diff --git a/build_pyodide_world.sh b/build_pyodide_world.sh index a815b0d..dc07fec 100755 --- a/build_pyodide_world.sh +++ b/build_pyodide_world.sh @@ -20,6 +20,8 @@ TARGET_PYODIDE_DIR="${THIS_REPO_ROOT}/static/pyodide" PYODIDE_RECIPES_DIR="${PYODIDE_RECIPES_DIR:-${THIS_REPO_ROOT}/_pyodide-recipes}" CUSTOM_RECIPES_DIR="${THIS_REPO_ROOT}/pyodide-custom-recipes" PYODIDE_ENV_NAME="${PYODIDE_ENV_NAME:-pyodide-env}" +CONDA_ENVS_PATH="${CONDA_ENVS_PATH:-${THIS_REPO_ROOT}/.conda-envs}" +export CONDA_ENVS_PATH # By default we only ask pyodide-build to build the packages needed for # the sc2ts / tskit stack: @@ -41,6 +43,7 @@ echo "Repo root : ${THIS_REPO_ROOT}" echo "Target pyodide dir : ${TARGET_PYODIDE_DIR}" echo "pyodide-recipes dir : ${PYODIDE_RECIPES_DIR}" echo "Conda env name : ${PYODIDE_ENV_NAME}" +echo "Conda envs path : ${CONDA_ENVS_PATH}" echo "Recipe targets : ${PYODIDE_RECIPES_TARGETS}" echo @@ -113,7 +116,7 @@ pyodide xbuildenv install echo echo "=== Installing and configuring Emscripten SDK ===" -python tools/install_and_patch_emscripten.py +pyodide xbuildenv install-emscripten echo echo "=== Building recipes: ${PYODIDE_RECIPES_TARGETS} ===" diff --git a/content-hash.txt b/content-hash.txt index 5501ad6..62ed183 100644 --- a/content-hash.txt +++ b/content-hash.txt @@ -1 +1 @@ -f468ef7ef8a11d8922fde09b94ef1e2748f8b5a3f80adac729665ca28aa93d2c +30f06c09863a10ca8c74a467e139c305f2ee63524613a21f420182ce52b628ee diff --git a/pyodide-custom-recipes/asciitree/meta.yaml b/pyodide-custom-recipes/asciitree/meta.yaml new file mode 100644 index 0000000..70e14be --- /dev/null +++ b/pyodide-custom-recipes/asciitree/meta.yaml @@ -0,0 +1,18 @@ +package: + name: asciitree + version: 0.3.3 + top-level: + - asciitree + +source: + url: https://files.pythonhosted.org/packages/2d/6a/885bc91484e1aa8f618f6f0228d76d0e67000b0fdd6090673b777e311913/asciitree-0.3.3.tar.gz + sha256: 4aa4b9b649f85e3fcb343363d97564aa1fb62e249677f2e18a96765145cc0f6e + +build: + type: package + +about: + home: https://github.com/mbr/asciitree + PyPI: https://pypi.org/project/asciitree + summary: Draws ASCII trees. + license: MIT diff --git a/pyodide-custom-recipes/humanize/meta.yaml b/pyodide-custom-recipes/humanize/meta.yaml index 3316b88..73d779b 100644 --- a/pyodide-custom-recipes/humanize/meta.yaml +++ b/pyodide-custom-recipes/humanize/meta.yaml @@ -1,16 +1,15 @@ package: name: humanize - version: 4.14.0 + version: 4.15.0 top-level: - humanize source: - url: https://files.pythonhosted.org/packages/c3/5b/9512c5fb6c8218332b530f13500c6ff5f3ce3342f35e0dd7be9ac3856fd3/humanize-4.14.0-py3-none-any.whl - sha256: d57701248d040ad456092820e6fde56c930f17749956ac47f4f655c0c547bfff + url: https://files.pythonhosted.org/packages/c5/7b/bca5613a0c3b542420cf92bd5e5fb8ebd5435ce1011a091f66bb7693285e/humanize-4.15.0-py3-none-any.whl + sha256: b1186eb9f5a9749cd9cb8565aee77919dd7c8d076161cf44d70e59e3301e1769 about: home: https://github.com/python-humanize/humanize PyPI: https://pypi.org/project/humanize summary: Python humanize utilities license: MIT - diff --git a/pyodide-custom-recipes/sc2ts/meta.yaml b/pyodide-custom-recipes/sc2ts/meta.yaml index 89bb2bf..0922952 100644 --- a/pyodide-custom-recipes/sc2ts/meta.yaml +++ b/pyodide-custom-recipes/sc2ts/meta.yaml @@ -1,12 +1,12 @@ package: name: sc2ts - version: 1.0.1 + version: 1.0.2 top-level: - sc2ts source: - url: https://files.pythonhosted.org/packages/7d/b7/763bfbd2a4bbaa810acdbffdb24acd4bcecacc2de0786f5f011a058b1005/sc2ts-1.0.1-py3-none-any.whl - sha256: 639ea91a515e7fd19914ecad3d2c6e36694b62f14e70fad45f24a832f409600b + url: https://files.pythonhosted.org/packages/81/1f/43b692dd0e1add2551899aa9371217118d2850ef8ae1bb84145b3c476da8/sc2ts-1.0.2-py3-none-any.whl + sha256: 95f03b2d658d95dd857507878ea48f7f5ac7d1fe39bc758750604e9ac183c09c requirements: run: @@ -24,4 +24,3 @@ about: PyPI: https://pypi.org/project/sc2ts summary: Infer ARGs for SARS-CoV-2 in tskit format license: GPL-3.0-or-later - diff --git