optimade-maker 0.7.2__tar.gz → 0.9.0__tar.gz

{optimade_maker-0.7.2 → optimade_maker-0.9.0}/.github/workflows/ci.yml

@@ -63,21 +63,21 @@ jobs:
           version: "0.8.x"
           enable-cache: true
 
-      - name: Install latest compatible versions of immediate dependencies
+      - name: Install the minimum environment with testing
         run: |
-          uv sync --locked --all-extras --dev
+          uv sync --locked --extra dev
 
       - name: Run tests
         run: |
           uv run pytest -vv --cov=./src/optimade_maker --cov-report=xml --cov-report=term ./tests
 
-      - name: Reinstall environment without aiida
+      - name: Reinstall the full environment with all extras
         run: |
-          uv sync --locked --extra core --extra tests
+          uv sync --locked --all-extras --dev
 
-      - name: Rerun tests without aiida
+      - name: Rerun tests
         run: |
-          uv run pytest -vv --cov=./src/optimade_maker --cov-report=xml --cov-report=term ./tests --ignore=./tests/aiida
+          uv run pytest -vv --cov=./src/optimade_maker --cov-report=xml --cov-report=term ./tests
 
       - name: Upload coverage
         uses: codecov/codecov-action@v3

{optimade_maker-0.7.2 → optimade_maker-0.9.0}/.gitignore

@@ -129,3 +129,4 @@ dmypy.json
 .pyre/
 
 .vscode
+.ruff_cache

{optimade_maker-0.7.2 → optimade_maker-0.9.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: optimade-maker
-Version: 0.7.2
+Version: 0.9.0
 Summary: Tools for making OPTIMADE APIs from raw structural data.
 License: MIT
 Keywords: optimade,jsonapi,materials
@@ -15,30 +15,27 @@ Classifier: Topic :: Scientific/Engineering
 Requires-Python: <3.13,>=3.10
 Description-Content-Type: text/markdown
 License-File: LICENSE
-Requires-Dist: pydantic~=2.2
-Requires-Dist: optimade[server]~=1.3.1
-Requires-Dist: pymongo
+Requires-Dist: pydantic<3,>=2
+Requires-Dist: optimade[server]~=1.4
+Requires-Dist: pymongo<5,>=4
 Requires-Dist: pyyaml~=6.0
 Requires-Dist: tqdm~=4.65
 Requires-Dist: requests~=2.31
-Requires-Dist: numpy<3,>=1.22
 Requires-Dist: click~=8.1
-Provides-Extra: ase
-Requires-Dist: ase~=3.22; extra == "ase"
+Requires-Dist: pandas<3,>=1.5
+Requires-Dist: ase~=3.22
 Provides-Extra: pymatgen
 Requires-Dist: pymatgen>=2023.9; extra == "pymatgen"
-Provides-Extra: pandas
-Requires-Dist: pandas<3,>=1.5; extra == "pandas"
 Provides-Extra: aiida
-Requires-Dist: aiida-core>=2.6.3; extra == "aiida"
-Provides-Extra: core
-Requires-Dist: optimade-maker[ase,pandas,pymatgen]; extra == "core"
+Requires-Dist: aiida-core~=2.6; extra == "aiida"
 Provides-Extra: ingest
-Requires-Dist: optimade-maker[aiida,ase,pandas,pymatgen]; extra == "ingest"
+Requires-Dist: optimade-maker[aiida,pymatgen]; extra == "ingest"
 Provides-Extra: tests
 Requires-Dist: pytest~=8.3; extra == "tests"
 Requires-Dist: pytest-cov~=6.0; extra == "tests"
+Requires-Dist: numpy<3,>=1.22; extra == "tests"
 Provides-Extra: dev
+Requires-Dist: optimade-maker[tests]; extra == "dev"
 Requires-Dist: ruff; extra == "dev"
 Requires-Dist: pre-commit; extra == "dev"
 Requires-Dist: mypy; extra == "dev"
@@ -75,6 +72,8 @@ This repository contains the src/optimade-maker Python package and the correspon
 Install with
 
 ```bash
+pip install optimade-maker
+# or to get all ingestion plugins (e.g. pymatgen, aiida):
 pip install optimade-maker[ingest]
 ```
 
