Use nox instead of tox

.github/workflows/docs.yml

@@ -14,35 +14,26 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        example-name: 
-          - lode_linear
-          - roy_gch
-          - sample_selection
-          - gaas_map
-          - cp2k_run_batch
+        example-name:
+          - lode-linear
+          - roy-gch
+          - sample-selection
+          - gaas-map
+          # - batch-cp2k
 
     steps:
       - uses: actions/checkout@v4
-      - name: setup rust
-        uses: actions-rs/toolchain@v1
-        with:
-          profile: minimal
-          toolchain: stable
 
       - name: setup Python
         uses: actions/setup-python@v5
         with:
           python-version: "3.12"
 
-      - name: install tox
-        run: python -m pip install tox
-
-      - name: install cp2k
-        if: matrix.example-name == 'cp2k_run_batch'
-        run: sudo apt-get install -y cp2k
+      - name: install nox
+        run: python -m pip install nox
 
       - name: build example
-        run: tox -e ${{ matrix.example-name }}
+        run: nox -e ${{ matrix.example-name }}
 
       - name: store example as a github artifact
         uses: actions/upload-artifact@v4
@@ -56,18 +47,14 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v4
-      - name: setup rust
-        uses: actions-rs/toolchain@v1
-        with:
-          profile: minimal
-          toolchain: stable
+
       - name: setup Python
         uses: actions/setup-python@v5
         with:
           python-version: "3.12"
 
-      - name: install tox
-        run: python -m pip install tox
+      - name: install nox
+        run: python -m pip install nox
 
       - name: load github artifact for each example
         uses: actions/download-artifact@v4
@@ -77,7 +64,7 @@ jobs:
           merge-multiple: true
 
       - name: build documentation
-        run: tox -e build_docs
+        run: nox -e build_docs
 
       - name: store documentation as github artifact to be downloaded by users
         uses: actions/upload-artifact@v4

.github/workflows/lint.yml

@@ -21,7 +21,7 @@ jobs:
         python-version: "3.12"
 
     - name: install dependencies
-      run: pip install tox
+      run: pip install nox
 
     - name: test lint
-      run: tox -e lint
+      run: nox -e lint

.gitignore

@@ -2,4 +2,5 @@ docs/src/examples/
 
 *build*
 *egg-info/
-sg_execution_times.rst
+
+.nox/

examples/cp2k_run_batch/environment.yml → deactivated/batch-cp2k/environment.yml

@@ -1,4 +1,3 @@
-name: cp2k_run_batch
 dependencies:
   - python=3.11
   - pip

examples/cp2k_run_batch/setup_reftraj.py → deactivated/batch-cp2k/reference-trajectory.py

@@ -27,7 +27,6 @@
 
 import os
 import re
-import shutil
 import subprocess
 from os.path import basename, splitext
 from typing import List, Union
@@ -68,7 +67,7 @@ def write_reftraj(fname: str, frames: Union[ase.Atoms, List[ase.Atoms]]) -> None
                 "CP2K does not support changing atom types within a reftraj run!"
             )
 
-        out += f"{len(atoms):>8}\n i = {i+1:>8}, time = {0:>12.3f}\n"
+        out += f"{len(atoms):>8}\n i = {i + 1:>8}, time = {0:>12.3f}\n"
         for atom in atoms:
             pos = atom.position
             out += f"{atom.symbol}{pos[0]:24.15f}{pos[1]:24.15f}{pos[2]:24.15f}\n"
@@ -105,7 +104,7 @@ def write_cellfile(fname: str, frames: Union[ase.Atoms, List[ase.Atoms]]) -> Non
     )
 
     for i, atoms in enumerate(frames):
-        out += f"{i+1:>8}{0:>12.3f}"
+        out += f"{i + 1:>8}{0:>12.3f}"
         out += "".join([f"{c:>20.10f}" for c in atoms.cell.flatten()])
         out += f"{atoms.cell.volume:>25.10f}"
         out += "\n"
@@ -162,7 +161,7 @@ def mkdir_force(*args, **kwargs) -> None:
 # files for the structures, the ``project_name`` used to build the name of the
 # trajectory during the CP2K run, the ``project_directory`` where we store all
 # simulation output as well as the path ``write_to_file`` which is the name of the file
-# containing the computed energies and forces of the sinulation.
+# containing the computed energies and forces of the simulation.
 
 frames_full = ase.io.read("example.xyz", ":")
 project_name = "test_calcs"  # name of the global PROJECT
@@ -181,7 +180,7 @@ def mkdir_force(*args, **kwargs) -> None:
 plt.show()
 
 # %%
-# We now extreact the stoichiometry from the input dataset using ASE's
+# We now extract the stoichiometry from the input dataset using ASE's
 # :py:meth:`ase.symbols.Symbols.get_chemical_formula` method.
 
 frames_dict = {}
@@ -236,8 +235,8 @@ def mkdir_force(*args, **kwargs) -> None:
 # %%
 # .. note::
 #
-#    For a usage on an HPC environment you can parallize the loop over the subfolders
-#    and submit and single job per stoichiometry.
+#    For a usage on an HPC environment you can parallelize the loop over the
+#    sub-directories and submit and single job per stoichiometry.
 #
 # Load results
 # ------------
@@ -289,18 +288,13 @@ def mkdir_force(*args, **kwargs) -> None:
 # Perform calculations using ASE calculator
 # -----------------------------------------
 # Above we performed the calculations using an external bash script. ASE also provides a
-# calculator class that we can use the perform the caclulations with our input file
+# calculator class that we can use the perform the calculations with our input file
 # without a detour of writing files to disk.
 #
 # To use the ASE calculator together with a custom input script this requires some
 # adjustments. First the name of the executable that has the exact name ``cp2k_shell``.
 # We create a symlink to follow this requirement.
 
-try:
-    os.symlink(shutil.which("cp2k"), "cp2k_shell.ssmp")
-except OSError:
-    pass
-
 # %%
 # Next, we load the input file abd remove ``GLOBAL`` section because from it
 
@@ -326,11 +320,10 @@ def mkdir_force(*args, **kwargs) -> None:
     stress_tensor=False,
     poisson_solver=None,
     print_level=None,
-    command="./cp2k_shell.ssmp --shell",
 )
 
 # %%
-# We now load a new struture, add the calculator and perform the computation.
+# We now load a new structure, add the calculator and perform the computation.
 
 atoms = ase.io.read("example.xyz")
 atoms.set_calculator(calc)

examples/cp2k_run_batch/run_calcs.sh → deactivated/batch-cp2k/run_calcs.sh

@@ -5,4 +5,3 @@ for i in $(find ./production/ -mindepth 1 -type d); do
     cp2k -i in.cp2k
     cd -
 done
-

docs/src/.gitignore

@@ -0,0 +1,2 @@
+sg_execution_times.rst
+index.rst

docs/src/index.rst → docs/src/index.rst.in

@@ -5,12 +5,7 @@ COSMO Software Cookbook
    :start-after: marker-intro-start
    :end-before: marker-intro-end
 
+
 .. toctree::
    :caption: Table of Contents
    :maxdepth: 1
-
-   examples/roy_gch/roy_gch
-   examples/lode_linear/lode_tutorial
-   examples/sample_selection/sample_selection
-   examples/gaas_map/gaas_map
-   examples/cp2k_run_batch/setup_reftraj

examples/gaas-map/.gitignore

@@ -0,0 +1,2 @@
+gaas_training.xyz
+gaas_map.chemiscope.json.gz

examples/gaas_map/environment.yml → examples/gaas-map/environment.yml

@@ -1,12 +1,14 @@
-name: gaas_map
+channels:
+  - conda-forge
 dependencies:
   - python=3.11
   - pip
+  - rust
   - pip:
     - ase
     - chemiscope
     - matplotlib
     - metatensor
-    - skmatter
     - rascaline @ git+https://github.com/Luthaf/rascaline@ca957642f512e141c7570e987aadc05c7ac71983
     - scikit-learn
+    - skmatter

examples/lode_linear/environment.yml → examples/lode-linear/environment.yml

@@ -1,7 +1,9 @@
-name: lode_linear
+channels:
+  - conda-forge
 dependencies:
   - python=3.11
   - pip
+  - rust
   - pip:
     - ase
     - equisolve @ git+https://github.com/lab-cosmo/equisolve.git@c858bedef4b2799eb445e4c92535ee387224089a

examples/sample_selection/environment.yml → examples/roy-gch/environment.yml

@@ -1,11 +1,13 @@
-name: sample_selection
+channels:
+  - conda-forge
 dependencies:
   - python=3.11
   - pip
+  - rust
   - pip:
     - ase
     - chemiscope
     - matplotlib
-    - skmatter
     - metatensor
     - rascaline @ git+https://github.com/Luthaf/rascaline@ca957642f512e141c7570e987aadc05c7ac71983
+    - skmatter

examples/sample-selection/.gitignore

@@ -0,0 +1 @@
+sample-selection.json.gz

examples/roy_gch/environment.yml → examples/sample-selection/environment.yml

@@ -1,7 +1,9 @@
-name: roy_gch
+channels:
+  - conda-forge
 dependencies:
   - python=3.11
   - pip
+  - rust
   - pip:
     - ase
     - chemiscope

examples/sample_selection/sample_selection.py → examples/sample-selection/sample-selection.py

@@ -191,7 +191,7 @@
 
 # Display with chemiscope. This currently does not work - as raised in issue #8
 # https://github.com/lab-cosmo/software-cookbook/issues/8
-cs = chemiscope.show(
+widget = chemiscope.show(
     frames,
     properties=properties,
     settings={
@@ -209,9 +209,9 @@
 if chemiscope.jupyter._is_running_in_notebook():
     from IPython.display import display
 
-    display(cs)
+    display(widget)
 else:
-    cs.save("sample_selection.json.gz")
+    widget.save("sample-selection.json.gz")
 
 
 # %%