From f1d7c0172e874aa378c07cdb3039f6bc3b9893d0 Mon Sep 17 00:00:00 2001
From: AroneyS <samuel.aroney@qut.edu.au>
Date: Thu, 18 Jan 2024 11:12:37 +1000
Subject: [PATCH 1/2] add citation

---
 CITATION.cff | 18 ++++++++++++++++++
 1 file changed, 18 insertions(+)
 create mode 100644 CITATION.cff

diff --git a/CITATION.cff b/CITATION.cff
new file mode 100644
index 0000000..00dd825
--- /dev/null
+++ b/CITATION.cff
@@ -0,0 +1,18 @@
+cff-version: 1.2.0
+message: "If you use this software, please cite it as below."
+authors:
+  - family-names: Aroney
+    given-names: Samuel T. N.
+    orcid: https://orcid.org/0000-0001-9806-5846
+  - family-names: Camargo
+    given-names: Antonio P.
+    orcid: https://orcid.org/0000-0003-3913-2484
+  - family-names: Tyson
+    given-names: Gene W.
+    orcid: https://orcid.org/0000-0001-8559-9427
+  - family-names: Woodcroft
+    given-names: Ben J.
+    orcid: https://orcid.org/0000-0003-0670-7480
+title: "Galah: More scalable dereplication for metagenome assembled genomes"
+version: 0.3.1
+date-released: 2021-11-30

From 0aea34bfbee9cbf6fcdbfb42d66be7792b5eb8d8 Mon Sep 17 00:00:00 2001
From: AroneyS <samuel.aroney@qut.edu.au>
Date: Thu, 18 Jan 2024 11:33:26 +1000
Subject: [PATCH 2/2] add release script

---
 galah.yml  |  1 +
 release.py | 44 ++++++++++++++++++++++++++++++++++++++++++++
 2 files changed, 45 insertions(+)
 create mode 100644 release.py

diff --git a/galah.yml b/galah.yml
index f862975..759054f 100644
--- a/galah.yml
+++ b/galah.yml
@@ -5,3 +5,4 @@ channels:
 dependencies:
   - dashing >= 0.4.0
   - fastani >= 1.3
+  - extern
diff --git a/release.py b/release.py
new file mode 100644
index 0000000..f7bf1c3
--- /dev/null
+++ b/release.py
@@ -0,0 +1,44 @@
+#!/usr/bin/env python3
+
+import io
+from os.path import dirname, join
+import extern
+
+def get_version(relpath):
+  """Read version info from a file without importing it"""
+  for line in io.open(join(dirname(__file__), relpath), encoding="utf-8"):
+    if "version" in line:
+      if '"' in line:
+        return line.split('"')[1]
+      elif "'" in line:
+        return line.split("'")[1]
+
+if __name__ == "__main__":
+    print("running release.sh")
+    extern.run("release.sh")
+
+    version = get_version('Cargo.toml')
+    print("version is {}".format(version))
+
+    # Replace version in CITATION.cff
+    citations_lines = []
+    with open("CITATION.cff", "r") as f:
+        import re
+        r = re.compile(r"( *version: )")
+        r2 = re.compile(r"( *date-released: )")
+        for line in f:
+            if matches := r.match(line):
+                line = matches.group(1) + version + "\n"
+            elif matches := r2.match(line):
+                from datetime import datetime
+                line = matches.group(1) + datetime.today().strftime('%Y-%m-%d') + "\n"
+            citations_lines.append(line)
+    with open("CITATION.cff", "w") as f:
+        f.writelines(citations_lines)
+
+    print("Checking if repo is clean ..")
+    extern.run('if [[ $(git diff --shortstat 2> /dev/null | tail -n1) != "" ]]; then exit 1; fi')
+
+    extern.run('git tag v{}'.format(version))
+    print("Now run 'cargo publish' and then 'git push && git push --tags' and GitHub actions will build and upload to PyPI".format(version))
+    print("Then make a release, adding changelog info, so Zenodo picks it up")