docs: change 'kmcp' to 'KMCP'

taxprofiler · Aug 18, 2023 · 39b9517 · 39b9517
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -9,7 +9,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### Added
 
-- Added classifier support for kmcp files (#129)
+-   Added classifier support for KMCP files (#129)
 
 ## [0.4.1] - (2023-07-13)
 

diff --git a/docs/supported_profilers/kmcp.md b/docs/supported_profilers/kmcp.md
@@ -1,7 +1,6 @@
-# kmcp
-
-> [kmcp](https://github.com/shenwei356/kmcp) uses genome coverage information by splitting the reference genomes into chunks and stores k-mers in a modified and optimized Compact Bit-Sliced Signature (COBS) index for fast alignment-free sequence searching. KMCP combines k-mer similarity and genome coverage information to reduce the false positive rate of k-mer-based taxonomic classification and profiling methods.
+# KMCP
 
+> [KMCP](https://github.com/shenwei356/kmcp) uses genome coverage information by splitting the reference genomes into chunks and stores k-mers in a modified and optimized Compact Bit-Sliced Signature (COBS) index for fast alignment-free sequence searching. KMCP combines k-mer similarity and genome coverage information to reduce the false positive rate of k-mer-based taxonomic classification and profiling methods.
 
 ## Profile Format
 
@@ -27,4 +26,4 @@ Taxpasta expects a tab-separated file with seventeen columns. This is generated
 | taxpath           |             |
 | taxpathsn         |             |
 
- See [kmcp docs](https://bioinf.shenwei.me/kmcp/usage/#profile) for further description.
+See [KMCP docs](https://bioinf.shenwei.me/kmcp/usage/#profile) for further description.
diff --git a/src/taxpasta/infrastructure/application/kmcp/kmcp_profile.py b/src/taxpasta/infrastructure/application/kmcp/kmcp_profile.py
@@ -27,7 +27,7 @@
 
 
 class KMCPProfile(BaseDataFrameModel):
-    """Define the expected kmcp profile format."""
+    """Define the expected KMCP profile format."""
 
     reference: Series[str] = pa.Field(alias="ref")
     percentage: Series[float] = pa.Field(ge=0.0, le=100.0)

diff --git a/src/taxpasta/infrastructure/application/kmcp/kmcp_profile_reader.py b/src/taxpasta/infrastructure/application/kmcp/kmcp_profile_reader.py
@@ -16,7 +16,7 @@
 # limitations under the License.
 
 
-"""Provide a reader for kmcp profiles."""
+"""Provide a reader for KMCP profiles."""
 
 
 import pandas as pd
@@ -29,20 +29,20 @@
 
 
 class KMCPProfileReader(ProfileReader):
-    """Define a reader for kmcp profiles."""
+    """Define a reader for KMCP profiles."""
 
     @classmethod
     @raise_parser_warnings
     def read(cls, profile: BufferOrFilepath) -> DataFrame[KMCPProfile]:
         """
-        Read a kmcp taxonomic profile from the given source.
+        Read a KMCP taxonomic profile from the given source.
 
         Args:
             profile: A source that contains a tab-separated taxonomic profile generated
-                by kmcp.
+                by KMCP.
 
         Returns:
-            A data frame representation of the kmcp profile.
+            A data frame representation of the KMCP profile.
 
         """
         result = pd.read_table(

diff --git a/src/taxpasta/infrastructure/application/kmcp/kmcp_profile_standardisation_service.py b/src/taxpasta/infrastructure/application/kmcp/kmcp_profile_standardisation_service.py
@@ -16,7 +16,7 @@
 # limitations under the License.
 
 
-"""Provide a standardisation service for kmcp profiles."""
+"""Provide a standardisation service for KMCP profiles."""
 
 
 import logging
@@ -35,16 +35,16 @@
 
 
 class KMCPProfileStandardisationService(ProfileStandardisationService):
-    """Define a standardisation service for kmcp profiles."""
+    """Define a standardisation service for KMCP profiles."""
 
     @classmethod
     @pa.check_types(lazy=True)
     def transform(cls, profile: DataFrame[KMCPProfile]) -> DataFrame[StandardProfile]:
         """
-        Tidy up and standardize a given kmcp profile.
+        Tidy up and standardize a given KMCP profile.
 
         Args:
-            profile: A taxonomic profile generated by kmcp.
+            profile: A taxonomic profile generated by KMCP.
 
         Returns:
             A standardized profile.

diff --git a/tests/conftest.py b/tests/conftest.py
@@ -99,5 +99,5 @@ def ganon_data_dir(data_dir: Path) -> Path:
 
 @pytest.fixture(scope="session")
 def kmcp_data_dir(data_dir: Path) -> Path:
-    """Provide the path to the kmcp data directory."""
+    """Provide the path to the KMCP data directory."""
     return data_dir / "kmcp"
diff --git a/tests/unit/infrastructure/application/kmcp/test_kmcp_profile.py b/tests/unit/infrastructure/application/kmcp/test_kmcp_profile.py
@@ -16,7 +16,7 @@
 # limitations under the License.
 
 
-"""Test that the schema model validates kmcp profiles correctly."""
+"""Test that the schema model validates KMCP profiles correctly."""
 
 
 from collections import OrderedDict

diff --git a/tests/unit/infrastructure/application/kmcp/test_kmcp_profile_reader.py b/tests/unit/infrastructure/application/kmcp/test_kmcp_profile_reader.py
@@ -16,7 +16,7 @@
 # limitations under the License.
 
 
-"""Test that the reader can parse valid kmcp profiles."""
+"""Test that the reader can parse valid KMCP profiles."""
 
 
 from pathlib import Path
@@ -45,7 +45,7 @@ def test_read_correctness(
     filename: str,
     checks: List[Tuple[int, int, Union[float, int, str]]],
 ):
-    """Test that the reader can parse valid kmcp profiles."""
+    """Test that the reader can parse valid KMCP profiles."""
     profile = KMCPProfileReader.read(kmcp_data_dir / filename)
     for row, col, value in checks:
         assert profile.iat[row, col] == value