Rafal Stepien comments

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                                            Rafal Stepien

Peppy does not create correct list of `Sample()` objects stored in `self._samples`

Hi @vreuter thanks for the comment. You are absolutely right. I mentioned `self._samples` but I meant `self.samples`. If you look to the code, accessing `self.samples` simply returns `self._samples` if it...

`peppy` does not initialize correctly, when there is sample table index name other than default

[samplesheet.csv](https://github.com/pepkit/peppy/files/9383406/samplesheet.csv) [subsamplesheet.csv](https://github.com/pepkit/peppy/files/9383407/subsamplesheet.csv) Since I cannot attach `.yaml` files below you will find raw config: ``` pep_version: "2.0.0" sample_table: "samplesheet.csv" subsample_table: "subsamplesheet.csv" sample_table_index: "sample" subsample_table_index: "sample" ```

`peppy` does not initialize correctly, when there is sample table index name other than default

The direct cause of this error is that in `peppy.Project` initialization attributes `self.st_index` and `self.sst_index` are created. Unfortunately in further part of the script hardcoded variables (`SAMPLE_NAME_ATTR` and `SUBSAMPLE_NAME_ATTR`) are...

`peppy` does not initialize correctly, when there is sample table index name other than default

After resolving the first issue, the command `eido convert pep_files/config.yaml -f csv` finishes with success announcement, but there are warnings: ``` Could not set subsample_table index. At least one of...

Allow a merged sample where some attributes are missing values

https://github.com/pepkit/peppy/pull/396