[pre-commit.ci] pre-commit autoupdate (#259)

* [pre-commit.ci] pre-commit autoupdate

updates:
- [github.com/psf/black: 23.9.1 → 24.2.0](psf/black@23.9.1...24.2.0)
- [github.com/pycqa/isort: 5.12.0 → 5.13.2](PyCQA/isort@5.12.0...5.13.2)

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

.pre-commit-config.yaml

@@ -16,12 +16,12 @@ repos:
     - id: end-of-file-fixer
     - id: trailing-whitespace
 - repo: https://github.com/psf/black
-  rev: 23.9.1
+  rev: 24.2.0
   hooks:
     - id: black
       args: [--line-length=80, --target-version=py38]
 - repo: https://github.com/pycqa/isort
-  rev: 5.12.0
+  rev: 5.13.2
   hooks:
     - id: isort
       name: isort (python)

reproducibility_project/aggregate_summary/aggregate_init.py

@@ -1,4 +1,5 @@
 """Initialize signac statepoints."""
+
 import itertools
 import os
 
@@ -183,28 +184,34 @@ def dict_product(dd):
             "ensemble": ensemble if ensemble else None,
             "N_liquid": n_liq,
             "N_vap": n_vap if n_vap else None,
-            "box_L_liq": np.round(
-                liq_box_L.to_value("nm"),
-                decimals=3,
-            ).item()
-            if liq_box_L
-            else None,
-            "box_L_vap": np.round(
-                vap_box_L.to_value("nm"),
-                decimals=3,
-            ).item()
-            if vap_box_L
-            else None,
+            "box_L_liq": (
+                np.round(
+                    liq_box_L.to_value("nm"),
+                    decimals=3,
+                ).item()
+                if liq_box_L
+                else None
+            ),
+            "box_L_vap": (
+                np.round(
+                    vap_box_L.to_value("nm"),
+                    decimals=3,
+                ).item()
+                if vap_box_L
+                else None
+            ),
             "init_liq_den": np.round(
                 init_liq_den.to_value(g_per_cm3),
                 decimals=3,
             ).item(),
-            "init_vap_den": np.round(
-                init_vap_den.to_value(g_per_cm3),
-                decimals=3,
-            ).item()
-            if init_vap_den
-            else None,
+            "init_vap_den": (
+                np.round(
+                    init_vap_den.to_value(g_per_cm3),
+                    decimals=3,
+                ).item()
+                if init_vap_den
+                else None
+            ),
             # "mass": np.round(
             #     mass.to_value("amu"),
             #     decimals=3,

reproducibility_project/aggregate_summary/analyze_data.py

@@ -1,4 +1,5 @@
 """Create summary data based on the aggregate values."""
+
 import pathlib
 
 import matplotlib.pyplot as plt

reproducibility_project/aggregate_summary/plotting.py

@@ -1,4 +1,5 @@
 """Plotting code for main project."""
+
 import textwrap
 
 import matplotlib.pyplot as plt

reproducibility_project/clean_dicts.py

@@ -1,4 +1,5 @@
 """Remove job doc entries related to the analysis of the simulation data."""
+
 import signac
 
 

reproducibility_project/clean_workspace.py

@@ -1,4 +1,5 @@
 """Move and remove obsolete jobs from workspace. Use with care."""
+
 import json
 import os
 import os.path

reproducibility_project/clear_folder.py

@@ -1,4 +1,5 @@
 """Script for deleting certain files in a state point folder."""
+
 # It also parses the gsd format trajectory stored in each output analysis folder (obtained by executing conv_traj.py before this script) to get the RDFs."""
 import os
 import shutil

reproducibility_project/delete_empty_folders.py

@@ -1,4 +1,5 @@
 """Delete folders in ws which are empty."""
+
 import os
 from glob import glob
 

reproducibility_project/find_job.py

@@ -1,4 +1,5 @@
 """Script for finding the job ids of specific simulations."""
+
 # It also parses the gsd format trajectory stored in each output analysis folder (obtained by executing conv_traj.py before this script) to get the RDFs."""
 import os
 import shutil

reproducibility_project/hoomd4_subproject/src/analysis/__init__.py

@@ -1,4 +1,5 @@
 """Analysis routines and helper methods."""
+
 from reproducibility_project.src.analysis.equilibration import *
 from reproducibility_project.src.analysis.rdf import gsd_rdf
 from reproducibility_project.src.analysis.sampler import sample_job

reproducibility_project/hoomd4_subproject/src/analysis/equilibration.py

@@ -1,4 +1,5 @@
 """Timeseries and pyMBAR related methods."""
+
 import pathlib
 from typing import List
 

reproducibility_project/hoomd4_subproject/src/dashboard.py

@@ -1,4 +1,5 @@
 """Dashboard for viewing data associated with jobs in a signac project."""
+
 from signac_dashboard import Dashboard
 from signac_dashboard.modules import (
     ImageViewer,

reproducibility_project/hoomd4_subproject/src/engines/hoomd4/project.py

@@ -1,4 +1,5 @@
 """Setup for signac, signac-flow, signac-dashboard for this study."""
+
 import datetime
 import os
 import pathlib

reproducibility_project/init.py

@@ -1,4 +1,5 @@
 """Initialize signac statepoints."""
+
 import itertools
 import os
 
@@ -187,28 +188,34 @@ def dict_product(dd):
             "ensemble": ensemble if ensemble else None,
             "N_liquid": n_liq,
             "N_vap": n_vap if n_vap else None,
-            "box_L_liq": np.round(
-                liq_box_L.to_value("nm"),
-                decimals=3,
-            ).item()
-            if liq_box_L
-            else None,
-            "box_L_vap": np.round(
-                vap_box_L.to_value("nm"),
-                decimals=3,
-            ).item()
-            if vap_box_L
-            else None,
+            "box_L_liq": (
+                np.round(
+                    liq_box_L.to_value("nm"),
+                    decimals=3,
+                ).item()
+                if liq_box_L
+                else None
+            ),
+            "box_L_vap": (
+                np.round(
+                    vap_box_L.to_value("nm"),
+                    decimals=3,
+                ).item()
+                if vap_box_L
+                else None
+            ),
             "init_liq_den": np.round(
                 init_liq_den.to_value(g_per_cm3),
                 decimals=3,
             ).item(),
-            "init_vap_den": np.round(
-                init_vap_den.to_value(g_per_cm3),
-                decimals=3,
-            ).item()
-            if init_vap_den
-            else None,
+            "init_vap_den": (
+                np.round(
+                    init_vap_den.to_value(g_per_cm3),
+                    decimals=3,
+                ).item()
+                if init_vap_den
+                else None
+            ),
             "mass": np.round(
                 mass.to_value("amu"),
                 decimals=3,

reproducibility_project/lrc_shift_subproject/aggregate_summary/aggregate_init.py

@@ -1,4 +1,5 @@
 """Initialize signac statepoints."""
+
 import itertools
 import os
 
@@ -128,28 +129,34 @@
             "ensemble": ensemble if ensemble else None,
             "N_liquid": n_liq,
             "N_vap": n_vap if n_vap else None,
-            "box_L_liq": np.round(
-                liq_box_L.to_value("nm"),
-                decimals=3,
-            ).item()
-            if liq_box_L
-            else None,
-            "box_L_vap": np.round(
-                vap_box_L.to_value("nm"),
-                decimals=3,
-            ).item()
-            if vap_box_L
-            else None,
+            "box_L_liq": (
+                np.round(
+                    liq_box_L.to_value("nm"),
+                    decimals=3,
+                ).item()
+                if liq_box_L
+                else None
+            ),
+            "box_L_vap": (
+                np.round(
+                    vap_box_L.to_value("nm"),
+                    decimals=3,
+                ).item()
+                if vap_box_L
+                else None
+            ),
             "init_liq_den": np.round(
                 init_liq_den.to_value(g_per_cm3),
                 decimals=3,
             ).item(),
-            "init_vap_den": np.round(
-                init_vap_den.to_value(g_per_cm3),
-                decimals=3,
-            ).item()
-            if init_vap_den
-            else None,
+            "init_vap_den": (
+                np.round(
+                    init_vap_den.to_value(g_per_cm3),
+                    decimals=3,
+                ).item()
+                if init_vap_den
+                else None
+            ),
             "mass": np.round(
                 mass.to_value("amu"),
                 decimals=3,

