multipers 2.4.2b2__tar.gz → 2.5.0b1__tar.gz

{multipers-2.4.2b2/multipers.egg-info → multipers-2.5.0b1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: multipers
-Version: 2.4.2b2
+Version: 2.5.0b1
 Summary: Multiparameter Topological Persistence for Machine Learning
 Author-email: David Loiseaux <david.lapous@proton.me>, Hannah Schreiber <hannah.schreiber@inria.fr>
 Maintainer-email: David Loiseaux <david.lapous@proton.me>
@@ -93,16 +93,6 @@ We hence recommend Windows user to use [WSL](https://learn.microsoft.com/en-us/w
 Documentation and build instructions are available
 [here](https://davidlapous.github.io/multipers/compilation.html).
 
-## Licensing
-
-`multipers` distributions that include the compiled external interfaces are provided under
-**GPL-3.0-or-later**.
-
-This is due to linked GPL/LGPL third-party components used by the build, notably
-`AIDA`, `Persistence-Algebra`, `function_delaunay`, `mpfree`, `multi_critical`, and
-`multi_chunk`.
-
-See `THIRD_PARTY_NOTICES.md` for dependency details and pinned revisions used in this workspace.
 
 
 ## Features, and linked projects
@@ -134,8 +124,20 @@ If I missed something, or you want to add something, feel free to open an issue.
 [Luis Scoccola](https://luisscoccola.com/) 
 (Möbius inversion in python, degree-rips using [persistable](https://github.com/LuisScoccola/persistable) and [RIVET](https://github.com/rivetTDA/rivet/)),<br>
 [Mathieu Carrière](https://www-sop.inria.fr/members/Mathieu.Carriere/) (Sliced Wasserstein),<br>
-[Odin Hoff Gardå](https://odinhg.github.io/) (Delaunay Core bifiltration).<br>
-Jan Jendrysiak (Module Decomposition).<br>
+[Odin Hoff Gardå](https://odinhg.github.io/) (Delaunay Core bifiltration),<br>
+[Michael Kerber](https://www.geometrie.tugraz.at/kerber/) ([mpfree](https://bitbucket.org/mkerber/mpfree/src/master/), [function_delaunay](https://bitbucket.org/mkerber/function_delaunay), [multi_critical](https://bitbucket.org/mkerber/multi_critical) [multi_chunck](https://bitbucket.org/mkerber/multi_chunk) backends),<br>
+[Jan Jendrysiak](https://github.com/JanJend) ([Module Decomposition (AIDA)](https://github.com/JanJend/AIDA), [Persistence Algebra](https://github.com/JanJend/Persistence-Algebra)).<br>
+
+## Licensing
+
+`multipers` distributions that include the compiled external interfaces are provided under
+**GPL-3.0-or-later**.
+
+This is due to linked GPL/LGPL third-party components used by the build, notably
+`AIDA`, `Persistence-Algebra`, `function_delaunay`, `mpfree`, `multi_critical`, and
+`multi_chunk`.
+
+See `THIRD_PARTY_NOTICES.md` for dependency details and pinned revisions used in this workspace.
 
 ## Citation
 Please cite this library when using it in scientific publications;

{multipers-2.4.2b2 → multipers-2.5.0b1}/README.md

@@ -38,16 +38,6 @@ We hence recommend Windows user to use [WSL](https://learn.microsoft.com/en-us/w
 Documentation and build instructions are available
 [here](https://davidlapous.github.io/multipers/compilation.html).
 
-## Licensing
-
-`multipers` distributions that include the compiled external interfaces are provided under
-**GPL-3.0-or-later**.
-
-This is due to linked GPL/LGPL third-party components used by the build, notably
-`AIDA`, `Persistence-Algebra`, `function_delaunay`, `mpfree`, `multi_critical`, and
-`multi_chunk`.
-
-See `THIRD_PARTY_NOTICES.md` for dependency details and pinned revisions used in this workspace.
 
