Merge pull request #7 from andreped:linting

Implemented linting shell scripts and CI workflow

.github/workflows/linting.yml

@@ -0,0 +1,26 @@
+name: Check linting
+
+on:
+  push:
+    branches: ['main']
+  pull_request:
+    branches: ['main']
+  workflow_dispatch:
+
+jobs:
+  check-linting:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout repo
+        uses: actions/checkout@v1
+
+      - name: Set up Python 3.10
+        uses: actions/setup-python@v2
+        with:
+          python-version: '3.10'
+
+      - name: Install lint dependencies
+        run: pip install black==22.3.0 isort==5.10.1 flake8==4.0.1
+
+      - name: Lint the code
+        run: sh shell/lint.sh

setup.cfg

@@ -0,0 +1,14 @@
+[metadata]
+description-file = README.md
+
+[isort]
+force_single_line=True
+known_first_party=vsi2tif
+line_length=120
+profile=black
+
+[flake8]
+# imported but unused in __init__.py, that's ok.
+per-file-ignores=*__init__.py:F401
+ignore=E203,W503,W605,F632,E266,E731,E712,E741
+max-line-length=120

setup.py

@@ -22,6 +22,13 @@
         ]
     },
     install_requires=["tqdm", "numpy"],
+    extras_require={"dev": [
+        "wheel",
+        "setuptools",
+        "black==22.3.0",
+        "isort==5.10.1",
+        "flake8==4.0.1",
+    ]},
     classifiers=[
         "Programming Language :: Python :: 3.6",
         "Programming Language :: Python :: 3.7",

shell/format.sh

@@ -0,0 +1,4 @@
+#!/bin/bash
+isort --sl vsi2tif
+black --line-length 120 vsi2tif
+flake8 vsi2tif

shell/lint.sh

@@ -0,0 +1,23 @@
+#!/bin/bash
+isort --check --sl -c vsi2tif
+if ! [ $? -eq 0 ]
+then
+  echo "Please run \"sh shell/format.sh\" to format the code."
+  exit 1
+fi
+echo "no issues with isort"
+flake8 vsi2tif
+if ! [ $? -eq 0 ]
+then
+  echo "Please fix the code style issue."
+  exit 1
+fi
+echo "no issues with flake8"
+black --check --line-length 120 vsi2tif
+if ! [ $? -eq 0 ]
+then
+  echo "Please run \"sh shell/format.sh\" to format the code."
+    exit 1
+fi
+echo "no issues with black"
+echo "linting success!"

vsi2tif/src/benchmark.py

@@ -1,12 +1,14 @@
-from time import perf_counter
 from functools import wraps
+from time import perf_counter
+
 
 def benchmark(func):
     @wraps(func)
     def wrapper(*args, **kwargs):
         time_start = perf_counter()
         result = func(*args, **kwargs)
         time_duration = perf_counter() - time_start
-        print(f'Processing took {time_duration:.3f} seconds')
+        print(f"Processing took {time_duration:.3f} seconds")
         return result
+
     return wrapper

vsi2tif/src/convert.py

@@ -3,13 +3,23 @@
 from tempfile import TemporaryDirectory
 
 
-def vsi2raw(input_path: str, output_path: str, bfconvert: str, compression: str = "LZW", tz: int = 1024, plane: int = 0, max_mem: int = 32) -> str:
+def vsi2raw(
+    input_path: str,
+    output_path: str,
+    bfconvert: str,
+    compression: str = "LZW",
+    tz: int = 1024,
+    plane: int = 0,
+    max_mem: int = 32,
+) -> str:
     if not os.path.exists(bfconvert):
         raise FileNotFoundError(f"bfconvert not found at: {bfconvert}")
     if not os.path.exists(input_path):
         raise FileNotFoundError(f"Input file not found at: {input_path}")
-
-    cmd = f"{bfconvert} -tilex {tz} -tiley {tz} -nogroup -no-upgrade -overwrite -bigtiff -series {plane} -compression {compression} {input_path} {output_path}"
+
+    cmd = f"{bfconvert} -tilex {tz} -tiley {tz} -nogroup -no-upgrade -overwrite -bigtiff -series {plane}"
+    f"-compression {compression} {input_path} {output_path}"
+
     sp.check_call(cmd, shell=True, env={"BF_MAX_MEM": f"{max_mem}g"})
 
     return output_path
@@ -18,14 +28,25 @@ def vsi2raw(input_path: str, output_path: str, bfconvert: str, compression: str
 def raw2tiff(input_path: str, output_path: str, compression: str = "jpeg", quality: int = 85) -> None:
     if not os.path.exists(input_path):
         raise FileNotFoundError(f"Input file not found at: {input_path}")
-    if not os.path.exists(os.path.dirname(output_path)):    
+    if not os.path.exists(os.path.dirname(output_path)):
         raise FileNotFoundError(f"Output directory not found at: {os.path.dirname}")
-
-    cmd = f"vips tiffsave {input_path} {output_path} --bigtiff --tile --pyramid --compression={compression} --Q={quality}"
+
+    cmd = (
+        f"vips tiffsave {input_path} {output_path} --bigtiff --tile --pyramid --compression={compression} --Q={quality}"
+    )
     sp.check_call(cmd, shell=True)
 
