Upgrade Pyodide to 0.27.2

.gitmodules

@@ -13,6 +13,3 @@
 [submodule "packages/py-faicons"]
 	path = packages/py-faicons
 	url = https://github.com/posit-dev/py-faicons.git
-[submodule "packages/plotnine"]
-	path = packages/plotnine
-	url = https://github.com/wch/plotnine.git

Makefile

@@ -17,7 +17,7 @@
 
 SHINYLIVE_VERSION = $(shell node -p "require('./package.json').version")
 
-PYODIDE_VERSION = 0.26.3
+PYODIDE_VERSION = 0.27.2
 PYODIDE_DIST_FILENAME = pyodide-$(PYODIDE_VERSION).tar.bz2
 DOWNLOAD_DIR = ./downloads
 R_SHINY_VERSION = 1.9.1.8002
@@ -41,10 +41,6 @@ SHINY_WHEEL = shiny-$(SHINY_VERSION)-py3-none-any.whl
 SHINYWIDGETS_WHEEL = shinywidgets-$(SHINYWIDGETS_VERSION)-py3-none-any.whl
 FAICONS_WHEEL = faicons-$(FAICONS_VERSION)-py3-none-any.whl
 
-# Hard code these versions for now
-PLOTNINE_VERSION=0.0.0
-PLOTNINE_WHEEL=plotnine-$(PLOTNINE_VERSION)-py3-none-any.whl
-
 # libsass is built in gadenbuie/libsass-python
 # NOTE: Update https://github.com/gadenbuie/libsass-python/blob/dev/.github/workflows/pyodide.yml
 # Pyodide, Emscripten, or Python versions change here.
@@ -97,13 +93,11 @@ submodules:
 	git submodule init
 	git submodule update --depth=20
 	cd packages/py-shiny && git fetch --tags --unshallow
-	cd packages/plotnine && git fetch --tags --unshallow
 
 ## Pull latest changes in git submodules
 submodules-pull:
 	git submodule update --recursive --remote
 	cd packages/py-shiny && git fetch --tags
-	cd packages/plotnine && git fetch --tags
 submodules-pull-shiny:
 	git submodule update --remote packages/py-shiny
 	cd packages/py-shiny && git fetch --tags
@@ -178,7 +172,6 @@ pyodide_packages_local: $(BUILD_DIR)/shinylive/pyodide/$(HTMLTOOLS_WHEEL) \
 	$(BUILD_DIR)/shinylive/pyodide/$(SHINY_WHEEL) \
 	$(BUILD_DIR)/shinylive/pyodide/$(SHINYWIDGETS_WHEEL) \
 	$(BUILD_DIR)/shinylive/pyodide/$(FAICONS_WHEEL) \
-	$(BUILD_DIR)/shinylive/pyodide/$(PLOTNINE_WHEEL) \
 	$(BUILD_DIR)/shinylive/pyodide/$(LIBSASS_WHEEL) \
 	$(BUILD_DIR)/shinylive/pyodide/$(POLARS_WHEEL)
 
@@ -206,11 +199,6 @@ $(BUILD_DIR)/shinylive/pyodide/$(FAICONS_WHEEL): $(PACKAGE_DIR)/$(FAICONS_WHEEL)
 	rm -f $(BUILD_DIR)/shinylive/pyodide/faicons*.whl
 	cp $(PACKAGE_DIR)/$(FAICONS_WHEEL) $(BUILD_DIR)/shinylive/pyodide/$(FAICONS_WHEEL)
 
-$(BUILD_DIR)/shinylive/pyodide/$(PLOTNINE_WHEEL): $(PACKAGE_DIR)/$(PLOTNINE_WHEEL)
-	mkdir -p $(BUILD_DIR)/shinylive/pyodide
-	rm -f $(BUILD_DIR)/shinylive/pyodide/plotnine*.whl
-	cp $(PACKAGE_DIR)/$(PLOTNINE_WHEEL) $(BUILD_DIR)/shinylive/pyodide/$(PLOTNINE_WHEEL)
-
 $(BUILD_DIR)/shinylive/pyodide/$(LIBSASS_WHEEL): $(PACKAGE_DIR)/$(LIBSASS_WHEEL)
 	mkdir -p $(BUILD_DIR)/shinylive/pyodide
 	rm -f $(BUILD_DIR)/shinylive/pyodide/libsass*.whl
@@ -281,8 +269,7 @@ packages: clean-packages \
 	package-htmltools \
 	package-shiny \
 	package-shinywidgets \
-	package-faicons \
-	package-plotnine
+	package-faicons
 
 
 package-htmltools: $(PACKAGE_DIR)/$(HTMLTOOLS_WHEEL)
@@ -293,8 +280,6 @@ package-shinywidgets: $(PACKAGE_DIR)/$(SHINYWIDGETS_WHEEL)
 
 package-faicons: $(PACKAGE_DIR)/$(FAICONS_WHEEL)
 
-package-plotnine: $(PACKAGE_DIR)/$(PLOTNINE_WHEEL)
-
 
 $(PACKAGE_DIR)/$(HTMLTOOLS_WHEEL): $(PYBIN) $(PACKAGE_DIR)/py-htmltools
 	# Remove any old copies of the package
@@ -317,11 +302,6 @@ $(PACKAGE_DIR)/$(FAICONS_WHEEL): $(PYBIN) $(PACKAGE_DIR)/py-faicons
 	rm -f $(PACKAGE_DIR)/faicons*.whl
 	. $(PYBIN)/activate && cd $(PACKAGE_DIR)/py-faicons && make install && mv dist/*.whl ../
 
-$(PACKAGE_DIR)/$(PLOTNINE_WHEEL): $(PYBIN) $(PACKAGE_DIR)/plotnine
-	rm -f $(PACKAGE_DIR)/plotnine*.whl
-	$(PYBIN)/pip install -e $(PACKAGE_DIR)/plotnine[build]
-	. $(PYBIN)/activate && cd $(PACKAGE_DIR)/plotnine && make dist && mv dist/*.whl ../$(PLOTNINE_WHEEL)
-
 $(PACKAGE_DIR)/$(LIBSASS_WHEEL): $(PYBIN) $(PACKAGE_DIR)/$(LIBSASS_WHEEL)
 	rm -f $(PACKAGE_DIR)/libsass*.whl
 	curl --fail -L https://pkg.garrickadenbuie.com/libsass-python/$(LIBSASS_WHEEL) -o $(PACKAGE_DIR)/$(LIBSASS_WHEEL)

shinylive_lock.json

@@ -97,18 +97,17 @@
   },
   "plotnine": {
     "name": "plotnine",
-    "version": "0.10.1.post98+g64295e1a",
-    "filename": "plotnine-0.0.0-py3-none-any.whl",
-    "sha256": null,
-    "url": null,
+    "version": "0.14.5",
+    "filename": "plotnine-0.14.5-py3-none-any.whl",
+    "sha256": "4a8bc4360732dd69a0263def4abab285ed8f0f4386186f1e44c642f2cea79b88",
+    "url": "https://files.pythonhosted.org/packages/4d/c5/7cfda7ba9fa02243367fbfb4880b6de8039266f22c47c2dbbd39b6adc46f/plotnine-0.14.5-py3-none-any.whl",
     "depends": [
-      {"name": "matplotlib", "specs": [[">=", "3.5.0"]]},
-      {"name": "mizani", "specs": [[">=", "0.8.1"]]},
-      {"name": "numpy", "specs": [[">=", "1.23.0"]]},
-      {"name": "pandas", "specs": [[">=", "1.3.5"]]},
-      {"name": "patsy", "specs": [[">=", "0.5.1"]]},
-      {"name": "scipy", "specs": [[">=", "1.5.0"]]},
-      {"name": "statsmodels", "specs": [[">=", "0.13.2"]]}
+      {"name": "matplotlib", "specs": [[">=", "3.8.0"]]},
+      {"name": "pandas", "specs": [[">=", "2.2.0"]]},
+      {"name": "mizani", "specs": [["~=", "0.13.0"]]},
+      {"name": "numpy", "specs": [[">=", "1.23.5"]]},
+      {"name": "scipy", "specs": [[">=", "1.8.0"]]},
+      {"name": "statsmodels", "specs": [[">=", "0.14.0"]]}
     ],
     "imports": [
       "plotnine"
@@ -325,14 +324,14 @@
   },
   "mizani": {
     "name": "mizani",
-    "version": "0.11.4",
-    "filename": "mizani-0.11.4-py3-none-any.whl",
-    "sha256": "5b6271dc3da2c88694dca2e0e0a7e1879f0e2fb046c789776f54d090a5243735",
-    "url": "https://files.pythonhosted.org/packages/2a/11/f3777ad46c5d92e3ead121c22ea45fafb6c3b2c1edca0c0c6494969c125c/mizani-0.11.4-py3-none-any.whl",
+    "version": "0.13.1",
+    "filename": "mizani-0.13.1-py3-none-any.whl",
+    "sha256": "7da0dcacd43fbcc01c279ea06a76f1f064ae90dbb387c4a985ba24a92d3c7d7a",
+    "url": "https://files.pythonhosted.org/packages/29/85/16e17e75831ec01808c5f07e578f1552df87a4f5c827caa8be28f97b4c19/mizani-0.13.1-py3-none-any.whl",
     "depends": [
-      {"name": "numpy", "specs": [[">=", "1.23.0"]]},
-      {"name": "scipy", "specs": [[">=", "1.7.0"]]},
-      {"name": "pandas", "specs": [[">=", "2.1.0"]]},
+      {"name": "numpy", "specs": [[">=", "1.23.5"]]},
+      {"name": "scipy", "specs": [[">=", "1.8.0"]]},
+      {"name": "pandas", "specs": [[">=", "2.2.0"]]},
       {"name": "tzdata", "specs": []}
     ],
     "imports": [

shinylive_requirements.json

@@ -10,12 +10,7 @@
     "version": "latest",
     "comment": "Needed to suppress warning from shiny/ui/_markdown.py."
   },
-  {
-    "name": "plotnine",
-    "source": "local",
-    "version": "latest",
-    "comment": "Fixed version needed to avoid problem with mizani calling zoneinfo.ZoneInfo('UTC')."
-  },
+  { "name": "plotnine", "source": "pypi", "version": "latest" },
   { "name": "plotly", "source": "pypi", "version": "latest" },
   { "name": "seaborn", "source": "pypi", "version": "latest" },
   { "name": "ipywidgets", "source": "pypi", "version": "latest" },

src/pyodide/ffi.d.ts

@@ -1086,8 +1086,11 @@ declare class PythonError extends Error {
 	constructor(type: string, message: string, error_address: number);
 }
 /**
- * See :ref:`js-api-pyodide-ffi`
+ * Foreign function interface classes. Can be used for typescript type
+ * annotations or at runtime for `instanceof` checks.
+ * @summaryLink :ref:`ffi <js-api-pyodide-ffi>`
  * @hidetype
+ * @omitFromAutoModule
  */
 declare const ffi: {
 	PyProxy: typeof PyProxy;

src/pyodide/pyodide.d.ts

@@ -37,6 +37,75 @@ declare function setStderr(options?: {
 }): void;
 /** @deprecated Use `import type { TypedArray } from "pyodide/ffi"` instead */
 export type TypedArray = Int8Array | Uint8Array | Int16Array | Uint16Array | Int32Array | Uint32Array | Uint8ClampedArray | Float32Array | Float64Array;
+type FSNode = {
+	timestamp: number;
+	rdev: number;
+	contents: Uint8Array;
+	mode: number;
+};
+type FSStream = {
+	tty?: boolean;
+	seekable?: boolean;
+	stream_ops: FSStreamOps;
+	node: FSNode;
+};
+type FSStreamOps = FSStreamOpsGen<FSStream>;
+type FSStreamOpsGen<T> = {
+	open: (a: T) => void;
+	close: (a: T) => void;
+	fsync: (a: T) => void;
+	read: (a: T, b: Uint8Array, offset: number, length: number, pos: number) => number;
+	write: (a: T, b: Uint8Array, offset: number, length: number, pos: number) => number;
+};
+interface FS {
+	unlink: (path: string) => void;
+	mkdirTree: (path: string, mode?: number) => void;
+	chdir: (path: string) => void;
+	symlink: (target: string, src: string) => FSNode;
+	createDevice: ((parent: string, name: string, input?: (() => number | null) | null, output?: ((code: number) => void) | null) => FSNode) & {
+		major: number;
+	};
+	closeStream: (fd: number) => void;
+	open: (path: string, flags: string | number, mode?: number) => FSStream;
+	makedev: (major: number, minor: number) => number;
+	mkdev: (path: string, dev: number) => FSNode;
+	filesystems: any;
+	stat: (path: string, dontFollow?: boolean) => any;
+	readdir: (path: string) => string[];
+	isDir: (mode: number) => boolean;
+	isMountpoint: (mode: FSNode) => boolean;
+	lookupPath: (path: string, options?: {
+		follow_mount?: boolean;
+	}) => {
+		node: FSNode;
+	};
+	isFile: (mode: number) => boolean;
+	writeFile: (path: string, contents: any, o?: {
+		canOwn?: boolean;
+	}) => void;
+	chmod: (path: string, mode: number) => void;
+	utime: (path: string, atime: number, mtime: number) => void;
+	rmdir: (path: string) => void;
+	mount: (type: any, opts: any, mountpoint: string) => any;
+	write: (stream: FSStream, buffer: any, offset: number, length: number, position?: number) => number;
+	close: (stream: FSStream) => void;
+	ErrnoError: {
+		new (errno: number): Error;
+	};
+	registerDevice<T>(dev: number, ops: FSStreamOpsGen<T>): void;
+	syncfs(dir: boolean, oncomplete: (val: void) => void): void;
+	findObject(a: string, dontResolveLastLink?: boolean): any;
+	readFile(a: string): Uint8Array;
+}
+type PackageType = "package" | "cpython_module" | "shared_library" | "static_library";
+interface PackageData {
+	name: string;
+	version: string;
+	fileName: string;
+	/** @experimental */
+	packageType: PackageType;
+}
+type LoadedPackages = Record<string, string>;
 /** @deprecated Use `import type { PyProxy } from "pyodide/ffi"` instead */
