diff --git a/README.md b/README.md
index 8365a26eba41f80edfcd89ac48e9f17b62348b0f..96ef69972722aa6a4e037e8c86216c135356900b 100644
--- a/README.md
+++ b/README.md
@@ -1,7 +1,7 @@
[](https://biobb-common.readthedocs.io/en/latest/?badge=latest)
[](https://anaconda.org/bioconda/biobb_common)
[](https://quay.io/repository/biocontainers/biobb_common?tab=tags)
-[](https://depot.galaxyproject.org/singularity/biobb_common:3.8.1--pyhdfd78af_0)
+[](https://depot.galaxyproject.org/singularity/biobb_common:3.9.0--pyhdfd78af_0)
[](https://opensource.org/licenses/Apache-2.0)
@@ -17,7 +17,7 @@ The latest documentation of this package can be found in our readthedocs site:
[latest API documentation](http://biobb_common.readthedocs.io/en/latest/).
### Version
-v3.8.1 2022.3
+v3.9.0 2022.4
### Copyright & Licensing
This software has been developed in the [MMB group](http://mmb.irbbarcelona.org) at the [BSC](http://www.bsc.es/) & [IRB](https://www.irbbarcelona.org/) for the [European BioExcel](http://bioexcel.eu/), funded by the European Commission (EU H2020 [823830](http://cordis.europa.eu/projects/823830), EU H2020 [675728](http://cordis.europa.eu/projects/675728)).
diff --git a/biobb_common/__init__.py b/biobb_common/__init__.py
index 3fe3e645fa110da08366562e87ea29f0d2ec3377..539e65836f72ae29f5719fdfde695ed59c729ff2 100644
--- a/biobb_common/__init__.py
+++ b/biobb_common/__init__.py
@@ -1,2 +1,2 @@
name = "biobb_common"
-__version__ = "3.8.1"
+__version__ = "3.9.0"
diff --git a/biobb_common/command_wrapper/cmd_wrapper.py b/biobb_common/command_wrapper/cmd_wrapper.py
index 1c098b3c7b88df1d34beb025724b50e77b27581c..087b909012fdde74ecda2e969a63d2ed27e72e34 100644
--- a/biobb_common/command_wrapper/cmd_wrapper.py
+++ b/biobb_common/command_wrapper/cmd_wrapper.py
@@ -29,7 +29,7 @@ class CmdWrapper:
else:
self.out_log.info(cmd + '\n')
- new_env = self.env if self.env else os.environ.copy()
+ new_env = {**os.environ.copy(), **self.env} if self.env else os.environ.copy()
process = subprocess.Popen(cmd,
stdout=subprocess.PIPE,
stderr=subprocess.PIPE,
diff --git a/biobb_common/docs/source/conf.py b/biobb_common/docs/source/conf.py
index 43039d59fc0baded513fa7844fc2e60043ea8e93..923b1ebfb473f6de4b11e22347ac73ab5f7a409c 100644
--- a/biobb_common/docs/source/conf.py
+++ b/biobb_common/docs/source/conf.py
@@ -75,7 +75,7 @@ author = u'Bioexcel Project'
# built documents.
#
# The short X.Y version.
-version = u'3.8.1'
+version = u'3.9.0'
# The full version, including alpha/beta/rc tags.
release = u'2022.3'
diff --git a/biobb_common/docs/source/readme.md b/biobb_common/docs/source/readme.md
index 8365a26eba41f80edfcd89ac48e9f17b62348b0f..96ef69972722aa6a4e037e8c86216c135356900b 100644
--- a/biobb_common/docs/source/readme.md
+++ b/biobb_common/docs/source/readme.md
@@ -1,7 +1,7 @@
[](https://biobb-common.readthedocs.io/en/latest/?badge=latest)
[](https://anaconda.org/bioconda/biobb_common)
[](https://quay.io/repository/biocontainers/biobb_common?tab=tags)
-[](https://depot.galaxyproject.org/singularity/biobb_common:3.8.1--pyhdfd78af_0)
+[](https://depot.galaxyproject.org/singularity/biobb_common:3.9.0--pyhdfd78af_0)
[](https://opensource.org/licenses/Apache-2.0)
@@ -17,7 +17,7 @@ The latest documentation of this package can be found in our readthedocs site:
[latest API documentation](http://biobb_common.readthedocs.io/en/latest/).
