@gen3/workspaces 0.12.63 → 0.12.65

package/scripts/patch-pyidode-lock.py

@@ -0,0 +1,100 @@
+#!/usr/bin/env python3
+"""
+Localize CDN wheels referenced by a JupyterLite pyodide-lock.json.
+
+Replaces the inline heredoc in build-jupyterlite.sh. Two fixes over the
+original:
+
+  1. Writes ``file_name`` (the only field Pyodide reads) instead of ``url``,
+     which is not part of the pyodide-lock schema and is silently ignored.
+  2. Writes a bare filename. ``file_name`` is resolved relative to the
+     directory holding pyodide-lock.json, which is where we download to,
+     so no "../../static/..." prefix is needed.
+
+Fails loudly if any CDN reference survives, so a no-op patch can never be
+reported as success.
+
+Usage:
+    LOCK_FILE=... LOCK_OUT=... python3 patch-pyodide-lock.py
+"""
+
+import json
+import os
+import sys
+import urllib.request
+
+CDN_HOSTS = ("cdn.jsdelivr.net", "pypi.org", "files.pythonhosted.org")
+
+lock_file = os.environ["LOCK_FILE"]
+lock_out = os.environ["LOCK_OUT"]
+
+with open(lock_file) as fh:
+    lock = json.load(fh)
+
+packages = lock.get("packages", {})
+localized = 0
+failed = []
+
+for name, meta in packages.items():
+    ref = meta.get("file_name", "")
+    if not any(host in ref for host in CDN_HOSTS):
+        continue
+
+    fname = ref.split("/")[-1].split("?")[0]
+    dest = os.path.join(lock_out, fname)
+
+    if not os.path.exists(dest):
+        try:
+            urllib.request.urlretrieve(ref, dest)
+            print(f"  downloaded {fname}", flush=True)
+        except Exception as exc:
+            failed.append((name, fname, exc))
+            print(f"  WARN: {fname}: {exc}", file=sys.stderr, flush=True)
+            continue
+
+    # The only field Pyodide reads. sha256 is unchanged because it is the
+    # same artifact, so integrity checks still pass.
+    meta["file_name"] = fname
+    meta.pop("url", None)  # drop the stale no-op key if a prior run added it
+    localized += 1
+
+with open(lock_file, "w") as fh:
+    json.dump(lock, fh)
+
+# ---- verification: no CDN reference may survive -----------------------------
+with open(lock_file) as fh:
+    reloaded = json.load(fh)
+
+survivors = [
+    (n, m.get("file_name", ""))
+    for n, m in reloaded.get("packages", {}).items()
+    if any(host in m.get("file_name", "") for host in CDN_HOSTS)
+]
+
+print(f"Lock patched: {localized} localized, {len(failed)} download failures")
+
+if survivors:
+    print(
+        f"ERROR: {len(survivors)} package(s) still point at a remote host; "
+        "the browser will fetch these at import time and may hang:",
+        file=sys.stderr,
+    )
+    for n, ref in survivors[:20]:
+        print(f"  {n}: {ref}", file=sys.stderr)
+    sys.exit(1)
+
+# Every localized reference must actually exist on disk next to the lock.
+missing = [
+    (n, m["file_name"])
+    for n, m in reloaded.get("packages", {}).items()
+    if m.get("file_name")
+    and "/" not in m["file_name"]
+    and not os.path.exists(os.path.join(lock_out, m["file_name"]))
+]
+if missing:
+    print(f"ERROR: {len(missing)} lock entries reference missing files:", file=sys.stderr)
+    for n, f in missing[:20]:
+        print(f"  {n}: {f}", file=sys.stderr)
+    sys.exit(1)
+
+print("Verified: all package references are local and present.")

