sierra-research 1.3.11__py3-none-any.whl → 1.5.0__py3-none-any.whl

sierra/core/graphs/summary_line_graph.py

@@ -1,371 +0,0 @@
-# Copyright 2018 John Harwell, All rights reserved.
-#
-# SPDX-License-Identifier: MIT
-#
-"""
-Linegraph for summarizing the results of a batch experiment in different ways.
-"""
-
-# Core packages
-import typing as tp
-import logging
-import pathlib
-
-# 3rd party packages
-import matplotlib.ticker as mticker
-import matplotlib.pyplot as plt
-import pandas as pd
-
-# Project packages
-from sierra.core import config, utils, storage
-
-
-class SummaryLineGraph:
-    """Generates a linegraph from a :term:`Summary .csv`.
-
-    Possibly shows the 95% confidence interval or box and whisker plots,
-    according to configuration.
-
-    Attributes:
-
-        stats_root: The absolute path to the ``statistics/`` directory for the
-                    batch experiment.
-
-        input_stem: Stem of the :term:`Summary .csv` file to generate a graph
-                    from.
-
-        output_fpath: The absolute path to the output image file to save
-                      generated graph to.
-
-        title: Graph title.
-
-        xlabel: X-label for graph.
-
-        ylabel: Y-label for graph.
-
-        xticks: The xticks for the graph.
-
-        xtick_labels: The xtick labels for the graph (can be different than the
-                      xticks; e.g., if the xticxs are 1-10 for categorical data,
-                      then then labels would be the categories).
-
-        large_text: Should the labels, ticks, and titles be large, or regular
-                    size?
-
-        legend: Legend for graph.
-
-        logyscale: Should the Y axis be in the log2 domain ?
-
-        stats: The type of statistics to include on the graph (from
-               ``--dist-stats``).
-
-        model_root: The absolute path to the ``models/`` directory for the batch
-                     experiment.
-
-    """
-    kLineStyles = ['-', '--', '.-', ':', '-', '--', '.-', ':']
-    kMarkStyles = ['o', '^', 's', 'x', 'o', '^', 's', 'x']
-
-    def __init__(self,
-                 stats_root: pathlib.Path,
-                 input_stem: str,
-                 output_fpath: pathlib.Path,
-                 title: str,
-                 xlabel: str,
-                 ylabel: str,
-                 xticks: tp.List[float],
-                 xtick_labels: tp.Optional[tp.List[str]] = None,
-                 large_text: bool = False,
-                 legend: tp.List[str] = ['Empirical Data'],
-                 logyscale: bool = False,
-                 stats: str = 'none',
-                 model_root: tp.Optional[pathlib.Path] = None) -> None:
-
-        # Required arguments
-        self.stats_root = stats_root
-        self.input_stem = input_stem
-        self.output_fpath = output_fpath
-        self.title = title
-        self.xlabel = xlabel
-        self.ylabel = ylabel
-        self.xticks = xticks
-
-        # Optional arguments
-        if large_text:
-            self.text_size = config.kGraphTextSizeLarge
-        else:
-            self.text_size = config.kGraphTextSizeSmall
-
-        self.xtick_labels = xtick_labels
-        self.model_root = model_root
-        self.legend = legend
-        self.logyscale = logyscale
-        self.stats = stats
-
-        self.logger = logging.getLogger(__name__)
-
-    def generate(self) -> None:
-        input_fpath = self.stats_root / (self.input_stem +
-                                         config.kStats['mean'].exts['mean'])
-
-        if not utils.path_exists(input_fpath):
-            self.logger.debug("Not generating %s: %s does not exist",
-                              self.output_fpath,
-                              input_fpath)
-            return
-        else:
-            self.logger.debug("Generating %s from %s",
-                              self.output_fpath,
-                              input_fpath)
-
-        data_dfy = storage.DataFrameReader('storage.csv')(input_fpath)
-        model = self._read_models()
-
-        fig, ax = plt.subplots()
-
-        # Plot lines
-        self._plot_lines(data_dfy, model)
-
-        # Add legend
-        self._plot_legend(model)
-
-        # Add statistics according to configuration
-        stat_dfs = self._read_stats()
-        self._plot_stats(ax, self.xticks, data_dfy, stat_dfs)
-
-        # Add X,Y labels
-        plt.ylabel(self.ylabel, fontsize=self.text_size['xyz_label'])
-        plt.xlabel(self.xlabel, fontsize=self.text_size['xyz_label'])
-
-        # Add ticks
-        self._plot_ticks(ax)
-
-        # Add title
-        plt.title(self.title, fontsize=self.text_size['title'])
-
-        # Output figure
-        fig = ax.get_figure()
-        fig.set_size_inches(config.kGraphBaseSize,
-                            config.kGraphBaseSize)
-        fig.savefig(self.output_fpath, bbox_inches='tight',
-                    dpi=config.kGraphDPI)
-        # Prevent memory accumulation (fig.clf() does not close everything)
-        plt.close(fig)
-
-    def _plot_lines(self,
-                    data_dfy: pd.DataFrame,
-                    model: tp.Tuple[pd.DataFrame, tp.List[str]]) -> None:
-        for i in range(0, len(data_dfy.values)):
-            assert len(data_dfy.values[i]) == len(self.xticks),\
-                "Length mismatch between xticks,data: {0} vs {1}/{2} vs {3}".format(
-                    len(self.xticks),
-                    len(data_dfy.values[i]),
-                    self.xticks,
-                    data_dfy.values[i])
-
-            # Plot data
-            plt.plot(self.xticks,
-                     data_dfy.values[i],
-                     marker=self.kMarkStyles[i],
-                     color=f"C{i}")
-
-            # Plot model prediction(s)
-            if model[0] is not None:
-                # The model might be of different dimensions than the data. If
-                # so, truncate it to fit.
-                if len(self.xticks) < len(model[0].values[i]):
-                    self.logger.warning("Truncating model: model/data lengths disagree: %s vs. %s",
-                                        len(model[0].values[i]),
-                                        len(self.xticks))
-                    xvals = model[0].values[i][:len(self.xticks)]
-                else:
-                    xvals = model[0].values[i]
-
-                plt.plot(self.xticks,
-                         xvals,
-                         '--',
-                         marker=self.kMarkStyles[i],
-                         color="C{}".format(i + len(data_dfy.index)))
-
-    def _plot_stats(self,
-                    ax,
-                    xticks,
-                    data_dfy: pd.DataFrame,
-                    stat_dfs: tp.Dict[str, pd.DataFrame]) -> None:
-        """
-        Plot statistics for all lines on the graph.
-        """
-        self._plot_conf95_stats(xticks, data_dfy, stat_dfs)
-        self._plot_bw_stats(ax, xticks, data_dfy, stat_dfs)
-
-    def _plot_conf95_stats(self,
-                           xticks,
-                           data_dfy: pd.DataFrame,
-                           stat_dfs: tp.Dict[str, pd.DataFrame]) -> None:
-        if self.stats not in ['conf95', 'all']:
-            return
-
-        if not all(k in stat_dfs.keys() for k in config.kStats['conf95'].exts):
-            self.logger.warning(("Cannot plot 95%% confidence intervals: "
-                                 "missing some statistics: %s vs %s"),
-                                stat_dfs.keys(),
-                                config.kStats['conf95'].exts)
-            return
-
-        for i in range(0, len(data_dfy.values)):
-            stddev_i = stat_dfs['stddev'].abs().values[i]
-            # 95% interval = 2 std stdeviations
-            plt.fill_between(xticks,
-                             data_dfy.values[i] - 2 * stddev_i,
-                             data_dfy.values[i] + 2 * stddev_i,
-                             alpha=0.25,
-                             color="C{}".format(i),
-                             interpolate=True)
-
-    def _plot_bw_stats(self,
-                       ax,
-                       xticks,
-                       data_dfy: pd.DataFrame,
-                       stat_dfs: tp.Dict[str, pd.DataFrame]) -> None:
