Merge Release-0.8.4

.github/workflows/unit_test.yml

@@ -38,7 +38,7 @@ jobs:
     - name: Set up Python environment
       uses: actions/setup-python@v2
       with:
-        python-version: 3.7
+        python-version: 3.8
 
     - name: Some logging
       shell: bash

.pre-commit-config.yaml

@@ -1,12 +1,12 @@
 repos:
 - repo: https://github.com/psf/black
-  rev: stable   # Replace by any tag/version: https://github.com/psf/black/tags
+  rev: 22.3.0   # Replace by any tag/version: https://github.com/psf/black/tags
   hooks:
   - id: black
     language_version: python3     # Should be a command that runs python3.6+
 
 - repo: https://github.com/pre-commit/pre-commit-hooks
-  rev: v4.0.1    # Use the ref you want to point at
+  rev: v4.3.0    # Use the ref you want to point at
   hooks:
   - id: trailing-whitespace
   - id: check-yaml
@@ -15,13 +15,13 @@ repos:
   - id: check-toml
   - id: pretty-format-json
   - id: detect-private-key
-- repo: local
-  hooks:
-  - id: export_dev_requirements
-    name: Export dev requirements
-    language: system
-    pass_filenames: false
-    entry: peodd -o requirements-dev.txt
+#- repo: local
+#  hooks:
+#  - id: export_dev_requirements
+#    name: Export dev requirements
+#    language: system
+#    pass_filenames: false
+#    entry: peodd -o requirements-dev.txt
 #  - id: export-requirements
 #    name: Export requeriments.txt
 #    language: system
@@ -34,7 +34,7 @@ repos:
 #    pass_filenames: false
 #    entry: ~/anaconda3/bin/poetry2setup > setup.py
 - repo: https://github.com/macisamuele/language-formatters-pre-commit-hooks
-  rev: v2.1.0
+  rev: v2.3.0
   hooks:
   - id: pretty-format-yaml
     args: [--autofix, --indent, '2']

easyDiffractionLib/Interfaces/CFML.py

@@ -2,14 +2,15 @@
 __version__ = "0.0.2"
 
 import os
+import glob
 from easyCore import borg, np
 from easyCore.Objects.Inferface import ItemContainer
 
 from easyDiffractionLib import Lattice, SpaceGroup, Site, Phases, Phase
 
 from easyDiffractionLib.Interfaces.interfaceTemplate import InterfaceTemplate
 from easyDiffractionLib.Profiles.P1D import Instrument1DCWParameters, Powder1DParameters
-from easyDiffractionLib.Calculators.CFML import CFML as CFML_calc
+from easyDiffractionLib.calculators.CFML import CFML as CFML_calc
 
 
 class CFML(InterfaceTemplate):
@@ -52,7 +53,7 @@ class CFML(InterfaceTemplate):
     }
     _pattern_link = {"scale": "scale", "x_offset": "x_offset"}
 
-    feature_available = {"Npowder1DCW": True}
+    feature_available = {"Npowder1DCW": True, "Npowder1DCWunp": True}
 
     name = "CrysFML"
 
@@ -122,7 +123,7 @@ def create(self, model):
             self.calculator.add_phase(str(model_key), model.name)
         elif issubclass(t_, Sample):
             self.__createModel(model)
-        elif t_.__name__ in ["Powder1DCW", "powder1DCW", "Npowder1DCW"]:
+        elif t_.__name__ in ["Powder1DCW", "powder1DCW", "Npowder1DCW", "Npowder1DCWunp"]:
             self.__createModel(model)
         else:
             if self._borg.debug:
@@ -159,6 +160,8 @@ def get_hkl(self, x_array: np.ndarray = None, idx=None, phase_name=None, encoded
     def dump_cif(self, *args, **kwargs):
         if self._filename is None:
             return
+        # delete preexising cif files
+        self.remove_cif()
         with open(self._filename, "w") as fid:
             fid.write(str(self._phase.cif))
         base, file = os.path.split(self._filename)
@@ -168,6 +171,20 @@ def dump_cif(self, *args, **kwargs):
             with open(f"{os.path.join(base, file)}_{idx}.{ext}", "w") as fid:
                 fid.write(str(phase.cif))
 
+    def remove_cif(self):
+        if self._filename is None:
+            return
+        base, file = os.path.split(self._filename)
+        ext = file[-3:]
+        file = file[:-4]
+        file_wildcarded = os.path.join(base, file) + '_*.' + ext
+        fileList = glob.glob(file_wildcarded)
+        for f in fileList:
+            try:
+                os.remove(f)
+            except OSError:
+                pass
+
     def __createModel(self, model):
         self._filename = model.filename
         self.calculator.filename = model.filename
@@ -182,6 +199,9 @@ def get_value(self, key, item_key):
     def get_phase_components(self, phase_name):
         return None
 
+    def get_component(self, component_name):
+        return self.calculator.get_component(component_name)
+
     def get_calculated_y_for_phase(self, phase_idx: int) -> list:
         return self.calculator.get_calculated_y_for_phase(phase_idx)
 

easyDiffractionLib/Interfaces/GSASII.py

@@ -4,7 +4,7 @@
 from easyCore import borg, np
 from ..Interfaces.interfaceTemplate import InterfaceTemplate
 from easyCore.Objects.Inferface import ItemContainer
-from ..Calculators.GSASII import GSASII as GSAS_calc
+from ..calculators.GSASII import GSASII as GSAS_calc
 from easyDiffractionLib.Profiles.P1D import Instrument1DCWParameters, Powder1DParameters
 from easyDiffractionLib import Lattice, SpaceGroup, Site, Phases
 
@@ -54,7 +54,8 @@ class GSASII(InterfaceTemplate):
     }
 
     feature_available = {
-        'Npowder1DCW': True
+        'Npowder1DCW': True,
+        'Npowder1DCWunp': True
     }
 
     name = 'GSASII'
@@ -108,7 +109,7 @@ def create(self, model):
                                         self.dump_cif))
         elif issubclass(t_, Phases):
             self._phase = model
-        elif t_.__name__ in ['Powder1DCW', 'powder1DCW', 'Npowder1DCW']:
+        elif t_.__name__ in ['Powder1DCW', 'powder1DCW', 'Npowder1DCW', 'Npowder1DCWunp']:
         #     #TODO Check to see if parameters and pattern should be initialized here.
             self.__createModel(model_key, 'powder1DCW')
         elif issubclass(t_, Sample):
@@ -164,6 +165,15 @@ def __createModel(self, model):
     def get_phase_components(self, phase_name):
         return None
 
+    def get_component(self, component_name):
+        return None
+
+    def get_calculated_y_for_phase(self, phase_idx: int) -> list:
+        return self.calculator.get_calculated_y_for_phase(phase_idx)
+
+    def get_total_y_for_phases(self) -> list:
+        return self.calculator.get_total_y_for_phases()
+
     @staticmethod
     def __identify(obj):
         return borg.map.convert_id_to_key(obj)

easyDiffractionLib/Interfaces/__init__.py

@@ -12,6 +12,13 @@
     # TODO make this a proper message (use logging?)
     print('Warning: CrysPy is not installed')
 
+
+# try:
+#     from easyDiffractionLib.Interfaces.cryspyV2 import CryspyBase  # noqa: F401
+# except ImportError:
+#     # TODO make this a proper message (use logging?)
+#     print('Warning: CrysPy is not installed')
+
 try:
     from easyDiffractionLib.Interfaces.CFML import CFML  # noqa: F401
 except ImportError: