From d8517dae717ab73f6e9de79f168e75178459c8ca Mon Sep 17 00:00:00 2001 From: ChrisKent Date: Tue, 3 Sep 2024 09:58:29 +0100 Subject: [PATCH 1/5] Corrected spelling --- bed2idt/main.py | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/bed2idt/main.py b/bed2idt/main.py index 53ae965..823dc23 100644 --- a/bed2idt/main.py +++ b/bed2idt/main.py @@ -91,7 +91,7 @@ def plates_go( # If only one pool complain if len(all_refs) <= 1: raise typer.BadParameter( - "To few referances to split by. Please use other --splitby option" + "To few references to split by. Please use other --splitby option" ) plates = [[] for _ in all_refs] @@ -202,7 +202,7 @@ def plates( ] = pathlib.Path("output.xlsx"), splitby: Annotated[ PlateSplitBy, - typer.Option(help="Should the primers be split across differant plate"), + typer.Option(help="Should the primers be split across different plate"), ] = PlateSplitBy.POOL.value, # type: ignore fillby: Annotated[ PlateFillBy, typer.Option(help="How should the plate be filled") @@ -249,7 +249,7 @@ def tubes( ), ] = pathlib.Path("output.xlsx"), scale: Annotated[ - TubeScale, typer.Option(help="The conc of the primers") + TubeScale, typer.Option(help="The concentration of the primers") ] = TubeScale.NM25.value, # type: ignore purification: Annotated[ TubePurification, typer.Option(help="The purification of the primers") From df51958c2aa4f3878804872899f2b1e5f6cd90ba Mon Sep 17 00:00:00 2001 From: ChrisKent Date: Wed, 6 Nov 2024 10:53:45 +0000 Subject: [PATCH 2/5] Added check incase output is dir --- bed2idt/__init__.py | 2 +- bed2idt/main.py | 6 ++++-- pyproject.toml | 2 +- 3 files changed, 6 insertions(+), 4 deletions(-) diff --git a/bed2idt/__init__.py b/bed2idt/__init__.py index c68196d..a955fda 100644 --- a/bed2idt/__init__.py +++ b/bed2idt/__init__.py @@ -1 +1 @@ -__version__ = "1.2.0" +__version__ = "1.2.1" diff --git a/bed2idt/main.py b/bed2idt/main.py index 823dc23..a0d65a5 100644 --- a/bed2idt/main.py +++ b/bed2idt/main.py @@ -186,7 +186,7 @@ def common( pass -@app.command() +@app.command(no_args_is_help=True) def plates( bedfile: Annotated[ pathlib.Path, @@ -198,6 +198,7 @@ def plates( help="The output location of the file. Defaults to output.xlsx", writable=True, callback=append_xlsx, + dir_okay=False, ), ] = pathlib.Path("output.xlsx"), splitby: Annotated[ @@ -235,7 +236,7 @@ def plates( plates_go(primer_list, workbook, splitby, fillby, plateprefix, randomise) -@app.command() +@app.command(no_args_is_help=True) def tubes( bedfile: Annotated[ pathlib.Path, typer.Argument(help="The path to the bed file", readable=True) @@ -246,6 +247,7 @@ def tubes( help="The output location of the file. Defaults to output.xlsx", writable=True, callback=append_xlsx, + dir_okay=False, ), ] = pathlib.Path("output.xlsx"), scale: Annotated[ diff --git a/pyproject.toml b/pyproject.toml index 73d331e..20ba2bc 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,6 +1,6 @@ [tool.poetry] name = "bed2idt" -version = "1.2.0" +version = "1.2.1" description = "Converts primer.bed files to IDT ordering templates" authors = ["ChrisKent "] license = "CC-BY-SA-4.0" From 52dc191a1b483db939b1ae0d880b3125a975ff65 Mon Sep 17 00:00:00 2001 From: ChrisKent Date: Wed, 6 Nov 2024 10:57:01 +0000 Subject: [PATCH 3/5] Adding precommit --- .pre-commit-config.yaml | 16 ++++++++++++++++ 1 file changed, 16 insertions(+) create mode 100644 .pre-commit-config.yaml diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml new file mode 100644 index 0000000..392d31f --- /dev/null +++ b/.pre-commit-config.yaml @@ -0,0 +1,16 @@ +repos: + - repo: https://github.com/astral-sh/ruff-pre-commit + # Ruff version. + rev: v0.4.1 + hooks: + # Run the linter. + - id: ruff + args: [--fix, --show-fixes] + # Run the formatter. + - id: ruff-format + - repo: https://github.com/python-poetry/poetry + rev: "1.8.3" # add version here + hooks: + - id: poetry-check + - id: poetry-lock + - id: poetry-install From 6a3e80c9e8b67890b07a25da8471fb7341b6a482 Mon Sep 17 00:00:00 2001 From: ChrisKent Date: Wed, 6 Nov 2024 10:57:28 +0000 Subject: [PATCH 4/5] Turning off local variables in traceback --- bed2idt/main.py | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/bed2idt/main.py b/bed2idt/main.py index a0d65a5..fb337b8 100644 --- a/bed2idt/main.py +++ b/bed2idt/main.py @@ -9,7 +9,9 @@ from bed2idt.config import PlateFillBy, PlateSplitBy, TubePurification, TubeScale # Create the typer app -app = typer.Typer(name="bed2idt", no_args_is_help=True) +app = typer.Typer( + name="bed2idt", no_args_is_help=True, pretty_exceptions_show_locals=False +) def chunks(lst, n): From 35be88093bc6fada74fbb87e10301a0eeeaabe55 Mon Sep 17 00:00:00 2001 From: ChrisKent Date: Wed, 6 Nov 2024 10:58:58 +0000 Subject: [PATCH 5/5] Local files --- poetry.lock | 956 ++++++++++++++++++++++++++++--------------------- pyproject.toml | 1 + 2 files changed, 549 insertions(+), 408 deletions(-) diff --git a/poetry.lock b/poetry.lock index 863bbd9..9586624 100644 --- a/poetry.lock +++ b/poetry.lock @@ -2,13 +2,13 @@ [[package]] name = "babel" -version = "2.15.0" +version = "2.16.0" description = "Internationalization utilities" optional = false python-versions = ">=3.8" files = [ - {file = "Babel-2.15.0-py3-none-any.whl", hash = "sha256:08706bdad8d0a3413266ab61bd6c34d0c28d6e1e7badf40a2cebe67644e2e1fb"}, - {file = "babel-2.15.0.tar.gz", hash = "sha256:8daf0e265d05768bc6c7a314cf1321e9a123afc328cc635c18622a2f30a04413"}, + {file = "babel-2.16.0-py3-none-any.whl", hash = "sha256:368b5b98b37c06b7daf6696391c3240c938b37767d4584413e8438c5c435fa8b"}, + {file = "babel-2.16.0.tar.gz", hash = "sha256:d1f3554ca26605fe173f3de0c65f750f5a42f924499bf134de6423582298e316"}, ] [package.extras] @@ -16,112 +16,138 @@ dev = ["freezegun (>=1.0,<2.0)", "pytest (>=6.0)", "pytest-cov"] [[package]] name = "certifi" -version = "2024.6.2" +version = "2024.8.30" description = "Python package for providing Mozilla's CA Bundle." optional = false python-versions = ">=3.6" files = [ - {file = "certifi-2024.6.2-py3-none-any.whl", hash = "sha256:ddc6c8ce995e6987e7faf5e3f1b02b302836a0e5d98ece18392cb1a36c72ad56"}, - {file = "certifi-2024.6.2.tar.gz", hash = "sha256:3cd43f1c6fa7dedc5899d69d3ad0398fd018ad1a17fba83ddaf78aa46c747516"}, + {file = "certifi-2024.8.30-py3-none-any.whl", hash = "sha256:922820b53db7a7257ffbda3f597266d435245903d80737e34f8a45ff3e3230d8"}, + {file = "certifi-2024.8.30.tar.gz", hash = "sha256:bec941d2aa8195e248a60b31ff9f0558284cf01a52591ceda73ea9afffd69fd9"}, +] + +[[package]] +name = "cfgv" +version = "3.4.0" +description = "Validate configuration and produce human readable error messages." +optional = false +python-versions = ">=3.8" +files = [ + {file = "cfgv-3.4.0-py2.py3-none-any.whl", hash = "sha256:b7265b1f29fd3316bfcd2b330d63d024f2bfd8bcb8b0272f8e19a504856c48f9"}, + {file = "cfgv-3.4.0.tar.gz", hash = "sha256:e52591d4c5f5dead8e0f673fb16db7949d2cfb3f7da4582893288f0ded8fe560"}, ] [[package]] name = "charset-normalizer" -version = "3.3.2" +version = "3.4.0" description = "The Real First Universal Charset Detector. 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