diff --git a/manual/main/api/_modules/index.html b/manual/main/api/_modules/index.html index 83b4f2bc..c31bb200 100644 --- a/manual/main/api/_modules/index.html +++ b/manual/main/api/_modules/index.html @@ -41,7 +41,7 @@ @@ -68,11 +68,9 @@

All modules for which code is available

-
diff --git a/manual/main/api/_modules/odatse/_initialize.html b/manual/main/api/_modules/odatse/_initialize.html index 11465320..bcf36582 100644 --- a/manual/main/api/_modules/odatse/_initialize.html +++ b/manual/main/api/_modules/odatse/_initialize.html @@ -41,7 +41,7 @@ diff --git a/manual/main/api/_modules/odatse/_main.html b/manual/main/api/_modules/odatse/_main.html index 1c2f4bd1..31e3ff8b 100644 --- a/manual/main/api/_modules/odatse/_main.html +++ b/manual/main/api/_modules/odatse/_main.html @@ -41,7 +41,7 @@ diff --git a/manual/main/api/_modules/odatse/_runner.html b/manual/main/api/_modules/odatse/_runner.html deleted file mode 100644 index f388ca7e..00000000 --- a/manual/main/api/_modules/odatse/_runner.html +++ /dev/null @@ -1,282 +0,0 @@ - - - - - - - - odatse._runner — ODAT-SE API documentation - - - - - - - - - - - - - - - -
- - -
- -
-
-
- -
-
-
-
- -

Source code for odatse._runner

-# -*- coding: utf-8 -*-
-
-# 2DMAT -- Data-analysis software of quantum beam diffraction experiments for 2D material structure
-# Copyright (C) 2020- The University of Tokyo
-#
-# This program is free software: you can redistribute it and/or modify
-# it under the terms of the GNU General Public License as published by
-# the Free Software Foundation, either version 3 of the License, or
-# (at your option) any later version.
-#
-# This program is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-# GNU General Public License for more details.
-#
-# You should have received a copy of the GNU General Public License
-# along with this program. If not, see http://www.gnu.org/licenses/.
-
-from abc import ABCMeta, abstractmethod
-
-import numpy as np
-
-import odatse
-import odatse.util.read_matrix
-import odatse.util.mapping
-import odatse.util.limitation
-from odatse.util.logger import Logger
-from odatse.exception import InputError
-
-# type hints
-from pathlib import Path
-from typing import List, Optional
-from . import mpi
-
-
-

-[docs]
-class Run(metaclass=ABCMeta):
-

-[docs]
-    def __init__(self, nprocs=None, nthreads=None, comm=None):
-        """
-        Initialize the Run class.
-
-        Parameters
-        ----------
-        nprocs : int
-            Number of processes which one solver uses.
-        nthreads : int
-            Number of threads which one solver process uses.
-        comm : MPI.Comm
-            MPI Communicator.
-        """
-        self.nprocs = nprocs
-        self.nthreads = nthreads
-        self.comm = comm

-
-
-

-[docs]
-    @abstractmethod
-    def submit(self, solver):
-        """
-        Abstract method to submit a solver.
-
-        Parameters
-        ----------
-        solver : object
-            Solver object to be submitted.
-        """
-        pass

-

-
-
-
-

-[docs]
-class Runner(object):
-    #solver: "odatse.solver.SolverBase"
-    logger: Logger
-
-

-[docs]
-    def __init__(self,
-                 solver,
-                 info: Optional[odatse.Info] = None,
-                 mapping = None,
-                 limitation = None) -> None:
-        """
-        Initialize the Runner class.
-
-        Parameters
-        ----------
-        solver : odatse.solver.SolverBase
-            Solver object.
-        info : Optional[odatse.Info]
-            Information object.
-        mapping : object, optional
-            Mapping object.
-        limitation : object, optional
-            Limitation object.
-        """
-        self.solver = solver
-        self.solver_name = solver.name
-        self.logger = Logger(info)
-
-        if mapping is not None:
-            self.mapping = mapping
-        elif "mapping" in info.runner:
-            info_mapping = info.runner["mapping"]
-            # N.B.: only Affine mapping is supported at present
-            self.mapping = odatse.util.mapping.Affine.from_dict(info_mapping)
-        else:
-            # trivial mapping
-            self.mapping = odatse.util.mapping.TrivialMapping()
-
-        if limitation is not None:
-            self.limitation = limitation
-        elif "limitation" in info.runner:
-            info_limitation = info.runner["limitation"]
-            self.limitation = odatse.util.limitation.Inequality.from_dict(info_limitation)
-        else:
-            self.limitation = odatse.util.limitation.Unlimited()

-
-
-

-[docs]
-    def prepare(self, proc_dir: Path):
-        """
-        Prepare the logger with the given process directory.
-
-        Parameters
-        ----------
-        proc_dir : Path
-            Path to the process directory.
-        """
-        self.logger.prepare(proc_dir)

-
-
-

-[docs]
-    def submit(
-            self, x: np.ndarray, args = (), nprocs: int = 1, nthreads: int = 1
-    ) -> float:
-        """
-        Submit the solver with the given parameters.
-
-        Parameters
-        ----------
-        x : np.ndarray
-            Input array.
-        args : tuple, optional
-            Additional arguments.
-        nprocs : int, optional
-            Number of processes.
-        nthreads : int, optional
-            Number of threads.
-
-        Returns
-        -------
-        float
-            Result of the solver evaluation.
-        """
-        if self.limitation.judge(x):
-            xp = self.mapping(x)
-            result = self.solver.evaluate(xp, args)
-        else:
-            result = np.inf
-        self.logger.count(x, args, result)
-        return result

-
-
-

-[docs]
-    def post(self) -> None:
-        """
-        Write the logger data.
-        """
-        self.logger.write()

-

-
-
- -
-
- -
-
-
-
- - - - \ No newline at end of file diff --git a/manual/main/api/_modules/odatse/algorithm.html b/manual/main/api/_modules/odatse/algorithm.html index 89da868a..e652edc6 100644 --- a/manual/main/api/_modules/odatse/algorithm.html +++ b/manual/main/api/_modules/odatse/algorithm.html @@ -41,7 +41,7 @@ diff --git a/manual/main/api/_modules/odatse/algorithm/_algorithm.html b/manual/main/api/_modules/odatse/algorithm/_algorithm.html index 1d248898..7ff8e69c 100644 --- a/manual/main/api/_modules/odatse/algorithm/_algorithm.html +++ b/manual/main/api/_modules/odatse/algorithm/_algorithm.html @@ -41,7 +41,7 @@ diff --git a/manual/main/api/_modules/odatse/algorithm/bayes.html b/manual/main/api/_modules/odatse/algorithm/bayes.html index c71fcfaa..7410aab2 100644 --- a/manual/main/api/_modules/odatse/algorithm/bayes.html +++ b/manual/main/api/_modules/odatse/algorithm/bayes.html @@ -41,7 +41,7 @@ diff --git a/manual/main/api/_modules/odatse/algorithm/exchange.html b/manual/main/api/_modules/odatse/algorithm/exchange.html index 822cf57a..d8670bfc 100644 --- a/manual/main/api/_modules/odatse/algorithm/exchange.html +++ b/manual/main/api/_modules/odatse/algorithm/exchange.html @@ -41,7 +41,7 @@ diff --git a/manual/main/api/_modules/odatse/algorithm/mapper_mpi.html b/manual/main/api/_modules/odatse/algorithm/mapper_mpi.html index 957cde69..96cb5525 100644 --- a/manual/main/api/_modules/odatse/algorithm/mapper_mpi.html +++ b/manual/main/api/_modules/odatse/algorithm/mapper_mpi.html @@ -41,7 +41,7 @@ diff --git a/manual/main/api/_modules/odatse/algorithm/min_search.html b/manual/main/api/_modules/odatse/algorithm/min_search.html index 67fa8800..106014fe 100644 --- a/manual/main/api/_modules/odatse/algorithm/min_search.html +++ b/manual/main/api/_modules/odatse/algorithm/min_search.html @@ -41,7 +41,7 @@ diff --git a/manual/main/api/_modules/odatse/algorithm/montecarlo.html b/manual/main/api/_modules/odatse/algorithm/montecarlo.html index ee50a23b..4bbab774 100644 --- a/manual/main/api/_modules/odatse/algorithm/montecarlo.html +++ b/manual/main/api/_modules/odatse/algorithm/montecarlo.html @@ -41,7 +41,7 @@ diff --git a/manual/main/api/_modules/odatse/algorithm/pamc.html b/manual/main/api/_modules/odatse/algorithm/pamc.html index d6516954..627a3a5d 100644 --- a/manual/main/api/_modules/odatse/algorithm/pamc.html +++ b/manual/main/api/_modules/odatse/algorithm/pamc.html @@ -41,7 +41,7 @@ diff --git a/manual/main/api/_modules/odatse/domain/_domain.html b/manual/main/api/_modules/odatse/domain/_domain.html index 91c89bda..08fc4c79 100644 --- a/manual/main/api/_modules/odatse/domain/_domain.html +++ b/manual/main/api/_modules/odatse/domain/_domain.html @@ -41,7 +41,7 @@ diff --git a/manual/main/api/_modules/odatse/domain/meshgrid.html b/manual/main/api/_modules/odatse/domain/meshgrid.html index b0f2b647..aed9e7d5 100644 --- a/manual/main/api/_modules/odatse/domain/meshgrid.html +++ b/manual/main/api/_modules/odatse/domain/meshgrid.html @@ -41,7 +41,7 @@ diff --git a/manual/main/api/_modules/odatse/domain/region.html b/manual/main/api/_modules/odatse/domain/region.html index 11b280f6..5df22373 100644 --- a/manual/main/api/_modules/odatse/domain/region.html +++ b/manual/main/api/_modules/odatse/domain/region.html @@ -41,7 +41,7 @@ diff --git a/manual/main/api/_modules/odatse/exception.html b/manual/main/api/_modules/odatse/exception.html index 964a35f8..25237cfd 100644 --- a/manual/main/api/_modules/odatse/exception.html +++ b/manual/main/api/_modules/odatse/exception.html @@ -41,7 +41,7 @@ diff --git a/manual/main/api/_modules/odatse/mpi.html b/manual/main/api/_modules/odatse/mpi.html deleted file mode 100644 index 02a1f008..00000000 --- a/manual/main/api/_modules/odatse/mpi.html +++ /dev/null @@ -1,164 +0,0 @@ - - - - - - - - odatse.mpi — ODAT-SE API documentation - - - - - - - - - - - - - - - -
- - -
- -
-
-
- -
-
-
-
- -

