Merge pull request mala-project#658 from elcorto/feature-small-improvements

Various small improvements

Author: RandomDefaultUser

.gitignore

@@ -153,6 +153,7 @@ cython_debug/
 *.out
 *.npy
 *.pkl
+*.pk
 *.pth
 *.json
 

examples/advanced/ex01_checkpoint_training.py

@@ -57,10 +57,10 @@ def initial_setup():
         data_handler.output_dimension,
     ]
 
-    test_network = mala.Network(parameters)
-    test_trainer = mala.Trainer(parameters, test_network, data_handler)
+    network = mala.Network(parameters)
+    trainer = mala.Trainer(parameters, network, data_handler)
 
-    return parameters, test_network, data_handler, test_trainer
+    return parameters, network, data_handler, trainer
 
 
 if mala.Trainer.run_exists("ex01_checkpoint", path="./"):

examples/basic/ex01_train_network.py

@@ -101,7 +101,7 @@
     100,
     data_handler.output_dimension,
 ]
-test_network = mala.Network(parameters)
+network = mala.Network(parameters)
 
 ####################
 # 4. TRAINING THE NETWORK
@@ -113,9 +113,9 @@
 # side the model. This makes inference easier.
 ####################
 
-test_trainer = mala.Trainer(parameters, test_network, data_handler)
-test_trainer.train_network()
+trainer = mala.Trainer(parameters, network, data_handler)
+trainer.train_network()
 additional_calculation_data = os.path.join(data_path, "Be_snapshot0.out")
-test_trainer.save_run(
+trainer.save_run(
     "Be_model", additional_calculation_data=additional_calculation_data
 )

examples/basic/ex05_run_predictions.py

@@ -1,4 +1,5 @@
 import os
+from importlib.util import find_spec
 
 from ase.io import read
 import mala
@@ -39,7 +40,11 @@
 ldos_calculator: mala.LDOS = predictor.target_calculator
 ldos_calculator.read_from_array(ldos)
 printout("Predicted band energy: ", ldos_calculator.band_energy)
+
 # If the total energy module is installed, the total energy can also be
 # calculated.
-# parameters.targets.pseudopotential_path = data_path
-# printout("Predicted total energy", ldos_calculator.total_energy)
+if find_spec("total_energy"):
+    parameters.targets.pseudopotential_path = data_path
+    printout("Predicted total energy", ldos_calculator.total_energy)
+else:
+    print("total_energy module not found, skipping total energy calculation")

examples/clean.sh

@@ -1,36 +1,26 @@
 #!/bin/sh
 
+set -u
+
 # Remove artifact files that some example scripts write.
 
-cd basic
-rm -rvf \
-    *.pth \
-    *.pkl \
-    *.db \
-    *.pw* \
-    __pycache__ \
-    *.cube \
-    ex10_vis \
-    *.tmp \
-    *.npy \
-    *.json \
-    *.zip \
-    Be_snapshot* \
-    lammps*.tmp
-cd ..
-cd advanced
-rm -rvf \
-    *.pth \
-    *.pkl \
-    *.db \
-    *.pw* \
-    __pycache__ \
-    *.cube \
-    ex10_vis \
-    *.tmp \
-    *.npy \
-    *.json \
-    *.zip \
-    Be_snapshot* \
-    lammps*.tmp
-cd ..
+here=$(dirname $(readlink -f $0))
+for dir in $here $(find $here -mindepth 1 -type d | grep -vE '\.ruff_cache|__pycache__'); do
+    cd $dir
+    echo "cleaning: $(pwd)"
+    rm -rvf \
+        *.pth \
+        *.pkl \
+        *.pk \
+        *.db \
+        *.pw* \
+        *.cube \
+        ex10_vis \
+        *.tmp \
+        *.npy \
+        *.json \
+        *.zip \
+        Be_snapshot* \
+        lammps*.tmp \
+        mala_vis
+done

pyproject.toml

@@ -1,6 +1,18 @@
 [tool.black]
 line-length = 79
 
+[tool.ruff]
+lint.ignore = [
+    "E731", # Do not assign a lambda expression, use a def
+]
+
+[tool.mypy]
+ignore_missing_imports = true
+implicit_optional = true
+follow_imports = "skip"
+allow_untyped_calls = true
+allow_untyped_defs = true
+
 [build-system]
 requires = ["setuptools"]
 build-backend = "setuptools.build_meta"

test/clean.sh

@@ -2,4 +2,4 @@
 
 # Remove artifact files that some example scripts write.
 
-rm -rv *.pth *.pkl ex09.db *.pw* __pycache__ *.cube ex10_vis *.tmp *.npy *.json *.h5 *.bp
+rm -rv *.pth *.pkl *.db *.pw* __pycache__ *.cube *_vis *.tmp *.npy *.json *.h5 *.bp *.db *.zip