package/scripts/setup-env.sh

@@ -0,0 +1,81 @@
+#!/usr/bin/env bash
+# =============================================================================
+# setup-env.sh — Shared build-environment bootstrap
+#
+# Guarantees both build-gen3sdk-lite and build-jupyterlite use the same
+# Python interpreter and virtual environment.
+#
+# BUILD_DIR resolution (first match wins):
+#   1. Pre-set BUILD_DIR environment variable  (export BUILD_DIR=…)
+#   2. First positional argument               (source setup-env.sh [/tmp/mybuild | ./mybuild])
+#   3. Default: "builds"
+#
+# Usage:
+#   source setup-env.sh [build_dir]
+#
+# After sourcing, the venv at $BUILD_DIR/.venv is activated in the calling
+# shell, and VENV_DIR is exported.
+# =============================================================================
+
+# ── Configuration ────────────────────────────────────────────────────────────
+PYTHON_VERSION="3.14.2"
+
+# Resolves a possibly-relative path against INIT_CWD (or $PWD) rather than
+# whatever directory happens to be current when this runs.
+_resolve_against_init_cwd() {
+  local path="$1"
+  local base="${INIT_CWD:-$(pwd)}"
+  case "$path" in
+    /*) printf '%s' "$path" ;;
+    *)  printf '%s/%s' "$base" "$path" ;;
+  esac
+}
+
+BUILD_DIR="${BUILD_DIR:-$(_resolve_against_init_cwd "${1:-builds}")}"
+
+mkdir -p "$BUILD_DIR"
+BUILD_DIR="$(cd "$BUILD_DIR" && pwd)"
+
+VENV_DIR="$BUILD_DIR/.venv"
+export BUILD_DIR VENV_DIR PYTHON_VERSION
+
+# ── Colours / helpers ────────────────────────────────────────────────────────
+RED='\033[0;31m'
+GREEN='\033[0;32m'
+YELLOW='\033[1;33m'
+CYAN='\033[0;36m'
+NC='\033[0m'
+
+info()    { echo -e "${CYAN}[INFO]${NC}  $*"; }
+success() { echo -e "${GREEN}[OK]${NC}    $*"; }
+warn()    { echo -e "${YELLOW}[WARN]${NC}  $*"; }
+fail()    { echo -e "${RED}[FAIL]${NC}  $*"; return 1 2>/dev/null || exit 1; }
+
+# Export helpers so functions in the calling script can use them.
+export -f info success warn fail
+
+# ── uv ───────────────────────────────────────────────────────────────────────
+if ! command -v uv &>/dev/null; then
+  fail "uv is not installed. Install it first: https://docs.astral.sh/uv/getting-started/installation/"
+fi
+success "uv found: $(uv --version)"
+
+# ── Python (via uv) ─────────────────────────────────────────────────────────
+info "Ensuring Python ${PYTHON_VERSION} is available via uv …"
+uv python install "${PYTHON_VERSION}" 2>&1 | tail -1
+success "Python ${PYTHON_VERSION} ready"
+
+# ── Virtual environment (create once, reuse everywhere) ──────────────────────
+if [[ ! -d "${VENV_DIR}" ]]; then
+  info "Creating virtual environment at ${VENV_DIR} …"
+  uv venv --python "${PYTHON_VERSION}" "${VENV_DIR}"
+fi
+
+# shellcheck disable=SC1091
+source "${VENV_DIR}/bin/activate"
+success "Activated venv ($(python --version))"
+
+# ── Core Python tooling (idempotent — uv skips already-installed) ────────────
+info "Ensuring core Python build tooling …"
+uv pip install --upgrade pip build 2>&1 | tail -3
+success "Core tooling ready"

package/scripts/sync-jupyter-assets-into-package.sh

@@ -1,12 +1,23 @@
 #!/usr/bin/env bash
 set -euo pipefail
 
-
-BUILD_SRC="${1:-}"
+_resolve_against_init_cwd() {
+  local path="$1"
+  local base="${INIT_CWD:-$(pwd)}"
+  case "$path" in
+    /*) printf '%s' "$path" ;;
+    *)  printf '%s/%s' "$base" "$path" ;;
+  esac
+}
+
+BUILD_SRC="$(_resolve_against_init_cwd "${1:-builds}")"
 if [[ -z "$BUILD_SRC" ]]; then
   usage "set to the output of the juypterlite install"
 fi
 
+
+echo "Build directory is $BUILD_SRC"
+
 PKG_DIR="${2:-jupyter-workspaces}"
 echo "assets directory is: $PKG_DIR"
 
