transitioned csodiaq to use pyproject.toml for installation

xomicsdatascience · Aug 29, 2023 · 5046e28 · 5046e28
1 parent 72b4f00
commit 5046e28
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Showing 45 changed files with 43 additions and 75 deletions.
diff --git a/.github/workflows/python-app.yml b/.github/workflows/python-app.yml
@@ -27,6 +27,8 @@ jobs:
       run: |
         python -m pip install --upgrade pip
         pip install pytest
+        pip install pyopenms
+        pip install psims
         pip install -e .
     - name: Unzip system test file
       run: |

diff --git a/pyproject.toml b/pyproject.toml
@@ -0,0 +1,39 @@
+[build-system]
+requires = ["setuptools", "setuptools-scm"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "CsoDIAq"
+version = "2.0.0"
+authors = [
+  { name="Caleb Cranney", email="caleb.cranney.github@proton.me" },
+]
+description = "Bioinformatics software package for identifying peptides and proteins in DIA and DISPA mass spectrometry data files."
+readme = "README.md"
+requires-python = ">=3.8"
+classifiers = [
+    "Programming Language :: Python :: 3",
+    "License :: OSI Approved :: MIT License",
+    "Intended Audience :: Science/Research",
+    "Topic :: Scientific/Engineering :: Bio-Informatics",
+]
+
+dependencies = [
+    'pyteomics>=4.4.1',
+    'matplotlib>=3.3.4',
+    'numba>=0.53.1',
+    'numpy>=1.20.1',
+    'pandas>=1.2.2',
+    'Bio>=0.4.1',
+    'PyQt5>=5.15.4',
+    'lxml>=4.6.2',
+    'scikit-learn>=1.1.2',
+]
+
+
+[project.urls]
+"Homepage" = "https://github.com/xomicsdatascience/CsoDIAq"
+"Bug Tracker" = "https://github.com/xomicsdatascience/CsoDIAq/issues"
+
+[project.scripts]
+csodiaq = "csodiaq.csodiaq:main"
diff --git a/requirements.txt b/requirements.txt
diff --git a/setup.py b/setup.py
diff --git a/csodiaq/__init__.py → src/csodiaq/__init__.py b/csodiaq/__init__.py → src/csodiaq/__init__.py
diff --git a/csodiaq/csodiaq.py → src/csodiaq/csodiaq.py b/csodiaq/csodiaq.py → src/csodiaq/csodiaq.py
diff --git a/csodiaq/csodiaqParser.py → src/csodiaq/csodiaqParser.py b/csodiaq/csodiaqParser.py → src/csodiaq/csodiaqParser.py
diff --git a/csodiaq/gui/__init__.py → src/csodiaq/gui/__init__.py b/csodiaq/gui/__init__.py → src/csodiaq/gui/__init__.py
diff --git a/csodiaq/gui/gui.py → src/csodiaq/gui/gui.py b/csodiaq/gui/gui.py → src/csodiaq/gui/gui.py
@@ -2,7 +2,6 @@
     QApplication,
 )
 import sys
-import os
 
 from csodiaq.gui.windows import MainWindow
 

diff --git a/csodiaq/gui/windows/MainWindow.py → src/csodiaq/gui/windows/MainWindow.py b/csodiaq/gui/windows/MainWindow.py → src/csodiaq/gui/windows/MainWindow.py
@@ -1,7 +1,6 @@
 from PyQt5.QtWidgets import (
     QMainWindow,
 )
-from PyQt5.QtCore import Qt
 from csodiaq.gui.windows.TableWindow import TableWindow
 
 

diff --git a/csodiaq/gui/windows/TableWindow.py → src/csodiaq/gui/windows/TableWindow.py b/csodiaq/gui/windows/TableWindow.py → src/csodiaq/gui/windows/TableWindow.py
diff --git a/csodiaq/gui/windows/__init__.py → src/csodiaq/gui/windows/__init__.py b/csodiaq/gui/windows/__init__.py → src/csodiaq/gui/windows/__init__.py
diff --git a/...i/windows/tabs/IdentificationTabWindow.py → ...i/windows/tabs/IdentificationTabWindow.py b/...i/windows/tabs/IdentificationTabWindow.py → ...i/windows/tabs/IdentificationTabWindow.py
diff --git a/csodiaq/gui/windows/tabs/ScoringTabWindow.py → ...diaq/gui/windows/tabs/ScoringTabWindow.py b/csodiaq/gui/windows/tabs/ScoringTabWindow.py → ...diaq/gui/windows/tabs/ScoringTabWindow.py
diff --git a/csodiaq/gui/windows/tabs/TabWindow.py → src/csodiaq/gui/windows/tabs/TabWindow.py b/csodiaq/gui/windows/tabs/TabWindow.py → src/csodiaq/gui/windows/tabs/TabWindow.py
diff --git a/...ndows/tabs/TargetedReanalysisTabWindow.py → ...ndows/tabs/TargetedReanalysisTabWindow.py b/...ndows/tabs/TargetedReanalysisTabWindow.py → ...ndows/tabs/TargetedReanalysisTabWindow.py
diff --git a/csodiaq/gui/windows/tabs/__init__.py → src/csodiaq/gui/windows/tabs/__init__.py b/csodiaq/gui/windows/tabs/__init__.py → src/csodiaq/gui/windows/tabs/__init__.py
diff --git a/csodiaq/identification/__init__.py → src/csodiaq/identification/__init__.py b/csodiaq/identification/__init__.py → src/csodiaq/identification/__init__.py
diff --git a/csodiaq/identification/identifier.py → src/csodiaq/identification/identifier.py b/csodiaq/identification/identifier.py → src/csodiaq/identification/identifier.py
diff --git a/csodiaq/identification/matchingFunctions.py → ...odiaq/identification/matchingFunctions.py b/csodiaq/identification/matchingFunctions.py → ...odiaq/identification/matchingFunctions.py
diff --git a/...entification/outputFormattingFunctions.py → ...entification/outputFormattingFunctions.py b/...entification/outputFormattingFunctions.py → ...entification/outputFormattingFunctions.py
@@ -1,9 +1,5 @@
 import pandas as pd
 import numpy as np
-from csodiaq.scoring.scoringFunctions import (
-    calculate_fdr_rates_of_decoy_array,
-)
-from csodiaq.utils import format_protein_list_to_string, format_protein_string_to_list
 
 
 def format_output_line(libMetadata, queMetadata, matchMetadata):

diff --git a/csodiaq/identification/poolingFunctions.py → ...sodiaq/identification/poolingFunctions.py b/csodiaq/identification/poolingFunctions.py → ...sodiaq/identification/poolingFunctions.py
@@ -1,6 +1,3 @@
-from csodiaq.loaders.library.libraryLoaderContext import LibraryLoaderContext
-from csodiaq.loaders.query.queryLoaderContext import QueryLoaderContext
-import pandas as pd
 import warnings
 from bisect import bisect
 

diff --git a/csodiaq/loaders/__init__.py → src/csodiaq/loaders/__init__.py b/csodiaq/loaders/__init__.py → src/csodiaq/loaders/__init__.py
@@ -1,2 +1,2 @@
-from csodiaq.loaders.query import QueryLoaderContext
 from csodiaq.loaders.library import LibraryLoaderContext
+from csodiaq.loaders.query import QueryLoaderContext
diff --git a/csodiaq/loaders/library/__init__.py → src/csodiaq/loaders/library/__init__.py b/csodiaq/loaders/library/__init__.py → src/csodiaq/loaders/library/__init__.py
diff --git a/...q/loaders/library/libraryLoaderContext.py → ...q/loaders/library/libraryLoaderContext.py b/...q/loaders/library/libraryLoaderContext.py → ...q/loaders/library/libraryLoaderContext.py
@@ -4,7 +4,6 @@
 from csodiaq.loaders.library.libraryLoaderStrategyMgf import (
     LibraryLoaderStrategyMgf as Mgf,
 )
-from csodiaq.loaders.library.libraryLoaderStrategy import LibraryLoaderStrategy
 import os
 
