biobb-io 5.1.1__tar.gz → 5.2.0__tar.gz

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (31) hide show
  1. {biobb_io-5.1.1 → biobb_io-5.2.0}/PKG-INFO +9 -9
  2. {biobb_io-5.1.1 → biobb_io-5.2.0}/README.md +5 -5
  3. {biobb_io-5.1.1 → biobb_io-5.2.0}/biobb_io/__init__.py +1 -1
  4. {biobb_io-5.1.1 → biobb_io-5.2.0}/biobb_io/api/mddb.py +1 -0
  5. {biobb_io-5.1.1 → biobb_io-5.2.0}/biobb_io/api/memprotmd_sim_list.py +1 -1
  6. {biobb_io-5.1.1 → biobb_io-5.2.0}/biobb_io/api/memprotmd_sim_search.py +1 -1
  7. {biobb_io-5.1.1 → biobb_io-5.2.0}/biobb_io/api/pdb_cluster_zip.py +1 -1
  8. {biobb_io-5.1.1 → biobb_io-5.2.0}/biobb_io.egg-info/PKG-INFO +9 -9
  9. biobb_io-5.2.0/biobb_io.egg-info/requires.txt +1 -0
  10. {biobb_io-5.1.1 → biobb_io-5.2.0}/setup.py +4 -4
  11. biobb_io-5.1.1/biobb_io.egg-info/requires.txt +0 -1
  12. {biobb_io-5.1.1 → biobb_io-5.2.0}/LICENSE +0 -0
  13. {biobb_io-5.1.1 → biobb_io-5.2.0}/biobb_io/api/__init__.py +0 -0
  14. {biobb_io-5.1.1 → biobb_io-5.2.0}/biobb_io/api/alphafold.py +0 -0
  15. {biobb_io-5.1.1 → biobb_io-5.2.0}/biobb_io/api/api_binding_site.py +0 -0
  16. {biobb_io-5.1.1 → biobb_io-5.2.0}/biobb_io/api/canonical_fasta.py +0 -0
  17. {biobb_io-5.1.1 → biobb_io-5.2.0}/biobb_io/api/common.py +0 -0
  18. {biobb_io-5.1.1 → biobb_io-5.2.0}/biobb_io/api/ideal_sdf.py +0 -0
  19. {biobb_io-5.1.1 → biobb_io-5.2.0}/biobb_io/api/ligand.py +0 -0
  20. {biobb_io-5.1.1 → biobb_io-5.2.0}/biobb_io/api/memprotmd_sim.py +0 -0
  21. {biobb_io-5.1.1 → biobb_io-5.2.0}/biobb_io/api/mmcif.py +0 -0
  22. {biobb_io-5.1.1 → biobb_io-5.2.0}/biobb_io/api/pdb.py +0 -0
  23. {biobb_io-5.1.1 → biobb_io-5.2.0}/biobb_io/api/pdb_variants.py +0 -0
  24. {biobb_io-5.1.1 → biobb_io-5.2.0}/biobb_io/api/structure_info.py +0 -0
  25. {biobb_io-5.1.1 → biobb_io-5.2.0}/biobb_io/py.typed +0 -0
  26. {biobb_io-5.1.1 → biobb_io-5.2.0}/biobb_io/test/__init__.py +0 -0
  27. {biobb_io-5.1.1 → biobb_io-5.2.0}/biobb_io.egg-info/SOURCES.txt +0 -0
  28. {biobb_io-5.1.1 → biobb_io-5.2.0}/biobb_io.egg-info/dependency_links.txt +0 -0
  29. {biobb_io-5.1.1 → biobb_io-5.2.0}/biobb_io.egg-info/entry_points.txt +0 -0
  30. {biobb_io-5.1.1 → biobb_io-5.2.0}/biobb_io.egg-info/top_level.txt +0 -0
  31. {biobb_io-5.1.1 → biobb_io-5.2.0}/setup.cfg +0 -0
{biobb_io-5.1.1 → biobb_io-5.2.0}/PKG-INFO RENAMED
@@ -1,6 +1,6 @@
1
1
  Metadata-Version: 2.4
2
2
  Name: biobb_io
3
- Version: 5.1.1
3
+ Version: 5.2.0
4
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  Summary: Biobb_io is the Biobb module collection to fetch data to be consumed by the rest of the Biobb building blocks.
5
5
  Home-page: https://github.com/bioexcel/biobb_io
6
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  Author: Biobb developers
@@ -9,15 +9,15 @@ Project-URL: Documentation, http://biobb-io.readthedocs.io/en/latest/
