-
Notifications
You must be signed in to change notification settings - Fork 4
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
Merge branch 'main' into 647-bump-flask-release
- Loading branch information
Showing
84 changed files
with
10,377 additions
and
8,187 deletions.
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
|
|
@@ -2,7 +2,7 @@ default_language_version: | |
| python: python3 | ||
| repos: | ||
| - repo: https://github.com/pre-commit/pre-commit-hooks | ||
| rev: v4.6.0 | ||
| rev: v5.0.0 | ||
| hooks: | ||
| - id: check-added-large-files | ||
| - id: check-case-conflict | ||
|
|
@@ -19,28 +19,18 @@ repos: | |
| args: ["--fix=lf"] | ||
| - id: sort-simple-yaml | ||
| - id: trailing-whitespace | ||
| # - repo: https://github.com/pre-commit/mirrors-eslint | ||
| # rev: v8.53.0 | ||
| # hooks: | ||
| # - id: eslint | ||
| # args: | ||
| # - --fix | ||
| # - --config | ||
| # - app/.eslintrc.cjs | ||
| # additional_dependencies: | ||
| # - eslint@latest | ||
| # - eslint-config-prettier | ||
| - repo: https://github.com/codespell-project/codespell | ||
| rev: v2.3.0 | ||
| hooks: | ||
| - id: codespell | ||
| additional_dependencies: ["tomli"] | ||
| - repo: https://github.com/pre-commit/mirrors-prettier | ||
| rev: v4.0.0-alpha.8 | ||
| - repo: https://github.com/biomejs/pre-commit | ||
| rev: v0.5.0 # Use the sha / tag you want to point at | ||
| hooks: | ||
| - id: prettier | ||
| - id: biome-format # not using check becasue there are lots of things that need fixed | ||
| additional_dependencies: ["@biomejs/[email protected]"] | ||
| - repo: https://github.com/astral-sh/ruff-pre-commit | ||
| rev: v0.6.5 | ||
| rev: v0.8.1 | ||
| hooks: | ||
| - id: ruff | ||
| args: [--fix] | ||
|
|
||
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,20 @@ | ||
| version: 2 | ||
|
|
||
| build: | ||
| os: "ubuntu-22.04" | ||
| tools: | ||
| python: "3.12" | ||
| jobs: | ||
| post_create_environment: | ||
| # Install poetry | ||
| # https://python-poetry.org/docs/#installing-manually | ||
| - pip install poetry | ||
| post_install: | ||
| # Install dependencies with 'docs' dependency group | ||
| # https://python-poetry.org/docs/managing-dependencies/#dependency-groups | ||
| # VIRTUAL_ENV needs to be set manually for now. | ||
| # See https://github.com/readthedocs/readthedocs.org/pull/11152/ | ||
| - VIRTUAL_ENV=$READTHEDOCS_VIRTUALENV_PATH poetry install --with docs | ||
|
|
||
| sphinx: | ||
| configuration: docs/source/conf.py |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,18 +1,14 @@ | ||
| FROM continuumio/miniconda3 | ||
| FROM python:3.12 | ||
| SHELL ["/bin/bash", "--login", "-c"] | ||
|
|
||
| WORKDIR /usr/src/app | ||
| COPY ./ ./ | ||
| # required for h5py, chemfiles | ||
|
|
||
| # required for h5py | ||
| RUN apt update && apt install -y gcc pkg-config libhdf5-dev build-essential | ||
| RUN conda install python=3.11 nodejs | ||
| # RUN conda install conda-forge::packmol | ||
| RUN npm install -g bun | ||
| RUN curl -fsSL https://bun.sh/install | bash | ||
|
|
||
| # Make RUN commands use the new environment: | ||
| SHELL ["conda", "run", "--no-capture-output", "-n", "base", "/bin/bash", "-c"] | ||
| COPY ./ ./ | ||
| RUN cd app && bun install && bun vite build && cd .. | ||
| RUN pip install -e .[all] | ||
|
|
||
| RUN pip install -e . | ||
|
|
||
| EXPOSE 5003 | ||
| # # The code to run when container is started: | ||
| ENTRYPOINT ["conda", "run", "--no-capture-output", "-n", "base", "zndraw", "--port", "5003", "--no-browser"] | ||
| ENTRYPOINT ["zndraw", "--port", "5003", "--no-browser"] |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file was deleted.
Oops, something went wrong.
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,30 @@ | ||
| { | ||
| "$schema": "https://biomejs.dev/schemas/1.9.4/schema.json", | ||
| "vcs": { | ||
| "enabled": false, | ||
| "clientKind": "git", | ||
| "useIgnoreFile": false | ||
| }, | ||
| "files": { | ||
| "ignoreUnknown": false, | ||
| "ignore": [] | ||
| }, | ||
| "formatter": { | ||
| "enabled": true, | ||
| "indentStyle": "tab" | ||
| }, | ||
| "organizeImports": { | ||
| "enabled": true | ||
| }, | ||
| "linter": { | ||
| "enabled": true, | ||
| "rules": { | ||
| "recommended": true | ||
| } | ||
| }, | ||
| "javascript": { | ||
| "formatter": { | ||
| "quoteStyle": "double" | ||
| } | ||
| } | ||
| } |
Binary file not shown.