@@ -16,6 +27,7 @@ REMOTE_SRC="$BUILD_SRC/remote"
 FREE_DST="$PKG_DIR/assets/free"
 REMOTE_DST="$PKG_DIR/assets/remote"
 VALIDATE_SCRIPT="$SCRIPT_DIR/scripts/validate-jupyterlite-assets.sh"
+source "${SCRIPT_DIR}/scripts/setup-env.sh"
 
 if [[ ! -d "$FREE_SRC" ]]; then
   echo "Missing free JupyterLite build output: $FREE_SRC"
@@ -29,6 +41,11 @@ if [[ ! -d "$REMOTE_SRC" ]]; then
   exit 1
 fi
 
+echo $VALIDATE_SCRIPT
+echo $FREE_SRC
+echo $REMOTE_SRC
+
+
 bash "$VALIDATE_SCRIPT" --free-dir "$FREE_SRC" --remote-dir "$REMOTE_SRC"
 
 rm -rf "$FREE_DST" "$REMOTE_DST"

package/scripts/validate-jupyterlite-assets.sh

@@ -48,6 +48,9 @@ fi
 FREE_JSON="$FREE_DIR/jupyter-lite.json"
 REMOTE_JSON="$REMOTE_DIR/jupyter-lite.json"
 
+
+echo "Free $FREE_DIR, Remote $REMOTE_DIR"
+
 if [[ ! -f "$FREE_JSON" ]]; then
   echo "Missing free config: $FREE_JSON"
   exit 1

package/dist/jupyterlite-builds/free-private/.cache/pyodide-lock/_work/constraints.txt