Source code for odatse.mpi

-# 2DMAT -- Data-analysis software of quantum beam diffraction experiments for 2D material structure
-# Copyright (C) 2020- The University of Tokyo
-#
-# This program is free software: you can redistribute it and/or modify
-# it under the terms of the GNU General Public License as published by
-# the Free Software Foundation, either version 3 of the License, or
-# (at your option) any later version.
-#
-# This program is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-# GNU General Public License for more details.
-#
-# You should have received a copy of the GNU General Public License
-# along with this program. If not, see http://www.gnu.org/licenses/.
-
-try:
-    from mpi4py import MPI
-    Comm = MPI.Comm
-
-    __comm = MPI.COMM_WORLD
-    __size = __comm.size
-    __rank = __comm.rank
-
-    def comm() -> MPI.Comm:
-        return __comm
-
-    def size() -> int:
-        return __size
-
-    def rank() -> int:
-        return __rank
-
-    def enabled() -> bool:
-        return True
-
-
-except ImportError:
-    Comm = None
-
-

-[docs]
-    def comm() -> None:
-        return None

-
-
-

-[docs]
-    def size() -> int:
-        return 1

-
-
-

-[docs]
-    def rank() -> int:
-        return 0

-
-
-

-[docs]
-    def enabled() -> bool:
-        return False

-
-
- -
-
- -
-
-
-
- - - - \ No newline at end of file diff --git a/manual/main/api/_modules/odatse/solver/_solver.html b/manual/main/api/_modules/odatse/solver/_solver.html index dd3d9f1e..646684dc 100644 --- a/manual/main/api/_modules/odatse/solver/_solver.html +++ b/manual/main/api/_modules/odatse/solver/_solver.html @@ -41,7 +41,7 @@ diff --git a/manual/main/api/_modules/odatse/solver/analytical.html b/manual/main/api/_modules/odatse/solver/analytical.html index dfb382ed..dabd3e26 100644 --- a/manual/main/api/_modules/odatse/solver/analytical.html +++ b/manual/main/api/_modules/odatse/solver/analytical.html @@ -41,7 +41,7 @@ diff --git a/manual/main/api/_modules/odatse/solver/function.html b/manual/main/api/_modules/odatse/solver/function.html index 2e362f73..7818bd51 100644 --- a/manual/main/api/_modules/odatse/solver/function.html +++ b/manual/main/api/_modules/odatse/solver/function.html @@ -41,7 +41,7 @@ diff --git a/manual/main/api/_modules/odatse/util/graph.html b/manual/main/api/_modules/odatse/util/graph.html index 0f3aec70..509cd8bc 100644 --- a/manual/main/api/_modules/odatse/util/graph.html +++ b/manual/main/api/_modules/odatse/util/graph.html @@ -41,7 +41,7 @@ diff --git a/manual/main/api/_modules/odatse/util/limitation.html b/manual/main/api/_modules/odatse/util/limitation.html index 9264171d..c45200f9 100644 --- a/manual/main/api/_modules/odatse/util/limitation.html +++ b/manual/main/api/_modules/odatse/util/limitation.html @@ -41,7 +41,7 @@ diff --git a/manual/main/api/_modules/odatse/util/logger.html b/manual/main/api/_modules/odatse/util/logger.html index 5d5e1946..1a55c7e7 100644 --- a/manual/main/api/_modules/odatse/util/logger.html +++ b/manual/main/api/_modules/odatse/util/logger.html @@ -41,7 +41,7 @@ diff --git a/manual/main/api/_modules/odatse/util/mapping.html b/manual/main/api/_modules/odatse/util/mapping.html index 50a5201c..6f47b8a7 100644 --- a/manual/main/api/_modules/odatse/util/mapping.html +++ b/manual/main/api/_modules/odatse/util/mapping.html @@ -41,7 +41,7 @@ diff --git a/manual/main/api/_modules/odatse/util/neighborlist.html b/manual/main/api/_modules/odatse/util/neighborlist.html index df02bc9c..6595dca7 100644 --- a/manual/main/api/_modules/odatse/util/neighborlist.html +++ b/manual/main/api/_modules/odatse/util/neighborlist.html @@ -41,7 +41,7 @@ @@ -553,8 +553,6 @@

Source code for odatse.util.neighborlist

             f.write("\n")
-
-[docs] def main(): import argparse @@ -631,8 +629,7 @@

Source code for odatse.util.neighborlist

         comm=mpi.comm(),
     )
 
