Merge pull request #205 from medema-group/hotfix/fix-config-pip-install

Revert location of config yml file until a default/override config system is in place
medema-group · Nov 1, 2024 · ec88659 · ec88659
2 parents a34ee3e + 9a02758
commit ec88659
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Showing 4 changed files with 10 additions and 6 deletions.
diff --git a/config.yml → big_scape/config.yml b/config.yml → big_scape/config.yml
diff --git a/big_scape/paths.py b/big_scape/paths.py
@@ -2,8 +2,8 @@
 
 import pkg_resources
 
-DB_SCHEMA_FILE = pkg_resources.resource_filename(
-    "bigscape", "big_scape/data/schema.sql"
-)
-TEMPLATES_OUTPUT_DIR = pkg_resources.resource_filename("bigscape", "big_scape/output")
-DEFAULT_CONFIG_FILE = pkg_resources.resource_filename("bigscape", "config.yml")
+DB_SCHEMA_FILE = pkg_resources.resource_filename("big_scape", "data/schema.sql")
+TEMPLATES_OUTPUT_DIR = pkg_resources.resource_filename("big_scape", "output")
+# config is in base directory, not in module
+# get path to package directory
+DEFAULT_CONFIG_FILE = pkg_resources.resource_filename("big_scape", "config.yml")
diff --git a/pyproject.toml b/pyproject.toml
@@ -45,6 +45,10 @@ dev = [
 "Repository" = "https://github.com/medema-group/BiG-SCAPE"
 # TODO: documentation
 
+[tool.setuptools.package-data]
+'big_scape' = ['config.yml']
+'data' = ['data/schema.sql']
+
 [build-system]
 requires = ["hatchling"]
 build-backend = "hatchling.build"

diff --git a/test/integration/test_comparison.py b/test/integration/test_comparison.py
@@ -456,7 +456,7 @@ def test_calculate_scores_pair(self):
             "legacy_weights": True,
             "record_type": bs_enums.RECORD_TYPE.REGION,
             "cores": 1,
-            "config_file_path": Path("config.yml"),
+            "config_file_path": Path("big_scape/config.yml"),
         }
 
         gbks_with_hsp = [