[create-pull-request] automated change

build/lib/optimade_client/__init__.py

@@ -0,0 +1,20 @@
+"""
+OPTIMADE Client
+
+Voilà/Jupyter client for searching through OPTIMADE databases.
+"""
+from .informational import OptimadeClientFAQ, HeaderDescription, OptimadeLog
+from .query_provider import OptimadeQueryProviderWidget
+from .query_filter import OptimadeQueryFilterWidget
+from .summary import OptimadeSummaryWidget
+
+
+__version__ = "2022.9.19"
+__all__ = (
+    "HeaderDescription",
+    "OptimadeClientFAQ",
+    "OptimadeLog",
+    "OptimadeQueryProviderWidget",
+    "OptimadeQueryFilterWidget",
+    "OptimadeSummaryWidget",
+)

build/lib/optimade_client/cli/run.py

@@ -0,0 +1,105 @@
+import argparse
+import logging
+import os
+from pathlib import Path
+import subprocess
+import sys
+
+try:
+    from voila.app import main as voila
+except ImportError:
+    voila = None
+
+
+LOGGING_LEVELS = [logging.getLevelName(level).lower() for level in range(0, 51, 10)]
+VERSION = "2022.9.19"  # Avoid importing optimade-client package
+
+
+def main(args: list = None):
+    """Run the OPTIMADE Client."""
+    parser = argparse.ArgumentParser(
+        description=main.__doc__,
+        formatter_class=argparse.ArgumentDefaultsHelpFormatter,
+    )
+    parser.add_argument(
+        "--version",
+        action="version",
+        help="Show the version and exit.",
+        version=f"OPTIMADE Client version {VERSION}",
+    )
+    parser.add_argument(
+        "--log-level",
+        type=str,
+        help="Set the log-level of the server.",
+        choices=LOGGING_LEVELS,
+        default="info",
+    )
+    parser.add_argument(
+        "--debug",
+        action="store_true",
+        help="Will overrule log-level option and set the log-level to 'debug'.",
+    )
+    parser.add_argument(
+        "--open-browser",
+        action="store_true",
+        help="Attempt to open a browser upon starting the Voilà tornado server.",
+    )
+    parser.add_argument(
+        "--template",
+        type=str,
+        help="Use another template than the default.",
+    )
+    parser.add_argument(
+        "--dev",
+        action="store_true",
+        help="Use development servers where applicable.",
+    )
+
+    args = parser.parse_args(args)
+    log_level = args.log_level
+    debug = args.debug
+    open_browser = args.open_browser
+    template = args.template
+    dev = args.dev
+
+    # Make sure Voilà is installed
+    if voila is None:
+        sys.exit(
+            "Voilà is not installed.\nPlease run:\n\n     pip install optimade-client[server]\n\n"
+            "Or the equivalent, matching the installation in your environment, to install Voilà "
+            "(and ASE for a larger download format selection)."
+        )
+
+    notebook = str(
+        Path(__file__).parent.joinpath("static/OPTIMADE-Client.ipynb").resolve()
+    )
+    config_path = str(Path(__file__).parent.joinpath("static").resolve())
+
+    # "Trust" notebook
+    subprocess.run(["jupyter", "trust", notebook], check=False)
+
+    argv = [notebook]
+
+    argv.append(f"--Voila.config_file_paths={config_path}")
+
+    if debug:
+        if log_level not in ("debug", "info"):
+            print("[OPTIMADE-Client] Overwriting requested log-level to: 'debug'")
+        os.environ["OPTIMADE_CLIENT_DEBUG"] = "True"
+        argv.append("--debug")
+        argv.append("--show_tracebacks=True")
+    else:
+        os.environ.pop("OPTIMADE_CLIENT_DEBUG", None)
+
+    os.environ["OPTIMADE_CLIENT_DEVELOPMENT_MODE"] = "1" if dev else "0"
+
+    if not open_browser:
+        argv.append("--no-browser")
+
+    if "--debug" not in argv:
+        argv.append(f"--Voila.log_level={getattr(logging, log_level.upper())}")
+
+    if template:
+        argv.append(f"--template={template}")
+
+    voila(argv)