@@ -106,8 +105,8 @@ entries:
       - file: properties.csv
     property_definitions:
       - name: energy
-        title: Total energy per atom
-        description: DFT total energy per atom
+        title: Total energy
+        description: DFT total energy
         unit: eV/atom
         type: float
 ```

{optimade_maker-0.7.2 → optimade_maker-0.9.0}/README.md

@@ -29,6 +29,8 @@ This repository contains the src/optimade-maker Python package and the correspon
 Install with
 
 ```bash
+pip install optimade-maker
+# or to get all ingestion plugins (e.g. pymatgen, aiida):
 pip install optimade-maker[ingest]
 ```
 
@@ -60,8 +62,8 @@ entries:
       - file: properties.csv
     property_definitions:
       - name: energy
-        title: Total energy per atom
-        description: DFT total energy per atom
+        title: Total energy
+        description: DFT total energy
         unit: eV/atom
         type: float
 ```

optimade_maker-0.9.0/examples/properties/.testing/first_entry.json

@@ -0,0 +1 @@
+{"id": "set1/101", "type": "structures", "links": null, "meta": null, "attributes": {"immutable_id": "structures.zip/cifs/set1/101.cif", "last_modified": "2026-02-16T13:34:52.085191", "elements": ["Ba", "C", "N", "S"], "nelements": 4, "elements_ratios": [0.14285714285714285, 0.2857142857142857, 0.2857142857142857, 0.2857142857142857], "chemical_formula_descriptive": "C4Ba2N4S4", "chemical_formula_reduced": "BaC2N2S2", "chemical_formula_hill": null, "chemical_formula_anonymous": "A2B2C2D", "dimension_types": [1, 1, 1], "nperiodic_dimensions": 3, "lattice_vectors": [[6.3587627540404945, 0.0, 0.0], [-2.672647488887009, 5.769819681958754, 0.0], [0.25844951934994664, -0.16511343006546234, 8.71190314896161]], "space_group_symmetry_operations_xyz": null, "space_group_symbol_hall": null, "space_group_symbol_hermann_mauguin": null, "space_group_symbol_hermann_mauguin_extended": null, "space_group_it_number": null, "cartesian_site_positions": [[3.4987802863851005, 5.049341739457014, 6.533927361693402], [0.4457844982025419, 0.5553645123824795, 2.177975787264444], [0.37416734784252487, 2.642448780492868, 5.291889331690525], [2.6281157156591126, 1.202488098280357, 7.775965391700042], [3.5703974366609055, 2.962257471400425, 3.420013817271085], [1.316449068841148, 4.402218153614962, 0.9359377571616379], [0.3512600296798777, 4.156339511491648, 5.900755701251229], [4.011419364830723, 1.818004876809729, 7.167099022143105], [3.5933047547393455, 1.4483667404554434, 2.8111474477141454], [-0.06685458032729186, 3.786701375083563, 1.5448041268185058], [0.3773832460379156, 1.5350786992068879, 4.8597303327393915], [1.621957615426957, 0.7399681351855376, 8.208124390751108], [3.567181538468686, 4.069627552684378, 3.8521728163221476], [2.3226071690796486, 4.864738116705728, 0.5037787583104332]], "nsites": 14, "species": [{"name": "N", "chemical_symbols": ["N"], "concentration": [1.0], "mass": null, "original_name": null, "attached": null, "nattached": null}, {"name": "Ba", "chemical_symbols": ["Ba"], "concentration": [1.0], "mass": null, "original_name": null, "attached": null, "nattached": null}, {"name": "C", "chemical_symbols": ["C"], "concentration": [1.0], "mass": null, "original_name": null, "attached": null, "nattached": null}, {"name": "S", "chemical_symbols": ["S"], "concentration": [1.0], "mass": null, "original_name": null, "attached": null, "nattached": null}], "species_at_sites": ["Ba", "Ba", "C", "C", "C", "C", "S", "S", "S", "S", "N", "N", "N", "N"], "assemblies": null, "structure_features": [], "_optimake_json_list": [[1, 2.0, 3]], "_optimake_dict_property": {"a": 1, "b": 2}, "_optimake_list_property": [[1, 2.0, 3], [3, 2, 3], [1, 5, 6]], "_optimake_json_nested_dict": {"a": 1, "b": {"c": 2, "d": [1, 2, 3]}}, "_optimake_json_float": 2.5, "_optimake_energy": 2.5}, "relationships": null}