 
-def vsi2tiff(input_path: str, output_path: str, bfconvert: str, compression: str = "jpeg", tz: int = 1024, plane: int = 0, quality: int = 85, max_mem: int = 32) -> None:
+def vsi2tiff(
+    input_path: str,
+    output_path: str,
+    bfconvert: str,
+    compression: str = "jpeg",
+    tz: int = 1024,
+    plane: int = 0,
+    quality: int = 85,
+    max_mem: int = 32,
+) -> None:
     # create temporary directory to store intermediate files
     temp_dir = TemporaryDirectory()
 
@@ -34,7 +55,7 @@ def vsi2tiff(input_path: str, output_path: str, bfconvert: str, compression: str
 
     # first convert from Olympus format to raw TIFF
     vsi2raw(input_path, bigtiff_path, bfconvert, "LZW", tz, plane, max_mem)
-    
+
     # construct tiled, pyramidal TIFF
     raw2tiff(bigtiff_path, output_path, compression, quality)
 

vsi2tif/src/process.py

@@ -1,17 +1,36 @@
 import os
 
-from .benchmark import benchmark
 from tqdm import tqdm
+
+from .benchmark import benchmark
 from .convert import vsi2tiff
 
 
 @benchmark
-def vsi2tiff_single(input_path: str, output_path:str, bfconvert: str, compression: str = "jpeg", tz: int = 1024, plane: int = 0, quality: int = 85, max_mem: int = 32) -> None:
+def vsi2tiff_single(
+    input_path: str,
+    output_path: str,
+    bfconvert: str,
+    compression: str = "jpeg",
+    tz: int = 1024,
+    plane: int = 0,
+    quality: int = 85,
+    max_mem: int = 32,
+) -> None:
     vsi2tiff(input_path, output_path, bfconvert, compression, tz, plane, quality, max_mem)
 
 
 @benchmark
-def vsi2tiff_batch(input_path: str, output_path: str, bfconvert: str, compression: str = "jpeg", tz: int = 1024, plane: int = 0, quality: int = 85, max_mem: int = 32) -> None:
+def vsi2tiff_batch(
+    input_path: str,
+    output_path: str,
+    bfconvert: str,
+    compression: str = "jpeg",
+    tz: int = 1024,
+    plane: int = 0,
+    quality: int = 85,
+    max_mem: int = 32,
+) -> None:
     # find path to all cellSens VSI images to convert
     paths = [(root, file) for root, _, files in os.walk(input_path) for file in files if file.endswith(".vsi")]
 

vsi2tif/vsi2tif.py

@@ -1,19 +1,30 @@
 import os
 from argparse import ArgumentParser
-from .src.process import vsi2tiff_single, vsi2tiff_batch 
+
+from .src.process import vsi2tiff_batch
+from .src.process import vsi2tiff_single
 
 
 def main():
-    parser = ArgumentParser(description='vsi2tif - simple tool for converting images from cellSens VSI to Generic TIFF')
+    parser = ArgumentParser(description="vsi2tif - simple tool for converting images from cellSens VSI to Generic TIFF")
     parser.add_argument("-i", "--input", help="folder with input files", required=True)
     parser.add_argument("-o", "--output", help="folder for output files", required=True)
     parser.add_argument("-b", "--bfconvert", help="path to bfconvert tool", required=True)
-    parser.add_argument("-c", "--compression", help="compression technique used for last conversion step - default 'jpeg'", default="jpeg")
+    parser.add_argument(
+        "-c",
+        "--compression",
+        help="compression technique used for last conversion step - default 'jpeg'",
+        default="jpeg",
+    )
     parser.add_argument("-p", "--plane", help="which image plane to convert image from - default 0", default=0)
-    parser.add_argument("-s", "--tilesize", help="tile size to use during both conversion steps - default 1024", default=1024)
-    parser.add_argument("-q", "--quality", help="compression quality used with JPEG compression - default 85", default=85)
+    parser.add_argument(
+        "-s", "--tilesize", help="tile size to use during both conversion steps - default 1024", default=1024
+    )
+    parser.add_argument(
+        "-q", "--quality", help="compression quality used with JPEG compression - default 85", default=85
+    )
     argv = parser.parse_args()
-    
+
     if not os.path.isfile(argv.bfconvert):
         raise FileNotFoundError(f"bfconvert not found at: {argv.bfconvert}")
     if not os.path.exists(argv.input):
@@ -22,10 +33,14 @@ def main():
     os.makedirs(argv.output, exist_ok=True)
 
     if os.path.isdir(argv.input):
-        vsi2tiff_batch(argv.input, argv.output, argv.bfconvert, argv.compression, argv.tilesize, argv.plane, argv.quality)
+        vsi2tiff_batch(
+            argv.input, argv.output, argv.bfconvert, argv.compression, argv.tilesize, argv.plane, argv.quality
+        )
     else:
-        vsi2tiff_single(argv.input, argv.output, argv.bfconvert, argv.compression, argv.tilesize, argv.plane, argv.quality)
+        vsi2tiff_single(
+            argv.input, argv.output, argv.bfconvert, argv.compression, argv.tilesize, argv.plane, argv.quality
+        )
 
 
-if __name__ == '__main__':
+if __name__ == "__main__":
     main()