Update common

Author: RubenChM

.github/env.yaml

@@ -4,6 +4,6 @@ channels:
   - bioconda
   - anaconda
 dependencies:
-  - biobb_common ==5.1.0
+  - biobb_common ==5.1.1
   - godmd ==1.7
   - emboss

biobb_godmd/docs/source/command_line.md

@@ -13,13 +13,14 @@ Command:
 ```python
 godmd_prep -h
 ```
-    usage: godmd_prep [-h] [--config CONFIG] --input_pdb_orig_path INPUT_PDB_ORIG_PATH --input_pdb_target_path INPUT_PDB_TARGET_PATH --output_aln_orig_path OUTPUT_ALN_ORIG_PATH --output_aln_target_path OUTPUT_ALN_TARGET_PATH
+    usage: godmd_prep [-h] [-c CONFIG] --input_pdb_orig_path INPUT_PDB_ORIG_PATH --input_pdb_target_path INPUT_PDB_TARGET_PATH --output_aln_orig_path OUTPUT_ALN_ORIG_PATH --output_aln_target_path OUTPUT_ALN_TARGET_PATH
 
     Prepares input files for the GOdMD tool.
 
     options:
       -h, --help            show this help message and exit
-      --config CONFIG       Configuration file
+      -c CONFIG, --config CONFIG
+                            This file can be a YAML file, JSON file or JSON string
 
     required arguments:
       --input_pdb_orig_path INPUT_PDB_ORIG_PATH
@@ -50,7 +51,7 @@ Config parameters for this building block:
 * **restart** (*boolean*): (False) Do not execute if output files exist..
 * **sandbox_path** (*string*): (./) Parent path to the sandbox directory..
 ### YAML
-#### [Common config file](https://github.com/bioexcel/biobb_godmd/blob/main/biobb_godmd/test/data/config/config_godmd_prep.yml)
+#### [Common config file](https://github.com/bioexcel/biobb_godmd/blob/master/biobb_godmd/test/data/config/config_godmd_prep.yml)
 ```python
 properties:
   gapextend: '2'
@@ -62,7 +63,7 @@ properties:
 godmd_prep --config config_godmd_prep.yml --input_pdb_orig_path 1ake_A.pdb --input_pdb_target_path 4ake_A.pdb --output_aln_orig_path 1ake_A.aln --output_aln_target_path 4ake_A.aln
 ```
 ### JSON
-#### [Common config file](https://github.com/bioexcel/biobb_godmd/blob/main/biobb_godmd/test/data/config/config_godmd_prep.json)
+#### [Common config file](https://github.com/bioexcel/biobb_godmd/blob/master/biobb_godmd/test/data/config/config_godmd_prep.json)
 ```python
 {
   "properties": {
@@ -83,13 +84,14 @@ Command:
 ```python
 godmd_run -h
 ```
-    usage: godmd_run [-h] [--config CONFIG] --input_pdb_orig_path INPUT_PDB_ORIG_PATH --input_pdb_target_path INPUT_PDB_TARGET_PATH --input_aln_orig_path INPUT_ALN_ORIG_PATH --input_aln_target_path INPUT_ALN_TARGET_PATH [--input_config_path INPUT_CONFIG_PATH] --output_log_path OUTPUT_LOG_PATH --output_ene_path OUTPUT_ENE_PATH --output_trj_path OUTPUT_TRJ_PATH --output_pdb_path OUTPUT_PDB_PATH
+    usage: godmd_run [-h] [-c CONFIG] --input_pdb_orig_path INPUT_PDB_ORIG_PATH --input_pdb_target_path INPUT_PDB_TARGET_PATH --input_aln_orig_path INPUT_ALN_ORIG_PATH --input_aln_target_path INPUT_ALN_TARGET_PATH [--input_config_path INPUT_CONFIG_PATH] --output_log_path OUTPUT_LOG_PATH --output_ene_path OUTPUT_ENE_PATH --output_trj_path OUTPUT_TRJ_PATH --output_pdb_path OUTPUT_PDB_PATH
 
     Computing conformational transition trajectories for proteins using GOdMD tool.
 
     options:
       -h, --help            show this help message and exit
-      --config CONFIG       Configuration file
+      -c CONFIG, --config CONFIG
+                            This file can be a YAML file, JSON file or JSON string
 
     required arguments:
       --input_pdb_orig_path INPUT_PDB_ORIG_PATH
@@ -100,16 +102,18 @@ godmd_run -h
                             Input GOdMD alignment file corresponding to the origin structure of the conformational transition. Accepted formats: aln, txt.
       --input_aln_target_path INPUT_ALN_TARGET_PATH
                             Input GOdMD alignment file corresponding to the target structure of the conformational transition. Accepted formats: aln, txt.
-      --input_config_path INPUT_CONFIG_PATH
-                            Input configuration file (GOdMD run options). Accepted formats: in, txt.
       --output_log_path OUTPUT_LOG_PATH
-                            Output log file. Accepted formats: log, out, txt.
+                            Output log file. Accepted formats: log, out, txt, o.
       --output_ene_path OUTPUT_ENE_PATH
-                            Output energy file. Accepted formats: log, out, txt.
+                            Output energy file. Accepted formats: log, out, txt, o.
       --output_trj_path OUTPUT_TRJ_PATH
-                            Output trajectory file. Accepted formats: mdcrd.
+                            Output trajectory file. Accepted formats: trj, crd, mdcrd, x.
       --output_pdb_path OUTPUT_PDB_PATH
                             Output structure file. Accepted formats: pdb.
+    
+    optional arguments:
+      --input_config_path INPUT_CONFIG_PATH
+                            Input GOdMD configuration file. Accepted formats: in, txt.
 ### I / O Arguments
 Syntax: input_argument (datatype) : Definition
 
@@ -133,7 +137,7 @@ Config parameters for this building block:
 * **restart** (*boolean*): (False) Do not execute if output files exist..
 * **sandbox_path** (*string*): (./) Parent path to the sandbox directory..
 ### YAML
-#### [Common config file](https://github.com/bioexcel/biobb_godmd/blob/main/biobb_godmd/test/data/config/config_godmd_run.yml)
+#### [Common config file](https://github.com/bioexcel/biobb_godmd/blob/master/biobb_godmd/test/data/config/config_godmd_run.yml)
 ```python
 properties:
   remove_tmp: true
@@ -144,7 +148,7 @@ properties:
 godmd_run --config config_godmd_run.yml --input_pdb_orig_path 1ake_A.pdb --input_pdb_target_path 4ake_A.pdb --input_aln_orig_path 1ake_A.aln --input_aln_target_path 4ake_A.aln --input_config_path params.in --output_log_path godmd.log --output_ene_path godmd_ene.out --output_trj_path godmd_trj.mdcrd --output_pdb_path godmd_pdb.pdb
 ```
 ### JSON
-#### [Common config file](https://github.com/bioexcel/biobb_godmd/blob/main/biobb_godmd/test/data/config/config_godmd_run.json)
+#### [Common config file](https://github.com/bioexcel/biobb_godmd/blob/master/biobb_godmd/test/data/config/config_godmd_run.json)
 ```python
 {
   "properties": {

biobb_godmd/godmd/godmd_prep.py

@@ -1,11 +1,9 @@
 #!/usr/bin/env python3
 
 """Module containing the GOdMDPrep class and the command line interface."""
-import argparse
 from typing import Optional
 from pathlib import Path
 from biobb_common.generic.biobb_object import BiobbObject
-from biobb_common.configuration import settings
 from biobb_common.tools import file_utils as fu
 from biobb_common.tools.file_utils import launchlogger
 from biobb_godmd.godmd.common import check_input_path, check_output_path
@@ -326,41 +324,11 @@ def godmd_prep(input_pdb_orig_path: str, input_pdb_target_path: str,
                properties: Optional[dict] = None, **kwargs) -> int:
     """Create :class:`GOdMDPrep <godmd.godmd_prep.GOdMDPrep>`godmd.godmd_prep.GOdMDPrep class and
     execute :meth:`launch() <godmd.godmd_prep.GOdMDPrep.launch>` method"""
-
-    return GOdMDPrep(input_pdb_orig_path=input_pdb_orig_path,
-                     input_pdb_target_path=input_pdb_target_path,
-                     output_aln_orig_path=output_aln_orig_path,
-                     output_aln_target_path=output_aln_target_path,
-                     properties=properties).launch()
+    return GOdMDPrep(**dict(locals())).launch()
 
 
 godmd_prep.__doc__ = GOdMDPrep.__doc__
-
-
-def main():
-    parser = argparse.ArgumentParser(description='Prepares input files for the GOdMD tool.', formatter_class=lambda prog: argparse.RawTextHelpFormatter(prog, width=99999))
-    parser.add_argument('--config', required=False, help='Configuration file')
-
-    # Specific args
-    required_args = parser.add_argument_group('required arguments')
-    required_args.add_argument('--input_pdb_orig_path', required=True, help='Input PDB file to be used as origin in the conformational transition. Accepted formats: pdb.')
-    required_args.add_argument('--input_pdb_target_path', required=True, help='Input PDB file to be used as target in the conformational transition. Accepted formats: pdb.')
-    required_args.add_argument('--output_aln_orig_path', required=True, help='Output GOdMD alignment file corresponding to the origin structure of the conformational transition. Accepted formats: aln, txt.')
-    required_args.add_argument('--output_aln_target_path', required=True, help='Output GOdMD alignment file corresponding to the target structure of the conformational transition. Accepted formats: aln, txt.')
-
-    args = parser.parse_args()
-    # config = args.config if args.config else None
-    args.config = args.config or "{}"
-    # properties = settings.ConfReader(config=config).get_prop_dic()
-    properties = settings.ConfReader(config=args.config).get_prop_dic()
-
-    # Specific call
-    godmd_prep(input_pdb_orig_path=args.input_pdb_orig_path,
-               input_pdb_target_path=args.input_pdb_target_path,
-               output_aln_orig_path=args.output_aln_orig_path,
-               output_aln_target_path=args.output_aln_target_path,
-               properties=properties)
-
+main = GOdMDPrep.get_main(godmd_prep, "Prepares input files for the GOdMD tool.")
 
 if __name__ == '__main__':
     main()

biobb_godmd/godmd/godmd_run.py

@@ -2,12 +2,10 @@
 
 """Module containing the GOdMDRun class and the command line interface."""
 
-import argparse
 import shutil
 from pathlib import Path, PurePath
 from typing import Optional
 
-from biobb_common.configuration import settings
 from biobb_common.generic.biobb_object import BiobbObject
 from biobb_common.tools.file_utils import launchlogger
 
@@ -312,99 +310,11 @@ def godmd_run(
 ) -> int:
     """Create :class:`GOdMDRun <godmd.godmd_run.GOdMDRun>`godmd.godmd_run.GOdMDRun class and
     execute :meth:`launch() <godmd.godmd_run.GOdMDRun.launch>` method"""
-
-    return GOdMDRun(
-        input_pdb_orig_path=input_pdb_orig_path,
-        input_pdb_target_path=input_pdb_target_path,
-        input_aln_orig_path=input_aln_orig_path,
-        input_aln_target_path=input_aln_target_path,
-        input_config_path=input_config_path,
-        output_log_path=output_log_path,
-        output_ene_path=output_ene_path,
-        output_trj_path=output_trj_path,
-        output_pdb_path=output_pdb_path,
-        properties=properties,
-    ).launch()
+    return GOdMDRun(**dict(locals())).launch()
 
