Refactor: Logging, Module Restructure, and Codebase Streamlining

docs/source/03_api/core/edge_generators.rst

@@ -1,38 +1,38 @@
 Edge Generators
 ========================
 
-- :func:`element_element_neighborsByGroupPeriod <matgraphdb.core.edges.element_element_neighborsByGroupPeriod>` - A function that generates the neighbors of an element by group and period.
+- :func:`element_element_neighborsByGroupPeriod <matgraphdb.generators.edges.element_element_neighborsByGroupPeriod>` - A function that generates the neighbors of an element by group and period.
 
-- :func:`element_element_bonds <matgraphdb.core.edges.element_element_bonds>` - A function that generates the bonds of an element.
+- :func:`element_element_bonds <matgraphdb.generators.edges.element_element_bonds>` - A function that generates the bonds of an element.
 
-- :func:`element_oxiState_canOccur <matgraphdb.core.edges.element_oxiState_canOccur>` - A function that generates the possible oxidation states of an element.
+- :func:`element_oxiState_canOccur <matgraphdb.generators.edges.element_oxiState_canOccur>` - A function that generates the possible oxidation states of an element.
 
-- :func:`material_chemenv_containsSite <matgraphdb.core.edges.material_chemenv_containsSite>` - A function that generates the sites of a material.
+- :func:`material_chemenv_containsSite <matgraphdb.generators.edges.material_chemenv_containsSite>` - A function that generates the sites of a material.
 
-- :func:`material_crystalSystem_has <matgraphdb.core.edges.material_crystalSystem_has>` - A function that generates the crystal system of a material.
+- :func:`material_crystalSystem_has <matgraphdb.generators.edges.material_crystalSystem_has>` - A function that generates the crystal system of a material.
 
-- :func:`material_element_has <matgraphdb.core.edges.material_element_has>` - A function that generates the elements of a material.
+- :func:`material_element_has <matgraphdb.generators.edges.material_element_has>` - A function that generates the elements of a material.
 
-- :func:`material_lattice_has <matgraphdb.core.edges.material_lattice_has>` - A function that generates the lattice of a material.
+- :func:`material_lattice_has <matgraphdb.generators.edges.material_lattice_has>` - A function that generates the lattice of a material.
 
-- :func:`material_spg_has <matgraphdb.core.edges.material_spg_has>` - A function that generates the space group of a material.
+- :func:`material_spg_has <matgraphdb.generators.edges.material_spg_has>` - A function that generates the space group of a material.
 
-- :func:`element_chemenv_canOccur <matgraphdb.core.edges.element_chemenv_canOccur>` - A function that generates the possible oxidation states of an element.
+- :func:`element_chemenv_canOccur <matgraphdb.generators.edges.element_chemenv_canOccur>` - A function that generates the possible oxidation states of an element.
 
-- :func:`spg_crystalSystem_isApart <matgraphdb.core.edges.spg_crystalSystem_isApart>` - A function that generates the crystal system of a material.
+- :func:`spg_crystalSystem_isApart <matgraphdb.generators.edges.spg_crystalSystem_isApart>` - A function that generates the crystal system of a material.
 
 
 
 .. autosummary::
    :toctree: _autosummary
 
-   matgraphdb.core.edges.element_element_neighborsByGroupPeriod
-   matgraphdb.core.edges.element_element_bonds
-   matgraphdb.core.edges.element_oxiState_canOccur
-   matgraphdb.core.edges.material_chemenv_containsSite
-   matgraphdb.core.edges.material_crystalSystem_has
-   matgraphdb.core.edges.material_element_has
-   matgraphdb.core.edges.material_lattice_has
-   matgraphdb.core.edges.material_spg_has
-   matgraphdb.core.edges.element_chemenv_canOccur
-   matgraphdb.core.edges.spg_crystalSystem_isApart
+   matgraphdb.generators.edges.element_element_neighborsByGroupPeriod
+   matgraphdb.generators.edges.element_element_bonds
+   matgraphdb.generators.edges.element_oxiState_canOccur
+   matgraphdb.generators.edges.material_chemenv_containsSite
+   matgraphdb.generators.edges.material_crystalSystem_has
+   matgraphdb.generators.edges.material_element_has
+   matgraphdb.generators.edges.material_lattice_has
+   matgraphdb.generators.edges.material_spg_has
+   matgraphdb.generators.edges.element_chemenv_canOccur
+   matgraphdb.generators.edges.spg_crystalSystem_isApart

docs/source/03_api/core/material_store.rst

@@ -1,9 +1,9 @@
 MaterialStore
 ========================
 
-- :class:`MaterialStore <matgraphdb.core.nodes.materials.MaterialStore>` - A store for managing materials in a graph database.
+- :class:`MaterialStore <matgraphdb.core.material_store.MaterialStore>` - A store for managing materials in a graph database.
 