 

diff --git a/.../loaders/library/libraryLoaderStrategy.py → .../loaders/library/libraryLoaderStrategy.py b/.../loaders/library/libraryLoaderStrategy.py → .../loaders/library/libraryLoaderStrategy.py
diff --git a/...aders/library/libraryLoaderStrategyMgf.py → ...aders/library/libraryLoaderStrategyMgf.py b/...aders/library/libraryLoaderStrategyMgf.py → ...aders/library/libraryLoaderStrategyMgf.py
@@ -4,7 +4,6 @@
     remove_low_intensity_peaks_below_max_peak_num,
     finalVariableNames,
 )
-import pandas as pd
 import os
 from pyteomics import mgf
 import re

diff --git a/...ers/library/libraryLoaderStrategyTable.py → ...ers/library/libraryLoaderStrategyTable.py b/...ers/library/libraryLoaderStrategyTable.py → ...ers/library/libraryLoaderStrategyTable.py
diff --git a/csodiaq/loaders/library/mappings.py → src/csodiaq/loaders/library/mappings.py b/csodiaq/loaders/library/mappings.py → src/csodiaq/loaders/library/mappings.py
diff --git a/csodiaq/loaders/query/__init__.py → src/csodiaq/loaders/query/__init__.py b/csodiaq/loaders/query/__init__.py → src/csodiaq/loaders/query/__init__.py
diff --git a/csodiaq/loaders/query/queryLoaderContext.py → ...odiaq/loaders/query/queryLoaderContext.py b/csodiaq/loaders/query/queryLoaderContext.py → ...odiaq/loaders/query/queryLoaderContext.py
diff --git a/csodiaq/loaders/query/queryLoaderStrategy.py → ...diaq/loaders/query/queryLoaderStrategy.py b/csodiaq/loaders/query/queryLoaderStrategy.py → ...diaq/loaders/query/queryLoaderStrategy.py
diff --git a/...loaders/query/queryLoaderStrategyMzxml.py → ...loaders/query/queryLoaderStrategyMzxml.py b/...loaders/query/queryLoaderStrategyMzxml.py → ...loaders/query/queryLoaderStrategyMzxml.py
diff --git a/csodiaq/plotting/__init__.py → src/csodiaq/plotting/__init__.py b/csodiaq/plotting/__init__.py → src/csodiaq/plotting/__init__.py
diff --git a/csodiaq/plotting/spectra.py → src/csodiaq/plotting/spectra.py b/csodiaq/plotting/spectra.py → src/csodiaq/plotting/spectra.py
@@ -1,5 +1,5 @@
 from matplotlib import pyplot as plt
-from csodiaq.plotting.spectrum import Spectrum
+from src.csodiaq.plotting.spectrum import Spectrum
 
 
 def spectrum_lineplot(spectrum: Spectrum,

diff --git a/csodiaq/plotting/spectrum.py → src/csodiaq/plotting/spectrum.py b/csodiaq/plotting/spectrum.py → src/csodiaq/plotting/spectrum.py
diff --git a/csodiaq/scoring/__init__.py → src/csodiaq/scoring/__init__.py b/csodiaq/scoring/__init__.py → src/csodiaq/scoring/__init__.py
diff --git a/csodiaq/scoring/fdrCalculationFunctions.py → ...sodiaq/scoring/fdrCalculationFunctions.py b/csodiaq/scoring/fdrCalculationFunctions.py → ...sodiaq/scoring/fdrCalculationFunctions.py
diff --git a/csodiaq/scoring/idpickerFunctions.py → src/csodiaq/scoring/idpickerFunctions.py b/csodiaq/scoring/idpickerFunctions.py → src/csodiaq/scoring/idpickerFunctions.py
diff --git a/csodiaq/scoring/scoringFunctions.py → src/csodiaq/scoring/scoringFunctions.py b/csodiaq/scoring/scoringFunctions.py → src/csodiaq/scoring/scoringFunctions.py
diff --git a/csodiaq/targetedReanalysis/__init__.py → src/csodiaq/targetedReanalysis/__init__.py b/csodiaq/targetedReanalysis/__init__.py → src/csodiaq/targetedReanalysis/__init__.py
diff --git a/...Reanalysis/targetedReanalysisFunctions.py → ...Reanalysis/targetedReanalysisFunctions.py b/...Reanalysis/targetedReanalysisFunctions.py → ...Reanalysis/targetedReanalysisFunctions.py
diff --git a/csodiaq/utils/Printer.py → src/csodiaq/utils/Printer.py b/csodiaq/utils/Printer.py → src/csodiaq/utils/Printer.py
diff --git a/csodiaq/utils/__init__.py → src/csodiaq/utils/__init__.py b/csodiaq/utils/__init__.py → src/csodiaq/utils/__init__.py
diff --git a/csodiaq/utils/utils.py → src/csodiaq/utils/utils.py b/csodiaq/utils/utils.py → src/csodiaq/utils/utils.py