linting with ruff

pyproject.toml

@@ -14,12 +14,18 @@ license = "Beerware"
 requires = [
     "pyperclip >=1.8.0",
     "click >= 7.1.2",
-    "black",
+    "pandas",
+    "openpyxl",
+    "ruff",
     "py-gitea",
+    "PyPDFForm",
 ]
 
 
 [tool.flit.scripts]
+form_inspect = "work_helpers.fill_forms:inspect"
+form_prepare_payments = "work_helpers.fill_forms:prepare_payments"
+form_fill_payments = "work_helpers.fill_forms:payments"
 nice_path = "work_helpers.nice_path:make_nice_path"
 random_password = "work_helpers.password:get_random_password"
 random_ints = "work_helpers.random_int:generate_random_number_list"
@@ -30,3 +36,50 @@ sg_mbp_issue_ref = "work_helpers.sg_mbp_issue:sg_mbp_issue_ref"
 xls2changelog = "work_helpers.excel2changelog:cli"
 xls2markdown = "work_helpers.excel2markdown:cli"
 xls2pylist = "work_helpers.excel2pylist:cli"
+
+
+
+[tool.ruff]
+# see https://docs.astral.sh/ruff/configuration/
+
+line-length = 80
+indent-width = 4
+
+fix = true
+
+[tool.ruff.lint]
+# Enable Pyflakes (`F`) and a subset of the pycodestyle (`E`)  codes by default.
+# Unlike Flake8, Ruff doesn't enable pycodestyle warnings (`W`) or
+# McCabe complexity (`C901`) by default.
+fixable = ["ALL"]
+select = ["ALL"]
+ignore = [
+    # ignored for now, should be activated in the future
+    # docstrings
+    "D",
+
+    # don't complain about not annotating self or cls
+    "ANN101",
+    "ANN102",
+
+    # ignored, "ruff format" will handle this
+    "COM812", 
+    "ISC001",
+
+    # ignored, due to Windows / WSL2 setup
+    # flake8-executable
+    "EXE",
+]
+
+[tool.ruff.lint.pydocstyle]
+convention = "pep257"  # Accepts: "google", "numpy", or "pep257".
+
+[tool.ruff.lint.per-file-ignores]
+# see https://github.com/charliermarsh/ruff
+"tests/*" = ["FBT003", "INP001", "PLR2004", "S101", "SLF001", "ANN"]
+"noxfile.py" = ["ANN"]
+
+
+[tool.ruff.format]
+indent-style = "space"
+

work_helpers/__init__.py

@@ -1,3 +1,3 @@
-""" Some helper scripts for the day to day work with Ubuntu in WSL2 """
+"""Some helper scripts for the day to day work with Ubuntu in WSL2"""
 
 __version__ = "0.0.2"

work_helpers/_natural_sort.py

@@ -1,4 +1,4 @@
-""" Sort the content of an list in a natural way
+"""Sort the content of an list in a natural way
 
 > l = ["A2", "A10", "A1", "A3"]
 > sorted(l)
@@ -21,7 +21,8 @@ def _nartural_sort_convert(text):
 
 def _nartural_sort_alphanum_key(text):
     return tuple(
-        _nartural_sort_convert(part) for part in _NATURAL_SORT_REGEX_DIGITS.split(text)
+        _nartural_sort_convert(part)
+        for part in _NATURAL_SORT_REGEX_DIGITS.split(text)
     )
 
 

work_helpers/excel2changelog.py

@@ -13,13 +13,13 @@ sheet = "Input_Data_*"
 col_start = "A"
 row_start = 8
 
+
 def xls_formula_spacing(formula):
     for c in "();=":
         formula = formula.replace(c, f"{c} ")
     return formula
 
 
-
 def text_to_changelog(
     raw_text, sheet, start_column, start_row, compact=False, keep=False
 ):
@@ -55,9 +55,13 @@ def text_to_changelog(
         prev = current
 
 
-def clipboard_to_changelog(sheet, start_column, start_row, compact=False, keep=False):
+def clipboard_to_changelog(
+    sheet, start_column, start_row, compact=False, keep=False
+):
     xls = pyperclip.paste()
-    result = list(text_to_changelog(xls, sheet, start_column, start_row, compact, keep))
+    result = list(
+        text_to_changelog(xls, sheet, start_column, start_row, compact, keep)
+    )
     line_count = len(result)
     if line_count == 1:
         print(f"Copied one line to the clipboard")
@@ -74,7 +78,9 @@ def clipboard_to_changelog(sheet, start_column, start_row, compact=False, keep=F
 
 
 @click.command()
-@click.option("-s", "--sheet", prompt=True, required=True, default="Input_Data_*")
+@click.option(
+    "-s", "--sheet", prompt=True, required=True, default="Input_Data_*"
+)
 @click.option("-w", "--well", prompt=True, required=True, default="A1")
 @click.option("-c", "--compact", is_flag=True)
 @click.option("-k", "--keep", is_flag=True)

work_helpers/excel2pylist.py

@@ -1,12 +1,15 @@
 import click
 import pyperclip
 
+
 def _strip_parts(iterable):
     return [item.strip() for item in iterable]
 
+
 def _replace_empty_strings(iterable, replacement="None"):
     return [i or replacement for i in iterable]
 
+
 def prepare(text):
     lines = text.splitlines()
 
@@ -31,13 +34,17 @@ def pad_field(index, t):
     else:
         return value.ljust(length)
 
+
 def pad_fields(iterable, lengths):
     return [pad_field(i, t) for i, t in enumerate(zip(iterable, lengths))]
 
+
 def build_list(table, lengths):
     padded = (pad_fields(l, lengths) for l in table)
     padded_lines = (", ".join(l) for l in padded)
-    lines_as_list = (f"    [{l}],  # noqa: E201, E202, E203, E501," for l in padded_lines)
+    lines_as_list = (
+        f"    [{l}],  # noqa: E201, E202, E203, E501," for l in padded_lines
+    )
     list_content = "\n".join(lines_as_list)
     return f"[\n{list_content}\n]\n"
 
@@ -49,4 +56,4 @@ def cli():
     lengths = get_cell_lengths(table)
     result = build_list(table, lengths)
     print("copied to clipboard")
-    pyperclip.copy(result)
+    pyperclip.copy(result)

work_helpers/nice_path.py

@@ -1,4 +1,4 @@
-""" create a nice path representation from a copied windows path """
+"""create a nice path representation from a copied windows path"""
 
 import click
 import pyperclip
@@ -7,6 +7,7 @@ REPLACEMENTS = {
     "G:": "Google Drive",
 }
 
+
 def replace(segment, replacements=REPLACEMENTS):
     return replacements.get(segment, segment)
 

work_helpers/password.py

@@ -15,7 +15,7 @@ characters = list(lowers + uppers + decimals)
 @click.command()
 @click.option("--length", default=16, type=int)
 def get_random_password(length=16):
-    """ generates a random password and copies it to the clipboard """
+    """generates a random password and copies it to the clipboard"""
     choice = [random.choice(characters) for i in range(length)]
     groups = [iter(choice)] * 4
     grouped = ("".join(g) for g in itertools.zip_longest(*groups, fillvalue=""))
@@ -23,4 +23,3 @@ def get_random_password(length=16):
     pyperclip.copy(password)
     click.echo("Copied to clipboard:", err=True)
     click.echo(password)
-    

work_helpers/random_int.py

@@ -2,14 +2,14 @@ import click
 import random
 import pyperclip
 
+
 @click.command()
 @click.argument("length", default=100, type=int)
 def generate_random_number_list(length=100):
-    """ generates a new line separated list of integers and copies it to the clipboard """
+    """generates a new line separated list of integers and copies it to the clipboard"""
     numbers = list(range(1, length + 1))
     random.shuffle(numbers)
     integer_list = "\n".join(str(i) for i in numbers)
     pyperclip.copy(integer_list)
     click.echo("Copied to clipboard:", err=True)
     click.echo(integer_list)
-    

work_helpers/sensospot_rename.py

@@ -1,4 +1,4 @@
-""" rename sensospot images """
+"""rename sensospot images"""
 
 import click
 import pathlib
@@ -9,41 +9,43 @@ RENAME_MAP_NAME = "rename_map.txt"
 IMAGE_SUFFIXES = {".tif", ".jpg"}
 
 
-def get_map_file_path(directory:str) -> pathlib.Path:
+def get_map_file_path(directory: str) -> pathlib.Path:
     return pathlib.Path(directory) / RENAME_MAP_NAME
 
 
-def list_images(directory:str) -> list[pathlib.Path]:
+def list_images(directory: str) -> list[pathlib.Path]:
     parent = pathlib.Path(directory)
     non_hidden = (i for i in parent.iterdir() if not i.name.startswith("."))
     return [i for i in non_hidden if i.suffix.lower() in IMAGE_SUFFIXES]
 
 
-def get_image_parts(image_path:pathlib.Path) -> tuple[str, str, str]:
+def get_image_parts(image_path: pathlib.Path) -> tuple[str, str, str]:
     return image_path.stem.rsplit("_", maxsplit=2)
 
 
-def get_unique_parts(images:list[pathlib.Path]) -> list[list[str], list[str], list[str]]: 
+def get_unique_parts(
+    images: list[pathlib.Path],
+) -> list[list[str], list[str], list[str]]:
     parts = [get_image_parts(p) for p in images]
     return [sorted(set(items)) for items in zip(*parts)]
 