optimade_maker-0.9.0/examples/properties/optimade.yaml

@@ -0,0 +1,45 @@
+config_version: 0.1.1
+database_description: Simple database
+
+entries:
+  - entry_type: structures
+    entry_paths:
+      - file: structures.zip
+        matches:
+          - cifs/*/*.cif
+    # (optional) property file and definitions:
+    property_paths:
+      - file: prop1.csv
+      - file: prop2.json
+    property_definitions:
+      # properties in the csv file
+      - name: energy
+        title: Total energy per atom
+        description: The total energy per atom as computed by DFT
+        unit: eV/atom
+        type: float
+      - name: list_property
+        title: List property
+        description: A 3x3 matrix property
+        type: list
+      - name: dict_property
+        title: Dictionary property
+        description: A dictionary property
+        type: dictionary
+      # properties in the json file
+      - name: json_float
+        title: JSON float property
+        description: A JSON float property
+        type: float
+        aliases:
+          - json_float_alias1
+          - json_float_alias2
+          - json_float_alias3
+      - name: json_list
+        title: JSON list property
+        description: A JSON list property
+        type: list
+      - name: json_nested_dict
+        title: JSON nested dictionary property
+        description: A nested dictionary property in JSON format
+        type: dictionary

optimade_maker-0.9.0/examples/properties/prop1.csv

@@ -0,0 +1,3 @@
+id,energy,list_property,dict_property
+set1/101,2.5,"[[1, 2.0, 3], [3, 2, 3], [1, 5, 6]]","{""a"": 1, ""b"": 2}"
+structures.zip/cifs/set2/102.cif,3.2,,

optimade_maker-0.9.0/examples/properties/prop2.json

@@ -0,0 +1,18 @@
+{
+  "set1/101": {
+    "json_float_alias2": 2.5,
+    "json_list": [[1, 2.0, 3]],
+    "json_nested_dict": {
+      "a": 1,
+      "b": {
+        "c": 2,
+        "d": [1, 2, 3]
+      }
+    }
+  },
+  "structures.zip/cifs/set2/102.cif": {
+    "json_float_alias3": 3.2,
+    "json_list": null,
+    "json_nested_dict": null
+  }
+}

optimade_maker-0.9.0/examples/simple_zip_of_cif/.gitignore

@@ -0,0 +1,2 @@
+cifs
+optimade.jsonl

{optimade_maker-0.7.2 → optimade_maker-0.9.0}/examples/simple_zip_of_cif/.testing/first_entry.json

@@ -1 +1 @@
-{"id": "set1/101", "type": "structures", "links": null, "meta": null, "attributes": {"immutable_id": "structures.zip/cifs/set1/101.cif", "last_modified": "2025-07-22T13:03:07.681100", "elements": ["Ba", "C", "N", "S"], "nelements": 4, "elements_ratios": [0.14285714285714285, 0.2857142857142857, 0.2857142857142857, 0.2857142857142857], "chemical_formula_descriptive": "C4Ba2N4S4", "chemical_formula_reduced": "BaC2N2S2", "chemical_formula_hill": null, "chemical_formula_anonymous": "A2B2C2D", "dimension_types": [1, 1, 1], "nperiodic_dimensions": 3, "lattice_vectors": [[6.3587627540404945, 0.0, 0.0], [-2.672647488887009, 5.769819681958754, 0.0], [0.25844951934994664, -0.16511343006546234, 8.71190314896161]], "space_group_symmetry_operations_xyz": null, "space_group_symbol_hall": null, "space_group_symbol_hermann_mauguin": null, "space_group_symbol_hermann_mauguin_extended": null, "space_group_it_number": null, "cartesian_site_positions": [[3.4987802863851005, 5.049341739457014, 6.533927361693402], [0.4457844982025419, 0.5553645123824795, 2.177975787264444], [0.37416734784252487, 2.642448780492868, 5.291889331690525], [2.6281157156591126, 1.202488098280357, 7.775965391700042], [3.5703974366609055, 2.962257471400425, 3.420013817271085], [1.316449068841148, 4.402218153614962, 0.9359377571616379], [0.3512600296798777, 4.156339511491648, 5.900755701251229], [4.011419364830723, 1.818004876809729, 7.167099022143105], [3.5933047547393455, 1.4483667404554434, 2.8111474477141454], [-0.06685458032729186, 3.786701375083563, 1.5448041268185058], [0.3773832460379155, 1.5350786992068879, 4.8597303327393915], [1.621957615426957, 0.7399681351855376, 8.208124390751108], [3.567181538468686, 4.069627552684378, 3.8521728163221476], [2.3226071690796477, 4.864738116705728, 0.5037787583104332]], "nsites": 14, "species": [{"name": "Ba", "chemical_symbols": ["Ba"], "concentration": [1.0], "mass": null, "original_name": null, "attached": null, "nattached": null}, {"name": "C", "chemical_symbols": ["C"], "concentration": [1.0], "mass": null, "original_name": null, "attached": null, "nattached": null}, {"name": "N", "chemical_symbols": ["N"], "concentration": [1.0], "mass": null, "original_name": null, "attached": null, "nattached": null}, {"name": "S", "chemical_symbols": ["S"], "concentration": [1.0], "mass": null, "original_name": null, "attached": null, "nattached": null}], "species_at_sites": ["Ba", "Ba", "C", "C", "C", "C", "S", "S", "S", "S", "N", "N", "N", "N"], "assemblies": null, "structure_features": [], "_optimake_energy": 2.5, "_optimake_list_property": [[1, 2.0, 3], [3, 2, 3], [1, 5, 6]]}, "relationships": null}
+{"id": "set1/101", "type": "structures", "links": null, "meta": null, "attributes": {"immutable_id": "structures.zip/cifs/set1/101.cif", "last_modified": "2026-02-16T13:37:21.465430", "elements": ["Ba", "C", "N", "S"], "nelements": 4, "elements_ratios": [0.14285714285714285, 0.2857142857142857, 0.2857142857142857, 0.2857142857142857], "chemical_formula_descriptive": "C4Ba2N4S4", "chemical_formula_reduced": "BaC2N2S2", "chemical_formula_hill": null, "chemical_formula_anonymous": "A2B2C2D", "dimension_types": [1, 1, 1], "nperiodic_dimensions": 3, "lattice_vectors": [[6.3587627540404945, 0.0, 0.0], [-2.672647488887009, 5.769819681958754, 0.0], [0.25844951934994664, -0.16511343006546234, 8.71190314896161]], "space_group_symmetry_operations_xyz": null, "space_group_symbol_hall": null, "space_group_symbol_hermann_mauguin": null, "space_group_symbol_hermann_mauguin_extended": null, "space_group_it_number": null, "cartesian_site_positions": [[3.4987802863851005, 5.049341739457014, 6.533927361693402], [0.4457844982025419, 0.5553645123824795, 2.177975787264444], [0.37416734784252487, 2.642448780492868, 5.291889331690525], [2.6281157156591126, 1.202488098280357, 7.775965391700042], [3.5703974366609055, 2.962257471400425, 3.420013817271085], [1.316449068841148, 4.402218153614962, 0.9359377571616379], [0.3512600296798777, 4.156339511491648, 5.900755701251229], [4.011419364830723, 1.818004876809729, 7.167099022143105], [3.5933047547393455, 1.4483667404554434, 2.8111474477141454], [-0.06685458032729186, 3.786701375083563, 1.5448041268185058], [0.3773832460379156, 1.5350786992068879, 4.8597303327393915], [1.621957615426957, 0.7399681351855376, 8.208124390751108], [3.567181538468686, 4.069627552684378, 3.8521728163221476], [2.3226071690796486, 4.864738116705728, 0.5037787583104332]], "nsites": 14, "species": [{"name": "C", "chemical_symbols": ["C"], "concentration": [1.0], "mass": null, "original_name": null, "attached": null, "nattached": null}, {"name": "S", "chemical_symbols": ["S"], "concentration": [1.0], "mass": null, "original_name": null, "attached": null, "nattached": null}, {"name": "Ba", "chemical_symbols": ["Ba"], "concentration": [1.0], "mass": null, "original_name": null, "attached": null, "nattached": null}, {"name": "N", "chemical_symbols": ["N"], "concentration": [1.0], "mass": null, "original_name": null, "attached": null, "nattached": null}], "species_at_sites": ["Ba", "Ba", "C", "C", "C", "C", "S", "S", "S", "S", "N", "N", "N", "N"], "assemblies": null, "structure_features": [], "_optimake_energy": 2.5}, "relationships": null}

{optimade_maker-0.7.2 → optimade_maker-0.9.0}/examples/simple_zip_of_cif/optimade.yaml

@@ -9,15 +9,10 @@ entries:
           - cifs/*/*.cif
     # (optional) property file and definitions:
     property_paths:
-      - file: data.csv
+      - file: properties.csv
     property_definitions:
       - name: energy
-        title: Total energy per atom
-        description: The total energy per atom as computed by DFT
+        title: Total energy
+        description: DFT total energy
         unit: eV/atom
         type: float
-      - name: list_property
-        title: List property
-        description: A 3x3 matrix property encoded as a string
-        type: list
-        unit: null

optimade_maker-0.9.0/examples/simple_zip_of_cif/properties.csv

@@ -0,0 +1,3 @@
+id,energy
+set1/101,2.5
+structures.zip/cifs/set2/102.cif,3.2

{optimade_maker-0.7.2 → optimade_maker-0.9.0}/pyproject.toml

@@ -19,14 +19,15 @@ classifiers = [
 ]
 
 dependencies = [
-  "pydantic~=2.2",
-  "optimade[server]~=1.3.1",
-  "pymongo",
+  "pydantic>=2,<3",
+  "optimade[server]~=1.4",
+  "pymongo>=4,<5",
   "pyyaml~=6.0",
   "tqdm~=4.65",
   "requests~=2.31",
-  "numpy >= 1.22, < 3",
   "click~=8.1",
+  "pandas>=1.5,<3",
+  "ase~=3.22",
 ]
 
 [project.scripts]
@@ -41,14 +42,11 @@ fallback_version = "0.1.0"
 version_scheme = "post-release"
 
 [project.optional-dependencies]
-ase = ["ase ~= 3.22"]
 pymatgen = ["pymatgen >= 2023.9"]
-pandas = ["pandas >= 1.5, < 3"]
-aiida = ["aiida-core >= 2.6.3"]
-core = ["optimade-maker[ase,pymatgen,pandas]"]
-ingest = ["optimade-maker[ase,pymatgen,pandas,aiida]"]
-tests = ["pytest~=8.3", "pytest-cov~=6.0"]
-dev = ["ruff", "pre-commit", "mypy"]
+aiida = ["aiida-core ~= 2.6"]
+ingest = ["optimade-maker[pymatgen,aiida]"]
+tests = ["pytest~=8.3", "pytest-cov~=6.0", "numpy >= 1.22, < 3"]
+dev = ["optimade-maker[tests]", "ruff", "pre-commit", "mypy"]
 
 [tool.ruff]
 target-version = "py311"

{optimade_maker-0.7.2 → optimade_maker-0.9.0}/src/optimade_maker/convert.py

@@ -173,7 +173,7 @@ def inflate_archive(archive_path: Path, data_path: Path) -> None:
     # If .tar in filename suffixes, use `tarfile`'s compression detection
     elif ".tar" in real_path.suffixes:
         with tarfile.open(real_path, "r") as tar:
-            tar.extractall(path=real_path.parent)
+            tar.extractall(path=real_path.parent, filter="data")
 
     # Otherwise assume this is a single compressed file
     # Decompress it and write it using the appropriate
@@ -306,11 +306,11 @@ def _parse_entries(
                         entry_ids.append(id_root)
                     break
                 except Exception as exc:
-                    exceptions[parser] = exc
+                    exceptions[parser.__name__] = exc
                     continue
             else:
                 raise RuntimeError(
-                    f"None of the provided parsers {ENTRY_PARSERS[entry_type]} could parse {_path}. Errors: {exceptions}"
+                    f"None of the provided parsers could parse {_path}. Errors: {exceptions}"
                 )
 
     if len(set(entry_ids)) != len(entry_ids):
@@ -573,7 +573,7 @@ def construct_entries_from_files(
             try:
                 entry = converter(
                     entry,
-                    properties=entry_config.property_definitions,
+                    prop_defs=entry_config.property_definitions,
                     prefix=provider_prefix,
                 )  # type: ignore[call-arg]
                 if not isinstance(entry, dict):

