Add support for random seed

src/phylojunction/interface/cmdbox/cmd_parse.py

@@ -20,15 +20,19 @@
 
 
 def script2dag(script_file_path_or_model_spec: str,
-               in_pj_file: bool = True) -> pgm.DirectedAcyclicGraph:
+               in_pj_file: bool = True,
+               random_seed: ty.Optional[int] = None) -> pgm.DirectedAcyclicGraph:
     """Go through .pj lines and populate and return DAG.
 
     Args:
         script_file_path_or_model_spec (str): Path to script .pj
-            file or full string specifying model directly
+            file or full string specifying model directly.
+        random_seed (int): Random seed (integer) for simulation.
+            Defaults to None.
 
     Returns:
-        (DirectedAcyclicGraph): DAG object built from .pj commands.
+        (DirectedAcyclicGraph): DAG object (model) built from .pj
+            script commands.
     """
 
     def _execute_spec_lines(
@@ -40,14 +44,13 @@ def _execute_spec_lines(
             line = line.lstrip().rstrip()
             _ = cmdline2dag(dag_obj, line)
 
-    # handle seed if specified
-    np.random.seed(seed=123)
-    random.seed(123)
-
+    # initialize model DAG
     dag = pgm.DirectedAcyclicGraph()
+    if random_seed is not None:
+        dag.random_seed = random_seed
 
-    all_lines_list: ty.List[str] = []
-
+    # get script strings
+    all_lines_list: ty.List[str] = list()
     if in_pj_file:
         with open(script_file_path_or_model_spec, "r") as infile:
             all_lines_list = infile.readlines()

src/phylojunction/interface/cmdbox/cmd_parse.pyi

@@ -1,6 +1,8 @@
+import typing as ty
+
 import phylojunction.pgm.pgm as pgm
 
-def script2dag(script_file_path: str) -> pgm.DirectedAcyclicGraph: ...
+def script2dag(script_file_path: str, in_pj_file: bool=True, random_seed: ty.Optional[int]=None) -> pgm.DirectedAcyclicGraph: ...
 def cmdline2dag(dag_obj: pgm.DirectedAcyclicGraph, cmd_line: str): ...
 def parse_variable_assignment(dag_obj: pgm.DirectedAcyclicGraph, stoch_node_name: str, stoch_node_spec: str, cmd_line: str) -> None: ...
 def parse_samp_dn_assignment(dag_obj, stoch_node_name, stoch_node_dn_spec, cmd_line) -> None: ...

src/phylojunction/interface/pjcli/pj_cli.py

@@ -20,20 +20,25 @@ def execute_pj_script(
         write_data: bool = False,
         write_figures: str = "",
         write_inference: bool = False,
-        write_nex_states: bool = False) -> None:
+        write_nex_states: bool = False,
+        a_random_seed: ty.Optional[int] = None) -> None:
     """
-    Execute .pj script
+    Execute .pj script.
 
     This is called by application 'pjcli' from the terminal,
     but can also be called from a .py script importing phylojunction
     """
 
     # Reading model #
-    dag_obj: pgm.DirectedAcyclicGraph = \
-        pgm.DirectedAcyclicGraph()
+    random_seed: int = None
+    if a_random_seed is not None:
+        random_seed = int(a_random_seed)
 
     print("Reading script " + model)
-    dag_obj = cmd.script2dag(model, in_pj_file=True)
+    dag_obj: pgm.DirectedAcyclicGraph \
+        = cmd.script2dag(model,
+                        in_pj_file=True,
+                        random_seed=random_seed)
     print("    ... done!")
 
     n_samples = dag_obj.sample_size
@@ -135,8 +140,8 @@ def call_cli() -> None:
         dest="out_dir",
         type=str,
         default="./",
-        help=("Path to project root directory, where automatic "
-              "subdirectories will be created"))
+        help=("Path to project root directory, where subdirectories "
+              "will be automatically created"))
     parser.add_argument(
         "-p",
         "--prefix",
@@ -150,6 +155,12 @@ def call_cli() -> None:
         action="store_true",
         default=False,
         help="Toggle states nexus file output")
+    parser.add_argument(
+        "-r", "--random-seed",
+        dest="random_seed",
+        action="store",
+        default=None,
+        help="Random seed (integer)")
 
     args = parser.parse_args()
 
@@ -160,7 +171,8 @@ def call_cli() -> None:
         write_data=args.write_data,
         write_figures=args.write_figures,
         write_inference=args.write_inference,
-        write_nex_states=args.write_nex_states
+        write_nex_states=args.write_nex_states,
+        a_random_seed=args.random_seed
     )
 
 # if one wants to run pj_cli.py for some reason

src/phylojunction/interface/pysidegui/pj_gui.py

@@ -34,11 +34,15 @@ def __init__(self):
         self.dag_obj = DirectedAcyclicGraph()
         self.cmd_log_list = []
 
+    def update_dag_random_seed(self, a_random_seed: int):
+        self.dag_obj.random_seed = a_random_seed
+
     def parse_cmd_update_pgm(
             self,
             cmd_line_list,
             gui_main_window_obj,
             clear_cmd_log_list: bool = False):
+
         # in case we read two scripts
         # consecutively, we want to clear
         # the comand line history list
@@ -53,6 +57,17 @@ def parse_cmd_update_pgm(
             line = line.strip()
             print("  " + line)
 
+            # will set random seed once if DAG does not already have one
+            if not isinstance(self.dag_obj.random_seed, int):
+                a_random_seed: str = \
+                    gui_main_window_obj.ui.ui_pages. \
+                        random_seed_prefix_textbox.toPlainText()
+
+                # random seed is not None and not empty string
+                if a_random_seed:
+                    random_seed: int = int(a_random_seed)
+                    self.dag_obj.random_seed = random_seed
+
             # side-effect in cmdline2dag
             try:
                 valid_cmd_line = cmdp.cmdline2dag(self.dag_obj, line)
@@ -317,7 +332,7 @@ def show_compare_page(self):
     def show_coverage_page(self):
         self.reset_selection()
         self.ui.pages.setCurrentWidget(self.ui.ui_pages.coverage_page)
-        self.ui.compare_button.set_active(True)
+        self.ui.covg_button.set_active(True)
         self.ui.top_label_left.setText("COVERAGE VALIDATION")
 
     def show_cmd_log_page(self):
@@ -704,6 +719,14 @@ def read_execute_script(self):
             # reset everything #
             self.clean_disable_everything()
 
+            # set seed
+            a_random_seed = self.ui.ui_pages.random_seed_prefix_textbox.toPlainText()
+            # is not None and is not an empty string
+            if a_random_seed:
+                random_seed: int = int(a_random_seed)
+                self.gui_modeling.update_dag_random_seed(random_seed)
+
+            # read all command line strings
             cmd_line_list = pjread.read_text_file(script_fp)
 
             # (side-effect: gui_modeling stores cmd hist) #
@@ -800,12 +823,17 @@ def read_coverage_hpd_csv(self):
 
     def load_model(self):
         # read file path #
-        model_fp, filter = QFileDialog.getOpenFileName(parent=self, caption="Load model", dir=".", filter="*.pickle")
+        model_fp, filter = QFileDialog.getOpenFileName(
+            parent=self,
+            caption="Load model",
+            dir=".",
+            filter="*.pickle")
 
         if model_fp:
             self.clean_disable_everything()
             self.ui.ui_pages.cmd_log_textbox.clear()
-            self.gui_modeling.dag_obj, self.gui_modeling.cmd_log_list = pjread.read_serialized_pgm(model_fp)
+            self.gui_modeling.dag_obj, self.gui_modeling.cmd_log_list = \
+                pjread.read_serialized_pgm(model_fp)
             self.refresh_node_lists()
             self.ui.ui_pages.cmd_log_textbox.setText(self.gui_modeling.cmd_log())
 
@@ -1059,10 +1087,10 @@ def _prepare_for_tree(potential_repl: bool = False):
             self.ui.ui_pages.sample_idx_spin.setMinimum(1)
             self.ui.ui_pages.sample_idx_spin.setValue(1)
 
+            self.ui.ui_pages.repl_idx_spin.setMinimum(1)
+            self.ui.ui_pages.repl_idx_spin.setValue(1)
             if potential_repl:
                 self.ui.ui_pages.repl_idx_spin.setEnabled(True)
-                self.ui.ui_pages.repl_idx_spin.setMinimum(1)
-                self.ui.ui_pages.repl_idx_spin.setValue(1)
 
         def _prepare_for_scalar(potential_repl: bool = False):
             # radio #
@@ -1109,7 +1137,7 @@ def _nothing_to_spin_through():
         # (basically: non-deterministic nodes)
         if isinstance(node_dag.value, list):
             if isinstance(node_dag.value[0], pjdt.AnnotatedTree):
-                if node_dag.repl_size > 1:
+                if node_dag.repl_size >= 2:
                     _prepare_for_tree(potential_repl=True)
 
                 else:

src/phylojunction/interface/pysidegui/pjguipages/gui_pages.py

@@ -1,8 +1,8 @@
 # -*- coding: utf-8 -*-
 
-# Form implementation generated from reading ui file 'src/phylojunction/interface/pysidegui/pjguipages/pjgui_pages.ui'
+# Form implementation generated from reading ui file 'pjgui_pages.ui'
 #
-# Created by: PyQt5 UI code generator 5.15.7
+# Created by: PyQt5 UI code generator 5.15.9
 #
 # WARNING: Any manual changes made to this file will be lost when pyuic5 is
 # run again.  Do not edit this file unless you know what you are doing.
@@ -25,26 +25,45 @@ def setupUi(self, PJGUIPages):
         self.settings_page_grid_layout = QtWidgets.QGridLayout(self.gridLayoutWidget_4)
         self.settings_page_grid_layout.setContentsMargins(0, 0, 0, 0)
         self.settings_page_grid_layout.setObjectName("settings_page_grid_layout")
-        self.label = QtWidgets.QLabel(self.gridLayoutWidget_4)
-        self.label.setMinimumSize(QtCore.QSize(0, 24))
-        self.label.setMaximumSize(QtCore.QSize(16777215, 24))
-        self.label.setObjectName("label")
-        self.settings_page_grid_layout.addWidget(self.label, 0, 0, 1, 1)
-        self.filename_prefix_hor_layout = QtWidgets.QHBoxLayout()
-        self.filename_prefix_hor_layout.setObjectName("filename_prefix_hor_layout")
         self.filename_prefix_label = QtWidgets.QLabel(self.gridLayoutWidget_4)
         self.filename_prefix_label.setMinimumSize(QtCore.QSize(110, 24))
         self.filename_prefix_label.setMaximumSize(QtCore.QSize(110, 24))
         self.filename_prefix_label.setObjectName("filename_prefix_label")
-        self.filename_prefix_hor_layout.addWidget(self.filename_prefix_label, 0, QtCore.Qt.AlignTop)
+        self.settings_page_grid_layout.addWidget(self.filename_prefix_label, 1, 0, 1, 1)
+        self.random_seed_prefix_label = QtWidgets.QLabel(self.gridLayoutWidget_4)
+        self.random_seed_prefix_label.setMinimumSize(QtCore.QSize(110, 24))
+        self.random_seed_prefix_label.setMaximumSize(QtCore.QSize(110, 24))
+        self.random_seed_prefix_label.setObjectName("random_seed_prefix_label")
+        self.settings_page_grid_layout.addWidget(self.random_seed_prefix_label, 2, 0, 1, 1)
+        self.settings_label = QtWidgets.QLabel(self.gridLayoutWidget_4)
+        self.settings_label.setMinimumSize(QtCore.QSize(0, 24))
+        self.settings_label.setMaximumSize(QtCore.QSize(16777215, 24))
+        font = QtGui.QFont()
+        font.setBold(True)
+        self.settings_label.setFont(font)
+        self.settings_label.setObjectName("settings_label")
+        self.settings_page_grid_layout.addWidget(self.settings_label, 0, 0, 1, 1)
+        spacerItem = QtWidgets.QSpacerItem(20, 40, QtWidgets.QSizePolicy.Minimum, QtWidgets.QSizePolicy.Expanding)
+        self.settings_page_grid_layout.addItem(spacerItem, 3, 0, 1, 1)
         self.filename_prefix_textbox = QtWidgets.QTextEdit(self.gridLayoutWidget_4)
         self.filename_prefix_textbox.setMinimumSize(QtCore.QSize(0, 24))
         self.filename_prefix_textbox.setMaximumSize(QtCore.QSize(16777215, 24))
         self.filename_prefix_textbox.setVerticalScrollBarPolicy(QtCore.Qt.ScrollBarAlwaysOff)
         self.filename_prefix_textbox.setHorizontalScrollBarPolicy(QtCore.Qt.ScrollBarAlwaysOff)
         self.filename_prefix_textbox.setObjectName("filename_prefix_textbox")
-        self.filename_prefix_hor_layout.addWidget(self.filename_prefix_textbox, 0, QtCore.Qt.AlignTop)
-        self.settings_page_grid_layout.addLayout(self.filename_prefix_hor_layout, 1, 0, 1, 1)
+        self.settings_page_grid_layout.addWidget(self.filename_prefix_textbox, 1, 1, 1, 1)
+        self.random_seed_prefix_textbox = QtWidgets.QTextEdit(self.gridLayoutWidget_4)
+        self.random_seed_prefix_textbox.setMinimumSize(QtCore.QSize(0, 24))
+        self.random_seed_prefix_textbox.setMaximumSize(QtCore.QSize(16777215, 24))
+        self.random_seed_prefix_textbox.setVerticalScrollBarPolicy(QtCore.Qt.ScrollBarAlwaysOff)
+        self.random_seed_prefix_textbox.setHorizontalScrollBarPolicy(QtCore.Qt.ScrollBarAlwaysOff)
+        self.random_seed_prefix_textbox.setObjectName("random_seed_prefix_textbox")
+        self.settings_page_grid_layout.addWidget(self.random_seed_prefix_textbox, 2, 1, 1, 1)
+        self.line = QtWidgets.QFrame(self.gridLayoutWidget_4)
+        self.line.setFrameShape(QtWidgets.QFrame.HLine)
+        self.line.setFrameShadow(QtWidgets.QFrame.Sunken)
+        self.line.setObjectName("line")
+        self.settings_page_grid_layout.addWidget(self.line, 0, 1, 1, 1)
         PJGUIPages.addWidget(self.settings_page)
         self.pgm_page = QtWidgets.QWidget()
         self.pgm_page.setMinimumSize(QtCore.QSize(980, 700))
@@ -108,7 +127,7 @@ def setupUi(self, PJGUIPages):
 "    color: #ec4a8a;\n"
 "}")
         icon = QtGui.QIcon()
-        icon.addPixmap(QtGui.QPixmap("src/phylojunction/interface/pysidegui/pjguipages/../images/icons/icon_clear.svg"), QtGui.QIcon.Normal, QtGui.QIcon.Off)
+        icon.addPixmap(QtGui.QPixmap("../images/icons/icon_clear.svg"), QtGui.QIcon.Normal, QtGui.QIcon.Off)
         self.clear_model.setIcon(icon)
         self.clear_model.setIconSize(QtCore.QSize(20, 20))
         self.clear_model.setObjectName("clear_model")
@@ -131,16 +150,16 @@ def setupUi(self, PJGUIPages):
         self.all_samples_radio.setAutoExclusive(True)
         self.all_samples_radio.setObjectName("all_samples_radio")
         self.radio_spin_hor_layout.addWidget(self.all_samples_radio)
-        spacerItem = QtWidgets.QSpacerItem(20, 20, QtWidgets.QSizePolicy.Maximum, QtWidgets.QSizePolicy.Minimum)
-        self.radio_spin_hor_layout.addItem(spacerItem)
+        spacerItem1 = QtWidgets.QSpacerItem(20, 20, QtWidgets.QSizePolicy.Maximum, QtWidgets.QSizePolicy.Minimum)
+        self.radio_spin_hor_layout.addItem(spacerItem1)
         self.sample_idx_spin = QtWidgets.QSpinBox(self.gridLayoutWidget)
         self.sample_idx_spin.setEnabled(False)
         self.sample_idx_spin.setStyleSheet("color: black;")
         self.sample_idx_spin.setAccelerated(True)
         self.sample_idx_spin.setObjectName("sample_idx_spin")
         self.radio_spin_hor_layout.addWidget(self.sample_idx_spin)
-        spacerItem1 = QtWidgets.QSpacerItem(20, 20, QtWidgets.QSizePolicy.Maximum, QtWidgets.QSizePolicy.Minimum)
-        self.radio_spin_hor_layout.addItem(spacerItem1)
+        spacerItem2 = QtWidgets.QSpacerItem(20, 20, QtWidgets.QSizePolicy.Maximum, QtWidgets.QSizePolicy.Minimum)
+        self.radio_spin_hor_layout.addItem(spacerItem2)
         self.repl_idx_spin = QtWidgets.QSpinBox(self.gridLayoutWidget)
