Run tutorials and tests in CI

.ci_support/environment.yml

@@ -3,7 +3,7 @@ channels:
   - conda-forge
 dependencies:
   - python
-  - xtb
+  - xtb>6.5
   - ase
   - numpy
   - openbabel

.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 }}

.github/workflows/test-tutorials.yml

@@ -0,0 +1,100 @@
+name: Tutorial Tests
+
+on:
+  push:
+    branches: [main, Secondary_Solvation_Shell]
+  pull_request:
+    branches: [main, Secondary_Solvation_Shell]
+
+jobs:
+  find-tutorials:
+    runs-on: ubuntu-latest
+    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: ${{ fromJson(needs.find-tutorials.outputs.tutorials) }}
+    defaults:
+      run:
+        shell: bash -el {0}
+
+    steps:
+      - name: Check out repo
+        uses: actions/checkout@v5
+
+      - name: Setup micromamba
+        uses: mamba-org/setup-micromamba@v2
+        with:
+          micromamba-version: 'latest'
+          environment-name: tutorial-env
+          create-args: >-
+            python=3.12
+            openbabel
+            crest
+            xtb>6.5
+            tblite-python
+            jupytext
+          init-shell: bash
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@v5
+        with:
+          version: "latest"
+
+      - name: Install package with optional dependencies
+        run: |
+          uv pip install -e ".[mace,dftd,tutorials]"
+
+      - name: Convert notebook to Python script
+        run: |
+          jupytext --to py:percent "${{ matrix.tutorial }}"
+
+      - name: Run tutorial
+        run: |
+          cd $(dirname "${{ matrix.tutorial }}")
+          SCRIPT=$(basename "${{ matrix.tutorial }}" .ipynb).py
+
+          echo "Running $SCRIPT...!"
+          timeout 600 python "$SCRIPT"
+
+      - name: Cleanup
+        run: |
+          rm -rf documentation/tutorials/pymol_renders
+          rm -f documentation/tutorials/*.xyz
+          rm -f documentation/tutorials/*.py
+        if: always()

.github/workflows/test.yml

@@ -0,0 +1,49 @@
+name: Tests
+
+on:
+  push:
+    branches: [main, Secondary_Solvation_Shell]
+  pull_request:
+    branches: [main, Secondary_Solvation_Shell]
+
+jobs:
+  test:
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        # Python 3.13 blocked by openbabel not yet available on conda-forge
+        python-version: ['3.11', '3.12']
+    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=${{ matrix.python-version }}
+            xtb>6.5
+            openbabel
+            crest
+            tblite-python
+          init-shell: bash
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@v5
+        with:
+          version: "latest"
+
+      - name: Install package
+        run: |
+          uv pip install -e .
+
+      - name: Run tests
+        run: |
+          python -m unittest discover tests

.gitignore

@@ -11,4 +11,5 @@
 meta_production_sample.pkl
 development/**/*.csv
 development/**/*.mol2
-pymol_renders/
+pymol_renders/
+build/

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:

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:

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