ms-components 0.3.5__tar.gz → 0.4.0__tar.gz

ms_components-0.4.0/MANIFEST.in

@@ -0,0 +1,3 @@
+# setuptools-scm puts every git-tracked file in the sdist; docs/ is repo
+# working material.  licenses/ stays -- it is third-party attribution.
+prune docs

{ms_components-0.3.5 → ms_components-0.4.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: ms_components
-Version: 0.3.5
+Version: 0.4.0
 Summary: PySide6 UI components for MolSuite: smart table, project browser, job monitor, PyMOL dock, steppers.
 Author: Mario S. Valdés-Tresanco, Mario E. Valdés-Tresanco
 License-Expression: MIT
@@ -17,12 +17,21 @@ Classifier: Environment :: X11 Applications :: Qt
 Requires-Python: >=3.12
 Description-Content-Type: text/markdown
 License-File: LICENSE
-Requires-Dist: ms_env>=0.2.0
-Requires-Dist: ms_flow>=0.2.0
 Requires-Dist: PySide6>=6.5
-Requires-Dist: pymol-open-source>=3.2.0a0
-Requires-Dist: sqlmodel>=0.0.14
+Provides-Extra: monitor
+Requires-Dist: pydantic>=2.0; extra == "monitor"
+Provides-Extra: projects
+Requires-Dist: ms_flow>=0.2.0; extra == "projects"
+Provides-Extra: pymol
+Requires-Dist: pymol-open-source>=3.2.0a0; extra == "pymol"
+Provides-Extra: steps
+Requires-Dist: ms_env>=0.2.0; extra == "steps"
+Provides-Extra: table
+Requires-Dist: sqlmodel>=0.0.14; extra == "table"
+Provides-Extra: all
+Requires-Dist: ms_components[monitor,projects,pymol,steps,table]; extra == "all"
 Provides-Extra: dev
+Requires-Dist: ms_components[all]; extra == "dev"
 Requires-Dist: pytest>=7.0; extra == "dev"
 Dynamic: license-file
 
@@ -35,18 +44,39 @@ PyMOL dock, steppers and the shared theming (`themes/` + `base.qss`).
 Python binds existing widgets/signals, while content can be defined in Python or
 TOML. Try `PYTHONPATH=src python examples/tutorial_demo.py` from a source checkout.
 
-Part of the [MolSuite](https://molsuite.github.io/) stack. Built on top of
-[`ms_flow`](https://github.com/MolSuite/ms_flow).
+Part of the [MolSuite](https://molsuite.github.io/) stack. The project catalog integrates
+with [`ms_flow`](https://github.com/MolSuite/ms_flow) when that backend is needed.
 
 ## Install
 
-PyMOL is installed automatically from the `pymol-open-source` alpha wheels on
-PyPI (`>=3.2.0a0`):
+The base installation provides Qt widgets and themes:
 
 ```bash
 pip install ms_components
 ```
 
+Choose the integrations your application uses, or install all of them:
+
+```bash
+pip install "ms_components[table,pymol]"
+pip install "ms_components[all]"
+```
+
+| Extra | Dependency / use |
+| --- | --- |
+| `table` | SQLModel tables |
+| `monitor` | Pydantic monitor configuration |
+| `projects` | `ms_flow` project catalog and standalone project browser |
+| `pymol` | `pymol-open-source` alpha wheels (`>=3.2.0a0`) |
+| `steps` | `ms_env` provisioning steps |
+| `dev` | All integrations and pytest |
+
+Extras select dependencies; all component source files remain in the package.
+Project widgets accept a supplied backend without importing `ms_flow`. When no backend is
+supplied, they use the optional MolSuite catalog, which creates its database on first use.
+Run the standalone browser with `python -m ms_components.ms_projects.app` after installing
+`ms_components[projects]`.
+
 ## Documentation
 
 <https://molsuite.github.io/ms_components/>: a guide to each component, examples,

ms_components-0.4.0/README.md

@@ -0,0 +1,50 @@
+# ms_components
+
+PySide6 UI components for MolSuite: smart table, project browser, job monitor,
+PyMOL dock, steppers and the shared theming (`themes/` + `base.qss`).
+
+[`ms_tutorial`](docs/ms_tutorial.md) provides informative and interactive tours:
+Python binds existing widgets/signals, while content can be defined in Python or
+TOML. Try `PYTHONPATH=src python examples/tutorial_demo.py` from a source checkout.
+
+Part of the [MolSuite](https://molsuite.github.io/) stack. The project catalog integrates
+with [`ms_flow`](https://github.com/MolSuite/ms_flow) when that backend is needed.
+
+## Install
+
+The base installation provides Qt widgets and themes:
+
+```bash
+pip install ms_components
+```
+
+Choose the integrations your application uses, or install all of them:
+
+```bash
+pip install "ms_components[table,pymol]"
+pip install "ms_components[all]"
+```
+
+| Extra | Dependency / use |
+| --- | --- |
+| `table` | SQLModel tables |
+| `monitor` | Pydantic monitor configuration |
+| `projects` | `ms_flow` project catalog and standalone project browser |
+| `pymol` | `pymol-open-source` alpha wheels (`>=3.2.0a0`) |
+| `steps` | `ms_env` provisioning steps |
+| `dev` | All integrations and pytest |
+
+Extras select dependencies; all component source files remain in the package.
+Project widgets accept a supplied backend without importing `ms_flow`. When no backend is
+supplied, they use the optional MolSuite catalog, which creates its database on first use.
+Run the standalone browser with `python -m ms_components.ms_projects.app` after installing
+`ms_components[projects]`.
+
+## Documentation
+
+<https://molsuite.github.io/ms_components/>: a guide to each component, examples,
+and the API reference.
+
+## License
+
+MIT — see [LICENSE](LICENSE). Third-party icon/asset licenses live in `licenses/`.

ms_components-0.4.0/licenses/qt-themes-LICENSE.txt

@@ -0,0 +1,24 @@
+qt-themes  —  https://github.com/beatreichenbach/qt-themes
+Palette values in src/ms_components/theme.py are derived from this project.
+
+MIT License
+
+Copyright (c) 2024 Beat Reichenbach
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

{ms_components-0.3.5 → ms_components-0.4.0}/pyproject.toml

@@ -24,18 +24,20 @@ classifiers = [
     "Environment :: X11 Applications :: Qt",
 ]
 
-# UI components sit on top of the orchestrator (molsuite_flow), Qt and PyMOL.
+# Shared widgets need Qt; each integration declares its own dependencies below.
 dependencies = [
-    "ms_env>=0.2.0",
-    "ms_flow>=0.2.0",
     "PySide6>=6.5",
-    "pymol-open-source>=3.2.0a0",
-    "sqlmodel>=0.0.14",
 ]
 
 [project.optional-dependencies]
+monitor = ["pydantic>=2.0"]
+projects = ["ms_flow>=0.2.0"]
+pymol = ["pymol-open-source>=3.2.0a0"]
+steps = ["ms_env>=0.2.0"]
+table = ["sqlmodel>=0.0.14"]
+all = ["ms_components[monitor,projects,pymol,steps,table]"]
 # Test + development tooling.
-dev = ["pytest>=7.0"]
+dev = ["ms_components[all]", "pytest>=7.0"]
 
