Merge pull request #554 from maurov/fix553

Fix issue #553

.github/workflows/test-ubuntu.yml

@@ -18,23 +18,25 @@ jobs:
       run:
         shell: bash -l {0}
     steps:
-    - uses: actions/checkout@v4
-    - name: Set up Python from Miniconda/conda
-      uses: conda-incubator/[email protected]
-      with:
-        miniconda-version: latest
-        channels: conda-forge,defaults
-        channel-priority: true
-        activate-environment: anaconda-client-env
-        python-version: ${{ matrix.python-version }}
-    - name: Install conda dependencies
-      run: |
-        printenv
-        conda install -y -c conda-forge python=${{ matrix.python-version }} "numpy>=1.23" "scipy>=1.12" "matplotlib>=3.8" "h5py>=3.5" "wxpython>=4.2" scikit-learn jupyter plotly pytest pytest-cov coverage
-    - name: Install xraylarch and other dependencies with pip
-      run: |
-        pip install ".[all]"
-    - name: Run test suite
-      run: |
-        cd tests
-        python -m pytest
+      - uses: actions/checkout@v4
+      - name: Install dependencies
+        run: |
+          sudo apt-get update
+          sudo apt-get install -y xvfb
+      - name: Set up Python from Miniconda/conda
+        uses: conda-incubator/[email protected]
+        with:
+          miniconda-version: latest
+          channels: conda-forge,defaults
+          channel-priority: true
+          activate-environment: anaconda-client-env
+          python-version: ${{ matrix.python-version }}
+      - name: Install conda dependencies
+        run: |
+          printenv
+          conda install -y -c conda-forge python=${{ matrix.python-version }} "numpy>=1.23" "scipy>=1.12" "matplotlib>=3.8" "h5py>=3.5" "wxpython>=4.2" scikit-learn jupyter plotly pytest pytest-cov coverage
+      - name: Install xraylarch and other dependencies with pip
+        run: |
+          pip install ".[all]"
+      - name: Run test suite
+        run: pytest --xvfb-backend xvfb tests/

larch/wxlib/cif_browser.py

@@ -551,7 +551,7 @@ def onGetFeff(self, event=None):
 
         etitles.append(f'Cell Parameters (A, degrees): {", ".join(cell)}')
         etitles.append(f'Cell Volume (A^3): {cif.cell_volume:.5f}')
-        etitles.append(f'Crystal Density (gr/cm^3): {cif.crystal_density:.5f}')
+        etitles.append(f'Crystal Density (gr/cm^3): {cif.crystal_density}')
         etitles.append(f'Compound: {cif.compound}')
 
         fefftext = cif2feffinp(cif.ciftext, catom, edge=edge, cluster_size=csize,
@@ -693,11 +693,12 @@ def onExportCIF(self, event=None):
                 fh.write(cc.ciftext)
             self.write_message("Wrote CIF file %s" % path, 0)
 
-    def onImportCIF(self, event=None):
-        wildcard = 'CIF files (*.cif)|*.cif|All files (*.*)|*.*'
-        path = FileOpen(self, message='Open CIF File',
-                        wildcard=wildcard, default_file='My.cif')
-        path = unixpath(path)
+    def onImportCIF(self, event=None, path=None):
+        if path is None:
+            wildcard = 'CIF files (*.cif)|*.cif|All files (*.*)|*.*'
+            path = FileOpen(self, message='Open CIF File',
+                            wildcard=wildcard, default_file='My.cif')
+            path = unixpath(path)
         if path is not None:
             try:
                 cif_data = parse_cif_file(path)
@@ -722,13 +723,14 @@ def onImportCIF(self, event=None):
                 message = [f"Error displaying CIF File: {path}"]
                 ExceptionPopup(self, title, message)
 
-    def onImportFeff(self, event=None):
+    def onImportFeff(self, event=None, path=None):
         if not self.with_feff:
             return
-        wildcard = 'Feff input files (*.inp)|*.inp|All files (*.*)|*.*'
-        path = FileOpen(self, message='Open Feff Input File',
-                        wildcard=wildcard, default_file='feff.inp')
-        path = unixpath(path)
+        if path is None:
+            wildcard = 'Feff input files (*.inp)|*.inp|All files (*.*)|*.*'
+            path = FileOpen(self, message='Open Feff Input File',
+                            wildcard=wildcard, default_file='feff.inp')
+            path = unixpath(path)
         if path is not None:
             fefftext = None
             fname = Path(path).name
@@ -848,13 +850,15 @@ def onClose(self, event=None):
 
 
 class CIFViewer(LarchWxApp):
-    def __init__(self, filename=None, version_info=None,  **kws):
+    def __init__(self, filename=None, version_info=None, with_feff=False, **kws):
         self.filename = filename
+        self.with_feff = with_feff
         LarchWxApp.__init__(self, version_info=version_info, **kws)
 
     def createApp(self):
         frame = CIFFrame(filename=self.filename,
-                         version_info=self.version_info)
+                         version_info=self.version_info,
+                         with_feff=self.with_feff)
         self.SetTopWindow(frame)
         return True
 

larch/wxlib/structure2feff_browser.py

@@ -292,7 +292,7 @@ def onRunFeff(self, event=None):
         out = self.wids['feffout_text']
         out.Clear()
         out.SetInsertionPoint(0)
-        out.WriteText(f'########\n###\n# Run Feff in folder: {folder:s}\n')
+        out.WriteText(f'########\n###\n# Run Feff in folder: {self.folder:s}\n')
         out.SetInsertionPoint(out.GetLastPosition())
         out.WriteText('###\n########\n')
         out.SetInsertionPoint(out.GetLastPosition())
@@ -377,10 +377,11 @@ def onExportStructure(self, event=None):
                 fh.write(cc['structure_text'])
             self.write_message("Wrote structure file %s" % path, 0)
 
-    def onImportStructure(self, event=None):
-        wildcard = 'Strucuture files (*.cif/*.postcar/*.contcar/*.chgcar/*locpot/*.cssr)|*.cif;*.postcar;*.contcar;*.chgcar;*locpot;*.cssr|Molecule files (*.xyz/*.gjf/*.g03/*.g09/*.com/*.inp)|*.xyz;*.gjf;*.g03;*.g09;*.com;*.inp|All other files readable with Openbabel (*.*)|*.*'
-        path = FileOpen(self, message='Open Structure File',
-                        wildcard=wildcard, default_file='My.cif')
+    def onImportStructure(self, event=None, path=None):
+        if path is None:
+            wildcard = 'Strucuture files (*.cif/*.postcar/*.contcar/*.chgcar/*locpot/*.cssr)|*.cif;*.postcar;*.contcar;*.chgcar;*locpot;*.cssr|Molecule files (*.xyz/*.gjf/*.g03/*.g09/*.com/*.inp)|*.xyz;*.gjf;*.g03;*.g09;*.com;*.inp|All other files readable with Openbabel (*.*)|*.*'
+            path = FileOpen(self, message='Open Structure File',
+                            wildcard=wildcard, default_file='My.cif')
 
         if path is not None:
             fmt = path.split('.')[-1]
@@ -426,10 +427,11 @@ def onImportStructure(self, event=None):
         i, p = self.get_nbpage('Structure Text')
         self.nb.SetSelection(i)
 
-    def onImportFeff(self, event=None):
-        wildcard = 'Feff input files (*.inp)|*.inp|All files (*.*)|*.*'
-        path = FileOpen(self, message='Open Feff Input File',
-                        wildcard=wildcard, default_file='feff.inp')
+    def onImportFeff(self, event=None, path=None):
+        if path is None:
+            wildcard = 'Feff input files (*.inp)|*.inp|All files (*.*)|*.*'
+            path = FileOpen(self, message='Open Feff Input File',
+                            wildcard=wildcard, default_file='feff.inp')
         if path is not None:
             fefftext = None
             fname = Path(path).name.replace('.inp', '_run')
@@ -511,7 +513,7 @@ def __init__(self, filename=None, version_info=None,  **kws):
 