-    write_neighbor_list(outputfile, nnlist, radius=radius, unit=unit)
- + write_neighbor_list(outputfile, nnlist, radius=radius, unit=unit)
diff --git a/manual/main/api/_modules/odatse/util/read_matrix.html b/manual/main/api/_modules/odatse/util/read_matrix.html index 56f57af5..f00dbf29 100644 --- a/manual/main/api/_modules/odatse/util/read_matrix.html +++ b/manual/main/api/_modules/odatse/util/read_matrix.html @@ -41,7 +41,7 @@ diff --git a/manual/main/api/_modules/odatse/util/resampling.html b/manual/main/api/_modules/odatse/util/resampling.html index 1a7802ea..105a2f17 100644 --- a/manual/main/api/_modules/odatse/util/resampling.html +++ b/manual/main/api/_modules/odatse/util/resampling.html @@ -41,7 +41,7 @@ @@ -98,19 +98,13 @@

Source code for odatse.util.resampling

 

 [docs]
 class Resampler(abc.ABC):
-

-[docs]
     @abc.abstractmethod
     def reset(self, weights: Iterable):
-        ...

-
+        ...
 
-

-[docs]
     @abc.abstractmethod
     def sample(self, rs: np.random.RandomState, size=None) -> Union[int, np.ndarray]:
         ...

-

 
 
