Apply ruff check rules, add pre-commit configuration (#45)

* Rewrite os module with pathlib and subrocess modules
* Apply I isort rule
* Apply E, W pycodestyle rules, also a few ruff format fixes
* Apply UP pyupgrade rule
* Apply F Pyflakes rule, with a few TODOs added
* Apply RET flake8-return rule
* Apply D pydocstyle rule

Author: mwtoews

.pre-commit-config.yaml

@@ -0,0 +1,16 @@
+ci:
+  autoupdate_schedule: quarterly
+exclude: \.grb$
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v5.0.0
+    hooks:
+    - id: check-yaml
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.9.3
+    hooks:
+      # Run the linter.
+      - id: ruff
+        args: [ --fix ]
+      # Run the formatter.
+      - id: ruff-format

docs/pestutilslib/docx_to_md.py

@@ -1,9 +1,8 @@
-import sys
-import os
+from subprocess import run
 
 
 def processFile(inFile, outFile):
-    mdFile = open(inFile, "r")
+    mdFile = open(inFile)
     toc = []
     levels = [0, 0, 0, 0, 0]
     newFile = open(outFile, "w")
@@ -14,8 +13,7 @@ def processFile(inFile, outFile):
     for line in mdFile:
         if partOfToc and line != "\n":
             continue
-        else:
-            partOfToc = False
+        partOfToc = False
         if "Table of Contents" in line:
             tocLoc = len(tempFile) + 1
             partOfToc = True
@@ -39,8 +37,7 @@ def processFile(inFile, outFile):
 
 def addSectionTag(line, secId):
     startIndex = line.find(" ")
-    line = line[: startIndex + 1] + "<a id='" + secId + "' />" + line[startIndex + 1 :]
-    return line
+    return line[: startIndex + 1] + "<a id='" + secId + "' />" + line[startIndex + 1 :]
 
 
 def buildToc(line, toc, levels):
@@ -78,8 +75,7 @@ def buildToc(line, toc, levels):
 
 def cleanLine(text):
     text = stripNewline(text)
-    text = removeAnchors(text)
-    return text
+    return removeAnchors(text)
 
 
 def stripNewline(text):
@@ -96,13 +92,21 @@ def removeAnchors(text):
 
 def clean(docx_file, inFile, outFile, run_pandoc=True):
     if run_pandoc:
-        os.system(
-            "pandoc -t gfm --wrap=none --extract-media . -o file.md {0} --mathjax".format(
-                docx_file
-            )
-        )
-    num_str = [str(i) for i in range(1, 11)]
-    lines = open(inFile, "r").readlines()
+        cmds = [
+            "pandoc",
+            "-t",
+            "gfm",
+            "--wrap=none",
+            "--extract-media",
+            ".",
+            "-o",
+            "file.md",
+            docx_file,
+            "--mathjax",
+        ]
+        run(cmds, check=True)
+    # num_str = [str(i) for i in range(1, 11)]
+    lines = open(inFile).readlines()
 
