31 | const handle = repo.create(content); 32 | 33 | if (!handle) { 34 | console.error(`Failed to create document for ref ${id}`); 35 | continue; 36 | } 37 | 38 | await pool.query("UPDATE snapshots SET doc_id = $2 WHERE id = $1", [id, handle.documentId]); 39 | 40 | console.log(`created automerge doc for snapshot ${id}`); 41 | } 42 | 43 | console.log("Done!"); 44 | } 45 | -------------------------------------------------------------------------------- /packages/automerge-doc-server/src/types.ts: -------------------------------------------------------------------------------- 1 | export type NewDocSocketResponse = 2 | | { 3 | Ok: { 4 | docId: string; 5 | docJson: any; 6 | }; 7 | } 8 | | { Err: string }; 9 | export type StartListeningSocketResponse = { Ok: null } | { Err: string }; 10 | -------------------------------------------------------------------------------- /packages/automerge-doc-server/tsconfig.json: -------------------------------------------------------------------------------- 1 | { 2 | "compilerOptions": { 3 | "target": "ESNext", 4 | "module": "NodeNext", 5 | "moduleResolution": "Node16", 6 | "esModuleInterop": true, 7 | "outDir": "./dist", 8 | 9 | "strict": true, 10 | "skipLibCheck": true, 11 | "noUnusedLocals": true, 12 | "noUnusedParameters": true, 13 | "noUncheckedIndexedAccess": true, 14 | "noFallthroughCasesInSwitch": true 15 | }, 16 | "include": ["src/**/*.ts"] 17 | } 18 | -------------------------------------------------------------------------------- /packages/backend/.gitignore: -------------------------------------------------------------------------------- 1 | *.env 2 | -------------------------------------------------------------------------------- /packages/backend/.sqlx/query-05183554f0c9207cdd1e89a948d3da5238ede1773a9507446694e9f7b4d2b16c.json: -------------------------------------------------------------------------------- 1 | { 2 | "db_name": "PostgreSQL", 3 | "query": "\n WITH snapshot AS (\n INSERT INTO snapshots(for_ref, content, last_updated, doc_id)\n VALUES ($1, $2, NOW(), $3)\n RETURNING id\n )\n UPDATE refs\n SET head = (SELECT id FROM snapshot)\n WHERE id = $1\n ", 4 | "describe": { 5 | "columns": [], 6 | "parameters": { 7 | "Left": [ 8 | "Uuid", 9 | "Jsonb", 10 | "Text" 11 | ] 12 | }, 13 | "nullable": [] 14 | }, 15 | "hash": "05183554f0c9207cdd1e89a948d3da5238ede1773a9507446694e9f7b4d2b16c" 16 | } 17 | -------------------------------------------------------------------------------- /packages/backend/.sqlx/query-1ddd7b172b0db3b5e7818013b6bb9e2d57dc2e2bc13e1d7faa82e48a77964dcc.json: -------------------------------------------------------------------------------- 1 | { 2 | "db_name": "PostgreSQL", 3 | "query": "SELECT 1 FROM refs WHERE id = $1", 4 | "describe": { 5 | "columns": [ 6 | { 7 | "ordinal": 0, 8 | "name": "?column?", 9 | "type_info": "Int4" 10 | } 11 | ], 12 | "parameters": { 13 | "Left": [ 14 | "Uuid" 15 | ] 16 | }, 17 | "nullable": [ 18 | null 19 | ] 20 | }, 21 | "hash": "1ddd7b172b0db3b5e7818013b6bb9e2d57dc2e2bc13e1d7faa82e48a77964dcc" 22 | } 23 | -------------------------------------------------------------------------------- /packages/backend/.sqlx/query-3645a86b3df08de865372b02d588272bb950744a38d46079ca18b11e405058a3.json: -------------------------------------------------------------------------------- 1 | { 2 | "db_name": "PostgreSQL", 3 | "query": "\n SELECT EXISTS (\n SELECT 1 FROM users WHERE id = $1\n )\n ", 4 | "describe": { 5 | "columns": [ 6 | { 7 | "ordinal": 0, 8 | "name": "exists", 9 | "type_info": "Bool" 10 | } 11 | ], 12 | "parameters": { 13 | "Left": [ 14 | "Text" 15 | ] 16 | }, 17 | "nullable": [ 18 | null 19 | ] 20 | }, 21 | "hash": "3645a86b3df08de865372b02d588272bb950744a38d46079ca18b11e405058a3" 22 | } 23 | -------------------------------------------------------------------------------- /packages/backend/.sqlx/query-3e2b3e63a36ffa59ce60f8df19157edc1dfcee0d876d4b0c22c2db24feee6a3c.json: -------------------------------------------------------------------------------- 1 | { 2 | "db_name": "PostgreSQL", 3 | "query": "\n INSERT INTO users(id, created, signed_in)\n VALUES ($1, NOW(), NOW())\n ON CONFLICT (id) DO UPDATE\n SET signed_in = EXCLUDED.signed_in\n ", 4 | "describe": { 5 | "columns": [], 6 | "parameters": { 7 | "Left": [ 8 | "Text" 9 | ] 10 | }, 11 | "nullable": [] 12 | }, 13 | "hash": "3e2b3e63a36ffa59ce60f8df19157edc1dfcee0d876d4b0c22c2db24feee6a3c" 14 | } 15 | -------------------------------------------------------------------------------- /packages/backend/.sqlx/query-3e715aa995094feff20f8254dfd27323844efa31ece5d40ce8778122687cdefc.json: -------------------------------------------------------------------------------- 1 | { 2 | "db_name": "PostgreSQL", 3 | "query": "\n SELECT id, username, display_name FROM users WHERE username = $1\n ", 4 | "describe": { 5 | "columns": [ 6 | { 7 | "ordinal": 0, 8 | "name": "id", 9 | "type_info": "Text" 10 | }, 11 | { 12 | "ordinal": 1, 13 | "name": "username", 14 | "type_info": "Text" 15 | }, 16 | { 17 | "ordinal": 2, 18 | "name": "display_name", 19 | "type_info": "Text" 20 | } 21 | ], 22 | "parameters": { 23 | "Left": [ 24 | "Text" 25 | ] 26 | }, 27 | "nullable": [ 28 | false, 29 | true, 30 | true 31 | ] 32 | }, 33 | "hash": "3e715aa995094feff20f8254dfd27323844efa31ece5d40ce8778122687cdefc" 34 | } 35 | -------------------------------------------------------------------------------- /packages/backend/.sqlx/query-4f04b1b2b42a310d659df5700aa47b10a291e6e98d2b989036e8d78ee3b00afd.json: -------------------------------------------------------------------------------- 1 | { 2 | "db_name": "PostgreSQL", 3 | "query": "\n UPDATE snapshots\n SET content = $2, last_updated = NOW()\n WHERE id = (SELECT head FROM refs WHERE id = $1)\n ", 4 | "describe": { 5 | "columns": [], 6 | "parameters": { 7 | "Left": [ 8 | "Uuid", 9 | "Jsonb" 10 | ] 11 | }, 12 | "nullable": [] 13 | }, 14 | "hash": "4f04b1b2b42a310d659df5700aa47b10a291e6e98d2b989036e8d78ee3b00afd" 15 | } 16 | -------------------------------------------------------------------------------- /packages/backend/.sqlx/query-513719212b96e260e9c4ce840f716b1b6cb43563371fb35f9677fcf949827363.json: -------------------------------------------------------------------------------- 1 | { 2 | "db_name": "PostgreSQL", 3 | "query": "\n SELECT subject as \"user_id\", username, display_name,\n level as \"level: PermissionLevel\"\n FROM permissions\n LEFT OUTER JOIN users ON id = subject\n WHERE object = $1\n ", 4 | "describe": { 5 | "columns": [ 6 | { 7 | "ordinal": 0, 8 | "name": "user_id", 9 | "type_info": "Text" 10 | }, 11 | { 12 | "ordinal": 1, 13 | "name": "username", 14 | "type_info": "Text" 15 | }, 16 | { 17 | "ordinal": 2, 18 | "name": "display_name", 19 | "type_info": "Text" 20 | }, 21 | { 22 | "ordinal": 3, 23 | "name": "level: PermissionLevel", 24 | "type_info": { 25 | "Custom": { 26 | "name": "permission_level", 27 | "kind": { 28 | "Enum": [ 29 | "read", 30 | "write", 31 | "maintain", 32 | "own" 33 | ] 34 | } 35 | } 36 | } 37 | } 38 | ], 39 | "parameters": { 40 | "Left": [ 41 | "Uuid" 42 | ] 43 | }, 44 | "nullable": [ 45 | true, 46 | true, 47 | true, 48 | false 49 | ] 50 | }, 51 | "hash": "513719212b96e260e9c4ce840f716b1b6cb43563371fb35f9677fcf949827363" 52 | } 53 | -------------------------------------------------------------------------------- /packages/backend/.sqlx/query-6425b7d75c5fd6482701adba8011472860299d4fc872194449e18682cfed5bab.json: -------------------------------------------------------------------------------- 1 | { 2 | "db_name": "PostgreSQL", 3 | "query": "\n SELECT doc_id FROM snapshots\n WHERE id = (SELECT head FROM refs WHERE id = $1)\n ", 4 | "describe": { 5 | "columns": [ 6 | { 7 | "ordinal": 0, 8 | "name": "doc_id", 9 | "type_info": "Text" 10 | } 11 | ], 12 | "parameters": { 13 | "Left": [ 14 | "Uuid" 15 | ] 16 | }, 17 | "nullable": [ 18 | false 19 | ] 20 | }, 21 | "hash": "6425b7d75c5fd6482701adba8011472860299d4fc872194449e18682cfed5bab" 22 | } 23 | -------------------------------------------------------------------------------- /packages/backend/.sqlx/query-84f34c3f761dbab809edf2af4104e533a26a50310c90d340fdd90d64683b6b55.json: -------------------------------------------------------------------------------- 1 | { 2 | "db_name": "PostgreSQL", 3 | "query": "\n SELECT username, display_name FROM users\n WHERE id = $1\n ", 4 | "describe": { 5 | "columns": [ 6 | { 7 | "ordinal": 0, 8 | "name": "username", 9 | "type_info": "Text" 10 | }, 11 | { 12 | "ordinal": 1, 13 | "name": "display_name", 14 | "type_info": "Text" 15 | } 16 | ], 17 | "parameters": { 18 | "Left": [ 19 | "Text" 20 | ] 21 | }, 22 | "nullable": [ 23 | true, 24 | true 25 | ] 26 | }, 27 | "hash": "84f34c3f761dbab809edf2af4104e533a26a50310c90d340fdd90d64683b6b55" 28 | } 29 | -------------------------------------------------------------------------------- /packages/backend/.sqlx/query-92973a6dc72749d528465057e8bd674427db3a290d6db645dea5ac3c540167ef.json: -------------------------------------------------------------------------------- 1 | { 2 | "db_name": "PostgreSQL", 3 | "query": "\n SELECT content FROM snapshots\n WHERE id = (SELECT head FROM refs WHERE id = $1)\n ", 4 | "describe": { 5 | "columns": [ 6 | { 7 | "ordinal": 0, 8 | "name": "content", 9 | "type_info": "Jsonb" 10 | } 11 | ], 12 | "parameters": { 13 | "Left": [ 14 | "Uuid" 15 | ] 16 | }, 17 | "nullable": [ 18 | false 19 | ] 20 | }, 21 | "hash": "92973a6dc72749d528465057e8bd674427db3a290d6db645dea5ac3c540167ef" 22 | } 23 | -------------------------------------------------------------------------------- /packages/backend/.sqlx/query-a80368dbf3e74206cdbe08744b1d46924d0731475384201d7f2ddaf51e8e3644.json: -------------------------------------------------------------------------------- 1 | { 2 | "db_name": "PostgreSQL", 3 | "query": "SELECT 1 FROM users WHERE username = $1", 4 | "describe": { 5 | "columns": [ 6 | { 7 | "ordinal": 0, 8 | "name": "?column?", 9 | "type_info": "Int4" 10 | } 11 | ], 12 | "parameters": { 13 | "Left": [ 14 | "Text" 15 | ] 16 | }, 17 | "nullable": [ 18 | null 19 | ] 20 | }, 21 | "hash": "a80368dbf3e74206cdbe08744b1d46924d0731475384201d7f2ddaf51e8e3644" 22 | } 23 | -------------------------------------------------------------------------------- /packages/backend/.sqlx/query-a8934c50209e48af661186c7d1c2ff8d8f23b4d05f1a7f5783baf74165f464f1.json: -------------------------------------------------------------------------------- 1 | { 2 | "db_name": "PostgreSQL", 3 | "query": "\n UPDATE users SET username = COALESCE($2, username), display_name = $3\n WHERE id = $1\n ", 4 | "describe": { 5 | "columns": [], 6 | "parameters": { 7 | "Left": [ 8 | "Text", 9 | "Text", 10 | "Text" 11 | ] 12 | }, 13 | "nullable": [] 14 | }, 15 | "hash": "a8934c50209e48af661186c7d1c2ff8d8f23b4d05f1a7f5783baf74165f464f1" 16 | } 17 | -------------------------------------------------------------------------------- /packages/backend/.sqlx/query-a8cb9f26893bbf784cf8a71090e64c3603e238ea6786d327f64ae04aef205198.json: -------------------------------------------------------------------------------- 1 | { 2 | "db_name": "PostgreSQL", 3 | "query": "\n WITH snapshot AS (\n INSERT INTO snapshots(for_ref, content, last_updated, doc_id)\n VALUES ($1, $2, NOW(), $3)\n RETURNING id\n )\n INSERT INTO refs(id, head, created)\n VALUES ($1, (SELECT id FROM snapshot), NOW())\n ", 4 | "describe": { 5 | "columns": [], 6 | "parameters": { 7 | "Left": [ 8 | "Uuid", 9 | "Jsonb", 10 | "Text" 11 | ] 12 | }, 13 | "nullable": [] 14 | }, 15 | "hash": "a8cb9f26893bbf784cf8a71090e64c3603e238ea6786d327f64ae04aef205198" 16 | } 17 | -------------------------------------------------------------------------------- /packages/backend/.sqlx/query-cca19c531258c9500e4c27e139d15f8bfea54d7fd1b08728debfcacd5de174b4.json: -------------------------------------------------------------------------------- 1 | { 2 | "db_name": "PostgreSQL", 3 | "query": "\n INSERT INTO permissions(subject, object, level)\n VALUES ($1, $2, 'own')\n ", 4 | "describe": { 5 | "columns": [], 6 | "parameters": { 7 | "Left": [ 8 | "Text", 9 | "Uuid" 10 | ] 11 | }, 12 | "nullable": [] 13 | }, 14 | "hash": "cca19c531258c9500e4c27e139d15f8bfea54d7fd1b08728debfcacd5de174b4" 15 | } 16 | -------------------------------------------------------------------------------- /packages/backend/.sqlx/query-cd63d277bd2ae2905790e11cddb4b9bcb5b56e952b854a75dc724e1c253afcf5.json: -------------------------------------------------------------------------------- 1 | { 2 | "db_name": "PostgreSQL", 3 | "query": "\n DELETE FROM permissions WHERE object = $1 AND level < 'own'\n ", 4 | "describe": { 5 | "columns": [], 6 | "parameters": { 7 | "Left": [ 8 | "Uuid" 9 | ] 10 | }, 11 | "nullable": [] 12 | }, 13 | "hash": "cd63d277bd2ae2905790e11cddb4b9bcb5b56e952b854a75dc724e1c253afcf5" 14 | } 15 | -------------------------------------------------------------------------------- /packages/backend/.sqlx/query-e75b5c0a7da4bc3c0f52a62179d15289fd31d08d48d7a99d37cb1a6414656e7d.json: -------------------------------------------------------------------------------- 1 | { 2 | "db_name": "PostgreSQL", 3 | "query": "\n SELECT MAX(level) AS \"max: PermissionLevel\" FROM permissions\n WHERE object = $1 AND (subject IS NULL OR subject = $2)\n ", 4 | "describe": { 5 | "columns": [ 6 | { 7 | "ordinal": 0, 8 | "name": "max: PermissionLevel", 9 | "type_info": { 10 | "Custom": { 11 | "name": "permission_level", 12 | "kind": { 13 | "Enum": [ 14 | "read", 15 | "write", 16 | "maintain", 17 | "own" 18 | ] 19 | } 20 | } 21 | } 22 | } 23 | ], 24 | "parameters": { 25 | "Left": [ 26 | "Uuid", 27 | "Text" 28 | ] 29 | }, 30 | "nullable": [ 31 | null 32 | ] 33 | }, 34 | "hash": "e75b5c0a7da4bc3c0f52a62179d15289fd31d08d48d7a99d37cb1a6414656e7d" 35 | } 36 | -------------------------------------------------------------------------------- /packages/backend/.sqlx/query-eea510d03cc559aa11d46aafe38f57789f5c2e791800f78a751602cc8336c84f.json: -------------------------------------------------------------------------------- 1 | { 2 | "db_name": "PostgreSQL", 3 | "query": "\n INSERT INTO permissions(subject, object, level)\n SELECT * FROM UNNEST($1::text[], $2::uuid[], $3::permission_level[])\n ", 4 | "describe": { 5 | "columns": [], 6 | "parameters": { 7 | "Left": [ 8 | "TextArray", 9 | "UuidArray", 10 | { 11 | "Custom": { 12 | "name": "permission_level[]", 13 | "kind": { 14 | "Array": { 15 | "Custom": { 16 | "name": "permission_level", 17 | "kind": { 18 | "Enum": [ 19 | "read", 20 | "write", 21 | "maintain", 22 | "own" 23 | ] 24 | } 25 | } 26 | } 27 | } 28 | } 29 | } 30 | ] 31 | }, 32 | "nullable": [] 33 | }, 34 | "hash": "eea510d03cc559aa11d46aafe38f57789f5c2e791800f78a751602cc8336c84f" 35 | } 36 | -------------------------------------------------------------------------------- /packages/backend/Cargo.toml: -------------------------------------------------------------------------------- 1 | [package] 2 | name = "catcolab-backend" 3 | version = "0.1.0" 4 | edition = "2024" 5 | 6 | [dependencies] 7 | axum = "0.7.7" 8 | chrono = { version = "0.4.40", features = ["serde"] } 9 | dotenvy = "0.15.7" 10 | firebase-auth = { version = "0.4.3", default-features = false } 11 | http = "1.1.0" 12 | hyper = { version = "1.4.1", features = ["server"] } 13 | jsonrpsee = "0.24.6" 14 | jsonrpsee-server = "0.24.6" 15 | qubit = "0.10.2" 16 | regex = "1.11.1" 17 | serde = { version = "1.0.210", features = ["derive"] } 18 | serde_json = "1.0.128" 19 | socketioxide = { version = "0.14.1", features = ["tracing"] } 20 | sqlx = { version = "0.8.2", features = [ 21 | "runtime-tokio", 22 | "tls-native-tls", 23 | "postgres", 24 | "uuid", 25 | "json", 26 | "chrono", 27 | ] } 28 | thiserror = "1.0.64" 29 | tokio = { version = "1.40.0", features = ["full"] } 30 | tower = { version = "0.5.1", features = ["util"] } 31 | tower-http = { version = "0.6.1", features = ["cors", "trace"] } 32 | tracing = "0.1.40" 33 | tracing-subscriber = { version = "0.3.18", features = ["env-filter"] } 34 | ts-rs = { version = "10.1.0", features = [ 35 | "serde-json-impl", 36 | "uuid-impl", 37 | "chrono-impl", 38 | ] } 39 | uuid = { version = "1.10.0", features = ["v7", "serde"] } 40 | -------------------------------------------------------------------------------- /packages/backend/default.nix: -------------------------------------------------------------------------------- 1 | { 2 | pkgs, 3 | rustToolchain, 4 | ... 5 | }: 6 | let 7 | # Why do this instaed of creating a global overlay for rustc and cargo? 8 | # 9 | # Fenix can provide a rustc and cargo, however they are derivations, which means they are lacking many 10 | # of the attributes that other packages expect them to have. So creating an overlay with the fenix rustc 11 | # and cargo will cause other packages to break. 12 | # 13 | # The correct way to handle this is to use fenix to configure pkgs.rustPlatform, which other packages 14 | # should be using. However crate2nix does not use this API and instaed uses the older pkgs.buildRustCrate. 15 | # As a result we need to manually pass the rust toolchain to the cargoNix callsite. 16 | buildRustCrateForPkgs = 17 | crate: 18 | pkgs.buildRustCrate.override { 19 | rustc = rustToolchain; 20 | cargo = rustToolchain; 21 | }; 22 | 23 | cargoNix = import ../../Cargo.nix { inherit pkgs buildRustCrateForPkgs; }; 24 | backend = cargoNix.workspaceMembers.catcolab-backend.build; 25 | in 26 | backend 27 | -------------------------------------------------------------------------------- /packages/backend/pkg/package.json: -------------------------------------------------------------------------------- 1 | { 2 | "name": "catcolab-api", 3 | "version": "0.1.0", 4 | "author": "Evan Patterson ", 5 | "license": "MIT", 6 | "main": "src/index.ts", 7 | "scripts": { 8 | "build": "tsc -b" 9 | }, 10 | "dependencies": { 11 | "@qubit-rs/client": "^0.4.4", 12 | "typescript": "^5.6.3" 13 | } 14 | } 15 | -------------------------------------------------------------------------------- /packages/backend/pkg/pnpm-lock.yaml: -------------------------------------------------------------------------------- 1 | lockfileVersion: '9.0' 2 | 3 | settings: 4 | autoInstallPeers: true 5 | excludeLinksFromLockfile: false 6 | 7 | importers: 8 | 9 | .: 10 | dependencies: 11 | '@qubit-rs/client': 12 | specifier: ^0.4.4 13 | version: 0.4.4 14 | typescript: 15 | specifier: ^5.6.3 16 | version: 5.6.3 17 | 18 | packages: 19 | 20 | '@qubit-rs/client@0.4.4': 21 | resolution: {integrity: sha512-AdaF25aGRU4YkYYxxARH3eYlezzHhGECTFGZ5/zEc9y+iPxdIaaWf4/m8uEtdbzjMEsGaA4vVVd1kuriK6sDzQ==} 22 | 23 | typescript@5.6.3: 24 | resolution: {integrity: sha512-hjcS1mhfuyi4WW8IWtjP7brDrG2cuDZukyrYrSauoXGNgx0S7zceP07adYkJycEr56BOUTNPzbInooiN3fn1qw==} 25 | engines: {node: '>=14.17'} 26 | hasBin: true 27 | 28 | snapshots: 29 | 30 | '@qubit-rs/client@0.4.4': {} 31 | 32 | typescript@5.6.3: {} 33 | -------------------------------------------------------------------------------- /packages/backend/pkg/src/NewPermissions.ts: -------------------------------------------------------------------------------- 1 | // This file was generated by [ts-rs](https://github.com/Aleph-Alpha/ts-rs). Do not edit this file manually. 2 | import type { PermissionLevel } from "./PermissionLevel"; 3 | 4 | /** 5 | * A new set of permissions to assign to a document. 6 | */ 7 | export type NewPermissions = { 8 | /** 9 | * Base permission level for any person, logged in or not. 10 | */ 11 | anyone: PermissionLevel | null, 12 | /** Permission levels for users. 13 | 14 | A mapping from user IDs to permission levels. 15 | */ 16 | users: { [key in string]?: PermissionLevel }, }; 17 | -------------------------------------------------------------------------------- /packages/backend/pkg/src/Paginated.ts: -------------------------------------------------------------------------------- 1 | // This file was generated by [ts-rs](https://github.com/Aleph-Alpha/ts-rs). Do not edit this file manually. 2 | 3 | /** 4 | * A page of items along with pagination metadata. 5 | */ 6 | export type Paginated = { 7 | /** 8 | * The total number of items matching the query criteria. 9 | */ 10 | total: number, 11 | /** 12 | * The number of items skipped. 13 | */ 14 | offset: number, 15 | /** 16 | * The items in the current page. 17 | */ 18 | items: Array, }; 19 | -------------------------------------------------------------------------------- /packages/backend/pkg/src/PermissionLevel.ts: -------------------------------------------------------------------------------- 1 | // This file was generated by [ts-rs](https://github.com/Aleph-Alpha/ts-rs). Do not edit this file manually. 2 | 3 | /** 4 | * Levels of permission that a user can have on a document. 5 | */ 6 | export type PermissionLevel = "Read" | "Write" | "Maintain" | "Own"; 7 | -------------------------------------------------------------------------------- /packages/backend/pkg/src/Permissions.ts: -------------------------------------------------------------------------------- 1 | // This file was generated by [ts-rs](https://github.com/Aleph-Alpha/ts-rs). Do not edit this file manually. 2 | import type { PermissionLevel } from "./PermissionLevel"; 3 | import type { UserPermissions } from "./UserPermissions"; 4 | 5 | /** 6 | * Permissions set on a document. 7 | */ 8 | export type Permissions = { 9 | /** 10 | * Base permission level for any person, logged in or not. 11 | */ 12 | anyone: PermissionLevel | null, 13 | /** 14 | * Permission level for the current user. 15 | */ 16 | user: PermissionLevel | null, 17 | /** Permission levels for all other users. 18 | 19 | Only owners of the document have access to this information. 20 | */ 21 | users: Array | null, }; 22 | -------------------------------------------------------------------------------- /packages/backend/pkg/src/RefContent.ts: -------------------------------------------------------------------------------- 1 | // This file was generated by [ts-rs](https://github.com/Aleph-Alpha/ts-rs). Do not edit this file manually. 2 | import type { JsonValue } from "./serde_json/JsonValue"; 3 | 4 | /** 5 | * A document ref along with its content. 6 | */ 7 | export type RefContent = { refId: string, content: JsonValue, }; 8 | -------------------------------------------------------------------------------- /packages/backend/pkg/src/RefDoc.ts: -------------------------------------------------------------------------------- 1 | // This file was generated by [ts-rs](https://github.com/Aleph-Alpha/ts-rs). Do not edit this file manually. 2 | import type { JsonValue } from "./serde_json/JsonValue"; 3 | import type { Permissions } from "./Permissions"; 4 | 5 | /** 6 | * Document identified by a ref. 7 | */ 8 | export type RefDoc = { "tag": "Readonly", content: JsonValue, permissions: Permissions, } | { "tag": "Live", docId: string, permissions: Permissions, }; 9 | -------------------------------------------------------------------------------- /packages/backend/pkg/src/RefQueryParams.ts: -------------------------------------------------------------------------------- 1 | // This file was generated by [ts-rs](https://github.com/Aleph-Alpha/ts-rs). Do not edit this file manually. 