docs: draft widget-tutorials meta.json process and dummy 8x8 test (#3)

- docs: draft widget-tutorials meta.json process and dummy 8x8 test (46a78773368957d3d3ff08d1d7f9b5cb0db83910)
- docs: teach Hugging Face Write token setup for Community PRs (7b9bb147046b39661de5d5f191ee2eb859846ce8)
- refactor: run checker as python -m check_meta (183c2248c7f5d1df90d6eaa34d738d6d513507c1)
- docs: add coding-agent Community PR steps (383faf3845c136258fba42f09531a55af0bb27f8)
- remove dummy 8x8 process-test folder (966dd006cb35ea83bd4973695f41310bf6e3b6c1)

README.md

@@ -10,59 +10,207 @@ pretty_name: quantem-data
 
 # quantem-data
 
-Reference electron-microscopy datasets (gold 4D-STEM and HAADF) for browsing
-and learning with [quantem.widget](https://github.com/bobleesj/quantem.widget).
-This repo just hosts the data — all instructions live in one place:
+**This page is in draft mode. We are still exploring the upload process
+and the `meta.json` template.** Keys, the checker, and these instructions
+will change as we try real pull requests. Use the current required keys
+for new PRs, and expect the template to grow.
 
-**How to download and use this data:** follow the
-[Download data tutorial](https://bobleesj.github.io/quantem.widget/tutorials/download_data.html)
-in the quantem.widget docs. One call per dataset:
+**This repo is currently used primarily by
+[quantem.widget**](https://github.com/electronmicroscopy/quantem.widget)
+(tutorial notebooks and `quantem.widget.datasets`). Other QuantEM packages
+may use it later.
+
+Public electron-microscopy data. MIT license. Downloads need no token.
+This page is the upload and download protocol.
+
+## Download
 
 ```python
-from quantem.widget import Show4DSTEM
 from quantem.widget.datasets import show4dstem_gold
 
-Show4DSTEM(show4dstem_gold())
+ds = show4dstem_gold(size="small")
+```
+
+Notebook: [Example Data](https://github.com/electronmicroscopy/quantem.widget/blob/main/docs/tutorials/download_data.ipynb).
+
+## Add data (Hugging Face pull request)
+
+Anyone with a Hugging Face account can add data. We follow a pull request
+process. Do not use `quantem.widget.io.upload`.
+
+Downloads need no token. Opening a pull request does. Create an account,
+then a token at
+[huggingface.co/settings/tokens](https://huggingface.co/settings/tokens).
+Use a **Write** token (classic). A **Read** token can download; it cannot
+open a PR. A fine-grained token also works if `--create-pr` is allowed on
+a public dataset. You do not need collaborator access to this repo.
+
+```bash
+pip install huggingface_hub   # skip if `hf` is already on PATH
+hf auth login
 ```
 
-Layout — two trees:
+Paste the token. The prompt hides it. When asked `Add token as git
+credential? [y/N]`, answer `n`. `hf upload` reads
+`~/.cache/huggingface/token`. You do not need a git credential helper.
+Ignore any hint to run `git config --global credential.helper store`.
 
-- **`widget-tutorials/<widget>/<dataset>/<size>/`** — baseline tutorial
-  bundles for the core widgets (`show1d/`, `show4dstem/`, `showfolder/`;
-  data shared by Show2D and Show3D lives under `shared/`). These back the
-  one-call loaders in `quantem.widget.datasets` and the Colab workshops.
-  Baseline tutorials only — real work uses your own data.
-- **`4dstem/`, `haadf/`** — full-size originals (Arina h5, Velox EMD) for
-  power users.
+```bash
+hf auth whoami
+```
 
-Every NumPy bundle ships a `meta.json` (shape, dtype, sampling, units,
-optics) next to `data.npy`.
+That should print your username. If you already logged in with a Read
+token, run `hf auth login --force` and paste a Write token. If
+`--create-pr` returns 403 after a valid login, the token is Read or the
+fine-grained scopes omit Community PRs; make a Write token and login
+again. On SSH (no browser on that machine), paste a token. Do not use the
+browser login unless the browser and `hf` run on the same machine. Do not
+commit the token.
 
