Merge pull request #10 from mlf-core/development

Updated train/test datasets and runs

.github/workflows/publish_docker.yml

@@ -21,5 +21,5 @@ jobs:
         username: mlf-core
         password: '${{ secrets.MLF_CORE_SYNC_TOKEN}}'
         registry: ghcr.io
-        tags: "latest,1.0.0"
+        tags: "latest,1.0.1"
 

.github/workflows/train_cpu.yml

@@ -18,13 +18,13 @@ jobs:
         with:
           dockerfile: Dockerfile
           repository: ghcr.io/mlf-core/lcep
-          tags: 1.0.0
+          tags: 1.0.1
           push: false
 
       - name: Setup Python
         uses: actions/setup-python@v1
         with:
-          python-version:  ${{ matrix.python }} 
+          python-version:  ${{ matrix.python }}
 
       - name: Install mlflow
         run: pip install mlflow

.mlf_core.yml

@@ -15,5 +15,5 @@ email: [email protected]
 project_name: lcep
 project_short_description: Classifying cancerous liver samples from gene expression
   data.
-version: 1.0.0
+version: 1.0.1
 license: MIT

CHANGELOG.rst

@@ -5,6 +5,20 @@ Changelog
 This project adheres to `Semantic Versioning <https://semver.org/>`_.
 
 
+1.0.1 (2021-04-08)
+------------------
+
+**Added**
+
+**Fixed**
+
+* Fixed train/test dataset float point variation of some samples. The new dataset was generated by the nextflow-lcep pipeline.
+
+**Dependencies**
+
+**Deprecated**
+
+
 1.0.0 (2021-03-11)
 ------------------
 

MLproject

@@ -1,13 +1,13 @@
 # Author: Lukas Heumos
 # Email: [email protected]
-# Version: 1.0.0
+# Version: 1.0.1
 # License: MIT
 
 name: lcep
 
 # conda_env: environment.yml
 docker_env:
-  image: ghcr.io/mlf-core/lcep:1.0.0
+  image: ghcr.io/mlf-core/lcep:1.0.1
   volumes: ["${PWD}/data:/data"]
 
 entry_points:

docs/conf.py

@@ -53,9 +53,9 @@
 # the built documents.
 #
 # The short X.Y version.
-version = '1.0.0'
+version = '1.0.1'
 # The full version, including alpha/beta/rc tags.
-release = '1.0.0'
+release = '1.0.1'
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.

docs/usage.rst

@@ -40,10 +40,10 @@ You can replace ``all`` with specific GPU ids (e.g. 0) if desired.
 Parameters
 +++++++++++++++
 
-- training-data               Path to the training data csv file                          ['train.csv': string]
-- test-data                   Path to the test data csv file                              ['test.csv':  string]
-- cuda:                       Whether to train with CUDA support (=GPU)                   ['True': string]
-- max_epochs:                 Number of epochs to train                                   [1000:        int]
-- general-seed:               Python, Random, Numpy seed                                  [0:         int]
-- xgboost-seed:               XGBoost specific seed                                       [0:         int]
-- single-precision-histogram  Whether to enable `single precision for histogram building <https://xgboost.readthedocs.io/en/latest/parameter.html#additional-parameters-for-hist-and-gpu-hist-tree-method>`_ ['True': string]
+- ``training-data``              Path to the training data csv file                          ``['train.csv': string]``
+- ``test-data``                  Path to the test data csv file                              ``['test.csv': string]``
+- ``cuda``                       Whether to train with CUDA support (=GPU)                   ``['True': string]``
+- ``max_epochs``                 Number of epochs to train                                   ``[1000: int]``
+- ``general-seed``               Python, Random, Numpy seed                                  ``[0: int]``
+- ``xgboost-seed``               XGBoost specific seed                                       ``[0: int]``
+- ``single-precision-histogram`` Whether to enable `single precision for histogram building <https://xgboost.readthedocs.io/en/latest/parameter.html#additional-parameters-for-hist-and-gpu-hist-tree-method>`_ ``['True': string]``

mlf_core.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 1.0.0
+current_version = 1.0.1
 
 [bumpversion_files_whitelisted]
 dot_mlf_core = .mlf_core.yml