Update readme for build backend and new subcommand

README.md

@@ -8,7 +8,7 @@ The toolkit for validating and building tiling amplicon PCR primer scheme defini
 
 ## Install (Python 3.10+)
 
-```
+```shell
 # Latest stable release
 pip install primaschema
 
@@ -19,13 +19,13 @@ pip install ./primaschema
 # Development
 git clone https://github.com/pha4ge/primaschema.git
 cd primaschema
-pip install --editable ./
+pip install --editable '.[dev]'
 pytest
 ```
 
 Some Primaschema commands use components from the [primer-schemes](https://github.com/pha4ge/primer-schemes) repository. To show Primaschema where to find these, create the environment variable `PRIMER_SCHEMES_PATH` pointing to the location of the primer-schemes directory on your machine:
 
-```
+```shell
 git clone https://github.com/pha4ge/primer-schemes.git
 export PRIMER_SCHEMES_PATH="/path/to/primer-schemes"
 ```
@@ -36,12 +36,10 @@ export PRIMER_SCHEMES_PATH="/path/to/primer-schemes"
 
 ```
 % primaschema --help
-usage: primaschema [-h] [--version]
-                   {hash-ref,hash-bed,validate,validate-recursive,build,build-recursive,build-manifest,diff,6to7,7to6,show-non-ref-alts}
-                   ...
+usage: primaschema [-h] [--version] {hash-ref,hash-bed,validate,validate-recursive,build,build-recursive,build-manifest,diff,6to7,7to6,show-non-ref-alts,intervals} ...
 
 positional arguments:
-  {hash-ref,hash-bed,validate,validate-recursive,build,build-recursive,build-manifest,diff,6to7,7to6,show-non-ref-alts}
+  {hash-ref,hash-bed,validate,validate-recursive,build,build-recursive,build-manifest,diff,6to7,7to6,show-non-ref-alts,intervals}
     hash-ref            Generate reference sequence checksum
     hash-bed            Generate a bed file checksum
     validate            Validate a primer scheme bundle containing info.yml, primer.bed and reference.fasta
@@ -53,6 +51,7 @@ positional arguments:
     6to7                Convert a 6 column scheme.bed file to a 7 column primer.bed file using a reference sequence
     7to6                Convert a 7 column primer.bed file to a 6 column scheme.bed file by droppign a column
     show-non-ref-alts   Show primer records with sequences not matching the reference sequence
+    intervals           Show intervals covered by primers in a BED file
 
 options:
   -h, --help            show this help message and exit

pyproject.toml

@@ -26,10 +26,10 @@ classifiers = [
 dependencies = [
     "biopython>=1.80",
     "defopt==6.4.0",
-    "pandas>=1.5.3",
     "jsonschema",
-    "pyyaml",
     "linkml==1.5.2",
+    "pandas>=1.5.3",
+    "pyyaml",
 ]
 
 [project.scripts]

src/primaschema/cli.py

@@ -133,7 +133,7 @@ def show_non_ref_alts(scheme_dir: Path):
 
 def print_intervals(bed_path: Path):
     """
-    Print intervals covered by primers in a BED file
+    Show intervals covered by primers in a BED file
 
     :arg ref_path: Path of bed file
     """