From 3afbd16880c9e70738fa73f7adfcedda59825983 Mon Sep 17 00:00:00 2001 From: Matthew Wells Date: Mon, 29 Jul 2024 10:58:32 -0500 Subject: [PATCH 1/5] altered default date format for databases, and bumped version --- CHANGELOG.md | 18 ++++++++++++++++++ locidex/build.py | 2 +- locidex/version.py | 2 +- 3 files changed, 20 insertions(+), 2 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index b9bd75e..629ae25 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -3,6 +3,24 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html). +## v0.2.1 + +### `Fixed` + +- Changed default data format for database configs to year-month-day format + +## v0.2.0 + +### `Added` + +- Incorporated both unit tests and end-to-end tests for workflows + +- Introduced manifest module for management of multiple databases + +### `Fixed` + +- Reduced code coupling issue by removing incorporating dataclasses over dictionaries. Changes were made in a backwards compatible fashion. + ## v1.0dev - [date] Initial release of phac-nml/locidex diff --git a/locidex/build.py b/locidex/build.py index 75d4eed..adf3baf 100644 --- a/locidex/build.py +++ b/locidex/build.py @@ -157,7 +157,7 @@ def run(cmd_args=None): db_version =cmd_args.db_ver, db_desc=cmd_args.db_desc, db_author=cmd_args.author, - db_date=datetime.now().strftime("%Y/%d/%m"), + db_date=datetime.now().strftime("%Y-%m-%d"), ) run_params = vars(cmd_args) diff --git a/locidex/version.py b/locidex/version.py index 7fd229a..fc79d63 100644 --- a/locidex/version.py +++ b/locidex/version.py @@ -1 +1 @@ -__version__ = '0.2.0' +__version__ = '0.2.1' From 7df678fdc6fa082fea30d47f4ca2cdd6afb26828 Mon Sep 17 00:00:00 2001 From: Matthew Wells Date: Mon, 29 Jul 2024 11:00:36 -0500 Subject: [PATCH 2/5] added pr number to changelog --- CHANGELOG.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 629ae25..d365801 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -7,7 +7,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### `Fixed` -- Changed default data format for database configs to year-month-day format +- Changed default data format for database configs to year-month-day format [PR 32](https://github.com/phac-nml/locidex/pull/32/commits/3afbd16880c9e70738fa73f7adfcedda59825983) ## v0.2.0 From 367fabc887535f87e99da772dbffcd6da0c7db2b Mon Sep 17 00:00:00 2001 From: Matthew Wells Date: Mon, 29 Jul 2024 11:01:54 -0500 Subject: [PATCH 3/5] added date to changelog --- CHANGELOG.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index d365801..a2d5775 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -3,7 +3,7 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html). -## v0.2.1 +## v0.2.1 - [2024-07-29] ### `Fixed` From a9e69907e7be09313ff687eb8013fc252c3e46c5 Mon Sep 17 00:00:00 2001 From: Matthew Wells Date: Thu, 1 Aug 2024 13:49:31 -0500 Subject: [PATCH 4/5] fixed issure 35 output database files were not being named properly --- locidex/build.py | 3 ++- locidex/report.py | 2 +- 2 files changed, 3 insertions(+), 2 deletions(-) diff --git a/locidex/build.py b/locidex/build.py index adf3baf..5dba127 100644 --- a/locidex/build.py +++ b/locidex/build.py @@ -55,11 +55,12 @@ def __init__(self, input_file: os.PathLike, outdir: os.PathLike, config: DBConfi blast_method = DBData.protein_db_type() self.init_dir(outfile) out_fasta = outfile.joinpath("{}.fasta".format(t)) + output_db_path = outfile.joinpath(t) self.write_seq_file(out_fasta, col_name) creating_db = BlastMakeDB(input_file=out_fasta, db_type=blast_method, parse_seqids=self.parse_seqids, - output_db_path=out_fasta) + output_db_path=output_db_path) creating_db.makeblastdb() self.config.is_nucl = self.is_dna self.config.is_prot = self.is_protein diff --git a/locidex/report.py b/locidex/report.py index 7d28dfb..09b9ae9 100644 --- a/locidex/report.py +++ b/locidex/report.py @@ -254,7 +254,7 @@ def allele_assignment(self,dbtype): hit_loci_names = self.get_hit_locinames() loci_lookup = self.get_loci_to_query_map(hit_loci_names,dbtype) - + print("loci names", hit_loci_names) for locus in loci_lookup: loci_lookup[locus] = list(set(loci_lookup[locus]) - self.failed_seqids) From 89daff71504e708ad9ca83eba002b007073f662e Mon Sep 17 00:00:00 2001 From: Matthew Wells Date: Thu, 1 Aug 2024 14:33:11 -0500 Subject: [PATCH 5/5] updated version and changelog --- CHANGELOG.md | 7 +++++++ locidex/version.py | 2 +- 2 files changed, 8 insertions(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index a2d5775..fefda0e 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -3,6 +3,13 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html). + +## v0.2.2 - [2024-08-01] + +### `Fixed` + +- Removed suffix from created databases, this resolves an issue where databases are not found as the wrong suffix is passed to the database option [PR 36](https://github.com/phac-nml/locidex/pull/36) + ## v0.2.1 - [2024-07-29] ### `Fixed` diff --git a/locidex/version.py b/locidex/version.py index fc79d63..020ed73 100644 --- a/locidex/version.py +++ b/locidex/version.py @@ -1 +1 @@ -__version__ = '0.2.1' +__version__ = '0.2.2'