Merge pull request #1 from mlf-core/release/2.0.0

Zethson · web-flow · commit e9cdbee518a0 · 2021-04-08T14:27:31.000+02:00
Release/2.0.0
diff --git a/.cookietemple.yml b/.cookietemple.yml
@@ -13,7 +13,7 @@ full_name: Lukas Heumos
 email: lukas.heumos@posteo.net
 project_name: lcep-package
 project_short_description: Python package for lcep.
-version: 1.2.0
+version: 2.0.0
 license: MIT
 command_line_interface: Click
 testing_library: pytest
diff --git a/.gitignore b/.gitignore
@@ -134,3 +134,6 @@ dmypy.json
 # Coala
 *.orig
 
+# Mac OS generated files 
+.DS_Store
+.DS_Store?
diff --git a/CHANGELOG.rst b/CHANGELOG.rst
@@ -4,6 +4,21 @@ Changelog
 
 This project adheres to `Semantic Versioning <https://semver.org/>`_.
 
+2.0.0 (2021-04-08)
+------------------
+
+**Added**
+
+* Added model (v2) trained on recount2 TCGA/GTEx liver(cancer) data obtained from mlf-core/lcep
+* Replaced test data
+
+**Fixed**
+
+**Dependencies**
+
+**Deprecated**
+
+
 1.2.0 (2020-08-28)
 ------------------
 
diff --git a/cookietemple.cfg b/cookietemple.cfg
@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 1.2.0
+current_version = 2.0.0
 
 [bumpversion_files_whitelisted]
 setup_file = setup.py
diff --git a/docs/conf.py b/docs/conf.py
@@ -53,9 +53,9 @@
 # the built documents.
 #
 # The short X.Y version.
-version = '1.2.0'
+version = '2.0.0'
 # The full version, including alpha/beta/rc tags.
-release = '1.2.0'
+release = '2.0.0'
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.
diff --git a/lcep_package/__init__.py b/lcep_package/__init__.py
@@ -2,4 +2,4 @@
 
 __author__ = """Lukas Heumos"""
 __email__ = 'lukas.heumos@posteo.net'
-__version__ = '1.2.0'
+__version__ = '2.0.0'
diff --git a/lcep_package/cli.py b/lcep_package/cli.py
@@ -30,7 +30,7 @@ def main(input: str, model: str, cuda: bool, output: str):
 
     print('[bold blue]Run [green]lcep-package --help [blue]for an overview of all commands\n')
     if not model:
-        model = get_xgboost_model(f'{WD}/models/model_28.08.2020_v1.xgb')
+        model = get_xgboost_model(f'{WD}/models/model_08.04.2021_v2.xgb')
     else:
         model = get_xgboost_model(model)
     if cuda:
diff --git a/lcep_package/data/test.tsv b/lcep_package/data/test.tsv
diff --git a/lcep_package/models/model_08.04.2021_v2.xgb b/lcep_package/models/model_08.04.2021_v2.xgb
diff --git a/requirements.txt b/requirements.txt
@@ -1,4 +1,4 @@
-rich==6.0.0
+rich==9.1.0
 click==7.1.2
-xgboost==1.2.0
+xgboost==1.2.1
 numpy==1.19.1
diff --git a/setup.py b/setup.py
@@ -72,6 +72,6 @@ def walker(base, *paths):
     test_suite='tests',
     tests_require=test_requirements,
     url='https://github.com/mlf-core/lcep-package',
-    version='1.2.0',
+    version='2.0.0',
     zip_safe=False,
 )
