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How to use _add_line method in tappy

Best Python code snippet using tappy_python

parser_generator.py

Source:parser_generator.py

...48        logging.debug(grammar)49        # Add standard generated warning at the top50        self._output_str = (51            '# NOTE: THIS FILE IS AUTOMATICALLY GENERATED BY ebnf_cc')52        self._add_line('# ONLY CHANGE THIS FILE IF YOU DO NOT MIND '53                       'LOSING ALL YOUR CHANGES')54        self._add_description()55        # Import files56        self._add_line('import _symbol')57        self._add_line('import _token_stream')58        # Create parser of language by traversing the Grammar object59        self._add_grammar(grammar)60        # Import custom definitions61        self._add_line('# Import any user-provided parser classes')62        self._add_line('# Necessary if the EBNF specification is incomplete')63        self._add_line('try:')64        self._push_depth()65        self._add_line('from _custom_definitions import *')66        self._pop_depth()67        self._add_line('except ImportError:')68        self._push_depth()69        self._add_line('pass')70        self._pop_depth()71        self._add_line('')72        with open(output_filename, 'w') as f:73            f.write(self._output_str)74        # Copy token_stream and symbol modules over75        for module in (token_stream, symbol):76            src_name = inspect.getfile(module)77            if src_name[-1] == 'c':78                src_name = src_name[:-1]79            shutil.copyfile(src_name, '_%s' % os.path.basename(src_name))80    def _add_description(self):81        """Add description to top of the file."""82        self._add_line('')83        self._add_line('# Description')84        self._add_line('# ###########')85        # TODO(akhouderchah) add full description + usage86        self._add_line('')87    def _add_grammar(self, grammar):88        """Add parser for the specified EBNF grammar."""89        for rule in grammar._children:90            self._add_rule(rule)91    def _add_rule(self, rule):92        """Add parser class for a single EBNF rule."""93        rule_name = rule.get_next()94        self._add_line('class %s(_symbol.BaseSymbol):' % rule_name)95        self._push_depth()96        self._add_line('def __init__(self):')97        self._push_depth()98        self._add_line('super(%s, self).__init__()' % rule_name)99        rhs = rule.get_next(ebnf_parser.Rhs)100        if rhs is None:101            raise Exception('Expected RHS in rule:\n%s' % rule)102        intermediate_repr = intermediate_language.ILGenerator().generate(rhs)103        self._add_intermediate(intermediate_repr)104        self._pop_depth()105        self._pop_depth()106        self._add_line('')107        self._add_line('')108    def _add_intermediate(self, intermediate, optional_mode=None):109        """Generates parser class body of a rule given its IL representation.110        Params:111          intermediate: intermediate_language._ILObject representing the112              rule to generate a parser class for.113          optional_mode: an _OPTIONAL_* value representing if the generated114              code currently resides in an if or elif statement.115        """116        if isinstance(intermediate, ebnf_parser.Terminal):117            self._add_terminal(intermediate, optional_mode)118        elif isinstance(intermediate, ebnf_parser.Identifier):119            self._add_identifier(intermediate, optional_mode)120        elif isinstance(intermediate, intermediate_language.Choice):121            self._add_choice(intermediate, optional_mode)122        elif isinstance(intermediate, intermediate_language.Sequence):123            self._add_sequence(intermediate, optional_mode)124        elif isinstance(intermediate, intermediate_language.Repetition):125            self._add_repetition(intermediate, optional_mode)126        elif isinstance(intermediate, intermediate_language.Optional):127            self._add_optional(intermediate, optional_mode)128        else:129            raise ValueError('Unexpected object type in IL representation')130    def _add_terminal(self, terminal, optional_mode):131        """Generate code to parse the given ebnf_parser.Terminal object.132        Params:133          terminal: ebnf_parser.Terminal representing the EBNF terminal.134          optional_mode: an _OPTIONAL_* value representing if the generated135              code currently resides in an if or elif statement.136        """137        terminal.get_next()  # Skip over ' token138        term = terminal.get_next()139        if not optional_mode:140            self._add_line("self.add_token('%s')" % term)141        elif optional_mode == self._OPTIONAL_IF:142            self._add_line("if self.add_token_optional('%s'):" % term)143            self._push_depth()144        elif optional_mode == self._OPTIONAL_ELIF:145            self._add_line("elif self.add_token_optional('%s'):" % term)146            self._push_depth()147    def _add_identifier(self, identifier, optional_mode):148        """Generate code to parse the given ebnf_parser.Identifier object.149        Params:150          identifier: ebnf_parser.Identnifier representing the EBNF identifier.151          optional_mode: an _OPTIONAL_* value representing if the generated152              code currently resides in an if or elif statement.153        """154        term = identifier.get_next()155        if not optional_mode:156            self._add_line('self.add(%s)' % term)157        elif optional_mode == self._OPTIONAL_IF:158            self._add_line('if self.add_optional(%s):' % term)159            self._push_depth()160        elif optional_mode == self._OPTIONAL_ELIF:161            self._add_line('elif self.add_optional(%s):' % term)162            self._push_depth()163    def _add_choice(self, il_choice, optional_mode):164        """Generate code to parse the given Choice object.165        Params:166          il_choice: intermediate_language.Choice representing the167              EBNF rule choice.168          optional_mode: an _OPTIONAL_* value representing if the generated169              code currently resides in an if or elif statement.170        """171        self._add_intermediate(il_choice._objs[0], self._OPTIONAL_IF)172        self._add_line('pass')173        self._pop_depth()174        for i in range(1, len(il_choice._objs)):175            self._add_intermediate(il_choice._objs[i],176                                   self._OPTIONAL_ELIF)177            self._add_line('pass')178            self._pop_depth()179        if optional_mode:180            self._push_depth()181        else:182            self._add_line('else:')183            self._push_depth()184            # TODO(akhouderchah) add error message185            self._add_line('raise _symbol.SymbolException(\'\')')186            self._pop_depth()187    def _add_sequence(self, il_sequence, optional_mode):188        """Generate code to parse the given Sequence object.189        Params:190          il_sequence: intermediate_language.Sequence representing the191              EBNF rule sequence.192          optional_mode: an _OPTIONAL_* value representing if the generated193              code currently resides in an if or elif statement.194        """195        self._add_intermediate(il_sequence._objs[0], optional_mode)196        for i in range(1, len(il_sequence._objs)):197            obj = il_sequence._objs[i]198            self._add_intermediate(obj)199    def _add_repetition(self, il_repetition, optional_mode):200        """Generate code to parse the given Repetition object.201        Params:202          il_optional: intermediate_language.Repetition representing the203              repeating EBNF rule sequence.204          optional_mode: an _OPTIONAL_* value representing if the generated205              code currently resides in an if or elif statement.206        """207        self._add_line('while True:')208        self._push_depth()209        self._add_intermediate(il_repetition._objs[0], self._OPTIONAL_IF)210        self._add_line('pass')211        self._pop_depth()212        self._add_line('else:')213        self._push_depth()214        self._add_line('break')215        self._pop_depth()216        self._pop_depth()217    def _add_optional(self, il_optional, optional_mode):218        """Generate code to parse the given Optional object.219        Params:220          il_optional: intermediate_language.Optional representing the221              optional EBNF rule sequence.222          optional_mode: an _OPTIONAL_* value representing if the generated223              code currently resides in an if or elif statement.224        """225        self._add_intermediate(il_optional._objs[0], self._OPTIONAL_IF)226        # Special casing optional terminals227        if not isinstance(il_optional._objs[0],228                          intermediate_language._ILObject):229            self._add_line('pass')230        self._pop_depth()231    def _add_line(self, line):232        """Adds line to file."""233        self._output_str += '\n%s%s' % (self.TAB * self._depth, line)234    def _push_depth(self):235        """Decrements indentation level for subsequent _add_line calls."""236        self._depth += 1237    def _pop_depth(self):238        """Increments indentation level for subsequent _add_line calls."""...