a/pyodide-custom-recipes/tszip/meta.yaml b/pyodide-custom-recipes/tszip/meta.yaml index c5105e6..131f79f 100644 --- a/pyodide-custom-recipes/tszip/meta.yaml +++ b/pyodide-custom-recipes/tszip/meta.yaml @@ -1,21 +1,20 @@ package: name: tszip - version: 0.2.6 + version: 0.3.1 tag: - always top-level: - tszip source: - url: https://files.pythonhosted.org/packages/70/53/200fba914ebb68ac1f11897fafdb9523238eb0b0f1852529f4a59edcc2d2/tszip-0.2.6-py3-none-any.whl - sha256: 1f2a3568f87b28e7435ec881c49e7e3b9d98d1283b8cec9ca38537ab27ed70bb + url: https://files.pythonhosted.org/packages/ac/cf/046c626d9d4acc9af08ea2492d9b4ba221a15983abee5db5da2f5d192295/tszip-0.3.1-py3-none-any.whl + sha256: 459ea5d2cf456840c86b6a119f2da7b6e41b09d302169a9ea000ec5bbf6037b2 requirements: run: - numpy - humanize - tskit - - numcodecs - zarr about: @@ -23,4 +22,3 @@ about: PyPI: https://pypi.org/project/tszip summary: Compression utilities for tree sequences license: MIT - diff --git a/requirements.txt b/requirements.txt index e99dcdc..505d370 100644 --- a/requirements.txt +++ b/requirements.txt @@ -1,11 +1,11 @@ # Core modules (mandatory) -jupyterlite-core>=0.7,<1 -jupyterlab~=4.4.3 -notebook~=7.4.3 +jupyterlite-core>=0.7.6,<1 +jupyterlab~=4.5.7 +notebook~=7.5.6 # Python kernel (optional) -jupyterlite-pyodide-kernel>=0.7,<1 +jupyterlite-pyodide-kernel>=0.7.2,<1 # JupyterLab: Fasta file renderer (optional) @@ -15,19 +15,19 @@ jupyterlab-geojson>=3.4.0,<4 # JupyterLab: guided tour (optional) jupyterlab-tour # JupyterLab: dark theme -jupyterlab-night +jupyterlab-night>=0.5.2 # JupyterLab: Miami nights theme (optional) -jupyterlab_miami_nights +jupyterlab_miami_nights>=0.4.3 # Python: ipywidget library for Jupyter notebooks (optional) -ipywidgets>=8.1.3,<9 +ipywidgets>=8.1.8,<9 # Python: ipyevents library for Jupyter notebooks (optional) -ipyevents>=2.0.1 +ipyevents>=2.0.4 # Python: interative Matplotlib library for Jupyter notebooks (optional) -ipympl>=0.8.2 +ipympl>=0.10.0 # Python: ipycanvas library for Jupyter notebooks (optional) -ipycanvas>=0.9.1 +ipycanvas>=0.14.3 # For running tests of the notebooks demesdraw -stdpopsim>=0.3 \ No newline at end of file +stdpopsim>=0.3 diff --git a/tests/test_notebooks_pyodide.py b/tests/test_notebooks_pyodide.py index 1904c0e..0e5bd67 100644 --- a/tests/test_notebooks_pyodide.py +++ b/tests/test_notebooks_pyodide.py @@ -25,6 +25,18 @@ def _execute_notebook(notebook_path: Path, *, cells: int | None = None, timeout: If `cells` is provided, only the first `cells` code cells are executed. """ nb = nbformat.read(notebook_path, as_version=4) + for cell in nb.cells: + if cell.cell_type == "code": + cell.source = cell.source.replace('"/drive/', f'"{notebook_path.parent}/') + cell.source = cell.source.replace( + "from pyodide.http import pyfetch", + "from pathlib import Path", + ) + cell.source = cell.source.replace( + 'response = await pyfetch("/files/data/demo.trees")\n' + "ts = tskit.load(io.BytesIO(await response.bytes()))", + 'ts = tskit.load(Path("data/demo.trees"))', + ) if cells is not None: code_cells = [c for c in nb.cells if c.cell_type == "code"] diff --git a/tskit-launcher/package-lock.json b/tskit-launcher/package-lock.json index a5b16e3..9a17bdb 100644 --- a/tskit-launcher/package-lock.json +++ b/tskit-launcher/package-lock.json @@ -9,41 +9,43 @@ "version": "0.1.0", "license": "BSD-3-Clause", "dependencies": { - "@jupyterlab/application": "^4.0.0", - "@jupyterlab/apputils": "^4.0.0", - "@jupyterlab/launcher": "^4.0.0" + "@jupyterlab/application": "^4.5.7", + "@jupyterlab/apputils": "^4.6.7", + "@jupyterlab/launcher": "^4.5.7" }, "devDependencies": { - 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"yjs": "^13.5.0" + "yjs": "^13.6.30" } }, "node_modules/@babel/code-frame": { - "version": "7.27.1", + "version": "7.29.0", + "resolved": "https://registry.npmjs.org/@babel/code-frame/-/code-frame-7.29.0.tgz", + "integrity": "sha512-9NhCeYjq9+3uxgdtp20LSiJXJvN0FeCtNGpJxuMFZ1Kv3cWUNb6DOhJwUvcVCzKGR66cw4njwM6hrJLqgOwbcw==", "dev": true, "license": "MIT", "dependencies": { - "@babel/helper-validator-identifier": "^7.27.1", + "@babel/helper-validator-identifier": "^7.28.5", "js-tokens": "^4.0.0", "picocolors": "^1.1.1" }, @@ -53,21 +55,112 @@ }, "node_modules/@babel/helper-validator-identifier": { "version": "7.28.5", + "resolved": "https://registry.npmjs.org/@babel/helper-validator-identifier/-/helper-validator-identifier-7.28.5.tgz", + "integrity": "sha512-qSs4ifwzKJSV39ucNjsvc6WVHs6b7S03sOh2OcHF9UHfVPqWWALUsNUVzhSBiItjRZoLHx7nIarVjqKVusUZ1Q==", "dev": true, "license": "MIT", "engines": { "node": ">=6.9.0" } }, + "node_modules/@cacheable/memory": { + "version": "2.0.9", + "resolved": "https://registry.npmjs.org/@cacheable/memory/-/memory-2.0.9.tgz", + "integrity": "sha512-HdMx6DoGywB30vacDbBsITbIX4pgFqj1zsrV58jZBUw3klzkNoXhj7qOqAgledhxG7YZI5rBSJg7Zp8/VG0DuA==", + "dev": true, + "license": "MIT", + "dependencies": { + "@cacheable/utils": "^2.4.1", + "@keyv/bigmap": "^1.3.1", + "hookified": "^1.15.1", + "keyv": "^5.6.0" + } + }, + "node_modules/@cacheable/memory/node_modules/@keyv/bigmap": { + "version": "1.3.1", + "resolved": "https://registry.npmjs.org/@keyv/bigmap/-/bigmap-1.3.1.tgz", + "integrity": "sha512-WbzE9sdmQtKy8vrNPa9BRnwZh5UF4s1KTmSK0KUVLo3eff5BlQNNWDnFOouNpKfPKDnms9xynJjsMYjMaT/aFQ==", + "dev": true, + "license": "MIT", + "dependencies": { + "hashery": "^1.4.0", + "hookified": "^1.15.0" + }, + "engines": { + "node": ">= 18" + }, + "peerDependencies": { + "keyv": "^5.6.0" + } + }, + "node_modules/@cacheable/memory/node_modules/keyv": { + "version": "5.6.0", + "resolved": "https://registry.npmjs.org/keyv/-/keyv-5.6.0.tgz", + "integrity": "sha512-CYDD3SOtsHtyXeEORYRx2qBtpDJFjRTGXUtmNEMGyzYOKj1TE3tycdlho7kA1Ufx9OYWZzg52QFBGALTirzDSw==", + "dev": true, + "license": "MIT", + "dependencies": { + "@keyv/serialize": "^1.1.1" + } + }, + "node_modules/@cacheable/utils": { + "version": "2.4.1", + "resolved": "https://registry.npmjs.org/@cacheable/utils/-/utils-2.4.1.tgz", + "integrity": "sha512-eiFgzCbIneyMlLOmNG4g9xzF7Hv3Mga4LjxjcSC/ues6VYq2+gUbQI8JqNuw/ZM8tJIeIaBGpswAsqV2V7ApgA==", + "dev": true, + "license": "MIT", + "dependencies": { + "hashery": "^1.5.1", + "keyv": "^5.6.0" + } + }, + "node_modules/@cacheable/utils/node_modules/keyv": { + "version": "5.6.0", + "resolved": "https://registry.npmjs.org/keyv/-/keyv-5.6.0.tgz", + "integrity": "sha512-CYDD3SOtsHtyXeEORYRx2qBtpDJFjRTGXUtmNEMGyzYOKj1TE3tycdlho7kA1Ufx9OYWZzg52QFBGALTirzDSw==", + "dev": true, + "license": "MIT", + "dependencies": { + "@keyv/serialize": "^1.1.1" + } + }, "node_modules/@codemirror/state": { - 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"node": ">=12" - }, - "funding": { - "url": "https://github.com/chalk/ansi-styles?sponsor=1" - } - }, - "node_modules/wrap-ansi/node_modules/emoji-regex": { - "version": "9.2.2", - "dev": true, - "license": "MIT" - }, - "node_modules/wrap-ansi/node_modules/string-width": { - "version": "5.1.2", - "dev": true, - "license": "MIT", - "dependencies": { - "eastasianwidth": "^0.2.0", - "emoji-regex": "^9.2.2", - "strip-ansi": "^7.0.1" - }, - "engines": { - "node": ">=12" - }, - "funding": { - "url": "https://github.com/sponsors/sindresorhus" - } - }, - "node_modules/wrap-ansi/node_modules/strip-ansi": { - "version": "7.1.2", - "dev": true, - "license": "MIT", - "dependencies": { - "ansi-regex": "^6.0.1" - }, - "engines": { - "node": ">=12" - }, - "funding": { - "url": "https://github.com/chalk/strip-ansi?sponsor=1" - } - }, "node_modules/wrappy": { "version": "1.0.2", "dev": true, "license": "ISC" }, "node_modules/write-file-atomic": { - "version": "5.0.1", + "version": "7.0.1", + "resolved": "https://registry.npmjs.org/write-file-atomic/-/write-file-atomic-7.0.1.tgz", + "integrity": "sha512-OTIk8iR8/aCRWBqvxrzxR0hgxWpnYBblY1S5hDWBQfk/VFmJwzmJgQFN3WsoUKHISv2eAwe+PpbUzyL1CKTLXg==", "dev": true, "license": "ISC", "dependencies": { - "imurmurhash": "^0.1.4", "signal-exit": "^4.0.1" }, "engines": { - "node": "^14.17.0 || ^16.13.0 || >=18.0.0" + "node": "^20.17.0 || >=22.9.0" } }, "node_modules/ws": { - "version": "8.18.3", + "version": "8.20.1", + "resolved": "https://registry.npmjs.org/ws/-/ws-8.20.1.tgz", + "integrity": "sha512-It4dO0K5v//JtTXuPkfEOaI3uUN87iYPnqo/ZzqCoG3g8uhA66QUMs/SrM0YK7/NAu+r4LMh/9dq2A7k+rHs+w==", "license": "MIT", "engines": { "node": ">=10.0.0" @@ -5716,7 +5951,9 @@ } }, "node_modules/y-protocols": { - "version": "1.0.6", + "version": "1.0.7", + "resolved": "https://registry.npmjs.org/y-protocols/-/y-protocols-1.0.7.tgz", + "integrity": "sha512-YSVsLoXxO67J6eE/nV4AtFtT3QEotZf5sK5BHxFBXso7VDUT3Tx07IfA6hsu5Q5OmBdMkQVmFZ9QOA7fikWvnw==", "license": "MIT", "dependencies": { "lib0": "^0.2.85" @@ -5733,21 +5970,10 @@ "yjs": "^13.0.0" } }, - "node_modules/yallist": { - "version": "4.0.0", - "dev": true, - "license": "ISC" - }, - "node_modules/yargs-parser": { - "version": "20.2.9", - "dev": true, - "license": "ISC", - "engines": { - "node": ">=10" - } - }, "node_modules/yjs": { - "version": "13.6.27", + "version": "13.6.30", + "resolved": "https://registry.npmjs.org/yjs/-/yjs-13.6.30.tgz", + "integrity": "sha512-vv/9h42eCMC81ZHDFswuu/MKzkl/vyq1BhaNGfHyOonwlG4CJbQF4oiBBJPvfdeCt/PlVDWh7Nov9D34YY09uQ==", "license": "MIT", "dependencies": { "lib0": "^0.2.99" diff --git a/tskit-launcher/package.json b/tskit-launcher/package.json index f468941..c204c5d 100644 --- a/tskit-launcher/package.json +++ b/tskit-launcher/package.json @@ -29,59 +29,59 @@ "url": "n/a.git" }, "scripts": { - "build": "jlpm build:lib && jlpm build:labextension:dev", - "build:prod": "jlpm clean && jlpm build:lib:prod && jlpm build:labextension", + "build": "npm run build:lib && npm run build:labextension:dev", + "build:prod": "npm run clean && npm run build:lib:prod && npm run build:labextension", "build:labextension": "jupyter labextension build .", "build:labextension:dev": "jupyter labextension build --development True .", "build:lib": "tsc --sourceMap", "build:lib:prod": "tsc", - "clean": "jlpm clean:lib", + "clean": "npm run clean:lib", "clean:lib": "rimraf lib tsconfig.tsbuildinfo", "clean:lintcache": "rimraf .eslintcache .stylelintcache", "clean:labextension": "rimraf tskit_launcher/labextension tskit_launcher/_version.py", - "clean:all": "jlpm clean:lib && jlpm clean:labextension && jlpm clean:lintcache", - "eslint": "jlpm eslint:check --fix", + "clean:all": "npm run clean:lib && npm run clean:labextension && npm run clean:lintcache", + "eslint": "npm run eslint:check -- --fix", "eslint:check": "eslint . --cache --ext .ts,.tsx", - "install:extension": "jlpm build", - "lint": "jlpm stylelint && jlpm prettier && jlpm eslint", - "lint:check": "jlpm stylelint:check && jlpm prettier:check && jlpm eslint:check", - "prettier": "jlpm prettier:base --write --list-different", + "install:extension": "npm run build", + "lint": "npm run stylelint && npm run prettier && npm run eslint", + "lint:check": "npm run stylelint:check && npm run prettier:check && npm run eslint:check", + "prettier": "npm run prettier:base -- --write --list-different", "prettier:base": "prettier \"**/*{.ts,.tsx,.js,.jsx,.css,.json,.md}\"", - "prettier:check": "jlpm prettier:base --check", - "stylelint": "jlpm stylelint:check --fix", + "prettier:check": "npm run prettier:base -- --check", + "stylelint": "npm run stylelint:check -- --fix", "stylelint:check": "stylelint --cache \"style/**/*.css\"", "watch": "run-p watch:src watch:labextension", "watch:src": "tsc -w --sourceMap", "watch:labextension": "jupyter labextension watch ." }, "dependencies": { - "@jupyterlab/application": "^4.0.0", - "@jupyterlab/apputils": "^4.0.0", - "@jupyterlab/launcher": "^4.0.0" + "@jupyterlab/application": "^4.5.7", + "@jupyterlab/apputils": "^4.6.7", + "@jupyterlab/launcher": "^4.5.7" }, "devDependencies": { - "@jupyterlab/builder": "^4.0.0", + "@jupyterlab/builder": "^4.5.7", "@types/json-schema": "^7.0.11", - "@types/react": "^18.0.26", + "@types/react": "^19.2.15", "@types/react-addons-linked-state-mixin": "^0.14.22", - "@typescript-eslint/eslint-plugin": "^6.1.0", - "@typescript-eslint/parser": "^6.1.0", - "css-loader": "^6.7.1", + "@typescript-eslint/eslint-plugin": "^8.59.4", + "@typescript-eslint/parser": "^8.59.4", + "css-loader": "^7.1.4", "eslint": "^8.36.0", - "eslint-config-prettier": "^8.8.0", - "eslint-plugin-prettier": "^5.0.0", - "npm-run-all2": "^7.0.1", - "prettier": "^3.0.0", - "rimraf": "^5.0.1", - "source-map-loader": "^1.0.2", - "style-loader": "^3.3.1", - "stylelint": "^15.10.1", - "stylelint-config-recommended": "^13.0.0", - "stylelint-config-standard": "^34.0.0", - "stylelint-csstree-validator": "^3.0.0", - "stylelint-prettier": "^4.0.0", + "eslint-config-prettier": "^10.1.8", + "eslint-plugin-prettier": "^5.5.5", + "npm-run-all2": "^8.0.4", + "prettier": "^3.8.3", + "rimraf": "^6.1.3", + "source-map-loader": "^5.0.0", + "style-loader": "^4.0.0", + "stylelint": "^17.11.1", + "stylelint-config-recommended": "^18.0.0", + "stylelint-config-standard": "^40.0.0", + "stylelint-csstree-validator": "^4.0.0", + "stylelint-prettier": "^5.0.3", "typescript": "^5.6.3", - "yjs": "^13.5.0" + "yjs": "^13.6.30" }, "sideEffects": [ "style/*.css", @@ -143,14 +143,6 @@ "@typescript-eslint/no-explicit-any": "off", "@typescript-eslint/no-namespace": "off", "@typescript-eslint/no-use-before-define": "off", - "@typescript-eslint/quotes": [ - "error", - "single", - { - "avoidEscape": true, - "allowTemplateLiterals": false - } - ], "curly": [ "error", "all" @@ -189,5 +181,8 @@ "selector-no-vendor-prefix": null, "value-no-vendor-prefix": null } + }, + "overrides": { + "sanitize-html": "2.17.4" } } diff --git a/tskit-launcher/pyproject.toml b/tskit-launcher/pyproject.toml index 971ffa1..4749910 100644 --- a/tskit-launcher/pyproject.toml +++ b/tskit-launcher/pyproject.toml @@ -1,5 +1,5 @@ [build-system] -requires = ["hatchling>=1.5.0", "jupyterlab>=4.0.0,<5", "hatch-nodejs-version>=0.3.2"] +requires = ["hatchling>=1.5.0", "jupyterlab>=4.5.7,<5", "hatch-nodejs-version>=0.3.2"] build-backend = "hatchling.build" [project] @@ -51,11 +51,11 @@ skip-if-exists = ["tskit_launcher/labextension/static/style.js"] [tool.hatch.build.hooks.jupyter-builder.build-kwargs] build_cmd = "build:prod" -npm = ["jlpm"] +npm = ["npm"] [tool.hatch.build.hooks.jupyter-builder.editable-build-kwargs] build_cmd = "install:extension" -npm = ["jlpm"] +npm = ["npm"] source_dir = "src" build_dir = "tskit_launcher/labextension" @@ -64,11 +64,11 @@ version_cmd = "hatch version" [tool.jupyter-releaser.hooks] before-build-npm = [ - "python -m pip install 'jupyterlab>=4.0.0,<5'", - "jlpm", - "jlpm build:prod" + "python -m pip install 'jupyterlab>=4.5.7,<5'", + "npm install", + "npm run build:prod" ] -before-build-python = ["jlpm clean:all"] +before-build-python = ["npm run clean:all"] [tool.check-wheel-contents] ignore = ["W002"] diff --git a/tskit-launcher/src/index.ts b/tskit-launcher/src/index.ts index 4897724..80112ce 100644 --- a/tskit-launcher/src/index.ts +++ b/tskit-launcher/src/index.ts @@ -10,7 +10,7 @@ import { ILauncher } from '@jupyterlab/launcher'; /** * Configuration for content hash checking */ -interface ContentConfig { +interface IContentConfig { contentHash: string; lastUpdated: string; version?: string; @@ -21,9 +21,12 @@ interface ContentConfig { */ class CustomLauncher extends Widget implements ILauncher { private app: JupyterFrontEnd | null = null; - private contentConfig: ContentConfig | null = null; + private contentConfig: IContentConfig | null = null; private readonly STORAGE_KEY = 'tskit-launcher-content-hash'; - private readonly CONFIG_URL = './content-config.json'; + private readonly AUTO_RESET_KEY = 'tskit-launcher-auto-reset-content-hash'; + private readonly UI_STATE_VERSION_KEY = 'tskit-launcher-ui-state-version'; + private readonly UI_STATE_VERSION = 'pyodide-2026-0'; + private readonly CONFIG_URL = './content-config.json'; constructor() { super(); @@ -119,8 +122,8 @@ class CustomLauncher extends Widget implements ILauncher { const resetButton = this.node.querySelector('#reset-button'); if (resetButton) { - resetButton.addEventListener('click', () => { - this.resetLocalState(); + resetButton.addEventListener('click', async () => { + await this.resetLocalState(); }); } } @@ -135,13 +138,27 @@ class CustomLauncher extends Widget implements ILauncher { } this.contentConfig = await response.json(); - + + if (this.shouldResetUiStateForVersion()) { + await this.resetUiState(this.UI_STATE_VERSION); + return; + } + // Get stored hash from localStorage const storedData = localStorage.getItem(this.STORAGE_KEY); const storedConfig = storedData ? JSON.parse(storedData) : null; // Check if content has been updated - if (this.contentConfig && storedConfig && storedConfig.contentHash !== this.contentConfig.contentHash) { + if ( + this.contentConfig && + storedConfig && + storedConfig.contentHash !== this.contentConfig.contentHash + ) { + if (this.shouldAutoResetUiState(this.contentConfig.contentHash)) { + await this.resetUiState(this.contentConfig.contentHash); + return; + } + this.showUpdateWarning(); } else if (!storedConfig) { // First time visit - store the current hash @@ -152,8 +169,20 @@ class CustomLauncher extends Widget implements ILauncher { } } + private shouldResetUiStateForVersion(): boolean { + return ( + localStorage.getItem(this.UI_STATE_VERSION_KEY) !== this.UI_STATE_VERSION + ); + } + + private shouldAutoResetUiState(resetMarker: string): boolean { + return sessionStorage.getItem(this.AUTO_RESET_KEY) !== resetMarker; + } + private showUpdateWarning(): void { - const warningElement = this.node.querySelector('#update-warning') as HTMLElement; + const warningElement = this.node.querySelector( + '#update-warning' + ) as HTMLElement; if (warningElement) { warningElement.style.display = 'block'; } @@ -161,18 +190,35 @@ class CustomLauncher extends Widget implements ILauncher { private storeCurrentHash(): void { if (this.contentConfig) { - localStorage.setItem(this.STORAGE_KEY, JSON.stringify(this.contentConfig)); + localStorage.setItem( + this.STORAGE_KEY, + JSON.stringify(this.contentConfig) + ); } } - private resetLocalState(): void { + private async resetUiState(resetMarker: string): Promise { + if (!this.contentConfig) { + return; + } + + sessionStorage.setItem(this.AUTO_RESET_KEY, resetMarker); + + this.clearJupyterLiteLocalStorage(); + await this.deleteIndexedDBDatabases(['JupyterLite Storage']); + this.storeCurrentHash(); + localStorage.setItem(this.UI_STATE_VERSION_KEY, this.UI_STATE_VERSION); + window.location.reload(); + } + + private async resetLocalState(): Promise { try { // Clear JupyterLite state - this.clearJupyterLiteState(); - + await this.clearJupyterLiteState(); + // Update stored hash this.storeCurrentHash(); - + // Force refresh window.location.reload(); } catch (error) { @@ -182,19 +228,31 @@ class CustomLauncher extends Widget implements ILauncher { } } - private clearJupyterLiteState(): void { + private async clearJupyterLiteState(): Promise { + this.clearJupyterLiteLocalStorage(); + await this.clearJupyterLiteIndexedDBDatabases(); + await this.clearJupyterLiteCaches(); + await this.unregisterJupyterLiteServiceWorkers(); + } + + private clearJupyterLiteLocalStorage(): void { // Clear JupyterLite-specific localStorage items const keysToRemove: string[] = []; - + for (let i = 0; i < localStorage.length; i++) { const key = localStorage.key(i); - if (key && ( - key.startsWith('jupyter-') || - key.startsWith('jupyterlab-') || - key.startsWith('lumino-') || - key.includes('notebook') || - key.includes('kernel') - )) { + if ( + key && + (key.startsWith('jupyter-') || + key.startsWith('jupyterlab-') || + key.startsWith('lumino-') || + key.startsWith('@jupyterlab/') || + key.startsWith('@jupyterlite/') || + key.includes('filebrowser') || + key.includes('notebook') || + key.includes('kernel') || + key.includes('workspace')) + ) { keysToRemove.push(key); } } @@ -202,26 +260,91 @@ class CustomLauncher extends Widget implements ILauncher { keysToRemove.forEach(key => { localStorage.removeItem(key); }); - - // Clear IndexedDB databases used by JupyterLite - this.clearIndexedDBDatabases(); } - private clearIndexedDBDatabases(): void { - // Common JupyterLite IndexedDB database names - const dbNames = [ + private async clearJupyterLiteIndexedDBDatabases(): Promise { + const knownDbNames = [ 'JupyterLite Storage', + 'JupyterLite Contents', 'jupyter-config-data', 'jupyter-lab-workspaces', 'pyodide-packages' ]; - dbNames.forEach(dbName => { - const deleteRequest = indexedDB.deleteDatabase(dbName); - deleteRequest.onerror = () => { - console.warn(`Could not delete database: ${dbName}`); - }; - }); + const dbNames = new Set(knownDbNames); + const indexedDBWithDatabases = indexedDB as IDBFactory & { + databases?: () => Promise>; + }; + + if (indexedDBWithDatabases.databases) { + const databases = await indexedDBWithDatabases.databases(); + for (const database of databases) { + const name = database.name; + if (name && this.isJupyterLiteDatabase(name)) { + dbNames.add(name); + } + } + } + + await this.deleteIndexedDBDatabases([...dbNames]); + } + + private isJupyterLiteDatabase(name: string): boolean { + return ( + name.startsWith('JupyterLite') || + name.startsWith('jupyter') || + name.startsWith('pyodide') + ); + } + + private async deleteIndexedDBDatabases(dbNames: string[]): Promise { + await Promise.all( + dbNames.map( + dbName => + new Promise(resolve => { + const deleteRequest = indexedDB.deleteDatabase(dbName); + deleteRequest.onsuccess = () => resolve(); + deleteRequest.onerror = () => { + console.warn(`Could not delete database: ${dbName}`); + resolve(); + }; + deleteRequest.onblocked = () => { + console.warn(`Database deletion blocked: ${dbName}`); + resolve(); + }; + }) + ) + ); + } + + private async clearJupyterLiteCaches(): Promise { + if (!('caches' in window)) { + return; + } + + const cacheNames = await caches.keys(); + await Promise.all( + cacheNames + .filter( + cacheName => cacheName.includes('jupyter') || cacheName === 'precache' + ) + .map(cacheName => caches.delete(cacheName)) + ); + } + + private async unregisterJupyterLiteServiceWorkers(): Promise { + if (!navigator.serviceWorker) { + return; + } + + const registrations = await navigator.serviceWorker.getRegistrations(); + await Promise.all( + registrations + .filter(registration => + registration.active?.scriptURL.includes(location.origin) + ) + .map(registration => registration.unregister()) + ); } setApp(app: JupyterFrontEnd): void { @@ -263,4 +386,4 @@ const launcher: JupyterFrontEndPlugin = { autoStart: true }; -export default launcher; \ No newline at end of file +export default launcher; diff --git a/tskit-launcher/style/base.css b/tskit-launcher/style/base.css index 3e89366..8b4d5c6 100644 --- a/tskit-launcher/style/base.css +++ b/tskit-launcher/style/base.css @@ -27,7 +27,7 @@ color: var(--jp-ui-font-color0); font-size: 24px; font-weight: 600; - margin: 0 0 16px 0; + margin: 0 0 16px; text-align: center; } @@ -55,7 +55,7 @@ border-color: var(--jp-brand-color1); background: var(--jp-layout-color2); transform: translateY(-2px); - box-shadow: 0 4px 8px rgba(0, 0, 0, 0.1); + box-shadow: 0 4px 8px rgb(0 0 0 / 10%); } .jp-LauncherCard-icon { @@ -74,28 +74,30 @@ .tskit-launcher { background: linear-gradient(135deg, #f8f9fa 0%, #e9ecef 100%); min-height: 100vh; + max-width: 800px; + margin: 0 auto; padding: 20px; } .tskit-header { text-align: center; - margin-bottom: 40px; + margin-bottom: 30px; padding: 30px; background: white; border-radius: 12px; - box-shadow: 0 4px 6px rgba(0, 0, 0, 0.1); + box-shadow: 0 4px 6px rgb(0 0 0 / 10%); border-top: 4px solid #204e66; } .tskit-logo { - height: 80px; - margin-bottom: 20px; + height: 60px; + margin-bottom: 10px; } .tskit-header h1 { color: #204e66; font-size: 2.5rem; - margin: 0 0 10px 0; + margin: 0 0 10px; font-weight: 