Merge pull request #1 from ideaconsult/pydantic2

Pydantic2 migration & multidimensional matrices for nexus

.pre-commit-config.yaml

@@ -0,0 +1,40 @@
+---
+repos:
+  - repo: https://github.com/python-poetry/poetry
+    rev: 1.8.3
+    hooks:
+      - id: poetry-check
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.6.0
+    hooks:
+      - id: check-docstring-first
+      - id: check-json
+      - id: check-merge-conflict
+      - id: debug-statements
+      - id: detect-private-key
+      - id: end-of-file-fixer
+      - id: name-tests-test
+      - id: pretty-format-json
+        args: [--autofix, --no-ensure-ascii]
+      - id: trailing-whitespace
+  - repo: https://github.com/facebook/usort
+    rev: v1.0.8
+    hooks:
+      - id: usort
+  - repo: https://github.com/psf/black-pre-commit-mirror
+    rev: 24.8.0
+    hooks:
+      - id: black
+        args: [--preview]
+  - repo: https://github.com/pycqa/flake8
+    rev: 7.1.1
+    hooks:
+      - id: flake8
+        args: [--exit-zero]
+        verbose: true
+        additional_dependencies:
+          - flake8-bugbear == 24.4.26
+  - repo: https://github.com/adrienverge/yamllint
+    rev: v1.35.1
+    hooks:
+      - id: yamllint

examples/demo.ipynb

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+{
+  "cells": [
+    {
+      "cell_type": "code",
+      "execution_count": null,
+      "metadata": {},
+      "outputs": [],
+      "source": [
+        "import requests\n",
+        "from pyambit.datamodel import Substances, Study \n",
+        "import nexusformat.nexus.tree as nx\n",
+        "import os.path\n",
+        "import tempfile\n",
+        "# to_nexus is not added without this import\n",
+        "from pyambit import nexus_writer\n",
+        "import json"
+      ]
+    },
+    {
+      "cell_type": "code",
+      "execution_count": null,
+      "metadata": {},
+      "outputs": [],
+      "source": [
+        "def query(url = \"https://apps.ideaconsult.net/gracious/substance/\" ,params = {\"max\" : 1}):\n",
+        "    substances = None\n",
+        "    headers = {'Accept': 'application/json'}\n",
+        "    result = requests.get(url,params=params,headers=headers)\n",
+        "    if result.status_code==200:\n",
+        "        response =  result.json()\n",
+        "        substances = Substances.model_construct(**response)\n",
+        "        for substance in substances.substance:\n",
+        "            url_study = \"{}/study\".format(substance.URI)\n",
+        "            study = requests.get(url_study,headers=headers)\n",
+        "            if study.status_code==200:\n",
+        "                response_study = study.json()\n",
+        "                substance.study = Study.model_construct(**response_study).study\n",
+        "\n",
+        "    return substances\n",
+        "\n",
+        "def write_studies_nexus(substances):\n",
+        "    for substance in substances.substance:\n",
+        "        for study in substance.study:\n",
+        "            file = os.path.join(tempfile.gettempdir(), \"study_{}.nxs\".format(study.uuid))\n",
+        "            nxroot = nx.NXroot()\n",
+        "            try:\n",
+        "                study.to_nexus(nxroot)\n",
+        "                nxroot.save(file, mode=\"w\")\n",
+        "            except Exception as err:\n",
+        "                #print(\"error\",file,str(err))\n",
+        "                print(file)"
+      ]
+    },
+    {
+      "cell_type": "code",
+      "execution_count": null,
+      "metadata": {},
+      "outputs": [],
+      "source": [
+        "\n",
+        "try:\n",
+        "    substances = query(params = {\"max\" : 10})   \n",
+        "    _json = substances.model_dump(exclude_none=True)\n",
+        "    new_substances = Substances.model_construct(**_json)\n",
+        "    #test roundtrip\n",
+        "    assert substances == new_substances\n",
+        "\n",
+        "    file = os.path.join(tempfile.gettempdir(), \"remote.json\")\n",
+        "    print(file)\n",
+        "    with open(file, 'w', encoding='utf-8') as file:\n",
+        "        file.write(substances.model_dump_json(exclude_none=True))\n",
+        "    write_studies_nexus(substances)\n",
+        "except Exception as x:\n",
+        "    print(x)"
+      ]
+    },
+    {
+      "cell_type": "code",
+      "execution_count": null,
+      "metadata": {},
+      "outputs": [],
+      "source": []
+    }
+  ],
+  "metadata": {
+    "kernelspec": {
+      "display_name": ".venv",
+      "language": "python",
+      "name": "python3"
+    },
+    "language_info": {
+      "name": "python",
+      "version": "3.12.5"
+    }
+  },
+  "nbformat": 4,
+  "nbformat_minor": 2
+}

examples/test.py

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+import pyambit
+
+print("test")