setupEM 0.14.1__tar.gz → 0.14.2__tar.gz

{setupem-0.14.1/src/setupEM.egg-info → setupem-0.14.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: setupEM
-Version: 0.14.1
+Version: 0.14.2
 Summary: Python tool for configuration of gds2palace workflow with GUI.
 Author-email: Volker Muehlhaus <volker@muehlhaus.com>
 License-Expression: GPL-3.0-or-later
@@ -11,7 +11,7 @@ Requires-Python: >=3.9
 Description-Content-Type: text/markdown
 License-File: LICENSE
 Requires-Dist: gds2palace>=0.9.0
-Requires-Dist: gds_prepare_for_EM>=1.3.0
+Requires-Dist: gds_prepare_for_EM>=1.6.0
 Requires-Dist: PySide6
 Requires-Dist: shiboken6
 Requires-Dist: scipy
@@ -38,6 +38,12 @@ https://github.com/VolkerMuehlhaus/setupEM
 
 ## Recent changes
 
+# What's New - October 21, 2026
+
+**Tools > Simplify GDS:** the simplification code moved to gds_prepare_for_EM (module `gds_simplify_for_em`), where the gds2palace MCP server uses it too. setupEM now requires gds_prepare_for_EM 1.6.0 or later; `pip install --upgrade setupEM` updates it.
+
+Fix: with **Merge via arrays** (and no fill removal or merging per layer), the simplified file still contained the original subcells as extra top-level cells. Without a cell name, gds2palace reads the first top-level cell, which could be one of them, e.g. a pad cell instead of the design. These left-over cells are now removed.
+
 # What's New - October 19, 2026
 
 **Stackup Editor, ADS Momentum (*.ltd) import:** metals with an EXPAND thickness operation now make the dielectric next to them thicker, as in ADS, instead of reaching into the dielectric below. Before, a thick EXPAND DOWN metal (e.g. MET1/MET2 in a GaAs stackup) overlapped the layers underneath it, and a via could end up with zero height. Files where long lines are wrapped or END_... markers follow the last entry on the same line now import too; before, they failed with "No usable dielectric slabs".
@@ -46,10 +52,6 @@ https://github.com/VolkerMuehlhaus/setupEM
 
 **Touchstone files with different port impedances:** the option line of the combined `.sNp` file now has one Z0 per port, in port order. Before, ports with the same Z0 as port 1 were left out.
 
-# What's New - October 17, 2026
-
-**Conductor model** replaces **Conductor meshing** on the Mesh and Boundaries tab (Palace only), with a third choice: **Surface impedance** (default, as before), **Solve inside (volume mesh)** and the new **Solve inside + skin layers**, which adds thin layers along the conductor faces for accurate Q and loss at high frequency. Generated model scripts now use `settings['conductor_model']` instead of `settings['filled_metals']`. Older projects and model scripts with `filled_metals` still load. setupEM now requires gds2palace 0.9.0 or later; `pip install --upgrade setupEM` updates it.
-
 Full history: [CHANGES.md](https://github.com/VolkerMuehlhaus/setupEM/blob/main/doc/CHANGES.md)
 
 ---
@@ -57,7 +59,7 @@ Full history: [CHANGES.md](https://github.com/VolkerMuehlhaus/setupEM/blob/main/
 **Note:** the `setupEM` PyPI package itself requires:
 
 - gds2palace>=0.9.0
-- gds_prepare_for_EM>=1.3.0
+- gds_prepare_for_EM>=1.6.0
 - PySide6
 - shiboken6
 - scipy

{setupem-0.14.1 → setupem-0.14.2}/README_pypi.md

@@ -11,6 +11,12 @@ https://github.com/VolkerMuehlhaus/setupEM
 
 ## Recent changes
 
+# What's New - October 21, 2026
+
+**Tools > Simplify GDS:** the simplification code moved to gds_prepare_for_EM (module `gds_simplify_for_em`), where the gds2palace MCP server uses it too. setupEM now requires gds_prepare_for_EM 1.6.0 or later; `pip install --upgrade setupEM` updates it.
+
+Fix: with **Merge via arrays** (and no fill removal or merging per layer), the simplified file still contained the original subcells as extra top-level cells. Without a cell name, gds2palace reads the first top-level cell, which could be one of them, e.g. a pad cell instead of the design. These left-over cells are now removed.
+
 # What's New - October 19, 2026
 
 **Stackup Editor, ADS Momentum (*.ltd) import:** metals with an EXPAND thickness operation now make the dielectric next to them thicker, as in ADS, instead of reaching into the dielectric below. Before, a thick EXPAND DOWN metal (e.g. MET1/MET2 in a GaAs stackup) overlapped the layers underneath it, and a via could end up with zero height. Files where long lines are wrapped or END_... markers follow the last entry on the same line now import too; before, they failed with "No usable dielectric slabs".
@@ -19,10 +25,6 @@ https://github.com/VolkerMuehlhaus/setupEM
 
 **Touchstone files with different port impedances:** the option line of the combined `.sNp` file now has one Z0 per port, in port order. Before, ports with the same Z0 as port 1 were left out.
 
-# What's New - October 17, 2026
-
-**Conductor model** replaces **Conductor meshing** on the Mesh and Boundaries tab (Palace only), with a third choice: **Surface impedance** (default, as before), **Solve inside (volume mesh)** and the new **Solve inside + skin layers**, which adds thin layers along the conductor faces for accurate Q and loss at high frequency. Generated model scripts now use `settings['conductor_model']` instead of `settings['filled_metals']`. Older projects and model scripts with `filled_metals` still load. setupEM now requires gds2palace 0.9.0 or later; `pip install --upgrade setupEM` updates it.
-
 Full history: [CHANGES.md](https://github.com/VolkerMuehlhaus/setupEM/blob/main/doc/CHANGES.md)
 
 ---
@@ -30,7 +32,7 @@ Full history: [CHANGES.md](https://github.com/VolkerMuehlhaus/setupEM/blob/main/
 **Note:** the `setupEM` PyPI package itself requires:
 
 - gds2palace>=0.9.0
-- gds_prepare_for_EM>=1.3.0
+- gds_prepare_for_EM>=1.6.0
 - PySide6
 - shiboken6
 - scipy

{setupem-0.14.1 → setupem-0.14.2}/pyproject.toml

@@ -13,7 +13,7 @@ authors = [
 ]
 dependencies = [
     "gds2palace>=0.9.0",
-    "gds_prepare_for_EM>=1.3.0",
+    "gds_prepare_for_EM>=1.6.0",
     "PySide6",
     "shiboken6",
     "scipy",

{setupem-0.14.1 → setupem-0.14.2}/src/setupEM/__init__.py

@@ -24,4 +24,4 @@ A Python tool for EM setup using gds2palace.
 from .setupEM import main
 
 __all__ = ["main"]
-__version__ = "0.14.1"
+__version__ = "0.14.2"

{setupem-0.14.1 → setupem-0.14.2}/src/setupEM/gds_hierarchy_scan.py

@@ -30,69 +30,16 @@ cell/reference tree directly instead, recursing into referenced cells
 without expanding them, so cost scales with the (small) number of distinct
 cells rather than the (potentially huge) number of instantiated copies.
 
+open_gds_cell() and estimate_polygon_count() live in gds_prepare_for_EM's
+gds_simplify_for_em module (shared with the gds2palace MCP server) and are
+re-exported here, so callers keep using gds_hierarchy_scan.<name>.
+
 No PySide6/setup_common/layout_preview dependency here - keeps this a leaf
 module importable from both without any circular-import concern (setup_common.py
 and layout_preview.py already need a deferred import between each other).
 """
 