 
 godmd_run.__doc__ = GOdMDRun.__doc__
-
-
-def main():
-    parser = argparse.ArgumentParser(
-        description="Computing conformational transition trajectories for proteins using GOdMD tool.",
-        formatter_class=lambda prog: argparse.RawTextHelpFormatter(prog, width=99999),
-    )
-    parser.add_argument("--config", required=False, help="Configuration file")
-
-    # Specific args
-    required_args = parser.add_argument_group("required arguments")
-    required_args.add_argument(
-        "--input_pdb_orig_path",
-        required=True,
-        help="Input PDB file to be used as origin in the conformational transition. Accepted formats: pdb.",
-    )
-    required_args.add_argument(
-        "--input_pdb_target_path",
-        required=True,
-        help="Input PDB file to be used as target in the conformational transition. Accepted formats: pdb.",
-    )
-    required_args.add_argument(
-        "--input_aln_orig_path",
-        required=True,
-        help="Input GOdMD alignment file corresponding to the origin structure of the conformational transition. Accepted formats: aln, txt.",
-    )
-    required_args.add_argument(
-        "--input_aln_target_path",
-        required=True,
-        help="Input GOdMD alignment file corresponding to the target structure of the conformational transition. Accepted formats: aln, txt.",
-    )
-    required_args.add_argument(
-        "--input_config_path",
-        required=False,
-        help="Input configuration file (GOdMD run options). Accepted formats: in, txt.",
-    )
-    required_args.add_argument(
-        "--output_log_path",
-        required=True,
-        help="Output log file. Accepted formats: log, out, txt.",
-    )
-    required_args.add_argument(
-        "--output_ene_path",
-        required=True,
-        help="Output energy file. Accepted formats: log, out, txt.",
-    )
-    required_args.add_argument(
-        "--output_trj_path",
-        required=True,
-        help="Output trajectory file. Accepted formats: mdcrd.",
-    )
-    required_args.add_argument(
-        "--output_pdb_path",
-        required=True,
-        help="Output structure file. Accepted formats: pdb.",
-    )
-
-    args = parser.parse_args()
-    # config = args.config if args.config else None
-    args.config = args.config or "{}"
-    # properties = settings.ConfReader(config=config).get_prop_dic()
-    properties = settings.ConfReader(config=args.config).get_prop_dic()
-
-    # Specific call
-    godmd_run(
-        input_pdb_orig_path=args.input_pdb_orig_path,
-        input_pdb_target_path=args.input_pdb_target_path,
-        input_aln_orig_path=args.input_aln_orig_path,
-        input_aln_target_path=args.input_aln_target_path,
-        input_config_path=args.input_config_path,
-        output_log_path=args.output_log_path,
-        output_ene_path=args.output_ene_path,
-        output_trj_path=args.output_trj_path,
-        output_pdb_path=args.output_pdb_path,
-        properties=properties,
-    )
-
+main = GOdMDRun.get_main(godmd_run, "Computing conformational transition trajectories for proteins using GOdMD tool.")
 
 if __name__ == "__main__":
     main()

biobb_godmd/json_schemas/biobb_godmd.json

@@ -27,12 +27,12 @@
         }
     ],
     "dep_pypi": [
-        "install_requires=['biobb_common==5.1.0']",
+        "install_requires=['biobb_common==5.1.1']",
         "python_requires='>=3.9'"
     ],
     "dep_conda": [
         "python >=3.9",
-        "biobb_common ==5.1.0",
+        "biobb_common ==5.1.1",
         "godmd ==1.7",
         "emboss"
     ],

setup.py

@@ -19,7 +19,7 @@
     },
     packages=setuptools.find_packages(exclude=["docs", "test"]),
     package_data={"biobb_godmd": ["py.typed"]},
-    install_requires=["biobb_common==5.1.0"],
+    install_requires=["biobb_common==5.1.1"],
     python_requires=">=3.9",
     entry_points={
         "console_scripts": [