2 | import type { PermissionLevel } from "./PermissionLevel"; 3 | 4 | /** 5 | * Parameters for filtering a search of refs 6 | */ 7 | export type RefQueryParams = { ownerUsernameQuery: string | null, refNameQuery: string | null, searcherMinLevel: PermissionLevel | null, includePublicDocuments: boolean | null, limit: number | null, offset: number | null, }; 8 | -------------------------------------------------------------------------------- /packages/backend/pkg/src/RefStub.ts: -------------------------------------------------------------------------------- 1 | // This file was generated by [ts-rs](https://github.com/Aleph-Alpha/ts-rs). Do not edit this file manually. 2 | import type { PermissionLevel } from "./PermissionLevel"; 3 | import type { UserSummary } from "./UserSummary"; 4 | 5 | /** 6 | * A subset of user relevant information about a ref. Used for showing 7 | * users information on a variety of refs without having to load whole 8 | * refs. 9 | */ 10 | export type RefStub = { name: string, typeName: string, refId: string, permissionLevel: PermissionLevel, owner: UserSummary | null, createdAt: string, }; 11 | -------------------------------------------------------------------------------- /packages/backend/pkg/src/RpcResult.ts: -------------------------------------------------------------------------------- 1 | // This file was generated by [ts-rs](https://github.com/Aleph-Alpha/ts-rs). Do not edit this file manually. 2 | 3 | /** 4 | * Result returned by an RPC handler. 5 | */ 6 | export type RpcResult = { "tag": "Ok", content: T, } | { "tag": "Err", code: number, message: string, }; 7 | -------------------------------------------------------------------------------- /packages/backend/pkg/src/UserPermissions.ts: -------------------------------------------------------------------------------- 1 | // This file was generated by [ts-rs](https://github.com/Aleph-Alpha/ts-rs). Do not edit this file manually. 2 | import type { PermissionLevel } from "./PermissionLevel"; 3 | import type { UserSummary } from "./UserSummary"; 4 | 5 | /** 6 | * Permissions of a user on a document. 7 | */ 8 | export type UserPermissions = { user: UserSummary, level: PermissionLevel, }; 9 | -------------------------------------------------------------------------------- /packages/backend/pkg/src/UserProfile.ts: -------------------------------------------------------------------------------- 1 | // This file was generated by [ts-rs](https://github.com/Aleph-Alpha/ts-rs). Do not edit this file manually. 2 | 3 | /** 4 | * Data of a user profile. 5 | */ 6 | export type UserProfile = { username: string | null, displayName: string | null, }; 7 | -------------------------------------------------------------------------------- /packages/backend/pkg/src/UserSummary.ts: -------------------------------------------------------------------------------- 1 | // This file was generated by [ts-rs](https://github.com/Aleph-Alpha/ts-rs). Do not edit this file manually. 2 | 3 | /** Summary of a user. 4 | 5 | The minimal information needed to uniquely identify a user and display the user 6 | in human-readable form. 7 | */ 8 | export type UserSummary = { id: string, username: string | null, displayName: string | null, }; 9 | -------------------------------------------------------------------------------- /packages/backend/pkg/src/UsernameStatus.ts: -------------------------------------------------------------------------------- 1 | // This file was generated by [ts-rs](https://github.com/Aleph-Alpha/ts-rs). Do not edit this file manually. 2 | 3 | /** 4 | * Status of a username. 5 | */ 6 | export type UsernameStatus = "Available" | "Unavailable" | "Invalid"; 7 | -------------------------------------------------------------------------------- /packages/backend/pkg/src/serde_json/JsonValue.ts: -------------------------------------------------------------------------------- 1 | // This file was generated by [ts-rs](https://github.com/Aleph-Alpha/ts-rs). Do not edit this file manually. 2 | 3 | export type JsonValue = number | string | boolean | Array | { [key in string]?: JsonValue } | null; 4 | -------------------------------------------------------------------------------- /packages/backend/pkg/tsconfig.json: -------------------------------------------------------------------------------- 1 | { 2 | "compilerOptions": { 3 | "target": "ESNext", 4 | "module": "NodeNext", 5 | "moduleResolution": "Node16", 6 | "esModuleInterop": true, 7 | "noEmit": true, 8 | "allowImportingTsExtensions": true, 9 | "outDir": "./dist", 10 | 11 | "strict": true, 12 | "skipLibCheck": true, 13 | "noUnusedLocals": true, 14 | "noUnusedParameters": true, 15 | "noUncheckedIndexedAccess": true, 16 | "noFallthroughCasesInSwitch": true 17 | }, 18 | "include": ["src/**/*.ts"] 19 | } 20 | -------------------------------------------------------------------------------- /packages/backend/src/socket.rs: -------------------------------------------------------------------------------- 1 | use socketioxide::extract::{Data, SocketRef}; 2 | use tracing::{error, info}; 3 | 4 | use super::app::AppState; 5 | use super::document as doc; 6 | 7 | /// Set up the socket that communicates with the Automerge doc server. 8 | pub fn setup_automerge_socket(state: AppState) { 9 | let io = state.automerge_io.clone(); 10 | 11 | io.ns("/", |socket: SocketRef| { 12 | info!("Automerge socket connected at namespace {}", socket.ns()); 13 | 14 | socket.on("autosave", |_: SocketRef, Data::(data)| async move { 15 | if let Err(err) = doc::autosave(state, data).await { 16 | error!("Autosave failed with error: {}", err); 17 | } 18 | }); 19 | }); 20 | } 21 | -------------------------------------------------------------------------------- /packages/catlog-wasm/.gitignore: -------------------------------------------------------------------------------- 1 | /target 2 | **/*.rs.bk 3 | bin/ 4 | pkg/ 5 | wasm-pack.log 6 | -------------------------------------------------------------------------------- /packages/catlog-wasm/Cargo.toml: -------------------------------------------------------------------------------- 1 | [package] 2 | name = "catlog-wasm" 3 | version = "0.1.0" 4 | authors = ["Evan Patterson "] 5 | edition = "2024" 6 | 7 | [lib] 8 | crate-type = ["cdylib", "rlib"] 9 | 10 | [features] 11 | default = ["console_error_panic_hook"] 12 | 13 | [dependencies] 14 | all-the-same = "1.1.0" 15 | catlog = { path = "../catlog", features = ["ode", "serde-wasm"] } 16 | console_error_panic_hook = { version = "0.1.7", optional = true } 17 | derive_more = { version = "1", features = ["from", "try_into"] } 18 | egglog = { version = "0.4", default-features = false, features = [ 19 | "wasm-bindgen", 20 | ] } 21 | getrandom = { version = "0.2", features = ["js"] } 22 | js-sys = "0.3.77" 23 | nonempty = { version = "0.10", features = ["serialize"] } 24 | notebook-types = { version = "0.1.0", path = "../notebook-types" } 25 | serde = { version = "1", features = ["derive"] } 26 | tsify = { version = "0.5", features = ["js"] } 27 | ustr = "1" 28 | uuid = { version = "=1.11", features = ["v7", "serde", "js"] } 29 | wasm-bindgen = "0.2.100" 30 | 31 | [dev-dependencies] 32 | wasm-bindgen-test = "0.3.50" 33 | -------------------------------------------------------------------------------- /packages/catlog-wasm/src/analyses.rs: -------------------------------------------------------------------------------- 1 | use serde::{Deserialize, Serialize}; 2 | use tsify::Tsify; 3 | use uuid::Uuid; 4 | 5 | use super::result::JsResult; 6 | use catlog::stdlib::analyses; 7 | 8 | #[derive(Serialize, Deserialize, Tsify)] 9 | #[tsify(into_wasm_abi, from_wasm_abi)] 10 | pub struct ODEResult(pub JsResult, String>); 11 | 12 | #[derive(Serialize, Deserialize, Tsify)] 13 | #[tsify(into_wasm_abi, from_wasm_abi)] 14 | pub struct LotkaVolterraModelData(pub analyses::ode::LotkaVolterraProblemData); 15 | 16 | #[derive(Serialize, Deserialize, Tsify)] 17 | #[tsify(into_wasm_abi, from_wasm_abi)] 18 | pub struct MassActionModelData(pub analyses::ode::MassActionProblemData); 19 | -------------------------------------------------------------------------------- /packages/catlog-wasm/src/lib.rs: -------------------------------------------------------------------------------- 1 | pub mod result; 2 | 3 | pub mod model; 4 | pub mod model_diagram; 5 | pub mod model_morphism; 6 | pub mod theory; 7 | 8 | pub mod analyses; 9 | #[allow(clippy::new_without_default)] 10 | pub mod theories; 11 | 12 | use wasm_bindgen::prelude::*; 13 | 14 | /** Produce type defs for dependencies supporting `serde` but not `tsify`. 