downstream 0.4.2__tar.gz

downstream-0.4.2/LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2024 Matthew Andres Moreno
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

downstream-0.4.2/PKG-INFO

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+Metadata-Version: 2.1
+Name: downstream
+Version: 0.4.2
+Summary: downstream provides efficient, constant-space instrumentation for heredity stratigraphic phylogenetic inference over distributed digital evolution populations.
+Author-email: Matthew Andres Moreno <m.more500@gmail.com>
+License: MIT license
+Project-URL: homepage, https://github.com/mmore500/downstream.git
+Project-URL: repository, https://github.com/mmore500/downstream
+Keywords: downstream
+Classifier: Development Status :: 2 - Pre-Alpha
+Classifier: Intended Audience :: Developers
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Natural Language :: English
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Requires-Python: >=3.10
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: Deprecated
+Requires-Dist: hstrat>=1.7.4
+Requires-Dist: interval_search>=0.5.2
+Requires-Dist: IPython
+Requires-Dist: matplotlib
+Requires-Dist: more_itertools
+Requires-Dist: numpy
+Requires-Dist: opytional
+Requires-Dist: pandas
+Requires-Dist: scipy
+Requires-Dist: seaborn
+Requires-Dist: teeplot>=0.5.0
+Provides-Extra: testing
+Requires-Dist: black==22.10.0; extra == "testing"
+Requires-Dist: isort==5.12.0; extra == "testing"
+Requires-Dist: pytest==7.2.2; extra == "testing"
+Requires-Dist: pytest-xdist==3.2.1; extra == "testing"
+Requires-Dist: ruff==0.0.260; extra == "testing"
+Requires-Dist: tqdm==4.64.1; extra == "testing"
+Provides-Extra: release
+Requires-Dist: bumpver==2022.1120; extra == "release"
+Requires-Dist: twine==1.14.0; extra == "release"
+Requires-Dist: wheel==0.33.6; extra == "release"
+Requires-Dist: pip==22.0.4; extra == "release"
+Requires-Dist: pip_tools==6.10.0; extra == "release"
+Requires-Dist: setuptools==65.6.3; extra == "release"
+
+# Downstream
+
+[![CI](https://github.com/mmore500/downstream/actions/workflows/ci.yaml/badge.svg)](https://github.com/mmore500/downstream/actions/workflows/ci.yaml)
+[![GitHub stars](https://img.shields.io/github/stars/mmore500/downstream.svg?style=flat-square&logo=github&label=Stars&logoColor=white)](https://github.com/mmore500/downstream)
+<!-- [
+![PyPi](https://img.shields.io/pypi/v/downstream.svg)
+](https://pypi.python.org/pypi/downstream) -->
+<!-- [![DOI](https://zenodo.org/badge/652063401.svg)](https://zenodo.org/doi/10.5281/zenodo.10779240) -->
+<!-- [![Documentation Status](https://readthedocs.org/projects/downstream/badge/?version=latest)](https://downstream.readthedocs.io/en/latest/?badge=latest) -->
+<!-- [![documentation coverage](https://img.shields.io/endpoint?url=https%3A%2F%2Fmmore500.github.io%2Fdownstream%2Fdocumentation-coverage-badge.json)](https://downstream.readthedocs.io/en/latest/) -->
+<!-- [![code coverage status](https://codecov.io/gh/mmore500/downstream/branch/master/graph/badge.svg)](https://codecov.io/gh/mmore500/downstream) -->
+<!-- [![dotos](https://img.shields.io/endpoint?url=https%3A%2F%2Fmmore500.com%2Fdownstream%2Fdoto-badge.json)](https://github.com/mmore500/downstream/search?q=todo+OR+fixme&type=) -->
+
+downstream provides efficient, constant-space implementations of stream curation algorithms.
+
+-   Free software: MIT license
+
+<!---
+-   Documentation: <https://downstream.readthedocs.io>.
+-->
+
+## Installation
+
+`python3 -m pip install "git+https://github.com/mmore500/downstream.git@v0.4.2#egg=downstream"`
+
+## Documentation
+
+Slide deck & graphics for this project are at <https://hopth.ru/ce>.
+
+See `https://github.com/mmore500/hstrat-surface-concept` for usage examples.
+
+## Citing
+
+If downstream contributes to a scientific publication, please cite it as
+
+> Matthew Andres Moreno. (2024). mmore500/downstream. Zenodo. https://zenodo.org/doi/TODO
+
+```bibtex
+@software{moreno2024downstream,
+  author = {Matthew Andres Moreno},
+  title = {mmore500/downstream},
+  month = mar,
+  year = 2024,
+  publisher = {Zenodo},
+  doi = {TODO},
+  url = {https://zenodo.org/doi/TODO}
+}
+```
+
+Consider also citing [hstrat](https://hstrat.readthedocs.io/en/stable/citing.html).
+And don't forget to leave a [star on GitHub](https://github.com/mmore500/downstream/stargazers)!
+
+## Credits
+
+This package was created with [Cookiecutter](https://github.com/audreyr/cookiecutter) and the [mmore500/cookiecutter-dishtiny-project](https://github.com/mmore500/cookiecutter-dishtiny-project) project template.
+
+<!---
+This package uses [Empirical](https://github.com/devosoft/Empirical#readme), a library of tools for scientific software development, with emphasis on also being able to build web interfaces using Emscripten.
+-->

downstream-0.4.2/README.md

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+# Downstream
+
+[![CI](https://github.com/mmore500/downstream/actions/workflows/ci.yaml/badge.svg)](https://github.com/mmore500/downstream/actions/workflows/ci.yaml)
+[![GitHub stars](https://img.shields.io/github/stars/mmore500/downstream.svg?style=flat-square&logo=github&label=Stars&logoColor=white)](https://github.com/mmore500/downstream)
+<!-- [
+![PyPi](https://img.shields.io/pypi/v/downstream.svg)
+](https://pypi.python.org/pypi/downstream) -->
+<!-- [![DOI](https://zenodo.org/badge/652063401.svg)](https://zenodo.org/doi/10.5281/zenodo.10779240) -->
+<!-- [![Documentation Status](https://readthedocs.org/projects/downstream/badge/?version=latest)](https://downstream.readthedocs.io/en/latest/?badge=latest) -->
+<!-- [![documentation coverage](https://img.shields.io/endpoint?url=https%3A%2F%2Fmmore500.github.io%2Fdownstream%2Fdocumentation-coverage-badge.json)](https://downstream.readthedocs.io/en/latest/) -->
+<!-- [![code coverage status](https://codecov.io/gh/mmore500/downstream/branch/master/graph/badge.svg)](https://codecov.io/gh/mmore500/downstream) -->
+<!-- [![dotos](https://img.shields.io/endpoint?url=https%3A%2F%2Fmmore500.com%2Fdownstream%2Fdoto-badge.json)](https://github.com/mmore500/downstream/search?q=todo+OR+fixme&type=) -->
+
+downstream provides efficient, constant-space implementations of stream curation algorithms.
+
+-   Free software: MIT license
+
+<!---
+-   Documentation: <https://downstream.readthedocs.io>.
+-->
+
+## Installation
+
+`python3 -m pip install "git+https://github.com/mmore500/downstream.git@v0.4.2#egg=downstream"`
+
+## Documentation
+
+Slide deck & graphics for this project are at <https://hopth.ru/ce>.
+
+See `https://github.com/mmore500/hstrat-surface-concept` for usage examples.
+
+## Citing
+
+If downstream contributes to a scientific publication, please cite it as
+
+> Matthew Andres Moreno. (2024). mmore500/downstream. Zenodo. https://zenodo.org/doi/TODO
+
+```bibtex
+@software{moreno2024downstream,
+  author = {Matthew Andres Moreno},
+  title = {mmore500/downstream},
+  month = mar,
+  year = 2024,
+  publisher = {Zenodo},
+  doi = {TODO},
+  url = {https://zenodo.org/doi/TODO}
+}
+```
+
+Consider also citing [hstrat](https://hstrat.readthedocs.io/en/stable/citing.html).
+And don't forget to leave a [star on GitHub](https://github.com/mmore500/downstream/stargazers)!
+
+## Credits
+
+This package was created with [Cookiecutter](https://github.com/audreyr/cookiecutter) and the [mmore500/cookiecutter-dishtiny-project](https://github.com/mmore500/cookiecutter-dishtiny-project) project template.
+
+<!---
+This package uses [Empirical](https://github.com/devosoft/Empirical#readme), a library of tools for scientific software development, with emphasis on also being able to build web interfaces using Emscripten.
+-->

