More efficient gui spec and new publish

Author: Alirezak2n

.github/workflows/publish.yml

@@ -29,14 +29,13 @@ jobs:
         uses: actions/setup-python@v5
         with:
           python-version: "3.11"
-      - name: Install dependencies
+      - name: Install build tooling
         run: |
           python -m pip install --upgrade pip
           python -m pip install --upgrade build
           
       - name: Build source and wheel
-        run: |
-          python -m build 
+        run: python -m build
 
       - name: Upload build artifacts
         uses: actions/upload-artifact@v4
@@ -62,31 +61,20 @@ jobs:
         with:
           python-version: "3.11"
 
-      - name: Install dependencies
+      - name: Install dependencies for building EXE
         run: |
           python -m pip install --upgrade pip
-          pip install --only-binary :all: . pyinstaller pillow requests
+          pip install --only-binary :all: .[gui] pyinstaller
 
       - name: Build Windows EXE with PyInstaller
-        working-directory: ./ideeplc
-        run: |
-          pyinstaller gui.spec --noconfirm
-#         working-directory: ${{ github.workspace }}
+        run: pyinstaller ideeplc/gui.spec --noconfirm
 
       - name: Upload EXE to artifact
         uses: actions/upload-artifact@v4
         with:
           name: iDeepLC-gui
           path: dist/*.exe
 
-      - name: Upload EXE to GitHub Release
-        uses: svenstaro/upload-release-action@v2
-        with:
-          repo_token: ${{ secrets.GITHUB_TOKEN }}
-          tag: ${{ github.ref }}
-          file: dist/*.exe
-          file_glob: true
-
       - name: Upload EXE to GitHub Release page
         uses: softprops/action-gh-release@v1
         with:

ideeplc/gui.spec

@@ -17,7 +17,7 @@ app_name = f"iDeepLC_{version}"
 script_path = "gui.py"
 icon_path = str(project_root / "ideeplc" / "logo" / "ideeplc.ico")
 
-packages = ["PIL", "requests", "torch", "ideeplc", "lxml", "pyteomics", "tqdm"]
+packages = ["ideeplc"]
 hiddenimports = set()
 datas, binaries = [], []
 

ideeplc/utilities.py

@@ -3,7 +3,6 @@
 
 import numpy as np
 import pandas as pd
-import tqdm
 from numpy import ndarray
 from pyteomics import proforma, mass
 from importlib.resources import files
@@ -316,7 +315,7 @@ def df_to_matrix(
     aa_to_feature = aa_chemical_feature()
     amino_acids_atoms = aa_atomic_composition_array()
 
-    for idx, peptide in tqdm.tqdm(enumerate(seqs), total=len(seqs)):
+    for idx, peptide in enumerate(seqs):
         try:
             parsed_sequence, modifiers, sequence, modifications = peptide_parser(
                 peptide

pyproject.toml

@@ -19,21 +19,26 @@ classifiers = [
     "Development Status :: 5 - Production/Stable",
 ]
 dynamic = ["version"]
-requires-python = ">=3.7"
+requires-python = ">=3.8"
 dependencies = [
     "matplotlib>=3.7,<4",
     "numpy>=1.25,<2",
     "pandas>=2,<3",
     "pyteomics>=4.5,<5",
-    "seaborn>=0.13,<1",
     "torch>=2.2.1,<3",
     "scikit-learn>=1.4,<2",
-    "tqdm>=4.65,<5",
     "rich>=13",
     "lxml>=4.9,<5",
 ]
 
 [project.optional-dependencies]
+
+gui = [
+    "pillow>=9.5",
+    "requests>=2.31",
+]
+
+
 dev = [
     "pytest",
     "pytest-cov",
@@ -42,6 +47,12 @@ dev = [
     "flake8"
 ]
 
+[tool.setuptools.package-data]
+ideeplc = [
+  "models/*.pth",
+  "structure_feature/*.csv",
+]
+
 [build-system]
 requires = ["setuptools"]
 build-backend = "setuptools.build_meta"