{optimade_maker-0.7.2 → optimade_maker-0.9.0}/src/optimade_maker/parsers.py

@@ -3,19 +3,8 @@ import warnings
 from pathlib import Path
 from typing import Any, Callable
 
-import numpy as np
-
-try:
-    import ase.io
-    import pandas
-    import pymatgen.core
-    import pymatgen.entries.computed_entries
-    from pymatgen.entries.computed_entries import ComputedStructureEntry
-except ImportError as exc:
-    raise ImportError(
-        "The parsers module requires the `ingest` extra of this package to be installed."
-    ) from exc
-
+import ase.io
+import pandas
 from optimade.adapters import Structure
 from optimade.models import DataType, EntryResource
 
@@ -24,7 +13,7 @@ from optimade_maker.config import PropertyDefinition
 
 def load_csv_file(
     p: Path,
-    properties: list[PropertyDefinition] | None = None,
+    prop_defs: list[PropertyDefinition] | None = None,
 ) -> dict[str, dict[str, Any]]:
     """Parses a CSV file found at path `p` and returns a dictionary
     of properties keyed by ID.
@@ -34,7 +23,7 @@ def load_csv_file(
 
     Parameters:
         p: Path to the CSV file.
-        properties: List of property definitions to extract from the CSV file.
+        prop_defs: List of property definitions to extract from the CSV file.
 
     Returns:
         A dictionary of ID -> properties.
@@ -55,40 +44,79 @@ def load_csv_file(
         df["id"] = df[id_key]
     df = df.set_index("id")
 
-    for prop in properties or []:
+    for prop_def in prop_defs or []:
         # loop through any property aliases, saving the value if found and only checking
         # the real name if not
-        for alias in prop.aliases or []:
+        for alias in prop_def.aliases or []:
             if alias in df:
-                df[prop.name] = df[alias]
+                df[prop_def.name] = df[alias]
                 df.drop(columns=[alias], inplace=True)
                 break
 
-    # Check for list/array-valued properties, being careful
-    # to reinterpret NaNs back into JSON `null` before trying
-    for prop in properties or []:
-        if prop.type == DataType.LIST:
+    # For list and dict types, interpret string values as JSON
+    for prop_def in prop_defs or []:
+        if (
+            prop_def.type in (DataType.LIST, DataType.DICTIONARY)
+            and prop_def.name in df.columns
+        ):
+            # Replace NaN -> "null"
+            df[prop_def.name] = df[prop_def.name].fillna("null")
             try:
-                df[prop.name] = (
-                    df[prop.name]
-                    .fillna(np.nan)
-                    .replace([np.nan], ["null"])
-                    .apply(json.loads)
+                df[prop_def.name] = df[prop_def.name].apply(
+                    lambda v: json.loads(v) if isinstance(v, str) else v
                 )
             except Exception as exc:
                 warnings.warn(
-                    f"Tried to interpret property {prop.name!r} as a list, but an error was raised: {exc.__class__.__name__}: {exc!r}"
+                    f"Tried to interpret property {prop_def.name!r} as JSON, but got "
+                    f"{exc.__class__.__name__}: {exc!r}"
                 )
-                pass
 
     return df.to_dict(orient="index")
 
