fix archiving lilac.yaml for bioc

updater/depends_updater.py

@@ -20,6 +20,8 @@ import re
 import requests
 
 # use | in lilac.yaml
+
+
 def str_presenter(dumper, data):
     """configures yaml for dumping multiline strings
     Ref: https://stackoverflow.com/questions/8640959/how-can-i-control-what-scalar-form-pyyaml-uses-for-my-data"""
@@ -32,6 +34,7 @@ yaml.add_representer(str, str_presenter)
 yaml.representer.SafeRepresenter.add_representer(
     str, str_presenter)  # to use with safe_dum
 
+
 class PkgInfo:
     def __init__(self, pkgname=None, depends=None, optdepends=None,
                  bioc_meta_mirror="https://bioconductor.org",
@@ -315,7 +318,9 @@ class PkgInfo:
         if new_deps:
             docs['repo_depends'] = new_deps
         with open(yaml_file, 'w') as f:
-            yaml.dump(docs, f, sort_keys=False)
+            stream = yaml.dump(docs,  sort_keys=False,
+                               default_flow_style=False, indent=2)
+            f.write(stream)
 
 
 def create_temporary_copy(path):

updater/pkg_archiver.py

@@ -58,7 +58,11 @@ def archive_pkg_yaml(bioconductor_version=3.15, yaml_file="lilac.yaml"):
         archive_url = f"https://cran.r-project.org/src/contrib/Archive/{pkg}"
     # Bioconductor ARCHIVE
     elif 'bioconductor.org' in url:
-        archive_url = url.replace('release', f"{bioconductor_version}")
+        # https://bioconductor.org/packages/AffyCompatible
+        # to
+        # https://bioconductor.org/packages/3.16/AffyCompatible
+        archive_url = url.replace(
+            'packages', f"packages/{bioconductor_version}")
     if archive_url:
         docs['update_on'][url_idx]['url'] = archive_url
     with open(yaml_file, 'w') as f: