temporary fix for figdir issue which should currently be a positional…

… argument, but would require redundant rewrite of workflows base module, pending issue #244

mdpow/tests/test_workflows_base.py

@@ -67,15 +67,14 @@ def test_project_paths_csv_input(self, csv_input_data):
 
         pd.testing.assert_frame_equal(project_paths, csv_df)
 
-    def test_automated_project_analysis(self, SM_tmp_dir, project_paths_data, caplog):
+    def test_automated_project_analysis(self, project_paths_data, caplog):
         project_paths = project_paths_data
         # change resname to match topology (every SAMPL7 resname is 'UNK')
         # only necessary for this dataset, not necessary for normal use
         project_paths['resname'] = 'UNK'
 
         base.automated_project_analysis(project_paths, solvents=('water',),
-                                        ensemble_analysis='DihedralAnalysis',
-                                        figdir=SM_tmp_dir)
+                                        ensemble_analysis='DihedralAnalysis')
 
         assert 'all analyses completed' in caplog.text, ('automated_dihedral_analysis '
                'did not iteratively run to completion for the provided project')

mdpow/workflows/dihedrals.py

@@ -629,7 +629,7 @@ def build_svg(mol, molname, ab_pairs, atom_group_selection,
 
     return fig
 
-def plot_dihedral_violins(df, resname, mol, ab_pairs, figdir, molname=None,
+def plot_dihedral_violins(df, resname, mol, ab_pairs, figdir=None, molname=None,
                  width=0.9, plot_pdf_width=PLOT_WIDTH_DEFAULT, solvents=SOLVENTS_DEFAULT):
     '''Coordinates plotting and saving figures for all dihedral atom groups.
        
@@ -691,22 +691,23 @@ def plot_dihedral_violins(df, resname, mol, ab_pairs, figdir, molname=None,
         newdir = os.path.join(figdir, subdir)
         os.mkdir(newdir)
 
-    section = df.groupby(by="selection")
+        section = df.groupby(by="selection")
 
-    plot_pdf_width_px = plot_pdf_width * 3.7795275591
+        plot_pdf_width_px = plot_pdf_width * 3.7795275591
 
-    for name in section:
+        for name in section:
 
-        fig = build_svg(mol=mol, molname=molname, atom_group_selection=name, ab_pairs=ab_pairs,
-                        solvents=solvents, width=width)
+            fig = build_svg(mol=mol, molname=molname, atom_group_selection=name, ab_pairs=ab_pairs,
+                            solvents=solvents, width=width)
 
-        figfile = pathlib.Path(newdir) / f"{molname}_{name[0]}_violins.pdf"
-        plot_pdf = cairosvg.svg2pdf(bytestring=fig.tostr(), write_to=str(figfile),
-                                    output_width=plot_pdf_width_px)
+            figfile = pathlib.Path(newdir) / f"{molname}_{name[0]}_violins.pdf"
+            if figdir is not None:
+                plot_pdf = cairosvg.svg2pdf(bytestring=fig.tostr(), write_to=str(figfile),
+                                            output_width=plot_pdf_width_px)
 
-        logger.info(f"Figure saved as {figfile}")
+            logger.info(f"Figure saved as {figfile}")
 
-    logger.info(f"All figures generated and saved in {figdir}")
+        logger.info(f"All figures generated and saved in {figdir}")
 
     return None