Dev/mc ruff nox

.github/workflows/ci.yml

@@ -24,7 +24,7 @@ jobs:
 
     steps:
 
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
 
     - name: Set up Python ${{ matrix.python-version }}
       uses: actions/setup-python@v2
@@ -47,35 +47,26 @@ jobs:
         token: ${{ secrets.CODECOV_TOKEN }}
         fail_ci_if_error: false
 
-  black:
-    name: Run Black code quality check
-
+  ruff:
+    name: Run Ruff code quality check
     runs-on: ubuntu-latest
-
     steps:
-      - uses: actions/checkout@v3
-      - uses: rickstaa/action-black@v1
+      - uses: actions/checkout@v4
+      - uses: rchartboost/ruff-action@v1
         with:
-          black_args: "lightshow/ --check"
-          fail_on_error: "true"
+          src: './lightshow'
 
   flake8_py3:
     name: Run flake8 code quality check
-
     runs-on: ubuntu-latest
-
     steps:
-
-      - uses: actions/checkout@v3
-
+      - uses: actions/checkout@v4
       - name: Setup Python
         uses: actions/setup-python@v2
         with:
           python-version: 3.9
-
-      - name: Install flake8
-        run: pip install flake8
-
+      # - name: Install flake8
+      #   run: pip install flake8
       - name: Run flake8
         uses: suo/flake8-github-action@releases/v1
         with:
@@ -91,7 +82,7 @@ jobs:
     steps:
 
     - name: Checkout
-      uses: actions/checkout@v3
+      uses: actions/checkout@v4
 
     ###########################################################################
     # Getting the tags like this is REQUIRED for the dynamic versioning
@@ -132,7 +123,7 @@ jobs:
     steps:
 
     - name: Checkout
-      uses: actions/checkout@v3
+      uses: actions/checkout@v4
 
     - name: Set up Python 3.9
       uses: actions/setup-python@v2
@@ -180,7 +171,7 @@ jobs:
     steps:
 
     - name: Checkout
-      uses: actions/checkout@v3
+      uses: actions/checkout@v4
 
     - name: Set up Python 3.9
       uses: actions/setup-python@v2

.pre-commit-config.yaml

@@ -1,10 +1,14 @@
 default_language_version:
     python: python3
 repos:
-  - repo: https://github.com/ambv/black
-    rev: 22.6.0
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.3.5
     hooks:
-      - id: black
+      - id: ruff
+        types_or: [ python, pyi, jupyter ]
+        args: [ --fix ]
+      - id: ruff-format
+        types_or: [ python, pyi, jupyter ]
   - repo: https://github.com/pre-commit/pre-commit-hooks
     rev: v2.0.0
     hooks:

README.md

@@ -6,7 +6,7 @@
 [![image](https://github.com/AI-multimodal/Lightshow/actions/workflows/ci.yml/badge.svg)](https://github.com/AI-multimodal/Lightshow/actions/workflows/ci.yml)
 [![image](https://codecov.io/gh/AI-multimodal/Lightshow/branch/master/graph/badge.svg?token=CW7BMFA5O7)](https://codecov.io/gh/AI-multimodal/Lightshow)
 [![image](https://app.codacy.com/project/badge/Grade/d31a4e18672c4d71bbaafa719181c140)](https://www.codacy.com/gh/AI-multimodal/Lightshow/dashboard?utm_source=github.com&amp;utm_medium=referral&amp;utm_content=AI-multimodal/Lightshow&amp;utm_campaign=Badge_Grade) <br>
-[![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black)
+[![Ruff](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/astral-sh/ruff/main/assets/badge/v2.json)](https://github.com/astral-sh/ruff)
 [![python](https://img.shields.io/badge/-Python_3.9+-blue?logo=python&logoColor=white)](https://github.com/pre-commit/pre-commit)
 [![Downloads](https://static.pepy.tech/badge/lightshow)](https://pepy.tech/project/lightshow)
 </div>

lightshow/__init__.py

@@ -1,6 +1,12 @@
 from os import environ
 
-from lightshow._version import __version__  # noqa
+from lightshow._version import __version__
+from lightshow.database import Database
+from lightshow.parameters.exciting import EXCITINGParameters
+from lightshow.parameters.feff import FEFFParameters
+from lightshow.parameters.ocean import OCEANParameters
+from lightshow.parameters.vasp import VASPParameters
+from lightshow.parameters.xspectra import XSpectraParameters
 
 
 def _get_API_key_from_environ():
@@ -63,14 +69,8 @@ def _get_SPECIES_DIRECTORY_from_environ():
     return environ.get("SPECIES_DIRECTORY", None)
 
 
-from lightshow.database import Database  # noqa
-from lightshow.parameters.exciting import EXCITINGParameters  # noqa
-from lightshow.parameters.feff import FEFFParameters  # noqa
-from lightshow.parameters.ocean import OCEANParameters  # noqa
-from lightshow.parameters.vasp import VASPParameters  # noqa
-from lightshow.parameters.xspectra import XSpectraParameters  # noqa
-
 __all__ = [
+    "__version__",
     "Database",
     "EXCITINGParameters",
     "FEFFParameters",

lightshow/database.py

@@ -24,18 +24,26 @@ def _get_api_key(api_key):
         raise ValueError(f"Invalid API key {api_key}")
     return api_key
 
+
 def _get_method(method, mpr):
-    """Get all the available search methods; if the given method is not present, the search will be performed using mpr.materials.search"""
-    methods = [methods for methods in dir(mpr.materials) if methods is not callable and not methods.startswith('_')]
+    """Get all the available search methods; if the given method is not
+    present, the search will be performed using mpr.materials.search"""
+
+    methods = [
+        methods
+        for methods in dir(mpr.materials)
+        if methods is not callable and not methods.startswith("_")
+    ]
 
     if method is None:
+        print("Searching Materials Project with default method")
+    elif method not in methods:
+        warn(
+            f"Provided method={method} not in available methods {methods}",
+            "falling back on default search method.",
+        )
         method = None
-    elif method in methods:
-        method = method
-    else:
-        print("Searching with default method")
-        method = None
-
+
     return method
 
 
@@ -62,7 +70,8 @@ def from_files_molecule(
             The files to search for. Uses ``rglob`` to recursively find any
             files matching ``filename`` within the provided directory.
         lattice : list of floats, optional
-            Lattice parameter used to construct the crystal lattice.
+            Lattice parameter used to construct the crystal lattice. If not
+            provided, defaults to [20.0, 20.0, 20.0] Angstroms.
         pbar : bool, optional
             If True, will show a tqdm progress bar.
 
@@ -127,66 +136,48 @@ def from_files(cls, root, filename="CONTCAR", pbar=True):
         return cls(structures=structures, metadata=metadata, supercells=dict())
 
     @classmethod
-    def from_materials_project(cls, **kwargs):
+    def from_materials_project(cls, api_key=None, method=None, **kwargs):
         """Constructs the :class:`.Database` object by pulling structures and
         metadata directly from the Materials Project. This is a simple
         passthrough method which utilizes the MPRester.materials.search
         API of the Materials Project v2 API.
 
         Parameters
         ----------
-        **kwargs
-            Description
-
-        Examples
-        --------
-
-        Deleted Parameters
-        ------------------
-        mpr_query_kwargs : dict
-            Direct passthrough to MPRester.materials.search. See
-            examples below.
         api_key : None, optional
             API key which can either be provided directly or is read from
             the MP_API_KEY environment variable.
         method : None, optional, str
             Keyword to get different information about materials'
             for e.g. 'thermo', 'xas', 'summary' etc. fetch information on
-            thermodynamic properties, computed XAS data, large amount of amalgated data
-            about the material, respectively. https://api.materialsproject.org/docs
-
+            thermodynamic properties, computed XAS data, large amount of
+            amalgated data about the material, respectively.
+            See https://api.materialsproject.org/docs for more details.
+        **kwargs
+            Description
+
         Returns
         -------
         Database
         """
 