-        if self.stats not in ['bw', 'all']:
-            return
-
-        if not all(k in stat_dfs.keys() for k in config.kStats['bw'].exts):
-            self.logger.warning(("Cannot plot box-and-whisker plots: "
-                                 "missing some statistics: %s vs %s"),
-                                stat_dfs.keys(),
-                                config.kStats['bw'].exts)
-            return
-
-        for i in range(0, len(data_dfy.values)):
-            boxes = []
-            for j in range(0, len(data_dfy.columns)):
-                boxes.append({
-                    # Bottom whisker position
-                    'whislo': stat_dfs['whislo'].iloc[i, j],
-                    # Top whisker position
-                    'whishi': stat_dfs['whishi'].iloc[i, j],
-                    # First quartile (25th percentile)
-                    'q1': stat_dfs['q1'].iloc[i, j],
-                    # Median         (50th percentile)
-                    'med': stat_dfs['median'].iloc[i, j],
-                    # Third quartile (75th percentile)
-                    'q3': stat_dfs['q3'].iloc[i, j],
-                    # Confidence interval lower bound
-                    'cilo': stat_dfs['cilo'].iloc[i, j],
-                    # Confidence interval upper bound
-                    'cihi': stat_dfs['cihi'].iloc[i, j],
-                    'fliers': []  # Ignoring outliers
-                })
-            ax.bxp(boxes,
-                   manage_ticks=False,
-                   positions=self.xticks,
-                   shownotches=True)
-
-    def _plot_ticks(self, ax) -> None:
-        if self.logyscale:
-            ax.set_yscale('symlog', base=2)
-            ax.yaxis.set_minor_formatter(mticker.ScalarFormatter())
-
-            # Use scientific or decimal notation--whichever has fewer chars
-            # ax.yaxis.set_major_formatter(mticker.FormatStrFormatter("%.02g"))
-
-        ax.tick_params(labelsize=self.text_size['tick_label'])
-
-        # For ordered, qualitative data
-        if self.xtick_labels is not None:
-            ax.set_xticks(self.xticks)
-            ax.set_xticklabels(self.xtick_labels, rotation='vertical')
-
-    def _plot_legend(self, model: tp.Tuple[pd.DataFrame, tp.List[str]]) -> None:
-        legend = self.legend
-
-        if model[1]:
-            legend = [val for pair in zip(self.legend, model[1])
-                      for val in pair]
-
-        plt.legend(legend,
-                   fontsize=self.text_size['legend_label'],
-                   ncol=max(1, int(len(legend) / 3.0)))
-
-    def _read_stats(self) -> tp.Dict[str, tp.List[pd.DataFrame]]:
-        dfs = {}
-
-        dfs.update(self._read_conf95_stats())
-        dfs.update(self._read_bw_stats())
-
-        return dfs
-
-    def _read_conf95_stats(self) -> tp.Dict[str, tp.List[pd.DataFrame]]:
-        dfs = {}
-        reader = storage.DataFrameReader('storage.csv')
-        exts = config.kStats['conf95'].exts
-
-        if self.stats in ['conf95', 'all']:
-            for k in exts:
-                ipath = self.stats_root / (self.input_stem + exts[k])
-
-                if utils.path_exists(ipath):
-                    dfs[k] = reader(ipath)
-                else:
-                    self.logger.warning("%s file not found for '%s'",
-                                        exts[k],
-                                        self.input_stem)
-
-        return dfs
-
-    def _read_bw_stats(self) -> tp.Dict[str, tp.List[pd.DataFrame]]:
-        dfs = {}
-        reader = storage.DataFrameReader('storage.csv')
-        exts = config.kStats['bw'].exts
-
-        if self.stats in ['bw', 'all']:
-            for k in exts:
-                ipath = self.stats_root / (self.input_stem + exts[k])
-
-                if utils.path_exists(ipath):
-                    dfs[k] = reader(ipath)
-                else:
-                    self.logger.warning("%s file not found for '%s'",
-                                        exts[k],
-                                        self.input_stem)
-
-        return dfs
-
-    # 2024/09/13 [JRH]: The union is for compatability with type checkers in
-    # python {3.8,3.11}.
-    def _read_models(self) -> tp.Tuple[pd.DataFrame, tp.Union[tp.List[str], tp.List[bytes]]]:
-        if self.model_root is None:
-            return (None, [])
-
-        self.logger.trace("Model root='%s'",   # type: ignore
-                          self.model_root)
-
-        exts = config.kModelsExt
-        modelf = self.model_root / (self.input_stem + exts['model'])
-        legendf = self.model_root / (self.input_stem + exts['legend'])
-
-        if not utils.path_exists(modelf):
-            self.logger.trace("No model='%s' found in model root",  # type: ignore
-                              modelf)
-            return (None, [])
-
-        model = storage.DataFrameReader('storage.csv')(modelf)
-        if utils.path_exists(legendf):
-            with utils.utf8open(legendf, 'r') as f:
-                legend = f.read().splitlines()
-        else:
-            self.logger.warning("No legend file for model '%s' found",
-                                modelf)
-            legend = ['Model Prediction']
-
-        self.logger.trace("Loaded model='%s',legend='%s'",  # type: ignore
-                          modelf.relative_to(self.model_root),
-                          legendf.relative_to(self.model_root))
-
-        return (model, legend)
-
-
-__api__ = [
-    'SummaryLineGraph'
-]

sierra/core/hpc/cmdline.py

@@ -1,142 +0,0 @@
-# Copyright 2020 John Harwell, All rights reserved.
-#
-#  SPDX-License-Identifier: MIT
-"""Common cmdline classes for the various HPC plugins.
-
-"""
-
-# Core packages
-import argparse
-import typing as tp
-
-# 3rd party packages
-
-# Project packages
-from sierra.core import types, cmdline
-
-
-class HPCCmdline(cmdline.BaseCmdline):
-    def __init__(self, stages: tp.List[int]) -> None:
-        self.parser = argparse.ArgumentParser(add_help=False,
-                                              allow_abbrev=False)
-
-        self.scaffold_cli()
-        self.init_cli(stages)
-
-    def scaffold_cli(self) -> None:
-        desc = ("For platforms which are simulators (and can "
-                "therefore be run in HPC environments).")
-        self.hpc = self.parser.add_argument_group('HPC options', desc)
-
-    def init_cli(self, stages: tp.List[int]) -> None:
-        if 2 in stages:
-            self.init_stage2()
-
-    def init_stage2(self) -> None:
-        """Add HPC cmdline options.
-
-        Options may be interpreted differently between :term:`Platforms
-        <Platform>`, or ignored, depending. These include:
-
-        - ``--exec-jobs-per-node``
-
-        - ``--exec-no-devnull``
-
-        - ``--exec-resume``
-
-        - ``--exec-strict``
-
-        """
-        self.hpc.add_argument("--exec-jobs-per-node",
-                              help="""
-
-                              Specify the maximum number of parallel jobs to run
-                              per allocated node. By default this is computed
-                              from the selected HPC environment for maximum
-                              throughput given the desired ``--n-runs`` and CPUs
-                              per allocated node. However, for some environments
-                              being able to override the computed default can be
-                              useful.
-
-                              """ + self.stage_usage_doc([2]),
-                              type=int,
-                              default=None)
-
-        self.hpc.add_argument("--exec-devnull",
-                              help="""
-
-                              Redirect ALL output from simulations to
-                              /dev/null. Useful for platform where you can't
-                              disable all INFO messages at compile time, and
-                              don't want to have to grep through lots of
-                              redundant stdout files to see if there were any
-                              errors.
-
-                              """ + self.stage_usage_doc([1, 2]),
-                              action='store_true',
-                              dest='exec_devnull',
-                              default=True)
-
-        self.hpc.add_argument("--exec-no-devnull",
-                              help="""
-
-                              Don't redirect ALL output from simulations to
-                              /dev/null. Useful for platform where you can't
-                              disable all INFO messages at compile time, and
-                              don't want to have to grep through lots of
-                              redundant stdout files to see if there were any
-                              errors.
-
-                              """ + self.stage_usage_doc([1, 2]),
-                              action='store_false',
-                              dest='exec_devnull')
-
-        self.hpc.add_argument("--exec-resume",
-                              help="""
-
-                              Resume a batch experiment that was
-                              killed/stopped/etc last time SIERRA was run.
-
-                              """ + self.stage_usage_doc([2]),
-                              action='store_true',
-                              default=False)
-
-        self.hpc.add_argument("--exec-strict",
-                              help="""
-
-                              If passed, then if any experimental commands fail
-                              during stage 2 SIERRA will exit, rather than try
-                              to keep going and execute the rest of the
-                              experiments.
-
-                              Useful for:
-
-                              - "Correctness by construction" experiments, where
-                                you know if SIERRA doesn't crash and it makes it
-                                to the end of your batch experiment then none of
-                                the individual experiments crashed.
