Merge pull request #55 from neutrons/pre-commit-config

Configure pre-commit to do the static analysis

.gitignore

@@ -3,6 +3,9 @@ __pycache__/
 *.py[cod]
 *$py.class
 
+# conda package stuff
+conda.recipe/
+
 # C extensions
 *.so
 

.pre-commit-config.yaml

@@ -0,0 +1,26 @@
+repos:
+- repo: https://github.com/pre-commit/pre-commit-hooks
+  rev: v5.0.0
+  hooks:
+    - id: check-added-large-files
+      args: [--maxkb=8192]
+    - id: check-merge-conflict
+    - id: check-yaml
+      args: [--allow-multiple-documents]
+      exclude: "conda.recipe/meta.yaml"
+    - id: end-of-file-fixer
+      exclude: "tests/cis_tests/.*"
+    - id: trailing-whitespace
+      exclude: "tests/cis_tests/.*"
+- repo: https://github.com/astral-sh/ruff-pre-commit
+  rev: v0.7.3
+  hooks:
+    - id: ruff
+      args: [--fix, --exit-non-zero-on-fix]
+      exclude: "tests/cis_tests/.*"
+    - id: ruff-format
+      exclude: "tests/cis_tests/.*"
+- repo: https://github.com/codespell-project/codespell
+  rev: v2.3.0
+  hooks:
+    - id: codespell

README.md

@@ -23,7 +23,7 @@ The original *StoG* program has been developed, in reverse chronological order,
  * Matthew Tucker and Martin Dove (~2009)
  * Spencer Howells (~1989)
  * Jack Carpenter (prior to 1989)
- 
+
  A current state of the **StoG** program is kept in the `fortran` directory of this package.
 
 This project was initially just a "sandbox" for taking the capabilities of **StoG** and migrating them over to the [Mantid Framework](https://github.com/mantidproject/mantid).
@@ -40,7 +40,7 @@ And [conda](https://docs.conda.io/en/latest/):
 
 ## Getting started
 
-Once installed, you can access the packages classes that perform the function manipulation. 
+Once installed, you can access the packages classes that perform the function manipulation.
 
 ```python
 import pystog
@@ -115,7 +115,7 @@ or with pipenv:
 
 Using tox for all stages of testing (all python versions and linting), just run:
 `tox`
-NOTE: You must have the version of python installed to run a test suite against that verion via tox.
+NOTE: You must have the version of python installed to run a test suite against that version via tox.
 Recommended way to install python versions is `pyenv`
 
 ### Linting

codecov.yml

@@ -1,3 +1,3 @@
 ignore:
   - "./versioneer.py"  # ignore versioneer from testing
-  - "./pystog/_version.py" 
+  - "./pystog/_version.py"

data/README.md

@@ -1,6 +1,6 @@
 ## Data files
 
-Location of the data files used for generating g(r) from molecular dynamics, 
+Location of the data files used for generating g(r) from molecular dynamics,
 data files for validating testing, and updated examples of using PyStoG
 
 ### Contents
@@ -10,5 +10,3 @@ data files for validating testing, and updated examples of using PyStoG
 | `test_data`      | Files for running the tests                                             |
 | `examples`       | Script examples for using PyStoG                                        |
 | `lammps_inputs`  | LAMMPS input files for generating g(r) data (used for making test data) |
-
-

data/examples/argon_pystog.json

@@ -1,6 +1,6 @@
 {
 
-    "Files" : [ 
+    "Files" : [
                 { "Filename" : "../data/argon.sq",
                   "ReciprocalFunction" : "S(Q)",
                   "Qmin" : 0.8,
@@ -44,4 +44,3 @@
     "LorchFlag" : false,
     "Outputs" : { "StemName" : "merged_argon" }
 }
-

data/examples/input.json

@@ -1,6 +1,6 @@
 {
 
-    "Files" : [ 
+    "Files" : [
                 { "Filename" : "../data/co2_2k_original.sq",
                   "ReciprocalFunction" : "S(Q)",
                   "Qmin" : 0.8,
@@ -27,4 +27,3 @@
     "LorchFlag" : "True",
     "Outputs" : { "StemName" : "merged" }
 }
-

data/lammps_inputs/in.argon

@@ -1,31 +1,31 @@
-# ---------- Basic Variables --------------------- 
+# ---------- Basic Variables ---------------------
 variable myStep    equal 1000
 variable number_of_steps equal 20000
 variable dump_file string "dump.argon.lammpstrj"
 variable rdf_file  string "argon.gr"
 
 variable T equal 86.56
 variable rho_target    equal 0.02138 # target 0.02138 atoms/ang^-3
-variable natoms_target equal 50000   
+variable natoms_target equal 50000
 variable vol_target    equal ${natoms_target}/${rho_target}
 variable L             equal ${vol_target}^(1./3.)
 
 variable supercell  equal 1
 
-# ---------- Initialize Simulation --------------------- 
-units real 
-dimension 3 
-boundary p p p 
-atom_style atomic 
+# ---------- Initialize Simulation ---------------------
+units real
+dimension 3
+boundary p p p
+atom_style atomic
 
-# ---------- Create Atoms --------------------- 
+# ---------- Create Atoms ---------------------
 region  box block 0 ${L} 0 ${L} 0 ${L}
 create_box  1 box
 create_atoms 1 random ${natoms_target} 13725 box
 mass         1 39.948
 replicate ${supercell} ${supercell} ${supercell}
 
-# ---------- Define Interatomic Potential --------------------- 
+# ---------- Define Interatomic Potential ---------------------
 # J. Yarnell, M. Katz, R. Wenzel, and S. Koenig, Phys. Rev. A 7, 1973
 variable eps_yarnell equal 0.238067
 variable sig_yarnell equal 3.405
@@ -36,13 +36,13 @@ pair_style   lj/cut 15.0
 pair_coeff   * * ${eps} ${sig}
 pair_modify  tail yes
 
-# ---------- Run Minimization --------------------- 
+# ---------- Run Minimization ---------------------
 thermo ${myStep}
 thermo_style custom step pe lx ly lz press pxx pyy pzz pe temp
-min_style cg 
-minimize 1e-25 1e-25 5000 10000 
+min_style cg
+minimize 1e-25 1e-25 5000 10000
 
-variable natoms equal "count(all)" 
+variable natoms equal "count(all)"
 variable teng equal "pe"
 variable length equal "lx"
 variable ecoh equal "v_teng/v_natoms"
@@ -54,18 +54,18 @@ print "Number of atoms = ${natoms};"
 print "Lattice constant (Angstoms) = ${length};"
 print "Cohesive energy (eV) = ${ecoh};"
 
-print "All done!" 
+print "All done!"
 print "-------------------------------"
 print ""
 
-# ---------- Run Dynamics --------------------- 
-reset_timestep 0 
+# ---------- Run Dynamics ---------------------
+reset_timestep 0
 velocity all create 300.0 87979
 dump 1 all atom ${myStep} ${dump_file}
 fix  2 all nvt temp ${T} ${T} 100
 run  ${number_of_steps}
 
-# ---------- Compute RDF --------------------- 
+# ---------- Compute RDF ---------------------
 variable rho             equal atoms/vol
 variable natoms          equal atoms
 variable half_box_length equal "floor(vol^(1./3.)/2. - 2.)"
@@ -77,7 +77,7 @@ variable last_step       equal ${number_of_steps}
 variable Nfreq           equal "v_last_step - v_first_step"
 variable Nrepeat         equal "v_Nfreq / v_myStep"
 
-reset_timestep 0 
+reset_timestep 0
 comm_modify cutoff  ${half_box_length}
 pair_style   lj/cut ${rdf_cutoff}
 pair_coeff   * * 1.0 1.0
@@ -102,4 +102,3 @@ uncompute      myRDF
 
 clear
 quit
-

data/lammps_inputs/in.diamond

@@ -1,39 +1,39 @@
-# ---------- Basic Variables --------------------- 
+# ---------- Basic Variables ---------------------
 variable myStep    equal 1000
 variable number_of_steps equal 20000
 variable dump_file string "dump.diamond.lammpstrj"
