Hotfix remove the tracked output files from pytest (#46)

* feat: add use_gui option in run command.  default use_gui is false, whic means dptb will only save the figure not plot and show the figure in a window. this suits for the servers where no gui.

* test: rm the run_config and add it to gitignore.

.gitignore

@@ -5,6 +5,8 @@ dptb/tests/data/test_all/test_config.json
 dptb/tests/data/test_all/checkpoint/best_nnsk_b5.000_c6.615_w0.265.json
 dptb/tests/data/test_all/checkpoint/best_nnsk_b4.000_c4.000_w0.300.json
 dptb/tests/data/test_all/fancy_ones/checkpoint/best_nnsk_b4.000_c4.000_w0.300.json
+dptb/tests/data/test_negf/test_negf_run/out_negf/run_config.json
+run_config.json
 dptb/nnet/__pycache__/
 dptb/sktb/__pycache__/
 dptb/negf/__pycache__/

dptb/entrypoints/run.py

@@ -95,6 +95,9 @@ def run(
 
     task_options = j_must_have(jdata, "task_options")
     task = task_options["task"]
+    use_gui = jdata.get("use_gui", False)
+    task_options.update({"use_gui": use_gui})
+
     model_ckpt = run_opt["init_model"]["path"]
     # init_type = model_ckpt.split(".")[-1]
     # if init_type not in ["json", "pth"]:

dptb/postprocess/bandstructure/band.py

@@ -24,7 +24,8 @@ def __init__ (self, apiHrk, run_opt, jdata):
         self.apiH.update_struct(self.structase)
 
         self.ref_band = self.band_plot_options.get("ref_band", None)
-
+        self.use_gui = self.band_plot_options.get("use_gui", False)
+
     def get_bands(self):
         kline_type = self.band_plot_options['kline_type']
 
@@ -153,4 +154,5 @@ def band_plot(self):
         # remove the box around the plot
         ax.set_frame_on(False)
         plt.savefig(f'{self.results_path}/band.png',dpi=300)
-        plt.show()
+        if self.use_gui:
+            plt.show()

dptb/postprocess/bandstructure/dos.py

@@ -21,7 +21,7 @@ def __init__ (self, apiHrk, run_opt, jdata):
         self.dos_plot_options = jdata
         self.results_path = run_opt.get('results_path')
         self.apiH.update_struct(self.structase)
-
+        self.use_gui = self.dos_plot_options.get("use_gui", False)
 
     def get_dos(self):
         self.mesh_grid = self.dos_plot_options['mesh_grid']
@@ -59,7 +59,8 @@ def dos_plot(self):
         plt.tick_params(direction='in')
         plt.tight_layout()
         plt.savefig(f'{self.results_path}/dos.png',dpi=300)
-        plt.show()
+        if self.use_gui:
+            plt.show()
 
 
     def _calc_dos(self, sigma=0.1, npoints=100,  width=None, updata=False, kpoints=None):
@@ -123,6 +124,8 @@ def __init__ (self, apiHrk, run_opt, jdata):
         for itype in apiHrk.structure.proj_atom_symbols:
             norbs = apiHrk.structure.proj_atomtype_norbs[itype]
             self.num_orbs_per_atom.append(norbs)
+
+        self.use_gui = self.pdos_plot_options.get("use_gui", False)
 
     def get_pdos(self):
         self.mesh_grid = self.pdos_plot_options['mesh_grid']
@@ -183,7 +186,8 @@ def pdos_plot(self, atom_index=None, orbital_index=None):
         plt.tick_params(direction='in')
         plt.tight_layout()
         plt.savefig(f'{self.results_path}/proj_dos.png',dpi=300)
-        plt.show()
+        if self.use_gui:
+            plt.show()
 
 
     def _calc_pdos(self, sigma=0.1, npoints=100,  width=None, updata=False, kpoints=None):

dptb/utils/argcheck.py

@@ -593,6 +593,7 @@ def normalize_run(data):
     doc_structure = ""
     doc_use_correction = ""
     doc_overlap = ""
+    doc_gui = ""
 
     args = [
         Argument("onsite_cutoff", float, optional = False, doc = doc_onsite_cutoff),
@@ -621,6 +622,7 @@ def normalize_run(data):
         mo,
         Argument("structure", [str,None], optional=True, default=None, doc = doc_structure),
         Argument("use_correction", [str,None], optional=True, default=None, doc = doc_use_correction),
+        Argument("use_gui", bool, optional=True, default=False, doc = doc_gui),
         Argument("task_options", dict, sub_fields=[], optional=True, sub_variants=[task_options()], doc = doc_property)
     ]