 
 ## Features, and linked projects
@@ -79,8 +69,20 @@ If I missed something, or you want to add something, feel free to open an issue.
 [Luis Scoccola](https://luisscoccola.com/) 
 (Möbius inversion in python, degree-rips using [persistable](https://github.com/LuisScoccola/persistable) and [RIVET](https://github.com/rivetTDA/rivet/)),<br>
 [Mathieu Carrière](https://www-sop.inria.fr/members/Mathieu.Carriere/) (Sliced Wasserstein),<br>
-[Odin Hoff Gardå](https://odinhg.github.io/) (Delaunay Core bifiltration).<br>
-Jan Jendrysiak (Module Decomposition).<br>
+[Odin Hoff Gardå](https://odinhg.github.io/) (Delaunay Core bifiltration),<br>
+[Michael Kerber](https://www.geometrie.tugraz.at/kerber/) ([mpfree](https://bitbucket.org/mkerber/mpfree/src/master/), [function_delaunay](https://bitbucket.org/mkerber/function_delaunay), [multi_critical](https://bitbucket.org/mkerber/multi_critical) [multi_chunck](https://bitbucket.org/mkerber/multi_chunk) backends),<br>
+[Jan Jendrysiak](https://github.com/JanJend) ([Module Decomposition (AIDA)](https://github.com/JanJend/AIDA), [Persistence Algebra](https://github.com/JanJend/Persistence-Algebra)).<br>
+
+## Licensing
+
+`multipers` distributions that include the compiled external interfaces are provided under
+**GPL-3.0-or-later**.
+
+This is due to linked GPL/LGPL third-party components used by the build, notably
+`AIDA`, `Persistence-Algebra`, `function_delaunay`, `mpfree`, `multi_critical`, and
+`multi_chunk`.
+
+See `THIRD_PARTY_NOTICES.md` for dependency details and pinned revisions used in this workspace.
 
 ## Citation
 Please cite this library when using it in scientific publications;

{multipers-2.4.2b2 → multipers-2.5.0b1}/multipers/__init__.py

@@ -8,6 +8,7 @@ from multipers import (
     filtrations,
     grids,
     io,
+    logs,
     multiparameter_module_approximation,
     simplex_tree_multi,
     slicer,
@@ -28,6 +29,7 @@ __all__ = [
     "filtrations",
     "grids",
     "io",
+    "logs",
     "multiparameter_module_approximation",
     "simplex_tree_multi",
     "slicer",

{multipers-2.4.2b2 → multipers-2.5.0b1}/multipers/array_api/numpy.py

@@ -2,6 +2,7 @@ from contextlib import nullcontext
 
 import numpy as _np
 from scipy.spatial.distance import cdist, pdist
+import multipers.logs as _mp_logs
 
 backend = _np
 cat = _np.concatenate
@@ -80,9 +81,7 @@ def check_keops():
         _is_keops_available = _np.allclose(my_conv(x, y).flatten(), expected_res)
         LazyTensor = LT
     except:
-        from warnings import warn
-
-        warn("Could not initialize keops (numpy). using workarounds")
+        _mp_logs.warn_fallback("Could not initialize keops (numpy). using workarounds")
         _is_keops_available = False
 
     return _is_keops_available

{multipers-2.4.2b2 → multipers-2.5.0b1}/multipers/array_api/torch.py

@@ -1,6 +1,7 @@
 import torch as _t
 import multipers.array_api as _mpapi
 import sys
+import multipers.logs as _mp_logs
 
 _mpapi.available_api.append(sys.modules[__name__])
 
@@ -74,9 +75,7 @@ def check_keops():
         LazyTensor = LT
 
     except:
-        from warnings import warn
-
-        warn("Could not initialize keops (torch). using workarounds")
+        _mp_logs.warn_fallback("Could not initialize keops (torch). using workarounds")
 
         _is_keops_available = False
 

{multipers-2.4.2b2 → multipers-2.5.0b1}/multipers/ext_interface/_multi_critical_interface.pyx