     def createApp(self):
         frame = Structure2FeffFrame(filename=self.filename,
-                         version_info=self.version_info)
+                                    version_info=self.version_info)
         self.SetTopWindow(frame)
         return True
 

larch/xrd/struct2xas.py

@@ -260,7 +260,7 @@ def read_structure(self, file):
             self.nframes = 1
             self.cif = CifParser(self.file, occupancy_tolerance=10, site_tolerance=5e-3)
             self.struct = Structure.from_file(self.file)
-            # self.struct = self.cif.parse_structures()[0] #: TODO
+            # self.struct = self.cif.parse_structures(primitive=False)[0] #: TODO
             # self.struct = self.cif.get_structures()[0]  #: DEPRECATED / NOT WORKING!
             logger.debug("structure created from a CIF file")
         elif self.file_ext == ".xyz":

setup.cfg

@@ -104,6 +104,7 @@ doc =
 dev =
     pytest
     pytest-cov
+    pytest-xvfb  #: For GUI testing
     coverage
     build
     pre-commit

tests/test_athena_addgroup.py

@@ -2,18 +2,24 @@
 from pathlib import Path
 from larch.io import read_ascii, AthenaProject
 
+data_dir = Path(__file__).parent.parent / "examples" / "xafsdata"
+
 
 def test_add_athena_group():
-    a = read_ascii('../examples/xafsdata/cu_10k.xmu')
-    b = read_ascii('../examples/xafsdata/cu_10k.xmu')
+    a = read_ascii(data_dir / "cu_10k.xmu")
+    b = read_ascii(data_dir / "cu_10k.xmu")
     b.mutrans = b.mu[:]
-    b.filename = 'cu_10k_copy.xmu'
+    b.filename = "cu_10k_copy.xmu"
     del b.mu
 
-    p = AthenaProject('x1.prj')
+    p = AthenaProject("x1.prj")
     p.add_group(a)
     p.add_group(b)
     p.save()
 
     # remove file after test
-    Path('x1.prj').unlink(missing_ok=True)
+    Path("x1.prj").unlink(missing_ok=True)
+
+
+if __name__ == "__main__":
+    test_add_athena_group()

tests/test_wxlib_cif_browser.py

@@ -0,0 +1,25 @@
+#!/usr/bin/env python
+"""Test larch.wxlib.cif_browser"""
+
+import sys, os
+import pytest
+from pathlib import Path
+from larch.wxlib.cif_browser import CIFViewer
+
+toppath = Path(__file__).parent.parent
+structpath = toppath / "examples" / "structuredata" / "struct2xas"
+
+
+@pytest.mark.skipif(os.name == "nt" and sys.version_info < (3,10), reason="fails for windows and python3.9")
+def test_cif2feff():
+    cif_file = structpath / "ZnO_mp-2133.cif"
+    viewer = CIFViewer(with_feff=True)
+    frame = viewer.GetTopWindow()
+    frame.onImportCIF(path=cif_file.as_posix())
+    frame.onGetFeff()
+    frame.onRunFeff()
+    # viewer.MainLoop()
+
+
+if __name__ == "__main__":
+    test_cif2feff()

tests/test_wxlib_structure2feff_browser.py

@@ -0,0 +1,23 @@
+#!/usr/bin/env python
+"""Test larch.wxlib.structure2feff_browser"""
+
+import pytest
+from pathlib import Path
+from larch.wxlib.structure2feff_browser import Structure2FeffViewer
+
+toppath = Path(__file__).parent.parent
+structpath = toppath / "examples" / "structuredata" / "struct2xas"
+
+
+def test_structure2feff():
+    struct_file = structpath / "GaBr_single_frame.xyz"
+    viewer = Structure2FeffViewer()
+    frame = viewer.GetTopWindow()
+    frame.onImportStructure(path=struct_file.as_posix())
+    frame.onGetFeff()
+    frame.onRunFeff()
+    # viewer.MainLoop()
+
+
+if __name__ == "__main__":
+    test_structure2feff()