-import gdspy
-
-
-def open_gds_cell(gds_path, cellname):
-    """Open gds_path and resolve the target cell: cellname if given and
-    found, else the file's first top-level cell. Shared first step for
-    every walker below. Raises on a bad file or a library with no top-level
-    cell, same as gdspy itself would - callers already wrap their own call
-    sites in a broad try/except.
-    """
-    library = gdspy.GdsLibrary(infile=gds_path)
-    top_level = library.top_level()
-    if not top_level:
-        raise ValueError(f"no top-level cell in {gds_path}")
-    cell = library.cells.get(cellname, top_level[0])
-    return library, cell
-
-
-def estimate_polygon_count(gds_path, cellname, layernumbers, purposelist):
-    """Fast pre-check of how many polygons a full read_gds()-based load
-    would end up processing, without flattening the GDS hierarchy. Walks
-    the cell/reference tree directly: a plain CellReference contributes its
-    referenced cell's own (memoized) count once, a CellArray contributes it
-    columns*rows times - the same arithmetic flatten() would otherwise do
-    by actually generating that many polygon objects. Returns None if the
-    file can't even be opened here (the real read_gds() call is expected to
-    surface that error properly instead).
-    """
-    try:
-        library, cell = open_gds_cell(gds_path, cellname)
-    except Exception:
-        return None
-
-    layernumbers = set(int(n) for n in layernumbers)
-    purposeset = set(int(p) for p in purposelist) if purposelist else None
-
-    memo = {}
-
-    def count(c):
-        if c.name in memo:
-            return memo[c.name]
-        total = 0
-        for polygonset in c.polygons:
-            for layer, datatype in zip(polygonset.layers, polygonset.datatypes):
-                if int(layer) in layernumbers and (purposeset is None or int(datatype) in purposeset):
-                    total += 1
-        for ref in c.references:
-            ref_cell = ref.ref_cell
-            if isinstance(ref_cell, str):
-                ref_cell = library.cells.get(ref_cell)
-            if ref_cell is None:
-                continue
-            sub = count(ref_cell)
-            total += sub * ref.columns * ref.rows if isinstance(ref, gdspy.CellArray) else sub
-        memo[c.name] = total
-        return total
-
-    return count(cell)
+from gds_simplify_for_em import open_gds_cell, estimate_polygon_count  # noqa: F401 (re-export)
 
 
 def layers_present_in_range(gds_path, cellname, layer_min, layer_max, purposelist):

{setupem-0.14.1 → setupem-0.14.2}/src/setupEM/setup_common.py

@@ -4912,8 +4912,8 @@ class MainWindowBase(QMainWindow):
         self.layout_preview_window.show()
 
     def open_simplify_gds(self):
-        # local import: simplify_gds.py imports gds_prepare_for_EM lazily
-        # inside run_simplify() too, but import the dialog module itself here
+        # local import: gds_simplify_for_em.run_simplify() imports gds_prepare_for_EM
+        # lazily, but import the dialog module itself here
         # (not at module load time) for the same circular-import reason as
         # open_stackup_editor()/open_layout_preview() above
         if __package__ in (None, ""):

{setupem-0.14.1 → setupem-0.14.2}/src/setupEM/simplify_gds.py

@@ -21,19 +21,18 @@ simplify_gds.py
 
 Tools > Simplify GDS... : removes floating (unconnected) metal fill, fills
 in small cutouts and/or merges via arrays on the currently loaded GDS file,
-writing the result to a new GDS file. All operations come from
-gds_prepare_for_EM (a sibling package, already an editable install in this
-venv) and are called in-process - no subprocess/CLI involved.
+writing the result to a new GDS file. The pipeline itself is
+gds_prepare_for_EM's gds_simplify_for_em.run_simplify() (shared with the
+gds2palace MCP server), called in-process - no subprocess/CLI involved.
 
 No technology-specific layer numbers are hardcoded here: the metal layers to
 process, the via layers and the metal layers above/below each via are derived
 entirely from the XML stackup already parsed into MainWindow.metals_list
-(gds2palace's stackup_reader), same as every other setupEM feature that needs
-to know "which GDS layers are metal".
+(gds2palace's stackup_reader), with gds_simplify_for_em.layers_from_stackup().
 """
 
-import os, io, contextlib, traceback, tempfile
-import gdspy
+import os, io, contextlib, traceback
+from gds_simplify_for_em import run_simplify, layers_from_stackup
 from PySide6.QtWidgets import (
     QDialog, QVBoxLayout, QHBoxLayout, QGroupBox, QLabel, QLineEdit,
     QPushButton, QPlainTextEdit, QFileDialog, QMessageBox, QCheckBox,
@@ -112,138 +111,6 @@ def _parse_layer_list(text):
                           f"comma-separated list of layer numbers: {text!r}")
 