 [project.urls]
 Homepage = "https://github.com/MolSuite/ms_components"

ms_components-0.4.0/src/ms_components/ketcher.py

@@ -0,0 +1,156 @@
+"""Draw or edit a small molecule in Ketcher (EPAM's web editor), embedded in a QWebEngineView.
+
+`folder` is an unpacked Ketcher standalone build (the folder holding its index.html); the
+application installs it. Ketcher's JS API answers with Promises, which runJavaScript cannot
+await: the settled value is parked in a window variable and polled from here.
+
+`run_editor` opens the dialog in its own process (`python -m ms_components.ketcher`): in an
+application's process, PySide 6.10 segfaults as soon as the pointer hovers a QWebEngineView
+while any Python application-wide event filter is installed. It also keeps Chromium's memory
+and GPU use away from the rest of the application (an embedded PyMOL, for one)."""
+from __future__ import annotations
+
+import json
+import subprocess
+import sys
+import tempfile
+from collections.abc import Callable
+from pathlib import Path
+
+from PySide6.QtCore import QCoreApplication, Qt, QTimer, QUrl, QUrlQuery
+from PySide6.QtWidgets import QApplication, QDialog, QDialogButtonBox, QLabel, QMessageBox, QVBoxLayout
+
+# Resolves once Ketcher has built `window.ketcher`, some time after the page itself loads.
+_READY = "new Promise(r => { const t = setInterval(() => { if (window.ketcher) { clearInterval(t); r(true); } }, 100); })"
+
+# Ketcher 3.18 standalone's URL options configure the editor before it mounts.
+_HIDDEN_CONTROLS = (
+    "open", "save", "arrows", "reaction-plus", "reaction-mapping-tools", "reaction-map", "reaction-unmap",
+    "rgroup", "rgroup-label", "rgroup-fragment", "rgroup-attpoints", "sgroup", "create-monomer",
+    "shapes", "shape-ellipse", "shape-rectangle", "shape-line", "text", "images",
+    "recognize", "analyse", "miew", "settings", "help", "about", "fullscreen",
+)
+
+
+class KetcherDialog(QDialog):
+    """Ketcher opened on `molblock`; after exec() == Accepted, `molblock` holds the drawing.
+    `note` is shown under the editor (e.g. what Apply will do)."""
+
+    def __init__(self, folder: Path, molblock: str, *, title: str, note: str = "", parent=None):
+        from PySide6.QtWebEngineWidgets import QWebEngineView  # heavy: only when someone edits
+
+        super().__init__(parent)
+        self.setWindowTitle(title)
+        self.resize(1100, 750)
+        self.molblock = molblock
+        self._done: Callable[[dict], None] | None = None
+        self._poll = QTimer(self, interval=100)
+        # As JSON: a JS object comes back to Python empty, a string intact.
+        self._poll.timeout.connect(
+            lambda: self._view.page().runJavaScript("JSON.stringify(window.__ketcher ?? null)", 0, self._polled)
+        )
+
+        self._view = QWebEngineView(self)
+        self._view.loadFinished.connect(self._loaded)
+        url = QUrl.fromLocalFile(str(Path(folder) / "index.html"))
+        query = QUrlQuery()
+        query.addQueryItem("hiddenControls", ",".join(_HIDDEN_CONTROLS))
+        query.addQueryItem("disableMacromoleculesEditor", "true")  # initialize without waiting for macromolecules
+        url.setQuery(query)
+        self._view.load(url)
+        self._buttons = QDialogButtonBox(QDialogButtonBox.StandardButton.Apply | QDialogButtonBox.StandardButton.Cancel, self)
+        self._buttons.button(QDialogButtonBox.StandardButton.Apply).clicked.connect(self._apply)
+        self._buttons.button(QDialogButtonBox.StandardButton.Apply).setEnabled(False)
+        self._buttons.rejected.connect(self.reject)
+        layout = QVBoxLayout(self)
+        layout.addWidget(self._view, 1)
+        if note:
+            label = QLabel(note, self)
+            label.setWordWrap(True)
+            layout.addWidget(label)
+        layout.addWidget(self._buttons)
+
+    def _call(self, promise: str, done: Callable[[dict], None]) -> None:
+        """Evaluate a JS Promise; `done({"ok": value} | {"error": text})` once it settles."""
+        self._done = done
+        self._view.page().runJavaScript(
+            "window.__ketcher = undefined;"
+            f"Promise.resolve({promise}).then(v => window.__ketcher = {{ok: v ?? ''}},"
+            " e => window.__ketcher = {error: String(e)});"
+        )
+        self._poll.start()
+
+    def _polled(self, value) -> None:
+        result = json.loads(value or "null")
+        if not result or self._done is None:
+            return
+        self._poll.stop()
+        done, self._done = self._done, None
+        done(result)
+
+    def _loaded(self, ok: bool) -> None:
+        if not ok:
+            QMessageBox.critical(self, "Ketcher", "Ketcher could not be loaded.")
+            return
+        self._call(f"{_READY}.then(() => window.ketcher.setMolecule({json.dumps(self.molblock)}))", self._ready)
+
+    def _ready(self, result: dict) -> None:
+        if "error" in result:
+            QMessageBox.warning(self, "Ketcher", f"Ketcher could not open the molecule:\n{result['error']}")
+            return
+        self._buttons.button(QDialogButtonBox.StandardButton.Apply).setEnabled(True)
+
+    def _apply(self) -> None:
+        self._buttons.setEnabled(False)
+        self._call("window.ketcher.getMolfile()", self._got)
+
+    def _got(self, result: dict) -> None:
+        self._buttons.setEnabled(True)
+        if "error" in result:
+            QMessageBox.critical(self, "Ketcher", f"Could not read the drawing:\n{result['error']}")
+            return
+        self.molblock = str(result.get("ok") or "")
+        self.accept()
+
+
+def run_editor(
+    folder: Path,
+    molblock: str,
+    title: str,
+    *,
+    note: str = "",
+    theme: str = "auto",
+    base_font_pt: float | None = None,
+) -> str | None:
+    """Open a KetcherDialog in a child process and wait; the drawing after Apply, None on Cancel.
+    Blocking: call it off the GUI thread. `theme`/`base_font_pt` go to ms_components.theme."""
+    options = {"folder": str(folder), "title": title, "note": note, "theme": theme, "base_font_pt": base_font_pt}
+    with tempfile.TemporaryDirectory() as tmp:
+        out = Path(tmp) / "edited.mol"
+        proc = subprocess.run(
+            [sys.executable, "-m", __name__, json.dumps(options), str(out)],
+            input=molblock, capture_output=True, text=True,
+        )
+        if proc.returncode != 0:
+            raise RuntimeError(f"The editor stopped (exit code {proc.returncode}):\n{proc.stderr[-2000:]}")
+        return out.read_text() if out.exists() else None
+
+
+def _main(options: str, out: str) -> int:
+    """The child process: molblock on stdin; the drawing is written to `out` only on Apply."""
+    from ms_components.theme import apply_theme
+
+    opts = json.loads(options)
+    QCoreApplication.setAttribute(Qt.ApplicationAttribute.AA_ShareOpenGLContexts)  # QtWebEngine wants it before the app
+    app = QApplication(["ms-ketcher"])
+    apply_theme(opts.get("theme") or "auto", app, base_font_pt=opts.get("base_font_pt"))
+    dialog = KetcherDialog(Path(opts["folder"]), sys.stdin.read(), title=opts["title"], note=opts.get("note", ""))
+    if dialog.exec() == QDialog.DialogCode.Accepted:
+        Path(out).write_text(dialog.molblock)
+    return 0
+
+
+__all__ = ["KetcherDialog", "run_editor"]
+
+if __name__ == "__main__":
+    sys.exit(_main(*sys.argv[1:3]))

