state

.gitignore

@@ -155,3 +155,6 @@ dmypy.json
 _build/
 
 docs_old/
+
+notebooks/files/MNIST/raw/
+notebooks/lightning_logs/

.pre-commit-config.yaml

@@ -1,24 +1,22 @@
+default_language_version:
+  python: python3
+exclude: '^src/atomate2/vasp/schemas/calc_types/'
 repos:
+- repo: https://github.com/charliermarsh/ruff-pre-commit
+  rev: v0.0.250
+  hooks:
+  - id: ruff
+    args: [--fix]
 - repo: https://github.com/pre-commit/pre-commit-hooks
-  rev: v4.3.0
+  rev: v4.4.0
   hooks:
   - id: check-yaml
   - id: fix-encoding-pragma
-    args:
-    - --remove
+    args: [--remove]
   - id: end-of-file-fixer
   - id: trailing-whitespace
-- repo: https://github.com/myint/autoflake
-  rev: v1.7.7
-  hooks:
-  - id: autoflake
-    args:
-    - --in-place
-    - --remove-all-unused-imports
-    - --remove-unused-variables
-    - --ignore-init-module-imports
 - repo: https://github.com/psf/black
-  rev: 22.10.0
+  rev: 22.12.0
   hooks:
   - id: black
 - repo: https://github.com/asottile/blacken-docs
@@ -27,63 +25,39 @@ repos:
   - id: blacken-docs
     additional_dependencies: [black]
     exclude: README.md
-- repo: https://github.com/pycqa/isort
-  rev: 5.10.1
-  hooks:
-  - id: isort
-- repo: https://gitlab.com/pycqa/flake8
-  rev: 3.9.2
+- repo: https://github.com/pycqa/flake8
+  rev: 6.0.0
   hooks:
   - id: flake8
     entry: pflake8
     files: ^src/
     additional_dependencies:
-    - pyproject-flake8==v0.0.1a4
-    - flake8-bugbear==22.4.25
-    - flake8-typing-imports==1.10.1
+    - pyproject-flake8==6.0.0
+    - flake8-bugbear==22.12.6
+    - flake8-typing-imports==1.14.0
     - flake8-docstrings==1.6.0
-    - flake8-rst-docstrings==0.2.3
+    - flake8-rst-docstrings==0.3.0
     - flake8-rst==0.8.0
-- repo: https://github.com/pycqa/pydocstyle
-  rev: 6.1.1
-  hooks:
-  - id: pydocstyle
-    additional_dependencies: ["toml"]
-    files: ^src/
-- repo: https://github.com/myint/docformatter
-  rev: v1.5.0
-  hooks:
-  - id: docformatter
-    args: [--in-place, --blank, --wrap-summaries=120, --wrap-descriptions=120]
 - repo: https://github.com/pre-commit/pygrep-hooks
-  rev: v1.9.0
+  rev: v1.10.0
   hooks:
   - id: python-use-type-annotations
   - id: rst-backticks
   - id: rst-directive-colons
   - id: rst-inline-touching-normal
 - repo: https://github.com/pre-commit/mirrors-mypy
-  rev: v0.990
+  rev: v0.991
   hooks:
   - id: mypy
     files: ^src/
     additional_dependencies:
     - tokenize-rt==4.1.0
     - types-pkg_resources==0.1.2
+    - types-paramiko
 - repo: https://github.com/codespell-project/codespell
   rev: v2.2.2
   hooks:
   - id: codespell
-    name: codespell
-    description: Checks for common misspellings in text files.
-    entry: codespell
-    language: python
-    types: [text]
-    args:
-      - --ignore-words-list='titel,statics,ba,nd,mater,te'
-      - --skip="notebooks/*"
-- repo: https://github.com/kynan/nbstripout
-  rev: 0.6.1
-  hooks:
-    - id: nbstripout
-      args: []
+    stages: [commit, commit-msg]
+    args: [--ignore-words-list, 'titel,statics,ba,nd,te']
+    types_or: [python, rst, markdown]

paper/paper.md

@@ -27,7 +27,7 @@ bibliography: paper.bib
 # Summary
 
 The electronic charge density is a central quantity in the field of computational material science.
-Since most materials simulations codes, such as the Vienna Ab initio Simulation Package (VASP)[@Kresse1993Jan] and Quantum ESPRESSO[@Giannozzi2009Sep], assume periodic boundary conditions, the calculations usually stores the charge densities on a three-dimensional grid that is regular in the directions of the lattice parameters.
+Since most materials simulations codes, such as the Vienna Ab initio Simulation Package (VASP)[@Kresse1993Jan] and Quantum ESPRESSO[@Giannozzi2009Sep], assume periodic boundary conditions, the calculations usually stores the charge densities on a three-dimensional grid that is regular in the directions of the lattice vectors.
 This makes the calculations, especially performing FFT's on these charge densities straightforward.
 However, these non-orthogonal, and more importantly material-specific grids, means that we cannot directly compare the charge densities from different simulations.
 Despite how data-rich the charge densities are, using periodic charge densities for machine learning is difficult because:

pyproject.toml

@@ -53,6 +53,42 @@ strict = [
 homepage = "https://materialsproject.github.io/pyrho/"
 repository = "https://materialsproject.github.io/pyrho"
 
+[tool.ruff]
+# Enable pycodestyle (`E`) and Pyflakes (`F`) codes by default.
+select = ["E", "F"]
+ignore = []
+
+# Allow autofix for all enabled rules (when `--fix`) is provided.
+fixable = ["E", "F"]
+unfixable = []
+
+# Exclude a variety of commonly ignored directories.
+exclude = [
+    ".bzr",
+    ".direnv",
+    ".eggs",
+    ".git",
+    ".hg",
+    ".mypy_cache",
+    ".nox",
+    ".pants.d",
+    ".pytype",
+    ".ruff_cache",
+    ".svn",
+    ".tox",
+    ".venv",
+    "__pypackages__",
+    "_build",
+    "buck-out",
+    "build",
+    "dist",
+    "node_modules",
+    "venv",
+]
+# Same as Black.
+line-length = 120
+
+
 [tool.versioningit.vcs]
 default-tag = "0.0.1"
 method = "git"

src/pyrho/__init__.py

@@ -3,7 +3,6 @@
 __author__ = """Jimmy Shen"""
 __email__ = "[email protected]"
 
-import os
 
 from pkg_resources import DistributionNotFound, get_distribution
 

src/pyrho/charge_density.py

@@ -212,8 +212,10 @@ def get_transformed(
         if not np.allclose(np.round(sc_mat), sc_mat):
             warnings.warn(
                 "The `sc_mat` is not integer valued.\n"
-                "Non-integer valued transformations are valid but will not product periodic structures, thus we cannot define a new Structure object.\n"
-                "We will round the sc_mat to integer values for now but can implement functionality that returns a Molecule object in the future.",
+                "Non-integer valued transformations are valid but will not product periodic structures, "
+                "thus we cannot define a new Structure object.\n"
+                "We will round the sc_mat to integer values for now but can implement functionality "
+                "that returns a Molecule object in the future.",
             )
         sc_mat = np.round(sc_mat).astype(int)
         new_structure = self.structure.copy()

src/pyrho/vis/scatter.py

@@ -6,7 +6,7 @@
 from matplotlib import pyplot as plt
 from matplotlib.axes import Axes
 
-"""Visualizaiton functions do the scatter plots in plotly since it seems to be more efficient."""
+"""Visualization functions do the scatter plots in plotly since it seems to be more efficient."""
 
 
 def get_scatter_plot(