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  Project-URL: Bioexcel, https://bioexcel.eu/
10
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  Keywords: Bioinformatics Workflows BioExcel Compatibility
11
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  Classifier: Development Status :: 5 - Production/Stable
12
- Classifier: Programming Language :: Python :: 3.9
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+ Classifier: Programming Language :: Python :: 3.10
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13
  Classifier: License :: OSI Approved :: Apache Software License
14
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  Classifier: Operating System :: MacOS :: MacOS X
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  Classifier: Operating System :: POSIX
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  Classifier: Operating System :: Unix
17
- Requires-Python: >=3.9
17
+ Requires-Python: >=3.10
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  Description-Content-Type: text/markdown
19
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  License-File: LICENSE
20
- Requires-Dist: biobb_common==5.1.1
20
+ Requires-Dist: biobb_common==5.2.0
21
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  Dynamic: author
22
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  Dynamic: author-email
23
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  Dynamic: classifier
@@ -36,7 +36,7 @@ Dynamic: summary
36
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  [![](https://img.shields.io/conda/vn/bioconda/biobb_io?label=Conda)](https://anaconda.org/bioconda/biobb_io)
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  [![](https://img.shields.io/conda/dn/bioconda/biobb_io?label=Conda%20Downloads)](https://anaconda.org/bioconda/biobb_io)
38
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  [![](https://img.shields.io/badge/Docker-Quay.io-blue)](https://quay.io/repository/biocontainers/biobb_io?tab=tags)
39
- [![](https://img.shields.io/badge/Singularity-GalaxyProject-blue)](https://depot.galaxyproject.org/singularity/biobb_io:5.1.1--pyhdfd78af_0)
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+ [![](https://img.shields.io/badge/Singularity-GalaxyProject-blue)](https://depot.galaxyproject.org/singularity/biobb_io:5.2.0--pyhdfd78af_0)
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41
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  [![](https://img.shields.io/badge/OS-Unix%20%7C%20MacOS-blue)](https://github.com/bioexcel/biobb_io)
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  [![](https://img.shields.io/pypi/pyversions/biobb-io.svg?label=Python%20Versions)](https://pypi.org/project/biobb-io/)
@@ -74,7 +74,7 @@ The latest documentation of this package can be found in our readthedocs site:
74
74
  [latest API documentation](http://biobb-io.readthedocs.io/en/latest/).
75
75
 