15 | 16 | Somewhat amazingly, the type system in TypeScript can express the constraint 17 | that an array be nonempty, with certain usage caveats: 18 | 19 | https://stackoverflow.com/q/56006111 20 | 21 | For now, though, we will not attempt to enforce this in the TypeScript layer. 22 | */ 23 | #[wasm_bindgen(typescript_custom_section)] 24 | const TS_APPEND_CONTENT: &'static str = r#" 25 | export type Uuid = string; 26 | export type Ustr = string; 27 | 28 | export type NonEmpty = Array; 29 | "#; 30 | 31 | #[wasm_bindgen] 32 | pub fn set_panic_hook() { 33 | // When the `console_error_panic_hook` feature is enabled, we can call the 34 | // `set_panic_hook` function at least once during initialization, and then 35 | // we will get better error messages if our code ever panics. 36 | // 37 | // For more details see 38 | // https://github.com/rustwasm/console_error_panic_hook#readme 39 | #[cfg(feature = "console_error_panic_hook")] 40 | console_error_panic_hook::set_once(); 41 | } 42 | -------------------------------------------------------------------------------- /packages/catlog-wasm/src/result.rs: -------------------------------------------------------------------------------- 1 | //! Result of fallible computation that translates to/from JavaScript. 2 | 3 | use serde::{Deserialize, Serialize}; 4 | use tsify::Tsify; 5 | 6 | /** A `Result`-like type that translates to/from JavaScript. 7 | 8 | In `wasm-bindgen`, returning a [`Result`] raises an exception in JavaScript when 9 | the `Err` variant is given: 10 | 11 | 12 | 13 | When an error should be handled in the UI, it is often more convenient to return 14 | an error value than to raise an exception. That's what this enum does. 15 | */ 16 | #[derive(Clone, Debug, PartialEq, Eq, Serialize, Deserialize, Tsify)] 17 | #[serde(tag = "tag", content = "content")] 18 | #[tsify(into_wasm_abi, from_wasm_abi)] 19 | pub enum JsResult { 20 | /// Contains the success value 21 | Ok(T), 22 | 23 | /// Contains the error value 24 | Err(E), 25 | } 26 | 27 | impl From> for JsResult { 28 | fn from(value: Result) -> Self { 29 | match value { 30 | Result::Ok(x) => JsResult::Ok(x), 31 | Result::Err(x) => JsResult::Err(x), 32 | } 33 | } 34 | } 35 | 36 | impl From> for JsResult { 37 | fn from(value: Option) -> Self { 38 | match value { 39 | Option::Some(x) => JsResult::Ok(x), 40 | Option::None => JsResult::Err(()), 41 | } 42 | } 43 | } 44 | -------------------------------------------------------------------------------- /packages/catlog-wasm/tests/web.rs: -------------------------------------------------------------------------------- 1 | //! Test suite for the Web and headless browsers. 2 | 3 | #![cfg(target_arch = "wasm32")] 4 | 5 | extern crate wasm_bindgen_test; 6 | use wasm_bindgen_test::*; 7 | 8 | wasm_bindgen_test_configure!(run_in_browser); 9 | 10 | #[wasm_bindgen_test] 11 | fn pass() { 12 | assert_eq!(1 + 1, 2); 13 | } 14 | -------------------------------------------------------------------------------- /packages/catlog/.gitignore: -------------------------------------------------------------------------------- 1 | # Generated by Cargo 2 | # will have compiled files and executables 3 | debug/ 4 | target/ 5 | 6 | # Remove Cargo.lock from gitignore if creating an executable, leave it for libraries 7 | # More information here https://doc.rust-lang.org/cargo/guide/cargo-toml-vs-cargo-lock.html 8 | 9 | # These are backup files generated by rustfmt 10 | **/*.rs.bk 11 | 12 | # MSVC Windows builds of rustc generate these, which store debugging information 13 | *.pdb 14 | -------------------------------------------------------------------------------- /packages/catlog/Cargo.toml: -------------------------------------------------------------------------------- 1 | [package] 2 | name = "catlog" 3 | description = "A toolbox for catgorical logic based on double theories" 4 | authors = ["Evan Patterson"] 5 | version = "0.1.0" 6 | edition = "2024" 7 | 8 | [features] 9 | ode = ["dep:ode_solvers", "dep:nalgebra"] 10 | serde = ["dep:serde", "nonempty/serialize", "ustr/serde"] 11 | serde-wasm = ["serde", "dep:wasm-bindgen", "dep:tsify"] 12 | 13 | [dependencies] 14 | derivative = "2" 15 | derive_more = { version = "1", features = ["from", "into"] } 16 | duplicate = "2" 17 | egglog = { version = "0.4", default-features = false } 18 | ego-tree = "0.10" 19 | itertools = "0.14" 20 | nalgebra = { version = "0.33", optional = true } 21 | nonempty = "0.10" 22 | num-traits = "0.2" 23 | ode_solvers = { version = "0.5.0", optional = true } 24 | ref-cast = "1" 25 | serde = { version = "1", features = ["derive"], optional = true } 26 | thiserror = "1" 27 | tsify = { version = "0.5", features = ["js"], optional = true } 28 | ustr = "1" 29 | uuid = { version = "=1.11", optional = true } 30 | wasm-bindgen = { version = "0.2.100", optional = true } 31 | 32 | [dev-dependencies] 33 | expect-test = "1.5" 34 | textplots = "0.8.6" 35 | -------------------------------------------------------------------------------- /packages/catlog/src/dbl/mod.rs: -------------------------------------------------------------------------------- 1 | //! Double category theory and two-dimensional categorical logic. 2 | 3 | pub mod category; 4 | pub mod graph; 5 | pub mod tree; 6 | 7 | pub mod model; 8 | pub mod model_diagram; 9 | pub mod model_morphism; 10 | pub mod theory; 11 | -------------------------------------------------------------------------------- /packages/catlog/src/lib.rs: -------------------------------------------------------------------------------- 1 | /*! A toolbox for categorical logic based on double-categorical theories. 2 | 3 | # Organization 4 | 5 | While the purpose of this package is to implement double theories and their 6 | models and morphisms, a certain amount of lower-dimensional category theory is 7 | necessary as background. The package is organized into top-level modules 8 | according to dimensionality: 9 | 10 | 0. [`zero`]: Sets and mappings, known semi-seriously as zero-dimensional 11 | category theory, and a bit of abstract algebra. 12 | 1. [`one`]: Ordinary, or one-dimensional, category theory. 13 | 2. [`dbl`]: Double category theory. 14 | 15 | The prerequisite modules make no pretence to completeness, but if they become 16 | sufficiently useful in their own right, they may be spun off into their own 17 | crates. 18 | */ 19 | 20 | // Unicode identifiers. 21 | #![allow(mixed_script_confusables)] 22 | #![allow(confusable_idents)] 23 | #![warn(missing_docs)] 24 | 25 | #[cfg(doc)] 26 | pub mod refs; 27 | 28 | pub mod egglog_util; 29 | pub mod validate; 30 | 31 | pub mod dbl; 32 | pub mod one; 33 | pub mod simulate; 34 | pub mod stdlib; 35 | pub mod zero; 36 | -------------------------------------------------------------------------------- /packages/catlog/src/one/mod.rs: -------------------------------------------------------------------------------- 1 | //! Category theory in dimension one. 2 | 3 | pub mod category; 4 | pub mod fp_category; 5 | pub mod graph; 6 | pub mod graph_algorithms; 7 | pub mod path; 8 | pub mod tree; 9 | pub mod tree_algorithms; 10 | 11 | pub use self::category::*; 12 | pub use self::graph::*; 13 | pub use self::path::*; 14 | -------------------------------------------------------------------------------- /packages/catlog/src/simulate/mod.rs: -------------------------------------------------------------------------------- 1 | /*! Simulation of dynamical systems. 2 | 3 | "Modeling and simulation" is a major part of science and engineering. The 4 | purpose of the `catlog` crate is to specify models using the machinery of 5 | double-categorical logic. This module simulates dynamical systems derived from 6 | models. It is intended as a stopgap pending interoperation with a language 7 | having a better scientific computing ecosystem than Rust, such as Julia. 8 | However, if it does stick around it should eventually become its own crate. For 9 | now it's convenient to keep everything in the same place. 10 | */ 11 | 12 | #[cfg(feature = "ode")] 13 | pub mod ode; 14 | -------------------------------------------------------------------------------- /packages/catlog/src/stdlib/analyses/mod.rs: -------------------------------------------------------------------------------- 1 | //! Various analyses that can be performed on models. 2 | 3 | #[cfg(feature = "ode")] 4 | pub mod ode; 5 | -------------------------------------------------------------------------------- /packages/catlog/src/stdlib/mod.rs: -------------------------------------------------------------------------------- 1 | //! Standard library of double theories, models, and analyses. 2 | 3 | pub mod models; 4 | pub mod theories; 5 | 6 | pub mod analyses; 7 | 8 | pub use models::*; 9 | pub use theories::*; 10 | -------------------------------------------------------------------------------- /packages/catlog/src/zero/mod.rs: -------------------------------------------------------------------------------- 1 | //! Sets and functions, and a little abstract algebra. 2 | 3 | pub mod alg; 4 | pub mod column; 5 | pub mod rig; 6 | pub mod set; 7 | 8 | pub use self::column::*; 9 | pub use self::set::*; 10 | -------------------------------------------------------------------------------- /packages/frontend/.env.development: -------------------------------------------------------------------------------- 1 | VITE_APP_TITLE="CatColab [dev]" 2 | 3 | VITE_SERVER_URL=http://127.0.0.1:8000 4 | VITE_AUTOMERGE_REPO_URL=ws://127.0.0.1:8010 5 | 6 | VITE_FIREBASE_OPTIONS='{ 7 | "apiKey": "AIzaSyAsFvrzQg_V8cVhGi9PNkZiueGF0iDH9Ws", 8 | "authDomain": "catcolab-next.firebaseapp.com", 9 | "projectId": "catcolab-next", 10 | "storageBucket": "catcolab-next.appspot.com", 11 | "messagingSenderId": "666779369059", 12 | "appId": "1:666779369059:web:f0319c1513d77996650256", 13 | "measurementId": "G-WKFYSTDYLF" 14 | }' 15 | -------------------------------------------------------------------------------- /packages/frontend/.env.production: -------------------------------------------------------------------------------- 1 | VITE_APP_TITLE="CatColab" 2 | 3 | VITE_SERVER_URL=https://backend.catcolab.org 4 | VITE_AUTOMERGE_REPO_URL=wss://automerge.catcolab.org 5 | 6 | VITE_FIREBASE_OPTIONS='{ 7 | "apiKey": "AIzaSyA9zb9RPri76DXB0Bnq3LZYa2u61l-K9oA", 8 | "authDomain": "catcolab-prod.firebaseapp.com", 9 | "projectId": "catcolab-prod", 10 | "storageBucket": "catcolab-prod.firebasestorage.app", 11 | "messagingSenderId": "192417001062", 12 | "appId": "1:192417001062:web:9089adb3abceac686187a7", 13 | "measurementId": "G-TQXNCW7D84" 14 | }' 15 | -------------------------------------------------------------------------------- /packages/frontend/.env.staging: -------------------------------------------------------------------------------- 1 | VITE_APP_TITLE="CatColab [next]" 2 | 3 | VITE_SERVER_URL=https://backend-next.catcolab.org 4 | VITE_AUTOMERGE_REPO_URL=wss://automerge-next.catcolab.org 5 | 6 | VITE_FIREBASE_OPTIONS='{ 7 | "apiKey": "AIzaSyAsFvrzQg_V8cVhGi9PNkZiueGF0iDH9Ws", 8 | "authDomain": "catcolab-next.firebaseapp.com", 9 | "projectId": "catcolab-next", 10 | "storageBucket": "catcolab-next.appspot.com", 11 | "messagingSenderId": "666779369059", 12 | "appId": "1:666779369059:web:f0319c1513d77996650256", 13 | "measurementId": "G-WKFYSTDYLF" 14 | }' 15 | -------------------------------------------------------------------------------- /packages/frontend/.gitignore: -------------------------------------------------------------------------------- 1 | # Logs 2 | logs 3 | *.log 4 | npm-debug.log* 5 | yarn-debug.log* 6 | yarn-error.log* 7 | pnpm-debug.log* 8 | lerna-debug.log* 9 | 10 | node_modules 11 | dist 12 | dist-ssr 13 | *.local 14 | 15 | # Editor directories and files 16 | .vscode/* 17 | !.vscode/extensions.json 18 | .idea 19 | .DS_Store 20 | *.suo 21 | *.ntvs* 22 | *.njsproj 23 | *.sln 24 | *.sw? 25 | -------------------------------------------------------------------------------- /packages/frontend/README.md: -------------------------------------------------------------------------------- 1 | # CatColab frontend 2 | 3 | This directory contains the web frontend for the CatColab application, written 4 | in TypeScript using the framework [Solid.js](https://www.solidjs.com/). 5 | 6 | ## Setup 7 | 8 | Install Rust and [pnpm](https://pnpm.io/), then run 9 | 10 | ```sh 11 | cd packages/frontend 12 | pnpm install 13 | pnpm run build 14 | ``` 15 | 16 | This command compiles the Rust dependencies to WebAssembly and then builds the 17 | frontend bundle. 18 | 19 | ## Usage 20 | 21 | To develop the frontend locally, run 22 | 23 | ```sh 24 | pnpm run dev --mode $MODE 25 | ``` 26 | 27 | where `$MODE` is replaced with one of the following: 28 | 29 | - `development`: assumes that the [backend](../backend/) is running locally (the 30 | default if `--mode` is omitted) 31 | - `staging`: uses the staging deployment of CatColab at `next.catcolab.org` 32 | (recommended for fronten dev) 33 | - `production`: uses the production deployment of CatColab at `catcolab.org` 34 | (*not* recommended) 35 | -------------------------------------------------------------------------------- /packages/frontend/index.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | 6 | 7 | %VITE_APP_TITLE% 8 | 9 | 10 |
