Fixed an issue with paths, patch version

primal_page/__init__.py

@@ -1 +1 @@
-__version__ = "1.8.0"
+__version__ = "1.8.1"

primal_page/build_index.py

@@ -16,6 +16,8 @@ def parse_version(
 ) -> dict[str, str]:
     version_dict = dict()
 
+    log.info(f"parsing {version_path}")
+
     # Read in the info.json file
     with open(version_path / "info.json") as f:
         info_dict = json.load(f)

primal_page/modify.py

@@ -100,7 +100,11 @@ def write_info_json(info: Info, schemeinfo: pathlib.Path):
 
 def generate_files(info: Info, schemeinfo: pathlib.Path):
     # Write the validated info.json
-    write_info_json(info, schemeinfo / "info.json")
+
+    if schemeinfo.name != "info.json":
+        schemeinfo = schemeinfo / "info.json"
+
+    write_info_json(info, schemeinfo)
 
     # Update the README
     scheme_path = schemeinfo.parent
@@ -151,7 +155,10 @@ def remove_link(
     schemeinfo: Annotated[
         pathlib.Path,
         typer.Argument(
-            help="The path to info.json", readable=True, exists=True, writable=True
+            help="The path to info.json",
+            readable=True,
+            exists=True,
+            writable=True,
         ),
     ],
     linkfield: Annotated[

pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "primal-page"
-version = "1.8.0"
+version = "1.8.1"
 description = "Tooling and schemas for the primerschemes index"
 authors = ["ChrisKent <[email protected]>"]
 readme = "README.md"
@@ -11,9 +11,9 @@ python = "^3.10"
 pydantic = "^2.4.2"
 requests = "^2.31.0"
 biopython = "^1.83"
-
 typer = "^0.12.3"
 pre-commit = "^3.7.1"
+
 [tool.poetry.group.dev.dependencies]
 pytest = "^7.4.3"
 ruff = "^0.3.4"

tests/test_bedfile.py

@@ -18,8 +18,8 @@ class TestBedfile(unittest.TestCase):
     v1bedfile = pathlib.Path("tests/test_input/v1.primer.bed")
     v2bedfile = pathlib.Path("tests/test_input/v2.primer.bed")
     v3bedfile = pathlib.Path("tests/test_input/v3.primer.bed")
-    invalidbedfile = pathlib.Path("tests/test_input/invalid.primer.bed")
-    invalidstructbedfile = pathlib.Path("tests/test_input/invalid.struct.primer.bed")
+    invalid_bedfile = pathlib.Path("tests/test_input/invalid.primer.bed")
+    invalid_struct_bedfile = pathlib.Path("tests/test_input/invalid.struct.primer.bed")
 
     def test_validate_bedfile(self):
         # Test v1
@@ -31,11 +31,11 @@ def test_validate_bedfile(self):
         self.assertEqual(validate_bedfile(self.v3bedfile), BEDFileResult.VALID)
         # Test invalid raises
         with self.assertRaises(PrimerVersionError):
-            validate_bedfile(self.invalidbedfile)
+            validate_bedfile(self.invalid_bedfile)
 
         # Test invalid structure
         with self.assertRaises(InvalidBedFileLine):
-            validate_bedfile(self.invalidstructbedfile)
+            validate_bedfile(self.invalid_struct_bedfile)
 
 
 class TestDeterminePrimernameVersion(unittest.TestCase):
@@ -122,7 +122,7 @@ class TestValidateBedfileLineStructure(unittest.TestCase):
     v1bedfile = pathlib.Path("tests/test_input/v1.primer.bed")
     v2bedfile = pathlib.Path("tests/test_input/v2.primer.bed")
     v3bedfile = pathlib.Path("tests/test_input/v3.primer.bed")
-    invalidbedfile = pathlib.Path("tests/test_input/invalid.struct.primer.bed")
+    invalid_bedfile = pathlib.Path("tests/test_input/invalid.struct.primer.bed")
 
     def test_bed_file_structure_v3(self):
         """
@@ -154,7 +154,7 @@ def test_bed_file_structure_invalid(self):
         """
         Test that the bed file structure is correct
         """
-        with open(self.invalidbedfile) as bedfile:
+        with open(self.invalid_bedfile) as bedfile:
             results = [
                 validate_bedfile_line_structure(line) for line in bedfile.readlines()
             ]

tests/test_output/test_covid/test-data-covid/400/v1.0.0/README.md

@@ -32,7 +32,7 @@
     "articbedversion": "v3.0",
     "collections": [],
     "links": {
-        "protocals": [],
+        "protocols": [],
         "validation": [],
         "homepage": [],
         "vendors": [],

tests/test_output/test_covid/test-data-covid/400/v1.0.0/info.json

@@ -21,7 +21,7 @@
     "articbedversion": "v3.0",
     "collections": [],
     "links": {
-        "protocals": [],
+        "protocols": [],
         "validation": [],
         "homepage": [],
         "vendors": [],