 
-def _flatten_cell(lib, cellname):
-    """Return (lib, top_cell) with top_cell flattened in place. Round-trips
-    through a temporary GDS file first: gdspy's flatten()/get_polygonsets()
-    hits an internal bug on some in-memory-only reference structures ('tuple'
-    object does not support item assignment) that only a GDS write+read
-    cycle avoids - same workaround gds_prepare_for_EM.py's own CLI pipeline
-    uses before every flatten() call in its main()."""
-    with tempfile.TemporaryDirectory(prefix="setupEM_simplify_") as tmp_dir:
-        tmp_path = os.path.join(tmp_dir, "pre_flatten.gds")
-        lib.write_gds(tmp_path)
-        lib = gdspy.GdsLibrary(infile=tmp_path)
-    top_cell = lib.cells.get(cellname, lib.top_level()[0])
-    top_cell.flatten()
-    return lib, top_cell
-
-
-def run_simplify(gds_path, metal_layers, output_path, cellname="",
-                  do_cutouts=False, max_hole_area=None,
-                  do_floating=False, fill_minsize=1.0, fill_maxsize=None, fill_mincount=20,
-                  do_merge=False, via_layers=None, via_merge_size=0):
-    """Load gds_path, optionally fill small cutouts, remove floating metal
-    fill, and/or merge (boolean OR) polygons per layer as a final pass, on
-    the given metal_layers, write the result to output_path. Mirrors the
-    step order gds_prepare_for_EM.py's own main() uses: cutout removal first
-    (works on the hierarchical design), floating-fill removal after that
-    (needs a flattened, per-layer-merged cell first so that touching fill
-    tiles aren't mistaken for isolated ones - see
-    find_isolated_same_size_polygons_by_layer()'s own docstring), per-layer
-    merge, then via array merging.
-
-    via_layers: list of (via layer, metal layers above, metal layers below),
-    GDS layer numbers. Vias closer than via_merge_size (microns) are merged
-    if they connect the same metal shapes above and below, see
-    gds_prepare_for_EM.merge_via_array_by_metal_overlap(). Vias without metal
-    above or below are kept unchanged. None or via_merge_size <= 0: no via
-    merging.
-    """
-    from gds_prepare_for_EM import (
-        remove_cutout_keep_hierarchy,
-        merge_polygons_by_layer,
-        find_isolated_same_size_polygons_by_layer,
-        merge_polygons,
-        merge_via_array_by_metal_overlap,
-    )
-    from gds_geometry_utils import validate_and_repair_polygons
-
-    # merge_polygons_by_layer()/find_isolated_same_size_polygons_by_layer()
-    # create cells via the bare gdspy.Cell(...) constructor, which
-    # auto-registers each one into gdspy's persistent global
-    # gdspy.current_library - harmless for the CLI (a fresh process every
-    # run) but in this long-running GUI, a second Run on the same file
-    # would reuse the same cell names and gdspy raises "already present in
-    # library". Starting from a fresh current_library each call clears that
-    # accumulated state without touching gds_prepare_for_EM itself.
-    gdspy.current_library = gdspy.GdsLibrary()
-
-    lib = gdspy.GdsLibrary()
-    lib.read_gds(gds_path)
-    top_cell = lib.cells.get(cellname, lib.top_level()[0])
-
-    if do_cutouts:
-        design_bbox = top_cell.get_bounding_box()
-        lib = remove_cutout_keep_hierarchy(lib, metal_layers, design_bbox=design_bbox,
-                                            max_hole_area=max_hole_area)
-        top_cell = lib.cells.get(cellname, lib.top_level()[0])
-
-    # floating-fill removal already ends with a flattened, per-layer-merged
-    # cell (it needs that itself, to tell a floating fill cluster apart from
-    # touching real metal) - so a separate final merge pass is only extra
-    # work when floating-fill removal did NOT already run
-    already_merged_flat = False
-
-    if do_floating:
-        lib, top_cell = _flatten_cell(lib, cellname)
-        merged_lib = merge_polygons_by_layer(top_cell, layers_list=metal_layers)
-        merged_top = merged_lib.top_level()[0]
-        lib = find_isolated_same_size_polygons_by_layer(
-            merged_top, metal_layers,
-            minsize=fill_minsize, maxsize=fill_maxsize, mincount=fill_mincount)