@@ -1,354 +0,0 @@
-affine @ https://cdn.jsdelivr.net/pyodide/v314.0.4/full/affine-2.4.0-py3-none-any.whl
-affine-tests @ https://cdn.jsdelivr.net/pyodide/v314.0.4/full/affine-tests.tar
-aiohappyeyeballs @ https://cdn.jsdelivr.net/pyodide/v314.0.4/full/aiohappyeyeballs-2.6.1-py3-none-any.whl
-aiohttp @ https://cdn.jsdelivr.net/pyodide/v314.0.4/full/aiohttp-3.13.5-cp314-cp314-pyemscripten_2026_0_wasm32.whl
-aiohttp-tests @ https://cdn.jsdelivr.net/pyodide/v314.0.4/full/aiohttp-tests.tar
-aiosignal @ https://cdn.jsdelivr.net/pyodide/v314.0.4/full/aiosignal-1.4.0-py3-none-any.whl
-altair @ https://cdn.jsdelivr.net/pyodide/v314.0.4/full/altair-6.0.0-py3-none-any.whl
-annotated-doc @ https://cdn.jsdelivr.net/pyodide/v314.0.4/full/annotated_doc-0.0.4-py3-none-any.whl
-annotated-types @ https://cdn.jsdelivr.net/pyodide/v314.0.4/full/annotated_types-0.7.0-py3-none-any.whl
-annotated-types-tests @ https://cdn.jsdelivr.net/pyodide/v314.0.4/full/annotated-types-tests.tar
-anyio @ https://cdn.jsdelivr.net/pyodide/v314.0.4/full/anyio-4.13.0-py3-none-any.whl
-apsw @ https://cdn.jsdelivr.net/pyodide/v314.0.4/full/apsw-3.51.3.0-cp314-cp314-pyemscripten_2026_0_wasm32.whl
-apsw-tests @ https://cdn.jsdelivr.net/pyodide/v314.0.4/full/apsw-tests.tar
-argon2-cffi @ https://cdn.jsdelivr.net/pyodide/v314.0.4/full/argon2_cffi-23.1.0-py3-none-any.whl
-argon2-cffi-bindings @ https://cdn.jsdelivr.net/pyodide/v314.0.4/full/argon2_cffi_bindings-25.1.0-cp314-abi3-pyemscripten_2026_0_wasm32.whl
-astropy @ https://cdn.jsdelivr.net/pyodide/v314.0.4/full/astropy-7.2.0-cp314-cp314-pyemscripten_2026_0_wasm32.whl
-astropy-iers-data @ https://cdn.jsdelivr.net/pyodide/v314.0.4/full/astropy_iers_data-0.2026.4.1.15.5.49-py3-none-any.whl
-astropy-iers-data-tests @ https://cdn.jsdelivr.net/pyodide/v314.0.4/full/astropy-iers-data-tests.tar
-asttokens @ https://cdn.jsdelivr.net/pyodide/v314.0.4/full/asttokens-3.0.1-py3-none-any.whl
-async-timeout @ https://cdn.jsdelivr.net/pyodide/v314.0.4/full/async_timeout-5.0.1-py3-none-any.whl
-atomicwrites @ https://cdn.jsdelivr.net/pyodide/v314.0.4/full/atomicwrites-1.4.1-py2.py3-none-any.whl
-attrs @ https://cdn.jsdelivr.net/pyodide/v314.0.4/full/attrs-26.1.0-py3-none-any.whl
-audioop-lts @ https://cdn.jsdelivr.net/pyodide/v314.0.4/full/audioop_lts-0.2.2-cp313-abi3-pyemscripten_2026_0_wasm32.whl
-awkward-cpp @ https://cdn.jsdelivr.net/pyodide/v314.0.4/full/awkward_cpp-52-cp314-cp314-pyemscripten_2026_0_wasm32.whl
-b2d @ https://cdn.jsdelivr.net/pyodide/v314.0.4/full/b2d-0.7.4-cp314-cp314-pyemscripten_2026_0_wasm32.whl
-bcrypt @ https://cdn.jsdelivr.net/pyodide/v314.0.4/full/bcrypt-5.0.0-cp314-cp314-pyemscripten_2026_0_wasm32.whl
-beautifulsoup4 @ https://cdn.jsdelivr.net/pyodide/v314.0.4/full/beautifulsoup4-4.14.3-py3-none-any.whl
-bilby-cython @ https://cdn.jsdelivr.net/pyodide/v314.0.4/full/bilby_cython-0.5.4-cp314-cp314-pyemscripten_2026_0_wasm32.whl
-bilby-cython-tests @ https://cdn.jsdelivr.net/pyodide/v314.0.4/full/bilby-cython-tests.tar
-biopython @ https://cdn.jsdelivr.net/pyodide/v314.0.4/full/biopython-1.87-cp314-cp314-pyemscripten_2026_0_wasm32.whl
-bitarray @ https://cdn.jsdelivr.net/pyodide/v314.0.4/full/bitarray-3.8.1-cp314-cp314-pyemscripten_2026_0_wasm32.whl