     # notoc_lines = []
     i = 0
@@ -112,9 +116,11 @@ def clean(docx_file, inFile, outFile, run_pandoc=True):
     #         while True:
     #             i += 1
     #             line = lines[i]
-    #             if line.lower().strip().startswith("introduction") or line.lower().strip().startswith("# introduction") :
+    #             if line.lower().strip().startswith(
+    #                 "introduction"
+    #             ) or line.lower().strip().startswith("# introduction"):
     #                 break
-    #             #print(line)
+    #             # print(line)
     #     notoc_lines.append(line)
     #     i += 1
     # lines = notoc_lines
@@ -132,19 +138,18 @@ def clean(docx_file, inFile, outFile, run_pandoc=True):
             )
         if "blockquote" in lines[i]:
             lines[i] = lines[i].replace("<blockquote>", "").replace("</blockquote>", "")
-        if lines[i].strip().startswith("$") and not "bmatrix" in lines[i].lower():
+        if lines[i].strip().startswith("$") and "bmatrix" not in lines[i].lower():
             label = lines[i].split()[-1]
             eq_str = lines[i].replace("$$", "$").split("$")[1]
             eq_str = (
-                r"{0}".format(eq_str)
-                .replace("\\\\", "\\")
+                rf"{eq_str}".replace("\\\\", "\\")
                 .replace(" \\ ", " ")
                 .replace("\\_", "_")
             )
-            math_str_pre = '<img src="https://latex.codecogs.com/svg.latex?\Large&space;{0}'.format(
-                eq_str
+            math_str_pre = (
+                rf'<img src="https://latex.codecogs.com/svg.latex?\Large&space;{eq_str}'
             )
-            math_str_post = '" title="\Large {0}" />  {1}  <br>'.format(eq_str, label)
+            math_str_post = rf'" title="\Large {eq_str}" />  {label}  <br>'
             lines[i] = math_str_pre + " " + math_str_post
         if lines[i].strip().startswith("<table>"):  # and "pcf" in lines[i].lower():
             lines[i] = '<div style="text-align: left">' + lines[i] + "</div>"
@@ -165,9 +170,17 @@ def clean(docx_file, inFile, outFile, run_pandoc=True):
         #         lines.pop(i)
         #         if "bmatrix" in lines[i].lower():
         #             break
-        #     eq_str = r"{0}".format(eq_str).replace("\\\\", "\\").replace(" \\ ", " ").replace("\\_", "_")
-        #     math_str_pre = "<img src=\"https://latex.codecogs.com/svg.latex?\Large&space;{0}".format(eq_str)
-        #     math_str_post = "\" title=\"\Large {0}\" />".format(eq_str)
+        #     eq_str = (
+        #         r"{0}".format(eq_str)
+        #         .replace("\\\\", "\\")
+        #         .replace(" \\ ", " ")
+        #         .replace("\\_", "_")
+        #     )
+        #     math_str_pre = '<img src="https://latex.codecogs.com/svg.latex'\
+        #         '?\Large&space;{0}'.format(
+        #         eq_str
+        #     )
+        #     math_str_post = '" title="\Large {0}" />'.format(eq_str)
         #     lines[i] = math_str_pre + " " + math_str_post
 
         i += 1

examples/clear_output_all.py

@@ -1,17 +1,19 @@
-import os
+from pathlib import Path
+from subprocess import run
 
-dirs = ["."]
 notebook_count = 0
-for d in dirs:
-    nb_files = [
-        os.path.join(d, f) for f in os.listdir(d) if f.lower().endswith(".ipynb")
-    ]
-    for nb_file in nb_files:
-        print("clearing", nb_file)
-        os.system(
-            "jupyter nbconvert --ClearOutputPreprocessor.enabled=True --ClearMetadataPreprocessor.enabled=True --inplace {0}".format(
-                nb_file
-            )
-        )
-        notebook_count += 1
-print(notebook_count, " notebooks cleared")
+for nb_file in Path(__file__).parent.rglob("*.ipynb"):
+    print("clearing", nb_file)
+    run(
+        [
+            "jupyter",
+            "nbconvert",
+            "--ClearOutputPreprocessor.enabled=True",
+            "--ClearMetadataPreprocessor.enabled=True",
+            "--inplace",
+            nb_file,
+        ],
+        check=True,
+    )
+    notebook_count += 1
+print(notebook_count, "notebooks cleared")

examples/exploring_lowlevel_pypestutils_functions.ipynb

@@ -16,15 +16,13 @@
    "outputs": [],
    "source": [
     "import os\n",
-    "import sys\n",
     "import shutil\n",
-    "import subprocess as sp\n",
+    "from datetime import datetime\n",
     "\n",
-    "import numpy as np\n",
-    "import pandas as pd\n",
+    "import flopy\n",
     "import matplotlib.pyplot as plt\n",
-    "\n",
-    "import flopy"
+    "import numpy as np\n",
+    "import pandas as pd"
    ]
   },
   {
@@ -293,7 +291,7 @@
     "    ax.pcolormesh(Easting, Northing, mtop)\n",
     "    ax.scatter(kdf.x, kdf.y, marker=\"^\", c=\"k\", label=\"gw level loc\")\n",
     "    ax.legend(loc=\"upper left\")\n",
-    "    ax.set_title(\"gw level locations in layer {0}\".format(lay), loc=\"left\")"
+    "    ax.set_title(f\"gw level locations in layer {lay}\", loc=\"left\")"
    ]
   },
   {
@@ -850,7 +848,6 @@
     "aa_pp = aa * pp_space * 10  # ?\n",
     "zone_pp = np.ones_like(ppeasting, dtype=int)\n",
     "fac_file = os.path.join(w_d, \"factors.bin\")\n",
-    "from datetime import datetime\n",
     "\n",
     "s = datetime.now()\n",
     "ipts = lib.calc_kriging_factors_2d(\n",

examples/exploring_pypestutils_helpers.ipynb

@@ -16,13 +16,11 @@
    "outputs": [],
    "source": [
     "import os\n",
-    "import sys\n",
     "import shutil\n",
-    "import subprocess as sp\n",
     "\n",
+    "import matplotlib.pyplot as plt\n",
     "import numpy as np\n",
-    "import pandas as pd\n",
-    "import matplotlib.pyplot as plt"
+    "import pandas as pd"
    ]
   },
   {

examples/ppu_helpers.py

@@ -1,5 +1,4 @@
 import os
-import pyemu
 
 
 def setup_pps(d):
@@ -10,10 +9,11 @@ def setup_pps(d):
 
 
 def apply_pps():
-    from pypestutils import helpers
     import numpy as np
     import pandas as pd
 
+    from pypestutils import helpers
+
     df = pd.read_csv("pp_info.csv")
     gridspec_fname = "org.grb"
     for model_file, pp_file in zip(df.model_file, df.pp_file):

examples/pypestutils_pstfrom_quadtree_mf6.ipynb

@@ -22,9 +22,10 @@
    "source": [
     "import os\n",
     "import shutil\n",
+    "\n",
+    "import matplotlib.pyplot as plt\n",
     "import numpy as np\n",
-    "import pandas as pd\n",
-    "import matplotlib.pyplot as plt"
+    "import pandas as pd"
    ]
   },
   {
@@ -40,8 +41,8 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "import pyemu\n",
-    "import flopy"
+    "import flopy\n",
+    "import pyemu"
    ]
   },
   {
@@ -529,7 +530,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "with open(os.path.join(template_ws, tpl_files[0]), \"r\") as f:\n",
+    "with open(os.path.join(template_ws, tpl_files[0])) as f:\n",
     "    for _ in range(4):\n",
     "        print(f.readline().strip())"
    ]
@@ -560,7 +561,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "_ = [print(line.rstrip()) for line in open(\"ppu_helpers.py\", \"r\").readlines()]"
+    "_ = [print(line.rstrip()) for line in open(\"ppu_helpers.py\").readlines()]"
    ]
   },
   {

examples/pypestutils_pstfrom_structured_mf6.ipynb

@@ -22,9 +22,10 @@
    "source": [
     "import os\n",
     "import shutil\n",
+    "\n",
+    "import matplotlib.pyplot as plt\n",
     "import numpy as np\n",
-    "import pandas as pd\n",
-    "import matplotlib.pyplot as plt"
+    "import pandas as pd"
    ]
   },
   {
@@ -40,8 +41,8 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "import pyemu\n",
-    "import flopy"
+    "import flopy\n",
+    "import pyemu"
    ]
   },
   {
@@ -612,7 +613,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "with open(os.path.join(template_ws, tpl_files[0]), \"r\") as f:\n",
+    "with open(os.path.join(template_ws, tpl_files[0])) as f:\n",
     "    for _ in range(4):\n",
     "        print(f.readline().strip())"
    ]
@@ -643,7 +644,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "_ = [print(line.rstrip()) for line in open(\"ppu_helpers.py\", \"r\").readlines()]"
+    "_ = [print(line.rstrip()) for line in open(\"ppu_helpers.py\").readlines()]"
    ]
   },
   {