 interface PyProxy {
 	[x: string]: any;
@@ -977,19 +1046,6 @@ declare class PyBufferView {
 	 */
 	release(): void;
 }
-type PackageType = "package" | "cpython_module" | "shared_library" | "static_library";
-interface PackageData {
-	name: string;
-	version: string;
-	fileName: string;
-	/** @experimental */
-	packageType: PackageType;
-}
-declare function loadPackage(names: string | PyProxy | Array<string>, options?: {
-	messageCallback?: (message: string) => void;
-	errorCallback?: (message: string) => void;
-	checkIntegrity?: boolean;
-}): Promise<Array<PackageData>>;
 declare class PythonError extends Error {
 	/**
 	 * The address of the error we are wrapping. We may later compare this
@@ -1013,11 +1069,13 @@ declare class PyodideAPI {
 	/** @hidden */
 	static version: string;
 	/** @hidden */
-	static loadPackage: typeof loadPackage;
+	static loadPackage: (names: string | PyProxy | Array<string>, options?: {
+		messageCallback?: (message: string) => void;
+		errorCallback?: (message: string) => void;
+		checkIntegrity?: boolean;
+	}) => Promise<Array<PackageData>>;
 	/** @hidden */
-	static loadedPackages: {
-		[key: string]: string;
-	};
+	static loadedPackages: LoadedPackages;
 	/** @hidden */
 	static ffi: {
 		PyProxy: typeof PyProxy;
@@ -1069,7 +1127,7 @@ declare class PyodideAPI {
 	 * are available as members of ``FS.filesystems``:
 	 * ``IDBFS``, ``NODEFS``, ``PROXYFS``, ``WORKERFS``.
 	 */
-	static FS: any;
+	static FS: FS;
 	/**
 	 * An alias to the `Emscripten Path API
 	 * <https://github.com/emscripten-core/emscripten/blob/main/src/library_path.js>`_.
@@ -1079,8 +1137,9 @@ declare class PyodideAPI {
 	 */
 	static PATH: any;
 	/**
-	 * See :ref:`js-api-pyodide-canvas`.
-	 * @hidetype
+	 * APIs to set a canvas for rendering graphics.
+	 * @summaryLink :ref:`canvas <js-api-pyodide-canvas>`
+	 * @omitFromAutoModule
 	 */
 	static canvas: CanvasInterface;
 	/**
@@ -1119,7 +1178,6 @@ declare class PyodideAPI {
 	 *    (optional)
 	 * @param options.checkIntegrity If true, check the integrity of the downloaded
 	 *    packages (default: true)
-	 * @async
 	 */
 	static loadPackagesFromImports(code: string, options?: {
 		messageCallback?: (message: string) => void;
@@ -1203,7 +1261,6 @@ declare class PyodideAPI {
 	 *        traceback for any exception that is thrown will show source lines
 	 *        (unless the given file name starts with ``<`` and ends with ``>``).
 	 * @returns The result of the Python code translated to JavaScript.
-	 * @async
 	 */
 	static runPythonAsync(code: string, options?: {
 		globals?: PyProxy;
@@ -1385,7 +1442,14 @@ declare class PyodideAPI {
 	 * @returns The old value of the debug flag.
 	 */
 	static setDebug(debug: boolean): boolean;
-	static makeMemorySnapshot(): Uint8Array;
+	/**
+	 *
+	 * @param param0
+	 * @returns
+	 */
+	static makeMemorySnapshot({ serializer, }?: {
+		serializer?: (obj: any) => any;
+	}): Uint8Array;
 }
 /** @hidden */
 export type PyodideInterface = typeof PyodideAPI;
@@ -1412,13 +1476,12 @@ type ConfigType = {
 	_makeSnapshot: boolean;
 	enableRunUntilComplete: boolean;
 	checkAPIVersion: boolean;
+	BUILD_ID: string;
 };
 /**
  * Load the main Pyodide wasm module and initialize it.
  *
  * @returns The :ref:`js-api-pyodide` module.
- * @memberof globalThis
- * @async
  * @example
  * async function main() {
  *   const pyodide = await loadPyodide({
@@ -1547,14 +1610,12 @@ export declare function loadPyodide(options?: {
 	 * @ignore
 	 */
 	_node_mounts?: string[];
-	/**
-	 * @ignore
-	 */
+	/** @ignore */
 	_makeSnapshot?: boolean;
-	/**
-	 * @ignore
-	 */
+	/** @ignore */
 	_loadSnapshot?: Uint8Array | ArrayBuffer | PromiseLike<Uint8Array | ArrayBuffer>;
+	/** @ignore */
+	_snapshotDeserializer?: (obj: any) => any;
 }): Promise<PyodideInterface>;
 
 export type {};