cleaned up the cli interface

I was annoyed by the cli interface quite some time. It should now adhere more to what is expected from a POSIX cli

README.md

@@ -18,7 +18,7 @@ There is no affiliation on my side regarding Sensovation or Miltenyi, I just use
     raw_data = sensospot_parser.parse_folder(<path to results directory>)
 
     sorted(raw_data.columns) == [
-        'Analysis.Datetime', 'Analysis.Image', 'Analysis.Name',
+        'Analysis.Datetime', 'Analysis.Image', 'Analysis.Name', 
         'Bkg.Area', 'Bkg.Mean', 'Bkg.Median', 'Bkg.StdDev', 'Bkg.Sum',
         'Exposure.Id',
         'Parameters.Channel', 'Parameters.Time',
@@ -54,18 +54,17 @@ There is a `columns` module available, providing constans that define the column
 
 ## CLI
 
-For the (propably) most important function, there is even a cli command
+For the (propably) most important function, there is a cli command
+
 ```sh
-Usage: sensospot_parse [OPTIONS] SOURCE
+Usage: sensospot_parse [OPTIONS] SOURCES
 
 Arguments:
-  SOURCE:             Folder with Sensospot measurement
+  SOURCES:             One or more folders with Sensospot measurements
 
 Options:
-  -o, --outfile TEXT  Output file name, use a dash '-' for stdout, default:
-                      'collected_data.csv'
+  -o, --output FILE  Output file path, defaults to 'collected_data.csv'
   -q, --quiet         Ignore Sanity Check
-  -r, --recurse       Recurse into folders one level down
   --help              Show this message and exit.
 ```
 

pyproject.toml

@@ -15,12 +15,14 @@ authors = [
 
 # see https://pypi.org/classifiers/
 classifiers = [
-    "Development Status :: 2 - Pre-Alpha",
+    "Development Status :: 5 - Production/Stable",
     "Intended Audience :: Developers",
+    "Intended Audience :: Science/Research",
     "Programming Language :: Python :: 3.8",
     "Programming Language :: Python :: 3.9",
     "Programming Language :: Python :: 3.10",
     "Programming Language :: Python :: 3 :: Only",
+    "Topic :: Scientific/Engineering",
     "License :: Freely Distributable",
 ]
 

src/sensospot_parser/__init__.py

@@ -3,10 +3,10 @@
 Parsing the numerical output from Sensovations Sensospot image analysis.
 """
 
-__version__ = "0.9.1"
+__version__ = "1.0.0"
 
 
-from pathlib import Path
+import pathlib
 
 import click
 import pandas
@@ -19,23 +19,23 @@ DEFAULT_OUTPUT_FILENAME = "collected_data.csv"
 
 @click.command()
 @click.argument(
-    "source",
+    "sources",
     type=click.Path(
         exists=True,
         file_okay=False,
         dir_okay=True,
         readable=True,
-        writable=True,
     ),
+    required=True,
+    nargs=-1,
 )
 @click.option(
     "-o",
-    "--outfile",
-    default=DEFAULT_OUTPUT_FILENAME,
-    help=(
-        "Output file name, use a dash '-' for stdout, "
-        f"default: '{DEFAULT_OUTPUT_FILENAME}'"
-    ),
+    "--output",
+    is_flag=False,
+    flag_value=DEFAULT_OUTPUT_FILENAME,
+    type=click.Path(exists=False, dir_okay=False),
+    help=f"Output file path, defaults to '{DEFAULT_OUTPUT_FILENAME}'",
 )
 @click.option(
     "-q",
@@ -44,54 +44,18 @@ DEFAULT_OUTPUT_FILENAME = "collected_data.csv"
     default=False,
     help="Ignore Sanity Check",
 )
-@click.option(
-    "-r",
-    "--recurse",
-    is_flag=True,
-    default=False,
-    help="Recurse into folders one level down",
-)
-def main(source, outfile, quiet=False, recurse=False):
-    if recurse:
-        _parse_recursive(source, outfile, quiet)
-    else:
-        _parse_one_folder(source, outfile, quiet)
+def main(sources, output, quiet=False):
+    """Parses the measurement results of the Sensospot reader
 
+    The resulting output is either echoed to stdout or saved to a file.
 
-def _output(data, folder, outfile):
-    """output a datafarme to stdout or csv file
-
-    data:    the pandas dataframe
-    folder:  the folder to save the file to
-    outfile: the name of the outfile, '-' will output to stdout
     """
-    if outfile.strip() == "-":
-        click.echo(data.to_csv(None, sep="\t", index=False))
-    else:
-        csv_file = Path(folder) / outfile
-        data.to_csv(csv_file, sep="\t", index=False)
-
-
-def _parse_one_folder(source, outfile, quiet):
-    """parses the data of one folder"""
-    source_path = Path(source)
-    # read the raw data of a folder
-    raw_data = parse_folder(source_path, quiet=quiet)
-    _output(raw_data, source_path, outfile)
-    return raw_data
-
-
-def _parse_recursive(source, outfile, quiet):
-    """parses all folders one level down and collects the data"""
-    child_outfile = DEFAULT_OUTPUT_FILENAME
-    source_path = Path(source)
-    folders = (i for i in source_path.iterdir() if i.is_dir())
-    non_hidden = (i for i in folders if not i.name.startswith("."))
-    collection = (
-        _parse_one_folder(f, child_outfile, quiet) for f in non_hidden
+    paths = (pathlib.Path(source) for source in sources)
+    collection = (parse_folder(source) for source in paths)
+    result = pandas.concat(collection, ignore_index=True).to_csv(
+        output, sep="\t", index=False
     )
-    try:
-        collected = pandas.concat(collection, ignore_index=True)
-        _output(collected.reset_index(), source_path, outfile)
-    except ValueError as e:
-        print(str(e))
+    # if 'output' is None, the call to 'to_csv()' returns the csv as text
+    # if 'output' is not None, 'to_csv()' writes to the file and returns None
+    if result:
+        click.echo(result)