76
76
  ### Version
77
- v5.1.1 2025.1
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+ v5.2.0 2025.2
78
78
 
79
79
  ### Installation
80
80
  Using PIP:
@@ -100,12 +100,12 @@ Using DOCKER:
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  * Installation:
101
101
 
102
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103
- docker pull quay.io/biocontainers/biobb_io:5.1.1--pyhdfd78af_0
103
+ docker pull quay.io/biocontainers/biobb_io:5.2.0--pyhdfd78af_0
104
104
 
105
105
  * Usage:
106
106
 
107
107
 
108
- docker run quay.io/biocontainers/biobb_io:5.1.1--pyhdfd78af_0 <command>
108
+ docker run quay.io/biocontainers/biobb_io:5.2.0--pyhdfd78af_0 <command>
109
109
 
110
110
 
111
111
  The command list and specification can be found at the [Command Line documentation](https://biobb-io.readthedocs.io/en/latest/command_line.html).
@@ -117,7 +117,7 @@ Using SINGULARITY:
117
117
  * Installation:
118
118
 
119
119
 
120
- singularity pull --name biobb_io.sif https://depot.galaxyproject.org/singularity/biobb_io:5.1.1--pyhdfd78af_0
120
+ singularity pull --name biobb_io.sif https://depot.galaxyproject.org/singularity/biobb_io:5.2.0--pyhdfd78af_0
121
121
 
122
122
 
123
123
  * Usage:
{biobb_io-5.1.1 → biobb_io-5.2.0}/README.md RENAMED
@@ -3,7 +3,7 @@
3
3
  [![](https://img.shields.io/conda/vn/bioconda/biobb_io?label=Conda)](https://anaconda.org/bioconda/biobb_io)
4
4
  [![](https://img.shields.io/conda/dn/bioconda/biobb_io?label=Conda%20Downloads)](https://anaconda.org/bioconda/biobb_io)
5
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  [![](https://img.shields.io/badge/Docker-Quay.io-blue)](https://quay.io/repository/biocontainers/biobb_io?tab=tags)
6
- [![](https://img.shields.io/badge/Singularity-GalaxyProject-blue)](https://depot.galaxyproject.org/singularity/biobb_io:5.1.1--pyhdfd78af_0)
6
+ [![](https://img.shields.io/badge/Singularity-GalaxyProject-blue)](https://depot.galaxyproject.org/singularity/biobb_io:5.2.0--pyhdfd78af_0)
7
7
 
8
8
  [![](https://img.shields.io/badge/OS-Unix%20%7C%20MacOS-blue)](https://github.com/bioexcel/biobb_io)
9
9
  [![](https://img.shields.io/pypi/pyversions/biobb-io.svg?label=Python%20Versions)](https://pypi.org/project/biobb-io/)
@@ -41,7 +41,7 @@ The latest documentation of this package can be found in our readthedocs site:
41
41
  [latest API documentation](http://biobb-io.readthedocs.io/en/latest/).
42
42
 
43
43
  ### Version
44
- v5.1.1 2025.1
44
+ v5.2.0 2025.2
45
45
 
46
46
  ### Installation
47
47
  Using PIP:
@@ -67,12 +67,12 @@ Using DOCKER:
67
67
  * Installation:
68
68
 
69
69
 
70
- docker pull quay.io/biocontainers/biobb_io:5.1.1--pyhdfd78af_0
70
+ docker pull quay.io/biocontainers/biobb_io:5.2.0--pyhdfd78af_0
71
71
 
72
72
  * Usage:
73
73
 
74
74
 
75
- docker run quay.io/biocontainers/biobb_io:5.1.1--pyhdfd78af_0 <command>
75
+ docker run quay.io/biocontainers/biobb_io:5.2.0--pyhdfd78af_0 <command>
76
76
 
77
77
 
78
78
  The command list and specification can be found at the [Command Line documentation](https://biobb-io.readthedocs.io/en/latest/command_line.html).
@@ -84,7 +84,7 @@ Using SINGULARITY:
84
84
  * Installation:
85
85
 
86
86
 
87
- singularity pull --name biobb_io.sif https://depot.galaxyproject.org/singularity/biobb_io:5.1.1--pyhdfd78af_0
87
+ singularity pull --name biobb_io.sif https://depot.galaxyproject.org/singularity/biobb_io:5.2.0--pyhdfd78af_0
88
88
 
89
89
 
90
90
  * Usage:
{biobb_io-5.1.1 → biobb_io-5.2.0}/biobb_io/__init__.py RENAMED
@@ -2,4 +2,4 @@ from . import api
2
2
 
3
3
  name = "biobb_io"
4
4
  __all__ = ["api"]
5
- __version__ = "5.1.1"
5
+ __version__ = "5.2.0"
{biobb_io-5.1.1 → biobb_io-5.2.0}/biobb_io/api/mddb.py RENAMED
@@ -169,6 +169,7 @@ mddb.__doc__ = MDDB.__doc__
169
169
  main = MDDB.get_main(
170
170
  mddb,
171
171
  "This class is a wrapper for downloading a trajectory / topology pair from the MDDB Database.",
172
+ custom_flags={"output_top_path": "-o", "output_trj_path": "-t"}
172
173
  )
173
174
 
174
175
  if __name__ == "__main__":
{biobb_io-5.1.1 → biobb_io-5.2.0}/biobb_io/api/memprotmd_sim_list.py RENAMED
@@ -15,7 +15,7 @@ class MemProtMDSimList(BiobbObject):
15
15
  | Wrapper for the `MemProtMD DB REST API <http://memprotmd.bioch.ox.ac.uk/>`_ to get all available membrane-protein systems (simulations).
16
16
 
17
17
  Args:
18
- output_simulations (str): Path to the output JSON file. File type: output. `Sample file <https://github.com/bioexcel/biobb_io/raw/master/biobb_io/test/reference/api/output_sim_list.json>`_. Accepted formats: json (edam:format_3464).
18
+ output_simulations (str): Path to the output JSON file. File type: output. `Sample file <https://github.com/bioexcel/biobb_io/raw/master/biobb_io/test/reference/api/output_sim_list_schema_validator.json>`_. Accepted formats: json (edam:format_3464).
19
19
  properties (dic - Python dictionary object containing the tool parameters, not input/output files):
20
20
  * **remove_tmp** (*bool*) - (True) [WF property] Remove temporal files.
21
21
  * **restart** (*bool*) - (False) [WF property] Do not execute if output files exist.
{biobb_io-5.1.1 → biobb_io-5.2.0}/biobb_io/api/memprotmd_sim_search.py RENAMED
@@ -16,7 +16,7 @@ class MemProtMDSimSearch(BiobbObject):
16
16
  | Wrapper for the `MemProtMD DB REST API <http://memprotmd.bioch.ox.ac.uk/>`_ to perform advanced searches.
17
17
 
18
18
  Args:
19
- output_simulations (str): Path to the output JSON file. File type: output. `Sample file <https://github.com/bioexcel/biobb_io/raw/master/biobb_io/test/reference/api/output_sim_search.json>`_. Accepted formats: json (edam:format_3464).
19
+ output_simulations (str): Path to the output JSON file. File type: output. `Sample file <https://github.com/bioexcel/biobb_io/raw/master/biobb_io/test/reference/api/output_sim_search_schema_validator.json>`_. Accepted formats: json (edam:format_3464).
20
20
  properties (dic - Python dictionary object containing the tool parameters, not input/output files):
21
21
  * **collection_name** (*str*) - ("refs") Name of the collection to query.
22
22
  * **keyword** (*str*) - (None) String to search for in the database metadata. Examples are families like gpcr or porin. Values: porin, outer membrane protein, membrane protein, gpcr (7-transmembrane domain receptors transducing extracellular signals into cells), ion channels, rhodopsin (The most famous GPCRs), abc, mip (Major Intrinsic Protein (MIP)/FNT superfamily: specific for the transport of water and small neutral solutes), ligand-gated (Ligand-dependent signal conversion from chemical signals to electric signals), ammonia (Regulating transepithelial ammonia secretion), mapeg (Eicosanoid and Glutathione metabolism proteins), transmembrane (Heme biosynthesis), protein, kinase (Tyrosine-protein kinases: regulate central nervous system; gene transcription and cell differentiation), glycoprotein (Expression of TCR complex), immunoglobulin (Recognition; binding and adhesion process of cells), integrin (Bridges for cell-cell and cell-extracellular matrix interaction), bnip3 (BNip3 protein family: protect cell from apoptosis), bcl-2 (Regulating cell-death; either induce apoptotic or inhibit apoptosis), atpase (ATPase regulators; P-P-bond hydrolysis-driven transporter), cytochrome (Terminal oxidase enzyme in electron transfer chain), nadp (Transmembrane proteins with NAD(P)-binding Rossmann-fold domains: monoamine oxidase; deaminates norepinephrine; epinephrine; serotonin and dopamine), a4 (Amyloid beta A4 protein; involved in alzheimer's diseases), lysosome (Lysosome-associated membrane glycoprotein: specific to lysosomes; CD107), necrosis (Tumor necrosis factor recepto: binding with TNF and NGF; interacting with a variety of signal molecules; highly associated with apoptosis), oxidoreductase (DHODH; biosynthesis of orotate), ceramidase (Neutral/alkaline ceramidase: converting sphingolipid to sphingosine), dehydrogenase (Aldehyde dehydrogenase:ALDH; Oxidation of aldehydes), mitochondrial, plastid.
{biobb_io-5.1.1 → biobb_io-5.2.0}/biobb_io/api/pdb_cluster_zip.py RENAMED
@@ -129,7 +129,7 @@ class PdbClusterZip(BiobbObject):
129
129
  fu.log("Zipping the pdb files to: %s" % self.output_pdb_zip_path)
130
130
  fu.zip_list(self.output_pdb_zip_path, file_list, out_log=self.out_log)
131
131
 
132
- self.tmp_files.extend([unique_dir])
132
+ self.tmp_files.append(unique_dir)
133
133
  self.remove_tmp_files()
134
134
 
135
135
  self.check_arguments(output_files_created=True, raise_exception=False)
{biobb_io-5.1.1 → biobb_io-5.2.0}/biobb_io.egg-info/PKG-INFO RENAMED
@@ -1,6 +1,6 @@
1
1
  Metadata-Version: 2.4
2
2
  Name: biobb_io
3
- Version: 5.1.1
3
+ Version: 5.2.0
4
4
  Summary: Biobb_io is the Biobb module collection to fetch data to be consumed by the rest of the Biobb building blocks.
5
5
  Home-page: https://github.com/bioexcel/biobb_io
6
6
  Author: Biobb developers
@@ -9,15 +9,15 @@ Project-URL: Documentation, http://biobb-io.readthedocs.io/en/latest/
9
9
  Project-URL: Bioexcel, https://bioexcel.eu/
10
10
  Keywords: Bioinformatics Workflows BioExcel Compatibility
11
11
  Classifier: Development Status :: 5 - Production/Stable
12
- Classifier: Programming Language :: Python :: 3.9
12
+ Classifier: Programming Language :: Python :: 3.10
13
13
  Classifier: License :: OSI Approved :: Apache Software License
14
14
  Classifier: Operating System :: MacOS :: MacOS X
15
15
  Classifier: Operating System :: POSIX
16
16
  Classifier: Operating System :: Unix
17
- Requires-Python: >=3.9
17
+ Requires-Python: >=3.10
18
18
  Description-Content-Type: text/markdown
19
19
  License-File: LICENSE
20
- Requires-Dist: biobb_common==5.1.1
20
+ Requires-Dist: biobb_common==5.2.0
21
21
  Dynamic: author
22
22
  Dynamic: author-email
23
23
  Dynamic: classifier
@@ -36,7 +36,7 @@ Dynamic: summary
36
36
  [![](https://img.shields.io/conda/vn/bioconda/biobb_io?label=Conda)](https://anaconda.org/bioconda/biobb_io)
37
37
  [![](https://img.shields.io/conda/dn/bioconda/biobb_io?label=Conda%20Downloads)](https://anaconda.org/bioconda/biobb_io)
38
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  [![](https://img.shields.io/badge/Docker-Quay.io-blue)](https://quay.io/repository/biocontainers/biobb_io?tab=tags)
39
- [![](https://img.shields.io/badge/Singularity-GalaxyProject-blue)](https://depot.galaxyproject.org/singularity/biobb_io:5.1.1--pyhdfd78af_0)
39
+ [![](https://img.shields.io/badge/Singularity-GalaxyProject-blue)](https://depot.galaxyproject.org/singularity/biobb_io:5.2.0--pyhdfd78af_0)
40
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41
41
  [![](https://img.shields.io/badge/OS-Unix%20%7C%20MacOS-blue)](https://github.com/bioexcel/biobb_io)
42
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  [![](https://img.shields.io/pypi/pyversions/biobb-io.svg?label=Python%20Versions)](https://pypi.org/project/biobb-io/)
@@ -74,7 +74,7 @@ The latest documentation of this package can be found in our readthedocs site:
74
74
  [latest API documentation](http://biobb-io.readthedocs.io/en/latest/).
75
75
 
76
76
  ### Version
77
- v5.1.1 2025.1
77
+ v5.2.0 2025.2
78
78
 
79
79
  ### Installation
80
80
  Using PIP:
@@ -100,12 +100,12 @@ Using DOCKER:
100
100
  * Installation:
101
101
 
102
102
 
103
- docker pull quay.io/biocontainers/biobb_io:5.1.1--pyhdfd78af_0
103
+ docker pull quay.io/biocontainers/biobb_io:5.2.0--pyhdfd78af_0
104
104
 
105
105
  * Usage:
106
106
 
107
107
 
108
- docker run quay.io/biocontainers/biobb_io:5.1.1--pyhdfd78af_0 <command>
108
+ docker run quay.io/biocontainers/biobb_io:5.2.0--pyhdfd78af_0 <command>
109
109
 
110
110
 
111
111
  The command list and specification can be found at the [Command Line documentation](https://biobb-io.readthedocs.io/en/latest/command_line.html).
@@ -117,7 +117,7 @@ Using SINGULARITY:
117
117
  * Installation:
118
118
 
119
119
 
120
- singularity pull --name biobb_io.sif https://depot.galaxyproject.org/singularity/biobb_io:5.1.1--pyhdfd78af_0
120
+ singularity pull --name biobb_io.sif https://depot.galaxyproject.org/singularity/biobb_io:5.2.0--pyhdfd78af_0
121
121
 
122
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123
123
  * Usage:
biobb_io-5.2.0/biobb_io.egg-info/requires.txt ADDED
@@ -0,0 +1 @@
1
+ biobb_common==5.2.0
{biobb_io-5.1.1 → biobb_io-5.2.0}/setup.py RENAMED
@@ -5,7 +5,7 @@ with open("README.md", "r") as fh:
5
5
 
6
6
  setuptools.setup(
7
7
  name="biobb_io",
8
- version="5.1.1",
8
+ version="5.2.0",
9
9
  author="Biobb developers",
10
10
  author_email="pau.andrio@bsc.es",
11
11
  description="Biobb_io is the Biobb module collection to fetch data to be consumed by the rest of the Biobb building blocks.",
@@ -19,8 +19,8 @@ setuptools.setup(
19
19
  },
20
20
  packages=setuptools.find_packages(exclude=["docs", "test"]),
21
21
  package_data={"biobb_io": ["py.typed"]},
22
- install_requires=["biobb_common==5.1.1"],
23
- python_requires=">=3.9",
22
+ install_requires=["biobb_common==5.2.0"],
23
+ python_requires=">=3.10",
24
24
  entry_points={
25
25
  "console_scripts": [
26
26
  "alphafold = biobb_io.api.alphafold:main",
@@ -41,7 +41,7 @@ setuptools.setup(
41
41
  },
42
42
  classifiers=[
43
43
  "Development Status :: 5 - Production/Stable",
44
- "Programming Language :: Python :: 3.9",
44
+ "Programming Language :: Python :: 3.10",
45
45
  "License :: OSI Approved :: Apache Software License",
46
46
  "Operating System :: MacOS :: MacOS X",
47
47
  "Operating System :: POSIX",
biobb_io-5.1.1/biobb_io.egg-info/requires.txt DELETED
@@ -1 +0,0 @@
1
- biobb_common==5.1.1
{biobb_io-5.1.1 → biobb_io-5.2.0}/LICENSE RENAMED
File without changes
{biobb_io-5.1.1 → biobb_io-5.2.0}/biobb_io/api/mmcif.py RENAMED
File without changes
{biobb_io-5.1.1 → biobb_io-5.2.0}/biobb_io/api/pdb.py RENAMED
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{biobb_io-5.1.1 → biobb_io-5.2.0}/biobb_io/py.typed RENAMED
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{biobb_io-5.1.1 → biobb_io-5.2.0}/setup.cfg RENAMED
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