From cc133f1873d8e2cce81c8e53dcd6615f94c6288c Mon Sep 17 00:00:00 2001 From: Holger Frey Date: Wed, 31 Aug 2022 16:18:27 +0200 Subject: [PATCH] added build instructions for documentation --- README.md | 24 +++++++++++++----------- 1 file changed, 13 insertions(+), 11 deletions(-) diff --git a/README.md b/README.md index 6f00ce3..d84e037 100644 --- a/README.md +++ b/README.md @@ -3,7 +3,7 @@ Sensospot Data Parser Parsing the numerical output from [SensoSpot][sensospot] microarray analysis. -The [SensoSpot][sensospot] microarray analyzer is an automated fluorescence microscope with an image analysis software for detecting and measuring microarrays. The original name of the product was "FLAIR" by the company Sensovation, that was later acquired by Miltenyi. +The [SensoSpot][sensospot] microarray analyzer is an automated fluorescence microscope with an image analysis software for detecting and measuring microarrays. The original name of the product was "FLAIR" by the company Sensovation, that was later acquired by Miltenyi. There is no affiliation on my side regarding Sensovation or Miltenyi, I just use the product and needed a way to make the data available for further analysis. @@ -18,13 +18,13 @@ There is no affiliation on my side regarding Sensovation or Miltenyi, I just use raw_data = sensospot_parser.parse_folder() sorted(raw_data.columns) == [ - 'Analysis.Name', - 'Bkg.Area', 'Bkg.Mean', 'Bkg.Median', 'Bkg.StdDev', 'Bkg.Sum', - 'Exposure.Id', - 'Parameters.Channel', 'Parameters.Time', - 'Pos.Id', 'Pos.Nom.X', 'Pos.Nom.Y', 'Pos.X', 'Pos.Y', - 'Spot.Area', 'Spot.Diameter', 'Spot.Found', 'Spot.Mean', 'Spot.Median', - 'Spot.Saturation', 'Spot.StdDev', 'Spot.Sum', + 'Analysis.Name', + 'Bkg.Area', 'Bkg.Mean', 'Bkg.Median', 'Bkg.StdDev', 'Bkg.Sum', + 'Exposure.Id', + 'Parameters.Channel', 'Parameters.Time', + 'Pos.Id', 'Pos.Nom.X', 'Pos.Nom.Y', 'Pos.X', 'Pos.Y', + 'Spot.Area', 'Spot.Diameter', 'Spot.Found', 'Spot.Mean', 'Spot.Median', + 'Spot.Saturation', 'Spot.StdDev', 'Spot.Sum', 'Well.Column', 'Well.Name', 'Well.Row' ] ``` @@ -44,8 +44,8 @@ There is a `columns` module available, providing constans that define the column ## Avaliable public functions: - **parse_folder(path_to_folder)** - Searches the folder for parsable Sensospot .csv files, parses them into one - big pandas data frame and will add additional meta data from parameters folder, + Searches the folder for parsable Sensospot .csv files, parses them into one + big pandas data frame and will add additional meta data from parameters folder, if it is present. - **parse_file(path_to_csv_file)** Parses a Sensospot csv file into a pandas data frame and will add some additional @@ -81,5 +81,7 @@ To install the development version of Sensovation Data Parser: To run the tests, use `make tests` (failing on first error) or `make coverage` for a complete report. +To generate the documentation pages use `make docs` or `make serve-docs` for +starting a webserver with the generated documentation -[sensospot]: https://www.miltenyi-imaging.com/products/sensospot \ No newline at end of file +[sensospot]: https://www.miltenyi-imaging.com/products/sensospot