sierra-research 1.3.6__py3-none-any.whl → 1.5.0__py3-none-any.whl

sierra/core/pipeline/stage4/pipeline_stage4.py

@@ -2,34 +2,25 @@
 #
 # SPDX-License-Identifier: MIT
 
-"""Stage 4 of the experimental pipeline: generating deliverables.
-
-"""
+"""Stage 4 of the experimental pipeline: generating products."""
 
 # Core packages
-import typing as tp
 import time
 import datetime
 import logging
 import pathlib
 
 # 3rd party packages
-import yaml
 
 # Project packages
-from sierra.core.pipeline.stage4.graph_collator import GraphParallelCollator
-from sierra.core.pipeline.stage4.intra_exp_graph_generator import BatchIntraExpGraphGenerator
-from sierra.core.pipeline.stage4.model_runner import IntraExpModelRunner
-from sierra.core.pipeline.stage4.model_runner import InterExpModelRunner
 import sierra.core.variables.batch_criteria as bc
 
-from sierra.core.pipeline.stage4 import rendering
-import sierra.core.plugin_manager as pm
-from sierra.core import types, config, utils
+import sierra.core.plugin as pm
+from sierra.core import types, batchroot
 
 
 class PipelineStage4:
-    """Generates end-result experimental deliverables.
+    """Generates end-result experimental products.
 
     Delvirables can be within a single experiment (intra-experiment) and across
     experiments in a batch (inter-experiment).  Currently this includes:
@@ -41,7 +32,6 @@ class PipelineStage4:
     This stage is idempotent.
 
     Attributes:
-
         cmdopts: Dictionary of parsed cmdline options.
 
         controller_config: YAML configuration file found in
@@ -51,361 +41,53 @@ class PipelineStage4:
                            graphs in both inter- and intra-experiment graph
                            generation.
 
-        inter_LN_config: YAML configuration file found in
-                         ``<project_config_root>/inter-graphs-line.yaml``
-                         Contains configuration for categories of linegraphs
-                         that can potentially be generated for all controllers
-                         `across` experiments in a batch. Which linegraphs are
-                         actually generated for a given controller is controlled
-                         by ``<project_config_root>/controllers.yaml``.
-
-        intra_LN_config: YAML configuration file found in
-                         ``<project_config_root>/intra-graphs-line.yaml``
-                         Contains configuration for categories of linegraphs
-                         that can potentially be generated for all controllers
-                         `within` each experiment in a batch. Which linegraphs
-                         are actually generated for a given controller in each
-                         experiment is controlled by
-                         ``<project_config_root>/controllers.yaml``.
-
-        intra_HM_config: YAML configuration file found in
-                         ``<project_config_root>/intra-graphs-hm.yaml`` Contains
-                         configuration for categories of heatmaps that can
-                         potentially be generated for all controllers `within`
-                         each experiment in a batch. Which heatmaps are actually
-                         generated for a given controller in each experiment is
+        graphs_config: YAML configuration file found in
+                         ``<project_config_root>/graphs.yaml``
+                         Contains configuration for categories of graphs
+                         that *can* potentially be generated for all controllers
+                         *across* experiments in a batch and *within* each
+                         experiment in a batch. Which linegraphs are
+                         *actually* generated for a given controller is
                          controlled by
                          ``<project_config_root>/controllers.yaml``.
-
-        inter_HM_config: YAML configuration file found in
-                         ``<project_config_root>/inter-graphs-hm.yaml`` Contains
-                         configuration for categories of heatmaps that can
-                         potentially be generated for all controllers `across`
-                         each experiment in a batch. Which heatmaps are actually
-                         generated for a given controller in each experiment is
-                         controlled by
-                         ``<project_config_root>/controllers.yaml``.
-
     """
 
-    def __init__(self,
-                 main_config: types.YAMLDict,
-                 cmdopts: types.Cmdopts) -> None:
-        self.cmdopts = cmdopts
+    def __init__(
+        self,
+        main_config: types.YAMLDict,
+        cmdopts: types.Cmdopts,
+        pathset: batchroot.PathSet,
+    ) -> None:
         self.main_config = main_config
+        self.cmdopts = cmdopts
+        self.pathset = pathset
 
-        self.project_config_root = pathlib.Path(self.cmdopts['project_config_root'])
-        controllers_yaml = self.project_config_root / config.kYAML.controllers
+        self.project_config_root = pathlib.Path(self.cmdopts["project_config_root"])
 
-        with utils.utf8open(controllers_yaml) as f:
-            self.controller_config = yaml.load(f, yaml.FullLoader)
         self.logger = logging.getLogger(__name__)
 