         self.repl_idx_spin.setEnabled(False)
         self.repl_idx_spin.setStyleSheet("color: black;\n"
@@ -149,8 +168,8 @@ def setupUi(self, PJGUIPages):
         self.repl_idx_spin.setAccelerated(True)
         self.repl_idx_spin.setObjectName("repl_idx_spin")
         self.radio_spin_hor_layout.addWidget(self.repl_idx_spin)
-        spacerItem2 = QtWidgets.QSpacerItem(40, 20, QtWidgets.QSizePolicy.Expanding, QtWidgets.QSizePolicy.Minimum)
-        self.radio_spin_hor_layout.addItem(spacerItem2)
+        spacerItem3 = QtWidgets.QSpacerItem(40, 20, QtWidgets.QSizePolicy.Expanding, QtWidgets.QSizePolicy.Minimum)
+        self.radio_spin_hor_layout.addItem(spacerItem3)
         self.save_pgm_node_plot = QtWidgets.QPushButton(self.gridLayoutWidget)
         self.save_pgm_node_plot.setEnabled(True)
         self.save_pgm_node_plot.setMinimumSize(QtCore.QSize(130, 24))
@@ -290,8 +309,8 @@ def setupUi(self, PJGUIPages):
         self.avg_replicate_check_button.setCursor(QtGui.QCursor(QtCore.Qt.PointingHandCursor))
         self.avg_replicate_check_button.setObjectName("avg_replicate_check_button")
         self.node_stat_vert_layout.addWidget(self.compare_node_frame)
-        spacerItem3 = QtWidgets.QSpacerItem(20, 40, QtWidgets.QSizePolicy.Minimum, QtWidgets.QSizePolicy.Expanding)
-        self.node_stat_vert_layout.addItem(spacerItem3)
+        spacerItem4 = QtWidgets.QSpacerItem(20, 40, QtWidgets.QSizePolicy.Minimum, QtWidgets.QSizePolicy.Expanding)
+        self.node_stat_vert_layout.addItem(spacerItem4)
         self.compare_stats_label = QtWidgets.QLabel(self.gridLayoutWidget_2)
         self.compare_stats_label.setMinimumSize(QtCore.QSize(0, 16))
         self.compare_stats_label.setMaximumSize(QtCore.QSize(16777215, 16))
@@ -521,8 +540,8 @@ def setupUi(self, PJGUIPages):
         self.coverage_node_label.setAlignment(QtCore.Qt.AlignCenter)
         self.coverage_node_label.setObjectName("coverage_node_label")
         self.cov_node_stat_vert_layout.addWidget(self.coverage_frame, 0, QtCore.Qt.AlignHCenter)
-        spacerItem4 = QtWidgets.QSpacerItem(20, 40, QtWidgets.QSizePolicy.Minimum, QtWidgets.QSizePolicy.Expanding)
-        self.cov_node_stat_vert_layout.addItem(spacerItem4)
+        spacerItem5 = QtWidgets.QSpacerItem(20, 40, QtWidgets.QSizePolicy.Minimum, QtWidgets.QSizePolicy.Expanding)
+        self.cov_node_stat_vert_layout.addItem(spacerItem5)
         self.compare_stats_label_2 = QtWidgets.QLabel(self.gridLayoutWidget_3)
         self.compare_stats_label_2.setMinimumSize(QtCore.QSize(0, 16))
         self.compare_stats_label_2.setMaximumSize(QtCore.QSize(16777215, 16))
@@ -586,14 +605,15 @@ def setupUi(self, PJGUIPages):
 
         self.retranslateUi(PJGUIPages)
         PJGUIPages.setCurrentIndex(1)
-        self.node_content_tabs.setCurrentIndex(0)
+        self.node_content_tabs.setCurrentIndex(1)
         QtCore.QMetaObject.connectSlotsByName(PJGUIPages)
 
     def retranslateUi(self, PJGUIPages):
         _translate = QtCore.QCoreApplication.translate
         PJGUIPages.setWindowTitle(_translate("PJGUIPages", "StackedWidget"))
-        self.label.setText(_translate("PJGUIPages", "Output configuration"))
         self.filename_prefix_label.setText(_translate("PJGUIPages", "File name prefix:"))
+        self.random_seed_prefix_label.setText(_translate("PJGUIPages", "Random seed:"))
+        self.settings_label.setText(_translate("PJGUIPages", "Output configuration"))
         self.model_label.setText(_translate("PJGUIPages", "Model nodes"))
         self.clear_model.setText(_translate("PJGUIPages", " Clear model"))
         self.one_sample_radio.setText(_translate("PJGUIPages", "One sample"))