feat: Add GUI, Windows installer, and Docker web server deployment

.github/workflows/publish.yml

@@ -4,6 +4,11 @@ on:
   release:
     types: [created]
   workflow_dispatch:
+    inputs:
+      dry_run:
+        description: "Dry run: build and test everything, but skip publishing to PyPI, GHCR, and GitHub releases"
+        type: boolean
+        default: true
 
 jobs:
   build-python-package:
@@ -12,13 +17,13 @@ jobs:
       contents: read
 
     steps:
-      - uses: actions/checkout@v6
+      - uses: actions/checkout@v7
 
-      - uses: actions/setup-python@v5
+      - uses: actions/setup-python@v6
         with:
           python-version-file: "pyproject.toml"
 
-      - uses: astral-sh/setup-uv@v7
+      - uses: astral-sh/setup-uv@v8.2.0
         with:
           enable-cache: true
 
@@ -46,62 +51,87 @@ jobs:
           path: dist/
 
       - name: Publish to PyPI
+        if: github.event_name == 'release' || inputs.dry_run == 'false'
         uses: pypa/gh-action-pypi-publish@release/v1
 
-  # windows-installer:
-  #   runs-on: windows-latest
-  #   needs: python-package
-  #   steps:
-  #   - uses: actions/checkout@v6
-  #   - uses: actions/setup-python@v5
-  #     with:
-  #       python-version: '3.11'
-  #   - name: Install dependencies
-  #     run: |
-  #       python -m pip install --upgrade pip
-  #       pip install .[gui] pyinstaller
-  #   - name: Install Inno Setup
-  #     uses: crazy-max/ghaction-chocolatey@v3
-  #     with:
-  #       args: install innosetup -y --allow-unofficial --force
-  #   - name: Run pyinstaller
-  #     run: pyinstaller ./deeplc_pyinstaller.spec --clean --noconfirm
-  #   - name: Test built DeepLC exe
-  #     run: dist/deeplc/deeplc.exe --ignore-gooey --help
-  #   - name: Run Inno Setup
-  #     run: ISCC.exe ./deeplc_innosetup.iss /DAppVersion=${{  github.ref_name }}
-  #   - name: Upload installer
-  #     uses: actions/upload-artifact@v4
-  #     with:
-  #       name: windows-installer
-  #       path: dist/*.exe
-  #   - name: Upload installer to release
-  #     uses: svenstaro/upload-release-action@v2
-  #     with:
-  #       repo_token: ${{ secrets.GITHUB_TOKEN }}
-  #       tag: ${{ github.ref }}
-  #       file_glob: true
-  #       file: dist/*.exe
-
-  # build-streamlit-image:
-  #   runs-on: ubuntu-latest
-  #   needs: publish-python-package
-
-  #   steps:
-  #     - uses: actions/checkout@v6
-
-  #     - name: Login to GitHub Container Registry
-  #       uses: docker/login-action@v3
-  #       with:
-  #         registry: ghcr.io
-  #         username: ${{ github.repository_owner }}
-  #         password: ${{ secrets.GITHUB_TOKEN }}
-
-  #     - name: Build and push to ghcr.io
-  #       uses: docker/build-push-action@v5
-  #       with:
-  #         context: streamlit
-  #         push: true
-  #         tags: |
-  #           ghcr.io/compomics/deeplc-streamlit:${{ github.ref }}
-  #           ghcr.io/compomics/deeplc-streamlit:latest
+  windows-installer:
+    runs-on: windows-latest
+    needs: build-python-package
+    steps:
+      - uses: actions/checkout@v7
+
+      - uses: actions/setup-python@v6
+        with:
+          python-version: "3.13"
+
+      - uses: astral-sh/setup-uv@v8
+        with:
+          enable-cache: true
+
+      - name: Install dependencies
+        run: uv pip install --system ".[gui]" pyinstaller
+
+      - name: Install Inno Setup
+        uses: crazy-max/ghaction-chocolatey@v3
+        with:
+          args: install innosetup -y --allow-unofficial --force
+
+      - name: Run PyInstaller
+        run: pyinstaller ./deeplc.spec --clean --noconfirm
+
+      - name: Test built executable
+        run: dist/deeplc/deeplc.exe predict --help
+
+      - name: Run Inno Setup
+        run: ISCC.exe ./deeplc_innosetup.iss /DAppVersion=${{ github.ref_name }}
+
+      - name: Upload installer artifact
+        uses: actions/upload-artifact@v7
+        with:
+          name: windows-installer
+          path: dist/*.exe
+
+      - name: Upload installer to release
+        if: github.event_name == 'release' || inputs.dry_run == 'false'
+        uses: svenstaro/upload-release-action@v2
+        with:
+          repo_token: ${{ secrets.GITHUB_TOKEN }}
+          tag: ${{ github.ref }}
+          file_glob: true
+          file: dist/*.exe
+
+  build-docker-image:
+    runs-on: ubuntu-latest
+    needs: publish-python-package
+    permissions:
+      packages: write
+
+    steps:
+      - uses: actions/checkout@v7
+
+      - name: Download wheel artifact
+        uses: actions/download-artifact@v8
+        with:
+          name: python-package-distributions
+          path: docker/dist/
+
+      - name: Login to GitHub Container Registry
+        if: github.event_name == 'release' || inputs.dry_run == 'false'
+        uses: docker/login-action@v4
+        with:
+          registry: ghcr.io
+          username: ${{ github.repository_owner }}
+          password: ${{ secrets.GITHUB_TOKEN }}
+
+      - name: Build and push to ghcr.io
+        uses: docker/build-push-action@v7
+        with:
+          context: docker
+          push: ${{ github.event_name == 'release' || inputs.dry_run == 'false' }}
+          tags: |
+            ghcr.io/compomics/deeplc:${{ github.ref_name }}
+            ghcr.io/compomics/deeplc:latest
+
+      - name: Test Docker image
+        if: github.event_name == 'release' || inputs.dry_run == 'false'
+        run: docker run --rm ghcr.io/compomics/deeplc:${{ github.ref_name }} deeplc --help

.github/workflows/test.yml

@@ -42,7 +42,7 @@ jobs:
         with:
           python-version: ${{ matrix.python-version }}
 
-      - uses: astral-sh/setup-uv@v7
+      - uses: astral-sh/setup-uv@v8.2.0
         with:
           enable-cache: true
 

.gitignore

@@ -1,3 +1,11 @@
+# Local
+*.ipynb
+examples/datasets/*_predictions.csv
+
+# IDE
+.vscode/
+.claude/
+
 # DeepLC
 data/
 ./*.png

CHANGELOG.md

@@ -6,6 +6,25 @@ 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).
 
+## [Unreleased]
+
+### Added
+
+- NiceGUI-based web interface, launchable as a browser app (`deeplc gui`) or native desktop window (`deeplc gui --native`)
+- `[gui]` optional dependency group (nicegui, plotly, pywebview) for desktop use
+- `[web]` optional dependency group (nicegui, plotly) for server/Docker use
+- Docker image for containerized web server deployment
+- Updated Windows installer (PyInstaller and Inno Setup) to new GUI
+- `predict_and_calibrate()` core function combining prediction and calibration in one call, with optional automatic reference PSM selection
+- `finetune_and_predict()` core function for transfer learning followed by calibrated prediction
+- Automatic calibration reference selection from input PSMs using q-value filtering or top-scoring fraction
+- Publish workflow with Windows installer build, Docker image build, and dry-run mode for CI testing without publishing
+
+### Changed
+
+- CLI restructured into `predict` and `gui` subcommands
+- Example datasets updated from legacy CSV format to psm_utils TSV and peprec formats
+
 ## [4.0.0-alpha.1]
 
 ### Changed

deeplc.spec

@@ -1,132 +1,71 @@
 # -*- mode: python ; coding: utf-8 -*-
 
-
-import os
-import sys
-from PyInstaller.building.build_main import Analysis, PYZ, EXE, COLLECT, BUNDLE, TOC
-import PyInstaller.utils.hooks
 import importlib.metadata
 
