From 50e0665c3464da31a37082ebd801c6db055e6e59 Mon Sep 17 00:00:00 2001
From: Joaquin Matres <4514346+joamatab@users.noreply.github.com>
Date: Tue, 1 Jul 2025 04:14:15 +0200
Subject: [PATCH] update to gdsfactory9

---
 piel/analysis/metrics/metadata.py                  | 4 ++--
 piel/types/digital.py                              | 4 ++--
 piel/types/digital_electro_optic.py                | 2 +-
 pyproject.toml                                     | 8 ++++----
 tests/analysis/metrics/test_units.py               | 2 +-
 tests/analysis/signals/time/core/test_dimension.py | 4 ++--
 tests/analysis/signals/time/core/test_transiton.py | 8 ++++----
 tests/integration/signal/frequency/test_convert.py | 2 ++
 tests/tools/amaranth/test_construct.py             | 2 ++
 tests/tools/amaranth/test_export.py                | 2 ++
 tests/tools/amaranth/test_verify.py                | 2 ++
 tests/tools/skrf/test_convert.py                   | 2 ++
 tests/types/test_type_conversion.py                | 2 ++
 13 files changed, 28 insertions(+), 16 deletions(-)

diff --git a/piel/analysis/metrics/metadata.py b/piel/analysis/metrics/metadata.py
index 17bac932..a04aa7c4 100644
--- a/piel/analysis/metrics/metadata.py
+++ b/piel/analysis/metrics/metadata.py
@@ -26,8 +26,8 @@ def rename_metrics_collection(
     # Create a new list of metrics with updated names
     updated_metrics = []
     for metric, new_name in zip(collection.metrics, new_names):
-        updated_metric = metric.copy(update={"name": new_name})
+        updated_metric = metric.model_copy(update={"name": new_name})
         updated_metrics.append(updated_metric)
 
     # Return a new ScalarMetricCollection with the updated metrics
-    return collection.copy(update={"metrics": updated_metrics})
+    return collection.model_copy(update={"metrics": updated_metrics})
diff --git a/piel/types/digital.py b/piel/types/digital.py
index c0cbdafd..453f9cae 100644
--- a/piel/types/digital.py
+++ b/piel/types/digital.py
@@ -103,7 +103,7 @@ def dataframe(self) -> pd.DataFrame:
         """
         data = {
             k: v
-            for k, v in self.dict().items()
+            for k, v in self.model_dump().items()
             if k not in {"input_ports", "output_ports"}
         }
         return pd.DataFrame(data)
@@ -117,7 +117,7 @@ def implementation_dictionary(self) -> dict:
             dict: A dictionary with keys that are part of the input and output connection.
         """
         selected_ports = set(self.input_ports + self.output_ports)
-        filtered_dict = {k: v for k, v in self.dict().items() if k in selected_ports}
+        filtered_dict = {k: v for k, v in self.model_dump().items() if k in selected_ports}
         return filtered_dict
 
 
diff --git a/piel/types/digital_electro_optic.py b/piel/types/digital_electro_optic.py
index 2d90a422..0b1cd05a 100644
--- a/piel/types/digital_electro_optic.py
+++ b/piel/types/digital_electro_optic.py
@@ -46,7 +46,7 @@ def dataframe(self) -> pd.DataFrame:
         Returns:
             pd.DataFrame: A DataFrame containing the bits and their corresponding phases.
         """
-        return pd.DataFrame(self.dict())
+        return pd.DataFrame(self.model_dump())
 
 
 """
diff --git a/pyproject.toml b/pyproject.toml
index 122a0b54..46428613 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -28,19 +28,19 @@ jaxlib = ">=0.4.14,<0.5.0"
 jaxtyping = "*"
 matplotlib = "*"
 networkx = ">=3.1,<4.0"
-numpy = ">=1.24.4,<2.0.0"
+numpy = "==2.2"
 pandas = ">=1.5.3,<2.0.0"
 pydantic = ">=2.0,<3.0"
 scipy = ">=1.11.4,<2.0.0"
 setuptools = "*"
-xarray = ">=2024.1.0,<2024.10.0"
+xarray = "==2025.1.2"
 
 # TOOLS
 amaranth = { version = ">=0.4.0,<0.5.0", optional = true }
 amaranth-yosys = { version = ">=0.40.0.0.post94,<0.41.0", optional = true }
 cocotb = { version = "==1.9.1", optional = true }
-gdsfactory = { version = "==7.27.2", optional = true }
-gplugins = { version = ">=0.14.0,<0.15.0", extras = ["schematic"], optional = true }
+gdsfactory = { version = ">=9.3.5", optional = true }
+gplugins = { version = ">=1.4.0", extras = ["schematic"], optional = true }
 hdl21 = { version = ">=6.0.0,<7.0.0", optional = true }
 qutip = { version = ">=4.7,<5.0", optional = true }
 sax = { version = "==0.12.2", optional = true }  # Pinned for pydantic <v2 compatibility
diff --git a/tests/analysis/metrics/test_units.py b/tests/analysis/metrics/test_units.py
index 192e4c1c..2f4f503d 100644
--- a/tests/analysis/metrics/test_units.py
+++ b/tests/analysis/metrics/test_units.py
@@ -113,7 +113,7 @@ def test_convert_scalar_metric_unit_incompatible_units():
     # Call function and expect ValueError
     with pytest.raises(
         ValueError,
-        match="Cannot convert from unit 'volt' \(datum: voltage\) to unit 'ampere' \(datum: ampere\). Units are incompatible.",
+        match=r"Cannot convert from unit 'volt' \(datum: voltage\) to unit 'ampere' \(datum: ampere\). Units are incompatible.",
     ):
         convert_scalar_metric_unit(metric, target_unit)
 
diff --git a/tests/analysis/signals/time/core/test_dimension.py b/tests/analysis/signals/time/core/test_dimension.py
index 21d7d4d9..269f69d7 100644
--- a/tests/analysis/signals/time/core/test_dimension.py
+++ b/tests/analysis/signals/time/core/test_dimension.py
@@ -57,7 +57,7 @@ def create_scalar_metric(
         standard_deviation=std_dev,
         count=count,
         unit=unit,
-    ).copy(update={"name": name})
+    ).model_copy(update={"name": name})
 
 
 # Helper function to create ScalarMetricCollection
@@ -108,7 +108,7 @@ def test_rename_metrics_collection_length_mismatch():
 
     new_names = ["New Metric1", "Extra Metric"]
 
-    with pytest.raises(ValueError, match="Number of new names \(2\) does not match"):
+    with pytest.raises(ValueError, match=r"Number of new names \(2\) does not match"):
         rename_metrics_collection(collection, new_names)
 
 
diff --git a/tests/analysis/signals/time/core/test_transiton.py b/tests/analysis/signals/time/core/test_transiton.py
index e7c1bab7..f7f34b86 100644
--- a/tests/analysis/signals/time/core/test_transiton.py
+++ b/tests/analysis/signals/time/core/test_transiton.py
@@ -86,7 +86,7 @@ def test_offset_time_signals_empty_time_s():
     multi_signal = [signal]
 
     with pytest.raises(
-        ValueError, match="Signal 'EmptySignal' has an empty time_s array\."
+        ValueError, match=r"Signal 'EmptySignal' has an empty time_s array\."
     ):
         offset_time_signals(multi_signal)
 
@@ -329,7 +329,7 @@ def test_extract_rising_edges_empty_data():
     )
 
     with pytest.raises(
-        ValueError, match="time_s and data must be of the same length\."
+        ValueError, match=r"time_s and data must be of the same length\."
     ):
         extract_rising_edges(
             signal, lower_threshold_ratio=0.1, upper_threshold_ratio=0.9
@@ -571,7 +571,7 @@ def test_extract_rising_edges_mismatched_time_data_lengths():
     )
 
     with pytest.raises(
-        ValueError, match="time_s and data must be of the same length\."
+        ValueError, match=r"time_s and data must be of the same length\."
     ):
         extract_rising_edges(
             signal, lower_threshold_ratio=0.1, upper_threshold_ratio=0.9
@@ -623,7 +623,7 @@ def test_extract_rising_edges_signal_with_no_data():
     )
 
     with pytest.raises(
-        ValueError, match="time_s and data must be of the same length\."
+        ValueError, match=r"time_s and data must be of the same length\."
     ):
         extract_rising_edges(
             signal, lower_threshold_ratio=0.1, upper_threshold_ratio=0.9
diff --git a/tests/integration/signal/frequency/test_convert.py b/tests/integration/signal/frequency/test_convert.py
index 1b26d3fa..933dc6f1 100644
--- a/tests/integration/signal/frequency/test_convert.py
+++ b/tests/integration/signal/frequency/test_convert.py
@@ -1,6 +1,8 @@
 # test_network_conversion.py
 
 import pytest
+
+pytest.importorskip("skrf")
 import skrf
 import numpy as np
 
diff --git a/tests/tools/amaranth/test_construct.py b/tests/tools/amaranth/test_construct.py
index af6e80f9..ccde9d97 100644
--- a/tests/tools/amaranth/test_construct.py
+++ b/tests/tools/amaranth/test_construct.py
@@ -1,4 +1,6 @@
 import pytest
+
+pytest.importorskip("amaranth")
 import amaranth as am
 from piel.tools.amaranth import (
     construct_amaranth_module_from_truth_table,
diff --git a/tests/tools/amaranth/test_export.py b/tests/tools/amaranth/test_export.py
index 9557ffd4..67597579 100644
--- a/tests/tools/amaranth/test_export.py
+++ b/tests/tools/amaranth/test_export.py
@@ -1,4 +1,6 @@
 import pytest
+
+pytest.importorskip("amaranth")
 import amaranth as am
 from piel.tools.amaranth import generate_verilog_from_amaranth_truth_table
 from piel.types import TruthTable
diff --git a/tests/tools/amaranth/test_verify.py b/tests/tools/amaranth/test_verify.py
index 6fc7f37a..43a9bbb9 100644
--- a/tests/tools/amaranth/test_verify.py
+++ b/tests/tools/amaranth/test_verify.py
@@ -1,4 +1,6 @@
 import pytest
+
+pytest.importorskip("amaranth")
 import amaranth as am
 from piel.tools.amaranth import verify_amaranth_truth_table
 from piel.types import TruthTable  # Adjust the import based on your actual module path
diff --git a/tests/tools/skrf/test_convert.py b/tests/tools/skrf/test_convert.py
index 9a09d3c8..0782b120 100644
--- a/tests/tools/skrf/test_convert.py
+++ b/tests/tools/skrf/test_convert.py
@@ -1,5 +1,7 @@
 import pytest
 import numpy as np
+
+pytest.importorskip("skrf")
 import skrf as rf
 
 # Import the function to be tested
diff --git a/tests/types/test_type_conversion.py b/tests/types/test_type_conversion.py
index 8dea5341..ed8b9ec4 100644
--- a/tests/types/test_type_conversion.py
+++ b/tests/types/test_type_conversion.py
@@ -2,6 +2,8 @@
 import numpy as np
 import jax.numpy as jnp
 import pandas as pd
+
+pytest.importorskip("qutip")
 import qutip
 
 import piel.types