v1.5.0

1.5.0 (2025-01-24)

Bug Fixes

• #111 - Do not change python working dir to requested output directory as this is no longer necessary (8180c56)
• add required dryrun option to container cache configuration for github workflow (df8b9ee)
• always regenerate incomplete files when a previous analysis was shut down unexpectedly (i.e. sigterm or power loss) (bb3b16f)
• create an empty {sample}_primers.bed file when no input primers were given (--primers NONE) to ensure workflow completion (f7c90e3)
• do not download containers in dryrun mode (4f6e45d)
• ensure proper parsing and assigning of input data when handling an integer sampleID (253a601)
• modify ask_prompt variable assignment based on auto_update configuration (5fab54f)
• resolve snakemake AmbiguousRuleException for certain combinations of primer inputs (5cf5fbd)
• update script path handling for breadth of coverage rule based on conda and singularity configuration (c8b4cc9)

Dependencies

• limit mamba version to <2.0.0 (941c19b)
• pin package versions in child conda environments (941c19b)
• set flexible pyopenssl dependency to version 24.x.x (0dc3d58)
• update pysam to version 0.21 in downstream env and pin package versions in setup.py (5140811)

Documentation

• enhance documentation with reproducibility settings and multi-reference analysis guidance (71b39ea)

Continuous Integration

• avoid triggering the entire workflow for markdown and docs files (533a971)

v1.4.6

1.4.6 (2024-10-08)

Bug Fixes

• properly solve DAG workflow for nonsegmented matched-ref samples (02a821a)

v1.4.5

1.4.5 (2024-09-25)

Bug Fixes

• incorrect renaming of matched references in non-segmented mode (c42740e)

v1.4.4

1.4.4 (2024-09-16)

Bug Fixes

• remove intel channel from selfupdater repositories (43fe508)

Dependencies

• reorder and add details to the conda dependency files for compatibility with strict_channel_priority in conda config (dc9b993)

v1.4.3

1.4.3 (2024-07-03)

Dependencies

• Remove 'intel' channel from conda environments (a2e918a)

v1.4.2

1.4.2 (2024-04-03)

Dependencies

• update AmpliGone to version 1.3.1 (b6a92c8)

v1.4.1

1.4.1 (2024-03-22)

Bug Fixes

• resolve pandas FutureWarning for integer casting on a series with a single element (bb76d06)

Dependencies

• update AmpliGone to version 1.3.0 (6f28568)
• update python and pysam version in Consensus conda environment (18e4ffb)

v1.4.0

1.4.0 (2023-09-18)

Features

• add "NONE" input for primers and gff's support to the match_ref process (1581c78)
• add all the match_ref analysis scripts (1581c78)
• add the match_ref snakemake workflow (1581c78)
• add the match_reference process (1581c78)
• only initiate the match_ref wrapping process whenever it is set on the commandline or through the samplesheet (1581c78)

Bug Fixes

• add fix for unformatted printed message (98386c1)
• enforce a "None" string instead of a Nonetype used for reference prep (f4f7490)
• ensure "match-ref" and "segmented" columns are always added to samplesheet (98386c1)
• ensure a string value like "NA" will not be interpreted as NaN in pandas.read_csv() (ecaca5e)
• pad the number in primer names in the amplicon_coverages script so the amplicons are sorted correctly (cab3a8c)
• solve index out of range bug in amplicon_coverages script (ca95a8a)
• suppress the strict-channel-priorities logmessage from snakemake (1654891)
• workaround to make sure the found segments can properly be 'exploded' in the resulting dataframe (9db4a42)

Dependencies

• remove anaconda channel from selfupdating method (3db1cfb)
• remove the anaconda and defaults channels as providers in conda environment recipes, set nodefaults (08ed236)
• replace gffpandas in script to AminoExtract functions (599da1f)
• update AminoExtract to version 0.3.1 (08e4a22)
• use a forked/patched version of gffpandas instead of the pypi version (circumvent a bug in the original repo) (08e4a22)

Documentation

• update the documentation site to represent the new match-ref and segmented arguments both on commandline and and in samplesheet (94c5ca0)
• updated docstring for function check_samplesheet_rows() (98386c1)

v1.3.1

1.3.1 (2023-05-26)

Bug Fixes

• enforce absolute paths for files given through the samplesheet (40889bf)

Dependencies

• use only snakemake-minimal as workaround for protobuf error in py3.11 (47c70db)

v1.3.0

1.3.0 (2023-05-03)

Features

• addition of proper logging functionality for the ViroConstrictor package (20a952b)
• replace snakemake logging output through our own log handler for unified output (20a952b)

Bug Fixes

• always use the absolute path of given files when parsing from the commandline options (a5b56e5)
• change certainty values of match_preset_name() function to be explicitly floating points to ensure correct datatypes in downstream check (a74249c)
• change preset fallback certainty threshold to be slightly more conservative (7542c46)
• clean-handling of mamba solver mismatching (i.e. CDN mismatch with upstream) (680730b)
• ensure variables for preset-warning fallbacks are properly set when no fallbackwarnings have to be logged (d7ddf0a)
• print the sample key instead of dictionary contents in non-existing reference error log (f8c7a12)
• Properly show all preset-fallback warnings instead of just the first in the index (48662db)
• suppress snakemake logging output (workaround for snakemake/snakemake#2089) (20a952b)
• ensure samples_df and samples_dict always contain the same information (20a952b)

Documentation

• add citation and DOI information to readme and documentation site (a2cf117)
• add explanatory docstrings to various functions (0e1a368)
• fix typo in installation docs (acc30d9)
• update documentation with dedicated page for presets (7b2a66f)
• updated manual with links to more detailed presets functionality explanation page (7b2a66f)
• updated mkdocs configuration to include new page (7b2a66f)
• updated mkdocs configuration to include the direct copy-button for code blocks (7b2a66f)

Code Refactoring

• Use a generic (__main__.py) top level entry-point instead of the named ViroConstrictor.py entrypoint (20a952b)
• re-structure argument parsing functionalities into its own class (20a952b)
• re-structure snakemake run-information and config functionalities into its own class (20a952b)
• remove old shell stdout-coloring method with the rich library (20a952b)
• simplify several functions to ensure a properly defined return (20a952b)
• Use f-strings more consistently for i.e. string concatenation with variables (20a952b)
• add type-hints to all functions (20a952b)

Miscellaneous Chores

• empty commit (84a34b9)

Dependencies

• change biopython version to 1.81 (6bd437a)
• change openpyxl version to 3.1.* (6bd437a)
• change pandas version to 2.0.* (6bd437a)
• change snakemake version to 7.25.* in base environment (6bd437a)
• change urllib3 version to be more lenient (1.26.*) (6bd437a)
• pin AminoExtract version to 0.2.1 (6bd437a)
• use more lenient package requirements in setup.py to allow for both py3.10 and py3.11 builds (944f39d)