Merge pull request #320 from medema-group/release/2.0.0

Release/2.0.0

Author: adraismawur

.github/ISSUE_TEMPLATE/bug_report.md

@@ -0,0 +1,28 @@
+---
+name: Bug report
+about: Create a report to help us improve
+title: ''
+labels: bug
+assignees: ''
+
+---
+
+**Describe the bug**
+A clear and concise description of what the bug is.
+
+**To Reproduce**
+Please describe the steps used to reproduce the issue in this section
+
+**Expected behavior**
+A clear and concise description of what you expected to happen.
+
+**Screenshots**
+If applicable, add screenshots to help explain your problem.
+
+**System (please complete the following information):**
+ - OS: [e.g. iOS]
+- Hardware [e.g. x64 or ARM, memory size]
+ - BiG-SCAPE Version [e.g. 2.0.0-beta.3, use bigscape --version to confirm]
+
+**Additional context**
+Add any other context about the problem here.

.github/ISSUE_TEMPLATE/feature_request.md

@@ -0,0 +1,20 @@
+---
+name: Feature request
+about: Suggest an idea for this project
+title: ''
+labels: enhancement
+assignees: ''
+
+---
+
+**Is your feature request related to a problem? Please describe.**
+A clear and concise description of what the problem is. Ex. I'm always frustrated when [...]
+
+**Describe the solution you'd like**
+A clear and concise description of what you want to happen.
+
+**Describe alternatives you've considered**
+A clear and concise description of any alternative solutions or features you've considered.
+
+**Additional context**
+Add any other context or screenshots about the feature request here.

.github/ISSUE_TEMPLATE/question-about-big-scape-process-or-results.md

@@ -0,0 +1,10 @@
+---
+name: Question about BiG-SCAPE process or results
+about: For questions about BiG-SCAPE in general
+title: ''
+labels: question
+assignees: ''
+
+---
+
+

.github/workflows/deploy-docker.yml

@@ -2,8 +2,7 @@ name: Publish Docker image
 
 on:
   release:
-    types: [published, edited]
-
+    types: [published]
 
 env:
   REGISTRY: ghcr.io
@@ -31,8 +30,8 @@ jobs:
         # set latest tag for master branch
         with:
           tags: |
-            type=semver,pattern={{version}}
-            type=raw,value=latest,enable=${{ github.ref == format('refs/heads/{0}', 'master') }}
+            type=semver,pattern={{GITHUB_REF}}
+            type=raw,value=latest
           images: ${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}
 
       - name: Login to GitHub Container Registry

CITATION.cff

@@ -0,0 +1,23 @@
+cff-version: 1.2.0
+message: "If you use this software, please cite it as below"
+authors:
+  - family-names: Draisma
+    given-names: Arjan
+    orcid: 0009-0004-0503-6261
+  - family-names: Loureiro
+    given-names: Catarina
+    orcid: 0000-0002-6258-2080
+  - family-names: Louwen
+    given-names: Nico L.L.
+    orcid: 0000-0002-4431-5499
+  - family-names: Medema
+    given-names: Marnix H.
+    orcid: 0000-0002-2191-2821
+title: "BiG-SCAPE: Biosynthetic Gene Similarity Clustering and Prospecting Engine"
+version: 2.0.0
+identifiers:
+  - type: doi
+    value: 10.1101/2025.08.20.671210
+  - type: doi
+    value: 10.1038/s41589-019-0400-9
+date-released: 24-07-2025

CONTRIBUTING.md

@@ -0,0 +1,38 @@
+# Contributing
+
+We welcome contributions to this repository.
+In order to do so, please fork this repository and submit pull requests according to
+the section below.
+
+## Submitting a pull request
+
+1. Fork this repository
+2. Create a new branch from our dev branch, and give it a descriptive name
+3. Commit your work to this branch
+4. Submit a new PR
+
+In this PR, please include the following information:
+
+- What did you change?
+- Why did you change it? (Please link to issues if available)
+- How did you implement the change?
+
+These points help us review your PR.
+
+
+## Submitting an issue
+
+Please feel free to submit new issues.
+You can use the search function on GitHub to check if an issue for the problem you are
+experiencing already exists.
+But if you cannot find an issue that matches your exact problem, please feel free to
+submit a new issue.
+
+We use a number of templates for issues that you can use, but if your issue does not fit
+within the templates, please feel free to submit a custom issue.
+
+## Code guidelines
+
+The codebase largely follows the PEP8 standards, and uses flake8 for linting.
+We use black for auto formatting.
+Please ensure you have run a formatting tool on your code.