-
-                              - CI pipelines
-
-                              """,
-                              action='store_true')
-
-    @staticmethod
-    def cmdopts_update(cli_args: argparse.Namespace,
-                       cmdopts: types.Cmdopts) -> None:
-        """Update cmdopts dictionary with the HPC-specific cmdline options.
-
-        """
-        updates = {
-            # Multistage
-            'exec_devnull': cli_args.exec_devnull,
-            'exec_jobs_per_node': cli_args.exec_jobs_per_node,
-            'exec_resume': cli_args.exec_resume,
-            'exec_strict': cli_args.exec_strict
-        }
-        cmdopts.update(updates)
-
-
-__api__ = [
-    'HPCCmdline',
-]

sierra/core/models/graphs.py

@@ -1,87 +0,0 @@
-# Copyright 2020 John Harwell, All rights reserved.
-#
-#  SPDX-License-Identifier: MIT
-"""
-Graphs which can always be generated, irrespective of model specifics.
-
-For example, you can always compare the model value to the empirical value, and
-plot the difference as error.
-"""
-# Core packages
-import pathlib
-
-# 3rd party packages
-
-# Project packages
-from sierra.core.graphs.heatmap import HeatmapSet
-from sierra.core import utils, config, storage
-
-
-class IntraExpModel2DGraphSet():
-    """
-    Generates 4 :class:`~sierra.core.graphs.heatmap.Heatmap` plots.
-
-    - One for the empirical data
-    - One for the stddev of the empirical data
-    - One for the model prediction
-    - One for the difference between the model and the empirical data
-    """
-    @staticmethod
-    def model_exists(exp_model_root: pathlib.Path, target_stem: str):
-        leaf = target_stem + config.kModelsExt['model']
-        return utils.path_exists(exp_model_root / leaf)
-
-    def __init__(self,
-                 exp_stat_root: pathlib.Path,
-                 exp_model_root: pathlib.Path,
-                 exp_graph_root: pathlib.Path,
-                 target_stem: str,
-                 target_title: str,
-                 **kwargs):
-        self.exp_stat_root = exp_stat_root
-        self.exp_model_root = exp_model_root
-        self.exp_graph_root = exp_graph_root
-        self.target_stem = target_stem
-        self.target_title = target_title
-        self.kwargs = kwargs
-
-    def generate(self):
-        stat_path = self.exp_stat_root / self.target_stem
-        graph_path = self.exp_graph_root / self.target_stem
-        model_path = self.exp_model_root / self.target_stem
-
-        data_ipath = stat_path.with_suffix(config.kStats['mean'].exts['mean'])
-
-        data_opath = self.exp_graph_root / \
-            (self.target_stem + '-HM').with_suffix(config.kImageExt)
-
-        stddev_ipath = stat_path.with_suffix(config.kStats['conf95'].exts['stddev'])
-        stddev_opath = graph_path.with_name(
-            self.target_stem + '-HM-stddev' + config.kImageExt)
-
-        model_ipath = model_path.with_suffix(config.kModelsExt['model'])
-        model_opath = graph_path.with_name(
-            self.target_stem + '-HM-model' + config.kImageExt)
-
-        model_error_ipath = model_path.with_name(
-            self.target_stem + '-HM-model-error' + config.kStats['mean'].exts['mean'])
-        model_error_opath = model_path.with_name(
-            self.target_stem + '-HM-model-error' + config.kImageExt)
-
-        # Write the error .csv to the filesystem
-        reader = storage.DataFrameReader('storage.csv')
-        writer = storage.DataFrameWriter('storage.csv')
-        data_df = reader(data_ipath)
-        model_df = reader(model_ipath)
-        writer(model_df - data_df, model_error_ipath, index=False)
-
-        HeatmapSet(ipaths=[data_ipath, stddev_ipath, model_ipath, model_error_ipath],
-                   opaths=[data_opath, stddev_opath,
-                           model_opath, model_error_opath],
-                   titles=[self.target_title,
-                           self.target_title + ' (Stddev)',
-                           self.target_title + ' (Model)',
-                           self.target_title + ' (Model Error)'],
-                   xlabel='X',
-                   ylabel='Y',
-                   **self.kwargs).generate()