downstream-0.4.2/downstream/__init__.py

@@ -0,0 +1,15 @@
+"""Top-level package for downstream."""
+
+__author__ = "Matthew Andres Moreno"
+__email__ = "m.more500@gmail.com"
+__version__ = "0.4.2"
+
+
+from . import genome_instrumentation, interop, site_selection_strategy
+
+__all__ = [
+    "interop",
+    "genome_instrumentation",
+    "serialization",
+    "site_selection_strategy",
+]

downstream-0.4.2/downstream/downstream/__init__.py

@@ -0,0 +1,4 @@
+from ..genome_instrumentation import *  # noqa: F403
+from ..interop import *  # noqa: F403
+from ..serialization import *  # noqa: F403
+from ..site_selection_strategy import *  # noqa: F403

downstream-0.4.2/downstream/genome_instrumentation/_BitSurface.py

@@ -0,0 +1,2 @@
+class BitSurface:
+    """Placeholder."""

downstream-0.4.2/downstream/genome_instrumentation/_StructSurface.py

@@ -0,0 +1,2 @@
+class StructSurface:
+    """Placeholder."""

downstream-0.4.2/downstream/genome_instrumentation/__init__.py

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+from ._BitSurface import BitSurface
+from ._StructSurface import StructSurface
+
+__all__ = [
+    "BitSurface",
+    "StructSurface",
+]

downstream-0.4.2/downstream/interop/__init__.py

@@ -0,0 +1,23 @@
+from . import (
+    _stratum_retention_interop_hybrid_algo as stratum_retention_interop_hybrid_algo,
+)
+from . import (
+    _stratum_retention_interop_steady_algo as stratum_retention_interop_steady_algo,
+)
+from . import (
+    _stratum_retention_interop_tilted_algo as stratum_retention_interop_tilted_algo,
+)
+from . import (
+    _stratum_retention_interop_tilted_sticky_algo as stratum_retention_interop_tilted_sticky_algo,
+)
+from ._make_stratum_retention_policy_from_site_selection_algo import (
+    make_stratum_retention_policy_from_site_selection_algo,
+)
+
+__all__ = [
+    "make_stratum_retention_policy_from_site_selection_algo",
+    "stratum_retention_interop_hybrid_algo",
+    "stratum_retention_interop_steady_algo",
+    "stratum_retention_interop_tilted_algo",
+    "stratum_retention_interop_tilted_sticky_algo",
+]

downstream-0.4.2/downstream/interop/_make_stratum_retention_policy_from_site_selection_algo.py

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+import numbers
+import types
+import typing
+
+from hstrat.stratum_retention_strategy.stratum_retention_algorithms._detail import (
+    PolicyCouplerBase,
+    PolicyCouplerFactory,
+    PolicySpecBase,
+)
+import more_itertools as mit
+
+
+class _PolicySpecBase:
+    pass
+
+
+class _GenDropRanksFtorBase:
+    pass
+
+
+class _CalcNumStrataRetainedExactFtorBase:
+    pass
+
+
+class _CalcRankAtColumnIndexFtorBase:
+    pass
+
+
+class _IterRetainedRanksFtorBase:
+    pass
+
+
+class _CalcNumStrataRetainedUpperBoundFtorBase:
+    pass
+
+
+def make_stratum_retention_policy_from_site_selection_algo(
+    site_selection_algo: types.ModuleType,
+) -> PolicyCouplerBase:
+    """Create object infrastructure for a stratum retention policy equivalent
+    to provided surface site selection algorithm."""
+
+    class PolicySpec(PolicySpecBase, _PolicySpecBase):
+        """Contains all policy parameters, if any."""
+
+        _site_selection_algo: types.ModuleType = site_selection_algo
+        _surface_size: int
+
+        def __init__(
+            self: "PolicySpec",
+            surface_size: int,
+        ):
+            """Construct the policy spec.
+
+            Parameters
+            ----------
+            surface_size : int
+                How many sites does surface contain?
+            """
+            assert surface_size > 1
+            self._surface_size = surface_size
+
+        def __eq__(self: "PolicySpec", other: typing.Any) -> bool:
+            return isinstance(other, _PolicySpecBase) and (
+                self._surface_size,
+                self._site_selection_algo,
+            ) == (
+                other._surface_size,
+                other._site_selection_algo,
+            )
+
+        def __repr__(self: "PolicySpec") -> str:
+            return f"""{
+                self.GetAlgoIdentifier()
+            }.{
+                PolicySpec.__qualname__
+            }(surface_size={
+                self._surface_size
+            })"""
+
+        def __str__(self: "PolicySpec") -> str:
+            return f"""{
+                self.GetAlgoTitle()
+            } (surface size: {
+                self._surface_size
+            })"""
+
+        def GetEvalCtor(self: "PolicySpec") -> str:
+            return (
+                "downstream.interop.stratum_retention_interop_"
+                f"{site_selection_algo.__name__}.{self!r}"
+            )
+
+        def GetSurfaceSize(self: "PolicySpec") -> int:
+            return self._surface_size
+
+        @staticmethod
+        def GetAlgoIdentifier() -> str:
+            """Get programatic name for underlying retention algorithm."""
+            return site_selection_algo.__name__
+
+        @staticmethod
+        def GetAlgoTitle() -> str:
+            """Get human-readable name for underlying retention algorithm."""
+            return site_selection_algo.__name__.replace("_", " ")
+
+    class CalcNumStrataRetainedExactFtor(_CalcNumStrataRetainedExactFtorBase):
+        def __init__(
+            self: "CalcNumStrataRetainedExactFtor",
+            policy_spec: typing.Optional[PolicySpec],
+        ) -> None:
+            pass
+
+        def __eq__(
+            self: "CalcNumStrataRetainedExactFtor",
+            other: typing.Any,
+        ) -> bool:
+            return isinstance(other, _CalcNumStrataRetainedExactFtorBase)
+
+        def __call__(
+            self: "CalcNumStrataRetainedExactFtor",
+            policy: PolicyCouplerBase,
+            num_strata_deposited: int,
+        ) -> int:
+            return sum(
+                1 for __ in policy.IterRetainedRanks(num_strata_deposited)
+            )
+
+    class CalcRankAtColumnIndexFtor(_CalcRankAtColumnIndexFtorBase):
+        def __init__(
+            self: "CalcRankAtColumnIndexFtor",
+            policy_spec: typing.Optional[PolicySpec],
+        ) -> None:
+            pass
+
+        def __eq__(
+            self: "CalcRankAtColumnIndexFtor",
+            other: typing.Any,
+        ) -> bool:
+            return isinstance(other, _CalcRankAtColumnIndexFtorBase)
+
+        def __call__(
+            self: "CalcRankAtColumnIndexFtor",
+            policy: PolicyCouplerBase,
+            index: int,
+            num_strata_deposited: int,
+        ) -> int:
+            if (
+                not 0
+                <= index
+                < policy.CalcNumStrataRetainedExact(num_strata_deposited)
+            ):
+                raise IndexError
+            res = mit.nth(
+                policy.IterRetainedRanks(num_strata_deposited), index
+            )
+            assert res is not None
+            return res
+
+    class GenDropRanksFtor(_GenDropRanksFtorBase):
+        def __init__(
+            self: "GenDropRanksFtor",
+            policy_spec: typing.Optional[PolicySpec],
+        ) -> None:
+            pass
+
+        def __eq__(
+            self: "GenDropRanksFtor",
+            other: typing.Any,
+        ) -> bool:
+            return isinstance(other, _GenDropRanksFtorBase)
+
+        def __call__(
+            self: "GenDropRanksFtor",
+            policy: PolicyCouplerBase,
+            num_stratum_depositions_completed: int,
+            retained_ranks: typing.Optional[typing.Iterable[int]] = None,
+        ) -> typing.Iterator[int]:
+            # convert for compat with numpy dtypes
+            assert isinstance(
+                num_stratum_depositions_completed, numbers.Integral
+            )
+            num_stratum_depositions_completed = int(
+                num_stratum_depositions_completed,
+            )
+
+            if num_stratum_depositions_completed == 0:
+                return
+
+            algo = site_selection_algo
+            surface_size = policy.GetSpec().GetSurfaceSize()
+
+            target_site = algo.pick_deposition_site(
+                num_stratum_depositions_completed, surface_size
+            )
+            target_rank = algo.calc_resident_deposition_rank(
+                target_site, surface_size, num_stratum_depositions_completed
+            )
+            if target_rank != 0:
+                yield target_rank
+                return
+            elif 0 not in algo.iter_resident_deposition_ranks(
+                surface_size,
+                num_stratum_depositions_completed + 1,
+            ):
+                yield 0
+                return
+
+    class IterRetainedRanksFtor(_IterRetainedRanksFtorBase):
+        def __init__(
+            self: "IterRetainedRanksFtor",
+            policy_spec: typing.Optional[PolicySpec],
+        ) -> None:
+            pass
+
+        def __eq__(
+            self: "IterRetainedRanksFtor",
+            other: typing.Any,
+        ) -> bool:
+            return isinstance(other, _IterRetainedRanksFtorBase)
+
+        def __call__(
+            self: "IterRetainedRanksFtor",
+            policy: PolicyCouplerBase,
+            num_strata_deposited: int,
+        ) -> typing.Iterator[int]:
+            # convert for compat with numpy dtypes
+            assert isinstance(num_strata_deposited, numbers.Integral)
+            num_strata_deposited = int(num_strata_deposited)
+
+            if num_strata_deposited == 0:
+                return
+            algo = site_selection_algo
+            surface_size = policy.GetSpec().GetSurfaceSize()
+            ranks = sorted(
+                algo.iter_resident_deposition_ranks(
+                    surface_size,
+                    num_strata_deposited,
+                )
+            )
+            last_zero = ranks.count(0) - (ranks[0] == 0)
+            assert 0 <= last_zero < len(ranks)
+            yield from ranks[last_zero:]
+
+    class CalcNumStrataRetainedUpperBoundFtor(
+        _CalcNumStrataRetainedUpperBoundFtorBase,
+    ):
+        def __init__(
+            self: "CalcNumStrataRetainedUpperBoundFtor",
+            policy_spec: typing.Optional[PolicySpec],
+        ) -> None:
+            pass
+
+        def __eq__(
+            self: "CalcNumStrataRetainedUpperBoundFtor",
+            other: typing.Any,
+        ) -> bool:
+            return isinstance(other, _CalcNumStrataRetainedUpperBoundFtorBase)
+
+        def __call__(
+            self: "CalcNumStrataRetainedUpperBoundFtor",
+            policy: PolicyCouplerBase,
+            num_strata_deposited: int,
+        ) -> typing.Iterator[int]:
+            surface_size = policy.GetSpec().GetSurfaceSize()
+            return min(
+                num_strata_deposited,
+                surface_size,
+            )
+
+    return PolicyCouplerFactory(
+        policy_spec_t=PolicySpec,
+        gen_drop_ranks_ftor_t=GenDropRanksFtor,
+        calc_num_strata_retained_exact_ftor_t=CalcNumStrataRetainedExactFtor,
+        calc_rank_at_column_index_ftor_t=CalcRankAtColumnIndexFtor,
+        iter_retained_ranks_ftor_t=IterRetainedRanksFtor,
+        calc_num_strata_retained_upper_bound_ftor_t=CalcNumStrataRetainedUpperBoundFtor,
+    )

downstream-0.4.2/downstream/interop/_stratum_retention_interop_hybrid_algo.py

@@ -0,0 +1,14 @@
+from ..site_selection_strategy.site_selection_algorithms import (
+    hybrid_algo as _site_selection_algo,
+)
+from ._make_stratum_retention_policy_from_site_selection_algo import (
+    make_stratum_retention_policy_from_site_selection_algo,
+)
+
+Policy = make_stratum_retention_policy_from_site_selection_algo(
+    _site_selection_algo
+)
+PolicySpec = Policy.policy_spec_t
+
+# prevent name leakage
+del make_stratum_retention_policy_from_site_selection_algo

downstream-0.4.2/downstream/interop/_stratum_retention_interop_steady_algo.py

@@ -0,0 +1,14 @@
+from ..site_selection_strategy.site_selection_algorithms import (
+    steady_algo as _site_selection_algo,
+)
+from ._make_stratum_retention_policy_from_site_selection_algo import (
+    make_stratum_retention_policy_from_site_selection_algo,
+)
+
+Policy = make_stratum_retention_policy_from_site_selection_algo(
+    _site_selection_algo
+)
+PolicySpec = Policy.policy_spec_t
+
+# prevent name leakage
+del make_stratum_retention_policy_from_site_selection_algo

downstream-0.4.2/downstream/interop/_stratum_retention_interop_tilted_algo.py

@@ -0,0 +1,14 @@
+from ..site_selection_strategy.site_selection_algorithms import (
+    tilted_algo as _site_selection_algo,
+)
+from ._make_stratum_retention_policy_from_site_selection_algo import (
+    make_stratum_retention_policy_from_site_selection_algo,
+)
+
+Policy = make_stratum_retention_policy_from_site_selection_algo(
+    _site_selection_algo,
+)
+PolicySpec = Policy.policy_spec_t
+
+# prevent name leakage
+del make_stratum_retention_policy_from_site_selection_algo

downstream-0.4.2/downstream/interop/_stratum_retention_interop_tilted_sticky_algo.py