-        already_merged_flat = True
-
-    if do_merge and not already_merged_flat:
-        lib, top_cell = _flatten_cell(lib, cellname)
-        lib = merge_polygons_by_layer(top_cell, layers_list=metal_layers)
-
-    if via_layers and via_merge_size > 0:
-        lib, top_cell = _flatten_cell(lib, cellname)
-        lpp = top_cell.get_polygons(by_spec=True)
-        print(f'Via array merging (distance {via_merge_size} um):')
-
-        def metal_polygons(layers):
-            polygons = [p for (layer, purpose), polys in lpp.items() if layer in layers for p in polys]
-            # touching metal pieces are one metal shape for via grouping
-            return merge_polygons(polygons) if polygons else []
-
-        for via_layer, above_layers, below_layers in via_layers:
-            purposes = [purpose for (layer, purpose) in lpp if layer == via_layer]
-            if not purposes:
-                continue
-            above, below = metal_polygons(above_layers), metal_polygons(below_layers)
-            for purpose in purposes:
-                vias = lpp[(via_layer, purpose)]
-                merged = merge_via_array_by_metal_overlap(
-                    vias, above, below, via_merge_size, keep_unmatched=True)
-                top_cell.remove_polygons(
-                    lambda pts, layer, datatype: layer == via_layer and datatype == purpose)
-                for pts in merged:
-                    top_cell.add(gdspy.Polygon(pts, layer=via_layer, datatype=purpose))
-                print(f'  layer {via_layer}:{purpose}: {len(vias)} -> {len(merged)} polygons')
-
-    # Final polygon validity check/repair - always runs, regardless of which
-    # operations above were selected. Catches any polygon still geometrically
-    # invalid (self-intersecting) no matter the reason - e.g. a cutout
-    # deliberately left alone by remove_cutout_keep_hierarchy() for being
-    # larger than max_hole_area, or a merge step re-introducing an invalid
-    # "bridge" hole encoding while fusing polygons back together. A
-    # solid-body mesher like gds2palace cannot handle this even though
-    # gdspy/GDSII themselves tolerate it.
-    repaired_count, unresolved = validate_and_repair_polygons(lib, metal_layers)
-    if repaired_count:
-        print(f'Final validity check: repaired {repaired_count} invalid polygon(s)')
-    if unresolved:
-        print(f'Final validity check: WARNING - {len(unresolved)} polygon(s) could not be '
-              f'auto-repaired, still geometrically invalid in the output file:')
-        for cell_name, n, layer, reason in unresolved:
-            print(f'  {cell_name} polygon #{n} layer {layer}: {reason}')
-    if not repaired_count and not unresolved:
-        print('Final validity check: no invalid polygons found')
-
-    lib.write_gds(output_path)
-
-
 class SimplifyGdsDialog(QDialog):
     """Own top-level window (WA_DeleteOnClose, non-modal), same lifecycle as
     LayoutPreviewWindow/StackupEditorWindow."""
@@ -266,18 +133,10 @@ class SimplifyGdsDialog(QDialog):
         app_name = self.MainWindow.APP_NAME
         port_layer_min, port_layer_max = _port_layer_range(app_name)
         metals_list = self.MainWindow.metals_list
-        self._metal_layers = sorted(
-            int(m.layernum) for m in metals_list.getallplanarmetals()
-            if not (port_layer_min <= int(m.layernum) <= port_layer_max)
-        ) if metals_list is not None else []
-        # via layers with the metal layers above/below them, for via array merging
-        self._via_layers = [
-            (int(m.layernum),
-             [int(n.layernum) for n in m.above if n.is_metal],
-             [int(n.layernum) for n in m.below if n.is_metal])
-            for m in metals_list.metals
-            if m.is_via and not (port_layer_min <= int(m.layernum) <= port_layer_max)
-        ] if metals_list is not None else []
+        # metal layers to process, and via layers with the metal layers above/below them
+        # for via array merging
+        self._metal_layers, self._via_layers = layers_from_stackup(
+            metals_list, (port_layer_min, port_layer_max)) if metals_list is not None else ([], [])
 
