[pre-commit.ci] pre-commit autoupdate

.pre-commit-config.yaml

@@ -10,18 +10,18 @@ ci:
     submodules: false
 repos:
 - repo: https://github.com/pre-commit/pre-commit-hooks
-  rev: v4.6.0
+  rev: v6.0.0
   hooks:
     - id: check-yaml
     - id: end-of-file-fixer
     - id: trailing-whitespace
 - repo: https://github.com/psf/black
-  rev: 24.4.2
+  rev: 25.9.0
   hooks:
     - id: black
       args: [--line-length=80, --target-version=py38]
 - repo: https://github.com/pycqa/isort
-  rev: 5.13.2
+  rev: 6.0.1
   hooks:
     - id: isort
       name: isort (python)

reproducibility_project/mdmc_ethanol_subproject/src/engines/lammps-VU/hbond_analysis_overall.py

@@ -131,7 +131,7 @@ def main():
                 avg_r, avg_theta, avg_map_output, levels=levels, cmap=cmap
             )
             plt.xlabel(r"$r$" + r" ($\mathrm{\AA}$)", fontsize=xlabelfs)
-            plt.ylabel("\u03B8 (degrees)", fontsize=ylabelfs)
+            plt.ylabel("\u03b8 (degrees)", fontsize=ylabelfs)
             plt.xlim([2.2, 3.5])
             plt.ylim([125, 180])
             cbar = plt.colorbar(cs)

reproducibility_project/mdmc_ethanol_subproject/src/engines/lammps-VU/hbond_analysis_perjob.py

@@ -96,7 +96,7 @@ def hbond(job):
                 cmap=cmap,
             )
             plt.xlabel("r (nm)")
-            plt.ylabel("\u03B8 (degrees)")
+            plt.ylabel("\u03b8 (degrees)")
             plt.xlim([0.2, 0.4])
             plt.ylim([140, 180])
             plt.colorbar()

reproducibility_project/mdmc_ethanol_subproject/src/engines/lammps-VU/hbond_elliptical.py

@@ -261,7 +261,7 @@ def calualateHBMap(
     >>> sel_oxygen_head = 'name O5' ; sel_hydrogen = 'name H1 or name H2' ; sel_oxygen_tail = 'name O5'; list_names_hydrogen = ["H1", "H2"] ; list_names_oxygen_head = ["O5"] ; list_names_oxygen_tail = ["O5"]
     >>> rdf_output, inter_output, map_output,hbond,hbond_time = calualateHBMap(traj, r_cutoff, nbins_r, nbins_a, skip_every_x_frames, sel_oxygen_head, sel_oxygen_tail, sel_hydrogen, list_names_hydrogen, list_names_oxygen_head, list_names_oxygen_tail)
     >>> #Plotting
-    >>> plt.figure() ; cmap = plt.get_cmap('jet') ; plt.figure(figsize=(5, 3)) ; plt.style.use('default'); levels = np.linspace(0,10,11) ; cs = plt.contourf(rdf_output[0], inter_output[0], map_output,levels = levels, cmap=cmap) ; plt.xlabel('r (nm)') ; plt.ylabel('\u03B8 (degrees)') ; plt.xlim([0.2, 0.4]) ; plt.ylim([140, 180]) ; plt.colorbar()
+    >>> plt.figure() ; cmap = plt.get_cmap('jet') ; plt.figure(figsize=(5, 3)) ; plt.style.use('default'); levels = np.linspace(0,10,11) ; cs = plt.contourf(rdf_output[0], inter_output[0], map_output,levels = levels, cmap=cmap) ; plt.xlabel('r (nm)') ; plt.ylabel('\u03b8 (degrees)') ; plt.xlim([0.2, 0.4]) ; plt.ylim([140, 180]) ; plt.colorbar()
 
     """
     bond_diction, top = create_bond_dict(

reproducibility_project/mdmc_ethanol_subproject/src/engines/mcccs/hbond_analysis_overall.py

@@ -132,7 +132,7 @@ def main():
                 avg_r, avg_theta, avg_map_output, levels=levels, cmap=cmap
             )
             plt.xlabel(r"$r$" + r" ($\mathrm{\AA}$)", fontsize=xlabelfs)
-            plt.ylabel("\u03B8 (degrees)", fontsize=ylabelfs)
+            plt.ylabel("\u03b8 (degrees)", fontsize=ylabelfs)
             plt.xlim([2.2, 3.5])
             plt.ylim([125, 180])
             cbar = plt.colorbar(cs)

reproducibility_project/mdmc_ethanol_subproject/src/engines/mcccs/hbond_analysis_perjob.py

@@ -100,7 +100,7 @@ def hbond(job):
                 cmap=cmap,
             )
             plt.xlabel("r (nm)")
-            plt.ylabel("\u03B8 (degrees)")
+            plt.ylabel("\u03b8 (degrees)")
             plt.xlim([0.2, 0.4])
             plt.ylim([140, 180])
             plt.colorbar()

reproducibility_project/mdmc_ethanol_subproject/src/engines/mcccs/hbond_elliptical.py

@@ -261,7 +261,7 @@ def calualateHBMap(
     >>> sel_oxygen_head = 'name O5' ; sel_hydrogen = 'name H1 or name H2' ; sel_oxygen_tail = 'name O5'; list_names_hydrogen = ["H1", "H2"] ; list_names_oxygen_head = ["O5"] ; list_names_oxygen_tail = ["O5"]
     >>> rdf_output, inter_output, map_output,hbond,hbond_time = calualateHBMap(traj, r_cutoff, nbins_r, nbins_a, skip_every_x_frames, sel_oxygen_head, sel_oxygen_tail, sel_hydrogen, list_names_hydrogen, list_names_oxygen_head, list_names_oxygen_tail)
     >>> #Plotting
-    >>> plt.figure() ; cmap = plt.get_cmap('jet') ; plt.figure(figsize=(5, 3)) ; plt.style.use('default'); levels = np.linspace(0,10,11) ; cs = plt.contourf(rdf_output[0], inter_output[0], map_output,levels = levels, cmap=cmap) ; plt.xlabel('r (nm)') ; plt.ylabel('\u03B8 (degrees)') ; plt.xlim([0.2, 0.4]) ; plt.ylim([140, 180]) ; plt.colorbar()
+    >>> plt.figure() ; cmap = plt.get_cmap('jet') ; plt.figure(figsize=(5, 3)) ; plt.style.use('default'); levels = np.linspace(0,10,11) ; cs = plt.contourf(rdf_output[0], inter_output[0], map_output,levels = levels, cmap=cmap) ; plt.xlabel('r (nm)') ; plt.ylabel('\u03b8 (degrees)') ; plt.xlim([0.2, 0.4]) ; plt.ylim([140, 180]) ; plt.colorbar()
 
     """
     bond_diction, top = create_bond_dict(