refactor: remove "include" option for global ruff format/check (#2065)

- Remove Ruff's "include" option to check all the files in the repo
- Apply the changes from ruff format / check for the new files that were previously not included
- Upgrade the Python version from py37 to py39, which applies a few minor changes, e.g. autotest/test_gwf_multimvr.py
- Ignore long lines (E501) in "doc/**.ipynb" files, and module import not at top of file (E402) for .build_rtd_docs/conf.py

.build_rtd_docs/conf.py

@@ -1,3 +1,4 @@
+# ruff: noqa: E402
 # Configuration file for the Sphinx documentation builder.
 #
 # This file only contains a selection of the most common options. For a full
@@ -14,7 +15,7 @@
 # documentation root, use os.path.abspath to make it absolute, like shown here.
 #
 import sys
-from subprocess import Popen, PIPE
+from subprocess import PIPE, Popen
 
 sys.path.insert(0, os.path.abspath(os.path.join("..", "doc")))
 sys.path.insert(0, os.path.abspath(os.path.join("..", "distribution")))
@@ -37,6 +38,7 @@
 # -- Update the modflow 6 version -------------------------------------------
 print("Update the modflow6 version")
 from update_version import update_version
+
 update_version()
 
 # -- import version from doc/version.py -------------------------------------

.github/common/check_format.py

@@ -3,10 +3,10 @@
 import sys
 import timeit
 from itertools import repeat
-from queue import Empty
+from multiprocessing import Manager, Pool, cpu_count
 from pathlib import Path
+from queue import Empty
 from subprocess import run
-from multiprocessing import cpu_count, Pool, Manager
 
 PROJ_ROOT = Path(__file__).parents[2]
 
@@ -20,13 +20,11 @@
     PROJ_ROOT / "src" / "Utilities" / "Libraries" / "sparskit2",
     PROJ_ROOT / "utils" / "mf5to6",
     PROJ_ROOT / "utils" / "zonebudget" / "msvs",
-    PROJ_ROOT / "msvs"
+    PROJ_ROOT / "msvs",
 ]
 
 # exclude these files from checks
-excludefiles = [
-    PROJ_ROOT / "src" / "Idm" / "gwf-stoidm.f90"
-]
+excludefiles = [PROJ_ROOT / "src" / "Idm" / "gwf-stoidm.f90"]
 
 # commands
 fprettify = "fprettify -c .fprettify.yaml"

.github/common/check_vfproj.py

@@ -4,7 +4,6 @@
 from pathlib import Path
 from pprint import pformat
 
-
 PROJ_ROOT = Path(__file__).parents[2]
 
 

.hpc/sstat_poll.py

@@ -141,9 +141,7 @@ def _run_command(
         )
         is None
     ):
-        raise ValueError(
-            f"SLURM command '{slurm_args.command}' does not exist"
-        )
+        raise ValueError(f"SLURM command '{slurm_args.command}' does not exist")
 
     end_tag = f"sstat:,error:,no,steps,running,for,job,{slurm_args.jobid}"
     # open file

autotest/test_gwf_multimvr.py

@@ -1000,9 +1000,10 @@ def check_output(idx, test):
     # cur_ws, gwfparent = ex[idx], gwf_names[idx]
     cur_ws = test.workspace
     gwfparent = "gwf_" + cases[idx] + "_p"
-    with open(os.path.join(cur_ws, gwfparent + ".lst"), "r") as gwf_lst, open(
-        os.path.join(cur_ws, "mfsim.lst"), "r"
-    ) as sim_lst:
+    with (
+        open(os.path.join(cur_ws, gwfparent + ".lst"), "r") as gwf_lst,
+        open(os.path.join(cur_ws, "mfsim.lst"), "r") as sim_lst,
+    ):
         gwf_lst_lines = gwf_lst.readlines()
         sim_lst_lines = sim_lst.readlines()