Merge branch 'master' of github.com:bioexcel/biobb_model

bioexcel · Jun 14, 2024 · 9ecaab6 · 9ecaab6
2 parents 603cf17 + 7b0a5a2
commit 9ecaab6
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Showing 9 changed files with 28 additions and 21 deletions.
diff --git a/README.md b/README.md
@@ -3,7 +3,7 @@
 [![](https://img.shields.io/conda/vn/bioconda/biobb_model?label=Conda)](https://anaconda.org/bioconda/biobb_model)
 [![](https://img.shields.io/conda/dn/bioconda/biobb_model?label=Conda%20downloads)](https://anaconda.org/bioconda/biobb_model)
 [![](https://img.shields.io/badge/Docker-Quay.io-blue)](https://quay.io/repository/biocontainers/biobb_model?tab=tags)
-[![](https://img.shields.io/badge/Singularity-GalaxyProject-blue)](https://depot.galaxyproject.org/singularity/biobb_model:4.2.2--pyhdfd78af_0)
+[![](https://img.shields.io/badge/Singularity-GalaxyProject-blue)](https://depot.galaxyproject.org/singularity/biobb_model:4.2.3--pyhdfd78af_0)
 
 [![](https://img.shields.io/badge/OS-Unix%20%7C%20MacOS-blue)](https://github.com/bioexcel/biobb_model)
 [![](https://img.shields.io/pypi/pyversions/biobb-model.svg?label=Python%20Versions)](https://pypi.org/project/biobb-model/)
@@ -41,7 +41,7 @@ The latest documentation of this package can be found in our readthedocs site:
 [latest API documentation](http://biobb-model.readthedocs.io/en/latest/).
 
 ### Version
-v4.2.2 2024.1
+v4.2.3 2024.1
 
 ### Installation
 Using PIP:
@@ -51,7 +51,7 @@ Using PIP:
 * Installation:
 
 
-        pip install "biobb_model>=4.2.2"
+        pip install "biobb_model>=4.2.3"
 
 
 * Usage: [Python API documentation](https://biobb-model.readthedocs.io/en/latest/modules.html)
@@ -61,7 +61,7 @@ Using ANACONDA:
 * Installation:
 
 
-        conda install -c bioconda "biobb_model>=4.2.2"
+        conda install -c bioconda "biobb_model>=4.2.3"
 
 
 * Usage: With conda installation BioBBs can be used with the [Python API documentation](https://biobb-model.readthedocs.io/en/latest/modules.html) and the [Command Line documentation](https://biobb-model.readthedocs.io/en/latest/command_line.html)
@@ -71,13 +71,13 @@ Using DOCKER:
 * Installation:
 
 
-        docker pull quay.io/biocontainers/biobb_model:4.2.2--pyhdfd78af_0
+        docker pull quay.io/biocontainers/biobb_model:4.2.3--pyhdfd78af_0
 
 
 * Usage:
 
 
-        docker run quay.io/biocontainers/biobb_model:4.2.2--pyhdfd78af_0 <command>
+        docker run quay.io/biocontainers/biobb_model:4.2.3--pyhdfd78af_0 <command>
 
 
 Using SINGULARITY:

diff --git a/biobb_model/__init__.py b/biobb_model/__init__.py
@@ -2,4 +2,4 @@
 
 name = "biobb_model"
 __all__ = ["model"]
-__version__ = "4.2.2"
+__version__ = "4.2.3"
diff --git a/biobb_model/docs/source/change_log.md b/biobb_model/docs/source/change_log.md
@@ -1,5 +1,11 @@
 # Biobb Model changelog
 
+## What's new in version [4.2.3](https://github.com/bioexcel/biobb_model/releases/tag/v4.2.3)?
+
+### Changes
+
+* [FIX] Minor fix in FixPdb
+
 ## What's new in version [4.2.2](https://github.com/bioexcel/biobb_model/releases/tag/v4.2.2)?
 
 ### Changes

diff --git a/biobb_model/docs/source/conf.py b/biobb_model/docs/source/conf.py
@@ -79,9 +79,9 @@
 # built documents.
 #
 # The short X.Y version.
-version = u'4.2.2'
+version = u'4.2.3'
 # The full version, including alpha/beta/rc tags.
-release = u'4.2.2'
+release = u'4.2.3'
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.

diff --git a/biobb_model/docs/source/readme.md b/biobb_model/docs/source/readme.md
@@ -3,7 +3,7 @@
 [![](https://img.shields.io/conda/vn/bioconda/biobb_model?label=Conda)](https://anaconda.org/bioconda/biobb_model)
 [![](https://img.shields.io/conda/dn/bioconda/biobb_model?label=Conda%20downloads)](https://anaconda.org/bioconda/biobb_model)
 [![](https://img.shields.io/badge/Docker-Quay.io-blue)](https://quay.io/repository/biocontainers/biobb_model?tab=tags)
-[![](https://img.shields.io/badge/Singularity-GalaxyProject-blue)](https://depot.galaxyproject.org/singularity/biobb_model:4.2.2--pyhdfd78af_0)
+[![](https://img.shields.io/badge/Singularity-GalaxyProject-blue)](https://depot.galaxyproject.org/singularity/biobb_model:4.2.3--pyhdfd78af_0)
 
 [![](https://img.shields.io/badge/OS-Unix%20%7C%20MacOS-blue)](https://github.com/bioexcel/biobb_model)
 [![](https://img.shields.io/pypi/pyversions/biobb-model.svg?label=Python%20Versions)](https://pypi.org/project/biobb-model/)
@@ -41,7 +41,7 @@ The latest documentation of this package can be found in our readthedocs site:
 [latest API documentation](http://biobb-model.readthedocs.io/en/latest/).
 
 ### Version
-v4.2.2 2024.1
+v4.2.3 2024.1
 
 ### Installation
 Using PIP:
@@ -51,7 +51,7 @@ Using PIP:
 * Installation:
 
 
-        pip install "biobb_model>=4.2.2"
+        pip install "biobb_model>=4.2.3"
 
 
 * Usage: [Python API documentation](https://biobb-model.readthedocs.io/en/latest/modules.html)
@@ -61,7 +61,7 @@ Using ANACONDA:
 * Installation:
 
 
-        conda install -c bioconda "biobb_model>=4.2.2"
+        conda install -c bioconda "biobb_model>=4.2.3"
 
 
 * Usage: With conda installation BioBBs can be used with the [Python API documentation](https://biobb-model.readthedocs.io/en/latest/modules.html) and the [Command Line documentation](https://biobb-model.readthedocs.io/en/latest/command_line.html)
@@ -71,13 +71,13 @@ Using DOCKER:
 * Installation:
 
 
-        docker pull quay.io/biocontainers/biobb_model:4.2.2--pyhdfd78af_0
+        docker pull quay.io/biocontainers/biobb_model:4.2.3--pyhdfd78af_0
 
 
 * Usage:
 
 
-        docker run quay.io/biocontainers/biobb_model:4.2.2--pyhdfd78af_0 <command>
+        docker run quay.io/biocontainers/biobb_model:4.2.3--pyhdfd78af_0 <command>
 
 
 Using SINGULARITY:

diff --git a/biobb_model/docs/source/schema.html b/biobb_model/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": "4.2.2",
+  "softwareVersion": "4.2.3",
   "applicationSuite": "BioBB BioExcel Building Blocks",
   "codeRepository": "https://github.com/bioexcel/biobb_model",
   "isAccessibleForFree": "True",

diff --git a/biobb_model/json_schemas/biobb_model.json b/biobb_model/json_schemas/biobb_model.json
@@ -4,9 +4,9 @@
     "github": "https://github.com/bioexcel/biobb_model",
     "readthedocs": "https://biobb-model.readthedocs.io/en/latest/",
     "conda": "https://anaconda.org/bioconda/biobb_model",
-    "docker": "https://quay.io/biocontainers/biobb_model:4.2.2--pyhdfd78af_0",
-    "singularity": "https://depot.galaxyproject.org/singularity/biobb_model:4.2.2--pyhdfd78af_0",
-    "version": "4.2.2",
+    "docker": "https://quay.io/biocontainers/biobb_model:4.2.3--pyhdfd78af_0",
+    "singularity": "https://depot.galaxyproject.org/singularity/biobb_model:4.2.3--pyhdfd78af_0",
+    "version": "4.2.3",
     "rest": true,
     "tools": [
         {

diff --git a/biobb_model/model/fix_pdb_utils.py b/biobb_model/model/fix_pdb_utils.py
@@ -798,7 +798,8 @@ def match_sequences() -> bool:
             continue
         # Run the blast
         sequence = structure_sequence['sequence']
-        uniprot_id = blast(sequence)[0]
+        # uniprot_id = blast(sequence)[0]
+        uniprot_id = blast(sequence)
         # Build a new reference from the resulting uniprot
         reference = get_uniprot_reference(uniprot_id)
         reference_sequences[reference['uniprot']] = reference['sequence']

diff --git a/setup.py b/setup.py
@@ -5,7 +5,7 @@
 
 setuptools.setup(
     name="biobb_model",
-    version="4.2.2",
+    version="4.2.3",
     author="Biobb developers",
     author_email="pau.andrio@bsc.es",
     description="Biobb_model is the Biobb module collection to check and model 3d structures, create mutations or reconstruct missing atoms.",