         # Load YAML config
-        loader = pm.module_load_tiered(project=self.cmdopts['project'],
-                                       path='pipeline.stage4.yaml_config_loader')
-        graphs_config = loader.YAMLConfigLoader()(self.cmdopts)
-        self.intra_LN_config = graphs_config['intra_LN']
-        self.intra_HM_config = graphs_config['intra_HM']
-        self.inter_HM_config = graphs_config['inter_HM']
-        self.inter_LN_config = graphs_config['inter_LN']
-
-        # Load models
-        if self.cmdopts['models_enable']:
-            self._load_models()
-
-    def run(self, criteria: bc.IConcreteBatchCriteria) -> None:
-        """Run the pipeline stage.
-
-        Intra-experiment graph generation: if intra-experiment graphs should be
-        generated, according to cmdline configuration, the following is run:
-
-        #. Model generation for each enabled and loaded model.
-
-        #. :class:`~sierra.core.pipeline.stage4.intra_exp_graph_generator.BatchIntraExpGraphGenerator`
-           to generate graphs for each experiment in the batch, or a subset.
-
-        Inter-experiment graph generation: if inter-experiment graphs should be
-        generated according to cmdline configuration, the following is run:
-
-        #. :class:`~sierra.core.pipeline.stage4.graph_collator.UnivarGraphCollator`
-           or
-           :class:`~sierra.core.pipeline.stage4.graph_collator.BivarGraphCollator`
-           as appropriate (depending on which type of
-           :class:`~sierra.core.variables.batch_criteria.BatchCriteria` was
-           specified on the cmdline).
-
-        #. Model generation for each enabled and loaded model.
-
-        #. :class:`~sierra.core.pipeline.stage4.inter_exp_graph_generator.InterExpGraphGenerator`
-           to perform graph generation from collated CSV files.
-
-
-        Video generation: The following is run:
-
-        #. :class:`~sierra.core.pipeline.stage4.rendering.PlatformFramesRenderer`,
-           if ``--platform-vc`` was passed
-
-        #. :class:`~sierra.core.pipeline.stage4.rendering.ProjectFramesRenderer`,
-           if ``--project-imagizing`` was passed previously to generate frames,
-           and ``--project-rendering`` is passed.
-
-        #. :class:`~sierra.core.pipeline.stage4.rendering.BivarHeatmapRenderer`,
-           if the batch criteria was bivariate and ``--HM-rendering`` was
-           passed.
-
-        """
-        if self.cmdopts['exp_graphs'] == 'all' or self.cmdopts['exp_graphs'] == 'intra':
-            if criteria.is_univar() and self.cmdopts['models_enable']:
-                self._run_intra_models(criteria)
-
-            self._run_intra_graph_generation(criteria)
-
-        # Collation must be after intra-experiment graph generation, so that all
-        # .csv files to be collated have been generated/modified according to
-        # parameters.
-        if self.cmdopts['exp_graphs'] == 'all' or self.cmdopts['exp_graphs'] == 'inter':
-            self._run_collation(criteria)
-
-            if criteria.is_univar() and self.cmdopts['models_enable']:
-                self._run_inter_models(criteria)
-
-            self._run_inter_graph_generation(criteria)
-
-        # Rendering must be after graph generation in case we should be
-        # rendering videos from generated graphs.
-        self._run_rendering(criteria)
-
-    def _load_models(self) -> None:
-        project_models = self.project_config_root / config.kYAML.models
-        self.models_intra = []
-        self.models_inter = []
-
-        if not utils.path_exists(project_models):
-            self.logger.debug("No models to load for project '%s': %s does not exist",
-                              self.cmdopts['project'],
-                              project_models)
-            return
 
-        self.logger.info("Loading models for project '%s'",
-                         self.cmdopts['project'])
+    def run(self, criteria: bc.XVarBatchCriteria) -> None:
+        """Run the pipeline stage."""
+        spec = self.cmdopts["prod"]
+        self.logger.info("Generating products %s product plugins: %s", len(spec), spec)
 
-        self.models_config = yaml.load(utils.utf8open(project_models),
-                                       yaml.FullLoader)
-        pm.models.initialize(self.cmdopts['project'],
-                             pathlib.Path(self.cmdopts['project_model_root']))
+        for s in spec:
+            module = pm.pipeline.get_plugin_module(s)
+            self.logger.info(
+                "Running %s in <batchroot>/%s",
+                s,
+                self.pathset.output_root.relative_to(self.pathset.root),
+            )
 
-        # All models present in the .yaml file are enabled/set to run
-        # unconditionally
-        available = pm.models.available_plugins()
-        self.logger.debug("Project %s has %d available model plugins",
-                          self.cmdopts['project'],
-                          len(available))
-
-        for module_name in pm.models.available_plugins():
-            # No models specified--nothing to do
-            if self.models_config.get('models') is None:
-                continue
-
-            for conf in self.models_config['models']:
-                if conf['pyfile'] == module_name:
-
-                    self.logger.debug("Model %s enabled by configuration",
-                                      module_name)
-                    pm.models.load_plugin(module_name)
-                    model_name = f'models.{module_name}'
-                    module = pm.models.get_plugin_module(model_name)
-                    self.logger.debug(("Configured model %s has %d "
-                                       "intra-experiment models"),
-                                      model_name,
-                                      len(module.available_models('intra')))
-
-                    self.logger.debug(("Configured model %s has %d "
-                                       "inter-experiment models"),
-                                      model_name,
-                                      len(module.available_models('inter')))
-
-                    for avail in module.available_models('intra'):
-                        model = getattr(module, avail)(self.main_config, conf)
-                        self.models_intra.append(model)
-
-                    for avail in module.available_models('inter'):
-                        model = getattr(module, avail)(self.main_config, conf)
-                        self.models_inter.append(model)
-                else:
-                    self.logger.debug("Model %s disabled by configuration",
-                                      module_name)
-
-        if len(self.models_intra) > 0:
-            self.logger.info("Loaded %s intra-experiment models for project '%s'",
-                             len(self.models_intra),
-                             self.cmdopts['project'])
-
-        if len(self.models_inter) > 0:
-            self.logger.info("Loaded %s inter-experiment models for project '%s'",
-                             len(self.models_inter),
-                             self.cmdopts['project'])
-
-    def _calc_inter_targets(self,
-                            name: str,
-                            category_prefix: str,
-                            loaded_graphs: types.YAMLDict) -> tp.List[types.YAMLDict]:
-        """Calculate what inter-experiment graphs to generate.
-
-        This also defines what CSV files need to be collated, as one graph is
-        always generated from one CSV file. Uses YAML configuration for
-        controllers and inter-experiment graphs.
-
-        """
-        keys = []
-        for category in list(self.controller_config.keys()):
-            if category not in self.cmdopts['controller']:
-                continue
-            for controller in self.controller_config[category]['controllers']:
-                if controller['name'] not in self.cmdopts['controller']:
-                    continue
-
-                # valid to specify no graphs, and only to inherit graphs
-                keys = controller.get('graphs', [])
-                if 'graphs_inherit' in controller:
-                    for inherit in controller['graphs_inherit']:
-                        keys.extend(inherit)   # optional
-
-        self.logger.debug("Loaded %s inter-experiment categories: %s",
-                          name,
-                          keys)
-
-        filtered_keys = [k for k in loaded_graphs if category_prefix in k]
-        filtered_keys = [k for k in loaded_graphs if k in keys]
-        targets = [loaded_graphs[k] for k in filtered_keys]
-
-        self.logger.debug("Enabled %s inter-experiment categories: %s", name,
-                          filtered_keys)
-        return targets
-
-    def _run_rendering(self, criteria: bc.IConcreteBatchCriteria) -> None:
-        """Render captured frames and/or imagized frames into videos.
-
-        """
-        if ((not self.cmdopts['platform_vc']) and
-            (not self.cmdopts['project_rendering']) and
-                (not (criteria.is_bivar() and self.cmdopts['bc_rendering']))):
-            return
-
-        self.logger.info("Rendering videos...")
-        start = time.time()
-
-        if self.cmdopts['platform_vc']:
-            rendering.PlatformFramesRenderer(self.main_config,
-                                             self.cmdopts)(criteria)
-        else:
-            self.logger.debug(("--platform-vc not passed--skipping rendering "
-                               "frames captured by the platform"))
-
-        if self.cmdopts['project_rendering']:
-            rendering.ProjectFramesRenderer(self.main_config,
-                                            self.cmdopts)(criteria)
-        else:
-            self.logger.debug(("--project-rendering not passed--skipping "
-                               "rendering frames captured by the project"))
-
-        if criteria.is_bivar() and self.cmdopts['bc_rendering']:
