2023.3

bioexcel · Sep 8, 2023 · 8e7e2ad · 8e7e2ad
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Showing 11 changed files with 48 additions and 34 deletions.
diff --git a/.github/workflows/linting_and_testing.yml b/.github/workflows/linting_and_testing.yml
@@ -19,7 +19,7 @@ jobs:
     strategy:
       matrix:
         os: [self-hosted]
-        python-version: ["3.8", "3.9", "3.10"]
+        python-version: ["3.8", "3.9"]
     runs-on: ${{ matrix.os }}
     steps:
       - name: Check out repository code

diff --git a/.readthedocs.yaml b/.readthedocs.yaml
@@ -11,7 +11,7 @@ sphinx:
 
 # Optionally set the version of Python and requirements required to build your docs
 python:
-   version: "3.7"
+   version: "3.8"
    install:
       - requirements: biobb_ml/docs/requirements.txt
       - method: pip

diff --git a/README.md b/README.md
@@ -3,7 +3,7 @@
 [![](https://img.shields.io/conda/vn/bioconda/biobb_ml?label=Conda)](https://anaconda.org/bioconda/biobb_ml)
 [![](https://img.shields.io/conda/dn/bioconda/biobb_ml?label=Conda%20Downloads)](https://anaconda.org/bioconda/biobb_ml)
 [![](https://img.shields.io/badge/Docker-Quay.io-blue)](https://quay.io/repository/biocontainers/biobb_ml?tab=tags)
-[![](https://img.shields.io/badge/Singularity-GalaxyProject-blue)](https://depot.galaxyproject.org/singularity/biobb_ml:4.0.0--pyhdfd78af_0)
+[![](https://img.shields.io/badge/Singularity-GalaxyProject-blue)](https://depot.galaxyproject.org/singularity/biobb_ml:4.1.0--pyhdfd78af_0)
 
 [![](https://img.shields.io/badge/OS-Unix%20%7C%20MacOS-blue)](https://github.com/bioexcel/biobb_ml)
 [![](https://img.shields.io/pypi/pyversions/biobb-ml.svg?label=Python%20Versions)](https://pypi.org/project/biobb-ml/)
@@ -33,7 +33,7 @@ The latest documentation of this package can be found in our readthedocs site:
 [latest API documentation](http://biobb_ml.readthedocs.io/en/latest/).
 
 ### Version
-v4.0.0 2023.1
+v4.1.0 2023.3
 
 ### Installation
 Using PIP:
@@ -43,7 +43,7 @@ Using PIP:
 * Installation:
 
 
-        pip install "biobb_ml>=4.0.0"
+        pip install "biobb_ml>=4.1.0"
 
 
 * Usage: [Python API documentation](https://biobb-ml.readthedocs.io/en/latest/modules.html)
@@ -53,7 +53,7 @@ Using ANACONDA:
 * Installation:
 
 
-        conda install -c bioconda "biobb_ml>=4.0.0"
+        conda install -c bioconda "biobb_ml>=4.1.0"
 
 
 * Usage: With conda installation BioBBs can be used with the [Python API documentation](https://biobb-ml.readthedocs.io/en/latest/modules.html) and the [Command Line documentation](https://biobb-ml.readthedocs.io/en/latest/command_line.html)
@@ -63,13 +63,13 @@ Using DOCKER:
 * Installation:
 
 
-        docker pull quay.io/biocontainers/biobb_ml:4.0.0--pyhdfd78af_0
+        docker pull quay.io/biocontainers/biobb_ml:4.1.0--pyhdfd78af_0
 
 
 * Usage:
 
 
-        docker run quay.io/biocontainers/biobb_ml:4.0.0--pyhdfd78af_0 <command>
+        docker run quay.io/biocontainers/biobb_ml:4.1.0--pyhdfd78af_0 <command>
 
 
 Using SINGULARITY:
@@ -79,7 +79,7 @@ Using SINGULARITY:
 * Installation:
 
 
-        singularity pull --name biobb_ml.sif https://depot.galaxyproject.org/singularity/biobb_ml:4.0.0--pyhdfd78af_0
+        singularity pull --name biobb_ml.sif https://depot.galaxyproject.org/singularity/biobb_ml:4.1.0--pyhdfd78af_0
 
 
 * Usage:

diff --git a/biobb_ml/__init__.py b/biobb_ml/__init__.py
@@ -1,3 +1,3 @@
 name = "biobb_ml"
 __all__ = ["classification", "clustering", "dimensionality_reduction", "regression", "resampling", "neural_networks", "utils"]
-__version__ = "4.0.0"
+__version__ = "4.1.0"
diff --git a/biobb_ml/docs/requirements.txt b/biobb_ml/docs/requirements.txt
@@ -1,3 +1,11 @@
 # Defining the exact version will make sure things don't break
-biobb_ml==3.7.0
-docutils==0.17.1
+# biobb_ml==3.7.0
+# docutils==0.17.1
+- numpy ==1.19.5
+- h5py ==2.10.0
+- scipy ==1.7.3
+- pandas >=1.3.0
+- scikit-learn ==0.24.2
+- seaborn ==0.10.1
+- tensorflow >=2.4.2
+- imbalanced-learn ==0.7.0
diff --git a/biobb_ml/docs/source/change_log.md b/biobb_ml/docs/source/change_log.md
@@ -1,5 +1,12 @@
 # Biobb Machine Learning changelog
 
+## What's new in version [4.1.0](https://github.com/bioexcel/biobb_ml/releases/tag/v4.1.0)?
+In version 4.1.0 the dependency biobb_common has been updated to 4.1.0 version.
+
+### New features
+
+* Update to biobb_common 4.1.0 (general)
+
 ## What's new in version [4.0.0](https://github.com/bioexcel/biobb_ml/releases/tag/v4.0.0)?
 In version 4.0.0 the dependency biobb_common has been updated to 4.0.0 version.
 

diff --git a/biobb_ml/docs/source/conf.py b/biobb_ml/docs/source/conf.py
@@ -75,9 +75,9 @@
 # built documents.
 #
 # The short X.Y version.
-version = u'4.0.0'
+version = u'4.1.0'
 # The full version, including alpha/beta/rc tags.
-release = u'4.0.0'
+release = u'4.1.0'
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.

diff --git a/biobb_ml/docs/source/readme.md b/biobb_ml/docs/source/readme.md
@@ -3,7 +3,7 @@
 [![](https://img.shields.io/conda/vn/bioconda/biobb_ml?label=Conda)](https://anaconda.org/bioconda/biobb_ml)
 [![](https://img.shields.io/conda/dn/bioconda/biobb_ml?label=Conda%20Downloads)](https://anaconda.org/bioconda/biobb_ml)
 [![](https://img.shields.io/badge/Docker-Quay.io-blue)](https://quay.io/repository/biocontainers/biobb_ml?tab=tags)
-[![](https://img.shields.io/badge/Singularity-GalaxyProject-blue)](https://depot.galaxyproject.org/singularity/biobb_ml:4.0.0--pyhdfd78af_0)
+[![](https://img.shields.io/badge/Singularity-GalaxyProject-blue)](https://depot.galaxyproject.org/singularity/biobb_ml:4.1.0--pyhdfd78af_0)
 
 [![](https://img.shields.io/badge/OS-Unix%20%7C%20MacOS-blue)](https://github.com/bioexcel/biobb_ml)
 [![](https://img.shields.io/pypi/pyversions/biobb-ml.svg?label=Python%20Versions)](https://pypi.org/project/biobb-ml/)
@@ -33,7 +33,7 @@ The latest documentation of this package can be found in our readthedocs site:
 [latest API documentation](http://biobb_ml.readthedocs.io/en/latest/).
 
 ### Version
-v4.0.0 2023.1
+v4.1.0 2023.3
 
 ### Installation
 Using PIP:
@@ -43,7 +43,7 @@ Using PIP:
 * Installation:
 
 
-        pip install "biobb_ml>=4.0.0"
+        pip install "biobb_ml>=4.1.0"
 
 
 * Usage: [Python API documentation](https://biobb-ml.readthedocs.io/en/latest/modules.html)
@@ -53,7 +53,7 @@ Using ANACONDA:
 * Installation:
 
 
-        conda install -c bioconda "biobb_ml>=4.0.0"
+        conda install -c bioconda "biobb_ml>=4.1.0"
 
 
 * Usage: With conda installation BioBBs can be used with the [Python API documentation](https://biobb-ml.readthedocs.io/en/latest/modules.html) and the [Command Line documentation](https://biobb-ml.readthedocs.io/en/latest/command_line.html)
@@ -63,13 +63,13 @@ Using DOCKER:
 * Installation:
 
 
-        docker pull quay.io/biocontainers/biobb_ml:4.0.0--pyhdfd78af_0
+        docker pull quay.io/biocontainers/biobb_ml:4.1.0--pyhdfd78af_0
 
 
 * Usage:
 
 
-        docker run quay.io/biocontainers/biobb_ml:4.0.0--pyhdfd78af_0 <command>
+        docker run quay.io/biocontainers/biobb_ml:4.1.0--pyhdfd78af_0 <command>
 
 
 Using SINGULARITY:
@@ -79,7 +79,7 @@ Using SINGULARITY:
 * Installation:
 
