@ai-ecoverse/slicc-bios 1.17.11 → 1.18.1

package/README.md

@@ -172,19 +172,19 @@ The Files panel lists `/opt/grammars/node_modules` but doesn't scan it.
 
 #### Optional packages
 
-Below the system rows, Install / Update offers **Optional packages** (spectrum ≥ 1.42.0): tools that seven doesn't preinstall, each at the version the homescoop coordinator certified. The catalog is [`src/packages/optional/`](src/packages/optional/): `package.json` pins each package exactly, `package-lock.json` (made with `npm install --package-lock-only --ignore-scripts`, never installed) holds its integrity, and `catalog.json` gives its id, label, description, commands, tarball size and `requires`. A test keeps the three in step. Today it offers git, the GitHub CLI, OpenSSH, `slicc` (see [Sevens this kernel follows](#network)), Python, Node.js (slicc-jsh's `node` and `jsh`), `sliccy:browser` for `.jsh` scripts, Ruby, Perl, Biome, the PDF tools (poppler), qpdf, rsync, screen, SQLite, dig, websocat, GnuPG and fnox.
+Below the system rows, Install / Update offers **Optional packages** (spectrum ≥ 1.42.0): tools that seven doesn't preinstall, each at the version the homescoop coordinator certified. The catalog is [`src/packages/optional/`](src/packages/optional/): `package.json` pins each package exactly, `package-lock.json` (made with `npm install --package-lock-only --ignore-scripts`, never installed) holds its integrity, and `catalog.json` gives its id, label, description, commands, tarball size and `requires`. A test keeps the three in step. Today it offers git, the GitHub CLI, OpenSSH, `slicc` (see [Sevens this kernel follows](#network)), Python, the Python data tools (numpy, pandas and matplotlib), Node.js (slicc-jsh's `node` and `jsh`), `sliccy:browser` for `.jsh` scripts, Ruby, Perl, Biome, the PDF tools (poppler), qpdf, rsync, screen, SQLite, dig, websocat, GnuPG and fnox.
 