         layout = QVBoxLayout(self)
 

{setupem-0.14.1 → setupem-0.14.2/src/setupEM.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: setupEM
-Version: 0.14.1
+Version: 0.14.2
 Summary: Python tool for configuration of gds2palace workflow with GUI.
 Author-email: Volker Muehlhaus <volker@muehlhaus.com>
 License-Expression: GPL-3.0-or-later
@@ -11,7 +11,7 @@ Requires-Python: >=3.9
 Description-Content-Type: text/markdown
 License-File: LICENSE
 Requires-Dist: gds2palace>=0.9.0
-Requires-Dist: gds_prepare_for_EM>=1.3.0
+Requires-Dist: gds_prepare_for_EM>=1.6.0
 Requires-Dist: PySide6
 Requires-Dist: shiboken6
 Requires-Dist: scipy
@@ -38,6 +38,12 @@ https://github.com/VolkerMuehlhaus/setupEM
 
 ## Recent changes
 
+# What's New - October 21, 2026
+
+**Tools > Simplify GDS:** the simplification code moved to gds_prepare_for_EM (module `gds_simplify_for_em`), where the gds2palace MCP server uses it too. setupEM now requires gds_prepare_for_EM 1.6.0 or later; `pip install --upgrade setupEM` updates it.
+
+Fix: with **Merge via arrays** (and no fill removal or merging per layer), the simplified file still contained the original subcells as extra top-level cells. Without a cell name, gds2palace reads the first top-level cell, which could be one of them, e.g. a pad cell instead of the design. These left-over cells are now removed.
+
 # What's New - October 19, 2026
 
 **Stackup Editor, ADS Momentum (*.ltd) import:** metals with an EXPAND thickness operation now make the dielectric next to them thicker, as in ADS, instead of reaching into the dielectric below. Before, a thick EXPAND DOWN metal (e.g. MET1/MET2 in a GaAs stackup) overlapped the layers underneath it, and a via could end up with zero height. Files where long lines are wrapped or END_... markers follow the last entry on the same line now import too; before, they failed with "No usable dielectric slabs".
@@ -46,10 +52,6 @@ https://github.com/VolkerMuehlhaus/setupEM
 
 **Touchstone files with different port impedances:** the option line of the combined `.sNp` file now has one Z0 per port, in port order. Before, ports with the same Z0 as port 1 were left out.
 
-# What's New - October 17, 2026
-
-**Conductor model** replaces **Conductor meshing** on the Mesh and Boundaries tab (Palace only), with a third choice: **Surface impedance** (default, as before), **Solve inside (volume mesh)** and the new **Solve inside + skin layers**, which adds thin layers along the conductor faces for accurate Q and loss at high frequency. Generated model scripts now use `settings['conductor_model']` instead of `settings['filled_metals']`. Older projects and model scripts with `filled_metals` still load. setupEM now requires gds2palace 0.9.0 or later; `pip install --upgrade setupEM` updates it.
-
 Full history: [CHANGES.md](https://github.com/VolkerMuehlhaus/setupEM/blob/main/doc/CHANGES.md)
 
 ---
@@ -57,7 +59,7 @@ Full history: [CHANGES.md](https://github.com/VolkerMuehlhaus/setupEM/blob/main/
 **Note:** the `setupEM` PyPI package itself requires:
 
 - gds2palace>=0.9.0
-- gds_prepare_for_EM>=1.3.0
+- gds_prepare_for_EM>=1.6.0
 - PySide6
 - shiboken6
 - scipy

{setupem-0.14.1 → setupem-0.14.2}/src/setupEM.egg-info/requires.txt

@@ -1,5 +1,5 @@
 gds2palace>=0.9.0
-gds_prepare_for_EM>=1.3.0
+gds_prepare_for_EM>=1.6.0
 PySide6
 shiboken6
 scipy