dev -> main for release v.0.1.6

.github/workflows/lint-workflow.yml

@@ -2,7 +2,7 @@ name: Run linter
 
 on:
   pull_request:
-    branches: [main]
+    branches: [main, dev]
 
 jobs:
   flake8:

.github/workflows/pytest-workflow.yml

@@ -4,7 +4,7 @@ on:
   push:
     branches: [main]
   pull_request:
-    branches: [main]
+    branches: [main, dev]
 
 jobs:
   pytest:

.pre-commit-config.yaml

@@ -8,6 +8,7 @@ repos:
     -   id: end-of-file-fixer
     -   id: check-yaml
     -   id: check-added-large-files
+        args: ['--maxkb=20000']
 -   repo: https://github.com/psf/black
     rev: 24.8.0
     hooks:

mgnify_pipelines_toolkit/analysis/shared/fastq_suffix_header_check.py

@@ -77,12 +77,10 @@ def main():
                 'No reverse file given, yet given forward file has the "_1" suffix implying it\'s paired-end. '
                 + "Either supply the reverse file, or supply a single-end file."
             )
-            exit(1)
         elif "_2" not in rev:
             logging.error(
                 'The expected suffix "_2" for a supplied reverse file is missing. Please verify your inputs.'
             )
-            exit(1)
         else:
             files_to_parse = [fwd, rev]
 

mgnify_pipelines_toolkit/utils/get_mpt_version.py

@@ -0,0 +1,26 @@
+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+
+# Copyright 2024 EMBL - European Bioinformatics Institute
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+import importlib.metadata
+
+
+def main():
+
+    print(importlib.metadata.version("mgnify-pipelines-toolkit"))
+
+
+if __name__ == "__main__":
+    main()

pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "mgnify_pipelines_toolkit"
-version = "0.1.5"
+version = "0.1.6"
 readme = "README.md"
 license = {text = "Apache Software License 2.0"}
 authors = [
@@ -56,6 +56,7 @@ mapseq_to_asv_table = "mgnify_pipelines_toolkit.analysis.amplicon.mapseq_to_asv_
 primer_val_classification = "mgnify_pipelines_toolkit.analysis.amplicon.primer_val_classification:main"
 # utils
 fasta_to_delimited = "mgnify_pipelines_toolkit.utils.fasta_to_delimited:main"
+get_mpt_version = "mgnify_pipelines_toolkit.utils.get_mpt_version:main"
 
 [project.optional-dependencies]
 tests = [

tests/unit/analysis/assembly/antismash_gff_builder/test_antismash_gff_builder.yml

@@ -0,0 +1,23 @@
+- name: antismash_gff_builder test_wrong_args
+  tags:
+    - antismash_gff_builder
+  exit_code: 2
+  command: python -m mgnify_pipelines_toolkit.analysis.assembly.antismash_gff_builder --chromosome X
+  stderr:
+    contains:
+      - "antismash_gff_builder.py: error: the following arguments are required: -i/--input, -o/--output"
+- name: antismash_gff_builder test_correct_args
+  tags:
+    - antismash_gff_builder
+  command: python -m mgnify_pipelines_toolkit.analysis.assembly.antismash_gff_builder -i tests/fixtures/misc/test_antismash.json -o test.gff --cds_tag ID
+  files:
+    - path: "test.gff"
+      md5sum: 381a0c0d7e221f8817d84f36153444c4
+- name: antismash_gff_builder test_correct_args_wrong_cds_tag
+  tags:
+    - antismash_gff_builder
+  exit_code: 1
+  command: python -m mgnify_pipelines_toolkit.analysis.assembly.antismash_gff_builder -i tests/fixtures/misc/test_antismash.json -o test.gff --cds_tag IDD
+  stderr:
+    contains:
+      - "KeyError: 'IDD'"

tests/unit/utils/get_mpt_version/test_get_mpt_version.yml

@@ -0,0 +1,8 @@
+- name: test_get_mpt_version
+  tags:
+    - test_get_mpt_version
+  exit_code: 0
+  stdout:
+    contains_regex:
+    - '\d\.\d\.\d'
+  command: python -m mgnify_pipelines_toolkit.utils.get_mpt_version