-bitarray-tests @ https://cdn.jsdelivr.net/pyodide/v314.0.4/full/bitarray-tests.tar
-bitstring @ https://cdn.jsdelivr.net/pyodide/v314.0.4/full/bitstring-4.4.0-py3-none-any.whl
-bleach @ https://cdn.jsdelivr.net/pyodide/v314.0.4/full/bleach-6.3.0-py3-none-any.whl
-bokeh @ https://cdn.jsdelivr.net/pyodide/v314.0.4/full/bokeh-3.9.0-py3-none-any.whl
-boost-histogram @ https://cdn.jsdelivr.net/pyodide/v314.0.4/full/boost_histogram-1.7.1-cp314-cp314-pyemscripten_2026_0_wasm32.whl
-bottleneck @ https://cdn.jsdelivr.net/pyodide/v314.0.4/full/bottleneck-1.6.0-cp314-cp314-pyemscripten_2026_0_wasm32.whl
-brotli @ https://cdn.jsdelivr.net/pyodide/v314.0.4/full/brotli-1.2.0-cp314-cp314-pyemscripten_2026_0_wasm32.whl
-cachetools @ https://cdn.jsdelivr.net/pyodide/v314.0.4/full/cachetools-7.0.5-py3-none-any.whl
-cartopy @ https://cdn.jsdelivr.net/pyodide/v314.0.4/full/cartopy-0.25.0-cp314-cp314-pyemscripten_2026_0_wasm32.whl
-cartopy-tests @ https://cdn.jsdelivr.net/pyodide/v314.0.4/full/cartopy-tests.tar
-casadi @ https://cdn.jsdelivr.net/pyodide/v314.0.4/full/casadi-3.7.2-cp314-cp314-pyemscripten_2026_0_wasm32.whl
-cbor-diag @ https://cdn.jsdelivr.net/pyodide/v314.0.4/full/cbor_diag-1.1.2-cp314-cp314-pyemscripten_2026_0_wasm32.whl
-certifi @ https://cdn.jsdelivr.net/pyodide/v314.0.4/full/certifi-2026.4.22-py3-none-any.whl
-cffi @ https://cdn.jsdelivr.net/pyodide/v314.0.4/full/cffi-2.0.0-cp314-cp314-pyemscripten_2026_0_wasm32.whl
-cffi-example @ https://cdn.jsdelivr.net/pyodide/v314.0.4/full/cffi_example-0.1-cp314-cp314-pyemscripten_2026_0_wasm32.whl
-cftime @ https://cdn.jsdelivr.net/pyodide/v314.0.4/full/cftime-1.6.5-cp314-cp314-pyemscripten_2026_0_wasm32.whl
-charset-normalizer @ https://cdn.jsdelivr.net/pyodide/v314.0.4/full/charset_normalizer-3.4.7-py3-none-any.whl
-clarabel @ https://cdn.jsdelivr.net/pyodide/v314.0.4/full/clarabel-0.11.1-cp39-abi3-pyemscripten_2026_0_wasm32.whl
-click @ https://cdn.jsdelivr.net/pyodide/v314.0.4/full/click-8.3.1-py3-none-any.whl
-cligj @ https://cdn.jsdelivr.net/pyodide/v314.0.4/full/cligj-0.7.2-py3-none-any.whl
-clingo @ https://cdn.jsdelivr.net/pyodide/v314.0.4/full/clingo-5.8.0-cp314-cp314-pyemscripten_2026_0_wasm32.whl
-cloudpickle @ https://cdn.jsdelivr.net/pyodide/v314.0.4/full/cloudpickle-3.1.2-py3-none-any.whl
-cmyt @ https://cdn.jsdelivr.net/pyodide/v314.0.4/full/cmyt-2.0.2-py3-none-any.whl
-cobs @ https://cdn.jsdelivr.net/pyodide/v314.0.4/full/cobs-1.2.2-cp314-cp314-pyemscripten_2026_0_wasm32.whl
-colorspacious @ https://cdn.jsdelivr.net/pyodide/v314.0.4/full/colorspacious-1.1.2-py2.py3-none-any.whl
-contourpy @ https://cdn.jsdelivr.net/pyodide/v314.0.4/full/contourpy-1.3.3-cp314-cp314-pyemscripten_2026_0_wasm32.whl
-coolprop @ https://cdn.jsdelivr.net/pyodide/v314.0.4/full/coolprop-7.2.0-cp314-cp314-pyemscripten_2026_0_wasm32.whl
-coolprop-tests @ https://cdn.jsdelivr.net/pyodide/v314.0.4/full/coolprop-tests.tar
-coverage @ https://cdn.jsdelivr.net/pyodide/v314.0.4/full/coverage-7.13.5-cp314-cp314-pyemscripten_2026_0_wasm32.whl
-crc32c @ https://cdn.jsdelivr.net/pyodide/v314.0.4/full/crc32c-2.8-cp314-cp314-pyemscripten_2026_0_wasm32.whl
-crcmod @ https://cdn.jsdelivr.net/pyodide/v314.0.4/full/crcmod-1.7-cp314-cp314-pyemscripten_2026_0_wasm32.whl