@@ -0,0 +1,14 @@
+from ..site_selection_strategy.site_selection_algorithms import (
+    tilted_sticky_algo as _site_selection_algo,
+)
+from ._make_stratum_retention_policy_from_site_selection_algo import (
+    make_stratum_retention_policy_from_site_selection_algo,
+)
+
+Policy = make_stratum_retention_policy_from_site_selection_algo(
+    _site_selection_algo,
+)
+PolicySpec = Policy.policy_spec_t
+
+# prevent name leakage
+del make_stratum_retention_policy_from_site_selection_algo

downstream-0.4.2/downstream/pylib/Literal.py

@@ -0,0 +1,4 @@
+try:
+    from typing import Literal  # noqa: F401
+except ImportError:
+    from typing_extensions import Literal  # noqa: F401

downstream-0.4.2/downstream/pylib/__init__.py

@@ -0,0 +1,69 @@
+from . import (
+    hanoi,
+    longevity_ordering_alternating,
+    longevity_ordering_descending,
+    longevity_ordering_naive,
+    longevity_ordering_piecewise_ascending,
+    oeis,
+    site_selection_eval,
+    site_selection_viz,
+)
+from .Literal import Literal
+from .bit_ceil import bit_ceil
+from .bit_count_immediate_zeros import bit_count_immediate_zeros
+from .bit_count_leading_ones import bit_count_leading_ones
+from .bit_decode_gray import bit_decode_gray
+from .bit_drop_msb import bit_drop_msb
+from .bit_encode_gray import bit_encode_gray
+from .bit_floor import bit_floor
+from .bit_invert import bit_invert
+from .bit_reverse import bit_reverse
+from .calc_dyadic_lcm_upper_bound import calc_dyadic_lcm_upper_bound
+from .count_factors_of_2 import count_factors_of_2
+from .enforce_typing import enforce_typing
+from .fast_pow2_divide import fast_pow2_divide
+from .fast_pow2_mod import fast_pow2_mod
+from .get_powersof2triangle_val_at_index import (
+    get_powersof2triangle_val_at_index,
+)
+from .jupyter_hide_toggle import jupyter_hide_toggle
+from .log_args_and_result import log_args_and_result
+from .modulo import modulo
+from .prepend_cmap_with_color import prepend_cmap_with_color
+from .round_to_one_sigfig import round_to_one_sigfig
+from .sign import sign
+from .tee_release import tee_release
+
+__all__ = [
+    "bit_ceil",
+    "bit_count_immediate_zeros",
+    "bit_count_leading_ones",
+    "bit_drop_msb",
+    "bit_decode_gray",
+    "bit_invert",
+    "bit_encode_gray",
+    "bit_floor",
+    "bit_reverse",
+    "calc_dyadic_lcm_upper_bound",
+    "count_factors_of_2",
+    "enforce_typing",
+    "fast_pow2_divide",
+    "fast_pow2_mod",
+    "get_powersof2triangle_val_at_index",
+    "jupyter_hide_toggle",
+    "Literal",
+    "log_args_and_result",
+    "modulo",
+    "prepend_cmap_with_color",
+    "round_to_one_sigfig",
+    "hanoi",
+    "longevity_ordering_naive",
+    "longevity_ordering_alternating",
+    "longevity_ordering_piecewise_ascending",
+    "longevity_ordering_descending",
+    "oeis",
+    "sign",
+    "site_selection_eval",
+    "site_selection_viz",
+    "tee_release",
+]

downstream-0.4.2/downstream/pylib/bit_ceil.py

@@ -0,0 +1,11 @@
+def bit_ceil(n: int) -> int:
+    """Calculate the smallest power of 2 not smaller than n."""
+    # adapted from https://github.com/mmore500/hstrat/blob/e9c2994c7a6514162f1ab685d88c374372dc1cf0/hstrat/_auxiliary_lib/_bit_ceil.py
+    assert n >= 0
+    if n:
+        # see https://stackoverflow.com/a/14267825/17332200
+        exp = (n - 1).bit_length()
+        res = 1 << exp
+        return res
+    else:
+        return 1