Workshop fixes (#114)

* Expose MLFFErrorAnalysis in `__init__.py`
* Fix calling plot with keyword arguments
* Fix string fix-length issue for MD energy plotting
* Replace calculations import with py4vasp import
* Fix access to HDF5 files for trajectories

---------
Co-authored-by: Martin Schlipf <martin.schlipf@gmail.com>

src/py4vasp/__init__.py

@@ -1,5 +1,6 @@
 # Copyright © VASP Software GmbH,
 # Licensed under the Apache License 2.0 (http://www.apache.org/licenses/LICENSE-2.0)
+from py4vasp._analysis.mlff import MLFFErrorAnalysis
 from py4vasp._calculation import Calculation
 from py4vasp._calculations import Calculations
 from py4vasp._third_party.graph import plot

src/py4vasp/_analysis/mlff.py

@@ -5,7 +5,8 @@
 
 import numpy as np
 
-from py4vasp import Calculations, exception
+import py4vasp
+from py4vasp import exception
 
 
 class MLFFErrorAnalysis:
@@ -71,7 +72,9 @@ def from_paths(cls, dft_data, mlff_data):
             Path to the MLFF data. Accepts wildcards.
         """
         mlff_error_analysis = cls(_internal=True)
-        calculations = Calculations.from_paths(dft_data=dft_data, mlff_data=mlff_data)
+        calculations = py4vasp.Calculations.from_paths(
+            dft_data=dft_data, mlff_data=mlff_data
+        )
         mlff_error_analysis._calculations = calculations
         set_appropriate_attrs(mlff_error_analysis)
         return mlff_error_analysis
@@ -92,7 +95,9 @@ def from_files(cls, dft_data, mlff_data):
             Path to the MLFF data. Accepts wildcards.
         """
         mlff_error_analysis = cls(_internal=True)
-        calculations = Calculations.from_files(dft_data=dft_data, mlff_data=mlff_data)
+        calculations = py4vasp.Calculations.from_files(
+            dft_data=dft_data, mlff_data=mlff_data
+        )
         mlff_error_analysis._calculations = calculations
         set_appropriate_attrs(mlff_error_analysis)
         return mlff_error_analysis

src/py4vasp/_data/energy.py

@@ -18,16 +18,16 @@ def _selection_string(default):
 
 
 _SELECTIONS = {
-    "ion-electron   TOTEN   ": ["ion_electron", "TOTEN"],
-    "kinetic energy EKIN    ": ["kinetic_energy", "EKIN"],
+    "ion-electron   TOTEN": ["ion_electron", "TOTEN"],
+    "kinetic energy EKIN": ["kinetic_energy", "EKIN"],
     "kin. lattice   EKIN_LAT": ["kinetic_lattice", "EKIN_LAT"],
-    "temperature    TEIN    ": ["temperature", "TEIN"],
-    "nose potential ES      ": ["nose_potential", "ES"],
-    "nose kinetic   EPS     ": ["nose_kinetic", "EPS"],
-    "total energy   ETOTAL  ": ["total_energy", "ETOTAL"],
-    "free energy    TOTEN   ": ["free_energy", "TOTEN"],
-    "energy without entropy ": ["without_entropy", "ENOENT"],
-    "energy(sigma->0)       ": ["sigma_0", "ESIG0"],
+    "temperature    TEIN": ["temperature", "TEIN"],
+    "nose potential ES": ["nose_potential", "ES"],
+    "nose kinetic   EPS": ["nose_kinetic", "EPS"],
+    "total energy   ETOTAL": ["total_energy", "ETOTAL"],
+    "free energy    TOTEN": ["free_energy", "TOTEN"],
+    "energy without entropy": ["without_entropy", "ENOENT"],
+    "energy(sigma->0)": ["sigma_0", "ESIG0"],
 }
 
 
@@ -168,7 +168,7 @@ def _init_selection_dict(self):
         return {
             selection: index
             for index, label in enumerate(self._raw_data.labels)
-            for selection in _SELECTIONS.get(convert.text_to_string(label), ())
+            for selection in _SELECTIONS.get(convert.text_to_string(label).strip(), ())
         }
 
     def _make_series(self, yaxes, tree):
@@ -188,9 +188,9 @@ def __init__(self, tree):
         self.y2label = "Temperature (K)" if self.use_both else None
 
     def _is_temperature(self, selection):
-        choices = _SELECTIONS["temperature    TEIN    "]
+        choices = _SELECTIONS["temperature    TEIN"]
         return any(select.contains(selection, choice) for choice in choices)
 
     def use_y2(self, label):
-        choices = _SELECTIONS["temperature    TEIN    "]
+        choices = _SELECTIONS["temperature    TEIN"]
         return self.use_both and label in choices

src/py4vasp/_data/structure.py

@@ -291,6 +291,8 @@ def _lattice_vectors(self):
         return self._scale() * lattice_vectors[self._get_steps()]
 
     def _scale(self):
+        if isinstance(self._raw_data.cell.scale, np.float_):
+            return self._raw_data.cell.scale
         if not self._raw_data.cell.scale.is_none():
             return self._raw_data.cell.scale[()]
         else:
@@ -324,6 +326,7 @@ def _step_string(self):
         else:
             return f" (step {self._steps + 1})"
 
+    @base.data_access
     def __getitem__(self, steps):
         if not self._is_trajectory:
             message = "The structure is not a Trajectory so accessing individual elements is not allowed."

src/py4vasp/_third_party/graph/plot.py

@@ -37,12 +37,19 @@ def plot(*args, **kwargs):
 
 
 def _parse_series(*args, **kwargs):
+    if series := _parse_multiple_series(*args, **kwargs):
+        return series
+    else:
+        return _parse_single_series(*args, **kwargs)
+
+
+def _parse_multiple_series(*args, **kwargs):
     try:
         return [Series(*arg) for arg in args]
     except TypeError:
-        # A TypeError is raised, if plot(x, y) is called instead of plot((x, y)).
-        # Because we creating the Series may raise another error, we leave the
-        # exception handling first to avoid reraising the TypeError.
-        pass
+        return []
+
+
+def _parse_single_series(*args, **kwargs):
     for_series = {key: val for key, val in kwargs.items() if key in Series._fields}
     return Series(*args, **for_series)

tests/conftest.py

@@ -438,13 +438,13 @@ def _polarization():
 
 def _MD_energy(randomize: bool = False):
     labels = (
-        "ion-electron   TOTEN   ",
-        "kinetic energy EKIN    ",
+        "ion-electron   TOTEN",
+        "kinetic energy EKIN",
         "kin. lattice   EKIN_LAT",
-        "temperature    TEIN    ",
-        "nose potential ES      ",
-        "nose kinetic   EPS     ",
-        "total energy   ETOTAL  ",
+        "temperature    TEIN",
+        "nose potential ES",
+        "nose kinetic   EPS",
+        "total energy   ETOTAL",
     )
     return _create_energy(labels, randomize=randomize)
 

tests/data/conftest.py

@@ -36,7 +36,7 @@ def inner(cls, data, parameters={}):
 def check_instance_accesses_data(instance, data, parameters, file=None):
     failed = []
     for name, method in inspect.getmembers(instance, inspect.ismethod):
-        if should_test_method(name):
+        if should_test_method(name, parameters):
             kwargs = parameters.get(name, {})
             try:
                 check_method_accesses_data(data, method, file, **kwargs)
@@ -50,7 +50,9 @@ def check_instance_accesses_data(instance, data, parameters, file=None):
         raise AssertionError(message)
 
 
-def should_test_method(name):
+def should_test_method(name, parameters):
+    if name in parameters:
+        return True
     if name in ("__str__", "_repr_html_"):
         return True
     if name.startswith("from") or name.startswith("_"):

tests/data/test_structure.py

@@ -360,4 +360,5 @@ def test_print_Ca3AsBr3(Ca3AsBr3, format_):
 
 def test_factory_methods(raw_data, check_factory_methods):
     data = raw_data.structure("Sr2TiO4")
-    check_factory_methods(Structure, data)
+    parameters = {"__getitem__": {"steps": slice(None)}}
+    check_factory_methods(Structure, data, parameters)

tests/third_party/graph/test_plot.py

@@ -19,6 +19,8 @@ def test_plot():
     assert plot((x1, y1)) == Graph([series0])
     assert plot((x1, y1), (x2, y2, "label2")) == Graph([series0, series2])
     assert plot((x1, y1), xlabel="xaxis") == Graph([series0], xlabel="xaxis")
+    assert plot(x1, y=y1) == Graph(series0)
+    assert plot(x=x1, y=y1) == Graph(series0)
 
 
 def test_plot_small_dataset():