 .. autosummary::
    :toctree: _autosummary
 
-   matgraphdb.core.nodes.materials.MaterialStore
+   matgraphdb.core.material_store.MaterialStore

docs/source/03_api/core/node_generators.rst

@@ -2,28 +2,39 @@ Node Generators
 ========================
 
 
-- :func:`element <matgraphdb.core.nodes.generators.element>` - A function that generates the elements of a material.
+- :func:`element <matgraphdb.generators.nodes.element>` - A function that generates the elements of a material.
 
-- :func:`chemenv <matgraphdb.core.nodes.generators.chemenv>` - A function that generates the chemical environments of a material.
+- :func:`chemenv <matgraphdb.generators.nodes.chemenv>` - A function that generates the chemical environments of a material.
 
-- :func:`crystal_system <matgraphdb.core.nodes.generators.crystal_system>` - A function that generates the crystal systems of a material.
+- :func:`crystal_system <matgraphdb.generators.nodes.crystal_system>` - A function that generates the crystal systems of a material.
+
+- :func:`magnetic_state <matgraphdb.generators.nodes.magnetic_state>` - A function that generates the magnetic states of a material.
+
+- :func:`oxidation_state <matgraphdb.generators.nodes.oxidation_state>` - A function that generates the oxidation states of a material.
+
+- :func:`space_group <matgraphdb.generators.nodes.space_group>` - A function that generates the space groups of a material.
+
+- :func:`wyckoff <matgraphdb.generators.nodes.wyckoff>` - A function that generates the wyckoffs of a material.
+
+- :func:`lattice <matgraphdb.generators.nodes.lattice>` - A function that generates the lattices of a material.
+
+- :func:`material_site <matgraphdb.generators.nodes.material_site>` - A function that generates the sites of a material.
 
-- :func:`magnetic_state <matgraphdb.core.nodes.generators.magnetic_state>` - A function that generates the magnetic states of a material.
 
-- :func:`oxidation_state <matgraphdb.core.nodes.generators.oxidation_state>` - A function that generates the oxidation states of a material.
 
-- :func:`space_group <matgraphdb.core.nodes.generators.space_group>` - A function that generates the space groups of a material.
 
-- :func:`wyckoff <matgraphdb.core.nodes.generators.wyckoff>` - A function that generates the wyckoffs of a material.
 
 
 .. autosummary::
    :toctree: _autosummary
 
-   matgraphdb.core.nodes.generators.element
-   matgraphdb.core.nodes.generators.chemenv
-   matgraphdb.core.nodes.generators.crystal_system
-   matgraphdb.core.nodes.generators.magnetic_state
-   matgraphdb.core.nodes.generators.oxidation_state
-   matgraphdb.core.nodes.generators.space_group
-   matgraphdb.core.nodes.generators.wyckoff
+   matgraphdb.generators.nodes.element
+   matgraphdb.generators.nodes.chemenv
+   matgraphdb.generators.nodes.crystal_system
+   matgraphdb.generators.nodes.magnetic_state
+   matgraphdb.generators.nodes.oxidation_state
+   matgraphdb.generators.nodes.space_group
+   matgraphdb.generators.nodes.wyckoff
+   matgraphdb.generators.nodes.lattice
+   matgraphdb.generators.nodes.material_site
+

