From 48f45801b474c2789217d045eaacd2c7b61df701 Mon Sep 17 00:00:00 2001
From: orionarcher <orioncohen@gmail.com>
Date: Tue, 20 Jan 2026 15:31:01 -0500
Subject: [PATCH 01/31] ignore build folder

---
 .gitignore | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/.gitignore b/.gitignore
index 86adcd8..c77ceb1 100644
--- a/.gitignore
+++ b/.gitignore
@@ -11,4 +11,5 @@
 meta_production_sample.pkl
 development/**/*.csv
 development/**/*.mol2
-pymol_renders/
\ No newline at end of file
+pymol_renders/
+build/
\ No newline at end of file

From 71b96dad101c46d6e64d77a270617826b2ba9eca Mon Sep 17 00:00:00 2001
From: orionarcher <orioncohen@gmail.com>
Date: Tue, 20 Jan 2026 15:31:14 -0500
Subject: [PATCH 02/31] new CI yml files

---
 .github/workflows/test-tutorials.yml | 108 +++++++++++++++++++++++++++
 .github/workflows/test.yml           |  53 +++++++++++++
 .github/workflows/unittests.yml      |  37 ---------
 3 files changed, 161 insertions(+), 37 deletions(-)
 create mode 100644 .github/workflows/test-tutorials.yml
 create mode 100644 .github/workflows/test.yml
 delete mode 100644 .github/workflows/unittests.yml

diff --git a/.github/workflows/test-tutorials.yml b/.github/workflows/test-tutorials.yml
new file mode 100644
index 0000000..74d585e
--- /dev/null
+++ b/.github/workflows/test-tutorials.yml
@@ -0,0 +1,108 @@
+name: Tutorial Tests
+
+on:
+  push:
+    branches: [main]
+  pull_request:
+    branches: [main]
+
+jobs:
+  tutorials:
+    runs-on: ubuntu-latest
+    timeout-minutes: 60
+    defaults:
+      run:
+        shell: bash -el {0}
+
+    steps:
+      - name: Check out repo
+        uses: actions/checkout@v5
+
+      - name: Setup micromamba
+        uses: mamba-org/setup-micromamba@v2
+        with:
+          micromamba-version: 'latest'
+          environment-name: tutorial-env
+          create-args: >-
+            python=3.12
+            xtb
+            ase
+            numpy
+            openbabel
+            scipy
+            numba
+            py3Dmol
+            pandas
+            crest
+            pynauty
+            tqdm
+            mendeleev
+            tblite-python
+            jupytext
+            matplotlib
+            pytorch
+          init-shell: bash
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@v5
+        with:
+          version: "latest"
+
+      - name: Install package and mace-torch
+        run: |
+          uv pip install --no-deps -e .
+          uv pip install mace-torch
+
+      - name: Convert notebooks to Python scripts
+        run: |
+          cd documentation/tutorials
+          for notebook in *.ipynb; do
+            jupytext --to py:percent "$notebook"
+          done
+
+      - name: Run tutorials
+        run: |
+          cd documentation/tutorials
+
+          # Tutorials to skip
+          SKIP_TUTORIALS=(
+            "10-Conformer_Searching.py"      # CREST sampling takes 6+ minutes
+            "12-Using_View_Structures.py"    # Visualization-focused, pymol renders
+          )
+
+          # Mock view_structures to avoid py3Dmol rendering issues
+          cat > mock_view.py << 'EOF'
+          import architector.visualization as viz
+          _original = viz.view_structures
+          def mock_view_structures(*args, **kwargs):
+              return None
+          viz.view_structures = mock_view_structures
+          import architector
+          architector.view_structures = mock_view_structures
+          EOF
+
+          # Run each tutorial
+          for script in *.py; do
+            skip=false
+            for skip_tutorial in "${SKIP_TUTORIALS[@]}"; do
+              if [[ "$script" == "$skip_tutorial" ]]; then
+                skip=true
+                echo "Skipping $script"
+                break
+              fi
+            done
+
+            if [[ "$skip" == "false" && "$script" != "mock_view.py" ]]; then
+              echo "Running $script..."
+              timeout 600 python -c "
+          import mock_view
+          exec(open('$script').read())
+          "
+            fi
+          done
+      - name: Cleanup
+        run: |
+          rm -rf documentation/tutorials/pymol_renders
+          rm -f documentation/tutorials/*.xyz
+          rm -f documentation/tutorials/*.py
+        if: always()
diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
new file mode 100644
index 0000000..2f4ea6c
--- /dev/null
+++ b/.github/workflows/test.yml
@@ -0,0 +1,53 @@
+name: Tests
+
+on:
+  push:
+    branches: [main]
+  pull_request:
+    branches: [main]
+
+jobs:
+  test:
+    runs-on: ubuntu-latest
+    defaults:
+      run:
+        shell: bash -el {0}
+
+    steps:
+      - name: Check out repo
+        uses: actions/checkout@v5
+
+      - name: Setup micromamba
+        uses: mamba-org/setup-micromamba@v2
+        with:
+          micromamba-version: 'latest'
+          environment-name: test-env
+          create-args: >-
+            python=3.12
+            xtb
+            ase
+            numpy
+            openbabel
+            scipy
+            numba
+            py3Dmol
+            pandas
+            crest
+            pynauty
+            tqdm
+            mendeleev
+            tblite-python
+          init-shell: bash
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@v5
+        with:
+          version: "latest"
+
+      - name: Install package
+        run: |
+          uv pip install --no-deps -e .
+
+      - name: Run tests
+        run: |
+          python -m unittest discover tests
diff --git a/.github/workflows/unittests.yml b/.github/workflows/unittests.yml
deleted file mode 100644
index f9617a9..0000000
--- a/.github/workflows/unittests.yml
+++ /dev/null
@@ -1,37 +0,0 @@
-# This workflow will install Python dependencies, run tests and lint with a variety of Python versions
-# For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions
-
-name: Python package
-
-on:
-  push:
-    branches: [ main ]
-  pull_request:
-    branches: [ main ]
-
-jobs:
-  build:
-
-    runs-on: ubuntu-latest
-    strategy:
-      matrix:
-        python-version: ['3.8', '3.9', '3.10']
-
-    steps:
-    - uses: actions/checkout@v2
-    - uses: conda-incubator/setup-miniconda@v2.2.0
-      with:
-        python-version: ${{ matrix.python-version }}
-        mamba-version: "*"
-        channels: conda-forge
-        channel-priority: strict
-        auto-update-conda: true  
-        environment-file: .ci_support/environment.yml
-        miniforge-variant: Mambaforge
-    - name: Setup
-      shell: bash -l {0}
-      run: |
-        pip install --no-deps .
-    - name: Test
-      shell: bash -l {0}
-      run: python -m unittest discover tests

From eff0f2cefbe0e0deb160b10c10ecd6cac56afcac Mon Sep 17 00:00:00 2001
From: orionarcher <orioncohen@gmail.com>
Date: Tue, 20 Jan 2026 16:04:43 -0500
Subject: [PATCH 03/31] run tutorials in parallel

---
 .github/workflows/test-tutorials.yml | 84 +++++++++++++++++-----------
 1 file changed, 51 insertions(+), 33 deletions(-)

diff --git a/.github/workflows/test-tutorials.yml b/.github/workflows/test-tutorials.yml
index 74d585e..d327d13 100644
--- a/.github/workflows/test-tutorials.yml
+++ b/.github/workflows/test-tutorials.yml
@@ -7,9 +7,48 @@ on:
     branches: [main]
 
 jobs:
-  tutorials:
+  find-tutorials:
     runs-on: ubuntu-latest
-    timeout-minutes: 60
+    outputs:
+      tutorials: ${{ steps.set-matrix.outputs.tutorials }}
+    steps:
+      - name: Check out repo
+        uses: actions/checkout@v5
+
+      - name: Find tutorial notebooks
+        id: set-matrix
+        run: |
+          # Tutorials to skip
+          SKIP_TUTORIALS=(
+            "10-Conformer_Searching.ipynb"   # CREST sampling takes 6+ minutes
+            "12-Using_View_Structures.ipynb" # Visualization-focused, pymol renders
+          )
+
+          # Find all notebooks and filter out skipped ones
+          TUTORIALS=$(find documentation/tutorials -name "*.ipynb" | while read notebook; do
+            basename=$(basename "$notebook")
+            skip=false
+            for skip_tutorial in "${SKIP_TUTORIALS[@]}"; do
+              if [[ "$basename" == "$skip_tutorial" ]]; then
+                skip=true
+                break
+              fi
+            done
+            if [[ "$skip" == "false" ]]; then
+              echo "$notebook"
+            fi
+          done | jq -R -s -c 'split("\n")[:-1]')
+
+          echo "tutorials=$TUTORIALS" >> $GITHUB_OUTPUT
+
+  run-tutorial:
+    needs: find-tutorials
+    runs-on: ubuntu-latest
+    timeout-minutes: 20
+    strategy:
+      fail-fast: false
+      matrix:
+        tutorial: ${{ fromJson(needs.find-tutorials.outputs.tutorials) }}
     defaults:
       run:
         shell: bash -el {0}
@@ -53,24 +92,16 @@ jobs:
           uv pip install --no-deps -e .
           uv pip install mace-torch
 
-      - name: Convert notebooks to Python scripts
+      - name: Convert notebook to Python script
         run: |
-          cd documentation/tutorials
-          for notebook in *.ipynb; do
-            jupytext --to py:percent "$notebook"
-          done
+          jupytext --to py:percent "${{ matrix.tutorial }}"
 
-      - name: Run tutorials
+      - name: Run tutorial
         run: |
-          cd documentation/tutorials
-
-          # Tutorials to skip
-          SKIP_TUTORIALS=(
-            "10-Conformer_Searching.py"      # CREST sampling takes 6+ minutes
-            "12-Using_View_Structures.py"    # Visualization-focused, pymol renders
-          )
+          cd $(dirname "${{ matrix.tutorial }}")
+          SCRIPT=$(basename "${{ matrix.tutorial }}" .ipynb).py
 
-          # Mock view_structures to avoid py3Dmol rendering issues
+          # Create mock for view_structures to avoid py3Dmol rendering issues
           cat > mock_view.py << 'EOF'
           import architector.visualization as viz
           _original = viz.view_structures
@@ -81,25 +112,12 @@ jobs:
           architector.view_structures = mock_view_structures
           EOF
 
-          # Run each tutorial
-          for script in *.py; do
-            skip=false
-            for skip_tutorial in "${SKIP_TUTORIALS[@]}"; do
-              if [[ "$script" == "$skip_tutorial" ]]; then
-                skip=true
-                echo "Skipping $script"
-                break
-              fi
-            done
-
-            if [[ "$skip" == "false" && "$script" != "mock_view.py" ]]; then
-              echo "Running $script..."
-              timeout 600 python -c "
+          echo "Running $SCRIPT..."
+          timeout 600 python -c "
           import mock_view
-          exec(open('$script').read())
+          exec(open('$SCRIPT').read())
           "
-            fi
-          done
+
       - name: Cleanup
         run: |
           rm -rf documentation/tutorials/pymol_renders

From ac6c5ce4192c3fe4360fc3398cc636edadd8d9c9 Mon Sep 17 00:00:00 2001
From: orionarcher <orioncohen@gmail.com>
Date: Wed, 21 Jan 2026 08:36:34 -0500
Subject: [PATCH 04/31] Add Secondary_Solvation_Shell to CI workflow triggers

---
 .github/workflows/test-tutorials.yml | 4 ++--
 .github/workflows/test.yml           | 4 ++--
 2 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/.github/workflows/test-tutorials.yml b/.github/workflows/test-tutorials.yml
index d327d13..c355f81 100644
--- a/.github/workflows/test-tutorials.yml
+++ b/.github/workflows/test-tutorials.yml
@@ -2,9 +2,9 @@ name: Tutorial Tests
 
 on:
   push:
-    branches: [main]
+    branches: [main, Secondary_Solvation_Shell]
   pull_request:
-    branches: [main]
+    branches: [main, Secondary_Solvation_Shell]
 
 jobs:
   find-tutorials:
diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index 2f4ea6c..e750a65 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -2,9 +2,9 @@ name: Tests
 
 on:
   push:
-    branches: [main]
+    branches: [main, Secondary_Solvation_Shell]
   pull_request:
-    branches: [main]
+    branches: [main, Secondary_Solvation_Shell]
 
 jobs:
   test:

From 9c3fc73dcd646289ae904876a5d974ab2bdb50b4 Mon Sep 17 00:00:00 2001
From: orionarcher <orioncohen@gmail.com>
Date: Wed, 21 Jan 2026 11:04:45 -0500
Subject: [PATCH 05/31] Remove view_structures mock from tutorial tests

---
 .github/workflows/test-tutorials.yml | 16 +---------------
 1 file changed, 1 insertion(+), 15 deletions(-)

diff --git a/.github/workflows/test-tutorials.yml b/.github/workflows/test-tutorials.yml
index c355f81..97c478b 100644
--- a/.github/workflows/test-tutorials.yml
+++ b/.github/workflows/test-tutorials.yml
@@ -101,22 +101,8 @@ jobs:
           cd $(dirname "${{ matrix.tutorial }}")
           SCRIPT=$(basename "${{ matrix.tutorial }}" .ipynb).py
 
-          # Create mock for view_structures to avoid py3Dmol rendering issues
-          cat > mock_view.py << 'EOF'
-          import architector.visualization as viz
-          _original = viz.view_structures
-          def mock_view_structures(*args, **kwargs):
-              return None
-          viz.view_structures = mock_view_structures
-          import architector
-          architector.view_structures = mock_view_structures
-          EOF
-
           echo "Running $SCRIPT..."
-          timeout 600 python -c "
-          import mock_view
-          exec(open('$SCRIPT').read())
-          "
+          timeout 600 python "$SCRIPT"
 
       - name: Cleanup
         run: |

From a9b13e5abb692277e34ceca1e1da075036fe2e6b Mon Sep 17 00:00:00 2001
From: orionarcher <orioncohen@gmail.com>
Date: Wed, 21 Jan 2026 11:38:30 -0500
Subject: [PATCH 06/31] insignificant change to test permissions

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

diff --git a/.github/workflows/test-tutorials.yml b/.github/workflows/test-tutorials.yml
index 97c478b..3c1d6e5 100644
--- a/.github/workflows/test-tutorials.yml
+++ b/.github/workflows/test-tutorials.yml
@@ -101,7 +101,7 @@ jobs:
           cd $(dirname "${{ matrix.tutorial }}")
           SCRIPT=$(basename "${{ matrix.tutorial }}" .ipynb).py
 
-          echo "Running $SCRIPT..."
+          echo "Running $SCRIPT...!"
           timeout 600 python "$SCRIPT"
 
       - name: Cleanup

From 3bf77a183064377894decdee49c33cac0667e90d Mon Sep 17 00:00:00 2001
From: orionarcher <orioncohen@gmail.com>
Date: Wed, 21 Jan 2026 11:44:08 -0500
Subject: [PATCH 07/31] Add XTB verification step to tutorial tests

---
 .github/workflows/test-tutorials.yml | 14 ++++++++++++++
 1 file changed, 14 insertions(+)

diff --git a/.github/workflows/test-tutorials.yml b/.github/workflows/test-tutorials.yml
index 3c1d6e5..91ebd12 100644
--- a/.github/workflows/test-tutorials.yml
+++ b/.github/workflows/test-tutorials.yml
@@ -92,6 +92,20 @@ jobs:
           uv pip install --no-deps -e .
           uv pip install mace-torch
 
+      - name: Verify XTB is working
+        run: |
+          xtb --version
+          python -c "
+          from architector import build_complex
+          out = build_complex({
+              'core': {'metal': 'Fe', 'coreCN': 6},
+              'ligands': [{'smiles': 'O', 'coordList': [0]}] * 6,
+              'parameters': {'metal_ox': 2}
+          })
+          assert len(out) > 0, 'XTB/build_complex failed - returned empty dict'
+          print('XTB verification passed:', list(out.keys()))
+          "
+
       - name: Convert notebook to Python script
         run: |
           jupytext --to py:percent "${{ matrix.tutorial }}"

From 5e1f3585977b4f36469be1f54d2f257bbae1e1f1 Mon Sep 17 00:00:00 2001
From: orionarcher <orioncohen@gmail.com>
Date: Wed, 21 Jan 2026 11:47:41 -0500
Subject: [PATCH 08/31] Fix: use xtb-python instead of xtb CLI package

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

diff --git a/.github/workflows/test-tutorials.yml b/.github/workflows/test-tutorials.yml
index 91ebd12..329c907 100644
--- a/.github/workflows/test-tutorials.yml
+++ b/.github/workflows/test-tutorials.yml
@@ -64,7 +64,7 @@ jobs:
           environment-name: tutorial-env
           create-args: >-
             python=3.12
-            xtb
+            xtb-python
             ase
             numpy
             openbabel
diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index e750a65..42496f7 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -24,7 +24,7 @@ jobs:
           environment-name: test-env
           create-args: >-
             python=3.12
-            xtb
+            xtb-python
             ase
             numpy
             openbabel

From dde23d5b19d8d44e5125c8bee69bb3dea68acc80 Mon Sep 17 00:00:00 2001
From: orionarcher <orioncohen@gmail.com>
Date: Wed, 21 Jan 2026 11:52:24 -0500
Subject: [PATCH 09/31] Remove XTB verification step

---
 .github/workflows/test-tutorials.yml | 14 --------------
 1 file changed, 14 deletions(-)

diff --git a/.github/workflows/test-tutorials.yml b/.github/workflows/test-tutorials.yml
index 329c907..a0afc92 100644
--- a/.github/workflows/test-tutorials.yml
+++ b/.github/workflows/test-tutorials.yml
@@ -92,20 +92,6 @@ jobs:
           uv pip install --no-deps -e .
           uv pip install mace-torch
 
-      - name: Verify XTB is working
-        run: |
-          xtb --version
-          python -c "
-          from architector import build_complex
-          out = build_complex({
-              'core': {'metal': 'Fe', 'coreCN': 6},
-              'ligands': [{'smiles': 'O', 'coordList': [0]}] * 6,
-              'parameters': {'metal_ox': 2}
-          })
-          assert len(out) > 0, 'XTB/build_complex failed - returned empty dict'
-          print('XTB verification passed:', list(out.keys()))
-          "
-
       - name: Convert notebook to Python script
         run: |
           jupytext --to py:percent "${{ matrix.tutorial }}"

From 6c26ef35fa9c6257e2919877285ff270faedb43e Mon Sep 17 00:00:00 2001
From: orionarcher <orioncohen@gmail.com>
Date: Wed, 21 Jan 2026 11:52:59 -0500
Subject: [PATCH 10/31] Add torch-dftd for MACE dispersion corrections

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

diff --git a/.github/workflows/test-tutorials.yml b/.github/workflows/test-tutorials.yml
index a0afc92..6b971c4 100644
--- a/.github/workflows/test-tutorials.yml
+++ b/.github/workflows/test-tutorials.yml
@@ -90,7 +90,7 @@ jobs:
       - name: Install package and mace-torch
         run: |
           uv pip install --no-deps -e .
-          uv pip install mace-torch
+          uv pip install mace-torch torch-dftd
 
       - name: Convert notebook to Python script
         run: |

From 1764cc63b1eaef101b0e4aa141b8285cfc8a64ee Mon Sep 17 00:00:00 2001
From: Michael Taylor <mgt16@lanl.gov>
Date: Wed, 21 Jan 2026 17:51:41 -0700
Subject: [PATCH 11/31] Update to remove xtb-python

---
 .github/workflows/test-tutorials.yml |   1 -
 .github/workflows/test.yml           |   1 -
 README.md                            |   4 +-
 architector/io_calc.py               |  20 +-
 architector/io_lig.py                |  13 +-
 architector/io_xtb_calc.py           | 609 ---------------------------
 6 files changed, 4 insertions(+), 644 deletions(-)
 delete mode 100644 architector/io_xtb_calc.py

diff --git a/.github/workflows/test-tutorials.yml b/.github/workflows/test-tutorials.yml
index 6b971c4..8627617 100644
--- a/.github/workflows/test-tutorials.yml
+++ b/.github/workflows/test-tutorials.yml
@@ -64,7 +64,6 @@ jobs:
           environment-name: tutorial-env
           create-args: >-
             python=3.12
-            xtb-python
             ase
             numpy
             openbabel
diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index 42496f7..c29906e 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -24,7 +24,6 @@ jobs:
           environment-name: test-env
           create-args: >-
             python=3.12
-            xtb-python
             ase
             numpy
             openbabel
diff --git a/README.md b/README.md
index ffbd993..09778cf 100644
--- a/README.md
+++ b/README.md
@@ -39,8 +39,8 @@ pip install -e .
 
 ## XTB (backend) Potentially Useful References:
 * [Available Solvents](https://xtb-docs.readthedocs.io/en/latest/gbsa.html)
-* [Available Methods](https://xtb-python.readthedocs.io/en/latest/general-api.html)
-* [ASE Calculator](https://xtb-python.readthedocs.io/en/latest/ase-calculator.html)
+* [Available Methods](https://xtb-docs.readthedocs.io/en/latest/commandline.html)
+* [ASE Calculator](https://tblite.readthedocs.io/en/latest/users/ase.html#tblite.ase.TBLite)
 * [XTB Documentation](https://xtb-docs.readthedocs.io/en/latest/contents.html)
 
 ## Basic Use of complex construction functionality:
diff --git a/architector/io_calc.py b/architector/io_calc.py
index 58bd999..590944c 100644
--- a/architector/io_calc.py
+++ b/architector/io_calc.py
@@ -21,15 +21,6 @@
 from ase.optimize import LBFGS
 from ase.constraints import FixAtoms, FixBondLengths, FixInternals
 
-# Add any other ASE calculator here.
-# To extend to other methods.
-has_xtb_python = False
-try:
-    from xtb.ase.calculator import XTB
-    has_xtb_python = True
-except ImportError:
-    pass
-
 from architector.arch_xtb_text_ase_calc import XTB_Calculator
 from tblite.ase import TBLite
 
@@ -455,7 +446,7 @@ def calculate(self):
                         electronic_temperature=self.xtb_electronic_temperature,
                         verbosity=-1,
                     )
-                elif (not has_xtb_python) or (self.xtb_relax):
+                else:
                     calc = XTB_Calculator(
                         xtb_method=self.method,
                         xtb_accuracy=self.xtb_accuracy,
@@ -464,15 +455,6 @@ def calculate(self):
                         xtb_solvent=self.xtb_solvent,
                         xtb_relax=self.xtb_relax,
                     )
-                else:  # legacy xtb-python
-                    calc = XTB(
-                        method=self.method,
-                        solvent=self.xtb_solvent,
-                        max_iterations=self.xtb_max_iterations,
-                        electronic_temperature=self.xtb_electronic_temperature,
-                        accuracy=self.xtb_accuracy,
-                    )
-                    # verbosity=0)
                 # Difference of more than 1. Still perform a ff_preoptimization if requested.
                 if np.abs(self.mol.xtb_charge - self.mol.charge) > 1:
                     if len(self.trans_oxo_triples) > 0:
diff --git a/architector/io_lig.py b/architector/io_lig.py
index b3c6922..e6cbc0e 100644
--- a/architector/io_lig.py
+++ b/architector/io_lig.py
@@ -38,14 +38,6 @@
 from ase.optimize.bfgslinesearch import BFGSLineSearch
 import ase.constraints as ase_con
 
-has_xtb_python = False
-try:
-    from xtb.ase.calculator import XTB
-
-    has_xtb_python = True
-except:
-    pass
-
 from architector.arch_xtb_text_ase_calc import XTB_Calculator
 
 # from tblite.ase import TBLite -> No GFN-FF support yet.
@@ -119,10 +111,7 @@ def set_XTB_calc(ase_atoms):
     """
     ase_atoms.set_initial_charges(np.zeros(len(ase_atoms)))
     ase_atoms.set_initial_magnetic_moments(np.zeros(len(ase_atoms)))
-    if has_xtb_python:
-        calc = XTB(method="GFN-FF")
-    else:
-        calc = XTB_Calculator(xtb_method="GFN-FF")
+    calc = XTB_Calculator(xtb_method="GFN-FF")
     # Default to only GFN-FF for ligand conformer relaxation.
     ase_atoms.calc = calc
     return ase_atoms
diff --git a/architector/io_xtb_calc.py b/architector/io_xtb_calc.py
deleted file mode 100644
index 797a532..0000000
--- a/architector/io_xtb_calc.py
+++ /dev/null
@@ -1,609 +0,0 @@
-# """
-# Assign XTB calculator to ase_atoms object following defualts or user input!
-# Written by Michael Taylor
-
-# This module is largely depricated in architector in favor of io_calc.py
-# It is useful still for xtb evalulations away from architector's main codebase.
-# """
-
-import numpy as np
-from xtb.ase.calculator import XTB
-from architector import arch_context_manage, io_molecule
-import architector.io_ptable as io_ptable
-import ase
-from ase.optimize import BFGSLineSearch
-from ase.atoms import Atom, Atoms
-
-
-def set_XTB_calc(ase_atoms, parameters=dict(), assembly=False, isCp_lig=False):
-    """set_XTB_calc
-    assign xtb calculator to atoms instance!
-
-    Parameters
-    ----------
-    ase_atoms : ase.atoms.Atoms
-        atoms to assign calculator to
-    parameters : dict, optional
-        parameters from input/ io_process_input!
-    assembly : bool, optional
-        whether or not this is assembly or final relaxation, by default False
-    isCP_lig : bool, optional
-        whether this is cP ligand evaluation or not, by default False
-    """
-    if isCp_lig:
-        ase_atoms.set_initial_charges(np.zeros(len(ase_atoms)))
-        ase_atoms.set_initial_magnetic_moments(np.zeros(len(ase_atoms)))
-        calc = XTB(
-            method="GFN-FF"
-        )  # ,verbosity=0) # Defaul to only GFN-FF for ligand conformer relaxation.
-    else:
-        # Charge -> charges already assigned to components during assembly
-        if (parameters["full_charge"] is not None) and (not assembly):
-            charge_vect = np.zeros(len(ase_atoms))
-            charge_vect[0] = parameters["full_charge"]
-            ase_atoms.set_initial_charges(charge_vect)
-        else:
-            charge_vect = ase_atoms.get_initial_charges()
-
-        mol_charge = np.sum(charge_vect)
-        symbols = ase_atoms.get_chemical_symbols()
-        metals = [x for x in symbols if x in io_ptable.all_metals]
-
-        f_in_core = False
-
-        if len(metals) == 1:
-            if metals[0] in io_ptable.heavy_metals:
-                f_in_core = True
-        else:
-            print(
-                "No metals - continuing anyway with obviously no f in core elements."
-            )
-
-        # Handle spin / magnetism
-        even_odd_electrons = (
-            np.sum([atom.number for atom in ase_atoms]) - mol_charge
-        ) % 2
-        if (parameters["full_spin"] is not None) and (not assembly):
-            uhf = parameters["full_spin"]
-            uhf_start = np.zeros(len(ase_atoms))
-            uhf_start[0] = uhf
-            ase_atoms.set_initial_magnetic_moments(uhf_start)
-        else:
-            uhf = parameters[
-                "metal_spin"
-            ]  # Metal spin set by io_process_input to defaults.
-            if (even_odd_electrons == 1) and (uhf == 0):
-                uhf = 1
-            elif (even_odd_electrons == 1) and (uhf < 7) and (uhf % 2 == 0):
-                uhf += 1
-            elif (even_odd_electrons == 1) and (uhf >= 7) and (uhf % 2 == 0):
-                uhf -= 1
-            if (even_odd_electrons == 0) and (uhf % 2 == 1):
-                uhf = uhf - 1
-            elif (even_odd_electrons == 1) and (uhf % 2 == 0):
-                uhf = uhf + 1
-            uhf_start = np.zeros(len(ase_atoms))
-            if not f_in_core:
-                uhf_start[0] = uhf
-            else:  # F in core assumes for a 3+ lanthanide there are 11 valence electrons (8 once the 3+ is taken into account)
-                even_odd_electrons = np.sum(
-                    [atom.number for atom in ase_atoms]
-                )
-                even_odd_electrons = (
-                    even_odd_electrons
-                    - io_ptable.elements.index(metals[0])
-                    + 11
-                    - mol_charge
-                )
-                even_odd_electrons = even_odd_electrons % 2
-                if even_odd_electrons == 0:
-                    uhf_start[0] = 0
-                else:
-                    uhf_start[0] = 1
-            ase_atoms.set_initial_magnetic_moments(uhf_start)
-
-        if assembly:
-            if (
-                parameters["assemble_method"] == "GFN-FF"
-            ):  # Need to turn off charges for GFN-FF evaluation. Probably an XTB-end bug.
-                ase_atoms.set_initial_charges(np.zeros(len(ase_atoms)))
-                ase_atoms.set_initial_magnetic_moments(
-                    np.zeros(len(ase_atoms))
-                )
-            calc = XTB(
-                method=parameters["assemble_method"],
-                solvent=parameters["solvent"],
-            )
-            # verbosity=0)
-        else:
-            if (
-                parameters["full_method"] == "GFN-FF"
-            ):  # Need to turn off charges for GFN-FF evaluation. Probably an XTB-end bug.
-                ase_atoms.set_initial_charges(np.zeros(len(ase_atoms)))
-                ase_atoms.set_initial_magnetic_moments(
-                    np.zeros(len(ase_atoms))
-                )
-            calc = XTB(
-                method=parameters["full_method"], solvent=parameters["solvent"]
-            )
-            #    verbosity=0)
-
-    #########################################################
-    ########### Calculator Now Set! #########################
-    #########################################################
-    ase_atoms.calc = calc
-    return ase_atoms
-
-
-def set_XTB_calc_lig(
-    ase_atoms, charge=None, uhf=None, method="GFN2-xTB", solvent="none"
-):
-    """set_XTB_calc
-    assign xtb calculator to ligand atoms instance!
-
-    Parameters
-    ----------
-    ase_atoms : ase.atoms.Atoms
-        atoms to assign calculator to
-    charge : int, optional
-        charge of the species, default to initial charges set on ase_atoms
-    uhf : int, optional
-        number of unpaired electrons in the system, default to 0
-    method : str, optional
-        which gfn family method to use, default GFN2-xTB
-    solvent: str, optional
-        use a solvent?, default 'none'
-    """
-    if charge:
-        mol_charge = charge
-    else:
-        mol_charge = np.sum(ase_atoms.get_initial_charges())
-
-    charge_vect = np.zeros(len(ase_atoms))
-    charge_vect[0] = mol_charge
-    ase_atoms.set_initial_charges(charge_vect)
-
-    # Handle spin / magnetism
-    even_odd_electrons = (
-        np.sum([atom.number for atom in ase_atoms]) - mol_charge
-    ) % 2
-    if uhf is not None:
-        uhf = uhf
-        if (even_odd_electrons == 1) and (uhf == 0):
-            uhf = 1
-        elif (even_odd_electrons == 1) and (uhf < 7) and (uhf % 2 == 0):
-            uhf += 1
-        elif (even_odd_electrons == 1) and (uhf >= 7) and (uhf % 2 == 0):
-            uhf -= 1
-        if (even_odd_electrons == 0) and (uhf % 2 == 1):
-            uhf = uhf - 1
-        elif (even_odd_electrons == 1) and (uhf % 2 == 0):
-            uhf = uhf + 1
-        uhf_start = np.zeros(len(ase_atoms))
-        uhf_start[0] = uhf
-        ase_atoms.set_initial_magnetic_moments(uhf_start)
-    else:
-        uhf = 0  # Set spin to LS by default
-        if (even_odd_electrons == 1) and (uhf == 0):
-            uhf = 1
-        elif (even_odd_electrons == 1) and (uhf < 7) and (uhf % 2 == 0):
-            uhf += 1
-        elif (even_odd_electrons == 1) and (uhf >= 7) and (uhf % 2 == 0):
-            uhf -= 1
-        if (even_odd_electrons == 0) and (uhf % 2 == 1):
-            uhf = uhf - 1
-        elif (even_odd_electrons == 1) and (uhf % 2 == 0):
-            uhf = uhf + 1
-        uhf_start = np.zeros(len(ase_atoms))
-        uhf_start[0] = uhf
-        ase_atoms.set_initial_magnetic_moments(uhf_start)
-
-    if (
-        method == "GFN-FF"
-    ):  # Need to turn off charges for GFN-FF evaluation. Probably an XTB-end bug.
-        ase_atoms.set_initial_charges(np.zeros(len(ase_atoms)))
-        ase_atoms.set_initial_magnetic_moments(np.zeros(len(ase_atoms)))
-    calc = XTB(method=method, solvent=solvent, verbosity=0)
-
-    #########################################################
-    ########### Calculator Now Set! #########################
-    #########################################################
-    ase_atoms.calc = calc
-
-
-def set_XTB_calc_straight(
-    ase_atoms, charge=None, uhf=None, method="GFN2-xTB", solvent="none"
-):
-    """set_XTB_calc_straight
-    assign xtb calculator atoms object with exaclty spin/charge requeste
-
-    Parameters
-    ----------
-    ase_atoms : ase.atoms.Atoms
-        atoms to assign calculator to
-    charge : int, optional
-        charge of the species, default to initial charges set on ase_atoms
-    uhf : int, optional
-        number of unpaired electrons in the system, default to 0
-    method : str, optional
-        which gfn family method to use, default GFN2-xTB
-    solvent: str, optional
-        use a solvent?, default 'none'
-    """
-    if charge:
-        mol_charge = charge
-    else:
-        mol_charge = np.sum(ase_atoms.get_initial_charges())
-
-    charge_vect = np.zeros(len(ase_atoms))
-    charge_vect[0] = mol_charge
-    ase_atoms.set_initial_charges(charge_vect)
-
-    uhf_start = np.zeros(len(ase_atoms))
-    uhf_start[0] = uhf
-    ase_atoms.set_initial_magnetic_moments(uhf_start)
-
-    if (
-        method == "GFN-FF"
-    ):  # Need to turn off charges for GFN-FF evaluation. Probably an XTB-end bug.
-        ase_atoms.set_initial_charges(np.zeros(len(ase_atoms)))
-        ase_atoms.set_initial_magnetic_moments(np.zeros(len(ase_atoms)))
-    calc = XTB(method=method, solvent=solvent)
-    #    verbosity=0)
-
-    #########################################################
-    ########### Calculator Now Set! #########################
-    #########################################################
-    ase_atoms.calc = calc
-
-
-def xtb_relax(
-    structure,
-    charge=None,
-    uhf=None,
-    method="GFN2-xTB",
-    solvent="none",
-    fmax=0.05,
-    detect_charge_spin=False,
-):
-    """xtb_relax relax the structure with xtb
-
-    Parameters
-    ----------
-    structure : any 3D structure
-       xyz, mol2string, ase atoms ...
-    charge :int, optional
-        total charge on the system, by default None
-    uhf : int, optional
-        number of unpaired electrons in the system, by default None
-    method : str, optional
-        which method to use, by default 'GFN2-xTB'
-    solvent : str, optional
-        any name xtb solvent, by default 'none'
-    fmax : float, optional
-        default 0.05 eV/Angstrom
-    detect_charge_spin : bool, optional
-        Use obmol and io_ptable metal defaults to assign charges and spins?, default False.
-
-    Returns
-    -------
-    ase_atoms : ase.atoms.Atoms
-        relaxed structure
-    good : bool
-        whether the relaxation was succesful!
-    """
-    if isinstance(structure, ase.atoms.Atoms):
-        ase_atoms = structure
-        if ase_atoms.calc is None:
-            set_XTB_calc_straight(
-                ase_atoms,
-                charge=charge,
-                uhf=uhf,
-                method=method,
-                solvent=solvent,
-            )
-    else:
-        mol = io_molecule.convert_io_molecule(
-            structure, detect_charge_spin=detect_charge_spin
-        )
-        ase_atoms = mol.ase_atoms
-        if detect_charge_spin:
-            set_XTB_calc_straight(
-                ase_atoms,
-                charge=mol.charge,
-                uhf=mol.xtb_uhf,
-                method=method,
-                solvent=solvent,
-            )
-        else:
-            set_XTB_calc_straight(
-                ase_atoms,
-                charge=charge,
-                uhf=uhf,
-                method=method,
-                solvent=solvent,
-            )
-    good = True
-    with arch_context_manage.make_temp_directory() as _:
-        try:
-            dyn = BFGSLineSearch(ase_atoms)
-            dyn.run(fmax=fmax)
-        except:
-            good = False
-    return ase_atoms, good
-
-
-def xtb_sp(
-    structure,
-    charge=None,
-    uhf=None,
-    method="GFN2-xTB",
-    solvent="none",
-    detect_charge_spin=False,
-):
-    """xtb_sp singlepoint on the structure with xtb
-
-    Parameters
-    ----------
-    structure : any 3D structure
-       xyz, mol2string, ase atoms ...
-    charge :int, optional
-        total charge on the system, by default None
-    uhf : int, optional
-        number of unpaired electrons in the system, by default None
-    method : str, optional
-        which method to use, by default 'GFN2-xTB'
-    solvent : str, optional
-        any name xtb solvent, by default 'none'
-
-    Returns
-    -------
-    ase_atoms : ase.atoms.Atoms
-        structure with calculator/energy calculated
-    good : bool
-        whether the relaxation was succesful!
-    """
-    if isinstance(structure, ase.atoms.Atoms):
-        ase_atoms = structure
-        if ase_atoms.calc is None:
-            set_XTB_calc_straight(
-                ase_atoms,
-                charge=charge,
-                uhf=uhf,
-                method=method,
-                solvent=solvent,
-            )
-    else:
-        mol = io_molecule.convert_io_molecule(
-            structure, detect_charge_spin=detect_charge_spin
-        )
-        ase_atoms = mol.ase_atoms
-        if detect_charge_spin:
-            set_XTB_calc_straight(
-                ase_atoms,
-                charge=mol.charge,
-                uhf=mol.xtb_uhf,
-                method=method,
-                solvent=solvent,
-            )
-        else:
-            set_XTB_calc_straight(
-                ase_atoms,
-                charge=charge,
-                uhf=uhf,
-                method=method,
-                solvent=solvent,
-            )
-    good = True
-    with arch_context_manage.make_temp_directory() as _:
-        try:
-            ase_atoms.get_total_energy()
-        except:
-            good = False
-    return ase_atoms, good
-
-
-eV2Hartree = 1 / 27.2114
-
-
-def get_rxyz_string(ase_atoms):
-    """dump the ase_atoms to rxyz file string"""
-    natom = len(ase_atoms)
-    ss = ""
-    # write an xyz file first
-    ss += "%d\n\n" % natom
-    for symb, coord in zip(
-        ase_atoms.get_chemical_symbols(), ase_atoms.positions
-    ):
-        ss += "%2s %12.6f %12.6f %12.6f\n" % (symb, *coord[:3])
-    ss += "\n"
-    # then force
-    ss += "FORCES\n"
-    for symb, force in zip(
-        ase_atoms.get_chemical_symbols(), ase_atoms.get_forces()
-    ):
-        ss += "%3s %22.14e %22.14e %22.14e\n" % (symb, *(force * eV2Hartree))
-    ss += "\n"
-    # then pbc, if needed
-    # Potentially usefull - ase_atoms.cell, ase_atoms.get_pbc(), ase_atoms.get_cell_lengths_and_angles(), get_celldisp(), get_cell()
-    # if ase_atoms.cell is not None:
-    #     ss += "PBC\n"
-    #     ss += "%12.6f %12.6f %12.6f\n" % (chemical.pbc.boxhi[0] -
-    #         chemical.pbc.boxlo[0], 0.0, 0.0))
-    #     ss += "%12.6f %12.6f %12.6f\n" % (chemical.pbc.xy,
-    #         chemical.pbc.boxhi[1] - chemical.pbc.boxlo[1], 0.0))
-    #     fp.write("%12.6f %12.6f %12.6f\n" % (chemical.pbc.xz,
-    #                                             chemical.pbc.yz,
-    #                     chemical.pbc.boxhi[2] - chemical.pbc.boxlo[2]))
-    #     fp.write('\n')
-    # then charge and spin
-    ss += "ATOM-CHARGE-SPIN\n"
-    for symb, charge, spin in zip(
-        ase_atoms.get_chemical_symbols(),
-        ase_atoms.get_charges(),
-        ase_atoms.get_initial_magnetic_moments(),
-    ):
-        ss += "%2s %12.6f %12.6f\n" % (symb, charge, spin)
-    ss += "\n"
-    # then different properties
-    ss += "ENERGY %22.14f\n" % (ase_atoms.get_total_energy() * eV2Hartree)
-    ss += "PA_BINDING_ENERGY %22.14f\n" % (
-        ase_atoms.get_total_energy() * eV2Hartree / len(ase_atoms)
-    )
-    dipole_vect = ase_atoms.get_dipole_moment()
-    ss += "DIPOLE_VEC %12.6f %12.6f %12.6f\n" % (
-        dipole_vect[0],
-        dipole_vect[1],
-        dipole_vect[2],
-    )
-    ss += "DIPOLE %12.6f\n" % np.linalg.norm(dipole_vect)
-    ss += "CHARGE %d\n" % ase_atoms.get_initial_charges().sum()
-    ss += "MULTIPLICITY %d\n" % round(
-        sum(ase_atoms.get_initial_magnetic_moments) + 1
-    )
-    # fp.write("DIFFAB %f\n" % sum(result['atomspin']))
-    # fp.write('BAND_GAP %12.6f\n' % (result["egap"] * eV2Hartree))
-    # fp.write('CONVERGED %s\n' % str(result["qconverged"]))
-    # for prop in more_props:
-    #     fp.write('%s %f\n' % (prop.upper(), result[prop]))
-    ss += "SOURCE %s\n" % ase_atoms.get_calculator().name
-    return ss
-
-
-def calc_xtb_ref_dict():
-    energydict = dict()
-    print("--------1---------")
-    for i, elem in enumerate(io_ptable.elements):
-        if i > 0 and i < 87:
-            atoms = Atoms([Atom(elem, (0, 0, 0))])
-            if elem in io_ptable.all_metals:
-                if elem in io_ptable.lanthanides:
-                    spin = 0
-                    charge = 3
-                else:
-                    spin = io_ptable.metal_spin_dict[elem]
-                    charge = io_ptable.metal_charge_dict[elem]
-            else:
-                if i % 2 == 0:
-                    spin = 0
-                else:
-                    spin = 1
-                charge = 0
-            set_XTB_calc_straight(atoms, charge=charge, uhf=spin)
-            try:
-                energy = atoms.get_total_energy()
-                energydict[elem] = energy
-            except:
-                energydict[elem] = None
-    print("--------2---------")
-    for elem, spin in io_ptable.second_choice_metal_spin_dict.items():
-        print(elem)
-        if io_ptable.elements.index(elem) < 87:
-            atoms = Atoms([Atom(elem, (0, 0, 0))])
-            charge = io_ptable.metal_charge_dict[elem]
-            set_XTB_calc_straight(atoms, charge=charge, uhf=spin)
-            try:
-                energy = atoms.get_total_energy()
-            except:
-                energy = None
-            failed = False
-            if (energydict[elem] is None) and isinstance(energy, float):
-                energydict[elem] = energy
-                print("Fixed {} with alternate spin".format(elem))
-            elif (energydict[elem] is None) and (energy is None):
-                failed = True
-                print("{}".format(elem) + " STILL FAILED")
-            if (not failed) and (energy is not None):
-                if energydict[elem] > energy:
-                    energydict[elem] = energy
-                    print("replaced {} with alternate spin".format(elem))
-    print("--------3---------")
-    for elem, spin in io_ptable.metal_spin_dict.items():
-        print(elem)
-        if io_ptable.elements.index(elem) < 87:
-            atoms = Atoms([Atom(elem, (0, 0, 0))])
-            charge = 0
-            if (i % 2 == 0) or (elem not in io_ptable.lanthanides):
-                spin = 0
-            else:
-                spin = 1
-            set_XTB_calc_straight(atoms, charge=charge, uhf=spin)
-            try:
-                energy = atoms.get_total_energy()
-            except:
-                energy = None
-            failed = False
-            if (energydict[elem] is None) and isinstance(energy, float):
-                energydict[elem] = energy
-                print("Fixed {} with 0 charge low spin".format(elem))
-            elif (energydict[elem] is None) and (energy is None):
-                failed = True
-                print("{}".format(elem) + " STILL FAILED")
-            if (not failed) and (energy is not None):
-                if energydict[elem] > (energy):
-                    energydict[elem] = energy
-                    print(
-                        "replaced {} with 0 charge alternate spin".format(elem)
-                    )
-    print("--------4---------")
-    for elem, spin in io_ptable.metal_spin_dict.items():
-        print(elem)
-        if io_ptable.elements.index(elem) < 87:
-            atoms = Atoms([Atom(elem, (0, 0, 0))])
-            charge = 0
-            if (i % 2 == 0) or (elem not in io_ptable.lanthanides):
-                spin = 2
-            else:
-                spin = 3
-            set_XTB_calc_straight(atoms, charge=charge, uhf=spin)
-            try:
-                energy = atoms.get_total_energy()
-            except:
-                energy = None
-            failed = False
-            if (energydict[elem] is None) and isinstance(energy, float):
-                energydict[elem] = energy
-                print("Fixed {} with 0 charge 2 spin".format(elem))
-            elif (energydict[elem] is None) and (energy is None):
-                failed = True
-                print("{}".format(elem) + " STILL FAILED")
-            if (not failed) and (energy is not None):
-                if energydict[elem] > energy:
-                    energydict[elem] = energy
-                    print("replaced {} with 0 charge 2 spin".format(elem))
-    print("--------5---------")
-    for elem, spin in io_ptable.metal_spin_dict.items():
-        print(elem)
-        if io_ptable.elements.index(elem) < 87:
-            atoms = Atoms([Atom(elem, (0, 0, 0))])
-            charge = 0
-            if (i % 2 == 0) or (elem not in io_ptable.lanthanides):
-                spin = 4
-            else:
-                spin = 5
-            set_XTB_calc_straight(atoms, charge=charge, uhf=spin)
-            try:
-                energy = atoms.get_total_energy()
-            except:
-                print("Failed 5 spin", elem)
-                energy = None
-            failed = False
-            if (energydict[elem] is None) and isinstance(energy, float):
-                energydict[elem] = energy
-                print("Fixed {} with 0 charge 4 spin".format(elem))
-            elif (energydict[elem] is None) and (energy is None):
-                failed = True
-                print("{}".format(elem) + " STILL FAILED")
-            if (not failed) and (energy is not None):
-                if energydict[elem] > energy:
-                    energydict[elem] = energy
-                    print("replaced {} with 0 charge 5 spin".format(elem))
-
-    # Fix Mo
-    atoms = Atoms([Atom("Mo", (0, 0, 0))])
-    charge = 0
-    set_XTB_calc_straight(atoms, charge=charge, uhf=6)
-    e = atoms.get_total_energy()
-    energydict["Mo"] = e
-    # energydict_scaled_ha = {sym:val/Hartree for sym,val in energydict.items()}
-    return energydict

From 661d6b553c4ac848d77d1a1fe693c7d8d3a252c6 Mon Sep 17 00:00:00 2001
From: Michael Taylor <mgt16@lanl.gov>
Date: Wed, 21 Jan 2026 18:21:27 -0700
Subject: [PATCH 12/31] Switch to pyproject.toml

---
 pyproject.toml | 34 ++++++++++++++++++++++++++++++++++
 setup.py       | 30 ------------------------------
 2 files changed, 34 insertions(+), 30 deletions(-)
 create mode 100644 pyproject.toml
 delete mode 100644 setup.py

diff --git a/pyproject.toml b/pyproject.toml
new file mode 100644
index 0000000..a681997
--- /dev/null
+++ b/pyproject.toml
@@ -0,0 +1,34 @@
+[build-system]
+requires = ["setuptools>=45", "wheel"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "architector"
+version = "0.1.0"
+description = "The architector python package - for 3D Coordination Complex Design."
+readme = "README.md"
+license = {text = "BSD 3-Clause License"}
+authors = [
+    {name = "Michael G. Taylor et al."}
+]
+classifiers = [
+    "Development Status :: 4 - Beta",
+    "Intended Audience :: Science/Research",
+    "Programming Language :: Python :: 3",
+    "Topic :: Scientific/Engineering :: Chemistry"
+]
+dependencies = [
+    "ase",
+    "numpy",
+    "py3Dmol",
+    "pynauty",
+    "scipy",
+    "pandas",
+    "mendeleev"
+]
+
+[tool.setuptools]
+packages = ["architector"]
+
+[tool.setuptools.package-data]
+"*" = ["data/*.csv"]
diff --git a/setup.py b/setup.py
deleted file mode 100644
index 57af8c6..0000000
--- a/setup.py
+++ /dev/null
@@ -1,30 +0,0 @@
-from setuptools import setup
-
-with open("README.md", "r") as fh:
-    long_description = fh.read()
-
-# 'xtb', # Xtb as install requirement is broken, installs correctly through conda.
-setup(
-    name='architector',
-    version='0.1.0',
-    author='Michael G. Taylor et al.',
-    packages=['architector'],
-    package_data={"": ["data/*.csv"]},
-    install_requires=[
-        'ase',
-        'numpy',
-        'py3Dmol',
-        'pynauty',
-        'scipy',
-        'pandas',
-        'mendeleev'
-    ],
-    license="BSD 3-Clause License",
-    classifiers=["Development Status :: 4 - Beta",
-                 "Intended Audience :: Science/Research",
-                 "Programming Language :: Python :: 3",
-                 "Topic :: Scientific/Engineering :: Chemistry"],
-    description="The architector python package - for 3D Coordination Complex Design.",
-    long_description=long_description,
-    long_description_content_type='text/markdown',
-)

From 764cf0dbb93f2018cb044866f96ed5eda9028ab1 Mon Sep 17 00:00:00 2001
From: Michael Taylor <mgt16@lanl.gov>
Date: Thu, 22 Jan 2026 10:36:42 -0700
Subject: [PATCH 13/31] Attempt XTB version pinning

---
 .ci_support/environment.yml          | 2 +-
 .github/workflows/test-tutorials.yml | 1 +
 .github/workflows/test.yml           | 1 +
 environment.yml                      | 2 +-
 4 files changed, 4 insertions(+), 2 deletions(-)

diff --git a/.ci_support/environment.yml b/.ci_support/environment.yml
index 5c43b6c..04eabf4 100644
--- a/.ci_support/environment.yml
+++ b/.ci_support/environment.yml
@@ -3,7 +3,7 @@ channels:
   - conda-forge
 dependencies:
   - python
-  - xtb
+  - xtb>6.4
   - ase
   - numpy
   - openbabel
diff --git a/.github/workflows/test-tutorials.yml b/.github/workflows/test-tutorials.yml
index 8627617..49ec507 100644
--- a/.github/workflows/test-tutorials.yml
+++ b/.github/workflows/test-tutorials.yml
@@ -73,6 +73,7 @@ jobs:
             pandas
             crest
             pynauty
+            xtb>6.4
             tqdm
             mendeleev
             tblite-python
diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index c29906e..a82b084 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -32,6 +32,7 @@ jobs:
             py3Dmol
             pandas
             crest
+            xtb>6.4
             pynauty
             tqdm
             mendeleev
diff --git a/environment.yml b/environment.yml
index 8d8e532..6f45604 100644
--- a/environment.yml
+++ b/environment.yml
@@ -4,7 +4,7 @@ channels:
 dependencies:
   - python
   - crest
-  - xtb
+  - xtb>6.4
   - ase
   - numpy
   - py3Dmol

From 58ecd1cfc9ccf21ebdbcdd02f10106301a83186d Mon Sep 17 00:00:00 2001
From: Michael Taylor <mgt16@lanl.gov>
Date: Thu, 22 Jan 2026 10:39:56 -0700
Subject: [PATCH 14/31] Attempt 2 xtb bump

---
 .ci_support/environment.yml          | 2 +-
 .github/workflows/test-tutorials.yml | 2 +-
 .github/workflows/test.yml           | 2 +-
 environment.yml                      | 2 +-
 4 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/.ci_support/environment.yml b/.ci_support/environment.yml
index 04eabf4..7b9bbf0 100644
--- a/.ci_support/environment.yml
+++ b/.ci_support/environment.yml
@@ -3,7 +3,7 @@ channels:
   - conda-forge
 dependencies:
   - python
-  - xtb>6.4
+  - xtb>6.5
   - ase
   - numpy
   - openbabel
diff --git a/.github/workflows/test-tutorials.yml b/.github/workflows/test-tutorials.yml
index 49ec507..bd3264a 100644
--- a/.github/workflows/test-tutorials.yml
+++ b/.github/workflows/test-tutorials.yml
@@ -73,7 +73,7 @@ jobs:
             pandas
             crest
             pynauty
-            xtb>6.4
+            xtb>6.5
             tqdm
             mendeleev
             tblite-python
diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index a82b084..15ba68f 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -32,7 +32,7 @@ jobs:
             py3Dmol
             pandas
             crest
-            xtb>6.4
+            xtb>6.5
             pynauty
             tqdm
             mendeleev
diff --git a/environment.yml b/environment.yml
index 6f45604..11cc471 100644
--- a/environment.yml
+++ b/environment.yml
@@ -4,7 +4,7 @@ channels:
 dependencies:
   - python
   - crest
-  - xtb>6.4
+  - xtb>6.5
   - ase
   - numpy
   - py3Dmol

From 3165e714d1a8c834028f991344968f3476bb8288 Mon Sep 17 00:00:00 2001
From: Michael Taylor <mgt16@lanl.gov>
Date: Thu, 22 Jan 2026 11:02:29 -0700
Subject: [PATCH 15/31] Generalize Types for view_structures labels

---
 architector/visualization.py | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/architector/visualization.py b/architector/visualization.py
index 2e25646..ebcda16 100644
--- a/architector/visualization.py
+++ b/architector/visualization.py
@@ -168,10 +168,10 @@ def add_bonds(
         for i, row in bondsdf.iterrows():
             # Allow for multiple different colors of interatomic distances.
             if (row["atom_pair"][0] in visited) and (
-                isinstance(distcolor, (list, np.ndarray))
+                hasattr(distcolor, "__len__")
             ):
                 tcolor = distcolor[visited.index(row["atom_pair"][0])]
-            elif isinstance(distcolor, (list, np.ndarray)):
+            elif hasattr(distcolor, "__len__"):
                 tcolor = distcolor[count]
                 visited.append(row["atom_pair"][0])
                 count += 1
@@ -442,7 +442,7 @@ def view_structures(
                 ]
             else:
                 labels = [str(i) for i in range(len(mols))]
-        elif isinstance(labels, list) or isinstance(labels, np.ndarray):
+        elif hasattr(labels, "__len__"):
             if len(labels) != len(mols):
                 print(
                     "Wrong amount of labels passed, defaulting to chemical formulas."
@@ -742,7 +742,7 @@ def view_structures(
                 label = [x.ase_atoms.get_chemical_formula() for x in mols]
             else:
                 label = []
-        elif isinstance(labels, list) or isinstance(labels, np.ndarray):
+        elif hasattr(labels, "__len__"):
             if len(labels) != len(mols):
                 print(
                     "Wrong amount of labels passed, defaulting to chemical formulas."

From a11d5e735f7cf63f016494543d6d08bd24198cd2 Mon Sep 17 00:00:00 2001
From: Michael Taylor <mgt16@lanl.gov>
Date: Thu, 22 Jan 2026 11:02:41 -0700
Subject: [PATCH 16/31] Fix tutorial 11 plots.

---
 documentation/tutorials/11-Distance_Analysis.ipynb | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/documentation/tutorials/11-Distance_Analysis.ipynb b/documentation/tutorials/11-Distance_Analysis.ipynb
index 957cdff..db8688a 100644
--- a/documentation/tutorials/11-Distance_Analysis.ipynb
+++ b/documentation/tutorials/11-Distance_Analysis.ipynb
@@ -331,8 +331,9 @@
     "import numpy as np\n",
     "g = df.groupby('atom_symbols')['distance']\n",
     "axes = g.plot(kind='hist',bins=np.arange(0.5,7.5,0.5),alpha=0.5,align='left')\n",
-    "for i, (groupname, group) in enumerate(g):\n",
-    "    axes[i].set_label(groupname)\n",
+    "# axes is keyed by group name; iterate key,value\n",
+    "for groupname, ax in axes.items():\n",
+    "    ax.set_label(groupname)\n",
     "plt.legend()\n",
     "plt.xlabel('Interatomic Distance ($\\AA$)')\n",
     "plt.title('Distance Plot')"

From d51d91e06d42277d92116d23f8134bd6fe777acb Mon Sep 17 00:00:00 2001
From: orionarcher <orioncohen@gmail.com>
Date: Thu, 22 Jan 2026 13:33:11 -0500
Subject: [PATCH 17/31] Modernize deploy.yml and pyproject.toml

---
 .github/workflows/deploy.yml | 41 ++++++++++++++++++------------------
 pyproject.toml               | 31 +++++++++++++++++++++------
 2 files changed, 46 insertions(+), 26 deletions(-)

diff --git a/.github/workflows/deploy.yml b/.github/workflows/deploy.yml
index 991cc15..e33b289 100644
--- a/.github/workflows/deploy.yml
+++ b/.github/workflows/deploy.yml
@@ -4,29 +4,30 @@
 name: PyPi Release
 
 on:
-    push:
-    pull_request:
-    workflow_dispatch:
+  push:
+  pull_request:
+  workflow_dispatch:
 
 jobs:
   build:
     runs-on: ubuntu-latest
 
     steps:
-    - uses: actions/checkout@v2
-    - uses: actions/setup-python@v2
-      with:
-        python-version: "3.10"
-
-    - name: Install dependencies
-      run: >-
-        python -m pip install --user --upgrade setuptools wheel
-    - name: Build
-      run: >-
-        python setup.py sdist bdist_wheel
-    - name: Publish distribution 📦 to PyPI
-      if: startsWith(github.event.ref, 'refs/tags') || github.event_name == 'release'
-      uses: pypa/gh-action-pypi-publish@master
-      with:
-        user: __token__
-        password: ${{ secrets.pypi_password }}
+      - uses: actions/checkout@v5
+
+      - uses: actions/setup-python@v5
+        with:
+          python-version: "3.12"
+
+      - name: Install build dependencies
+        run: python -m pip install --upgrade build
+
+      - name: Build package
+        run: python -m build
+
+      - name: Publish distribution to PyPI
+        if: startsWith(github.event.ref, 'refs/tags') || github.event_name == 'release'
+        uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          user: __token__
+          password: ${{ secrets.pypi_password }}
diff --git a/pyproject.toml b/pyproject.toml
index a681997..c88c9f5 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -7,26 +7,45 @@ name = "architector"
 version = "0.1.0"
 description = "The architector python package - for 3D Coordination Complex Design."
 readme = "README.md"
-license = {text = "BSD 3-Clause License"}
-authors = [
-    {name = "Michael G. Taylor et al."}
+license = { file = "LICENSE.txt" }
+authors = [{ name = "Michael G. Taylor et al." }]
+keywords = [
+    "chemistry",
+    "computational-chemistry",
+    "coordination-complexes",
+    "inorganic-chemistry",
+    "molecular-design",
 ]
 classifiers = [
     "Development Status :: 4 - Beta",
     "Intended Audience :: Science/Research",
+    "License :: OSI Approved :: BSD License",
+    "Operating System :: OS Independent",
     "Programming Language :: Python :: 3",
-    "Topic :: Scientific/Engineering :: Chemistry"
+    "Programming Language :: Python :: 3.10",
+    "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.12",
+    "Topic :: Scientific/Engineering :: Chemistry",
 ]
+requires-python = ">=3.10"
 dependencies = [
     "ase",
+    "mendeleev",
     "numpy",
+    "pandas",
     "py3Dmol",
     "pynauty",
     "scipy",
-    "pandas",
-    "mendeleev"
 ]
 
+[project.optional-dependencies]
+mace = ["mace-torch", "torch-dftd"]
+
+[project.urls]
+Homepage = "https://github.com/lanl/Architector"
+Repository = "https://github.com/lanl/Architector"
+Documentation = "https://lanl.github.io/Architector/"
+
 [tool.setuptools]
 packages = ["architector"]
 

From fbf3fe53db656067d1c72b9429810f234ca22e85 Mon Sep 17 00:00:00 2001
From: orionarcher <orioncohen@gmail.com>
Date: Thu, 22 Jan 2026 13:41:57 -0500
Subject: [PATCH 18/31] Minimize conda deps in test.yml, install package deps
 via pip

---
 .github/workflows/test.yml | 13 ++-----------
 pyproject.toml             |  2 ++
 2 files changed, 4 insertions(+), 11 deletions(-)

diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index 15ba68f..a347ec2 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -24,18 +24,9 @@ jobs:
           environment-name: test-env
           create-args: >-
             python=3.12
-            ase
-            numpy
+            xtb>6.5
             openbabel
-            scipy
-            numba
-            py3Dmol
-            pandas
             crest
-            xtb>6.5
-            pynauty
-            tqdm
-            mendeleev
             tblite-python
           init-shell: bash
 
@@ -46,7 +37,7 @@ jobs:
 
       - name: Install package
         run: |
-          uv pip install --no-deps -e .
+          uv pip install -e .
 
       - name: Run tests
         run: |
diff --git a/pyproject.toml b/pyproject.toml
index c88c9f5..efe556f 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -31,11 +31,13 @@ requires-python = ">=3.10"
 dependencies = [
     "ase",
     "mendeleev",
+    "numba",
     "numpy",
     "pandas",
     "py3Dmol",
     "pynauty",
     "scipy",
+    "tqdm",
 ]
 
 [project.optional-dependencies]

From f85fbb3e5b646679f635cb435c607bc3f4bbdc54 Mon Sep 17 00:00:00 2001
From: orionarcher <orioncohen@gmail.com>
Date: Thu, 22 Jan 2026 13:43:39 -0500
Subject: [PATCH 19/31] Minimize conda deps in test-tutorials.yml, add optional
 dependency groups

---
 .github/workflows/test-tutorials.yml | 18 +++---------------
 pyproject.toml                       |  4 +++-
 2 files changed, 6 insertions(+), 16 deletions(-)

diff --git a/.github/workflows/test-tutorials.yml b/.github/workflows/test-tutorials.yml
index bd3264a..6c69a57 100644
--- a/.github/workflows/test-tutorials.yml
+++ b/.github/workflows/test-tutorials.yml
@@ -64,21 +64,10 @@ jobs:
           environment-name: tutorial-env
           create-args: >-
             python=3.12
-            ase
-            numpy
+            xtb>6.5
             openbabel
-            scipy
-            numba
-            py3Dmol
-            pandas
             crest
-            pynauty
-            xtb>6.5
-            tqdm
-            mendeleev
             tblite-python
-            jupytext
-            matplotlib
             pytorch
           init-shell: bash
 
@@ -87,10 +76,9 @@ jobs:
         with:
           version: "latest"
 
-      - name: Install package and mace-torch
+      - name: Install package with optional dependencies
         run: |
-          uv pip install --no-deps -e .
-          uv pip install mace-torch torch-dftd
+          uv pip install -e ".[mace,dftd,tutorials]"
 
       - name: Convert notebook to Python script
         run: |
diff --git a/pyproject.toml b/pyproject.toml
index efe556f..7935f3a 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -41,7 +41,9 @@ dependencies = [
 ]
 
 [project.optional-dependencies]
-mace = ["mace-torch", "torch-dftd"]
+mace = ["mace-torch"]
+dftd = ["torch-dftd"]
+tutorials = ["jupytext", "matplotlib"]
 
 [project.urls]
 Homepage = "https://github.com/lanl/Architector"

From 83360a29e6e62518340267bbe59f3c7ea9474117 Mon Sep 17 00:00:00 2001
From: orionarcher <orioncohen@gmail.com>
Date: Thu, 22 Jan 2026 13:45:22 -0500
Subject: [PATCH 20/31] Remove unnecessary pytorch and tblite-python from
 tutorial conda deps

---
 .github/workflows/test-tutorials.yml | 2 --
 1 file changed, 2 deletions(-)

diff --git a/.github/workflows/test-tutorials.yml b/.github/workflows/test-tutorials.yml
index 6c69a57..4ce43d4 100644
--- a/.github/workflows/test-tutorials.yml
+++ b/.github/workflows/test-tutorials.yml
@@ -67,8 +67,6 @@ jobs:
             xtb>6.5
             openbabel
             crest
-            tblite-python
-            pytorch
           init-shell: bash
 
       - name: Install uv

From d7950c89fe5b8c31ff849a175991b80d296b6121 Mon Sep 17 00:00:00 2001
From: orionarcher <orioncohen@gmail.com>
Date: Thu, 22 Jan 2026 13:46:51 -0500
Subject: [PATCH 21/31] Move tblite to pyproject.toml optional dependency

---
 .github/workflows/test.yml | 3 +--
 pyproject.toml             | 3 ++-
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index a347ec2..de2129c 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -27,7 +27,6 @@ jobs:
             xtb>6.5
             openbabel
             crest
-            tblite-python
           init-shell: bash
 
       - name: Install uv
@@ -37,7 +36,7 @@ jobs:
 
       - name: Install package
         run: |
-          uv pip install -e .
+          uv pip install -e ".[tblite]"
 
       - name: Run tests
         run: |
diff --git a/pyproject.toml b/pyproject.toml
index 7935f3a..ffce340 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -41,8 +41,9 @@ dependencies = [
 ]
 
 [project.optional-dependencies]
-mace = ["mace-torch"]
 dftd = ["torch-dftd"]
+mace = ["mace-torch"]
+tblite = ["tblite"]
 tutorials = ["jupytext", "matplotlib"]
 
 [project.urls]

From a76e92905e8b9313175612e11e78e6f4e42685b7 Mon Sep 17 00:00:00 2001
From: orionarcher <orioncohen@gmail.com>
Date: Thu, 22 Jan 2026 13:49:32 -0500
Subject: [PATCH 22/31] clean up dependency placement

---
 .github/workflows/test-tutorials.yml | 1 +
 .github/workflows/test.yml           | 2 +-
 pyproject.toml                       | 4 ++--
 3 files changed, 4 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/test-tutorials.yml b/.github/workflows/test-tutorials.yml
index 4ce43d4..5b1b0c6 100644
--- a/.github/workflows/test-tutorials.yml
+++ b/.github/workflows/test-tutorials.yml
@@ -67,6 +67,7 @@ jobs:
             xtb>6.5
             openbabel
             crest
+            jupytext
           init-shell: bash
 
       - name: Install uv
diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index de2129c..82ed15f 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -36,7 +36,7 @@ jobs:
 
       - name: Install package
         run: |
-          uv pip install -e ".[tblite]"
+          uv pip install -e .
 
       - name: Run tests
         run: |
diff --git a/pyproject.toml b/pyproject.toml
index ffce340..7e93864 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -38,13 +38,13 @@ dependencies = [
     "pynauty",
     "scipy",
     "tqdm",
+    "tblite",
 ]
 
 [project.optional-dependencies]
 dftd = ["torch-dftd"]
 mace = ["mace-torch"]
-tblite = ["tblite"]
-tutorials = ["jupytext", "matplotlib"]
+tutorials = ["matplotlib"]
 
 [project.urls]
 Homepage = "https://github.com/lanl/Architector"

From da5ac6a42f4810dbdc88d9d632a2c83fde1d6c71 Mon Sep 17 00:00:00 2001
From: orionarcher <orioncohen@gmail.com>
Date: Thu, 22 Jan 2026 13:51:24 -0500
Subject: [PATCH 23/31] swap tblite dep back

---
 .github/workflows/test-tutorials.yml | 1 +
 .github/workflows/test.yml           | 1 +
 pyproject.toml                       | 1 -
 3 files changed, 2 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/test-tutorials.yml b/.github/workflows/test-tutorials.yml
index 5b1b0c6..eb94106 100644
--- a/.github/workflows/test-tutorials.yml
+++ b/.github/workflows/test-tutorials.yml
@@ -68,6 +68,7 @@ jobs:
             openbabel
             crest
             jupytext
+            tblite-python
           init-shell: bash
 
       - name: Install uv
diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index 82ed15f..a347ec2 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -27,6 +27,7 @@ jobs:
             xtb>6.5
             openbabel
             crest
+            tblite-python
           init-shell: bash
 
       - name: Install uv
diff --git a/pyproject.toml b/pyproject.toml
index 7e93864..ce02c54 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -38,7 +38,6 @@ dependencies = [
     "pynauty",
     "scipy",
     "tqdm",
-    "tblite",
 ]
 
 [project.optional-dependencies]

From 8b074b0fec435566622b2002c873b53c5bb20ede Mon Sep 17 00:00:00 2001
From: orionarcher <orioncohen@gmail.com>
Date: Thu, 22 Jan 2026 13:59:41 -0500
Subject: [PATCH 24/31] Revert test-tutorials.yml to working state from fbf3fe5

---
 .github/workflows/test-tutorials.yml | 20 ++++++++++++++++----
 1 file changed, 16 insertions(+), 4 deletions(-)

diff --git a/.github/workflows/test-tutorials.yml b/.github/workflows/test-tutorials.yml
index eb94106..bd3264a 100644
--- a/.github/workflows/test-tutorials.yml
+++ b/.github/workflows/test-tutorials.yml
@@ -64,11 +64,22 @@ jobs:
           environment-name: tutorial-env
           create-args: >-
             python=3.12
-            xtb>6.5
+            ase
+            numpy
             openbabel
+            scipy
+            numba
+            py3Dmol
+            pandas
             crest
-            jupytext
+            pynauty
+            xtb>6.5
+            tqdm
+            mendeleev
             tblite-python
+            jupytext
+            matplotlib
+            pytorch
           init-shell: bash
 
       - name: Install uv
@@ -76,9 +87,10 @@ jobs:
         with:
           version: "latest"
 
-      - name: Install package with optional dependencies
+      - name: Install package and mace-torch
         run: |
-          uv pip install -e ".[mace,dftd,tutorials]"
+          uv pip install --no-deps -e .
+          uv pip install mace-torch torch-dftd
 
       - name: Convert notebook to Python script
         run: |

From 537c65687cec652b515ec5bbc7faec6f32e0c634 Mon Sep 17 00:00:00 2001
From: orionarcher <orioncohen@gmail.com>
Date: Thu, 22 Jan 2026 14:01:19 -0500
Subject: [PATCH 25/31] Minimize conda deps, install pyproject.toml deps via
 pip

Keep in conda (required):
- openbabel (C++ bindings)
- crest (CLI)
- xtb>6.5 (CLI)
- tblite-python (Fortran)
- jupytext (needed before pip install)

Install via pip from pyproject.toml:
- Core deps: ase, numpy, scipy, etc.
- Optional: mace, dftd, tutorials
---
 .github/workflows/test-tutorials.yml | 16 ++--------------
 1 file changed, 2 insertions(+), 14 deletions(-)

diff --git a/.github/workflows/test-tutorials.yml b/.github/workflows/test-tutorials.yml
index bd3264a..e96eedd 100644
--- a/.github/workflows/test-tutorials.yml
+++ b/.github/workflows/test-tutorials.yml
@@ -64,22 +64,11 @@ jobs:
           environment-name: tutorial-env
           create-args: >-
             python=3.12
-            ase
-            numpy
             openbabel
-            scipy
-            numba
-            py3Dmol
-            pandas
             crest
-            pynauty
             xtb>6.5
-            tqdm
-            mendeleev
             tblite-python
             jupytext
-            matplotlib
-            pytorch
           init-shell: bash
 
       - name: Install uv
@@ -87,10 +76,9 @@ jobs:
         with:
           version: "latest"
 
-      - name: Install package and mace-torch
+      - name: Install package with optional dependencies
         run: |
-          uv pip install --no-deps -e .
-          uv pip install mace-torch torch-dftd
+          uv pip install -e ".[mace,dftd,tutorials]"
 
       - name: Convert notebook to Python script
         run: |

From 1d6eb434bd05fb39a7778aada44a964bd5ebe6a3 Mon Sep 17 00:00:00 2001
From: orionarcher <orioncohen@gmail.com>
Date: Thu, 22 Jan 2026 14:03:58 -0500
Subject: [PATCH 26/31] Revert "Minimize conda deps, install pyproject.toml
 deps via pip"

This reverts commit 537c65687cec652b515ec5bbc7faec6f32e0c634.
---
 .github/workflows/test-tutorials.yml | 16 ++++++++++++++--
 1 file changed, 14 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/test-tutorials.yml b/.github/workflows/test-tutorials.yml
index e96eedd..bd3264a 100644
--- a/.github/workflows/test-tutorials.yml
+++ b/.github/workflows/test-tutorials.yml
@@ -64,11 +64,22 @@ jobs:
           environment-name: tutorial-env
           create-args: >-
             python=3.12
+            ase
+            numpy
             openbabel
+            scipy
+            numba
+            py3Dmol
+            pandas
             crest
+            pynauty
             xtb>6.5
+            tqdm
+            mendeleev
             tblite-python
             jupytext
+            matplotlib
+            pytorch
           init-shell: bash
 
       - name: Install uv
@@ -76,9 +87,10 @@ jobs:
         with:
           version: "latest"
 
-      - name: Install package with optional dependencies
+      - name: Install package and mace-torch
         run: |
-          uv pip install -e ".[mace,dftd,tutorials]"
+          uv pip install --no-deps -e .
+          uv pip install mace-torch torch-dftd
 
       - name: Convert notebook to Python script
         run: |

From beb459ac9a86a010a1aabe9be908b5a34c775312 Mon Sep 17 00:00:00 2001
From: orionarcher <orioncohen@gmail.com>
Date: Thu, 22 Jan 2026 14:08:25 -0500
Subject: [PATCH 27/31] Minimize conda deps, add ipython to tutorials optional
 deps

The conda py3Dmol package depends on ipython, but pip py3Dmol doesn't.
Adding ipython to [tutorials] optional deps fixes the headless CI issue.

Conda (required):
- openbabel (C++ bindings)
- crest (CLI)
- xtb>6.5 (CLI)
- tblite-python (Fortran)
- jupytext (needed before pip install)

Pip via pyproject.toml:
- Core deps + [mace,dftd,tutorials]
---
 .github/workflows/test-tutorials.yml | 16 ++--------------
 pyproject.toml                       |  2 +-
 2 files changed, 3 insertions(+), 15 deletions(-)

diff --git a/.github/workflows/test-tutorials.yml b/.github/workflows/test-tutorials.yml
index bd3264a..e96eedd 100644
--- a/.github/workflows/test-tutorials.yml
+++ b/.github/workflows/test-tutorials.yml
@@ -64,22 +64,11 @@ jobs:
           environment-name: tutorial-env
           create-args: >-
             python=3.12
-            ase
-            numpy
             openbabel
-            scipy
-            numba
-            py3Dmol
-            pandas
             crest
-            pynauty
             xtb>6.5
-            tqdm
-            mendeleev
             tblite-python
             jupytext
-            matplotlib
-            pytorch
           init-shell: bash
 
       - name: Install uv
@@ -87,10 +76,9 @@ jobs:
         with:
           version: "latest"
 
-      - name: Install package and mace-torch
+      - name: Install package with optional dependencies
         run: |
-          uv pip install --no-deps -e .
-          uv pip install mace-torch torch-dftd
+          uv pip install -e ".[mace,dftd,tutorials]"
 
       - name: Convert notebook to Python script
         run: |
diff --git a/pyproject.toml b/pyproject.toml
index ce02c54..850a26c 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -43,7 +43,7 @@ dependencies = [
 [project.optional-dependencies]
 dftd = ["torch-dftd"]
 mace = ["mace-torch"]
-tutorials = ["matplotlib"]
+tutorials = ["ipython", "matplotlib"]
 
 [project.urls]
 Homepage = "https://github.com/lanl/Architector"

From 80610ad6a21aff42a58e0af836d450caa2255ced Mon Sep 17 00:00:00 2001
From: orionarcher <orioncohen@gmail.com>
Date: Thu, 22 Jan 2026 14:10:01 -0500
Subject: [PATCH 28/31] Test Python 3.11, 3.12, and 3.13 in matrix

---
 .github/workflows/test.yml | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index a347ec2..98fbb92 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -9,6 +9,10 @@ on:
 jobs:
   test:
     runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ['3.11', '3.12', '3.13']
     defaults:
       run:
         shell: bash -el {0}
@@ -23,7 +27,7 @@ jobs:
           micromamba-version: 'latest'
           environment-name: test-env
           create-args: >-
-            python=3.12
+            python=${{ matrix.python-version }}
             xtb>6.5
             openbabel
             crest

From 8f4aca82dd1b623fcc93ccfad52b60e0d2b22613 Mon Sep 17 00:00:00 2001
From: orionarcher <orioncohen@gmail.com>
Date: Thu, 22 Jan 2026 14:16:33 -0500
Subject: [PATCH 29/31] Drop Python 3.13 - blocked by openbabel conda-forge
 availability

---
 .github/workflows/test.yml | 3 ++-
 pyproject.toml             | 3 +--
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index 98fbb92..e85dfb4 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -12,7 +12,8 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ['3.11', '3.12', '3.13']
+        # Python 3.13 blocked by openbabel not yet available on conda-forge
+        python-version: ['3.11', '3.12']
     defaults:
       run:
         shell: bash -el {0}
diff --git a/pyproject.toml b/pyproject.toml
index 850a26c..950f768 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -22,12 +22,11 @@ classifiers = [
     "License :: OSI Approved :: BSD License",
     "Operating System :: OS Independent",
     "Programming Language :: Python :: 3",
-    "Programming Language :: Python :: 3.10",
     "Programming Language :: Python :: 3.11",
     "Programming Language :: Python :: 3.12",
     "Topic :: Scientific/Engineering :: Chemistry",
 ]
-requires-python = ">=3.10"
+requires-python = ">=3.11"
 dependencies = [
     "ase",
     "mendeleev",

From c7e659ce92fee343006c922eb7057511ffaeec95 Mon Sep 17 00:00:00 2001
From: orionarcher <orioncohen@gmail.com>
Date: Thu, 22 Jan 2026 14:20:03 -0500
Subject: [PATCH 30/31] Test 3.11 with lowest-direct resolution, 3.12 with
 highest

---
 .github/workflows/test.yml | 8 +++++---
 1 file changed, 5 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index e85dfb4..9c4b679 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -13,7 +13,9 @@ jobs:
       fail-fast: false
       matrix:
         # Python 3.13 blocked by openbabel not yet available on conda-forge
-        python-version: ['3.11', '3.12']
+        version:
+          - { python: '3.11', resolution: lowest-direct }
+          - { python: '3.12', resolution: highest }
     defaults:
       run:
         shell: bash -el {0}
@@ -28,7 +30,7 @@ jobs:
           micromamba-version: 'latest'
           environment-name: test-env
           create-args: >-
-            python=${{ matrix.python-version }}
+            python=${{ matrix.version.python }}
             xtb>6.5
             openbabel
             crest
@@ -42,7 +44,7 @@ jobs:
 
       - name: Install package
         run: |
-          uv pip install -e .
+          uv pip install -e . --resolution=${{ matrix.version.resolution }}
 
       - name: Run tests
         run: |

From dbd4c375c9664ce5ea5b4df9ab3c12abd984d88b Mon Sep 17 00:00:00 2001
From: orionarcher <orioncohen@gmail.com>
Date: Thu, 22 Jan 2026 14:23:21 -0500
Subject: [PATCH 31/31] Simplify test matrix: Python 3.11 and 3.12 with default
 resolution

---
 .github/workflows/test.yml | 8 +++-----
 1 file changed, 3 insertions(+), 5 deletions(-)

diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index 9c4b679..e85dfb4 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -13,9 +13,7 @@ jobs:
       fail-fast: false
       matrix:
         # Python 3.13 blocked by openbabel not yet available on conda-forge
-        version:
-          - { python: '3.11', resolution: lowest-direct }
-          - { python: '3.12', resolution: highest }
+        python-version: ['3.11', '3.12']
     defaults:
       run:
         shell: bash -el {0}
@@ -30,7 +28,7 @@ jobs:
           micromamba-version: 'latest'
           environment-name: test-env
           create-args: >-
-            python=${{ matrix.version.python }}
+            python=${{ matrix.python-version }}
             xtb>6.5
             openbabel
             crest
@@ -44,7 +42,7 @@ jobs:
 
       - name: Install package
         run: |
-          uv pip install -e . --resolution=${{ matrix.version.resolution }}
+          uv pip install -e .
 
       - name: Run tests
         run: |