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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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