-cryptography @ https://cdn.jsdelivr.net/pyodide/v314.0.4/full/cryptography-47.0.0-cp314-abi3-pyemscripten_2026_0_wasm32.whl
-cssselect @ https://cdn.jsdelivr.net/pyodide/v314.0.4/full/cssselect-1.4.0-py3-none-any.whl
-cvxpy-base @ https://cdn.jsdelivr.net/pyodide/v314.0.4/full/cvxpy_base-1.8.2-py3-none-any.whl
-cvxpy-base-tests @ https://cdn.jsdelivr.net/pyodide/v314.0.4/full/cvxpy-base-tests.tar
-cycler @ https://cdn.jsdelivr.net/pyodide/v314.0.4/full/cycler-0.12.1-py3-none-any.whl
-cysignals @ https://cdn.jsdelivr.net/pyodide/v314.0.4/full/cysignals-1.12.3-cp314-cp314-pyemscripten_2026_0_wasm32.whl
-cytoolz @ https://cdn.jsdelivr.net/pyodide/v314.0.4/full/cytoolz-1.1.0-cp314-cp314-pyemscripten_2026_0_wasm32.whl
-cytoolz-tests @ https://cdn.jsdelivr.net/pyodide/v314.0.4/full/cytoolz-tests.tar
-decorator @ https://cdn.jsdelivr.net/pyodide/v314.0.4/full/decorator-5.2.1-py3-none-any.whl
-demes @ https://cdn.jsdelivr.net/pyodide/v314.0.4/full/demes-0.2.3-py3-none-any.whl
-deprecated @ https://cdn.jsdelivr.net/pyodide/v314.0.4/full/deprecated-1.3.1-py2.py3-none-any.whl
-deprecation @ https://cdn.jsdelivr.net/pyodide/v314.0.4/full/deprecation-2.1.0-py2.py3-none-any.whl
-diskcache @ https://cdn.jsdelivr.net/pyodide/v314.0.4/full/diskcache-5.6.3-py3-none-any.whl
-distlib @ https://cdn.jsdelivr.net/pyodide/v314.0.4/full/distlib-0.4.0-py2.py3-none-any.whl
-distro @ https://cdn.jsdelivr.net/pyodide/v314.0.4/full/distro-1.9.0-py3-none-any.whl
-dnspython @ https://cdn.jsdelivr.net/pyodide/v314.0.4/full/dnspython-2.8.0-py3-none-any.whl
-docutils @ https://cdn.jsdelivr.net/pyodide/v314.0.4/full/docutils-0.22.4-py3-none-any.whl
-donfig @ https://cdn.jsdelivr.net/pyodide/v314.0.4/full/donfig-0.8.1.post1-py3-none-any.whl
-donfig-tests @ https://cdn.jsdelivr.net/pyodide/v314.0.4/full/donfig-tests.tar
-duckdb @ https://cdn.jsdelivr.net/pyodide/v314.0.4/full/duckdb-1.5.1-cp314-cp314-pyemscripten_2026_0_wasm32.whl
-ewah-bool-utils @ https://cdn.jsdelivr.net/pyodide/v314.0.4/full/ewah_bool_utils-1.3.0-cp314-cp314-pyemscripten_2026_0_wasm32.whl
-ewah-bool-utils-tests @ https://cdn.jsdelivr.net/pyodide/v314.0.4/full/ewah-bool-utils-tests.tar
-exceptiongroup @ https://cdn.jsdelivr.net/pyodide/v314.0.4/full/exceptiongroup-1.3.1-py3-none-any.whl
-executing @ https://cdn.jsdelivr.net/pyodide/v314.0.4/full/executing-2.2.1-py2.py3-none-any.whl
-fastapi @ https://cdn.jsdelivr.net/pyodide/v314.0.4/full/fastapi-0.136.1-py3-none-any.whl
-fiona @ https://cdn.jsdelivr.net/pyodide/v314.0.4/full/fiona-1.10.1-cp314-cp314-pyemscripten_2026_0_wasm32.whl
-fonttools @ https://cdn.jsdelivr.net/pyodide/v314.0.4/full/fonttools-4.62.1-py3-none-any.whl
-freesasa @ https://cdn.jsdelivr.net/pyodide/v314.0.4/full/freesasa-2.2.1-cp314-cp314-pyemscripten_2026_0_wasm32.whl
-frozenlist @ https://cdn.jsdelivr.net/pyodide/v314.0.4/full/frozenlist-1.8.0-cp314-cp314-pyemscripten_2026_0_wasm32.whl
-fsspec @ https://cdn.jsdelivr.net/pyodide/v314.0.4/full/fsspec-2026.3.0-py3-none-any.whl
-fsspec-tests @ https://cdn.jsdelivr.net/pyodide/v314.0.4/full/fsspec-tests.tar
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package/dist/jupyterlite-builds/free-private/.cache/pyodide-lock/_work/excludes.txt

@@ -1,3 +0,0 @@
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