README.md

@@ -4,7 +4,7 @@
 ![Test workflow](https://github.com/medema-group/BiG-SCAPE/actions/workflows/deploy-docker.yml/badge.svg)
 [![fair-software.eu](https://img.shields.io/badge/fair--software.eu-%E2%97%8F%20%20%E2%97%8F%20%20%E2%97%8F%20%20%E2%97%8B%20%20%E2%97%8B-orange)](https://fair-software.eu)
 
-## _Notes:<br>BiG-SCAPE 2.0 is still in beta. Please submit an issue if you find anything wrong with this release!<br>BiG-SCAPE 2.0 features several updates to input validation and reference usage. We encourage both experienced BiG-SCAPE 1 users as well as new BiG-SCAPE users to read the updated [documentation](https://github.com/medema-group/BiG-SCAPE/wiki)._
+## _Notes:<br>BiG-SCAPE 2.0 features several updates to input validation and reference usage.<br>We encourage both experienced BiG-SCAPE 1 users as well as new BiG-SCAPE users to read the updated [documentation](https://github.com/medema-group/BiG-SCAPE/wiki)._
 
 # BiG-SCAPE
 

big_scape/comparison/comparable_region.py

@@ -220,15 +220,15 @@ def __repr__(self) -> str:
         )
 
     @staticmethod
-    def cds_range_contains_biosynthetic(
+    def cds_range_contains_core(
         record: BGCRecord,
         cds_start: int,
         cds_stop: int,
         end_inclusive=False,
         reverse=False,
     ) -> bool:
         """Return true if a range of cds within this record contains a gene that is
-        marked as biosynthetic
+        marked as core
 
         Args:
             record (BGCRecord): BGC record object
@@ -240,7 +240,7 @@ def cds_range_contains_biosynthetic(
             cds_start and cds_stop. Defaults to False.
 
         Returns:
-            bool: True if the given range contains a biosynthetic gene
+            bool: True if the given range contains a core gene
         """
         stop = cds_stop
         if end_inclusive:
@@ -252,7 +252,7 @@ def cds_range_contains_biosynthetic(
             if cds.gene_kind is None:
                 continue
 
-            if cds.gene_kind == "biosynthetic":
+            if cds.is_core():
                 return True
 
         return False

big_scape/comparison/extend.py

@@ -53,17 +53,17 @@ def len_check(pair: RecordPair, min_len_perc: float) -> bool:
     return False
 
 
-def biosynthetic_check(pair: RecordPair) -> bool:
-    """Checks if any element of a pair contains a biosynthetic domain
+def core_check(pair: RecordPair) -> bool:
+    """Checks if any element of a pair contains a rule-triggering core domain
 
     returns true if
-    - the comparable region contains a biosynthetic gene
+    - the comparable region contains a core gene
 
     Args:
         pair: The record pair to check
     """
 
-    if ComparableRegion.cds_range_contains_biosynthetic(
+    if ComparableRegion.cds_range_contains_core(
         pair.record_a,
         pair.comparable_region.a_start,
         pair.comparable_region.a_stop,
@@ -72,7 +72,7 @@ def biosynthetic_check(pair: RecordPair) -> bool:
     ):
         return True
 
-    if ComparableRegion.cds_range_contains_biosynthetic(
+    if ComparableRegion.cds_range_contains_core(
         pair.record_b,
         pair.comparable_region.b_start,
         pair.comparable_region.b_stop,