diff --git a/CHANGELOG.md b/CHANGELOG.md index a445a50..077fb28 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -7,6 +7,9 @@ * .describe [] * .write_paths_to_file, .copy_files_to_dir(), .link_files_to_dir() +### v0.1.18a +* Patch file deserializer bug [x] + ### v0.1.18 * Add support for ProvStore API (#23) [x] * Add subparsers for CLI commands [x] diff --git a/bioprov/__init__.py b/bioprov/__init__.py index 03cd455..1dc35d6 100644 --- a/bioprov/__init__.py +++ b/bioprov/__init__.py @@ -2,7 +2,7 @@ __license__ = "MIT" __maintainer__ = "Vini Salazar" __url__ = "https://github.com/vinisalazar/bioprov" -__version__ = "0.1.18" +__version__ = "0.1.18a" """ diff --git a/bioprov/bioprov b/bioprov/bioprov index 796aca6..e8d3208 100644 --- a/bioprov/bioprov +++ b/bioprov/bioprov @@ -3,7 +3,7 @@ __author__ = "Vini Salazar" __license__ = "MIT" __maintainer__ = "Vini Salazar" __url__ = "https://github.com/vinisalazar/bioprov" -__version__ = "0.1.18" +__version__ = "0.1.18a" """ Executable that goes in $PATH. Code for the command-line is on the bioprov.py module. diff --git a/bioprov/bioprov.py b/bioprov/bioprov.py index 7c7eea0..24586e4 100644 --- a/bioprov/bioprov.py +++ b/bioprov/bioprov.py @@ -2,7 +2,7 @@ __license__ = "MIT" __maintainer__ = "Vini Salazar" __url__ = "https://github.com/vinisalazar/bioprov" -__version__ = "0.1.18" +__version__ = "0.1.18a" """ BioProv command-line application. This module holds the main executable. diff --git a/bioprov/data/__init__.py b/bioprov/data/__init__.py index 2fff155..192eb54 100644 --- a/bioprov/data/__init__.py +++ b/bioprov/data/__init__.py @@ -2,7 +2,7 @@ __license__ = "MIT" __maintainer__ = "Vini Salazar" __url__ = "https://github.com/vinisalazar/bioprov" -__version__ = "0.1.18" +__version__ = "0.1.18a" """ diff --git a/bioprov/programs/__init__.py b/bioprov/programs/__init__.py index 0051107..80874c0 100644 --- a/bioprov/programs/__init__.py +++ b/bioprov/programs/__init__.py @@ -2,7 +2,7 @@ __license__ = "MIT" __maintainer__ = "Vini Salazar" __url__ = "https://github.com/vinisalazar/bioprov" -__version__ = "0.1.18" +__version__ = "0.1.18a" from .programs import prodigal, diamond, blastn, blastp, prokka, kaiju, kaiju2table diff --git a/bioprov/programs/programs.py b/bioprov/programs/programs.py index 34018ae..de7a212 100644 --- a/bioprov/programs/programs.py +++ b/bioprov/programs/programs.py @@ -2,7 +2,7 @@ __license__ = "MIT" __maintainer__ = "Vini Salazar" __url__ = "https://github.com/vinisalazar/bioprov" -__version__ = "0.1.18" +__version__ = "0.1.18a" """ diff --git a/bioprov/src/__init__.py b/bioprov/src/__init__.py index 5b82e1b..7e9f807 100644 --- a/bioprov/src/__init__.py +++ b/bioprov/src/__init__.py @@ -2,7 +2,7 @@ __license__ = "MIT" __maintainer__ = "Vini Salazar" __url__ = "https://github.com/vinisalazar/bioprov" -__version__ = "0.1.18" +__version__ = "0.1.18a" """ diff --git a/bioprov/src/config.py b/bioprov/src/config.py index 7666493..6074e91 100644 --- a/bioprov/src/config.py +++ b/bioprov/src/config.py @@ -2,7 +2,7 @@ __license__ = "MIT" __maintainer__ = "Vini Salazar" __url__ = "https://github.com/vinisalazar/bioprov" -__version__ = "0.1.18" +__version__ = "0.1.18a" """ diff --git a/bioprov/src/files.py b/bioprov/src/files.py index 8dde293..532215a 100644 --- a/bioprov/src/files.py +++ b/bioprov/src/files.py @@ -2,7 +2,7 @@ __license__ = "MIT" __maintainer__ = "Vini Salazar" __url__ = "https://github.com/vinisalazar/bioprov" -__version__ = "0.1.18" +__version__ = "0.1.18a" """ @@ -489,5 +489,5 @@ def deserialize_files_dict(files_dict): try: setattr(files_dict[tag], attr_, value_) except AttributeError: - breakpoint() + pass return files_dict diff --git a/bioprov/src/main.py b/bioprov/src/main.py index c00d6d3..25b2c53 100644 --- a/bioprov/src/main.py +++ b/bioprov/src/main.py @@ -2,7 +2,7 @@ __license__ = "MIT" __maintainer__ = "Vini Salazar" __url__ = "https://github.com/vinisalazar/bioprov" -__version__ = "0.1.18" +__version__ = "0.1.18a" """ diff --git a/bioprov/src/prov.py b/bioprov/src/prov.py index aa30106..d0f6105 100644 --- a/bioprov/src/prov.py +++ b/bioprov/src/prov.py @@ -2,7 +2,7 @@ __license__ = "MIT" __maintainer__ = "Vini Salazar" __url__ = "https://github.com/vinisalazar/bioprov" -__version__ = "0.1.18" +__version__ = "0.1.18a" """ Module containing base provenance attributes. diff --git a/bioprov/src/workflow.py b/bioprov/src/workflow.py index 7bdabf0..6331335 100644 --- a/bioprov/src/workflow.py +++ b/bioprov/src/workflow.py @@ -2,7 +2,7 @@ __license__ = "MIT" __maintainer__ = "Vini Salazar" __url__ = "https://github.com/vinisalazar/bioprov" -__version__ = "0.1.18" +__version__ = "0.1.18a" """ Contains the Workflow class and related functions. diff --git a/bioprov/tests/__init__.py b/bioprov/tests/__init__.py index b4797eb..c57fe4a 100644 --- a/bioprov/tests/__init__.py +++ b/bioprov/tests/__init__.py @@ -2,7 +2,7 @@ __license__ = "MIT" __maintainer__ = "Vini Salazar" __url__ = "https://github.com/vinisalazar/bioprov" -__version__ = "0.1.18" +__version__ = "0.1.18a" """ diff --git a/bioprov/tests/test_bioprov_imports.py b/bioprov/tests/test_bioprov_imports.py index 29a22be..e1bd6c4 100644 --- a/bioprov/tests/test_bioprov_imports.py +++ b/bioprov/tests/test_bioprov_imports.py @@ -2,7 +2,7 @@ __license__ = "MIT" __maintainer__ = "Vini Salazar" __url__ = "https://github.com/vinisalazar/bioprov" -__version__ = "0.1.18" +__version__ = "0.1.18a" """ diff --git a/bioprov/tests/test_bioprov_integration.py b/bioprov/tests/test_bioprov_integration.py index e4bc3f3..c6edf86 100644 --- a/bioprov/tests/test_bioprov_integration.py +++ b/bioprov/tests/test_bioprov_integration.py @@ -2,7 +2,7 @@ __license__ = "MIT" __maintainer__ = "Vini Salazar" __url__ = "https://github.com/vinisalazar/bioprov" -__version__ = "0.1.18" +__version__ = "0.1.18a" """ diff --git a/bioprov/tests/test_bioprov_programs.py b/bioprov/tests/test_bioprov_programs.py index ad04330..f733214 100644 --- a/bioprov/tests/test_bioprov_programs.py +++ b/bioprov/tests/test_bioprov_programs.py @@ -2,7 +2,7 @@ __license__ = "MIT" __maintainer__ = "Vini Salazar" __url__ = "https://github.com/vinisalazar/bioprov" -__version__ = "0.1.18" +__version__ = "0.1.18a" """ diff --git a/bioprov/tests/test_bioprov_workflows.py b/bioprov/tests/test_bioprov_workflows.py index 5c55016..e0dfcd6 100644 --- a/bioprov/tests/test_bioprov_workflows.py +++ b/bioprov/tests/test_bioprov_workflows.py @@ -2,7 +2,7 @@ __license__ = "MIT" __maintainer__ = "Vini Salazar" __url__ = "https://github.com/vinisalazar/bioprov" -__version__ = "0.1.18" +__version__ = "0.1.18a" """ diff --git a/bioprov/tests/test_src_config.py b/bioprov/tests/test_src_config.py index d06f8be..c187398 100644 --- a/bioprov/tests/test_src_config.py +++ b/bioprov/tests/test_src_config.py @@ -2,7 +2,7 @@ __license__ = "MIT" __maintainer__ = "Vini Salazar" __url__ = "https://github.com/vinisalazar/bioprov" -__version__ = "0.1.18" +__version__ = "0.1.18a" """ diff --git a/bioprov/tests/test_src_file.py b/bioprov/tests/test_src_file.py index 75c990a..0b32fdd 100644 --- a/bioprov/tests/test_src_file.py +++ b/bioprov/tests/test_src_file.py @@ -2,7 +2,7 @@ __license__ = "MIT" __maintainer__ = "Vini Salazar" __url__ = "https://github.com/vinisalazar/bioprov" -__version__ = "0.1.18" +__version__ = "0.1.18a" """ diff --git a/bioprov/tests/test_src_main.py b/bioprov/tests/test_src_main.py index d80917f..d789d8a 100644 --- a/bioprov/tests/test_src_main.py +++ b/bioprov/tests/test_src_main.py @@ -2,7 +2,7 @@ __license__ = "MIT" __maintainer__ = "Vini Salazar" __url__ = "https://github.com/vinisalazar/bioprov" -__version__ = "0.1.18" +__version__ = "0.1.18a" """ diff --git a/bioprov/tests/test_src_prov.py b/bioprov/tests/test_src_prov.py index 5d94344..872b324 100644 --- a/bioprov/tests/test_src_prov.py +++ b/bioprov/tests/test_src_prov.py @@ -2,7 +2,7 @@ __license__ = "MIT" __maintainer__ = "Vini Salazar" __url__ = "https://github.com/vinisalazar/bioprov" -__version__ = "0.1.18" +__version__ = "0.1.18a" """ diff --git a/bioprov/utils.py b/bioprov/utils.py index 5eb3360..99aa68f 100644 --- a/bioprov/utils.py +++ b/bioprov/utils.py @@ -2,7 +2,7 @@ __license__ = "MIT" __maintainer__ = "Vini Salazar" __url__ = "https://github.com/vinisalazar/bioprov" -__version__ = "0.1.18" +__version__ = "0.1.18a" """ Helper functions. diff --git a/bioprov/workflows/__init__.py b/bioprov/workflows/__init__.py index 5d8d232..0dbe70b 100644 --- a/bioprov/workflows/__init__.py +++ b/bioprov/workflows/__init__.py @@ -2,7 +2,7 @@ __license__ = "MIT" __maintainer__ = "Vini Salazar" __url__ = "https://github.com/vinisalazar/bioprov" -__version__ = "0.1.18" +__version__ = "0.1.18a" from .genome_annotation import genome_annotation diff --git a/bioprov/workflows/blastn.py b/bioprov/workflows/blastn.py index 8a6d459..b43e19c 100644 --- a/bioprov/workflows/blastn.py +++ b/bioprov/workflows/blastn.py @@ -3,7 +3,7 @@ __license__ = "MIT" __maintainer__ = "Vini Salazar" __url__ = "https://github.com/vinisalazar/bioprov" -__version__ = "0.1.18" +__version__ = "0.1.18a" """ BLAST nucleotide alignment workflow diff --git a/bioprov/workflows/genome_annotation.py b/bioprov/workflows/genome_annotation.py index 5322bce..f84f21c 100644 --- a/bioprov/workflows/genome_annotation.py +++ b/bioprov/workflows/genome_annotation.py @@ -3,7 +3,7 @@ __license__ = "MIT" __maintainer__ = "Vini Salazar" __url__ = "https://github.com/vinisalazar/bioprov" -__version__ = "0.1.18" +__version__ = "0.1.18a" """ Genome annotation workflow module. diff --git a/bioprov/workflows/kaiju.py b/bioprov/workflows/kaiju.py index 66259fa..0626021 100644 --- a/bioprov/workflows/kaiju.py +++ b/bioprov/workflows/kaiju.py @@ -3,7 +3,7 @@ __license__ = "MIT" __maintainer__ = "Vini Salazar" __url__ = "https://github.com/vinisalazar/bioprov" -__version__ = "0.1.18" +__version__ = "0.1.18a" """ diff --git a/bioprov/workflows/wf_parser.py b/bioprov/workflows/wf_parser.py index 31ddd3f..bf02177 100644 --- a/bioprov/workflows/wf_parser.py +++ b/bioprov/workflows/wf_parser.py @@ -2,7 +2,7 @@ __license__ = "MIT" __maintainer__ = "Vini Salazar" __url__ = "https://github.com/vinisalazar/bioprov" -__version__ = "0.1.18" +__version__ = "0.1.18a" """ diff --git a/docs/source/conf.py b/docs/source/conf.py index 2c8046d..fcefef8 100644 --- a/docs/source/conf.py +++ b/docs/source/conf.py @@ -24,7 +24,7 @@ author = "Vini Salazar" # The full version, including alpha/beta/rc tags -release = "0.1.18" +release = "0.1.18a" # -- General configuration --------------------------------------------------- diff --git a/setup.py b/setup.py index cf007fe..06ac34a 100644 --- a/setup.py +++ b/setup.py @@ -2,7 +2,7 @@ __license__ = "MIT" __maintainer__ = "Vini Salazar" __url__ = "https://github.com/vinisalazar/bioprov" -__version__ = "0.1.18" +__version__ = "0.1.18a" import setuptools @@ -12,7 +12,7 @@ setuptools.setup( name="bioprov", - version="0.1.18", + version="0.1.18a", author="Vini Salazar", author_email="viniws@gmail.com", description="BioProv - Provenance capture for bioinformatics workflows",