build/lib/optimade_client/cli/static/OPTIMADE-Client.ipynb

@@ -0,0 +1,131 @@
+{
+ "cells": [
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "source": [
+    "# import os\n",
+    "\n",
+    "# This line will include DEBUG level log messages from the start of the app,\n",
+    "# as well as include a \"Local server\" as provider (at http://localhost:5000/optimade/v<MAJOR>),\n",
+    "# where <MAJOR> is the major version number of the currently supported OPTIMADE spec version.\n",
+    "#os.environ[\"OPTIMADE_CLIENT_DEBUG\"] = \"True\""
+   ],
+   "outputs": [],
+   "metadata": {}
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "source": [
+    "from optimade_client import (\n",
+    "    HeaderDescription,\n",
+    "    OptimadeClientFAQ,\n",
+    "    OptimadeLog,\n",
+    "    OptimadeQueryProviderWidget,\n",
+    "    OptimadeQueryFilterWidget,\n",
+    "    OptimadeSummaryWidget,\n",
+    ")\n",
+    "from ipywidgets import dlink, HTML\n",
+    "from IPython.display import display\n",
+    "\n",
+    "# NOTE: Temporarily disable providers NOT properly satisfying the OPTIMADE specification\n",
+    "# Follow issue #206: https://github.com/CasperWA/voila-optimade-client/issues/206\n",
+    "# For omdb: Follow issue #246: https://github.com/CasperWA/voila-optimade-client/issues/246\n",
+    "disable_providers = [\n",
+    "    \"cod\",\n",
+    "    \"tcod\",\n",
+    "    \"nmd\",\n",
+    "    \"oqmd\",\n",
+    "    \"aflow\",\n",
+    "    \"matcloud\",\n",
+    "    \"mpds\",\n",
+    "    \"necro\",\n",
+    "    \"jarvis\",\n",
+    "]\n",
+    "# Curate and group Materials Cloud databases\n",
+    "skip_databases = {\"Materials Cloud\": [\"li-ion-conductors\"]}\n",
+    "database_grouping = {\n",
+    "    \"Materials Cloud\": {\n",
+    "        \"General\": [\"curated-cofs\"],\n",
+    "        \"Projects\": [\n",
+    "            \"2dstructures\",\n",
+    "            \"2dtopo\",\n",
+    "            \"pyrene-mofs\",\n",
+    "            \"scdm\",\n",
+    "            \"sssp\",\n",
+    "            \"stoceriaitf\",\n",
+    "            \"tc-applicability\",\n",
+    "            \"threedd\",\n",
+    "        ]}\n",
+    "}\n",
+    "\n",
+    "selector = OptimadeQueryProviderWidget(\n",
+    "    disable_providers=disable_providers,\n",
+    "    skip_providers=[\"exmpl\", \"optimade\", \"aiida\"],\n",
+    "    skip_databases=skip_databases,\n",
+    "    provider_database_groupings=database_grouping,\n",
+    ")\n",
+    "filters = OptimadeQueryFilterWidget()\n",
+    "summary = OptimadeSummaryWidget(direction=\"horizontal\")\n",
+    "\n",
+    "_ = dlink((selector, 'database'), (filters, 'database'))\n",
+    "_ = dlink((filters, 'structure'), (summary, 'entity'))\n",
+    "\n",
+    "HeaderDescription()"
+   ],
+   "outputs": [],
+   "metadata": {}
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "source": [
+    "OptimadeClientFAQ()"
+   ],
+   "outputs": [],
+   "metadata": {}
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "source": [
+    "OptimadeLog()"
+   ],
+   "outputs": [],
+   "metadata": {}
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "source": [
+    "display(HTML('<h2 style=\"margin-below:0px;padding-below:0px;\">Query a provider\\'s database</h2>'))\n",
+    "\n",
+    "display(selector, filters, summary)"
+   ],
+   "outputs": [],
+   "metadata": {}
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 3",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.7.5"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 4
+}

build/lib/optimade_client/cli/static/voila.json

@@ -0,0 +1,12 @@
+{
+    "VoilaConfiguration": {
+        "enable_nbextensions": true
+    },
+    "VoilaExecutePreprocessor": {
+        "timeout": 180
+    },
+    "MappingKernelManager": {
+      "cull_idle_timeout": 900,
+      "cull_interval": 60
+    }
+}

build/lib/optimade_client/default_parameters.py

@@ -0,0 +1,51 @@
+"""Default initialization parameters
+
+The lists are set, based on the status of providers from
+https://www.optimade.org/providers-dashboard/.
+
+If the provider has no available databases, it should be put into the SKIP_PROVIDERS list,
+meaning it will not be supported.
+Providers in the DISABLE_PROVIDERS list are ones the client should support,
+but cannot because of one issue or another.
+"""
+
+SKIP_PROVIDERS = [
+    "exmpl",
+    "optimade",
+    "aiida",
+    "ccpnc",
+    "matcloud",
+    "necro",
+    "httk",
+    "pcod",
+]
+
+DISABLE_PROVIDERS = [
+    "cod",
+    "tcod",
+    "nmd",
+    "oqmd",
+    "aflow",
+    "mpds",
+    "jarvis",
+]
+
+PROVIDER_DATABASE_GROUPINGS = {
+    "Materials Cloud": {
+        "Main Projects": ["mc3d", "mc2d"],
+        "Contributed Projects": [
+            "2dtopo",
+            "pyrene-mofs",
+            "scdm",
+            "stoceriaitf",
+            "tc-applicability",
+            "tin-antimony-sulfoiodide",
+            "curated-cofs",
+        ],
+    }
+}
+
+
+SKIP_DATABASE = {
+    "Materials Cloud": ["optimade-sample", "li-ion-conductors", "sssp"],
+}