 
+def load_json_file(
+    p: Path,
+    prop_defs: list[PropertyDefinition] | None = None,
+) -> dict[str, dict[str, Any]]:
+    """Parses a JSON file found at path `p` and returns a dictionary
+    of properties keyed by ID.
+
+    Expects either a list of objects (each with an "id" field) or a dictionary
+    already keyed by IDs. If a list is provided, the "id" field of each object
+    will be used as the dictionary key.
+
+    Parameters:
+        p: Path to the JSON file.
+        prop_defs: List of property definitions to extract from the JSON data.
+
+    Returns:
+        A dictionary of ID -> properties.
+    """
+
+    with open(p, "r") as f:
+        data = json.load(f)
+
+    if isinstance(data, list):
+        data_dict = {}
+        for item in data:
+            id_value = item.get("id")
+            if not id_value:
+                raise RuntimeError(f"JSON item {item} missing 'id'")
+            data_dict[id_value] = item
+        data = data_dict
+
+    for prop_def in prop_defs or []:
+        for alias in prop_def.aliases or []:
+            for row_id, row in data.items():
+                if alias in row:
+                    row[prop_def.name] = row.pop(alias)
+
+    return data
+
+
 PROPERTY_PARSERS: dict[
     str, list[Callable[[Path, list[PropertyDefinition] | None], Any]]
-] = {
-    ".csv": [load_csv_file],
-}
+] = {".csv": [load_csv_file], ".json": [load_json_file]}
 
 TYPE_MAP: dict[DataType, type] = {
     DataType.FLOAT: float,
@@ -98,6 +126,29 @@ TYPE_MAP: dict[DataType, type] = {
 }
 
 
+ENTRY_PARSERS: dict[str, list[Callable[[Path], Any]]] = {
+    "structures": [ase.io.read],
+}
+
+
+def structure_ingest_wrapper(entry, prop_defs=None, prefix=None):  # type: ignore
+    return Structure.ingest_from(entry)
+
+
+OPTIMADE_CONVERTERS: dict[
+    str,
+    list[
+        Callable[
+            [Any, list[PropertyDefinition] | None, str | None], EntryResource | dict
+        ]
+    ],
+] = {
+    "structures": [structure_ingest_wrapper],
+}
+
+#### Wrappers for third-party parsers and converters, such as pymatgen ####
+
+
 def wrapped_json_parser(parser):
     """This wrapper allows `from_dict` parser functions to be called
     on a single JSON file.
@@ -133,20 +184,9 @@ def wrapped_json_parser(parser):
     return _wrapped_json_parser
 
 
-ENTRY_PARSERS: dict[str, list[Callable[[Path], Any]]] = {
-    "structures": [
-        ase.io.read,
-        wrapped_json_parser(
-            pymatgen.entries.computed_entries.ComputedStructureEntry.from_dict
-        ),
-        wrapped_json_parser(pymatgen.core.Structure.from_dict),
-    ],
-}
-
-
 def convert_pymatgen_computed_structure_entry(
-    pmg_entry: ComputedStructureEntry,
-    properties: list[PropertyDefinition] | None = None,
+    pmg_entry,
+    prop_defs: list[PropertyDefinition] | None = None,
     prefix: str | None = None,
 ) -> dict:
     """Convert a pymatgen ComputedStructureEntry to an OPTIMADE EntryResource."""
@@ -159,7 +199,7 @@ def convert_pymatgen_computed_structure_entry(
             entry["id"] = id
             break
 
-    for p in properties or []:
+    for p in prop_defs or []:
         # loop through any property aliases, saving the value if found and only checking
         # the real name if not
         for alias in p.aliases or []:
@@ -172,17 +212,28 @@ def convert_pymatgen_computed_structure_entry(
     return entry
 
 
-def structure_ingest_wrapper(entry, properties=None, prefix=None):  # type: ignore
-    return Structure.ingest_from(entry)
+def add_pymatgen_parsers():
+    try:
+        import pymatgen.core
+        import pymatgen.entries.computed_entries
 
+        ENTRY_PARSERS["structures"].extend(
+            [
+                wrapped_json_parser(
+                    pymatgen.entries.computed_entries.ComputedStructureEntry.from_dict
+                ),
+                wrapped_json_parser(pymatgen.core.Structure.from_dict),
+            ]
+        )
 
-OPTIMADE_CONVERTERS: dict[
-    str,
-    list[
-        Callable[
-            [Any, list[PropertyDefinition] | None, str | None], EntryResource | dict
-        ]
-    ],
-] = {
-    "structures": [structure_ingest_wrapper, convert_pymatgen_computed_structure_entry],
-}
+        OPTIMADE_CONVERTERS["structures"].append(
+            convert_pymatgen_computed_structure_entry
+        )
+    except ImportError:
+        warnings.warn(
+            "pymatgen is not installed, so corresponding parsers and converters will not be available. "
+            "To use these, install the 'pymatgen' extra."
+        )
+
+
+add_pymatgen_parsers()