+import PyInstaller.utils.hooks
 
-exe_name = 'deeplc'
-script_name = 'deeplc/__main__.py'
-#if sys.platform[:6] == "darwin":
-#	icon = 'deeplc_logo.icns'
-#else:
-#	icon = 'deeplc_logo.ico'
-block_cipher = None
-location = os.getcwd()
-project = "deeplc"
-remove_tests = True
-bundle_name = "deeplc"
-#bundle_identifier = f"{bundle_name}.{deeplc.__version__}"
-
-
-requirements = {
-    req.split()[0] for req in importlib.metadata.requires(project)
+# Collect all dependencies recursively
+requirements = {req.split()[0] for req in importlib.metadata.requires("deeplc")}
+requirements |= {
+    "deeplc", "sklearn", "sklearn.utils", "sklearn.neighbors", "sklearn.tree",
+    "distributed", "nicegui", "plotly", "pywebview", "onnx2torch",
 }
-requirements.add(project)
-requirements.add("sklearn")
-requirements.add("sklearn.utils")
-requirements.add("sklearn.neighbors")
-requirements.add("sklearn.tree")
-requirements.add("distributed")
 
 hidden_imports = set()
 datas = []
-binaries = []
 checked = set()
 while requirements:
     requirement = requirements.pop()
     checked.add(requirement)
-    if requirement in ["pywin32"]:
+    if requirement in {"pywin32"}:
         continue
     try:
-        module_version = importlib.metadata.version(requirement)
-    except (
-        importlib.metadata.PackageNotFoundError,
-        ModuleNotFoundError,
-        ImportError
-    ):
+        importlib.metadata.version(requirement)
+    except (importlib.metadata.PackageNotFoundError, ModuleNotFoundError, ImportError):
         continue
     try:
-        datas_, binaries_, hidden_imports_ = PyInstaller.utils.hooks.collect_all(
-            requirement,
-            include_py_files=True
+        datas_, _, hidden_imports_ = PyInstaller.utils.hooks.collect_all(
+            requirement, include_py_files=True
         )
     except ImportError:
         continue
     datas += datas_
-    # binaries += binaries_
     hidden_imports_ = set(hidden_imports_)
-    if "" in hidden_imports_:
-        hidden_imports_.remove("")
-    if None in hidden_imports_:
-        hidden_imports_.remove(None)
+    hidden_imports_.discard("")
+    hidden_imports_.discard(None)
     requirements |= hidden_imports_ - checked
     hidden_imports |= hidden_imports_
 
-if remove_tests:
-    hidden_imports = sorted(
-        [h for h in hidden_imports if "tests" not in h.split(".")]
-    )
-else:
-    hidden_imports = sorted(hidden_imports)
-
-
-hidden_imports = [h for h in hidden_imports if "__pycache__" not in h]
-
-datas = [d for d in datas if ("__pycache__" not in d[0]) and (d[1] not in [".", "build","dist","Output"])]
-
-block_cipher = None
-
+hidden_imports = sorted(
+    h for h in hidden_imports if "tests" not in h.split(".") and "__pycache__" not in h
+)
+datas = [
+    d for d in datas
+    if "__pycache__" not in d[0] and d[1] not in {".", "build", "dist", "Output"}
+]
 
 a = Analysis(
-    [script_name],
-    pathex=[location],
-    binaries=binaries,
+    ["deeplc/__main__.py"],
     datas=datas,
     hiddenimports=hidden_imports,
-    hookspath=[],
-    hooksconfig={},
-    runtime_hooks=[],
-    excludes=[],
-    win_no_prefer_redirects=False,
-    win_private_assemblies=False,
-    cipher=block_cipher,
-    noarchive=False
 )
 
-pyz = PYZ(
-    a.pure,
-    a.zipped_data,
-    cipher=block_cipher
-)
+pyz = PYZ(a.pure, a.zipped_data)
 
 exe = EXE(
     pyz,
     a.scripts,
     [],
     exclude_binaries=True,
-    name='deeplc',
-    debug=False,
-    bootloader_ignore_signals=False,
-    strip=False,
-    upx=True,
-    console=True,
-    disable_windowed_traceback=False,
-    target_arch=None,
-    codesign_identity=None,
-    entitlements_file=None
+    name="deeplc",
+    console=False,
+    icon="img/deeplc.ico",
 )
 
 coll = COLLECT(
     exe,
     a.binaries,
     a.zipfiles,
     a.datas,
-    strip=False,
-    upx=True,
-    upx_exclude=[],
-    name=exe_name
+    name="deeplc",
 )