feat: harmonization and import reshuffling (#50)

* refactor: some harmonization

* refactor: shuffle imports around and fix all resulting errors

* docs: modify new benchmark tutorial due to new import structure

* ci: remove requirements.txt fixer from pre-commits

* ci: upgrade ruff version

Author: chrbrunk

.pre-commit-config.yaml

@@ -8,19 +8,18 @@ default_install_hook_types:
 
 repos:
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.11.9
+    rev: v0.13.0
     hooks:
-      - id: ruff
+      - id: ruff-check
         types_or: [python, pyi, jupyter]
-        args: ["-v", "--config", "ruff.toml", "--fix"]
+        args: ["--config", "ruff.toml", "--fix"]
       - id: ruff-format
         types_or: [python, pyi, jupyter]
 
   - repo: https://github.com/pre-commit/pre-commit-hooks
     rev: v5.0.0
     hooks:
       - id: debug-statements # Check for debugger imports
-      - id: requirements-txt-fixer # Order requirements alphabetically
       - id: check-ast # Simply check whether the files parse as valid python
       - id: check-case-conflict # Check for files that would conflict in case-insensitive filesystems
       - id: check-builtin-literals # Require literal syntax when initializing empty or zero Python builtin types

docs/source/api_reference/biomolecules/folding_stability.rst

@@ -3,7 +3,7 @@
 Folding Stability
 =================
 
-.. module:: mlipaudit.folding_stability.folding_stability
+.. module:: mlipaudit.benchmarks.folding_stability.folding_stability
 
 .. autoclass:: FoldingStabilityBenchmark
 

docs/source/api_reference/biomolecules/sampling.rst

@@ -3,7 +3,7 @@
 Sampling
 ========
 
-.. module:: mlipaudit.sampling.sampling
+.. module:: mlipaudit.benchmarks.sampling.sampling
 
 .. autoclass:: SamplingBenchmark
 

docs/source/api_reference/general/scaling.rst

@@ -3,7 +3,7 @@
 Scaling
 =========
 
-.. module:: mlipaudit.scaling.scaling
+.. module:: mlipaudit.benchmarks.scaling.scaling
 
 .. autoclass:: ScalingBenchmark
 

docs/source/api_reference/general/stability.rst

@@ -3,7 +3,7 @@
 Stability
 =========
 
-.. module:: mlipaudit.stability.stability
+.. module:: mlipaudit.benchmarks.stability.stability
 
 .. autoclass:: StabilityBenchmark
 

docs/source/api_reference/small_molecules/bond_length_distribution.rst

@@ -3,7 +3,7 @@
 Bond length distribution
 ========================
 
-.. module:: mlipaudit.bond_length_distribution.bond_length_distribution
+.. module:: mlipaudit.benchmarks.bond_length_distribution.bond_length_distribution
 
 .. autoclass:: BondLengthDistributionBenchmark
 

docs/source/api_reference/small_molecules/conformer_selection.rst

@@ -3,7 +3,7 @@
 Conformer Selection
 ===================
 
-.. module:: mlipaudit.conformer_selection.conformer_selection
+.. module:: mlipaudit.benchmarks.conformer_selection.conformer_selection
 
 .. autoclass:: ConformerSelectionBenchmark
 

docs/source/api_reference/small_molecules/dihedral_scan.rst

@@ -3,7 +3,7 @@
 Dihedral Scan
 =============
 
-.. module:: mlipaudit.dihedral_scan.dihedral_scan
+.. module:: mlipaudit.benchmarks.dihedral_scan.dihedral_scan
 
 .. autoclass:: DihedralScanBenchmark
 

docs/source/api_reference/small_molecules/minimization.rst

@@ -3,7 +3,7 @@
 Small molecule minimization
 ===========================
 
-.. module:: mlipaudit.small_molecule_minimization.small_molecule_minimization
+.. module:: mlipaudit.benchmarks.small_molecule_minimization.small_molecule_minimization
 
 .. autoclass:: SmallMoleculeMinimizationBenchmark
 

docs/source/api_reference/small_molecules/noncovalent_interactions.rst

@@ -3,7 +3,7 @@
 Noncovalent Interactions
 ========================
 
-.. module:: mlipaudit.noncovalent_interactions.noncovalent_interactions
+.. module:: mlipaudit.benchmarks.noncovalent_interactions.noncovalent_interactions
 
 .. autoclass:: NoncovalentInteractionsBenchmark