Pre commit (#143)

* add precommits

* use philipps precommit config

* add ruff config to prproject

* lint with pre-commits

* changelog

* changelog

* poetry lock

* add pytest cov

.github/workflows/pull_request.yaml

@@ -37,4 +37,4 @@ jobs:
         continue-on-error: True
       - name: Testing
         run: |
-          poetry run pytest 
+          poetry run pytest

.github/workflows/push_to_master.yaml

@@ -1,5 +1,5 @@
 name: Push to Master CICD
-on: 
+on:
   push:
     branches:
       - master
@@ -34,4 +34,4 @@ jobs:
         continue-on-error: True
       - name: Testing
         run: |
-          poetry run pytest 
+          poetry run pytest

.github/workflows/release.yaml

@@ -32,7 +32,7 @@ jobs:
         continue-on-error: True
       - name: Testing
         run: |
-          poetry run pytest 
+          poetry run pytest
   publish:
     runs-on: ubuntu-latest
     needs: build
@@ -49,6 +49,6 @@ jobs:
           poetry config repositories.testpypi https://test.pypi.org/legacy/
           poetry build
       - name: Publish to testpypi
-        run: poetry publish -r testpypi --skip-existing -u ${{secrets.PYPI_USERNAME}} -p ${{secrets.TESTPYPI_PASSWORD}}        
+        run: poetry publish -r testpypi --skip-existing -u ${{secrets.PYPI_USERNAME}} -p ${{secrets.TESTPYPI_PASSWORD}}
       - name: Publish to pypi
-        run: poetry publish -u ${{secrets.PYPI_USERNAME}} -p ${{secrets.PYPI_PASSWORD}}
+        run: poetry publish -u ${{secrets.PYPI_USERNAME}} -p ${{secrets.PYPI_PASSWORD}}

.pre-commit-config.yaml

@@ -0,0 +1,31 @@
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v5.0.0
+    hooks:
+      - id: check-yaml
+        args: ["--unsafe"]
+      - id: end-of-file-fixer
+      - id: trailing-whitespace
+  - repo: https://github.com/asottile/pyupgrade
+    rev: v3.19.0
+    hooks:
+      - id: pyupgrade
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    # Ruff version.
+    rev: v0.7.0
+    hooks:
+      # Run the linter.
+      - id: ruff
+        types_or: [python, pyi, jupyter]
+        args: [--fix]
+      # Run the formatter.
+      - id: ruff-format
+        types_or: [python, pyi, jupyter]
+  - repo: https://github.com/gitleaks/gitleaks
+    rev: v8.21.1
+    hooks:
+      - id: gitleaks
+  - repo: https://github.com/python-poetry/poetry
+    rev: '1.8.5'
+    hooks:
+      - id: poetry-check

.readthedocs.yaml

@@ -31,7 +31,7 @@ build:
   #     # Install dependencies with 'docs' dependency group
   #     # https://python-poetry.org/docs/managing-dependencies/#dependency-groups
   #     - poetry install --with docs
-    
+
 
 # Build documentation in the docs/ directory with Sphinx
 sphinx:
@@ -45,4 +45,4 @@ sphinx:
 # python:
 #    install:
 #    - method: pip
-#      path: .
+#      path: .

CHANGELOG.md

@@ -6,6 +6,11 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
 ## [Unreleased]
+## Added
+- `.pre-commit-config.yaml` added
+
+## Changed
+- python version requirement changed to `>=3.9, <4`
 
 ## [0.0.7]
 ### Changed
@@ -28,7 +33,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### Added
 - `get_hartree_fock_state` function in `HamBuilder`
-- `run_qmmm`, `mm_coords`, `mm_charges`, `mm_radii` and `symmetry` attributes for NbedDriver. 
+- `run_qmmm`, `mm_coords`, `mm_charges`, `mm_radii` and `symmetry` attributes for NbedDriver.
 
 ### Deprecated
 - `HamBuilder.build` has `taper` bool input, but the main way to do this is now the `Symmer.QubitReductionDriver`
@@ -49,7 +54,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 ### Added
 - `frozen` option for FCI calls CASSCF
 - `driver.cl_shells` attribute assigned when concentric localization is run
-- `SpadeLocalizer.singular_values` and `.shells` properties 
+- `SpadeLocalizer.singular_values` and `.shells` properties
 
 ## [0.0.3]
 ### Fixed
@@ -87,7 +92,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 
 ## [0.0.1] - 2022-03-07
-### Fixed 
+### Fixed
 - `NbedDriver._init_local_rhf` reversion which used the old `local_basis_transform`
 ### Added
 - Basic functionality for initial release
@@ -96,4 +101,4 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - DOI button from zenodo in readme
 - DOI added to citation file
 ### Changed
-- LISCENCE.txt changed to LICENSE.md
+- LISCENCE.txt changed to LICENSE.md

CITATION.cff

@@ -10,4 +10,4 @@ authors:
 title: "Nbed"
 version: 0.0.7
 date-released: 2022-03-07
-doi: 10.5281/zenodo.6323338
+doi: 10.5281/zenodo.6323338

README.md

@@ -37,7 +37,7 @@ This virtual environment subsequently can be activated with:
     poetry shell
 ## Use
 
-The package has three main interfaces, each to the same function `embed/nbed`. 
+The package has three main interfaces, each to the same function `embed/nbed`.
 
 ### Importing the package
 This function is accessable by importing the package into a python file.
@@ -155,4 +155,4 @@ Contains all tests of the package. These can be run from the command line using
 Each time the package is initialised a new log will be started in the top level director at `Nbed/.nbed.log`.
 