 
-        singularity pull --name biobb_ml.sif https://depot.galaxyproject.org/singularity/biobb_ml:4.0.0--pyhdfd78af_0
+        singularity pull --name biobb_ml.sif https://depot.galaxyproject.org/singularity/biobb_ml:4.1.0--pyhdfd78af_0
 
 
 * Usage:

diff --git a/biobb_ml/docs/source/schema.html b/biobb_ml/docs/source/schema.html
@@ -10,7 +10,7 @@
   "applicationSubCategory": "http://www.edamontology.org/topic_3892",
   "citation": "https://www.nature.com/articles/s41597-019-0177-4",
   "license": "https://www.apache.org/licenses/LICENSE-2.0",
-  "softwareVersion": "4.0.0",
+  "softwareVersion": "4.1.0",
   "applicationSuite": "BioBB BioExcel Building Blocks",
   "codeRepository": "https://github.com/bioexcel/biobb_ml",
   "isAccessibleForFree": "True",

diff --git a/biobb_ml/json_schemas/biobb_ml.json b/biobb_ml/json_schemas/biobb_ml.json
@@ -4,9 +4,9 @@
     "github": "https://github.com/bioexcel/biobb_ml",
     "readthedocs": "https://biobb-ml.readthedocs.io/en/latest/",
     "conda": "https://anaconda.org/bioconda/biobb_ml",
-    "docker": "https://quay.io/biocontainers/biobb_ml:4.0.0--pyhdfd78af_0",
-    "singularity": "https://depot.galaxyproject.org/singularity/biobb_ml:4.0.0--pyhdfd78af_0",
-    "version": "4.0.0",
+    "docker": "https://quay.io/biocontainers/biobb_ml:4.1.0--pyhdfd78af_0",
+    "singularity": "https://depot.galaxyproject.org/singularity/biobb_ml:4.1.0--pyhdfd78af_0",
+    "version": "4.1.0",
     "rest": true,
     "tools" : [
         {
@@ -315,14 +315,14 @@
         }
     ],
     "dep_pypi" : [
-        "install_requires=['biobb_common==4.0.0', 'scikit-learn ==0.24.2', 'pandas ==1.3.0', 'seaborn ==0.10.1', 'tensorflow ==2.4.0', 'h5py ==2.10.0', 'imbalanced-learn ==0.7.0']", 
-        "python_requires='>=3.7,<3.10'"
+        "install_requires=['biobb_common==4.1.0', 'scikit-learn ==0.24.2', 'pandas >=1.3.0', 'seaborn ==0.10.1', 'tensorflow ==2.4.0', 'h5py ==2.10.0', 'imbalanced-learn ==0.7.0']", 
+        "python_requires='>=3.8'"
     ], 
     "dep_conda" : [
-        "python >=3.7,<3.10", 
-        "biobb_common ==4.0.0", 
+        "python >=3.8", 
+        "biobb_common ==4.1.0", 
         "scikit-learn ==0.24.2",
-        "pandas ==1.3.0",
+        "pandas >=1.3.0",
         "seaborn ==0.10.1",
         "tensorflow ==2.4.0",
         "h5py ==2.10.0",

diff --git a/setup.py b/setup.py
@@ -5,7 +5,7 @@
 
 setuptools.setup(
     name="biobb_ml",
-    version="4.0.0",
+    version="4.1.0",
     author="Biobb developers",
     author_email="genis.bayarri@irbbarcelona.org",
     description="Biobb_ml is the Biobb module collection to perform machine learning predictions.",
@@ -18,8 +18,8 @@
         "Bioexcel": "https://bioexcel.eu/"
     },
     packages=setuptools.find_packages(exclude=['docs', 'test']),
-    install_requires=['biobb_common==4.0.0', 'scikit-learn ==0.24.2', 'pandas ==1.3.0', 'seaborn ==0.10.1', 'tensorflow>=2.4.2', 'h5py ==2.10.0', 'imbalanced-learn ==0.7.0'],
-    python_requires='>=3.7,<3.10',
+    install_requires=['biobb_common==4.1.0', 'scikit-learn ==0.24.2', 'pandas >=1.3.0', 'seaborn ==0.10.1', 'tensorflow>=2.4.2', 'h5py ==2.10.0', 'imbalanced-learn ==0.7.0'],
+    python_requires='>=3.8',
     entry_points={
         "console_scripts": [
             "classification_predict = biobb_ml.classification.classification_predict:main",
@@ -64,7 +64,6 @@
     },
     classifiers=(
         "Development Status :: 3 - Alpha",
-        "Programming Language :: Python :: 3.7",
         "Programming Language :: Python :: 3.8",
         "Programming Language :: Python :: 3.9",
         "License :: OSI Approved :: Apache Software License",