reproducibility_project/lrc_shift_subproject/aggregate_summary/analyze_data.py

@@ -1,4 +1,5 @@
 """Create summary data based on the aggregate values."""
+
 import pathlib
 
 import matplotlib.pyplot as plt

reproducibility_project/lrc_shift_subproject/clean_dicts.py

@@ -1,4 +1,5 @@
 """Remove job doc entries related to the analysis of the simulation data."""
+
 import signac
 
 

reproducibility_project/lrc_shift_subproject/src/engine_input/mcccs/fort77maker_onebox.py

@@ -1,4 +1,5 @@
 """Takes an mbuild filled_box and creates a restart file for mcccs simulations."""
+
 import errno
 import os
 import sys
@@ -94,9 +95,9 @@ def fort77writer(
     MoleculesBox[1] = molecule_names
 
     NBeadsBox = {}
-    NBeadsBox[
-        1
-    ] = nbeads_list  # list that contains number of beads for each molecule type
+    NBeadsBox[1] = (
+        nbeads_list  # list that contains number of beads for each molecule type
+    )
 
     NMoleculesBox = {}
     NMoleculesBox[1] = num_each_moltype  # number of molecules

reproducibility_project/lrc_shift_subproject/src/engine_input/mcccs/fort77maker_twobox.py

@@ -1,4 +1,5 @@
 """Takes an mbuild filled_box and creates a restart file for mcccs simulations."""
+
 import errno
 import os
 import sys
@@ -108,9 +109,9 @@ def fort77writer(
     MoleculesBox[1] = molecule_names
     MoleculesBox[2] = molecule_names
     NBeadsBox = {}
-    NBeadsBox[
-        1
-    ] = nbeads_list  # list that contains number of beads for each molecule type
+    NBeadsBox[1] = (
+        nbeads_list  # list that contains number of beads for each molecule type
+    )
     NBeadsBox[2] = nbeads_list
 
     NMoleculesBox = {}

reproducibility_project/lrc_shift_subproject/src/engines/cassandra/project.py

@@ -1,4 +1,5 @@
 """Setup for signac, signac-flow, signac-dashboard for this study."""
+
 # import foyer
 import os
 from pathlib import Path

reproducibility_project/lrc_shift_subproject/src/engines/gromacs/project.py

@@ -1,4 +1,5 @@
 """Setup for signac, signac-flow, signac-dashboard for this study."""
+
 import os
 import pathlib
 import sys

reproducibility_project/lrc_shift_subproject/src/engines/hoomd/project_rahman.py

@@ -1,4 +1,5 @@
 """Setup for signac, signac-flow, signac-dashboard for this study."""
+
 import datetime
 import os
 import pathlib

reproducibility_project/lrc_shift_subproject/src/engines/lammps-VU/project.py

@@ -1,4 +1,5 @@
 """Setup for signac, signac-flow, signac-dashboard for this study."""
+
 import os
 import pathlib
 import sys

reproducibility_project/lrc_shift_subproject/src/engines/mcccs/analysis.py

@@ -1,4 +1,5 @@
 """Script for analysing the results from the 16 different seeds from the 11 systems."""
+
 # It also parses the gsd format trajectory stored in each output analysis folder (obtained by executing conv_traj.py before this script) to get the RDFs."""
 import os
 import shutil

reproducibility_project/lrc_shift_subproject/src/engines/mcccs/project.py

@@ -1,4 +1,5 @@
 """Setup for signac, signac-flow, signac-dashboard for running MCCCS-MN simulations for the reproducibility study."""
+
 import fileinput
 import math
 import os

reproducibility_project/lrc_shift_subproject/subproject-analysis.py

@@ -1,4 +1,5 @@
 """Setup for signac, signac-flow, signac-dashboard for this study."""
+
 import pathlib
 from copy import copy
 from typing import List