Fix and new readme (#6)

* Fix error with wells not in uppercase * New readme
nicolasboisseau · Aug 25, 2022 · 5be27f5 · 5be27f5
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diff --git a/docs/readme-cp-zoom.jpg b/docs/readme-cp-zoom.jpg
diff --git a/docs/readme-cp.jpg b/docs/readme-cp.jpg
diff --git a/docs/readme-qc-channel-1.jpg b/docs/readme-qc-channel-1.jpg
diff --git a/docs/readme-qc-channel-2.jpg b/docs/readme-qc-channel-2.jpg
diff --git a/docs/readme-qc-channel-3.jpg b/docs/readme-qc-channel-3.jpg
diff --git a/docs/readme-qc-channel-4.jpg b/docs/readme-qc-channel-4.jpg
diff --git a/docs/readme-qc-channel-5.jpg b/docs/readme-qc-channel-5.jpg
diff --git a/lumos/picasso.py b/lumos/picasso.py
@@ -504,15 504,22 @@ def picasso_generate_plate_image(
  well_list = sorted(data_df["well"].unique())
 
  # Handle the single-well request
- if single_well and single_well not in well_list:
- logger.error("Single-well parameter not a valid well")
- logger.err_print(f"ERROR: {single_well} is not a valid well.",
- color='bright_red')
- sys.exit(1)
- elif single_well:
- # Override the list of wells to be rendered
- # with the single well
- well_list = [single_well]
  if single_well:
  if single_well in well_list:
  # Override the list of wells to be rendered
  # with the single well
  well_list = [single_well]
  elif single_well.upper() in well_list:
  # Also accept if the well was not written in uppercase
  well_list = [single_well.upper()]
  elif single_well.lower() in well_list:
  # Also accept if the well was not written in lowercase
  well_list = [single_well.lower()]
  else:
  logger.error("Single-well parameter not a valid well")
  logger.err_print(f"ERROR: {single_well} is not a valid well.",
  color='bright_red')
  sys.exit(1)
 
  # Generate the Cell-painted well images
  generate_multiplexed_well_images(

diff --git a/lumoscli.py b/lumoscli.py
@@ -499,7 499,6 @@ def cell_painting(scope, single_well, source_path, output_path, temp_path, plate
  'classic' else list(config['channel_info'].keys())[:5])
  )
  elif scope != 'plate':
- single_well = single_well.upper()
  click.echo(
  "Process well "
    single_well

diff --git a/readme.md b/readme.md