From a2d451480eca5414e3ef8e66a5bf82f828d9aafb Mon Sep 17 00:00:00 2001 From: Pau Andrio <andriopau@gmail.com> Date: Mon, 19 Dec 2022 12:44:19 +0100 Subject: [PATCH] 2022.4 --- README.md | 4 ++-- biobb_common/__init__.py | 2 +- biobb_common/command_wrapper/cmd_wrapper.py | 2 +- biobb_common/docs/source/conf.py | 2 +- biobb_common/docs/source/readme.md | 4 ++-- biobb_common/docs/source/schema.html | 2 +- biobb_common/generic/biobb_object.py | 5 ++--- biobb_common/json_schemas/biobb_common.json | 6 +++--- setup.py | 4 ++-- 9 files changed, 15 insertions(+), 16 deletions(-) diff --git a/README.md b/README.md index 8365a26..96ef699 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 3fe3e64..539e658 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 1c098b3..087b909 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 43039d5..923b1eb 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 8365a26..96ef699 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 1a32b13..ffac064 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 4f2d857..37e8204 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 afbcd33..c033a2b 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 0cc69e2..ebf562c 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", -- GitLab