parseet 0.2.0__py3-none-any.whl

parseet/version.py

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+__version__ = "0.2.0"

parseet-0.2.0.dist-info/METADATA

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+Metadata-Version: 2.1
+Name: parseet
+Version: 0.2.0
+Summary: This package is used to parse ms samplesheet for further analyses.
+Keywords: samplesheet,parser,data analyses,mass spectrometry,msdial
+Author-Email: Matteo Miotto <miotsdata@gmail.com>
+License: MIT
+Classifier: Programming Language :: Python :: 3
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Operating System :: OS Independent
+Requires-Python: <3.13,>=3.12
+Requires-Dist: pandas>=2.3.3
+Requires-Dist: openpyxl>=3.1.5
+Provides-Extra: gui
+Requires-Dist: pyside6>=6.11.1; extra == "gui"
+Description-Content-Type: text/markdown
+
+# BULK METABOLOMICS SAMPLESHEET
+
+This folder contains the files necessary for the samplesheet of LC-MS and spatial metabolomics.
+Samplesheet template (LC-MS_metabolomics_samplesheet.xlsx or spatial_metabolomics_samplesheet.xlsx) should be given to clients to be compiled. Once received back, it should be tested with the parser (LC-MS_parse_samplesheet.py or spatial_parse_samplesheet.py).
+
+## Samplesheet template
+Samplesheet templates contains 3 sheets:
+
+- input: the one the user should fill. It contains two sections, one with user info and the other with samples metadata.
+- example_ok: an example of a good samplesheet
+- example_fail: an example of a problematic samplesheet
+
+## Parser
+The parser will check the samplesheet for its correct compilation and raises warnings and/or errors if any.
+If no errors are found, the samples metadata section is saved as a csv file (specified as -o). Warnings also prevent file to be saved, but this can be overruled by --ignore-warnings.
+
+## Test
+In test folder, 3 test samplesheet for each technology are found:
+
+- test_error.xlsx: a test samplesheet with errrors
+- test_ok.xlsx: a test samplesheet correctly compiled
+- test_warning.xlsx: a test samplesheet with warnings
+
+Several test should be run after changind any file:
+
+- `python LC-MS_parse_samplesheet.py` (this should result in an error for missing input and output) 
+- `python LC-MS_parse_samplesheet.py -i test_files/LC-MS_test_ok.xlsx -o test.csv --dry-run` (this should be ok, with no errors nor warnings, but no file should be saved due to --dry-run)
+- `python LC-MS_parse_samplesheet.py -i test_files/LC-MS_test_ok.xlsx -o test.csv` (this should be ok, with also test.csv file saved)
+- `python LC-MS_parse_samplesheet.py -i test_files/LC-MS_test_error.xlsx -o test.csv` (this should raise errors and no test.csv file should be created)
+- `python LC-MS_parse_samplesheet.py -i test_files/LC-MS_test_warning.xlsx -o test.csv` (this should raise warnings and no test.csv file should be created)
+- `python LC-MS_parse_samplesheet.py` (this should result in an error for missing input and output) 
+- `python spatial_parse_samplesheet.py -i test_files/spatial_test_ok.xlsx -o test.csv --dry-run` (this should be ok, with no errors nor warnings, but no file should be saved due to --dry-run)
+- `python LC-MS_parse_samplesheet.py -i test_files/LC-MS_test_ok_timecourse.xlsx -o test.csv` (this should be ok, with also test.csv file saved)
+- `python spatial_parse_samplesheet.py -i test_files/spatial_test_ok.xlsx -o test.csv` (this should be ok, with also test.csv file saved)
+- `python spatial_parse_samplesheet.py -i test_files/spatial_test_error.xlsx -o test.csv` (this should raise errors and no test.csv file should be created)
+- `python spatial_parse_samplesheet.py -i test_files/spatial_test_warning.xlsx -o test.csv` (this should raise warnings and no test.csv file should be created)
+- `python spatial_parse_samplesheet.py -i test_files/spatial_test_warning.xlsx -o test.csv` --ignore-warnings (this should raise warnings, but test.csv file should be created)
+- `python spatial_parse_samplesheet.py -i test_files/spatial_test_warning.xlsx -o test.csv` --ignore-warnings (this should raise warnings, but test.csv file should be created)
+

parseet-0.2.0.dist-info/RECORD

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+parseet-0.2.0.dist-info/entry_points.txt,sha256=oeHTCaYLLZDEnS0MJsV70nIccIwm07x6UJdE5wQZrBw,92
+parseet/.DS_Store,sha256=2JvCSFIsKyVMbIw8qiMatTYqT5qOo0VsZmsEPvMewLk,6148
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+parseet/core/utils/lcms_check_samples.py,sha256=I63s1T0V2vCYeLIPQeiwj95XypL-IuDcXxlNKy99bLs,12228
+parseet/core/utils/parse_samplesheet.py,sha256=0pj8vGhDisQAzCRrz42FWmuEhxrLZL0Uym606sPQnTs,12608
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+parseet/version.py,sha256=Zn1KFblwuFHiDRdRAiRnDBRkbPttWh44jKa5zG2ov0E,22
+parseet-0.2.0.dist-info/RECORD,,

parseet-0.2.0.dist-info/WHEEL

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+Wheel-Version: 1.0
+Generator: pdm-backend (2.4.9)
+Root-Is-Purelib: true
+Tag: py3-none-any

parseet-0.2.0.dist-info/entry_points.txt

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+[console_scripts]
+parseet = parseet.cli:main
+
+[gui_scripts]
+parseet-gui = parseet.app:main
+