diff --git a/docs/RELEASE.md b/docs/RELEASE.md index 16e8c8a..1f091c0 100644 --- a/docs/RELEASE.md +++ b/docs/RELEASE.md @@ -6,7 +6,7 @@ ## πŸ› Bug Fixes ## πŸ”§ Maintenance ## ⛔️ Deprecated -- XXX [Commit Detail](/~https://github.com/akikuno/DAJIN2/commit/xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx) +[Commit Detail](/~https://github.com/akikuno/DAJIN2/commit/xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx) --> -v0.4.5 (2024-04-24) +v0.4.6 (2024-04-24) -## πŸ› Bug Fixes +## πŸ’₯ Breaking -+ In version 0.4.4 of strand_bias_handler.remove_biased_clusters, there was an error in the continuation condition for removing biased clusters, which has now been corrected. The correct condition should be 'there are alleles with and without strand bias **and** the iteration count is less than or equal to 1000'. Instead, it was incorrectly set to 'there are alleles with and without strand bias **or** the iteration count is less than or equal to 1000'. [Commit Detail](/~https://github.com/akikuno/DAJIN2/commit/b72b3855121d0da6ac80636089315ecc26464657) ++ Update the log file [Commit Detail](/~https://github.com/akikuno/DAJIN2/commit/xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx) + + Add the version of DAJIN2 to the log file to track the version of the analysis. + + Rename the log file to `DAJIN2_log_.txt` from `_DAJIN2.log` to enabling open the file in any text editor. +## πŸ“ Documentation + ++ Enhance the descriptions in GitHub Issue templates to clarify their purpose. [Commit Detail](/~https://github.com/akikuno/DAJIN2/commit/08f3c71bf9f8b755e718eea79dd4a2562aa59297) + + +## πŸ”§ Maintenance + ++ Move `DAJIN2_VERSION` to `utils.config.py` from `main.py` to make it easier to recognize its location. [Commit Detail](/~https://github.com/akikuno/DAJIN2/commit/xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx) + + + ------------------------------------------------------------- # Past Releases +
+ v0.4.5 (2024-04-24) + +## πŸ› Bug Fixes + ++ In version 0.4.4 of strand_bias_handler.remove_biased_clusters, there was an error in the continuation condition for removing biased clusters, which has now been corrected. The correct condition should be 'there are alleles with and without strand bias **and** the iteration count is less than or equal to 1000'. Instead, it was incorrectly set to 'there are alleles with and without strand bias **or** the iteration count is less than or equal to 1000'. [Commit Detail](/~https://github.com/akikuno/DAJIN2/commit/b72b3855121d0da6ac80636089315ecc26464657) +
+ +
v0.4.4 (2024-04-23) diff --git a/src/DAJIN2/core/core.py b/src/DAJIN2/core/core.py index 30708fd..e9f650a 100644 --- a/src/DAJIN2/core/core.py +++ b/src/DAJIN2/core/core.py @@ -5,7 +5,7 @@ from pathlib import Path -from DAJIN2.utils import io, fastx_handler +from DAJIN2.utils import io, config, fastx_handler from DAJIN2.core import classification, clustering, consensus, preprocess, report from DAJIN2.core.preprocess.input_formatter import FormattedInputs @@ -18,6 +18,9 @@ def execute_control(arguments: dict): + + logger.info(f"\N{runner} Start running DAJIN2 version {config.DAJIN_VERSION}") + logger.info(f"{arguments['control']} is now processing...") ########################################################### diff --git a/src/DAJIN2/main.py b/src/DAJIN2/main.py index 2323f35..bb35f0b 100644 --- a/src/DAJIN2/main.py +++ b/src/DAJIN2/main.py @@ -20,9 +20,6 @@ from DAJIN2.utils import io, config, report_generator, input_validator, multiprocess -DAJIN_VERSION = "0.4.5" - - def generate_report(name: str) -> None: report_generator.report(name) print( @@ -165,7 +162,7 @@ def execute(): "-g", "--genome", type=str, default="", help="Reference genome ID (e.g hg38, mm39) [default: '']" ) parser.add_argument("-t", "--threads", type=int, default=1, help="Number of threads [default: 1]") - parser.add_argument("-v", "--version", action="version", version=f"DAJIN2 version {DAJIN_VERSION}") + parser.add_argument("-v", "--version", action="version", version=f"DAJIN2 version {config.DAJIN_VERSION}") parser.add_argument("-d", "--debug", action="store_true", help=argparse.SUPPRESS) ############################################################################### diff --git a/src/DAJIN2/utils/config.py b/src/DAJIN2/utils/config.py index 9b9d05f..1a9cd9a 100644 --- a/src/DAJIN2/utils/config.py +++ b/src/DAJIN2/utils/config.py @@ -9,7 +9,7 @@ from sklearn.exceptions import ConvergenceWarning - +DAJIN_VERSION = "0.4.6" DAJIN_RESULTS_DIR = Path("DAJIN_Results") TEMP_ROOT_DIR = Path(DAJIN_RESULTS_DIR, ".tempdir") @@ -28,7 +28,7 @@ def emit(self, record): def get_logfile() -> Path: current_time = datetime.datetime.now().strftime("%Y%m%d_%H%M%S") - return Path(f"{current_time}_DAJIN2.log") + return Path(f"DAJIN2_log_{current_time}.txt") def set_logging(path_logfile: Path) -> None: