Fix docs

docs/about/license.md

@@ -1,5 +1,4 @@
-License
-=======
+# License
 
 `atomate2` is developed under a modified BSD license, reproduced below:
 
@@ -51,3 +50,4 @@ modify, prepare derivative works, incorporate into other computer
 software, distribute, and sublicense such enhancements or derivative
 works thereof, in binary and source code form.
 ```
+

docs/conf.py

@@ -72,7 +72,7 @@
 napoleon_use_ivar = True
 
 # The suffix(es) of source filenames.
-source_suffix = [".rst", ".md"]
+source_suffix = {'.rst': 'restructuredtext', '.md': 'restructuredtext'}
 
 mathjax3_config = {
     "tex": {
@@ -92,10 +92,10 @@
 """
 }
 language = "en"
-html_extra_path = ["images/badge.svg"]
+#html_extra_path = ["images/badge.svg"]
 html_static_path = ["_static"]
 html_css_files = ["custom.css", "github.css"]
-suppress_warnings = "etoc.toctree"
+suppress_warnings = ["etoc.toctree"]
 
 # autodoc options
 autosummary_imported_members = False
@@ -172,6 +172,5 @@
     "python": ("https://docs.python.org/3.8", None),
     "matplotlib": ("https://matplotlib.org/stable/", None),
     "networkx": ("https://networkx.org/documentation/stable/", None),
-    "monty": ("https://materialsvirtuallab.github.io/monty/", None),
     "jobflow": ("https://materialsproject.github.io/jobflow", None),
 }

docs/index.md

@@ -5,6 +5,7 @@ user/index
 user/install
 user/running-workflows
 user/fireworks
+user/atomate-1-vs-2
 user/codes/index
 ```
 
@@ -20,6 +21,7 @@ reference/index
 dev/dev_install
 dev/workflow_tutorial
 dev/vasp_tests
+dev/abinit_tests
 ```
 
 ```{toctree}

docs/user/install.md

@@ -296,7 +296,7 @@ This is the command that you would use to run VASP with parallelization
 
 The directory structure of `<<INSTALL_DIR>>/config` should now look like
 
-```txt
+```
 config
 ├── jobflow.yaml
 └── atomate2.yaml

src/atomate2/amset/schemas.py

@@ -23,9 +23,6 @@
     amset = None
 
 
-if TYPE_CHECKING:
-    from typing_extensions import Self
-
 logger = logging.getLogger(__name__)
 
 
@@ -147,7 +144,7 @@ def from_directory(
         dir_name: Union[Path, str],
         additional_fields: dict[str, Any] = None,
         include_mesh: bool = False,
-    ) -> Self:
+    ):
         """Create a task document from a directory containing VASP files.
 
         Parameters

src/atomate2/common/flows/defect.py

@@ -182,6 +182,7 @@ class FormationEnergyMaker(Maker, ABC):
         lattice relaxation, you should manually set the grid size.
 
         .. code-block:: python
+
             relax_set = MPRelaxSet(defect.get_supercell_structure())
             ng, ngf = relax_set.calculate_ng()
             params = ["NGX", "NGY", "NGZ", "NGXF", "NGYF", "NGZF"]
@@ -217,32 +218,35 @@ class FormationEnergyMaker(Maker, ABC):
         energy diagrams.
 
         .. note::
-        Once we remove the requirement for explicit bulk supercell calculations,
-        this setting will be removed. It is only needed because the bulk supercell
-        locpot is currently needed for the finite-size correction calculation.
+            Once we remove the requirement for explicit bulk supercell calculations,
+            this setting will be removed. It is only needed because the bulk supercell
+            locpot is currently needed for the finite-size correction calculation.
 
         Output format for the DefectEntry data:
+
         .. code-block:: python
-        [
-            {
-                'bulk_dir_name': 'computer1:/folder1',
-                'bulk_locpot': {...},
-                'bulk_uuid': '48fb6da7-dc2b-4dcb-b1c8-1203c0f72ce3',
-                'defect_dir_name': 'computer1:/folder2',
-                'defect_entry': {...},
-                'defect_locpot': {...},
-                'defect_uuid': 'e9af2725-d63c-49b8-a01f-391540211750'
-            },
-            {
-                'bulk_dir_name': 'computer1:/folder3',
-                'bulk_locpot': {...},
-                'bulk_uuid': '48fb6da7-dc2b-4dcb-b1c8-1203c0f72ce3',
-                'defect_dir_name': 'computer1:/folder4',
-                'defect_entry': {...},
-                'defect_locpot': {...},
-                'defect_uuid': 'a1c31095-0494-4eed-9862-95311f80a993'
-            }
-        ]
+
+            [
+                {
+                    'bulk_dir_name': 'computer1:/folder1',
+                    'bulk_locpot': {...},
+                    'bulk_uuid': '48fb6da7-dc2b-4dcb-b1c8-1203c0f72ce3',
+                    'defect_dir_name': 'computer1:/folder2',
+                    'defect_entry': {...},
+                    'defect_locpot': {...},
+                    'defect_uuid': 'e9af2725-d63c-49b8-a01f-391540211750'
+                },
+                {
+                    'bulk_dir_name': 'computer1:/folder3',
+                    'bulk_locpot': {...},
+                    'bulk_uuid': '48fb6da7-dc2b-4dcb-b1c8-1203c0f72ce3',
+                    'defect_dir_name': 'computer1:/folder4',
+                    'defect_entry': {...},
+                    'defect_locpot': {...},
+                    'defect_uuid': 'a1c31095-0494-4eed-9862-95311f80a993'
+                }
+            ]
+
     """
 
