From a8640904840ede64007cb34893fdd107c282ff41 Mon Sep 17 00:00:00 2001
From: Usman Rashid <usman@smme.edu.pk>
Date: Mon, 29 Apr 2024 11:55:40 +1200
Subject: [PATCH] Added pyproject.toml

---
 .github/workflows/test.yml                 |  2 +-
 CHANGELOG.md                               |  1 +
 local_pangene                              |  5 ++---
 pyproject.toml                             | 15 +++++++++++++++
 tests/stub/{test_stub.json => params.json} |  3 ++-
 5 files changed, 21 insertions(+), 5 deletions(-)
 create mode 100644 pyproject.toml
 rename tests/stub/{test_stub.json => params.json} (89%)

diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index da21d2f..04497a0 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -50,7 +50,7 @@ jobs:
             main.nf \
             -profile local,docker \
             -stub \
-            -params-file tests/stub/test_stub.json
+            -params-file tests/stub/params.json
 
   confirm-pass:
     runs-on: ubuntu-latest
diff --git a/CHANGELOG.md b/CHANGELOG.md
index 135fb02..7936734 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -47,6 +47,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 38. Updated `pfr_pangene` and `pfr/profile.config`
 39. Now using local tests/stub files for GitHub CI
 40. Now removing iso-forms left by TSEBRA using `AGAT_SPFILTERFEATUREFROMKILLLIST`
+41. Added `pyproject.toml`
 
 ### `Fixed`
 
diff --git a/local_pangene b/local_pangene
index 9befef7..8a1aa8a 100755
--- a/local_pangene
+++ b/local_pangene
@@ -17,6 +17,5 @@ nextflow run \
     -profile local,docker \
     -resume \
     $stub \
-    -params-file pangene-test/test_params.json \
-    --eggnogmapper_db_dir ../../dbs/emapperdb/5.0.2 \
-    --eggnogmapper_tax_scope 33090
+    -params-file pangene-test/params.json \
+    --eggnogmapper_db_dir ../dbs/emapperdb/5.0.2
diff --git a/pyproject.toml b/pyproject.toml
new file mode 100644
index 0000000..5611062
--- /dev/null
+++ b/pyproject.toml
@@ -0,0 +1,15 @@
+# Config file for Python. Mostly used to configure linting of bin/*.py with Ruff.
+# Should be kept the same as nf-core/tools to avoid fighting with template synchronisation.
+[tool.ruff]
+line-length = 120
+target-version = "py38"
+cache-dir = "~/.cache/ruff"
+
+[tool.ruff.lint]
+select = ["I", "E1", "E4", "E7", "E9", "F", "UP", "N"]
+
+[tool.ruff.lint.isort]
+known-first-party = ["nf_core"]
+
+[tool.ruff.lint.per-file-ignores]
+"__init__.py" = ["E402", "F401"]
diff --git a/tests/stub/test_stub.json b/tests/stub/params.json
similarity index 89%
rename from tests/stub/test_stub.json
rename to tests/stub/params.json
index c49c3e9..db97d3b 100644
--- a/tests/stub/test_stub.json
+++ b/tests/stub/params.json
@@ -1,7 +1,8 @@
 {
     "input": "tests/stub/assemblysheet.csv",
-    "eggnogmapper_db_dir": "tests/stub/emapperdb/5.0.2",
     "external_protein_fastas": "tests/stub/external-protein-fastas.txt",
+    "eggnogmapper_db_dir": "tests/stub/emapperdb/5.0.2",
+    "eggnogmapper_tax_scope": 33090,
     "fastq": "tests/stub/fastqsheet.csv",
     "liftoff_annotations": "tests/stub/liftoffannotations.csv",
     "max_cpus": 2,