From 43a17d698b9b6285f049288cdfcfdabfa89ba000 Mon Sep 17 00:00:00 2001 From: Harrison Deng Date: Tue, 18 Feb 2025 19:16:39 +0000 Subject: [PATCH] Updated readme to reflect recent changes and discuss versioning --- README.md | 17 +++++++++++++++-- 1 file changed, 15 insertions(+), 2 deletions(-) diff --git a/README.md b/README.md index 13e291a..821f43a 100644 --- a/README.md +++ b/README.md @@ -12,6 +12,7 @@ This CLI is capable of exactly what [autoBIGS.engine](https://pypi.org/project/a - Fetch the available BIGSdb database schemas for a given MLST database - Retrieve exact/non-exact MLST allele variant IDs based off a sequence - Retrieve MLST sequence type IDs based off a sequence +- Inexact matches are annotated with an asterisk (\*) - Output all results to a single CSV ## Planned Features for CLI @@ -40,6 +41,18 @@ Let's say you have a fasta called `seq.fasta` which contains several sequences. 3. Then, run `autobigs st -h` and familiarize yourself with the parameters needed for sequence typing. -4. Namely, you should find that you will need to run `autobigs st seq.fasta pubmlst_bordetella_seqdef 3 output.csv`. You can optionally include multiple `FASTA` files, and/or `--exact` to only retrieve exact sequence types, and/or `--stop-on-fail` to stop typing if one of your sequences fail to retrieve any type. +4. Namely, you should find that you will need to run `autobigs st seq.fasta pubmlst_bordetella_seqdef 3 output.csv`. You can optionally include multiple `FASTA` files, and `--stop-on-fail` to stop typing if one of your sequences fail to retrieve any type. -5. Sit tight, and wait. The `output.csv` will contain your results once completed. \ No newline at end of file +5. Sit tight, and wait. The `output.csv` will contain your results once completed. + +## Versioning + +the autoBIGS project follows [semantic versioning](https://semver.org/) where the three numbers may be interpreted as MAJOR.MINOR.PATCH. + +Note regarding major version 0 ([spec item 4](https://semver.org/#spec-item-4)), the following adaptation of semantic versioning definition is as follows: + +1. Given x.Y.z, Y is only incremented when a backwards incompatible change is made. + +2. Given x.y.Z, Z is only incremented when a backwards compatible change is made. + +Versions of autoBIGS items with a major version number of 0 will introduce numerous changes and patches. As such, changes between such versions should be considered highly variable. \ No newline at end of file