script_generator.py

Source:script_generator.py

...9        self._build_script()10    @abstractmethod11    def _build_script(self) -> None:12        pass13    def _add_line(self, line: str, indent_level: int = 0) -> None:14        for i in range(indent_level):15            self._output += "\t"16        # add the line17        self._output += line18        # close the line19        self._end_line()20    @property21    def file_name(self) -> str:22        return self._file_name23    def _end_line(self):24        self._output += "\n"25    def write(self, directory: str = ".") -> None:26        out_file: Path = Path(directory) / self._file_name27        with out_file.open("w") as f:28            f.write(self._output)29class PythonGenerator(ScriptGenerator):30    def __init__(31        self,32        file_name: str,33        database_file: str,34        parameter_file: str,35        base_dir: str,36        import_line: str,37        n_procs: int,38        n_nodes: Optional[int] = None,39        linear_exceution: bool = False,40    ) -> None:41        """42        Generate the python script that will be run43        :param file_name:44        :type file_name: str45        :param database_file:46        :type database_file: str47        :param parameter_file:48        :type parameter_file: str49        :param base_dir:50        :type base_dir: str51        :param import_line:52        :type import_line: str53        :param n_procs:54        :type n_procs: int55        :param n_nodes:56        :type n_nodes: Optional[int]57        :param linear_exceution:58        :type linear_exceution: bool59        :returns:60        """61        self._import_line = import_line62        self._n_procs: int = n_procs63        self._n_nodes: Optional[int] = n_nodes64        self._parameter_file: str = parameter_file65        self._database_file: str = Path(database_file).absolute()66        self._base_dir: str = base_dir67        self._linear_execution: bool = linear_exceution68        super().__init__(file_name)69    def _build_script(self) -> None:70        self._add_line(self._import_line)71        self._add_line("from joblib import Parallel, delayed")72        self._add_line("from tqdm.auto import tqdm")73        self._add_line("from ronswanson import ParameterGrid")74        if self._n_nodes is not None:75            self._add_line("import sys")76            self._end_line()77            self._add_line("key_num = int(sys.argv[-1])")78        self._end_line()79        self._add_line(80            f"pg = ParameterGrid.from_yaml('{self._parameter_file}')"81        )82        self._add_line("def func(i):")83        self._add_line("params = pg.at_index(i)", indent_level=1)84        self._add_line(85            f"simulation = Simulation(i, params, pg.energy_grid,'{self._database_file}')",86            indent_level=1,87        )88        self._add_line("simulation.run()", indent_level=1)89        if self._n_nodes is None:90            self._add_line("iteration = [i for i in range(0, pg.n_points)]")91        else:92            self._add_line(93                f"with open(f'{self._base_dir}/key_file{{key_num}}.txt') as f:"94            )95            self._add_line("iteration = f.readlines()")96            pass97        if self._linear_execution:98            # just do a straight for loop99            self._add_line("for i in tqdm(iteration):")100            self._add_line("func(i)", indent_level=1)101        else:102            # use joblib103            if self._n_nodes is not None:104                self._add_line(105                    f"Parallel(n_jobs={self._n_procs})(delayed(func)(i) for i in iteration)"106                )107            else:108                self._add_line(109                    f"Parallel(n_jobs={self._n_procs})(delayed(func)(i) for i in tqdm(iteration, colour='#FC0A5A'))"110                )111class SLURMGenerator(ScriptGenerator):112    def __init__(113        self,114        file_name: str,115        n_procs: int,116        n_nodes: int,117        hrs: int,118        min: int,119        sec: int,120    ) -> None:121        self._n_procs: int = n_procs122        self._n_nodes: int = n_nodes123        self._hrs: int = hrs124        self._min: int = min125        self._sec: int = sec126        super().__init__(file_name)127    def _build_script(self) -> None:128        self._add_line("#!/bin/bash")129        self._add_line("")130        self._add_line(f"#SBATCH --array=0-{self._n_nodes} #generate array")131        self._add_line("#SBATCH -o ./output/%A_%a.out      #output file")132        self._add_line("#SBATCH -e ./output/%A_%a.err      #error file")133        self._add_line("#SBATCH -D ./                      #working directory")134        self._add_line("#SBATCH -J grid_mp                 #job name")135        self._add_line("#SBATCH -N 1               ")136        self._add_line("#SBATCH --ntasks-per-node=1")137        self._add_line(f"#SBATCH --cpus-per-task={self._n_procs}")138        self._add_line(f"#SBATCH --time={self._hrs}:{self._min}:{self._sec}")139        self._add_line("#SBATCH --mail-type=ALL ")140        self._add_line(141            f"#SBATCH --mail-user={ronswanson_config.slurm.user_email}"142        )143        self._add_line("")144        if ronswanson_config.slurm.modules is not None:145            for m in ronswanson_config.slurm.modules:146                self._add_line(f"module load {m}")147        self._add_line("")148        # self._add_line("module load gcc/11")149        # self._add_line("module load openmpi/4")150        # self._add_line("module load hdf5-serial/1.10.6")151        # self._add_line("module load anaconda/3/2021.05")152        self._add_line("")153        self._add_line("#add HDF5 library path to ld path")154        self._add_line("export LD_LIBRARY_PATH=$HDF5_HOME/lib:$LD_LIBRARY_PATH")155        self._add_line("")156        self._add_line(157            "srun /u/eschoe/conda-envs/py_env/bin/python3 run_sim_mp_rav.py ${SLURM_ARRAY_TASK_ID}"...

qc_plots.py

Source:qc_plots.py

...23        "pct_counts_mito",24    )25    fig, axs = plt.subplots(nrows=2, ncols=2, figsize=(12, 10))26    axs = {k: ax for k, ax in zip(KEYS, axs.flatten())}27    def _add_line(ax, val):28        if val is not None:29            if cumulative:30                ax.hlines(31                    y=val, color="red", linewidth=1, xmin=0, xmax=ax.get_xlim()[1]32                )33            else:34                ax.vlines(35                    x=val, color="red", linewidth=1, ymin=0, ymax=ax.get_ylim()[1]36                )37    for key, ax in axs.items():38        if key == "total_counts (< 5000)":39            values = adata.obs["total_counts"][adata.obs["total_counts"] < 5000]40        else:41            values = adata.obs[key]42        if not cumulative:43            sns.histplot(values, bins=100, ax=ax)44        else:45            ranks = values.rank(ascending=True, method="first")46            ax.scatter(x=ranks, y=values, marker=".", s=2)47        ax.set_xlabel(key)48    if cumulative:49        axs["total_counts"].set_yscale("log")50        axs["total_counts (< 5000)"].set_yscale("log")51    _add_line(axs["total_counts"], min_counts)52    _add_line(axs["total_counts (< 5000)"], min_counts)53    _add_line(axs["total_counts"], max_counts)54    _add_line(axs["n_genes_by_counts"], min_genes)55    _add_line(axs["pct_counts_mito"], max_pct_mito)56    if show:57        plt.show()58    else:...

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