     defect_relax_maker: Maker

src/atomate2/common/jobs/eos.py

@@ -26,6 +26,8 @@ class EOSPostProcessor(MSONable):
     """
     Fit data to an EOS.
 
+    Parameters
+    ----------
     name : str
         Name of the class
     eos_attrs : tuple[str,...]
@@ -72,16 +74,19 @@ def fit(self, eos_flow_output: dict[str, Any]) -> None:
         Parameters
         ----------
         eos_flow_output : dict
-            Volume, energy, and (optionally) stress and pressure data in dict form,
-            {
-                "relax" <required> and "static" <optional> : {
-                    "energy": list, <required>
-                    "volume": list, <required>
-                    "stress": list <optional>
-                },
-                "initial_<key>": {"E0": float, "V0": float} <optional>,
-                    for <key> in ("relax", "static")
-            }
+            Volume, energy, and (optionally) stress and pressure data in dict
+            form::
+
+                {
+                    "relax" <required> and "static" <optional> : {
+                        "energy": list, <required>
+                        "volume": list, <required>
+                        "stress": list <optional>
+                    },
+                    "initial_<key>": {"E0": float, "V0": float} <optional>,
+                        for <key> in ("relax", "static")
+                }
+
         """
         self.results.update(eos_flow_output)
         self._use_job_types = [key for key in self.job_types if self.results.get(key)]
@@ -103,16 +108,19 @@ def make(self, eos_flow_output: dict[str, Any]) -> Job:
         Parameters
         ----------
         eos_flow_output : dict
-            Volume, energy, and (optionally) stress and pressure data in dict form,
-            {
-                "relax" <required> and "static" <optional> : {
-                    "energy": list, <required>
-                    "volume": list, <required>
-                    "stress": list <optional>
-                },
-                "initial_<key>": {"E0": float, "V0": float} <optional>,
-                    for <key> in ("relax", "static")
-            }
+            Volume, energy, and (optionally) stress and pressure data in dict
+            form::
+
+                {
+                    "relax" <required> and "static" <optional> : {
+                        "energy": list, <required>
+                        "volume": list, <required>
+                        "stress": list <optional>
+                    },
+                    "initial_<key>": {"E0": float, "V0": float} <optional>,
+                        for <key> in ("relax", "static")
+                }
+
         """
         self.fit(eos_flow_output)
         return self.results
@@ -125,16 +133,19 @@ class PostProcessEosEnergy(EOSPostProcessor):
     Parameters
     ----------
     eos_flow_output : dict
-        Volume, energy, and (optionally) stress and pressure data in dict form,
-        {
-            "relax" <required> and "static" <optional> : {
-                "energy": list, <required>
-                "volume": list, <required>
-                "stress": list <optional>
-            },
-            "initial_<key>": {"E0": float, "V0": float} <optional>,
-                for <key> in ("relax", "static")
-        }
+        Volume, energy, and (optionally) stress and pressure data in dict
+        form::
+
+            {
+                "relax" <required> and "static" <optional> : {
+                    "energy": list, <required>
+                    "volume": list, <required>
+                    "stress": list <optional>
+                },
+                "initial_<key>": {"E0": float, "V0": float} <optional>,
+                    for <key> in ("relax", "static")
+            }
+
     name : str
         Name of the class
     eos_attrs : tuple[str,...]
@@ -158,7 +169,7 @@ class PostProcessEosEnergy(EOSPostProcessor):
     )
 
     def eval(self) -> None:
-        """Fit the input data to each EOS in `self.eos_models."""
+        """Fit the input data to each EOS in ``self.eos_models``."""
         for jobtype in self._use_job_types:
             self.results[jobtype]["EOS"] = {}
             for eos_name in self.eos_models:
@@ -181,16 +192,19 @@ class PostProcessEosPressure(EOSPostProcessor):
     Parameters
     ----------
     eos_flow_output : dict
-        Volume, energy, and (optionally) stress and pressure data in dict form,
-        {
-            "relax" <required> and "static" <optional> : {
-                "energy": list, <required>
-                "volume": list, <required>
-                "stress": list <optional>
-            },
-            "initial_<key>": {"E0": float, "V0": float} <optional>,
-                for <key> in ("relax", "static")
-        }
+        Volume, energy, and (optionally) stress and pressure data in dict
+        form::
+
+            {
+                "relax" <required> and "static" <optional> : {
+                    "energy": list, <required>
+                    "volume": list, <required>
+                    "stress": list <optional>
+                },
+                "initial_<key>": {"E0": float, "V0": float} <optional>,
+                    for <key> in ("relax", "static")
+            }
+
     name : str
         Name of the class
     eos_attrs : tuple[str,...]
@@ -201,8 +215,10 @@ class PostProcessEosPressure(EOSPostProcessor):
         Minimum number of data points needed to perform a fit.
 
     If only stresses are specified, it is assumed that the elements of "stress"
-    are 3 x 3 tensors, and the pressure is computed as
+    are 3 x 3 tensors, and the pressure is computed as::
+
         pressure = Trace(stress tensor)/3
+
     The overall sign is irrelevant for a successful fit, as the overall sign
     of the pressure indicates internal/external stress.
     """
@@ -232,14 +248,18 @@ def _birch_murnaghan_pressure(
         -------
         float : the BM pressure
 
-        BM EOS for E(V) has the form
+        BM EOS for E(V) has the form::
+
             E(V) = E0 + 9 B0 V0 / 16 * (
                 (B1 - 4)*eta**6 + (14 - 3*B1)*eta**4 + (3*B1 - 16)*eta**2 + 6 - B1
             )
             eta = (V0/V)**(1/3).
-        This function computes p = - dE / dV via the chain rule,
+
+        This function computes p = - dE / dV via the chain rule,::
+
             p = d E / d eta * (- d eta / dV)
             = eta**4/(3*V0) * d E / d eta
+
         """
         eta = (v0 / volume) ** (1.0 / 3.0)
         return (
@@ -253,7 +273,8 @@ def _birch_murnaghan_pressure(
     def _initial_fit(self) -> dict:
         """Generate initial polynomial fit for p(V) curve.
 
-        p(V) / V = a + b V + c V**2
+        ::
+            p(V) / V = a + b V + c V**2
         """
         init_pars = {}
         for jobtype in self._use_job_types:
@@ -337,9 +358,12 @@ def apply_strain_to_structure(structure: Structure, deformations: list) -> list:
     deformations: list[.Deformation]
         A list of deformations to apply **independently** to the input
         structure, in anticipation of performing an EOS fit.
-        Deformations should be of the form of a 3x3 matrix, e.g.,
+        Deformations should be of the form of a 3x3 matrix, e.g.,::
+
         [[1.2, 0., 0.], [0., 1.2, 0.], [0., 0., 1.2]]
-        or
+
+        or::
+
         ((1.2, 0., 0.), (0., 1.2, 0.), (0., 0., 1.2))
 
     Returns

src/atomate2/common/schemas/magnetism.py

@@ -350,10 +350,12 @@ def from_outputs(
     def from_tasks(cls, tasks: list[dict]) -> MagneticOrderingsDocument:
         """Construct a MagneticOrderingsDocument from a list of task dicts.
 
-        .. Note:: this function assumes the tasks contain the keys "output" and
-        "metadata". These keys are automatically constructed when jobflow stores its
-        outputs; however, you may need to put the data in this format if using this
-        manually (as in a postprocessing job).
+        .. Note::
+
+            this function assumes the tasks contain the keys "output" and "metadata".
+            These keys are automatically constructed when jobflow stores its outputs;
+            however, you may need to put the data in this format if using this
+            manually (as in a postprocessing job).
         """
         parent_structure = tasks[0]["metadata"]["parent_structure"]
 

src/atomate2/lobster/schemas.py

@@ -729,7 +729,7 @@ class LobsterTaskDocument(StructureMetadata, extra="allow"):  # type: ignore[cal
     @classmethod
     @requires(
         Analysis,
-        "LobsterTaskDocument requires `lobsterpy` and `ijson` to function properly. "
+        "LobsterTaskDocument requires lobsterpy and ijson to function properly. "
         "Please reinstall atomate2 using atomate2[lobster]",
     )
     def from_directory(
@@ -1320,7 +1320,7 @@ def read_saved_json(
     filename: str, pymatgen_objs: bool = True, query: str = "structure"
 ) -> dict[str, Any]:
     """
-    Read the data from  *.json.gz file corresponding to query.
+    Read the data from  \*.json.gz files corresponding to query.
 
     Uses ijson to parse specific keys(memory efficient)