-Workshop notebooks (Google Colab, no local install):
-[Show4DSTEM demo](https://colab.research.google.com/gist/bobleesj/54864ce5b2a6f0a4fd5ae1e5d5719b45/show4dstem_colab.ipynb)
-·
-[Workshop v1](https://colab.research.google.com/gist/bobleesj/a05a90185c6cddbb331342cae6d7e9c1/berk_workshop_v1.ipynb)
+A PR is the data file(s) plus one `meta.json`. Example already on the hub
+(2 files):
+
+```text
+widget-tutorials/show4dstem/gold-512-bin4/full/data.npy
+widget-tutorials/show4dstem/gold-512-bin4/full/meta.json
+```
+
+One EMD: `gold_haadf.emd` + `meta.json` (2 files). A session folder: the
+`.emd` files + `meta.json`.
+
+Copy this `meta.json`. Required: `name`, `source`, `date`, `sample`,
+`shape`, `dtype`, `permission`. Optional: `sampling`, `units`, optics.
+Omit a key if unknown. Do not invent a number.
+
+`shape` is `[row, col]` for an image, `[frame, row, col]` for a stack, or
+`[scan_row, scan_col, det_row, det_col]` for 4D-STEM. `dtype` is the NumPy
+name of the stored array (or of the EMD image). Examples already on this
+repo:
+
+
+| Data                      | `shape`              | `dtype`  |
+| ------------------------- | -------------------- | -------- |
+| 2D HAADF (`gold-haadf`)   | `[4096, 4096]`       | `uint16` |
+| 4D-STEM (`gold-512-bin4`) | `[512, 512, 48, 48]` | `uint16` |
+| One EMD HAADF             | `[4096, 4096]`       | `uint16` |
+
+
+Processed float data uses `"float32"`. Read both values from the file
+(`arr.shape`, `arr.dtype`, or the EMD image) and copy them into
+`meta.json`.
+
+```json
+{
+  "name": "gold_512_npy_bin4",
+  "source": "Arina 4D-STEM, Nano Titan, session 20260423, gold_004_master.h5",
+  "date": "2026-04-23",
+  "sample": "gold nanoparticles",
+  "shape": [512, 512, 48, 48],
+  "dtype": "uint16",
+  "permission": {
+    "received": true,
+    "from": ["Sangjoon Lee"],
+    "collectors": ["Sangjoon Lee"],
+    "date": "2026-04-23"
+  },
+  "sampling": [0.5, 0.5, 1.84, 1.84],
+  "units": ["A", "A", "mrad", "mrad"],
+  "voltage_kV": 300,
+  "semiangle_mrad": 30,
+  "camera_length_mm": 91
+}
+```
+
+`source` is microscope, facility, and original file. `date` is acquisition
+day (`YYYY-MM-DD`). `permission.received` must be `true`. `from` is who granted the share (one name or several). `collectors` is who
+used the instrument (one name or several). `permission.date` is when that
+share was granted.
+
+```bash
+python -m check_meta ./gold-512-bin4
+hf upload bobleesj/quantem-data ./gold-512-bin4 \
+  widget-tutorials/show4dstem/gold-512-bin4/full \
+  --repo-type dataset --create-pr
+```
+
+Run `python -m check_meta` from a checkout of this dataset so the
+`check_meta/` package is importable. `./gold-512-bin4` is your local
+folder (`data.npy` + `meta.json`). The last `hf upload` path is the
+folder on this repo. The hub path is
+`widget-tutorials/<widget>/<name>/<size>/`. For a new ShowBragg set that
+would be `widget-tutorials/showbragg/<name>/full`. Size is `small`,
+`medium`, `large`, or `full`. Use `widget-tutorials/shared/` only when
+more than one widget will read the same files.
+
+`python -m check_meta` must print `ok` or do not open the PR. Resume a stopped
+upload with `--revision refs/pr/N` (do not pass `--create-pr` again).
+Merge is on the
+[Community tab](https://huggingface.co/datasets/bobleesj/quantem-data/discussions).
+
+### Coding agents
+
+A coding agent can open the Community pull request. The human creates the
+Write token and attests permission. The agent does not invent
+`permission.*`, `sampling`, or optics. The agent does not run
+`hf auth login` (that prompt is interactive). The agent does not write the
+token into a repository file.
+
+```bash
+# human already ran `hf auth login` or exported HF_TOKEN (Write)
+hf auth whoami
+hf download bobleesj/quantem-data --repo-type dataset \
+  --include "check_meta/**" --include "templates/meta.json" \
+  --local-dir ./quantem-data-tools
+export PYTHONPATH="$PWD/quantem-data-tools${PYTHONPATH:+:$PYTHONPATH}"
+python -m check_meta ./gold-512-bin4
+hf upload bobleesj/quantem-data ./gold-512-bin4 \
+  widget-tutorials/show4dstem/gold-512-bin4/full \
+  --repo-type dataset --create-pr \
+  --commit-message "add show4dstem gold-512-bin4 full tutorial data"
+```
+
+`hf auth whoami` must print a username. If it fails or `--create-pr`
+returns 403, stop and ask the human for a Write token (`export HF_TOKEN=...`).
+If `python -m check_meta` is not `ok`, stop. After the upload, give the
+human the Community URL. Do not merge.
+
+Copyable widget prompt:
+[Add tutorial data](https://github.com/electronmicroscopy/quantem.widget/blob/main/docs/agent-prompts.md#add-tutorial-data-hugging-face-pull-request).
+
+If a notebook should call `quantem.widget.datasets`, open a GitHub PR after
+this one merges:
+[Contribute tutorial data](https://github.com/electronmicroscopy/quantem.widget/blob/main/docs/tutorials/contribute_data.md).
+
+Colab: [Show4DSTEM](https://colab.research.google.com/gist/bobleesj/54864ce5b2a6f0a4fd5ae1e5d5719b45/show4dstem_colab.ipynb)
+· [Workshop v1](https://colab.research.google.com/gist/bobleesj/a05a90185c6cddbb331342cae6d7e9c1/berk_workshop_v1.ipynb)
 