@@ -64,7 +64,9 @@ cdef object _slicer_from_multi_critical_output(
     int degree=-1,
 ):
     out_boundaries = vect_vect_boundary_to_numpy_slices(interface_output.boundaries)
-    out_dimensions = np.asarray(interface_output.dimensions, dtype=np.int32)
+    out_dimensions = np.array(interface_output.dimensions, dtype=np.int32) 
+    if mark_minpres:
+        out_dimensions -= 1 # cause presentation
     out_filtrations = vect_pair_double_to_array(interface_output.filtration_values)
     out = slicer_type(out_boundaries, out_dimensions, out_filtrations)
     if mark_minpres:
@@ -252,21 +254,21 @@ def one_criticalify(
                 use_swedish,
             )
         return tuple(
-            _slicer_from_multi_critical_output(newSlicer, all_outputs[i], True, i)
-            for i in range(all_outputs.size())
+            _slicer_from_multi_critical_output(newSlicer, all_outputs[i+1], True, i)
+            for i in range(all_outputs.size()-1)
         )
     elif reduce:
-        target_degree = degree
+        _degree =<int>(degree+1) # cause presentation
         with nogil:
             one_output = multi_critical_minpres_interface(
                 interface_input,
-                target_degree,
+                _degree, 
                 use_logpath,
                 True,
                 verbose,
                 use_swedish,
             )
-        return _slicer_from_multi_critical_output(newSlicer, one_output, True, target_degree)
+        return _slicer_from_multi_critical_output(newSlicer, one_output, True,degree)
     else:
         with nogil:
             one_output = multi_critical_resolution_interface(

{multipers-2.4.2b2 → multipers-2.5.0b1}/multipers/ext_interface/mpfree_interface.hpp

@@ -221,11 +221,11 @@ mpfree_interface_output<index_type> mpfree_minpres_interface(const mpfree_interf
     throw std::invalid_argument("Invalid multipers input: sizes of filtrations, boundaries and dimensions differ.");
   }
 
-  for (const auto& grade : input.filtration_values) {
-    if (!std::isfinite(grade.first) || !std::isfinite(grade.second)) {
-      throw std::invalid_argument("mpfree interface expects finite bifiltration values.");
-    }
-  }
+  // for (const auto& grade : input.filtration_values) {
+  //   if (!std::isfinite(grade.first) || !std::isfinite(grade.second)) {
+  //     throw std::invalid_argument("mpfree interface expects finite bifiltration values.");
+  //   }
+  // }
 
   if (!std::is_sorted(input.dimensions.begin(), input.dimensions.end())) {
     throw std::invalid_argument("Dimensions are expected to be sorted in non-decreasing order.");

{multipers-2.4.2b2 → multipers-2.5.0b1}/multipers/ext_interface/multi_critical_interface.hpp

@@ -218,9 +218,9 @@ class multi_critical_input_parser {
         }
         col.raw_grades.reserve(grades.size() * 2);
         for (const auto& grade : grades) {
-          if (!std::isfinite(grade.first) || !std::isfinite(grade.second)) {
-            throw std::invalid_argument("multi_critical interface expects finite bifiltration values.");
-          }
+          // if (!std::isfinite(grade.first) || !std::isfinite(grade.second)) {
+          //   throw std::invalid_argument("multi_critical interface expects finite bifiltration values.");
+          // }
           col.raw_grades.push_back(grade.first);
           col.raw_grades.push_back(grade.second);
         }

{multipers-2.4.2b2 → multipers-2.5.0b1}/multipers/filtrations/filtrations.py

@@ -1,7 +1,6 @@
 from collections.abc import Sequence
 from time import perf_counter
 from typing import Optional
-from warnings import warn
 
 import gudhi as gd
 import numpy as np
@@ -9,6 +8,7 @@ from numpy.typing import ArrayLike
 from scipy.spatial import KDTree
 
 from multipers.array_api import api_from_tensor, api_from_tensors
+import multipers.logs as _mp_logs
 from multipers.filtrations.density import DTM, available_kernels
 from multipers.grids import compute_grid, get_exact_grid
 from multipers.simplex_tree_multi import SimplexTreeMulti, SimplexTreeMulti_type
@@ -21,7 +21,7 @@ try:
 except ImportError:
     from sklearn.neighbors import KernelDensity
 
-    warn("pykeops not found. Falling back to sklearn.")
+    _mp_logs.warn_fallback("pykeops not found. Falling back to sklearn.")
 
     def KDE(bandwidth, kernel, return_log):
         assert return_log, "Sklearn returns log-density."
@@ -151,7 +151,9 @@ def DelaunayLowerstar(
     api = api_from_tensors(points, function)
     _log_step("resolved backend")
     if not flagify and (api.has_grad(points) or api.has_grad(function)):
-        warn("Cannot keep points gradient unless using `flagify=True`.")
+        _mp_logs.warn_autodiff(
+            "Cannot keep points gradient unless using `flagify=True`."
+        )
     points = api.astensor(points)
     function = api.astensor(function).squeeze()
     _log_step("converted inputs")
@@ -323,10 +325,8 @@ def DegreeRips(
         rips_filtration = None
 
     if ks is None or rips_filtration is None:
-        from warnings import warn
-
-        warn(
-            "(copy warning) Had to copy the rips to infer the `degrees` or recover the 1st filtration parameter."
+        _mp_logs.warn_copy(
+            "Had to copy the rips to infer the `degrees` or recover the 1st filtration parameter."
         )
         _temp_st = _mp.SimplexTreeMulti(
             st, num_parameters=1
@@ -494,9 +494,7 @@ def RhomboidBifiltration(
 
     api = api_from_tensor(x)
     if api.has_grad(x):
-        from warnings import warn
-
-        warn(
+        _mp_logs.warn_autodiff(
             "Found a gradient in input, which cannot be processed by RhomboidBifiltration."
         )
     x = api.asnumpy(x)

{multipers-2.4.2b2 → multipers-2.5.0b1}/multipers/grids.pyx

@@ -12,6 +12,7 @@ from itertools import product
 from multipers.array_api import api_from_tensor, api_from_tensors
 from multipers.array_api import numpy as npapi
 from multipers.array_api import check_keops
+import multipers.logs as _mp_logs
 
 available_strategies = ["exact","regular","regular_closest", "regular_left", "partition", "quantile", "precomputed"]
 Lstrategies = Literal["exact","regular","regular_closest", "regular_left", "partition", "quantile", "precomputed"]
@@ -309,8 +310,7 @@ def _compute_grid_numpy(
 
 def _todo_regular(f, int r, api):
     if api.has_grad(f):
-        from warnings import warn
-        warn("`strategy=regular` is not differentiable. Removing grad.")
+        _mp_logs.warn_autodiff("`strategy=regular` is not differentiable. Removing grad.")
     with api.no_grad():
         return api.linspace(api.min(f), api.max(f), r)
 
@@ -360,8 +360,7 @@ def _todo_regular_left_old(some_float[:] f, int r, bool unique):
 
 def _todo_partition(x, int resolution, bool unique, api):
     if api.has_grad(x):
-        from warnings import warn
-        warn("`strategy=partition` is not differentiable. Removing grad.")
+        _mp_logs.warn_autodiff("`strategy=partition` is not differentiable. Removing grad.")
     out = _todo_partition_(api.asnumpy(x), resolution, unique)
     return api.from_numpy(out)
 
@@ -615,5 +614,3 @@ def evaluate_mod_in_grid(mod, grid, box=None):
         )
     )
     return diff_mod
-
-

{multipers-2.4.2b2 → multipers-2.5.0b1}/multipers/io.pyx

@@ -11,6 +11,7 @@ from typing import Optional, Literal
 from collections import defaultdict
 import itertools
 import threading
+import multipers.logs as _mp_logs
 import cython
 cimport cython
 cimport numpy as cnp
@@ -103,8 +104,7 @@ def _path_init(soft:str|os.PathLike):
         verbose_arg = "> /dev/null 2>&1"
         test = os.system(pathes[soft] + " --help " + verbose_arg)
         if test % 256!=0:
-            from warnings import warn
-            warn(f"""
+            _mp_logs.warn_fallback(f"""
             Found external software {soft} at {pathes[soft]}
             but may not behave well.
             """)

multipers-2.5.0b1/multipers/logs.py

@@ -0,0 +1,113 @@
+"""Runtime warning classes and toggles for multipers.
+
+Usage:
+
+    import multipers as mp
+    mp.logs.CopyWarning.enabled = False
+"""
+
+from __future__ import annotations
+
+from warnings import warn
+
+
+class MultipersWarning(UserWarning):
+    enabled: bool = True
+
+
+class CopyWarning(MultipersWarning):
+    enabled: bool = False
+
+
+class SuperfluousComputationWarning(MultipersWarning):
+    enabled: bool = True
+
+
+class AutodiffWarning(MultipersWarning):
+    enabled: bool = True
+
+
+class ExperimentalWarning(MultipersWarning):
+    enabled: bool = True
+
+
+class FallbackWarning(MultipersWarning):
+    enabled: bool = True
+
+
+class GeometryWarning(MultipersWarning):
+    enabled: bool = True
+
+
+_WARNING_CLASSES = {
+    "copy": CopyWarning,
+    "superfluous_computation": SuperfluousComputationWarning,
+    "autodiff": AutodiffWarning,
+    "experimental": ExperimentalWarning,
+    "fallback": FallbackWarning,
+    "geometry": GeometryWarning,
+}
+
+_DEFAULTS = {
+    CopyWarning: False,
+    SuperfluousComputationWarning: True,
+    AutodiffWarning: True,
+    ExperimentalWarning: True,
+    FallbackWarning: True,
+    GeometryWarning: True,
+}
+
+_TOGGLE_HINT_SHOWN = {key: False for key in _WARNING_CLASSES}
+
+
+def _emit(kind: str, message: str, stacklevel: int = 2) -> None:
+    warning_cls = _WARNING_CLASSES[kind]
+    if not warning_cls.enabled:
+        return
+    if not _TOGGLE_HINT_SHOWN[kind]:
+        message = (
+            f"{message} "
+            f"\nSet `multipers.logs.{warning_cls.__name__}.enabled = False` to disable this warning."
+        )
+        _TOGGLE_HINT_SHOWN[kind] = True
+    warn(message, category=warning_cls, stacklevel=stacklevel)
+
+
+def warn_copy(message: str, *, stacklevel: int = 2) -> None:
+    _emit("copy", message, stacklevel=stacklevel)
+
+
+def warn_superfluous_computation(message: str, *, stacklevel: int = 2) -> None:
+    _emit("superfluous_computation", message, stacklevel=stacklevel)
+
+
+def warn_autodiff(message: str, *, stacklevel: int = 2) -> None:
+    _emit("autodiff", message, stacklevel=stacklevel)
+
+
+def warn_experimental(message: str, *, stacklevel: int = 2) -> None:
+    _emit("experimental", message, stacklevel=stacklevel)
+
+
+def warn_fallback(message: str, *, stacklevel: int = 2) -> None:
+    _emit("fallback", message, stacklevel=stacklevel)
+
+
+def warn_geometry(message: str, *, stacklevel: int = 2) -> None:
+    _emit("geometry", message, stacklevel=stacklevel)
+
+
+def set_level(level: int) -> None:
+    if level == 0:
+        for warning_cls in _DEFAULTS:
+            warning_cls.enabled = False
+        return
+    if level == 1:
+        for warning_cls, enabled in _DEFAULTS.items():
+            warning_cls.enabled = enabled
+        return
+    if level == 2:
+        for warning_cls in _DEFAULTS:
+            warning_cls.enabled = True
+        return
+    raise ValueError(f"Invalid level {level}. Expected 0, 1, or 2.")

{multipers-2.4.2b2 → multipers-2.5.0b1}/multipers/multiparameter_module_approximation.pyx

@@ -14,7 +14,7 @@ import numpy as np
 from typing import List
 from joblib import Parallel, delayed
 import sys
-from warnings import warn
+import multipers.logs as _mp_logs
 