 
-def write_rename_map(map_file:pathlib.Path) -> None:
+def write_rename_map(map_file: pathlib.Path) -> None:
     images = list_images(map_file.parent)
     parts = get_unique_parts(images)
     headers = ["stems", "wells", "exposures"]
-    
+
     lines = []
     for header, items in zip(headers, parts):
         lines.append(f"# {header}")
         lines.extend([f"{i}\t" for i in items])
         lines.append("")
     lines.append("")
-    
+
     map_file.write_text("\n".join(lines))
 
 
-def _parse_rename_map(content:str) -> tuple[str, str]:
+def _parse_rename_map(content: str) -> tuple[str, str]:
     lines = [line.strip() for line in content.splitlines()]
     for i, line in enumerate(lines, start=1):
         if not line or line.startswith("#"):
@@ -53,19 +55,23 @@ def _parse_rename_map(content:str) -> tuple[str, str]:
         yield line.split("\t", maxsplit=1)
 
 
-def read_rename_map(map_file:pathlib.Path) -> dict[str, str]:
+def read_rename_map(map_file: pathlib.Path) -> dict[str, str]:
     content = map_file.read_text()
     return {k: v for k, v in _parse_rename_map(content)}
 
 
-def prepare_rename(images:list[pathlib.Path], rename_map:dict[str, str], sep="_") -> list[tuple[pathlib.Path, pathlib.Path]]:
+def prepare_rename(
+    images: list[pathlib.Path], rename_map: dict[str, str], sep="_"
+) -> list[tuple[pathlib.Path, pathlib.Path]]:
     for path in images:
         renamed_parts = [rename_map[p] for p in get_image_parts(path)]
         yield path, path.with_stem(sep.join(renamed_parts))
 
 
 @click.command()
-@click.argument("directory", type=click.Path(exists=True, file_okay=False, dir_okay=True))
+@click.argument(
+    "directory", type=click.Path(exists=True, file_okay=False, dir_okay=True)
+)
 def sensospot_rename(directory):
     images = list_images(directory)
     if not images:
@@ -85,8 +91,10 @@ def sensospot_rename(directory):
         try:
             prepared = list(prepare_rename(images, rename_map))
         except Exception:
-            raise click.UsageError("Could not rename images. Please check the image directory and rename map file.")
+            raise click.UsageError(
+                "Could not rename images. Please check the image directory and rename map file."
+            )
 
         for src, dst in prepared:
             click.echo(f"renaming: {src} -> {dst}")
-            shutil.move(src, dst)
+            shutil.move(src, dst)

work_helpers/sg_mbp_build.py

@@ -103,7 +103,7 @@ def _get_issue_numbers(group: str, build_version: str):
     # print(list(_list_current_frms(group, build_version)))
     for path in _list_current_frms(group, build_version):
         rest, issue_info = path.name.lower().split("issue")
-        issue_info = issue_info.removeprefix("s") # might be "issues"
+        issue_info = issue_info.removeprefix("s")  # might be "issues"
         issue, *rest = issue_info.strip().split()
         yield issue.strip(" ,")
 
@@ -122,7 +122,9 @@ def _extract_changes_from_log(
 
 def _get_group_from_folder(folder: Pathlike) -> str:
     name = pathlib.Path(folder).name
-    middle = name.removeprefix(GROUP_FOLDER_PREFIX).removesuffix(GROUP_FOLDER_SUFFIX)
+    middle = name.removeprefix(GROUP_FOLDER_PREFIX).removesuffix(
+        GROUP_FOLDER_SUFFIX
+    )
     if middle in GROUPS:
         return middle
     msg = f"Folder '{name}' is not an MBP group folder"
@@ -166,7 +168,9 @@ class Version:
 ## functions for `sg_mbp_build`
 
 
-def copy_workbooks(group: str, destination: Pathlike, build_version: str) -> None:
+def copy_workbooks(
+    group: str, destination: Pathlike, build_version: str
+) -> None:
     source = _get_workbook_folder(group)
     all_xls_files = _files_in_folder(source, ".xlsx")
     mbp_files = (f for f in all_xls_files if f.name.lower().startswith("mbp"))
@@ -198,7 +202,9 @@ def copy_workbook_changelogs(
         shutil.copyfile(log_file, new_path)
 
 
-def copy_changelog(cwd: Pathlike, destination: Pathlike, build_version: str) -> None:
+def copy_changelog(
+    cwd: Pathlike, destination: Pathlike, build_version: str
+) -> None:
     changelog = _get_changelog_path(cwd)
     new_path = pathlib.Path(destination) / f"CHANGELOG {build_version}.txt"
     print(changelog.name, "->", new_path)

work_helpers/sg_mbp_issue.py

@@ -9,4 +9,4 @@ MBP_ISSUE_BASE = "Safeguard/MBP-issues"
 def sg_mbp_issue_ref(issue):
     reference = f"{MBP_ISSUE_BASE}#{issue}"
     pyperclip.copy(f"{MBP_ISSUE_BASE}#{issue}")
-    click.echo(reference)
+    click.echo(reference)