From 0afa8f960e9bb478832fdb0f07537f5ef75fb84c Mon Sep 17 00:00:00 2001
From: Helge Gehring <42973196+HelgeGehring@users.noreply.github.com>
Date: Thu, 5 Sep 2024 01:32:28 -0700
Subject: [PATCH 01/20] update poetry

---
 .github/workflows/build.yml | 2 +-
 .github/workflows/docs.yml  | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml
index 51f4e30b..75b1ca3f 100644
--- a/.github/workflows/build.yml
+++ b/.github/workflows/build.yml
@@ -62,7 +62,7 @@ jobs:
       - name: Install Poetry
         uses: snok/install-poetry@v1
         with:
-          version: 1.3.2
+          version: 1.8.3
           virtualenvs-create: false
           installer-parallel: true
       - name: Install dependencies
diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml
index 33805c7d..2671a74c 100644
--- a/.github/workflows/docs.yml
+++ b/.github/workflows/docs.yml
@@ -32,7 +32,7 @@ jobs:
       - name: Install Poetry
         uses: snok/install-poetry@v1
         with:
-          version: 1.8.1
+          version: 1.8.3
           virtualenvs-create: false
           installer-parallel: true
       - name: Install dependencies

From 7011a198d085322b7195fa3516f4e1e19344cdcb Mon Sep 17 00:00:00 2001
From: Helge Gehring <42973196+HelgeGehring@users.noreply.github.com>
Date: Thu, 5 Sep 2024 01:36:47 -0700
Subject: [PATCH 02/20] use setuptools as build backend

---
 pyproject.toml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/pyproject.toml b/pyproject.toml
index 6c6de116..6074ed52 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,6 +1,6 @@
 [build-system]
-requires = ["poetry-core>=1.6.0"]
-build-backend = "poetry.core.masonry.api"
+requires = ['setuptools>=74.0.0']
+build-backend = 'setuptools.build_meta'
 
 [tool.poetry]
 name = "femwell"

From cc457b99d4cd6cbc9d4fb3b4c36e471ca15791d9 Mon Sep 17 00:00:00 2001
From: Helge Gehring <42973196+HelgeGehring@users.noreply.github.com>
Date: Thu, 5 Sep 2024 01:50:39 -0700
Subject: [PATCH 03/20] accept older setuptools version

---
 pyproject.toml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index 6074ed52..9d209bf1 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,5 +1,5 @@
 [build-system]
-requires = ['setuptools>=74.0.0']
+requires = ['setuptools>=73.0.0']
 build-backend = 'setuptools.build_meta'
 
 [tool.poetry]

From 554d2745c57c59a1396bd9a550c819d7ef00a53d Mon Sep 17 00:00:00 2001
From: Helge Gehring <42973196+HelgeGehring@users.noreply.github.com>
Date: Thu, 5 Sep 2024 02:16:49 -0700
Subject: [PATCH 04/20] try without poetry install-parallel

---
 .github/workflows/docs.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml
index 2671a74c..4df40996 100644
--- a/.github/workflows/docs.yml
+++ b/.github/workflows/docs.yml
@@ -34,7 +34,7 @@ jobs:
         with:
           version: 1.8.3
           virtualenvs-create: false
-          installer-parallel: true
+          installer-parallel: false
       - name: Install dependencies
         run: |
           sudo apt-get install -y libglu1-mesa xvfb

From 97ce853bea2d714fdb6e73b6bf9ab350852c1b84 Mon Sep 17 00:00:00 2001
From: Helge Gehring <42973196+HelgeGehring@users.noreply.github.com>
Date: Thu, 3 Oct 2024 01:27:22 -0700
Subject: [PATCH 05/20] try older python version

---
 .github/workflows/build.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml
index 75b1ca3f..991d8d7b 100644
--- a/.github/workflows/build.yml
+++ b/.github/workflows/build.yml
@@ -55,7 +55,7 @@ jobs:
             miniforge-version: latest
             activate-environment: env
             use-mamba: true
-            python-version: "3.12"
+            python-version: "3.11"
       - name: Add conda to system path
         run: |
           echo $CONDA/bin >> $GITHUB_PATH