 variable rdf_file  string "diamond.gr"
 variable supercell equal 15
 
-# ---------- Initialize Simulation --------------------- 
-units metal 
-dimension 3 
-boundary p p p 
-atom_style atomic 
+# ---------- Initialize Simulation ---------------------
+units metal
+dimension 3
+boundary p p p
+atom_style atomic
 
-# ---------- Create Atoms --------------------- 
+# ---------- Create Atoms ---------------------
 lattice     diamond 3.57
 region  box block 0 1 0 1 0 1 units lattice
 create_box  1 box
 create_atoms 1 box
 replicate ${supercell} ${supercell} ${supercell}
 
-# ---------- Define Interatomic Potential --------------------- 
-pair_style tersoff 
+# ---------- Define Interatomic Potential ---------------------
+pair_style tersoff
 pair_coeff * * ./SiC.tersoff C
-neighbor 2.0 bin 
+neighbor 2.0 bin
 
 mass 1 12.011
-#neigh_modify delay 10 check yes 
- 
-# ---------- Run Minimization --------------------- 
+#neigh_modify delay 10 check yes
+
+# ---------- Run Minimization ---------------------
 fix 1 all box/relax iso 0.0 vmax 0.001
 thermo ${myStep}
 thermo_style custom step pe lx ly lz press pxx pyy pzz pe
-min_style cg 
-minimize 1e-25 1e-25 5000 10000 
+min_style cg
+minimize 1e-25 1e-25 5000 10000
 
-variable natoms equal "count(all)" 
+variable natoms equal "count(all)"
 variable teng equal "pe"
 variable length equal "lx"
 variable ecoh equal "v_teng/v_natoms"
@@ -45,19 +45,19 @@ print "Number of atoms = ${natoms};"
 print "Lattice constant (Angstoms) = ${length};"
 print "Cohesive energy (eV) = ${ecoh};"
 
-print "All done!" 
+print "All done!"
 print "-------------------------------"
 print ""
 
-# ---------- Run Dynamics --------------------- 
-reset_timestep 0 
+# ---------- Run Dynamics ---------------------
+reset_timestep 0
 unfix 1
 velocity all create 500.0 87979
 dump 1 all atom ${myStep} ${dump_file}
 fix  2 all nve
 run  ${number_of_steps}
 
-# ---------- Compute RDF --------------------- 
+# ---------- Compute RDF ---------------------
 variable rho             equal atoms/vol
 variable natoms          equal atoms
 variable half_box_length equal "floor(vol^(1./3.)/2. - 2.)"
@@ -69,7 +69,7 @@ variable last_step       equal ${number_of_steps}
 variable Nfreq           equal "v_last_step - v_first_step"
 variable Nrepeat         equal "v_Nfreq / v_myStep"
 
-reset_timestep 0 
+reset_timestep 0
 comm_modify cutoff  ${half_box_length}
 pair_style   lj/cut ${rdf_cutoff}
 pair_coeff   * * 1.0 1.0
@@ -94,4 +94,3 @@ uncompute      myRDF
 
 clear
 quit
-

data/lammps_inputs/in.nickel

@@ -1,37 +1,37 @@
-# ---------- Basic Variables --------------------- 
+# ---------- Basic Variables ---------------------
 variable myStep    equal 1000
 variable number_of_steps equal 20000
 variable dump_file string "dump.nickel.lammpstrj"
 variable rdf_file  string "nickel.gr"
 variable supercell equal 15
 
-# ---------- Initialize Simulation --------------------- 
-units metal 
-dimension 3 
-boundary p p p 
-atom_style atomic 
+# ---------- Initialize Simulation ---------------------
+units metal
+dimension 3
+boundary p p p
+atom_style atomic
 
-# ---------- Create Atoms --------------------- 
+# ---------- Create Atoms ---------------------
 lattice     fcc 3.5238
 region  box block 0 1 0 1 0 1 units lattice
 create_box  1 box
 create_atoms 1 box
 replicate ${supercell} ${supercell} ${supercell}
 
-# ---------- Define Interatomic Potential --------------------- 
-pair_style eam/alloy 
+# ---------- Define Interatomic Potential ---------------------
+pair_style eam/alloy
 pair_coeff * * ./Ni.eam.fs Ni
-neighbor 2.0 bin 
-#neigh_modify delay 10 check yes 
- 
-# ---------- Run Minimization --------------------- 
+neighbor 2.0 bin
+#neigh_modify delay 10 check yes
+
+# ---------- Run Minimization ---------------------
 fix 1 all box/relax iso 0.0 vmax 0.001
 thermo ${myStep}
 thermo_style custom step pe lx ly lz press pxx pyy pzz pe
-min_style cg 
-minimize 1e-25 1e-25 5000 10000 
+min_style cg
+minimize 1e-25 1e-25 5000 10000
 
-variable natoms equal "count(all)" 
+variable natoms equal "count(all)"
 variable teng equal "pe"
 variable length equal "lx"
 variable ecoh equal "v_teng/v_natoms"
@@ -43,19 +43,19 @@ print "Number of atoms = ${natoms};"
 print "Lattice constant (Angstoms) = ${length};"
 print "Cohesive energy (eV) = ${ecoh};"
 
-print "All done!" 
+print "All done!"
 print "-------------------------------"
 print ""
 
-# ---------- Run Dynamics --------------------- 
-reset_timestep 0 
+# ---------- Run Dynamics ---------------------
+reset_timestep 0
 unfix 1
 velocity all create 300.0 87979
 dump 1 all atom ${myStep} ${dump_file}
 fix  2 all nve
 run  ${number_of_steps}
 
-# ---------- Compute RDF --------------------- 
+# ---------- Compute RDF ---------------------
 variable rho             equal atoms/vol
 variable natoms          equal atoms
 variable half_box_length equal "floor(vol^(1./3.)/2. - 2.)"
@@ -67,7 +67,7 @@ variable last_step       equal ${number_of_steps}
 variable Nfreq           equal "v_last_step - v_first_step"
 variable Nrepeat         equal "v_Nfreq / v_myStep"
 
-reset_timestep 0 
+reset_timestep 0
 comm_modify cutoff  ${half_box_length}
 pair_style   lj/cut ${rdf_cutoff}
 pair_coeff   * * 1.0 1.0
@@ -92,4 +92,3 @@ uncompute      myRDF
 
 clear
 quit
-

docs/Makefile

@@ -16,4 +16,4 @@ help:
 # Catch-all target: route all unknown targets to Sphinx using the new
 # "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
 %: Makefile
-	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)