### Version
-v3.8.1 2022.3
+v3.9.0 2022.4
### Copyright & Licensing
This software has been developed in the [MMB group](http://mmb.irbbarcelona.org) at the [BSC](http://www.bsc.es/) & [IRB](https://www.irbbarcelona.org/) for the [European BioExcel](http://bioexcel.eu/), funded by the European Commission (EU H2020 [823830](http://cordis.europa.eu/projects/823830), EU H2020 [675728](http://cordis.europa.eu/projects/675728)).
diff --git a/biobb_common/docs/source/schema.html b/biobb_common/docs/source/schema.html
index 1a32b133b8fc1506424255c325f5c3339c1cc07a..ffac06421d6dbffc1da736d4d4db046c5de5e4ec 100644
--- a/biobb_common/docs/source/schema.html
+++ b/biobb_common/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": "3.8.1",
+ "softwareVersion": "3.9.0",
"applicationSuite": "BioBB BioExcel Building Blocks",
"codeRepository": "https://github.com/bioexcel/biobb_common",
"isAccessibleForFree": "True",
diff --git a/biobb_common/generic/biobb_object.py b/biobb_common/generic/biobb_object.py
index 4f2d857e478092961378ca1ac85ceb6d23ece744..37e820400ab8d7aa5c26b0a4544bb96677018bee 100644
--- a/biobb_common/generic/biobb_object.py
+++ b/biobb_common/generic/biobb_object.py
@@ -63,10 +63,9 @@ class BiobbObject:
self.remove_tmp = properties.get('remove_tmp', True)
self.restart = properties.get('restart', False)
self.cmd = []
- self.environment = None
self.return_code = None
self.tmp_files = []
- self.env_vars_dict: typing.Mapping = {}
+ self.env_vars_dict: typing.Mapping = properties.get('check_extensions', {})
self.dev = properties.get('dev', None)
self.check_extensions = properties.get('check_extensions', True)
@@ -258,7 +257,7 @@ class BiobbObject:
# fu.log('Not using any container', self.out_log, self.global_log)
def execute_command(self):
- self.return_code = cmd_wrapper.CmdWrapper(self.cmd, self.out_log, self.err_log, self.global_log, self.environment).launch()
+ self.return_code = cmd_wrapper.CmdWrapper(self.cmd, self.out_log, self.err_log, self.global_log, self.env_vars_dict).launch()
def copy_to_host(self):
for file_ref, file_path in self.stage_io_dict["out"].items():
diff --git a/biobb_common/json_schemas/biobb_common.json b/biobb_common/json_schemas/biobb_common.json
index afbcd332f72f3223e5f2dac3a1c361231cffd06d..c033a2b6ebf0287a0316c8350e35bfa5ec05f1c9 100644
--- a/biobb_common/json_schemas/biobb_common.json
+++ b/biobb_common/json_schemas/biobb_common.json
@@ -6,7 +6,7 @@
"conda": "https://anaconda.org/bioconda/biobb_common",
"docker": "https://quay.io/biocontainers/biobb_common:3.8.1--pyhdfd78af_0",
"singularity": "https://depot.galaxyproject.org/singularity/biobb_common:3.8.1--pyhdfd78af_0",
- "version": "3.8.1",
+ "version": "3.9.0",
"tools" : [
{
"block" : "",
@@ -16,10 +16,10 @@
],
"dep_pypi" : [
"install_requires=['pyyaml', 'requests', 'biopython==1.79']",
- "python_requires='>=3.7'"
+ "python_requires='>=3.7,<3.10'"
],
"dep_conda" : [
- "python >=3.7",
+ "python >=3.7,<3.10",
"pyyaml",
"requests",
"biopython ==1.79"
diff --git a/setup.py b/setup.py
index 0cc69e2de1eca44d78634d3978c972057afba103..ebf562cb7ddd33ce387c7cc38f8b49defaf05f84 100644
--- a/setup.py
+++ b/setup.py
@@ -5,7 +5,7 @@ with open("README.md", "r") as fh:
setuptools.setup(
name="biobb_common",
- version="3.8.1",
+ version="3.9.0",
author="Biobb developers",
author_email="pau.andrio@bsc.es",
description="Biobb_common is the base package required to use the biobb packages.",
@@ -19,7 +19,7 @@ setuptools.setup(
},
packages=setuptools.find_packages(exclude=['docs']),
install_requires=['pyyaml', 'requests', 'biopython==1.79'],
- python_requires='>=3.7',
+ python_requires='>=3.7,<3.10',
classifiers=(
"Development Status :: 3 - Alpha",
"Programming Language :: Python :: 3.7",