{optimade_maker-0.7.2 → optimade_maker-0.9.0}/src/optimade_maker/serve.py

@@ -287,11 +287,12 @@ class OptimakeServer:
             LOGGER.info("Using the MongoMock backend.")
             if skip_mock:
                 return
-            # Importing optimade python tools loads the config and creates the mongomock
-            # client that we need to populate.
-            from optimade.server.entry_collections.mongo import CLIENT
+            # Get the MongoMock client from optimade-python-tools
+            from optimade.server.config import ServerConfig
+            from optimade.server.entry_collections.mongo import get_mongo_client
 
-            mongo_db = CLIENT[db_name]
+            client = get_mongo_client(ServerConfig())
+            mongo_db = client[db_name]
         else:
             raise ValueError(
                 f"Unknown database backend '{db_backend}'. "

{optimade_maker-0.7.2 → optimade_maker-0.9.0}/src/optimade_maker.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: optimade-maker
-Version: 0.7.2
+Version: 0.9.0
 Summary: Tools for making OPTIMADE APIs from raw structural data.
 License: MIT
 Keywords: optimade,jsonapi,materials
@@ -15,30 +15,27 @@ Classifier: Topic :: Scientific/Engineering
 Requires-Python: <3.13,>=3.10
 Description-Content-Type: text/markdown
 License-File: LICENSE
-Requires-Dist: pydantic~=2.2
-Requires-Dist: optimade[server]~=1.3.1
-Requires-Dist: pymongo
+Requires-Dist: pydantic<3,>=2
+Requires-Dist: optimade[server]~=1.4
+Requires-Dist: pymongo<5,>=4
 Requires-Dist: pyyaml~=6.0
 Requires-Dist: tqdm~=4.65
 Requires-Dist: requests~=2.31
-Requires-Dist: numpy<3,>=1.22
 Requires-Dist: click~=8.1
-Provides-Extra: ase
-Requires-Dist: ase~=3.22; extra == "ase"
+Requires-Dist: pandas<3,>=1.5
+Requires-Dist: ase~=3.22
 Provides-Extra: pymatgen
 Requires-Dist: pymatgen>=2023.9; extra == "pymatgen"
-Provides-Extra: pandas
-Requires-Dist: pandas<3,>=1.5; extra == "pandas"
 Provides-Extra: aiida
-Requires-Dist: aiida-core>=2.6.3; extra == "aiida"
-Provides-Extra: core
-Requires-Dist: optimade-maker[ase,pandas,pymatgen]; extra == "core"
+Requires-Dist: aiida-core~=2.6; extra == "aiida"
 Provides-Extra: ingest
-Requires-Dist: optimade-maker[aiida,ase,pandas,pymatgen]; extra == "ingest"
+Requires-Dist: optimade-maker[aiida,pymatgen]; extra == "ingest"
 Provides-Extra: tests
 Requires-Dist: pytest~=8.3; extra == "tests"
 Requires-Dist: pytest-cov~=6.0; extra == "tests"
+Requires-Dist: numpy<3,>=1.22; extra == "tests"
 Provides-Extra: dev
+Requires-Dist: optimade-maker[tests]; extra == "dev"
 Requires-Dist: ruff; extra == "dev"
 Requires-Dist: pre-commit; extra == "dev"
 Requires-Dist: mypy; extra == "dev"
@@ -75,6 +72,8 @@ This repository contains the src/optimade-maker Python package and the correspon
 Install with
 
 ```bash
+pip install optimade-maker
+# or to get all ingestion plugins (e.g. pymatgen, aiida):
 pip install optimade-maker[ingest]
 ```
 
@@ -106,8 +105,8 @@ entries:
       - file: properties.csv
     property_definitions:
       - name: energy
-        title: Total energy per atom
-        description: DFT total energy per atom
+        title: Total energy
+        description: DFT total energy
         unit: eV/atom
         type: float
 ```