 
diff --git a/manual/main/api/_modules/odatse/util/separateT.html b/manual/main/api/_modules/odatse/util/separateT.html
index 9138e132..c1eb2a4e 100644
--- a/manual/main/api/_modules/odatse/util/separateT.html
+++ b/manual/main/api/_modules/odatse/util/separateT.html
@@ -41,7 +41,7 @@
diff --git a/manual/main/api/_modules/odatse/util/toml.html b/manual/main/api/_modules/odatse/util/toml.html index 7d8b28da..cfcb6313 100644 --- a/manual/main/api/_modules/odatse/util/toml.html +++ b/manual/main/api/_modules/odatse/util/toml.html @@ -41,7 +41,7 @@ diff --git a/manual/main/api/_sources/index.rst.txt b/manual/main/api/_sources/index.rst.txt index 0c1ac76b..c3cba7b1 100644 --- a/manual/main/api/_sources/index.rst.txt +++ b/manual/main/api/_sources/index.rst.txt @@ -10,7 +10,7 @@ Welcome to ODAT-SE API's documentation! :maxdepth: 4 :caption: Contents: - odatse + modules Indices and tables diff --git a/manual/main/api/_sources/modules.rst.txt b/manual/main/api/_sources/modules.rst.txt index 0df1f736..3a33c17e 100644 --- a/manual/main/api/_sources/modules.rst.txt +++ b/manual/main/api/_sources/modules.rst.txt @@ -2,6 +2,6 @@ odatse ====== .. toctree:: - :maxdepth: 4 + :maxdepth: 1 odatse diff --git a/manual/main/api/_sources/odatse._info.rst.txt b/manual/main/api/_sources/odatse._info.rst.txt index d3fd449a..37d6f1ed 100644 --- a/manual/main/api/_sources/odatse._info.rst.txt +++ b/manual/main/api/_sources/odatse._info.rst.txt @@ -3,6 +3,5 @@ odatse.\_info module .. automodule:: odatse._info :members: - :undoc-members: :show-inheritance: :private-members: diff --git a/manual/main/api/_sources/odatse._initialize.rst.txt b/manual/main/api/_sources/odatse._initialize.rst.txt index 555869e9..ab44e17b 100644 --- a/manual/main/api/_sources/odatse._initialize.rst.txt +++ b/manual/main/api/_sources/odatse._initialize.rst.txt @@ -3,6 +3,5 @@ odatse.\_initialize module .. automodule:: odatse._initialize :members: - :undoc-members: :show-inheritance: :private-members: diff --git a/manual/main/api/_sources/odatse._main.rst.txt b/manual/main/api/_sources/odatse._main.rst.txt index b6625ba4..122d809c 100644 --- a/manual/main/api/_sources/odatse._main.rst.txt +++ b/manual/main/api/_sources/odatse._main.rst.txt @@ -3,6 +3,5 @@ odatse.\_main module .. automodule:: odatse._main :members: - :undoc-members: :show-inheritance: :private-members: diff --git a/manual/main/api/_sources/odatse._runner.rst.txt b/manual/main/api/_sources/odatse._runner.rst.txt index 286957af..7a8916f7 100644 --- a/manual/main/api/_sources/odatse._runner.rst.txt +++ b/manual/main/api/_sources/odatse._runner.rst.txt @@ -3,6 +3,5 @@ odatse.\_runner module .. automodule:: odatse._runner :members: - :undoc-members: :show-inheritance: :private-members: diff --git a/manual/main/api/_sources/odatse.algorithm._algorithm.rst.txt b/manual/main/api/_sources/odatse.algorithm._algorithm.rst.txt index ef991943..a1465555 100644 --- a/manual/main/api/_sources/odatse.algorithm._algorithm.rst.txt +++ b/manual/main/api/_sources/odatse.algorithm._algorithm.rst.txt @@ -3,6 +3,5 @@ odatse.algorithm.\_algorithm module .. automodule:: odatse.algorithm._algorithm :members: - :undoc-members: :show-inheritance: :private-members: diff --git a/manual/main/api/_sources/odatse.algorithm.bayes.rst.txt b/manual/main/api/_sources/odatse.algorithm.bayes.rst.txt index cc18ee1e..66f571cc 100644 --- a/manual/main/api/_sources/odatse.algorithm.bayes.rst.txt +++ b/manual/main/api/_sources/odatse.algorithm.bayes.rst.txt @@ -3,6 +3,5 @@ odatse.algorithm.bayes module .. automodule:: odatse.algorithm.bayes :members: - :undoc-members: :show-inheritance: :private-members: diff --git a/manual/main/api/_sources/odatse.algorithm.exchange.rst.txt b/manual/main/api/_sources/odatse.algorithm.exchange.rst.txt index 1b54a140..6f3427b0 100644 --- a/manual/main/api/_sources/odatse.algorithm.exchange.rst.txt +++ b/manual/main/api/_sources/odatse.algorithm.exchange.rst.txt @@ -3,6 +3,5 @@ odatse.algorithm.exchange module .. automodule:: odatse.algorithm.exchange :members: - :undoc-members: :show-inheritance: :private-members: diff --git a/manual/main/api/_sources/odatse.algorithm.mapper_mpi.rst.txt b/manual/main/api/_sources/odatse.algorithm.mapper_mpi.rst.txt index c86bcc9a..ce3c74af 100644 --- a/manual/main/api/_sources/odatse.algorithm.mapper_mpi.rst.txt +++ b/manual/main/api/_sources/odatse.algorithm.mapper_mpi.rst.txt @@ -3,6 +3,5 @@ odatse.algorithm.mapper\_mpi module .. automodule:: odatse.algorithm.mapper_mpi :members: - :undoc-members: :show-inheritance: :private-members: diff --git a/manual/main/api/_sources/odatse.algorithm.min_search.rst.txt b/manual/main/api/_sources/odatse.algorithm.min_search.rst.txt index 3980305d..09d389e8 100644 --- a/manual/main/api/_sources/odatse.algorithm.min_search.rst.txt +++ b/manual/main/api/_sources/odatse.algorithm.min_search.rst.txt @@ -3,6 +3,5 @@ odatse.algorithm.min\_search module .. automodule:: odatse.algorithm.min_search :members: - :undoc-members: :show-inheritance: :private-members: diff --git a/manual/main/api/_sources/odatse.algorithm.montecarlo.rst.txt b/manual/main/api/_sources/odatse.algorithm.montecarlo.rst.txt index 75c48d1f..0cc7cb15 100644 --- a/manual/main/api/_sources/odatse.algorithm.montecarlo.rst.txt +++ b/manual/main/api/_sources/odatse.algorithm.montecarlo.rst.txt @@ -3,6 +3,5 @@ odatse.algorithm.montecarlo module .. automodule:: odatse.algorithm.montecarlo :members: - :undoc-members: :show-inheritance: :private-members: diff --git a/manual/main/api/_sources/odatse.algorithm.pamc.rst.txt b/manual/main/api/_sources/odatse.algorithm.pamc.rst.txt index 826f7041..1abe5109 100644 --- a/manual/main/api/_sources/odatse.algorithm.pamc.rst.txt +++ b/manual/main/api/_sources/odatse.algorithm.pamc.rst.txt @@ -3,6 +3,5 @@ odatse.algorithm.pamc module .. automodule:: odatse.algorithm.pamc :members: - :undoc-members: :show-inheritance: :private-members: diff --git a/manual/main/api/_sources/odatse.algorithm.rst.txt b/manual/main/api/_sources/odatse.algorithm.rst.txt index e2eb2ef3..1d94c41f 100644 --- a/manual/main/api/_sources/odatse.algorithm.rst.txt +++ b/manual/main/api/_sources/odatse.algorithm.rst.txt @@ -1,11 +1,16 @@ odatse.algorithm package ======================== +.. automodule:: odatse.algorithm + :members: + :show-inheritance: + :private-members: + Submodules ---------- .. toctree:: - :maxdepth: 4 + :maxdepth: 1 odatse.algorithm._algorithm odatse.algorithm.bayes @@ -14,12 +19,3 @@ Submodules odatse.algorithm.min_search odatse.algorithm.montecarlo odatse.algorithm.pamc - -Module contents ---------------- - -.. automodule:: odatse.algorithm - :members: - :undoc-members: - :show-inheritance: - :private-members: diff --git a/manual/main/api/_sources/odatse.domain._domain.rst.txt b/manual/main/api/_sources/odatse.domain._domain.rst.txt index a85cb1fd..475476fd 100644 --- a/manual/main/api/_sources/odatse.domain._domain.rst.txt +++ b/manual/main/api/_sources/odatse.domain._domain.rst.txt @@ -3,6 +3,5 @@ odatse.domain.\_domain module .. automodule:: odatse.domain._domain :members: - :undoc-members: :show-inheritance: :private-members: diff --git a/manual/main/api/_sources/odatse.domain.meshgrid.rst.txt b/manual/main/api/_sources/odatse.domain.meshgrid.rst.txt index 838632bc..45308619 100644 --- a/manual/main/api/_sources/odatse.domain.meshgrid.rst.txt +++ b/manual/main/api/_sources/odatse.domain.meshgrid.rst.txt @@ -3,6 +3,5 @@ odatse.domain.meshgrid module .. automodule:: odatse.domain.meshgrid :members: - :undoc-members: :show-inheritance: :private-members: diff --git a/manual/main/api/_sources/odatse.domain.region.rst.txt b/manual/main/api/_sources/odatse.domain.region.rst.txt index 500e891d..3b58537f 100644 --- a/manual/main/api/_sources/odatse.domain.region.rst.txt +++ b/manual/main/api/_sources/odatse.domain.region.rst.txt @@ -3,6 +3,5 @@ odatse.domain.region module .. automodule:: odatse.domain.region :members: - :undoc-members: :show-inheritance: :private-members: diff --git a/manual/main/api/_sources/odatse.domain.rst.txt b/manual/main/api/_sources/odatse.domain.rst.txt index 33ace0cc..ac5f6925 100644 --- a/manual/main/api/_sources/odatse.domain.rst.txt +++ b/manual/main/api/_sources/odatse.domain.rst.txt @@ -1,21 +1,17 @@ odatse.domain package ===================== +.. automodule:: odatse.domain + :members: + :show-inheritance: + :private-members: + Submodules ---------- .. toctree:: - :maxdepth: 4 + :maxdepth: 1 odatse.domain._domain odatse.domain.meshgrid odatse.domain.region - -Module contents ---------------- - -.. automodule:: odatse.domain - :members: - :undoc-members: - :show-inheritance: - :private-members: diff --git a/manual/main/api/_sources/odatse.exception.rst.txt b/manual/main/api/_sources/odatse.exception.rst.txt index 9c4fd827..5ff7200e 100644 --- a/manual/main/api/_sources/odatse.exception.rst.txt +++ b/manual/main/api/_sources/odatse.exception.rst.txt @@ -3,6 +3,5 @@ odatse.exception module .. automodule:: odatse.exception :members: - :undoc-members: :show-inheritance: :private-members: diff --git a/manual/main/api/_sources/odatse.mpi.rst.txt b/manual/main/api/_sources/odatse.mpi.rst.txt index fee18647..200fd450 100644 --- a/manual/main/api/_sources/odatse.mpi.rst.txt +++ b/manual/main/api/_sources/odatse.mpi.rst.txt @@ -3,6 +3,5 @@ odatse.mpi module .. automodule:: odatse.mpi :members: - :undoc-members: :show-inheritance: :private-members: diff --git a/manual/main/api/_sources/odatse.rst.txt b/manual/main/api/_sources/odatse.rst.txt index 9544a061..2450ea3b 100644 --- a/manual/main/api/_sources/odatse.rst.txt +++ b/manual/main/api/_sources/odatse.rst.txt @@ -1,11 +1,16 @@ odatse package ============== +.. automodule:: odatse + :members: + :show-inheritance: + :private-members: + Subpackages ----------- .. toctree:: - :maxdepth: 4 + :maxdepth: 1 odatse.algorithm odatse.domain @@ -16,7 +21,7 @@ Submodules ---------- .. toctree:: - :maxdepth: 4 + :maxdepth: 1 odatse._info odatse._initialize @@ -24,12 +29,3 @@ Submodules odatse._runner odatse.exception odatse.mpi - -Module contents ---------------- - -.. automodule:: odatse - :members: - :undoc-members: - :show-inheritance: - :private-members: diff --git a/manual/main/api/_sources/odatse.solver._solver.rst.txt b/manual/main/api/_sources/odatse.solver._solver.rst.txt index 7299a86a..019a394f 100644 --- a/manual/main/api/_sources/odatse.solver._solver.rst.txt +++ b/manual/main/api/_sources/odatse.solver._solver.rst.txt @@ -3,6 +3,5 @@ odatse.solver.