Release 0.50.0a1

[ClaudeHu]

Release 0.50.0a1

1. Merging EIDO
2. Merging PEPHubClient

merging eido

merging

eido is relocated and is now a module within peppy.

from peppy.eido.validation import validate_project
from peppy import Project

pep_proj = Project("path/to/project/config.yaml")
validate_project(pep_proj, "path/to/schema/file.yaml")

peppy didn't have CLI before relocation. After the relocation, the command is peppy:

$ peppy inspect config.yaml
$ peppy validate config.yaml -s schema.yaml
$ peppy convert config.yaml --format csv

pre-processd PEP validation

Config validation is extended. It can directly validate given path of config file against a schema.

validate the original samples

New function that validate a sample table against a given schema.

Relative path in schema to import

If the schema path is given, peppy.schema.read_schema parses relative paths if the initial schema path is the input.

Repeated warning

The warning message is now printed at the end. For an unpopulated environment variable, the relative paths under it are accumulated and printed once together. For example:

WARNING - Not all environment variables were populated in derived attribute source: $PROJECT/{frog_0h.fastq, pig_1h.fastq, pig_0h.fastq, frog_1h.fastq}

Confusing error

Corrected as suggested in issue.

To discuss

Integer type in PEP

Default dtype is str when a sample csv table is parsed. Would like to hear everyone's thought on that.

Other minor changes

In argparser for CLI relocated from eido, default args related to sample table indices is changed to None. Previous default values can interfere with project config when running CLI, like the attached PEP in integer type issue.

[khoroshevskyi]

Add peppy0_50 branch to pytests.
Then ready to merge

[khoroshevskyi]

TODO:

• Readme file is empty, just add everything that was before there back
• Confirm that we need mkdocs.yml and .readthedocs.yaml
• we have 3 files: update_test_data.sh,update_docs.sh, scripts/update_usage_docs.sh . It would be nice to consolidate them, test, and add docs to pep.databio.org
• We don't need docs in this repo anymore. We can remove them.
• Change version to 0.50.0a1
• Add release info in changelog to pep.databio.org