{ms_components-0.3.5 → ms_components-0.4.0}/src/ms_components/ms_projects/app.py

@@ -2,14 +2,20 @@ from __future__ import annotations
 
 import sys
 
-from PySide6.QtWidgets import QApplication
+from PySide6.QtWidgets import QApplication, QMessageBox
 
 from ms_components.ms_projects.browser import ProjectBrowserWindow
 
 
 def main(argv: list[str] | None = None) -> int:
     app = QApplication(list(sys.argv[1:] if argv is None else argv))
-    window = ProjectBrowserWindow()
+    try:
+        window = ProjectBrowserWindow()
+    except ModuleNotFoundError as exc:
+        if exc.name != "ms_flow":
+            raise
+        QMessageBox.critical(None, "Projects", str(exc))
+        return 1
     window.show()
     return app.exec()
 

ms_components-0.4.0/src/ms_components/ms_projects/backend.py

@@ -0,0 +1,15 @@
+"""Load MolSuite's default catalog only when a caller has not supplied a backend."""
+from __future__ import annotations
+
+
+def create_catalog_backend(*, app_id_filter: str | None = None):
+    try:
+        from ms_flow.core.project.catalog import ProjectCatalogBackend
+    except ModuleNotFoundError as exc:
+        if exc.name != "ms_flow":
+            raise
+        raise ModuleNotFoundError(
+            'The project catalog requires ms_flow. Install it with: pip install "ms_components[projects]"',
+            name="ms_flow",
+        ) from exc
+    return ProjectCatalogBackend(app_id_filter=app_id_filter)

{ms_components-0.3.5 → ms_components-0.4.0}/src/ms_components/ms_projects/browser.py

@@ -3,7 +3,7 @@ from __future__ import annotations
 import sys
 from dataclasses import dataclass, field
 from pathlib import Path
-from typing import Any, List, Optional
+from typing import TYPE_CHECKING, Any, List, Optional
 
 from PySide6.QtCore import (
     Qt, Signal, QRect, QSize, QAbstractTableModel, QModelIndex, QEvent,
@@ -21,11 +21,14 @@ from PySide6.QtWidgets import (
     QTreeView, QTreeWidget, QTreeWidgetItem, QVBoxLayout, QWidget,
 )
 
-from ms_flow.core.project.catalog import ProjectCatalogBackend
-from ms_flow.core.settings.manager import SettingsManager
-from ms_flow.core.settings.models import Settings
+from ms_components.ms_projects.backend import create_catalog_backend
 from ms_components.theme import color as theme_color
 
+if TYPE_CHECKING:
+    from ms_flow.core.project.catalog import ProjectCatalogBackend
+    from ms_flow.core.settings.manager import SettingsManager
+    from ms_flow.core.settings.models import Settings
+
 
 # ── Palette ───────────────────────────────────────────────────────────────────
 _TOOL_COLORS: list[str] = [
@@ -1108,7 +1111,7 @@ class ProjectBrowserPanel(QWidget):
                  _backend: ProjectCatalogBackend | None = None, parent=None):
         super().__init__(parent)
         self.app_id              = (app_id or "").strip() or None
-        self.backend             = _backend or ProjectCatalogBackend(app_id_filter=None)
+        self.backend             = _backend if _backend is not None else create_catalog_backend()
         self.header_title        = header_title
         self.hint_text           = hint_text
         self.allow_app_selection = (
@@ -2002,7 +2005,7 @@ class ProjectBrowserWindow(QMainWindow):
                  close_on_launch: bool = True, _backend: ProjectCatalogBackend | None = None):
         super().__init__()
         self.app_id          = (app_id or "").strip() or None
-        self.backend         = _backend or ProjectCatalogBackend(app_id_filter=None)
+        self.backend         = _backend if _backend is not None else create_catalog_backend()
         self.window_title    = window_title or "MolSuite Control Center"
         self.close_on_launch = close_on_launch
         eff_header = header_title or (self.app_id or "MolSuite Projects")
@@ -2082,7 +2085,6 @@ class ProjectBrowserWindow(QMainWindow):
 
 
 if __name__ == "__main__":
-    app = QApplication(sys.argv[1:])
-    w = ProjectBrowserWindow()
-    w.show()
-    sys.exit(app.exec())
+    from ms_components.ms_projects.app import main
+
+    sys.exit(main())