\_solver module .. automodule:: odatse.solver._solver :members: - :undoc-members: :show-inheritance: :private-members: diff --git a/manual/main/api/_sources/odatse.solver.analytical.rst.txt b/manual/main/api/_sources/odatse.solver.analytical.rst.txt index 024cc540..456ee162 100644 --- a/manual/main/api/_sources/odatse.solver.analytical.rst.txt +++ b/manual/main/api/_sources/odatse.solver.analytical.rst.txt @@ -3,6 +3,5 @@ odatse.solver.analytical module .. automodule:: odatse.solver.analytical :members: - :undoc-members: :show-inheritance: :private-members: diff --git a/manual/main/api/_sources/odatse.solver.function.rst.txt b/manual/main/api/_sources/odatse.solver.function.rst.txt index 5944a901..72c839e5 100644 --- a/manual/main/api/_sources/odatse.solver.function.rst.txt +++ b/manual/main/api/_sources/odatse.solver.function.rst.txt @@ -3,6 +3,5 @@ odatse.solver.function module .. automodule:: odatse.solver.function :members: - :undoc-members: :show-inheritance: :private-members: diff --git a/manual/main/api/_sources/odatse.solver.rst.txt b/manual/main/api/_sources/odatse.solver.rst.txt index 4a2b4883..a854a880 100644 --- a/manual/main/api/_sources/odatse.solver.rst.txt +++ b/manual/main/api/_sources/odatse.solver.rst.txt @@ -1,21 +1,17 @@ odatse.solver package ===================== +.. automodule:: odatse.solver + :members: + :show-inheritance: + :private-members: + Submodules ---------- .. toctree:: - :maxdepth: 4 + :maxdepth: 1 odatse.solver._solver odatse.solver.analytical odatse.solver.function - -Module contents ---------------- - -.. automodule:: odatse.solver - :members: - :undoc-members: - :show-inheritance: - :private-members: diff --git a/manual/main/api/_sources/odatse.util.graph.rst.txt b/manual/main/api/_sources/odatse.util.graph.rst.txt index 9752b6e9..361d976a 100644 --- a/manual/main/api/_sources/odatse.util.graph.rst.txt +++ b/manual/main/api/_sources/odatse.util.graph.rst.txt @@ -3,6 +3,5 @@ odatse.util.graph module .. automodule:: odatse.util.graph :members: - :undoc-members: :show-inheritance: :private-members: diff --git a/manual/main/api/_sources/odatse.util.limitation.rst.txt b/manual/main/api/_sources/odatse.util.limitation.rst.txt index 777689d8..c3c235d7 100644 --- a/manual/main/api/_sources/odatse.util.limitation.rst.txt +++ b/manual/main/api/_sources/odatse.util.limitation.rst.txt @@ -3,6 +3,5 @@ odatse.util.limitation module .. automodule:: odatse.util.limitation :members: - :undoc-members: :show-inheritance: :private-members: diff --git a/manual/main/api/_sources/odatse.util.logger.rst.txt b/manual/main/api/_sources/odatse.util.logger.rst.txt index 5b3e5a84..af38d240 100644 --- a/manual/main/api/_sources/odatse.util.logger.rst.txt +++ b/manual/main/api/_sources/odatse.util.logger.rst.txt @@ -3,6 +3,5 @@ odatse.util.logger module .. automodule:: odatse.util.logger :members: - :undoc-members: :show-inheritance: :private-members: diff --git a/manual/main/api/_sources/odatse.util.mapping.rst.txt b/manual/main/api/_sources/odatse.util.mapping.rst.txt index d2add125..3171120f 100644 --- a/manual/main/api/_sources/odatse.util.mapping.rst.txt +++ b/manual/main/api/_sources/odatse.util.mapping.rst.txt @@ -3,6 +3,5 @@ odatse.util.mapping module .. automodule:: odatse.util.mapping :members: - :undoc-members: :show-inheritance: :private-members: diff --git a/manual/main/api/_sources/odatse.util.neighborlist.rst.txt b/manual/main/api/_sources/odatse.util.neighborlist.rst.txt index 82f4154b..2736b613 100644 --- a/manual/main/api/_sources/odatse.util.neighborlist.rst.txt +++ b/manual/main/api/_sources/odatse.util.neighborlist.rst.txt @@ -3,6 +3,5 @@ odatse.util.neighborlist module .. automodule:: odatse.util.neighborlist :members: - :undoc-members: :show-inheritance: :private-members: diff --git a/manual/main/api/_sources/odatse.util.read_matrix.rst.txt b/manual/main/api/_sources/odatse.util.read_matrix.rst.txt index 5a2ece2d..b05fa52f 100644 --- a/manual/main/api/_sources/odatse.util.read_matrix.rst.txt +++ b/manual/main/api/_sources/odatse.util.read_matrix.rst.txt @@ -3,6 +3,5 @@ odatse.util.read\_matrix module .. automodule:: odatse.util.read_matrix :members: - :undoc-members: :show-inheritance: :private-members: diff --git a/manual/main/api/_sources/odatse.util.resampling.rst.txt b/manual/main/api/_sources/odatse.util.resampling.rst.txt index d3ea7f3d..c9fc2291 100644 --- a/manual/main/api/_sources/odatse.util.resampling.rst.txt +++ b/manual/main/api/_sources/odatse.util.resampling.rst.txt @@ -3,6 +3,5 @@ odatse.util.resampling module .. automodule:: odatse.util.resampling :members: - :undoc-members: :show-inheritance: :private-members: diff --git a/manual/main/api/_sources/odatse.util.rst.txt b/manual/main/api/_sources/odatse.util.rst.txt index 7a8c185c..22c8ed15 100644 --- a/manual/main/api/_sources/odatse.util.rst.txt +++ b/manual/main/api/_sources/odatse.util.rst.txt @@ -1,11 +1,16 @@ odatse.util package =================== +.. automodule:: odatse.util + :members: + :show-inheritance: + :private-members: + Submodules ---------- .. toctree:: - :maxdepth: 4 + :maxdepth: 1 odatse.util.graph odatse.util.limitation @@ -16,12 +21,3 @@ Submodules odatse.util.resampling odatse.util.separateT odatse.util.toml - -Module contents ---------------- - -.. automodule:: odatse.util - :members: - :undoc-members: - :show-inheritance: - :private-members: diff --git a/manual/main/api/_sources/odatse.util.separateT.rst.txt b/manual/main/api/_sources/odatse.util.separateT.rst.txt index 0ad5b72e..77176682 100644 --- a/manual/main/api/_sources/odatse.util.separateT.rst.txt +++ b/manual/main/api/_sources/odatse.util.separateT.rst.txt @@ -3,6 +3,5 @@ odatse.util.separateT module .. automodule:: odatse.util.separateT :members: - :undoc-members: :show-inheritance: :private-members: diff --git a/manual/main/api/_sources/odatse.util.toml.rst.txt b/manual/main/api/_sources/odatse.util.toml.rst.txt index d9e3a78e..c1f83185 100644 --- a/manual/main/api/_sources/odatse.util.toml.rst.txt +++ b/manual/main/api/_sources/odatse.util.toml.rst.txt @@ -3,6 +3,5 @@ odatse.util.toml module .. automodule:: odatse.util.toml :members: - :undoc-members: :show-inheritance: :private-members: diff --git a/manual/main/api/genindex.html b/manual/main/api/genindex.html index 958a0128..205c56a7 100644 --- a/manual/main/api/genindex.html +++ b/manual/main/api/genindex.html @@ -41,7 +41,7 @@ @@ -106,10 +106,6 @@