-- **Install** runs `pnpm add -g <package>@<version>` in the page's kernel, as a user would, under the Web Lock `slicc-optional`, so the commands work at once in every open shell. pnpm 12 gives each global add its own project under `$PNPM_HOME/global/v11/`; bios reads `PNPM_HOME` from the kernel's environment. Afterwards `os/packages.js` reads that project's `pnpm-lock.yaml`: every package in it, the one added and each dependency, must be a version in the catalog's lockfile or the base set's, with that integrity. homescoop pins `@ai-ecoverse/*` dependencies exactly (uv → Python, git → bash), so the catalog's lockfile names them all. Anything else, a dependency pnpm resolved to another version included, removes the package again and fails the row with *This version doesn't match the tested build*. An entry's `requires` (uv needs Python) are installed first.
+- **Install** runs `pnpm add -g <package>@<version>` in the page's kernel, as a user would, under the Web Lock `slicc-optional`, so the commands work at once in every open shell. pnpm 12 gives each global add its own project under `$PNPM_HOME/global/v11/`; bios reads `PNPM_HOME` from the kernel's environment. Afterwards `os/packages.js` reads that project's `pnpm-lock.yaml`: every package in it, the one added and each dependency, must be a version in the catalog's lockfile or the base set's, with that integrity. homescoop pins `@ai-ecoverse/*` dependencies exactly (uv → Python, git → bash), so the catalog's lockfile names them all. Anything else, a dependency pnpm resolved to another version included, removes the package again and fails the row with *This version doesn't match the tested build*. An entry's `requires` (uv needs Python) are installed first. A project entry also **updates** a required package that's older than the catalog's before it installs, since it runs on the catalog's version: the data tools override their own Python away, and their builds need the catalog's Python. A global add brings its own pinned dependencies, so it leaves an older required package as it is.
 - **State** comes from pnpm's global projects, not from a list of bios's own, so a package installed by hand shows as installed with its version. One older than the catalog's offers **Update**, which adds the catalog's version; one at or above it offers **Remove**. bios never downgrades.
 - **Remove** runs `pnpm remove -g <package>`. It asks first only when another installed entry needs it (*Remove Node.js (jsh)? Browser for jsh scripts needs it and stops working until Node.js (jsh) is back.*, accent); otherwise it doesn't ask, since pnpm's global projects hold no user data and the package can be installed again. A cancelled confirm changes nothing.
 - **Readable by everyone:** after every pnpm install of `/opt/agent`, `/opt/grammars` and an optional project in `/opt/slicc`, bios makes that tree readable by everyone, as root: one `find` selects the files without `a+r`, the executables without `a+x` and the directories without `a+x`, and runs `chmod a+rX` on only those, so a tree of 15,000 entries with one `0600` file pays for one walk and one `chmod`, not 15,000. pnpm writes some files `0600`, such as `node_modules/.pnpm-workspace-state-v1.json`, and with kernel users every user must be able to read seven's installed packages. An install from before this runs the same pass once at its next check, marked by `var/lib/slicc/<project>/readable`.
 - **Failures** lead with one sentence and keep pnpm's output, starting with the package and version, under *Install log*, with **Retry**.
 - **Withdrawn and kept as exceptions** (homescoop#858/#859, #864): uv, esbuild, tsc and buf are withdrawn until attested rebuilds. They're retired rows (*No longer offered*, with Remove for an earlier install), and their certs lines are gone. Instead, use `pip` for uv's work for now (uv returns as `@ai-ecoverse/wasi-uv`, Astral's uv, once that's certified), and install esbuild and typescript straight from npm with `pnpm add -g`; buf has no stand-in. **git** and **gh** stay as recorded supply-chain exceptions until their attested rebuilds: their `certs.json` entries carry an `exception` field, which `pins.test.mjs` lists, and any other uncertified pin still fails it.
-- **Python data tools are withdrawn** until numpy and pandas come from verified CI builds (homescoop#826, #730): py-numpy 2.3.2-4 to -10 and py-pandas 2.3.2-5 to -11 came from un-attested local builds, so their certs lines are gone and the catalog has no `pydata` row or project. `retired.json` lists it as a retired `kind: "project"` entry, so an earlier install shows as installed with only **Remove**, which deletes the project, its `.pth` and its receipt. Plain Python stays. The project support below is unchanged for when it returns.
-- **Project entries** (`kind: "project"`): **Python data tools** (numpy, pandas, scipy and matplotlib, about 270 MB on disk) can't be a global add. pnpm 12 gives each global add its own isolated project, so every py-* package would carry its own Python (about 1 GB in total), and Python wouldn't find the packages. So the entry is a pnpm project of its own in `src/packages/optional/projects/pydata/`:
+- **Python data tools are back** as homescoop's attested CI builds (A3, A4): py-numpy 2.3.2-12, py-pandas 2.3.2-12 and py-matplotlib 3.11.2-10, with contourpy, kiwisolver, pillow and their pure dependencies, on the catalog's Python 3.14.2-28. They replace the withdrawn builds (homescoop#826, #730): no py-numpy 2.3.2-4 to -10 or py-pandas 2.3.2-5 to -11 is certified, and an install from before the withdrawal (version 2026.10.12) shows as outdated, with **Update**. numpy 2.3.2-12 has homescoop#1082's fix: `numpy.linalg` raises `LinAlgError` on a singular matrix instead of returning NaN. **scipy is not back yet:** its build isn't attested, so the project leaves it out and `certs.json` has no scipy line.
+- **Project entries** (`kind: "project"`): **Python data tools** (numpy, pandas and matplotlib, about 160 MB on disk) can't be a global add. pnpm 12 gives each global add its own isolated project, so every py-* package would carry its own Python (about 1 GB in total), and Python wouldn't find the packages. So the entry is a pnpm project of its own in [`src/packages/optional/projects/pydata/`](src/packages/optional/projects/pydata/), which locks one numpy and no Python of its own:
   - **Install:** bios writes the project to `/opt/slicc/pydata` and installs it with `pnpm install --frozen-lockfile`, so pnpm checks every integrity against the lockfile bios ships. Its `pnpm-workspace.yaml` overrides `@ai-ecoverse/wasix-python` to nothing, and the entry `requires` the catalog's Python, which runs it.
   - **How Python finds it:** bios writes `/opt/slicc/python/slicc-pydata.pth`, which lists each package's site-packages (from its `slicc.python.sitePackages`), next to a `sitecustomize.py` that adds that folder as a site directory. The page's kernel puts `/opt/slicc/python` on every process's `PYTHONPATH`, so `python3` imports the packages from any shell or agent, as any user. Python's own discovery only looks in its own project, so the `.pth` stays. A `.pth` that an earlier version wrote to `/root/.local` is moved there the next time the optional packages are listed. The kernel's environment reaches every process, whichever client or user starts it, `sudo` included. `python -I` and `python -E` ignore `PYTHONPATH`, so they don't see the data tools; that's a known gap.
-  - **State and Remove:** a receipt in `var/lib/slicc/optional/pydata/` records the installed version. **Remove** deletes the project, the `.pth` and the receipt.
+  - **State and Remove:** a receipt in `var/lib/slicc/optional/pydata/` records the installed version. **Remove** deletes the project, the `.pth` and the receipt. A project that `retired.json` lists still shows while it's installed, with only **Remove**.
   - **Without Python:** if Python is removed while the data tools stay installed, the row warns that it needs Python (`warnings`, spectrum ≥ 1.49.1).
 - **Login shells:** bios writes `/etc/profile.d/slicc.sh` at every boot, which puts `~/.local/share/gem/ruby/3.4.0/bin` on `PATH`, so a command from `gem install` runs by name in a login shell. It also makes sure `/etc/profile` runs `/etc/profile.d/*.sh`: it writes one if there's none, and adds that loop once, after the lines already there, to an `/etc/profile` that doesn't mention `/etc/profile.d/`.
 - **The agent** reads the same catalog: bios writes it to `/etc/slicc/optional.json` at every boot (id, package, version, label, description, commands, requires).

