Flatten sunbeamlib dir

pyproject.toml

@@ -105,7 +105,6 @@ classifiers = [  # Optional
 # https://packaging.python.org/discussions/install-requires-vs-requirements/
 dependencies = [ # Optional
   "more-itertools",
-  "semantic-version",
   "ruamel.yaml",
 ]
 
@@ -149,7 +148,7 @@ sunbeam = "sunbeamlib.scripts.command:main"
 [tool.setuptools]
 # If there are data files included in your packages that need to be
 # installed, specify them here.
-package-data = {"sunbeamlib" = ["src/sunbeamlib/data/*.yml", "src/sunbeamlib/data/*.yaml"]}
+package-data = {"sunbeamlib" = ["*.yml", "*.yaml"]}
 
 [build-system]
 # These are the assumed default build requirements from pip:
@@ -158,9 +157,8 @@ requires = ["setuptools>=61.0.0", "wheel"]
 build-backend = "setuptools.build_meta"
 
 #[tool.setuptools.packages.find]
-#where = ["src/sunbeamlib"]
+#where = ["src/"]
 # include = ["pkg*"]  # alternatively: `exclude = ["additional*"]`
-#exclude = ["src/sunbeamlib/data"]
 #namespaces = false
 
 [tool.setuptools.dynamic]

src/sunbeamlib/__init__.py

@@ -8,10 +8,30 @@
 
 from pathlib import Path
 
-from semantic_version import Version
 from sunbeamlib.parse import parse_fasta
 
-__version__ = str(Version.coerce(os.environ.get("SUNBEAM_VER", "0.0.0")))
+class Version():
+    def __init__(self, version: str) -> None:
+        self.version = version
+        if self.version.startswith("v"):
+            self.version = self.version[1:]
+
+        version_parts = self.version.split(".")
+        self.major = version_parts[0]
+        try:
+            self.minor = version_parts[1]
+        except IndexError:
+            self.minor = 0
+        try:
+            self.patch = version_parts[2]
+        except IndexError:
+            self.patch = 0
+
+    def __str__(self) -> str:
+        return f"{self.major}.{self.minor}.{self.patch}"
+
+
+__version__ = str(Version(os.environ.get("SUNBEAM_VER", "0.0.0")))
 
 
 def load_sample_list(samplelist_fp, paired_end=True, root_proj=""):

src/sunbeamlib/scripts/command.py → src/sunbeamlib/command.py

@@ -1,11 +1,11 @@
 import sys
 import argparse
 import sunbeamlib
-from sunbeamlib.scripts.run import main as Run
-from sunbeamlib.scripts.init import main as Init
-from sunbeamlib.scripts._config import main as Config
-from sunbeamlib.scripts.list_samples import main as ListSamples
-from sunbeamlib.scripts.extend import main as Extend
+from sunbeamlib.script_run import main as Run
+from sunbeamlib.script_init import main as Init
+from sunbeamlib.script_config import main as Config
+from sunbeamlib.script_list_samples import main as ListSamples
+from sunbeamlib.script_extend import main as Extend
 
 
 def main():

src/sunbeamlib/config.py

@@ -1,12 +1,11 @@
 import os
+import ruamel.yaml
 import sys
 from collections.abc import Mapping
 from pathlib import Path
 from pkg_resources import resource_stream
 
-from semantic_version import Version
-import ruamel.yaml
-from sunbeamlib import __version__
+from sunbeamlib import __version__, Version
 
 
 def makepath(path):

src/sunbeamlib/scripts/init.py → src/sunbeamlib/script_init.py

@@ -5,7 +5,7 @@
 import ruamel.yaml
 from pathlib import Path
 
-from .list_samples import (
+from sunbeamlib.script_list_samples import (
     build_sample_list,
     MissingMatePairError,
     SampleFormatError,