v0.4.0

CITATION.cff

@@ -15,5 +15,5 @@ authors:
     given-names: Suzanne B.
     orcid: https://orcid.org/0000-0002-0489-9207
 title: "Kingfisher: A utility for procurement of public sequencing data"
-version: 0.3.1
+version: 0.4.0
 date-released: 2023-09-27

docs/usage/extract.md

@@ -16,6 +16,10 @@ uncompressed.
 
   Extract this SRA file [required]
 
+**\--output-directory** *OUTPUT_DIRECTORY*
+
+  Output directory to write to [default: current working directory]
+
 **-f**, **\--output-format-possibilities** {sra,fastq,fastq.gz,fasta,fasta.gz} [{sra,fastq,fastq.gz,fasta,fasta.gz} \...]
 
   Allowable output formats. If more than one is specified, downloaded

docs/usage/get.md

@@ -39,6 +39,10 @@ Download and extract sequence data from SRA or ENA
 | aws-cp   | Download .SRA file from AWS using aws s3 cp, which is then extracted with fasterq-dump. Does not usually require payment or an AWS account.        |
 | gcp-cp   | Download .SRA file from Google Cloud gsutil, which is then extracted with fasterq-dump. Requires payment and a Google Cloud account.               |
 
+**\--output-directory** *OUTPUT_DIRECTORY*
+
+  Output directory to write to [default: current working directory]
+
 # FURTHER DOWNLOAD OPTIONS
 
 **\--download-threads** *DOWNLOAD_THREADS*

kingfisher/version.py

@@ -1 +1 @@
-__version__ = "0.3.1"
+__version__ = "0.4.0"

release.py

@@ -2,6 +2,7 @@
 
 import io
 from os.path import dirname, join
+import re
 import extern
 
 def get_version(relpath):
@@ -17,6 +18,17 @@ def get_version(relpath):
     version = get_version('kingfisher/version.py')
     print("version is {}".format(version))
 
+    # Replace version in CITATION.cff
+    citations_lines = []
+    with open("CITATION.cff", "r") as f:
+        r = re.compile(r"( *version: )")
+        for line in f:
+            if matches := r.match(line):
+                line = matches.group(1) + version + "\n"
+            citations_lines.append(line)
+    with open("CITATION.cff", "w") as f:
+        f.writelines(citations_lines)
+
     print("building docs")
     extern.run("python3 build_docs.py")