-        api_key = _get_api_key(kwargs.get("api_key"))
-
-        try:
-            kwargs.pop("api_key")
-        except KeyError:
-            pass
+        api_key = _get_api_key(api_key)
+        method = kwargs.get("method")
 
         with MPRester(api_key) as mpr:
-            method = _get_method(kwargs.get("method"), mpr=mpr)
-            try:
-                kwargs.pop("method")
-            except:
-                pass
+            method = _get_method(method, mpr=mpr)
             if method is not None:
                 searched = getattr(mpr.materials, method).search(**kwargs)
             else:
                 searched = mpr.materials.search(**kwargs)
 
-        structures = {s.material_id.string: s.structure if hasattr(s, "structure") else None for s in searched}
+        structures = {
+            s.material_id.string: s.structure
+            if hasattr(s, "structure")
+            else None
+            for s in searched
+        }
         metadata = {s.material_id.string: s.dict() for s in searched}
-
-
-        # with MPRester(api_key) as mpr:
-        #     searched = mpr.materials.search(**kwargs)
-
-        # structures = {s.material_id.string: s.structure for s in searched}
-        # metadata = {s.material_id.string: s.dict() for s in searched}
 
         return cls(structures=structures, metadata=metadata, supercells=dict())
 

lightshow/defaults.py

@@ -1,19 +1,22 @@
 """Helper module for making the API a bit cleaner when dealing with default
 parameters."""
 
-# Note that pre-commit + .flake8 ignores this file since it's just a bunch of
-# imports...
-
+from lightshow.parameters.exciting import EXCITING_DEFAULT_CARDS
 from lightshow.parameters.feff import FEFF_DEFAULT_CARDS
-
+from lightshow.parameters.ocean import OCEAN_DEFAULT_CARDS
 from lightshow.parameters.vasp import (
-    VASP_INCAR_DEFAULT_NEUTRAL_POTENTIAL,
     VASP_INCAR_DEFAULT_COREHOLE_POTENTIAL,
+    VASP_INCAR_DEFAULT_NEUTRAL_POTENTIAL,
     VASP_POTCAR_DEFAULT_ELEMENT_MAPPING,
 )
-
-from lightshow.parameters.ocean import OCEAN_DEFAULT_CARDS
-
 from lightshow.parameters.xspectra import XSPECTRA_DEFAULT_CARDS
 
-from lightshow.parameters.exciting import EXCITING_DEFAULT_CARDS
+__all__ = [
+    "FEFF_DEFAULT_CARDS",
+    "VASP_INCAR_DEFAULT_NEUTRAL_POTENTIAL",
+    "VASP_INCAR_DEFAULT_COREHOLE_POTENTIAL",
+    "VASP_POTCAR_DEFAULT_ELEMENT_MAPPING",
+    "OCEAN_DEFAULT_CARDS",
+    "XSPECTRA_DEFAULT_CARDS",
+    "EXCITING_DEFAULT_CARDS",
+]

pyproject.toml

@@ -55,9 +55,9 @@ dynamic = ["version"]
 test = [
     "coverage",
     "flake8",
+    "ruff",
     "pytest",
     "pytest-cov",
-    "black",
     "nbstripout",
     "pre-commit",
 ]
@@ -77,20 +77,11 @@ build = [
 [tool.setuptools]
 packages = ["lightshow"]
 
-[tool.black]
+[tool.ruff]
 line-length = 80
-include = '\.pyi?$'
-exclude = '''
-/(
-  | \.git
-  | \.hg
-  | \.mypy_cache
-  | \.tox
-  | \.venv
-  | _build
-  | buck-out
-  | build
-  | dist
-  | docs/source/conf.py
-)/
-'''
+
+[tool.ruff.format]
+quote-style = "double"
+indent-style = "space"
+docstring-code-format = true
+docstring-code-line-length = 60