From 37b39f2ca78d2e4fc617d0c4dc5f484cec9498ab Mon Sep 17 00:00:00 2001
From: Helge Gehring <42973196+HelgeGehring@users.noreply.github.com>
Date: Thu, 3 Oct 2024 01:36:30 -0700
Subject: [PATCH 06/20] try uv

---
 .github/workflows/build.yml | 19 +++++++++----------
 1 file changed, 9 insertions(+), 10 deletions(-)

diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml
index 991d8d7b..dae1c859 100644
--- a/.github/workflows/build.yml
+++ b/.github/workflows/build.yml
@@ -59,18 +59,17 @@ jobs:
       - name: Add conda to system path
         run: |
           echo $CONDA/bin >> $GITHUB_PATH
-      - name: Install Poetry
-        uses: snok/install-poetry@v1
-        with:
-          version: 1.8.3
-          virtualenvs-create: false
-          installer-parallel: true
+      - name: Install uv
+        uses: astral-sh/setup-uv@v3
       - name: Install dependencies
+        env:
+          UV_SYSTEM_PYTHON: 1
         run: |
           sudo apt-get install -y libglu1-mesa
-          pip install git+https://github.com/kinnala/scikit-fem.git
-          poetry install --no-interaction --no-root
-          mamba install slepc4py=*=complex* -y
+          mamba install slepc4py=*=complex* uv -y
+          uv pip install -r requirements.txt
       - name: Build package
+        env:
+          UV_SYSTEM_PYTHON: 1
         run: |
-          poetry build
+          uv build

From da99af56591b840c620007262e624f4cb7d6f679 Mon Sep 17 00:00:00 2001
From: Helge Gehring <42973196+HelgeGehring@users.noreply.github.com>
Date: Thu, 3 Oct 2024 01:38:31 -0700
Subject: [PATCH 07/20] try python 3.11

---
 .github/workflows/docs.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml
index 4df40996..6dfbcce2 100644
--- a/.github/workflows/docs.yml
+++ b/.github/workflows/docs.yml
@@ -25,7 +25,7 @@ jobs:
             miniforge-version: latest
             activate-environment: env
             use-mamba: true
-            python-version: "3.12"
+            python-version: "3.11"
       - name: Add conda to system path
         run: |
           echo $CONDA/bin >> $GITHUB_PATH

From 40f0422cff812e34c85cecbf7bf6090d2f50a0dc Mon Sep 17 00:00:00 2001
From: Helge Gehring <42973196+HelgeGehring@users.noreply.github.com>
Date: Thu, 3 Oct 2024 01:41:20 -0700
Subject: [PATCH 08/20] use uv instead of poetry in docs

---
 .github/workflows/docs.yml | 17 ++++++++++-------
 1 file changed, 10 insertions(+), 7 deletions(-)

diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml
index 6dfbcce2..080463fc 100644
--- a/.github/workflows/docs.yml
+++ b/.github/workflows/docs.yml
@@ -25,7 +25,7 @@ jobs:
             miniforge-version: latest
             activate-environment: env
             use-mamba: true
-            python-version: "3.11"
+            python-version: "3.12"
       - name: Add conda to system path
         run: |
           echo $CONDA/bin >> $GITHUB_PATH
@@ -35,17 +35,20 @@ jobs:
           version: 1.8.3
           virtualenvs-create: false
           installer-parallel: false
+      - name: Install uv
+        uses: astral-sh/setup-uv@v3
       - name: Install dependencies
+        env:
+          UV_SYSTEM_PYTHON: 1
         run: |
           sudo apt-get install -y libglu1-mesa xvfb
-          poetry install --no-interaction
-          pip install --upgrade scipy
           mamba install slepc4py=*=complex* -y
           mamba install julia
-          pip install jupyter-book
-          pip install --upgrade jupytext
-          pip install gdsfactory gplugins
-          pip list
+          uv pip install .
+          uv pip install jupyter-book
+          uv pip install --upgrade jupytext
+          uv pip install gdsfactory gplugins
+          uv pip list
       
       - uses: julia-actions/setup-julia@v2
         with:

From 79fef8c41f9896a7df398842cea2a45733c0bb65 Mon Sep 17 00:00:00 2001
From: Helge Gehring <42973196+HelgeGehring@users.noreply.github.com>
Date: Thu, 3 Oct 2024 01:50:43 -0700
Subject: [PATCH 09/20] adjust for uv

---
 .pre-commit-config.yaml |  5 -----
 pyproject.toml          | 46 +++++++++++++++++++++--------------------
 2 files changed, 24 insertions(+), 27 deletions(-)

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 9aa65670..54141c37 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -15,11 +15,6 @@ repos:
     hooks:
       - id: black
 
-  - repo: https://github.com/python-poetry/poetry
-    rev: 1.8.0
-    hooks:
-      - id: poetry-check
-
   - repo: "https://github.com/domluna/JuliaFormatter.jl"
     rev: "v1.0.54"
     hooks:
diff --git a/pyproject.toml b/pyproject.toml
index 9d209bf1..a81755d5 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -2,7 +2,7 @@
 requires = ['setuptools>=73.0.0']
 build-backend = 'setuptools.build_meta'
 
-[tool.poetry]
+[project]
 name = "femwell"
 version = "0.0.1"
 authors = ["Helge Gehring"]
@@ -23,30 +23,32 @@ classifiers = [
 license = "GPLv3"
 readme = "README.md"
 
-[tool.poetry.urls]
-Documentation = "https://HelgeGehring.github.io/femwell/"
+dependencies = [
+    "python >=3.8",
+    "scikit-fem >=8.1.0",
+    "gmsh = 4.13.1",
+    "pygmsh",
+    "matplotlib",
+    "meshwell>=1.0.2"
+]
 
-[tool.poetry.dependencies]
-python = ">=3.8"
-scikit-fem = ">=8.1.0"
-gmsh = "4.13.1"
-pygmsh = "*"
-matplotlib = "*"
-meshwell = ">=1.0.2"
+[project.optional-dependencies]
+test = [
+    "pytest",
+    "flake8"
+]
 
-[tool.poetry.group.test.dependencies]
-pytest = "*"
-flake8 = "*"
+[project.urls]
+Documentation = "https://HelgeGehring.github.io/femwell/"
 
-[tool.poetry.group.docs.dependencies]
-python = ">=3.10"
-tqdm = "*"
-enlighten = "*"
-pint = ">0.20.1"
-# sphinx-book-theme = "*"
-jupytext = "*"
-# myst-parser = "*"
-pandas = "*"
+docs = [
+    "tqdm",
+    "enlighten",
+    "pint>0.20.1",
+    "sphinx-book-theme",
+    "jupytext",
+    "pandas"
+]
 
 [tool.black]
 line-length = 100

From 7a56f1049f80d94773811ed15cf15dae18aa7cb1 Mon Sep 17 00:00:00 2001
From: Helge Gehring <42973196+HelgeGehring@users.noreply.github.com>
Date: Thu, 3 Oct 2024 01:51:49 -0700
Subject: [PATCH 10/20] don't install poetry in docs workflow

---
 .github/workflows/docs.yml | 6 ------
 1 file changed, 6 deletions(-)

diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml
index 080463fc..19ddccab 100644
--- a/.github/workflows/docs.yml
+++ b/.github/workflows/docs.yml
@@ -29,12 +29,6 @@ jobs:
       - name: Add conda to system path
         run: |
           echo $CONDA/bin >> $GITHUB_PATH
-      - name: Install Poetry
-        uses: snok/install-poetry@v1
-        with:
-          version: 1.8.3
-          virtualenvs-create: false
-          installer-parallel: false
       - name: Install uv
         uses: astral-sh/setup-uv@v3
       - name: Install dependencies

From fefbb01fd9d90cde092e982ecc7b1177a1d87e8e Mon Sep 17 00:00:00 2001
From: Helge Gehring <42973196+HelgeGehring@users.noreply.github.com>
Date: Thu, 3 Oct 2024 01:53:29 -0700
Subject: [PATCH 11/20] fix pyproject.toml

---
 pyproject.toml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index a81755d5..5aa8f70b 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -20,7 +20,7 @@ classifiers = [
     "Programming Language :: Python :: 3",
     "Topic :: Scientific/Engineering"
 ]
-license = "GPLv3"
+license = {file = "LICENSE"}
 readme = "README.md"
 
 dependencies = [

From 9e3d53edc96d8340d1ce94c87e54165f236ad34f Mon Sep 17 00:00:00 2001
From: Helge Gehring <42973196+HelgeGehring@users.noreply.github.com>
Date: Thu, 3 Oct 2024 01:55:23 -0700
Subject: [PATCH 12/20] fix pyproject.toml

---
 pyproject.toml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index 5aa8f70b..3c8204f8 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -5,7 +5,7 @@ build-backend = 'setuptools.build_meta'
 [project]
 name = "femwell"
 version = "0.0.1"
-authors = ["Helge Gehring"]
+authors = [{name="Helge Gehring"}]
 description = "Mode solver for photonic and electric waveguides based on FEM"
 homepage = "https://github.com/HelgeGehring/femwell"
 keywords = [

From 092cbd553e201add62ede90dd69b4414f6c5a32a Mon Sep 17 00:00:00 2001
From: Helge Gehring <42973196+HelgeGehring@users.noreply.github.com>
Date: Thu, 3 Oct 2024 01:57:56 -0700
Subject: [PATCH 13/20] fix pyproject.toml

---
 pyproject.toml | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/pyproject.toml b/pyproject.toml
index 3c8204f8..919e5fdd 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -38,9 +38,6 @@ test = [
     "flake8"
 ]
 
-[project.urls]
-Documentation = "https://HelgeGehring.github.io/femwell/"
-
 docs = [
     "tqdm",
     "enlighten",
@@ -50,5 +47,8 @@ docs = [
     "pandas"
 ]
 
+[project.urls]
+Documentation = "https://HelgeGehring.github.io/femwell/"
+
 [tool.black]
 line-length = 100

From fa9b3883dd73ebaf18a9a022e7d2ef8cf8e5b0a5 Mon Sep 17 00:00:00 2001
From: Helge Gehring <42973196+HelgeGehring@users.noreply.github.com>
Date: Thu, 3 Oct 2024 01:59:53 -0700
Subject: [PATCH 14/20] fix pyproject.toml

---
 pyproject.toml | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/pyproject.toml b/pyproject.toml
index 919e5fdd..e4f4b8ea 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -24,9 +24,9 @@ license = {file = "LICENSE"}
 readme = "README.md"
 
 dependencies = [
-    "python >=3.8",
-    "scikit-fem >=8.1.0",
-    "gmsh = 4.13.1",
+    "python>=3.8",
+    "scikit-fem>=8.1.0",
+    "gmsh>=4.13.1",
     "pygmsh",
     "matplotlib",
     "meshwell>=1.0.2"

From cc3456fc479bab463ef94a0361f0d5c57d35adc8 Mon Sep 17 00:00:00 2001
From: Helge Gehring <42973196+HelgeGehring@users.noreply.github.com>
Date: Thu, 3 Oct 2024 02:02:14 -0700
Subject: [PATCH 15/20] fix pyproject.toml

---
 pyproject.toml | 1 -
 1 file changed, 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index e4f4b8ea..bee303ea 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -24,7 +24,6 @@ license = {file = "LICENSE"}
 readme = "README.md"
 
 dependencies = [
-    "python>=3.8",
     "scikit-fem>=8.1.0",
     "gmsh>=4.13.1",
     "pygmsh",

From 33f764aaa996f9ddc0374ac63257de5e51a1710c Mon Sep 17 00:00:00 2001
From: Helge Gehring <42973196+HelgeGehring@users.noreply.github.com>
Date: Thu, 3 Oct 2024 02:03:56 -0700
Subject: [PATCH 16/20] fix pyproject.toml

---
 pyproject.toml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index bee303ea..670a7a3f 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -7,7 +7,6 @@ name = "femwell"
 version = "0.0.1"
 authors = [{name="Helge Gehring"}]
 description = "Mode solver for photonic and electric waveguides based on FEM"
-homepage = "https://github.com/HelgeGehring/femwell"
 keywords = [
     "integrated photonics",
     "silicon photonics",
@@ -47,6 +46,7 @@ docs = [
 ]
 
 [project.urls]
+Homepage = "https://github.com/HelgeGehring/femwell"
 Documentation = "https://HelgeGehring.github.io/femwell/"
 
 [tool.black]

From 716c2f3123d4380a5937bc6a9ae9541dca06b921 Mon Sep 17 00:00:00 2001
From: Helge Gehring <42973196+HelgeGehring@users.noreply.github.com>
Date: Thu, 3 Oct 2024 02:32:07 -0700
Subject: [PATCH 17/20] add GridapODEs

---
 Project.toml           | 1 +
 src/Thermal/Thermal.jl | 2 ++
 2 files changed, 3 insertions(+)

diff --git a/Project.toml b/Project.toml
index 2016bdc2..f95d9d19 100644
--- a/Project.toml
+++ b/Project.toml
@@ -10,6 +10,7 @@ GLMakie = "e9467ef8-e4e7-5192-8a1a-b1aee30e663a"
 Gridap = "56d4f2e9-7ea1-5844-9cf6-b9c51ca7ce8e"
 GridapGmsh = "3025c34a-b394-11e9-2a55-3fee550c04c8"
 GridapMakie = "41f30b06-6382-4b60-a5f7-79d86b35bf5d"
+GridapODEs = "55e38337-5b6e-4c7c-9cfc-e00dd49102e6"
 GridapPETSc = "bcdc36c2-0c3e-11ea-095a-c9dadae499f1"
 IJulia = "7073ff75-c697-5162-941a-fcdaad2a7d2a"
 JuliaFormatter = "98e50ef6-434e-11e9-1051-2b60c6c9e899"
diff --git a/src/Thermal/Thermal.jl b/src/Thermal/Thermal.jl
index 7eee9e4c..4686ebd2 100644
--- a/src/Thermal/Thermal.jl
+++ b/src/Thermal/Thermal.jl
@@ -2,6 +2,8 @@ module Thermal
 
 using Gridap
 using Gridap.Algebra
+using GridapODEs.ODETools
+using GridapODEs.TransientFETools
 
 export calculate_temperature, temperature, calculate_temperature_transient, heat_flux
 

From 898722bb1398212095512c7202d7346d57c85ce5 Mon Sep 17 00:00:00 2001
From: Helge Gehring <42973196+HelgeGehring@users.noreply.github.com>
Date: Thu, 3 Oct 2024 02:48:05 -0700
Subject: [PATCH 18/20] fix location of python package

---
 pyproject.toml | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/pyproject.toml b/pyproject.toml
index 670a7a3f..124a99bd 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -45,6 +45,10 @@ docs = [
     "pandas"
 ]
 
+[tool.setuptools.packages.find]
+where = ["."]
+include = ["femwell*]
+
 [project.urls]
 Homepage = "https://github.com/HelgeGehring/femwell"
 Documentation = "https://HelgeGehring.github.io/femwell/"

From fffec9cd814e6a8278019c4556870e42ab054a17 Mon Sep 17 00:00:00 2001
From: Helge Gehring <42973196+HelgeGehring@users.noreply.github.com>
Date: Thu, 3 Oct 2024 02:51:16 -0700
Subject: [PATCH 19/20] fix pyproject.toml

---
 pyproject.toml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index 124a99bd..f39785c7 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -47,7 +47,7 @@ docs = [
 
 [tool.setuptools.packages.find]
 where = ["."]
-include = ["femwell*]
+include = ["femwell*"]
 
 [project.urls]
 Homepage = "https://github.com/HelgeGehring/femwell"

From 4cd998bb95de6f1ed3483ad798650922b6e71677 Mon Sep 17 00:00:00 2001
From: Helge Gehring <42973196+HelgeGehring@users.noreply.github.com>
Date: Thu, 3 Oct 2024 03:11:43 -0700
Subject: [PATCH 20/20] fix build.yml

---
 .github/workflows/build.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml
index dae1c859..959d81a0 100644
--- a/.github/workflows/build.yml
+++ b/.github/workflows/build.yml
@@ -67,7 +67,7 @@ jobs:
         run: |
           sudo apt-get install -y libglu1-mesa
           mamba install slepc4py=*=complex* uv -y
-          uv pip install -r requirements.txt
+          uv pip install -r pyproject.toml
       - name: Build package
         env:
           UV_SYSTEM_PYTHON: 1