{ms_components-0.3.5 → ms_components-0.4.0}/src/ms_components/ms_projects/widget.py

@@ -1,7 +1,7 @@
 from __future__ import annotations
 
 from pathlib import Path
-from typing import Optional
+from typing import TYPE_CHECKING, Optional
 
 from PySide6.QtCore import Qt, Signal
 from PySide6.QtWidgets import (
@@ -16,9 +16,12 @@ from PySide6.QtWidgets import (
     QWidget,
 )
 
-from ms_flow.core.project.catalog import ProjectCatalogBackend
+from ms_components.ms_projects.backend import create_catalog_backend
 from ms_components.ms_projects.browser import ProjectFormDialog, ProjectItem, ProjectTreeWidget
 
+if TYPE_CHECKING:
+    from ms_flow.core.project.catalog import ProjectCatalogBackend
+
 _PROJECT_MENU_COLORS = [
     "#4e95ff",
     "#a259ff",
@@ -56,7 +59,7 @@ class ProjectsMenuWidget(QFrame):
     ):
         super().__init__(parent)
         self.app_id = (app_id or "").strip() or None
-        self.backend = backend or ProjectCatalogBackend(app_id_filter=self.app_id)
+        self.backend = backend if backend is not None else create_catalog_backend(app_id_filter=self.app_id)
         self.title = title
         self.hint_text = hint_text
         self.allow_create = allow_create

ms_components-0.4.0/src/ms_components/ms_pymol/__init__.py

@@ -0,0 +1,49 @@
+from .scene import (
+    SceneMemory,
+    add_scene_actions,
+    clear_scene,
+    color_atoms,
+    color_by_residue_nature,
+    frame,
+    install_scene_memory,
+    is_additive,
+    is_interacting,
+    menu_action,
+    object_list,
+    prepare_scene,
+    select_atoms,
+    set_additive,
+    set_scene_context,
+)
+from .widget import (
+    COMPARISON_COLORS,
+    associate_scene_objects,
+    PymolControlBar,
+    PymolDockWidget,
+    PymolPresetSpec,
+    PymolSceneContext,
+)
+
+__all__ = [
+    "COMPARISON_COLORS",
+    "SceneMemory",
+    "add_scene_actions",
+    "associate_scene_objects",
+    "clear_scene",
+    "color_atoms",
+    "color_by_residue_nature",
+    "frame",
+    "install_scene_memory",
+    "is_additive",
+    "is_interacting",
+    "menu_action",
+    "object_list",
+    "prepare_scene",
+    "select_atoms",
+    "set_additive",
+    "set_scene_context",
+    "PymolControlBar",
+    "PymolDockWidget",
+    "PymolPresetSpec",
+    "PymolSceneContext",
+]

ms_components-0.4.0/src/ms_components/ms_pymol/icons/style.svg

@@ -0,0 +1 @@
+<svg xmlns="http://www.w3.org/2000/svg" width="24" height="24" viewBox="0 0 24 24" fill="none" stroke="currentColor" stroke-width="2" stroke-linecap="round" stroke-linejoin="round" class="lucide lucide-paintbrush-icon lucide-paintbrush"><path d="m14.622 17.897-10.68-2.913"/><path d="M18.376 2.622a1 1 0 1 1 3.002 3.002L17.36 9.643a.5.5 0 0 0 0 .707l.944.944a2.41 2.41 0 0 1 0 3.408l-.944.944a.5.5 0 0 1-.707 0L8.354 7.348a.5.5 0 0 1 0-.707l.944-.944a2.41 2.41 0 0 1 3.408 0l.944.944a.5.5 0 0 0 .707 0z"/><path d="M9 8c-1.804 2.71-3.97 3.46-6.583 3.948a.507.507 0 0 0-.302.819l7.32 8.883a1 1 0 0 0 1.185.204C12.735 20.405 16 16.792 16 15"/></svg>