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,11 +1,4 @@ | ||
| declare module "@json-editor/json-editor" { | ||
| const JSONEditor: any; | ||
| export default JSONEditor; | ||
| } | ||
| declare module "znsocket" { | ||
| function createClient(...args: any[]): any; | ||
| const Client: any; | ||
| const List: any; | ||
| const Dict: any; | ||
| export { createClient, List, Dict, Client }; | ||
| const JSONEditor: any; | ||
| export default JSONEditor; | ||
| } |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,51 +1,49 @@ | ||
| { | ||
| "name": "my-app", | ||
| "private": true, | ||
| "version": "0.0.0", | ||
| "type": "module", | ||
| "scripts": { | ||
| "dev": "vite", | ||
| "build": "tsc && vite build", | ||
| "lint": "eslint . --ext ts,tsx --report-unused-disable-directives --max-warnings 0", | ||
| "preview": "vite preview", | ||
| "format": "prettier . --write" | ||
| }, | ||
| "dependencies": { | ||
| "@json-editor/json-editor": "^2.15.2", | ||
| "@react-three/drei": "^9.115.0", | ||
| "@react-three/fiber": "^8.17.10", | ||
| "@types/three": "^0.165.0", | ||
| "bootstrap": "5.3.3", | ||
| "plotly.js": "^2.35.2", | ||
| "react": "^18.3.1", | ||
| "react-bootstrap": "^2.10.5", | ||
| "react-dom": "^18.3.1", | ||
| "react-icons": "^5.3.0", | ||
| "react-markdown": "^9.0.1", | ||
| "react-plotly.js": "^2.6.0", | ||
| "react-rnd": "^10.4.13", | ||
| "react-select": "^5.8.2", | ||
| "react-syntax-highlighter": "^15.6.1", | ||
| "rehype-katex": "^7.0.1", | ||
| "rehype-raw": "^7.0.0", | ||
| "remark-breaks": "^4.0.0", | ||
| "remark-gfm": "^4.0.0", | ||
| "remark-math": "^6.0.0", | ||
| "socket.io-client": "^4.8.1", | ||
| "three": "^0.165.0", | ||
| "znsocket": "^0.2.3" | ||
| }, | ||
| "devDependencies": { | ||
| "@types/react": "^18.3.12", | ||
| "@types/react-dom": "^18.3.1", | ||
| "@typescript-eslint/eslint-plugin": "^7.18.0", | ||
| "@typescript-eslint/parser": "^7.18.0", | ||
| "@vitejs/plugin-react-swc": "^3.7.1", | ||
| "eslint": "^8.57.1", | ||
| "eslint-plugin-react-hooks": "^4.6.2", | ||
| "eslint-plugin-react-refresh": "^0.4.14", | ||
| "prettier": "^3.3.3", | ||
| "typescript": "^5.6.3", | ||
| "vite": "^5.4.10" | ||
| } | ||
| "name": "my-app", | ||
| "private": true, | ||
| "version": "0.0.0", | ||
| "type": "module", | ||
| "scripts": { | ||
| "dev": "vite", | ||
| "build": "tsc && vite build", | ||
| "lint": "eslint . --ext ts,tsx --report-unused-disable-directives --max-warnings 0", | ||
| "preview": "vite preview", | ||
| "format": "prettier . --write" | ||
| }, | ||
| "dependencies": { | ||
| "@json-editor/json-editor": "^2.15.2", | ||
| "@react-three/drei": "^9.116.3", | ||
| "@react-three/fiber": "^8.17.10", | ||
| "@react-three/gpu-pathtracer": "^0.2.0", | ||
| "@types/lodash": "^4.17.13", | ||
| "@types/three": "^0.165.0", | ||
| "bootstrap": "5.3.3", | ||
| "lodash": "^4.17.21", | ||
| "plotly.js": "^2.35.2", | ||
| "react": "^18.3.1", | ||
| "react-bootstrap": "^2.10.5", | ||
| "react-dom": "^18.3.1", | ||
| "react-icons": "^5.3.0", | ||
| "react-markdown": "^9.0.1", | ||
| "react-plotly.js": "^2.6.0", | ||
| "react-rnd": "^10.4.13", | ||
| "react-select": "^5.8.3", | ||
| "react-syntax-highlighter": "^15.6.1", | ||
| "rehype-katex": "^7.0.1", | ||
| "rehype-raw": "^7.0.0", | ||
| "remark-breaks": "^4.0.0", | ||
| "remark-gfm": "^4.0.0", | ||
| "remark-math": "^6.0.0", | ||
| "socket.io-client": "^4.8.1", | ||
| "three": "^0.165.0", | ||
| "znsocket": "^0.2.6" | ||
| }, | ||
| "devDependencies": { | ||
| "@biomejs/biome": "1.9.4", | ||
| "@types/react": "^18.3.12", | ||
| "@types/react-dom": "^18.3.1", | ||
| "@vitejs/plugin-react-swc": "^3.7.1", | ||
| "typescript": "^5.6.3", | ||
| "vite": "^5.4.11" | ||
| } | ||
| } |
Oops, something went wrong.