 ## Acquisition parameters
 
-The 20260423 drift session's optics are **confirmed via the session's own
-HAADF EMD** (`AccelerationVoltage`, `BeamConvergence`, `CameraLength`).
-4D-STEM `scan_sampling` is an **operator pattern from a sibling SSB session**
-— the drift acquisition itself was never per-file calibrated.
+The 20260423 drift session optics are confirmed via the session HAADF EMD.
+4D-STEM `scan_sampling` is an operator pattern from a sibling SSB session.
+
+
+| dataset                          | voltage  | probe     | CL      | scan        | scan sampling  | det pitch    | mag         |
+| -------------------------------- | -------- | --------- | ------- | ----------- | -------------- | ------------ | ----------- |
+| `haadf/gold_haadf_npy`           | 300 kV ✓ | 30 mrad ✓ | 91 mm ✓ | 4096² image | 0.0186 nm/px   | n/a          | FOV 76.2 nm |
+| `4dstem/gold_512_npy_bin8`       | 300 kV ✓ | 30 mrad ✓ | 91 mm ✓ | 512²        | 0.5 Å (op)     | 3.68 mrad/px | unknown     |
+| `4dstem/gold_512_npy_bin4`       | 300 kV ✓ | 30 mrad ✓ | 91 mm ✓ | 512²        | 0.5 Å (op)     | 1.84 mrad/px | unknown     |
+| `4dstem/gold_512`                | 300 kV ✓ | 30 mrad ✓ | 91 mm ✓ | 512²        | 0.5 Å (op)     | 0.46 mrad/px | unknown     |
+| `4dstem/gold_30mrad1.3mx04`…`09` | 300 kV   | 30 mrad   | 91 mm   | smaller     | (session yaml) | 0.46 mrad/px | 1.3 Mx      |
+| `haadf/gold_haadf.emd`           | 300 kV ✓ | 30 mrad ✓ | 91 mm ✓ | 4096² image | 0.0186 nm/px   | n/a          | FOV 76.2 nm |
 
-| dataset | voltage | probe | CL | scan | scan sampling | det pitch | mag |
-|---|---|---|---|---|---|---|---|
-| `haadf/gold_haadf_npy` | 300 kV ✓ | 30 mrad ✓ | 91 mm ✓ | 4096² image | 0.0186 nm/px | n/a | FOV 76.2 nm |
-| `4dstem/gold_512_npy_bin8` | 300 kV ✓ | 30 mrad ✓ | 91 mm ✓ | 512² | 0.5 Å (op) | 3.68 mrad/px | unknown |
-| `4dstem/gold_512_npy_bin4` | 300 kV ✓ | 30 mrad ✓ | 91 mm ✓ | 512² | 0.5 Å (op) | 1.84 mrad/px | unknown |
-| `4dstem/gold_512` | 300 kV ✓ | 30 mrad ✓ | 91 mm ✓ | 512² | 0.5 Å (op) | 0.46 mrad/px | unknown |
-| `4dstem/gold_30mrad1.3mx04`…`09` | 300 kV | 30 mrad | 91 mm | smaller | (session yaml) | 0.46 mrad/px | 1.3 Mx |
-| `haadf/gold_haadf.emd` | 300 kV ✓ | 30 mrad ✓ | 91 mm ✓ | 4096² image | 0.0186 nm/px | n/a | FOV 76.2 nm |
 
 ✓ = confirmed via EMD/yaml. `(op)` = operator pattern, not file-certified.
 
 ## License
 
-MIT — free to use for anything. Citing
-[quantem.widget](https://github.com/bobleesj/quantem.widget) in publications
-is appreciated.
+Files on this repo are published under **MIT**.
+
+**You must have explicit written permission from the person who collected
+the data before you open a pull request**, unless you collected the data
+yourself. Put that receipt in `meta.json` (`permission.received`,
+`permission.from`, `permission.collectors`, `permission.date`). If you
+collected it yourself, set `from` and `collectors` to your name.
+
+Do not open a pull request without that permission. `python -m check_meta`
+must print `ok`.

check_meta/__init__.py

@@ -0,0 +1,97 @@
+"""Refuse a folder whose meta.json is missing required keys.
+
+Required: name, source, date, sample, shape, dtype, permission
+  (permission.received, permission.from, permission.collectors,
+  permission.date). from and collectors are one or more names.
+Optional: sampling, units, and optics keys.
+"""
+
+from __future__ import annotations
+
+import json
+import re
+from pathlib import Path
+
+REQUIRED = ("name", "source", "date", "sample", "shape", "dtype", "permission")
+PERMISSION_REQUIRED = ("received", "from", "collectors", "date")
+DATE_RE = re.compile(r"^\d{4}-\d{2}-\d{2}$")
+
+
+def _name_list(value: object) -> list[str] | None:
+    """Accept one name or a list of names. Empty is missing."""
+
+    if isinstance(value, str) and value.strip():
+        return [value.strip()]
+    if isinstance(value, list) and value and all(isinstance(item, str) and item.strip() for item in value):
+        return [item.strip() for item in value]
+    return None
+
+
+def check_meta(folder: Path) -> list[str]:
+    """Return a list of problems. Empty means the sidecar is complete."""
+
+    problems: list[str] = []
+    path = folder / "meta.json"
+    if not path.is_file():
+        return [f"missing {path}"]
+    try:
+        meta = json.loads(path.read_text(encoding="utf-8"))
+    except json.JSONDecodeError as exc:
+        return [f"{path} is not JSON: {exc}"]
+    if not isinstance(meta, dict):
+        return [f"{path} must be a JSON object"]
+    for key in REQUIRED:
+        value = meta.get(key)
+        if value in (None, "", []):
+            problems.append(f"missing {key}")
+    if "name" in meta and not isinstance(meta.get("name"), str):
+        problems.append("name must be a string")
+    if "source" in meta and not isinstance(meta.get("source"), str):
+        problems.append("source must be a string")
+    if "sample" in meta and not isinstance(meta.get("sample"), str):
+        problems.append("sample must be a string")
+    permission = meta.get("permission")
+    if permission not in (None, "", []):
+        if not isinstance(permission, dict):
+            problems.append("permission must be an object")
+        else:
+            for key in PERMISSION_REQUIRED:
+                value = permission.get(key)
+                if value in (None, "", []):
+                    problems.append(f"missing permission.{key}")
+            if permission.get("received") is not True:
+                problems.append("permission.received must be true")
+            if permission.get("from") not in (None, "", []) and _name_list(permission.get("from")) is None:
+                problems.append("permission.from must be one name or a list of names")
+            if permission.get("collectors") not in (None, "", []) and _name_list(permission.get("collectors")) is None:
+                problems.append("permission.collectors must be one name or a list of names")
+            perm_date = permission.get("date")
+            if perm_date not in (None, "") and not (isinstance(perm_date, str) and DATE_RE.match(perm_date)):
+                problems.append("permission.date must be YYYY-MM-DD")
+    date = meta.get("date")
+    if date not in (None, "", []) and not (isinstance(date, str) and DATE_RE.match(date)):
+        problems.append("date must be YYYY-MM-DD")
+    shape = meta.get("shape")
+    if shape not in (None, "", []):
+        if not (
+            isinstance(shape, list)
+            and len(shape) >= 2
+            and all(isinstance(n, int) and not isinstance(n, bool) for n in shape)
+        ):
+            problems.append("shape must be a list of ints, length >= 2")
+    dtype = meta.get("dtype")
+    if dtype not in (None, "", []) and not isinstance(dtype, str):
+        problems.append("dtype must be a string")
+    sampling = meta.get("sampling")
+    if sampling not in (None, "", []):
+        if not (isinstance(sampling, list) and all(isinstance(n, (int, float)) and not isinstance(n, bool) for n in sampling)):
+            problems.append("sampling must be a list of numbers")
+        if isinstance(shape, list) and isinstance(sampling, list) and len(sampling) != len(shape):
+            problems.append("sampling length must match shape length")
+    units = meta.get("units")
+    if units not in (None, "", []):
+        if not (isinstance(units, list) and all(isinstance(u, str) for u in units)):
+            problems.append("units must be a list of strings")
+        if isinstance(shape, list) and isinstance(units, list) and len(units) != len(shape):
+            problems.append("units length must match shape length")
+    return problems

check_meta/__main__.py

@@ -0,0 +1,31 @@
+"""CLI: python -m check_meta /path/to/folder"""
+
+from __future__ import annotations
+
+import argparse
+import sys
+from pathlib import Path
+
+from check_meta import REQUIRED, check_meta
+
+
+def main(argv: list[str] | None = None) -> int:
+    parser = argparse.ArgumentParser(prog="python -m check_meta")
+    parser.add_argument("folder", type=Path, help="folder that contains meta.json")
+    args = parser.parse_args(argv)
+    folder: Path = args.folder
+    if not folder.is_dir():
+        print(f"not a folder: {folder}", file=sys.stderr)
+        return 2
+    problems = check_meta(folder)
+    if problems:
+        print(f"{folder / 'meta.json'}:")
+        for item in problems:
+            print(f"  {item}")
+        return 1
+    print(f"{folder / 'meta.json'}: ok ({', '.join(REQUIRED)})")
+    return 0
+
+
+if __name__ == "__main__":
+    raise SystemExit(main())

templates/meta.json

@@ -0,0 +1,19 @@
+{
+  "name": "gold_512_npy_bin4",
+  "source": "Arina 4D-STEM, Nano Titan, session 20260423, gold_004_master.h5",
+  "date": "2026-04-23",
+  "sample": "gold nanoparticles",
+  "shape": [512, 512, 48, 48],
+  "dtype": "uint16",
+  "permission": {
+    "received": true,
+    "from": ["Sangjoon Lee"],
+    "collectors": ["Sangjoon Lee"],
+    "date": "2026-04-23"
+  },
+  "sampling": [0.5, 0.5, 1.84, 1.84],
+  "units": ["A", "A", "mrad", "mrad"],
+  "voltage_kV": 300,
+  "semiangle_mrad": 30,
+  "camera_length_mm": 91
+}