700; } @@ -117,9 +119,11 @@ border: 2px solid #e9ecef; border-radius: 12px; padding: 25px; - transition: all 0.3s ease; + transition: + transform 0.2s, + box-shadow 0.2s; cursor: pointer; - box-shadow: 0 2px 4px rgba(0, 0, 0, 0.1); + box-shadow: 0 2px 4px rgb(0 0 0 / 10%); width: 100%; max-width: 600px; min-height: 80px; @@ -133,7 +137,7 @@ .tskit-card:hover { border-color: #5dc694; transform: translateY(-2px); - box-shadow: 0 8px 16px rgba(93, 198, 148, 0.2); + box-shadow: 0 4px 12px rgb(0 0 0 / 10%); } .tskit-card .jp-LauncherCard-icon { @@ -170,7 +174,6 @@ text-align: left; line-height: 1.4; margin: 0; - word-wrap: break-word; overflow-wrap: break-word; } @@ -181,12 +184,12 @@ flex-wrap: wrap; } -[data-jp-item-name="new-launcher"] { - display: none !important; +[data-jp-item-name='new-launcher'] { + display: none !important; } .lm-TabBar-addButton { - display: none !important; + display: none !important; } .tskit-update-warning { @@ -195,7 +198,7 @@ border-radius: 8px; margin-bottom: 20px; padding: 16px; - box-shadow: 0 2px 4px rgba(0,0,0,0.1); + box-shadow: 0 2px 4px rgb(0 0 0 / 10%); } .tskit-warning-content { @@ -219,7 +222,7 @@ } .tskit-warning-text p { - margin: 4px 0 0 0; + margin: 4px 0 0; color: #856404; font-size: 13px; } @@ -234,7 +237,7 @@ font-size: 13px; font-weight: 600; transition: all 0.2s ease; - box-shadow: 0 3px 8px rgba(32, 78, 102, 0.3); + box-shadow: 0 3px 8px rgb(32 78 102 / 30%); position: relative; overflow: hidden; text-transform: uppercase; @@ -248,14 +251,19 @@ left: -100%; width: 100%; height: 100%; - background: linear-gradient(90deg, transparent, rgba(255, 255, 255, 0.2), transparent); + background: linear-gradient( + 90deg, + transparent, + rgb(255 255 255 / 20%), + transparent + ); transition: left 0.5s; } .tskit-reset-button:hover { background: linear-gradient(135deg, #1a3d52 0%, #204e66 100%); transform: translateY(-2px); - box-shadow: 0 5px 15px rgba(32, 78, 102, 0.4); + box-shadow: 0 5px 15px rgb(32 78 102 / 40%); } .tskit-reset-button:hover::before { @@ -263,36 +271,6 @@ } .tskit-reset-button:active { - transform: translateY(0px); - box-shadow: 0 2px 5px rgba(32, 78, 102, 0.3); -} - -.tskit-launcher { - max-width: 800px; - margin: 0 auto; - padding: 20px; -} - -.tskit-header { - text-align: center; - margin-bottom: 30px; + transform: translateY(0); + box-shadow: 0 2px 5px rgb(32 78 102 / 30%); } - -.tskit-logo { - height: 60px; - margin-bottom: 10px; -} - -.tskit-card { - cursor: pointer; - transition: transform 0.2s, box-shadow 0.2s; -} - -.tskit-card:hover { - transform: translateY(-2px); - box-shadow: 0 4px 12px rgba(0,0,0,0.1); -} - -.tskit-card-content { - flex-grow: 1; -} \ No newline at end of file diff --git a/tskit-launcher/yarn.lock b/tskit-launcher/yarn.lock deleted file mode 100644 index bd6f941..0000000 --- a/tskit-launcher/yarn.lock +++ /dev/null @@ -1,2687 +0,0 @@ -# THIS IS AN AUTOGENERATED FILE. DO NOT EDIT THIS FILE DIRECTLY. -# yarn lockfile v1 - - -"@babel/code-frame@^7.0.0": - version "7.27.1" - dependencies: - "@babel/helper-validator-identifier" "^7.27.1" - js-tokens "^4.0.0" - picocolors "^1.1.1" - -"@babel/helper-validator-identifier@^7.27.1": - version "7.28.5" - -"@codemirror/state@^6.5.2": - version "6.5.2" - dependencies: - "@marijn/find-cluster-break" "^1.0.0" - -"@csstools/css-parser-algorithms@^2.3.1", "@csstools/css-parser-algorithms@^2.7.1": - version "2.7.1" - -"@csstools/css-tokenizer@^2.2.0", "@csstools/css-tokenizer@^2.4.1": - version "2.4.1" - -"@csstools/media-query-list-parser@^2.1.4": - version "2.1.13" - -"@csstools/selector-specificity@^3.0.0": - version "3.1.1" - -"@discoveryjs/json-ext@^0.5.0": - version "0.5.7" - -"@eslint-community/eslint-utils@^4.2.0", "@eslint-community/eslint-utils@^4.4.0": - version "4.9.0" - dependencies: - eslint-visitor-keys "^3.4.3" - -"@eslint-community/regexpp@^4.5.1", "@eslint-community/regexpp@^4.6.1": - version "4.12.2" - 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