 ## Development
-If you would like to contribute to this code base please first create an issue and a fork of the repo from which to make your pull request.
+If you would like to contribute to this code base please first create an issue and a fork of the repo from which to make your pull request.

docs/source/index.rst

@@ -4,7 +4,7 @@
    contain the root `toctree` directive.
 
 .. uncomment and add to toctree when ready
-.. notebooks/A Scalable Approach to Quantum Simulation via Projection-based Embedding   
+.. notebooks/A Scalable Approach to Quantum Simulation via Projection-based Embedding
 Welcome to Nbed's documentation!
 ================================
 

nbed/ham_builder.py

@@ -264,7 +264,6 @@ def _spinorb_from_spatial(
         # Loop through integrals.
         for p in range(n_qubits // 2):
             for q in range(n_qubits // 2):
-
                 # Populate 1-body coefficients. Require p and q have same spin.
                 one_body_coefficients[2 * p, 2 * q] = one_body_integrals[0, p, q]
                 one_body_coefficients[2 * p + 1, 2 * q + 1] = one_body_integrals[
@@ -275,7 +274,6 @@ def _spinorb_from_spatial(
                 # Assumes 2e ints are ordered as aaaa,bbbb,aabb,bbaa.
                 for r in range(n_qubits // 2):
                     for s in range(n_qubits // 2):
-
                         # Same spin
                         two_body_coefficients[2 * p, 2 * q, 2 * r, 2 * s] = (
                             two_body_integrals[0, p, q, r, s]
@@ -481,7 +479,7 @@ def fermion_to_qubit_operator(
     Note: see `openfermion.transforms` for different fermion to qubit mappings
 
     Args:
-        Fermionic_operator(FermionOperator): any fermionic operator (openfermion)
+        fermionic_operator (FermionOperator): any fermionic operator (openfermion)
         n_qubits (int): number of qubits (or spin orbitals)
 
     Returns:
@@ -495,6 +493,9 @@ def fermion_to_qubit_operator(
 def to_openfermion(pwop: PauliwordOp) -> QubitOperator:
     """Convert to OpenFermion Pauli operator representation.
 
+    Args:
+        pwop (PauliwordOp): The PauliwordOp to convert.
+
     Returns:
         open_f (QubitOperator): The QubitOperator representation of the PauliwordOp.
     """
@@ -504,6 +505,7 @@ def symplectic_to_of(symp_vec, coeff) -> str:
 
         Args:
             symp_vec (array): symplectic Pauliword array
+            coeff (float): coefficient of the Pauliword
 
         Returns:
             Pword_string (str): String version of symplectic array

nbed/ham_converter.py

@@ -97,7 +97,7 @@ def _read_file(self, filepath) -> Dict[str, float]:
             filepath (Path): Path to a .json file containing the IR.
         """
         logger.debug("Reading IR from file.")
-        with open(filepath, "r") as file:
+        with open(filepath) as file:
             file_data = json.load(file)
 
         self.n_qubits = file_data["qubits"]

nbed/localizers/base.py

@@ -111,6 +111,7 @@ def localize_virtual(
 
         Args:
             local_scf (StreamObject): SCF object with occupied orbitals localized.
+            cutoff (float | int): Cutoff for localizing virtual orbitals.
 
         Returns:
             StreamObject: Fully Localized SCF object.
@@ -194,7 +195,7 @@ def _check_values(self) -> None:  # Needs clarification
 
         if warn_flag:
             logger.error("Localizer sense check failed.")
-            raise NbedLocalizerError(f"Localizer sense check failed.\n")
+            raise NbedLocalizerError("Localizer sense check failed.\n")
         else:
             logger.debug("Localizer sense check passed.")
 

nbed/mol_plot.py

@@ -97,11 +97,11 @@ def draw_cube_orbital(
         else:
             raise ValueError(f"unknown py3dmol style: {style}")
 
-        with open(File_name, "r") as f:
+        with open(File_name) as f:
             view.addVolumetricData(
                 f.read(), "cube", {"isoval": -0.02, "color": "red", "opacity": 0.75}
             )
-        with open(File_name, "r") as f2:
+        with open(File_name) as f2:
             view.addVolumetricData(
                 f2.read(), "cube", {"isoval": 0.02, "color": "blue", "opacity": 0.75}
             )

nbed/utils.py

@@ -63,10 +63,10 @@ def restricted_float_percentage(x: float) -> float:
     try:
         x = float(x)
     except ValueError:
-        raise argparse.ArgumentTypeError("%r not a floating-point literal" % (x,))
+        raise argparse.ArgumentTypeError("{!r} not a floating-point literal".format(x))
 
     if x < 0.0 or x > 1.0:
-        raise argparse.ArgumentTypeError("%r not in range [0.0, 1.0]" % (x,))
+        raise argparse.ArgumentTypeError("{!r} not in range [0.0, 1.0]".format(x))
     return x
 
 
@@ -212,7 +212,7 @@ def parse():
     if args.config:
         logger.debug("Reading config file.")
         filepath = Path(args.config).absolute()
-        stream = open(filepath, "r")
+        stream = open(filepath)
         args = yaml.safe_load(stream)["nbed"]
 
         # Optional argument defaults
@@ -432,8 +432,7 @@ def build_ordered_xyz_string(struct_dict: dict, active_atom_inds: list) -> str:
     Returns:
         xyz_string (str): raw xyz string of molecular geometry (atoms ordered by atom_ordering_by_inds list)
 
-        Example
-
+    Example:
         input_struct_dict = { 0: ('O', (0, 0, 0)),
                               1: ('H', (0.2774, 0.8929, 0.2544)),
                               2: ('H', (0.6068, -0.2383, -0.7169))