examples/notebooks/01 - Getting Started.ipynb

@@ -259,7 +259,6 @@
     }
    ],
    "source": [
-    "\n",
     "from matgraphdb import MatGraphDB\n",
     "\n",
     "if not os.path.exists(MATGRAPHDB_PATH):\n",
@@ -284,27 +283,24 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "from matgraphdb.core.nodes import (\n",
-    "    element, chemenv, crystal_system, magnetic_state, \n",
-    "    oxidation_state, space_group, wyckoff, material_site, material_lattice\n",
-    ")\n",
+    "from matgraphdb import generators\n",
     "\n",
     "# Here we define the generator functions and arguments if they are needed. \n",
     "# For instance, to get the materials sites and lattices, we need to pass the materials store to the generator function.\n",
     "node_generators = [\n",
-    "    {\"generator_func\": element},\n",
-    "    {\"generator_func\": chemenv},\n",
-    "    {\"generator_func\": crystal_system},\n",
-    "    {\"generator_func\": magnetic_state},\n",
-    "    {\"generator_func\": oxidation_state},\n",
-    "    {\"generator_func\": space_group},\n",
-    "    {\"generator_func\": wyckoff},\n",
+    "    {\"generator_func\": generators.element},\n",
+    "    {\"generator_func\": generators.chemenv},\n",
+    "    {\"generator_func\": generators.crystal_system},\n",
+    "    {\"generator_func\": generators.magnetic_state},\n",
+    "    {\"generator_func\": generators.oxidation_state},\n",
+    "    {\"generator_func\": generators.space_group},\n",
+    "    {\"generator_func\": generators.wyckoff},\n",
     "    {\n",
-    "        \"generator_func\": material_site,\n",
+    "        \"generator_func\": generators.material_site,\n",
     "        \"generator_args\": {\"material_store\": mdb.node_stores[\"material\"]},\n",
     "    },\n",
     "    {\n",
-    "        \"generator_func\": material_lattice,\n",
+    "        \"generator_func\": generators.material_lattice,\n",
     "        \"generator_args\": {\"material_store\": mdb.node_stores[\"material\"]},\n",
     "    },\n",
     "]\n"
@@ -805,86 +801,72 @@
     }
    ],
    "source": [
-    "from matgraphdb.core.edges import (\n",
-    "    material_element_has,\n",
-    "    material_lattice_has,\n",
-    "    material_spg_has,\n",
-    "    element_element_neighborsByGroupPeriod,\n",
-    "    element_element_bonds,\n",
-    "    element_oxiState_canOccur,\n",
-    "    material_chemenv_containsSite,\n",
-    "    material_crystalSystem_has,\n",
-    "    element_chemenv_canOccur,\n",
-    "    spg_crystalSystem_isApart,\n",
-    ")\n",
-    "\n",
-    "\n",
     "\n",
     "# List of edge generator configurations.\n",
     "edge_generators = [\n",
     "    {\n",
-    "        \"generator_func\": element_element_neighborsByGroupPeriod,\n",
+    "        \"generator_func\": generators.element_element_neighborsByGroupPeriod,\n",
     "        \"generator_args\": {\"element_store\": mdb.node_stores[\"element\"]},\n",
     "    },\n",
     "    {\n",
-    "        \"generator_func\": element_oxiState_canOccur,\n",
+    "        \"generator_func\": generators.element_oxiState_canOccur,\n",
     "        \"generator_args\": {\n",
     "            \"element_store\": mdb.node_stores[\"element\"],\n",
     "            \"oxiState_store\": mdb.node_stores[\"oxidation_state\"],\n",
     "        },\n",
     "    },\n",
     "    {\n",
-    "        \"generator_func\": material_chemenv_containsSite,\n",
+    "        \"generator_func\": generators.material_chemenv_containsSite,\n",
     "        \"generator_args\": {\n",
     "            \"material_store\": mdb.node_stores[\"material\"],\n",
     "            \"chemenv_store\": mdb.node_stores[\"chemenv\"],\n",
     "        },\n",
     "    },\n",
     "    {\n",
-    "        \"generator_func\": material_crystalSystem_has,\n",
+    "        \"generator_func\": generators.material_crystalSystem_has,\n",
     "        \"generator_args\": {\n",
     "            \"material_store\": mdb.node_stores[\"material\"],\n",
     "            \"crystal_system_store\": mdb.node_stores[\"crystal_system\"],\n",
     "        },\n",
     "    },\n",
     "    {\n",
-    "        \"generator_func\": material_element_has,\n",
+    "        \"generator_func\": generators.material_element_has,\n",
     "        \"generator_args\": {\n",
     "            \"material_store\": mdb.node_stores[\"material\"],\n",
     "            \"element_store\": mdb.node_stores[\"element\"],\n",
     "        },\n",
     "    },\n",
     "    {\n",
-    "        \"generator_func\": material_lattice_has,\n",
+    "        \"generator_func\": generators.material_lattice_has,\n",
     "        \"generator_args\": {\n",
     "            \"material_store\": mdb.node_stores[\"material\"],\n",
     "            \"lattice_store\": mdb.node_stores[\"material_lattice\"],\n",
     "        },\n",
     "    },\n",
     "    {\n",
-    "        \"generator_func\": material_spg_has,\n",
+    "        \"generator_func\": generators.material_spg_has,\n",
     "        \"generator_args\": {\n",
     "            \"material_store\": mdb.node_stores[\"material\"],\n",
     "            \"spg_store\": mdb.node_stores[\"space_group\"],\n",
     "        },\n",
     "    },\n",
     "    {\n",
-    "        \"generator_func\": element_chemenv_canOccur,\n",
+    "        \"generator_func\": generators.element_chemenv_canOccur,\n",
     "        \"generator_args\": {\n",
     "            \"element_store\": mdb.node_stores[\"element\"],\n",
     "            \"chemenv_store\": mdb.node_stores[\"chemenv\"],\n",
     "            \"material_store\": mdb.node_stores[\"material\"],\n",
     "        },\n",
     "    },\n",
     "    {\n",
-    "        \"generator_func\": spg_crystalSystem_isApart,\n",
+    "        \"generator_func\": generators.spg_crystalSystem_isApart,\n",
     "        \"generator_args\": {\n",
     "            \"spg_store\": mdb.node_stores[\"space_group\"],\n",
     "            \"crystal_system_store\": mdb.node_stores[\"crystal_system\"],\n",
     "        },\n",
     "    },\n",
     "    {\n",
-    "        \"generator_func\": element_element_bonds,\n",
+    "        \"generator_func\": generators.element_element_bonds,\n",
     "        \"generator_args\": {\n",
     "            \"element_store\": mdb.node_stores[\"element\"],\n",
     "            \"material_store\": mdb.node_stores[\"material\"],\n",

matgraphdb/__init__.py

@@ -1,3 +1,8 @@
+from parquetdb.utils.log_utils import setup_logging
+
 from matgraphdb._version import __version__
+
+setup_logging()
+
 from matgraphdb.core import MaterialStore, MatGraphDB
 from matgraphdb.utils.config import PKG_DIR, config