 ###########################################################################
 ## CPP CLASSES
@@ -67,7 +67,7 @@ def module_approximation_from_slicer(
     cdef intptr_t ptr
     if not slicer.is_vine:
         if warnings:
-            warn(r"(copy warning) Got a non-vine slicer as an input. Use `vineyard=True` to remove this copy.")
+            _mp_logs.warn_copy(r"Got a non-vine slicer as an input. Use `vineyard=True` to remove this copy.")
         from multipers._slicer_meta import Slicer
         slicer = Slicer(slicer, vineyard=True, backend="matrix")
     # if slicer.is_squeezed and unsqueeze_grid not None:
@@ -204,7 +204,7 @@ def module_approximation(
         if direction[i] == 0:
             is_degenerate=True
     if is_degenerate and not ignore_warnings:
-        warn("Got a degenerate direction. This function may fail if the first line is not generic.")
+        _mp_logs.warn_geometry("Got a degenerate direction. This function may fail if the first line is not generic.")
 
     if from_coordinates and not input.is_squeezed:
         input = input.grid_squeeze()
@@ -224,7 +224,7 @@ def module_approximation(
                 print(f"Updated  `{direction=}`, and `{max_error=}` ",end="")
         else:
             if not ignore_warnings:
-                warn("(copy warning) Got a squeezed input. ")
+                _mp_logs.warn_copy("Got a squeezed input.")
             input = input.unsqueeze()
         if verbose:
             print("Done.", flush=True)
@@ -244,7 +244,7 @@ def module_approximation(
     scales = box[1] - box[0]
     scales /= scales.max()
     if np.any(scales<.1):
-        warn(
+        _mp_logs.warn_geometry(
             f"Squewed filtration detected. Found {scales=}. "
             "Consider rescaling the filtration for interpretable results."
         )
@@ -253,7 +253,7 @@ def module_approximation(
     zero_idx = box[1] == box[0]
     if np.any(zero_idx):
         if not ignore_warnings:
-            warn(f"Got {(box[1] == box[0])=} trivial box coordinates.")
+            _mp_logs.warn_geometry(f"Got {(box[1] == box[0])=} trivial box coordinates.")
         box[1] += zero_idx
 
     for i in swap_box_coords:

{multipers-2.4.2b2 → multipers-2.5.0b1}/multipers/ops.pyx

@@ -1,5 +1,6 @@
 import numpy as np
 from typing import Iterable, Literal, Optional
+import multipers.logs as _mp_logs
 
 
 def aida(s, bool sort=True, bool verbose=False, bool progress=False):
@@ -22,7 +23,7 @@ def aida(s, bool sort=True, bool verbose=False, bool progress=False):
 
 def one_criticalify(
     slicer,
-    bool reduce=False,
+    reduce:Optional[bool] = None,
     degree: Optional[int] = None,
     bool clear=True,
     swedish: Optional[bool] = None,
@@ -30,6 +31,7 @@ def one_criticalify(
     bool kcritical=False,
     str algo: Literal["path", "tree"] = "path",
     str filtration_container="contiguous",
+    bool force_resolution = True,
 ):
     """
     Computes a free implicit representation of a given multi-critical
@@ -52,6 +54,8 @@ def one_criticalify(
         F = slicer.filtration_grid
     else:
         F = None
+    if reduce is None and degree is not None:
+        reduce = True
     out = _multi_critical_from_slicer(
         slicer,
         reduce=reduce,
@@ -63,12 +67,17 @@ def one_criticalify(
         kcritical=kcritical,
         filtration_container=filtration_container,
     )
-    if is_slicer(out, allow_minpres=False):
-        out.filtration_grid = F
-    else:
-        for stuff in out:
-            stuff.filtration_grid = F
-    return out
+    if not reduce:
+        return out
+    def _todo(x,i):
+        x.filtration_grid = F
+        x.minpres_degree=i
+        if reduce and force_resolution:
+            x = minimal_presentation(x, degree=i, force=True)
+        return x
+    if isinstance(out,tuple):
+        return tuple(_todo(out[i], i) for i in range(len(out)))
+    return _todo(out, degree)
 
 
 def minimal_presentation(
@@ -92,10 +101,8 @@ def minimal_presentation(
     from multipers.slicer import is_slicer
 
     if is_slicer(slicer) and slicer.is_minpres and not force:
-        from warnings import warn
-
-        warn(
-            f"(unnecessary computation) The slicer seems to be already reduced, "
+        _mp_logs.warn_superfluous_computation(
+            f"The slicer seems to be already reduced, "
             f"from homology of degree {slicer.minpres_degree}."
         )
         return slicer