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Merge pull request #199 from posit-dev/upgrade-pyodide
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Upgrade Pyodide to 0.27.2
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@wch
wch authored Jan 28, 2025
2 parents 17d3bc6 + d3f9fc6 commit 77938f9
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Showing 8 changed files with 119 additions and 85 deletions.
3 changes: 0 additions & 3 deletions .gitmodules
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Expand Up @@ -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
24 changes: 2 additions & 22 deletions Makefile
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Expand Up @@ -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-$(PYODIDE_VERSION).tar.bz2
DOWNLOAD_DIR = ./downloads
R_SHINY_VERSION = 1.9.1.8002
Expand All @@ -41,10 +41,6 @@ SHINY_WHEEL = shiny-$(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.
Expand Down Expand Up @@ -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
Expand Down Expand Up @@ -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)

Expand Down Expand Up @@ -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
Expand Down Expand Up @@ -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)
Expand All @@ -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
Expand All @@ -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)
Expand Down
1 change: 0 additions & 1 deletion packages/plotnine
Submodule plotnine deleted from 64295e
35 changes: 17 additions & 18 deletions shinylive_lock.json
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Expand Up @@ -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"
Expand Down Expand Up @@ -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": [
Expand Down
7 changes: 1 addition & 6 deletions shinylive_requirements.json
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Expand Up @@ -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" },
Expand Down
5 changes: 4 additions & 1 deletion src/pyodide/ffi.d.ts
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Expand Up @@ -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;
Expand Down
123 changes: 92 additions & 31 deletions src/pyodide/pyodide.d.ts
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Expand Up @@ -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;
Expand Down Expand Up @@ -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
Expand All @@ -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;
Expand Down Expand Up @@ -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>`_.
Expand All @@ -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;
/**
Expand Down Expand Up @@ -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;
Expand Down Expand Up @@ -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;
Expand Down Expand Up @@ -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;
Expand All @@ -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({
Expand Down Expand Up @@ -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 {};
Expand Down
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