-            rendering.BivarHeatmapRenderer(self.main_config,
-                                           self.cmdopts)(criteria)
-        else:
-            self.logger.debug(("--bc-rendering not passed or univariate batch "
-                               "criteria--skipping rendering generated graphs"))
-
-        elapsed = int(time.time() - start)
-        sec = datetime.timedelta(seconds=elapsed)
-        self.logger.info("Rendering complete in %s", str(sec))
-
-    def _run_intra_models(self, criteria: bc.IConcreteBatchCriteria) -> None:
-        self.logger.info("Running %d intra-experiment models...",
-                         len(self.models_intra))
-        start = time.time()
-        IntraExpModelRunner(self.cmdopts,
-                            self.models_intra)(self.main_config,
-                                               criteria)
-        elapsed = int(time.time() - start)
-        sec = datetime.timedelta(seconds=elapsed)
-        self.logger.info("Intra-experiment models finished in %s", str(sec))
-
-    def _run_inter_models(self, criteria: bc.IConcreteBatchCriteria) -> None:
-        self.logger.info("Running %d inter-experiment models...",
-                         len(self.models_inter))
-        start = time.time()
-
-        runner = InterExpModelRunner(self.cmdopts, self.models_inter)
-        runner(self.main_config, criteria)
-
-        elapsed = int(time.time() - start)
-        sec = datetime.timedelta(seconds=elapsed)
-        self.logger.info("Inter-experiment models finished in %s", str(sec))
-
-    def _run_intra_graph_generation(self, criteria: bc.IConcreteBatchCriteria) -> None:
-        """
-        Generate intra-experiment graphs (duh).
-        """
-        self.logger.info("Generating intra-experiment graphs...")
-        start = time.time()
-        BatchIntraExpGraphGenerator(self.cmdopts)(self.main_config,
-                                                  self.controller_config,
-                                                  self.intra_LN_config,
-                                                  self.intra_HM_config,
-                                                  criteria)
-        elapsed = int(time.time() - start)
-        sec = datetime.timedelta(seconds=elapsed)
-        self.logger.info(
-            "Intra-experiment graph generation complete: %s", str(sec))
-
-    def _run_collation(self, criteria: bc.IConcreteBatchCriteria) -> None:
-        LN_targets = self._calc_inter_targets(name='linegraph',
-                                              category_prefix='LN',
-                                              loaded_graphs=self.inter_LN_config)
-        HM_targets = self._calc_inter_targets(name='heatmap',
-                                              category_prefix='HM',
-                                              loaded_graphs=self.inter_HM_config)
-
-        if not self.cmdopts['skip_collate']:
-            self.logger.info("Collating inter-experiment CSV files...")
             start = time.time()
-            collator = GraphParallelCollator(self.main_config, self.cmdopts)
-            collator(criteria, LN_targets)
-            collator(criteria, HM_targets)
+            module.proc_batch_exp(
+                self.main_config, self.cmdopts, self.pathset, criteria
+            )
             elapsed = int(time.time() - start)
             sec = datetime.timedelta(seconds=elapsed)
-            self.logger.info("Collating inter-experiment CSV files complete: %s",
-                             str(sec))
-
-    def _run_inter_graph_generation(self, criteria: bc.IConcreteBatchCriteria) -> None:
-        """
-        Generate inter-experiment graphs (duh).
-        """
-        LN_targets = self._calc_inter_targets(name='linegraph',
-                                              category_prefix='LN',
-                                              loaded_graphs=self.inter_LN_config)
-        HM_targets = self._calc_inter_targets(name='heatmap',
-                                              category_prefix='HM',
-                                              loaded_graphs=self.inter_HM_config)
-
-        self.logger.info("Generating inter-experiment graphs...")
-        start = time.time()
-
-        module = pm.module_load_tiered(project=self.cmdopts['project'],
-                                       path='pipeline.stage4.inter_exp_graph_generator')
-        generator = module.InterExpGraphGenerator(self.main_config,
-                                                  self.cmdopts,
-                                                  LN_targets,
-                                                  HM_targets)
-        generator(criteria)
-        elapsed = int(time.time() - start)
-        sec = datetime.timedelta(seconds=elapsed)
-
-        self.logger.info("Inter-experiment graph generation complete: %s",
-                         str(sec))
+            self.logger.info("Generation with %s complete in %s", s, str(sec))
 
 
-__api__ = [
-    'PipelineStage4'
-]
+__all__ = ["PipelineStage4"]

sierra/core/pipeline/stage5/__init__.py

@@ -0,0 +1,12 @@
+#
+# Copyright 2025 John Harwell, All rights reserved.
+#
+# SPDX-License Identifier: MIT
+#
+"""Container module for stage 5 of the pipeline."""
+
+# Core packages
+
+# 3rd party packages
+
+# Project packages