11 | 12 | 13 | 14 | -------------------------------------------------------------------------------- /packages/frontend/netlify.toml: -------------------------------------------------------------------------------- 1 | [build] 2 | publish = "dist/" 3 | command = "rustup toolchain install stable && rustup target add wasm32-unknown-unknown && npm run build" 4 | 5 | [build.environment] 6 | RUST_VERSION = "1.81.0" 7 | -------------------------------------------------------------------------------- /packages/frontend/public/topos_icon.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ToposInstitute/CatColab/8e6e52655f51b402d22d43a52807a3529e131402/packages/frontend/public/topos_icon.png -------------------------------------------------------------------------------- /packages/frontend/src/analysis/context.ts: -------------------------------------------------------------------------------- 1 | import { type Accessor, createContext } from "solid-js"; 2 | 3 | import type { LiveAnalysisDocument } from "./document"; 4 | 5 | /** Context for a live analysis. */ 6 | export const LiveAnalysisContext = createContext>(); 7 | -------------------------------------------------------------------------------- /packages/frontend/src/analysis/index.ts: -------------------------------------------------------------------------------- 1 | export * from "./types"; 2 | export * from "./document"; 3 | export * from "./context"; 4 | -------------------------------------------------------------------------------- /packages/frontend/src/api/context.ts: -------------------------------------------------------------------------------- 1 | import { createContext, useContext } from "solid-js"; 2 | import invariant from "tiny-invariant"; 3 | 4 | import type { Api } from "./types"; 5 | 6 | /** Context for the CatColab API. */ 7 | export const ApiContext = createContext(); 8 | 9 | /** Retrieve CatColab API from application context. */ 10 | export function useApi(): Api { 11 | const api = useContext(ApiContext); 12 | invariant(api, "CatColab API should be provided as context"); 13 | return api; 14 | } 15 | -------------------------------------------------------------------------------- /packages/frontend/src/api/index.ts: -------------------------------------------------------------------------------- 1 | export * from "./context"; 2 | export * from "./document"; 3 | export * from "./rpc"; 4 | export * from "./types"; 5 | -------------------------------------------------------------------------------- /packages/frontend/src/components/alert.css: -------------------------------------------------------------------------------- 1 | .alert { 2 | --alert-color: black; 3 | 4 | box-sizing: border-box; 5 | border-left: 4px solid var(--alert-color); 6 | border-radius: 4px; 7 | padding-left: 1ex; 8 | } 9 | 10 | .alert-heading { 11 | display: flex; 12 | flex-direction: row; 13 | align-items: center; 14 | gap: 5px; 15 | 16 | color: var(--alert-color); 17 | font-weight: 500; 18 | } 19 | 20 | .alert-warning { 21 | --alert-color: rgb(102, 77, 3); 22 | } 23 | 24 | .alert-error { 25 | --alert-color: maroon; 26 | } 27 | -------------------------------------------------------------------------------- /packages/frontend/src/components/alert.tsx: -------------------------------------------------------------------------------- 1 | import { Alert } from "@kobalte/core/alert"; 2 | import type { JSX } from "solid-js"; 3 | 4 | import OctagonX from "lucide-solid/icons/octagon-x"; 5 | import TriangleAlert from "lucide-solid/icons/triangle-alert"; 6 | 7 | import "./alert.css"; 8 | 9 | /** Props for an alert component. */ 10 | export type AlertProps = { 11 | /** Title for the alert. */ 12 | title?: string; 13 | 14 | children?: JSX.Element; 15 | }; 16 | 17 | /** A warning alert. */ 18 | export const Warning = (props: AlertProps) => ( 19 | 20 |
21 | 22 | {props.title ?? "Warning"} 23 |
24 | {props.children} 25 | 26 | ); 27 | 28 | /** An error alert. 29 | 30 | Not called `Error` to avoid shadowing that name in JavaScript. 31 | */ 32 | export const ErrorAlert = (props: AlertProps) => ( 33 | 34 |
35 | 36 | {props.title ?? "Error"} 37 |
38 | {props.children} 39 | 40 | ); 41 | -------------------------------------------------------------------------------- /packages/frontend/src/components/completions.css: -------------------------------------------------------------------------------- 1 | .completion-list { 2 | list-style: none; 3 | padding: 0; 4 | margin: 0; 5 | } 6 | 7 | .completion-list li { 8 | cursor: pointer; 9 | padding: 5px; 10 | } 11 | 12 | .completion-list li.active { 13 | background: #f1f5f9; 14 | } 15 | 16 | .completion-head { 17 | display: flex; 18 | gap: 0.25em; 19 | justify-content: space-between; 20 | } 21 | 22 | .completion-description { 23 | font-size: 0.75em; 24 | color: dimgray; 25 | } 26 | 27 | .completion-shortcut { 28 | font-size: 0.9em; 29 | padding-left: 2ex; 30 | } 31 | 32 | .completion-empty { 33 | font-size: 0.75em; 34 | color: dimgray; 35 | } 36 | 37 | kbd.shortcut { 38 | display: flex; 39 | gap: 0.5em; 40 | } 41 | -------------------------------------------------------------------------------- /packages/frontend/src/components/dialog.css: -------------------------------------------------------------------------------- 1 | [data-corvu-dialog-overlay] { 2 | position: fixed; 3 | inset: 0px; 4 | } 5 | 6 | [data-corvu-dialog-content] { 7 | position: fixed; 8 | left: 50%; 9 | top: 50%; 10 | transform: translate(-50%, -50%); 11 | 12 | &.popup { 13 | padding: 1rem; 14 | } 15 | 16 | & .title-bar { 17 | display: flex; 18 | flex-direction: row; 19 | justify-content: space-between; 20 | padding-bottom: 0.5rem; 21 | } 22 | } 23 | 24 | [data-corvu-dialog-label] { 25 | font-size: larger; 26 | } 27 | 28 | [data-corvu-dialog-close] { 29 | & .lucide { 30 | color: dimgray; 31 | } 32 | } 33 | -------------------------------------------------------------------------------- /packages/frontend/src/components/fixed_table_editor.css: -------------------------------------------------------------------------------- 1 | .fixed-table-editor { 2 | background: white; 3 | --border-color: lightgray; 4 | --cell-padding: 5px; 5 | 6 | border-collapse: collapse; 7 | 8 | & tr { 9 | border-top: 1px solid var(--border-color); 10 | border-bottom: 1px solid var(--border-color); 11 | } 12 | & td { 13 | padding: var(--cell-padding); 14 | border-left: 1px solid var(--border-color); 15 | } 16 | & th { 17 | font-weight: normal; 18 | padding: var(--cell-padding); 19 | } 20 | & th[scope="col"] { 21 | font-weight: 500; 22 | border-right: 1px solid var(--border-color); 23 | } 24 | & th[scope="col"]:last-child { 25 | border-right: none; 26 | } 27 | } 28 | 29 | .fixed-table-cell-input { 30 | background: transparent; 31 | border: none; 32 | outline: none; 33 | font: inherit; 34 | 35 | width: 100%; 36 | } 37 | 38 | .fixed-table-cell-input.invalid { 39 | background: #f8d7da; 40 | } 41 | -------------------------------------------------------------------------------- /packages/frontend/src/components/foldable.css: -------------------------------------------------------------------------------- 1 | .foldable-trigger { 2 | background: none; 3 | border: none; 4 | cursor: pointer; 5 | outline: none; 6 | font: inherit; 7 | padding: 0; 8 | 9 | display: flex; 10 | flex-direction: row; 11 | align-items: center; 12 | 13 | & .lucide { 14 | color: darkgray; 15 | } 16 | } 17 | 18 | [data-corvu-disclosure-content] { 19 | overflow: hidden; 20 | } 21 | [data-corvu-disclosure-content][data-collapsed] { 22 | animation: collapse 200ms linear; 23 | } 24 | [data-corvu-disclosure-content][data-expanded] { 25 | animation: expand 200ms linear; 26 | } 27 | 28 | @keyframes collapse { 29 | 0% { 30 | height: var(--corvu-disclosure-content-height); 31 | } 32 | 100% { 33 | height: 0px; 34 | } 35 | } 36 | 37 | @keyframes expand { 38 | 0% { 39 | height: 0px; 40 | } 41 | 100% { 42 | height: var(--corvu-disclosure-content-height); 43 | } 44 | } 45 | -------------------------------------------------------------------------------- /packages/frontend/src/components/icon_button.css: -------------------------------------------------------------------------------- 1 | .icon-button { 2 | display: flex; 3 | flex-direction: row; 4 | justify-content: center; 5 | align-items: center; 6 | gap: 0.25rem; 7 | 8 | background: none; 9 | border: none; 10 | cursor: pointer; 11 | padding: 0; 12 | font-size: 1rem; 13 | 14 | &:hover:enabled { 15 | background: whitesmoke; 16 | border-radius: 5px; 17 | } 18 | } 19 | 20 | .tooltip-content { 21 | border-radius: 0.5rem; 22 | color: white; 23 | background-color: hsl(251, 9%, 23%); 24 | padding: 0.5rem; 25 | font-size: smaller; 26 | 27 | & p:first-child { 28 | margin-top: 0; 29 | } 30 | 31 | & p:last-child { 32 | margin-bottom: 0; 33 | } 34 | } 35 | -------------------------------------------------------------------------------- /packages/frontend/src/components/id_input.css: -------------------------------------------------------------------------------- 1 | .id-input.anonymous { 2 | background-color: color-mix(in srgb, lightsteelblue, black 10%); 3 | color: white; 4 | font-variant-numeric: tabular-nums; 5 | 6 | padding: 3px; 7 | border-radius: 10px; 8 | } 9 | -------------------------------------------------------------------------------- /packages/frontend/src/components/index.ts: -------------------------------------------------------------------------------- 1 | export * from "./alert"; 2 | export * from "./completions"; 3 | export * from "./dialog"; 4 | export * from "./fixed_table_editor"; 5 | export * from "./foldable"; 6 | export * from "./form"; 7 | export * from "./icon_button"; 8 | export * from "./id_input"; 9 | export * from "./inline_input"; 10 | export * from "./name_input"; 11 | export * from "./panel"; 12 | export * from "./resizable"; 13 | export * from "./rich_text_editor"; 14 | export * from "./json_import"; 15 | -------------------------------------------------------------------------------- /packages/frontend/src/components/inline_input.css: -------------------------------------------------------------------------------- 1 | .inline-input-container { 2 | display: inline-block; 3 | position: relative; 4 | } 5 | 6 | .inline-input-filler, 7 | .inline-input { 8 | border: none; 9 | border-bottom: 3px solid transparent; 10 | } 11 | 12 | .inline-input-filler { 13 | display: inline-block; 14 | visibility: hidden; 15 | white-space-collapse: preserve; 16 | padding-left: 5px; 17 | padding-right: 5px; 18 | min-width: 1ex; 19 | } 20 | 21 | .inline-input { 22 | position: absolute; 23 | top: 0; 24 | left: 0; 25 | right: 0; 26 | bottom: 0; 27 | 28 | background: transparent; 29 | outline: none; 30 | padding-left: 5px; 31 | padding-right: 5px; 32 | font: inherit; 33 | color: inherit; 34 | 35 | &.incomplete { 36 | border-bottom: 3px solid sandybrown; 37 | } 38 | &.invalid { 39 | border-bottom: 3px solid indianred; 40 | } 41 | } 42 | -------------------------------------------------------------------------------- /packages/frontend/src/components/json_import.css: -------------------------------------------------------------------------------- 1 | .json_import { 2 | min-width: 20em; 3 | max-width: 80vw; 4 | margin: 0 auto; 5 | width: auto; 6 | } 7 | 8 | .json_import textarea { 9 | font-family: monospace; 10 | } 11 | -------------------------------------------------------------------------------- /packages/frontend/src/components/name_input.tsx: -------------------------------------------------------------------------------- 1 | import { createEffect, createSignal, splitProps } from "solid-js"; 2 | 3 | import { InlineInput, type InlineInputErrorStatus, type InlineInputOptions } from "./inline_input"; 4 | 5 | /** Input a human-readable name for a formal element. 6 | 7 | In CatColab, a valid name is any string that is *not* a decimal numeral, since 8 | the latter are used as anonymous identifiers. See the `IdInput` component. 9 | */ 10 | export function NameInput( 11 | allProps: { 12 | name: string; 13 | setName: (name: string) => void; 14 | } & Omit, 15 | ) { 16 | const [props, inputProps] = splitProps(allProps, ["name", "setName"]); 17 | 18 | const [text, setText] = createSignal(""); 19 | 20 | createEffect(() => setText(props.name)); 21 | 22 | const status = (): InlineInputErrorStatus => (text() === props.name ? null : "invalid"); 23 | 24 | const handleNewText = (text: string) => { 25 | if (!/^\d+$/.test(text)) { 26 | props.setName(text); 27 | } 28 | setText(text); 29 | }; 30 | 31 | return ; 32 | } 33 | -------------------------------------------------------------------------------- /packages/frontend/src/components/panel.css: -------------------------------------------------------------------------------- 1 | .panel-header { 2 | display: flex; 3 | flex-direction: row; 4 | align-items: center; 5 | width: 100%; 6 | 7 | & .filler { 8 | flex: 1; 9 | } 10 | 11 | & .title { 12 | font-weight: 450; 13 | } 14 | } 15 | -------------------------------------------------------------------------------- /packages/frontend/src/components/panel.tsx: -------------------------------------------------------------------------------- 1 | import { type JSX, Show } from "solid-js"; 2 | 3 | import "./panel.css"; 4 | 5 | /** Header for a panel with a title. 6 | */ 7 | export function PanelHeader(props: { 8 | /** Title shown at the top of the panel. */ 9 | title: string | JSX.Element; 10 | /** Additional header content. */ 11 | children?: JSX.Element; 12 | }) { 13 | return ( 14 |
15 | {props.title} 16 | 17 | 18 | {props.children} 19 | 20 |
21 | ); 22 | } 23 | -------------------------------------------------------------------------------- /packages/frontend/src/components/resizable.css: -------------------------------------------------------------------------------- 1 | .resizable-handle { 2 | background: none; 3 | border: none; 4 | border-radius: 6px; 5 | padding: 3px; 6 | 7 | &.active { 8 | background: gray; 9 | } 10 | 11 | &:hover { 12 | background: gray; 13 | } 14 | } 15 | -------------------------------------------------------------------------------- /packages/frontend/src/components/resizable.tsx: -------------------------------------------------------------------------------- 1 | import Resizable from "@corvu/resizable"; 2 | import { createSignal } from "solid-js"; 3 | 4 | import "./resizable.css"; 5 | 6 | type ResizableHandleProps = Parameters[0]["props"]; 7 | 8 | /** A styled wrapper for corvu's `Resizable.Handle`. 9 | */ 10 | export const ResizableHandle = (props: ResizableHandleProps) => { 11 | const [isResizing, setIsResizing] = createSignal(false); 12 | 13 | return ( 14 | setIsResizing(true)} 20 | onHandleDragEnd={() => setIsResizing(false)} 21 | {...props} 22 | /> 23 | ); 24 | }; 25 | -------------------------------------------------------------------------------- /packages/frontend/src/components/rich_text_editor.css: -------------------------------------------------------------------------------- 1 | /* ProseMirror CSS seems not to be documented, but see the following sources: 2 | 3 | - https://github.com/ProseMirror/prosemirror-view/blob/master/style/prosemirror.css 4 | - https://github.com/ProseMirror/prosemirror-example-setup/blob/master/style/style.css 5 | */ 6 | 7 | .ProseMirror { 8 | background: transparent; 9 | } 10 | 11 | .ProseMirror-focused { 12 | outline: none; 13 | } 14 | 15 | .ProseMirror[data-placeholder]::before { 16 | color: darkgray; 17 | position: absolute; 18 | content: attr(data-placeholder); 19 | pointer-events: none; 20 | } 21 | -------------------------------------------------------------------------------- /packages/frontend/src/components/spinner.css: -------------------------------------------------------------------------------- 1 | .spinner { 2 | border: 4px solid rgba(0, 0, 0, 0.1); 3 | border-top-color: #333; 4 | border-radius: 50%; 5 | width: 24px; 6 | height: 24px; 7 | margin: auto; 8 | animation: spin 1s linear infinite; 9 | will-change: transform; 10 | } 11 | 12 | @keyframes spin { 13 | to { 14 | transform: rotate(360deg); 15 | } 16 | } 17 | -------------------------------------------------------------------------------- /packages/frontend/src/components/spinner.tsx: -------------------------------------------------------------------------------- 1 | import "./spinner.css"; 2 | 3 | export function Spinner() { 4 | return