_

  • __init__() (odatse._info.Info method)
  • __init_rng() (odatse.algorithm._algorithm.AlgorithmBase method)
    • -
  • _abc_impl (odatse._runner.Run attribute) - -
  • _asdict() (odatse.util.separateT.Entry method)
  • _check_parameters() (odatse.algorithm._algorithm.AlgorithmBase method) @@ -200,19 +160,11 @@

    _

  • _evaluate() (odatse.algorithm.montecarlo.AlgorithmBase method)
  • _exchange() (odatse.algorithm.exchange.Algorithm method) -
    • -
  • _field_defaults (odatse.util.separateT.Entry attribute) -
    • -
  • _fields (odatse.util.separateT.Entry attribute)
  • _find_scheduling() (odatse.algorithm.pamc.Algorithm method) -
    • -
  • _func (odatse.solver.function.Solver attribute)
  • _gather_information() (odatse.algorithm.pamc.Algorithm method)
    • - - + +

    N

    @@ -1023,6 +811,8 @@

    O

  • module
    • + + - -
  • out_of_bound() (odatse.util.neighborlist.Cells method)
    • -
  • output_dir (odatse.algorithm._algorithm.AlgorithmBase attribute) - -
    • @@ -1155,21 +937,11 @@

    P

    @@ -1213,8 +977,6 @@

    R

  • (odatse.algorithm.pamc.Algorithm attribute)
    • -
  • rank() (in module odatse.mpi) -
  • read_matrix() (in module odatse.util.read_matrix)
  • read_Ts() (in module odatse.algorithm.montecarlo) @@ -1223,50 +985,26 @@

    R

  • Region (class in odatse.domain.region)
    • -
  • rep2T (odatse.algorithm.exchange.Algorithm attribute), [1] + + - @@ -1278,8 +1016,6 @@

    S

  • sample() (odatse.util.resampling.BinarySearch method)
    • @@ -1288,67 +1024,41 @@

    S

  • separateT() (in module odatse.util.separateT)
  • set_function() (odatse.solver.function.Solver method) -
    • -
  • set_runner() (odatse.algorithm._algorithm.AlgorithmBase method) -
    • -
  • size() (in module odatse.mpi)

    • T

      -
    • to_write_input (odatse.util.logger.Logger attribute) -
      • -
    • to_write_result (odatse.util.logger.Logger attribute) -
    • TrivialMapping (class in odatse.util.mapping)
    • Ts (odatse.algorithm.montecarlo.AlgorithmBase attribute) @@ -1359,12 +1069,8 @@

      T

      U

      • Unlimited (class in odatse.util.limitation) @@ -1376,19 +1082,11 @@

        W

          -
        • wmax (odatse.util.resampling.BinarySearch attribute) -
          • -
        • work_dir (odatse.solver._solver.SolverBase attribute) -
        • write() (odatse.util.logger.Logger method)
        • write_neighbor_list() (in module odatse.util.neighborlist) @@ -1401,53 +1099,19 @@

          W

          X

          diff --git a/manual/main/api/index.html b/manual/main/api/index.html index a0d30f89..647a0a27 100644 --- a/manual/main/api/index.html +++ b/manual/main/api/index.html @@ -19,7 +19,7 @@ - + @@ -43,7 +43,7 @@ @@ -75,63 +75,26 @@

          Welcome to ODAT-SE API’s documentation!

          Contents:

            -
          • odatse package
              -
            • Subpackages
                -
              • odatse.algorithm package
                  -
                • Submodules
                  • -
                • Module contents
                  • +
                • odatse @@ -150,7 +113,7 @@

                  Indices and tables - +
                  diff --git a/manual/main/api/modules.html b/manual/main/api/modules.html index c46ccd9f..18b22474 100644 --- a/manual/main/api/modules.html +++ b/manual/main/api/modules.html @@ -18,7 +18,9 @@ - + + + @@ -41,8 +43,11 @@ @@ -73,65 +78,7 @@

                  odatse

                  @@ -139,7 +86,10 @@

                  odatse< -