From f052aa891490acae95dcbcf73a6c2645b1270e84 Mon Sep 17 00:00:00 2001
From: Pau Andrio <andriopau@gmail.com>
Date: Thu, 21 Nov 2019 16:35:10 +0100
Subject: [PATCH] 2019.4
---
README.md | 2 +-
biobb_common/configuration/settings.py | 26 ++++++++++++++++++++-
biobb_common/docs/source/readme.md | 2 +-
biobb_common/json_schemas/biobb_common.json | 2 +-
setup.py | 2 +-
5 files changed, 29 insertions(+), 5 deletions(-)
diff --git a/README.md b/README.md
index 8cbf1ed..510fbe8 100644
--- a/README.md
+++ b/README.md
@@ -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
-v2.0.0 2019.4
+v2.0.1 2019.4
### 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/configuration/settings.py b/biobb_common/configuration/settings.py
index 4f47a21..4844be9 100644
--- a/biobb_common/configuration/settings.py
+++ b/biobb_common/configuration/settings.py
@@ -4,6 +4,31 @@
This module contains the classes to read the different formats of the
configuration files.
+
+The configuration files are composed by paths to the files and properties. There are several common properties for all
+the building blocks.
+
+Syntax:
+* **property** (*dataType) - (Default value) Short description.
+
+Available Workflow properties:
+* **working_dir_path** (*str*) - (Current working dir) Directory where the workflow outputs will be created.
+* **can_write_console_log** (*bool*) - (True) Output log to console.
+* **restart** (*bool*) - (False) Do not execute steps if output files are already created.
+* **remove_tmp** (*bool*) - (True) Remove temporal files.
+
+Available common step properties: (Each Biobb step also has their specific properties)
+* **can_write_console_log** (*bool*) - (True) Overwrite **can_write_console_log** workflow property on this step.
+* **restart** (*bool*) - (False) Overwrite **restart** workflow property on this step.
+* **remove_tmp** (*bool*) - (True) Overwrite **remove_tmp** workflow property on this step.
+
+Available common step properties for containerized applications:
+* **container_path** (*string*) - (None) Path to the binary executable of your container.
+* **container_image** (*string*) - (None) Container Image identifier.
+* **container_volume_path** (*string*) - (None) Path to an internal directory in the container.
+* **container_working_dir** (*string*) - (None) Path to the internal CWD in the container.
+* **container_user_id** (*string*) - (None) User number id to be mapped inside the container.
+* **container_shell_path** (*string*) - ("/bin/bash") Path to the binary executable of the container shell.
"""
import yaml
@@ -149,7 +174,6 @@ class ConfReader():
prop_dic['restart']= self.properties.get('restart', False)
prop_dic['remove_tmp']= self.properties.get('remove_tmp', True)
-
return prop_dic
def get_paths_dic(self, prefix=None):
diff --git a/biobb_common/docs/source/readme.md b/biobb_common/docs/source/readme.md
index 8cbf1ed..510fbe8 100644
--- a/biobb_common/docs/source/readme.md
+++ b/biobb_common/docs/source/readme.md
@@ -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
-v2.0.0 2019.4
+v2.0.1 2019.4
### 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/json_schemas/biobb_common.json b/biobb_common/json_schemas/biobb_common.json
index 41c6c87..66eeee6 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/repository/biocontainers/biobb_common",
"singularity": "https://www.singularity-hub.org/collections/2734/usage",
- "version": "2.0.0",
+ "version": "2.0.1",
"tools" : [
{
"block" : "",
diff --git a/setup.py b/setup.py
index de0cb57..6e02b46 100644
--- a/setup.py
+++ b/setup.py
@@ -5,7 +5,7 @@ with open("README.md", "r") as fh:
setuptools.setup(
name="biobb_common",
- version="2.0.0",
+ version="2.0.1",
author="Biobb developers",
author_email="pau.andrio@bsc.es",
description="Biobb_common is the base package required to use the biobb packages.",
--
GitLab