Merge pull request #233 from medema-group/release/2.0.0-beta.2

Release/2.0.0 beta.2

.github/workflows/update-version.yml

@@ -18,7 +18,7 @@ jobs:
         run: |
           OLD_VERSION=$(grep ^version pyproject.toml | cut -d '"' -f 2)
           OLD_VERSION="\"$OLD_VERSION\""
-          NEW_VERSION="\"$GITHUB_REF_NAME\""
+          NEW_VERSION="\"$(echo $GITHUB_REF_NAME | cut -d '/' -f 2)\""
           sed -i "s+version = $OLD_VERSION+version = $NEW_VERSION+g" pyproject.toml
       - name: Commit Changes
         run: |

big_scape/cli/cli_common_options.py

@@ -150,13 +150,14 @@ def common_cluster_query(fn):
             type=str,
             required=False,
             help=(
-                "MIBiG release number (from 3.1 onwards). If not provided, MIBiG will not be "
-                "included in the analysis. If required, BiG-SCAPE will download the "
+                "MIBiG release number (from 3.1 onwards, antiSMASH processed files of "
+                "recent MIBiG releases might not be immediately available). If not "
+                "provided, MIBiG will not be required, BiG-SCAPE will download the "
                 "MIBiG database to ./big_scape/MIBiG/mibig_antismash_<version>_gbk. "
-                "For advanced users: any custom (antiSMASH-processed) MIBiG collection"
-                " can be used as long as the expected folder is present, e.g. provide"
-                " -m mymibig with ./big_scape/MIBiG/mibig_antismash_mymibig_gbk."
-                "For more information, see the wiki."
+                "For advanced users: any custom (antiSMASH-processed) MIBiG collection "
+                "can be used as long as the expected folder is present, e.g. provide "
+                "-m mymibig with ./big_scape/MIBiG/mibig_antismash_mymibig_gbk. "
+                "If you wish to use a recent release, see the wiki on how to proceed."
             ),
         ),
         click.option(

pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name ="big-scape"
-version = "release/2.0.0"
+version = "2.0.0-beta.2"
 description = "Biosynthetic Gene Similarity Clustering and Prospecting Engine"
 requires-python = ">=3.11"
 license = { file = "LICENSE" }