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@ai-ecoverse/slicc-bios",
-  "version": "1.17.11",
+  "version": "1.18.1",
   "description": "Slim loader that boots SLICC into OPFS and serves the UI from there",
   "type": "module",
   "license": "Apache-2.0",

package/src/packages/certs.json

@@ -7,6 +7,18 @@
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+    "sha256": "ffbbb748115e6ec0385ebd83e3d9867e3cf9b5062786b4e265f0b9f71a85eb3a"
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@@ -15,6 +27,26 @@
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@@ -23,22 +55,46 @@
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package/src/packages/optional/catalog.json

@@ -32,7 +32,16 @@
     "label": "Python",
     "description": "Python 3.14 with pip (pip, pip3 or python3 -m pip), for scripts and data work.",
     "commands": ["python3", "pip", "pip3"],
-    "size": 49598727
+    "size": 57417828
+  },
+  "slicc-py-datatools": {
+    "id": "pydata",
+    "kind": "project",
+    "label": "Python data tools",
+    "description": "numpy, pandas and matplotlib for Python, about 160 MB on disk.",
+    "commands": [],
+    "requires": ["python"],
+    "size": 46014414
   },
   "@ai-ecoverse/slicc-jsh": {
     "id": "node",

package/src/packages/optional/package-lock.json

@@ -16,7 +16,7 @@
         "@ai-ecoverse/wasix-gnupg": "2.4.9-11",
         "@ai-ecoverse/wasix-openssh": "10.6.0-6",
         "@ai-ecoverse/wasix-perl": "5.42.0-11",
-        "@ai-ecoverse/wasix-python": "3.14.2-20",
+        "@ai-ecoverse/wasix-python": "3.14.2-28",
         "@ai-ecoverse/wasix-ruby": "3.4.11-12",
         "@ai-ecoverse/wasix-websocat": "4.0.0-alpha3-3",
         "@ai-ecoverse/wasm-git": "2.55.0-15",
@@ -132,12 +132,12 @@
       }
     },
     "node_modules/@ai-ecoverse/wasix-python": {
-      "version": "3.14.2-20",
-      "resolved": "https://registry.npmjs.org/@ai-ecoverse/wasix-python/-/wasix-python-3.14.2-20.tgz",
-      "integrity": "sha512-Mbf9IERBIMo9aySMQ4dNNcWSjxK0+Oz14S0KJNIv+UvfYc5gFOGFIWwJSeik8Wo+BWhuKWk5LIEM3CvOeQ0oSw==",
+      "version": "3.14.2-28",
+      "resolved": "https://registry.npmjs.org/@ai-ecoverse/wasix-python/-/wasix-python-3.14.2-28.tgz",
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       "license": "PSF-2.0 AND GPL-3.0-or-later",
       "engines": {
-        "slicc-kernel": ">=1.51.0"
+        "slicc-kernel": ">=1.120.0"
       }
     },
     "node_modules/@ai-ecoverse/wasix-ruby": {

package/src/packages/optional/package.json

@@ -13,7 +13,7 @@
     "@ai-ecoverse/wasix-gnupg": "2.4.9-11",
     "@ai-ecoverse/wasix-openssh": "10.6.0-6",
     "@ai-ecoverse/wasix-perl": "5.42.0-11",
-    "@ai-ecoverse/wasix-python": "3.14.2-20",
+    "@ai-ecoverse/wasix-python": "3.14.2-28",
     "@ai-ecoverse/wasix-ruby": "3.4.11-12",
     "@ai-ecoverse/wasix-websocat": "4.0.0-alpha3-3",
     "@ai-ecoverse/wasm-git": "2.55.0-15",