Refactor usage of temporary files in multipers.io

multipers/io.pyx

@@ -1,4 +1,5 @@
 import re
+import tempfile
 from gudhi import SimplexTree
 import gudhi as gd
 import numpy as np
@@ -106,16 +107,6 @@ cdef dict[str,str|None] pathes = {
 # multi_chunk_out_path:str|os.PathLike = "multipers_multi_chunk_output.scc"
 # function_delaunay_out_path:str|os.PathLike = "function_delaunay_output.scc"
 # function_delaunay_in_path:str|os.PathLike = "function_delaunay_input.txt" # point cloud
-input_path:str|os.PathLike = "multipers_input.scc"
-output_path:str|os.PathLike = "multipers_output.scc"
-
-def _put_temp_files_to_ram():
-    global input_path,output_path
-    shm_memory = "/tmp/"  # on unix, we can write in RAM instead of disk.
-    if os.access(shm_memory, os.W_OK) and not input_path.startswith(shm_memory):
-        input_path = shm_memory + input_path
-        output_path = shm_memory + output_path
-_put_temp_files_to_ram()
 
 
 ## TODO : optimize with Python.h ?
@@ -221,7 +212,6 @@ def _init_external_softwares(requires=[]):
             any = any or (soft in requires) 
 
     if any:
-        _put_temp_files_to_ram()
         for soft in requires:
             if pathes[soft] is None:
                 global doc_soft_urls
@@ -309,7 +299,6 @@ def scc_reduce_from_str_to_slicer(
         bool full_resolution=True,
         int dimension: int | np.int64 = 1,
         bool clear: bool = True,
-        id: Optional[str] = None,  # For parallel stuff
         bool verbose:bool=False,
         backend:Literal["mpfree","multi_chunk","twopac"]="mpfree",
         shift_dimension=0
@@ -327,43 +316,38 @@ def scc_reduce_from_str_to_slicer(
     verbose: bool
     backend: "mpfree", "multi_chunk" or "2pac"
     """
-    global pathes, input_path, output_path
+    global pathes
     _init_external_softwares(requires=[backend])
 
+    with tempfile.TemporaryDirectory(prefix="multipers", delete=clear) as tmpdir:
+        output_path = os.path.join(tmpdir, "multipers_output.scc")
+
+        resolution_str = "--resolution" if full_resolution else ""
+
+        if not os.path.exists(path):
+            raise ValueError(f"No file found at {path}.")
+
+        verbose_arg = "> /dev/null 2>&1" if not verbose else ""
+        if backend == "mpfree":
+            more_verbose = "-v" if verbose else ""
+            command = (
+                    f"{pathes[backend]} {more_verbose} {resolution_str} --dim={dimension} {path} {output_path} {verbose_arg}"
+                    )
+        elif backend == "multi_chunk":
+            command = (
+                    f"{pathes[backend]}  {path} {output_path} {verbose_arg}"
+                    )
+        elif backend in ["twopac", "2pac"]:
+            command = (
+                    f"{pathes[backend]} -f {path} --scc-input -n{dimension} --save-resolution-scc {output_path} {verbose_arg}"
+                    )
+        else:
+            raise ValueError(f"Unsupported backend {backend}.")
+        if verbose:
+            print(f"Calling :\n\n {command}")
+        os.system(command)
 
-    resolution_str = "--resolution" if full_resolution else ""
-    # print(mpfree_in_path + id, mpfree_out_path + id)
-    if id is None:
-        id = str(threading.get_native_id())
-    if not os.path.exists(path):
-        raise ValueError(f"No file found at {path}.")
-    if os.path.exists(output_path + id):
-        os.remove(output_path + id)
-    verbose_arg = "> /dev/null 2>&1" if not verbose else ""
-    if backend == "mpfree":
-        more_verbose = "-v" if verbose else ""
-        command = (
-                f"{pathes[backend]} {more_verbose} {resolution_str} --dim={dimension} {path} {output_path+id} {verbose_arg}"
-                )
-    elif backend == "multi_chunk":
-        command = (
-                f"{pathes[backend]}  {path} {output_path+id} {verbose_arg}"
-                )
-    elif backend in ["twopac", "2pac"]:
-        command = (
-                f"{pathes[backend]} -f {path} --scc-input -n{dimension} --save-resolution-scc {output_path+id} {verbose_arg}"
-                )
-    else:
-        raise ValueError(f"Unsupported backend {backend}.")
-    if verbose:
-        print(f"Calling :\n\n {command}")
-    os.system(command)
-
-    slicer._build_from_scc_file(path=output_path+id, shift_dimension=shift_dimension)
-
-    if clear:
-        clear_io(input_path+id, output_path + id)
-
+        slicer._build_from_scc_file(path=output_path, shift_dimension=shift_dimension)
 
 # def reduce_complex(
 #         complex, # Simplextree, Slicer, or str
@@ -474,7 +458,6 @@ def function_delaunay_presentation_to_slicer(
         slicer,
         point_cloud:np.ndarray,
         function_values:np.ndarray,
-        id:Optional[str] = None,
         bool clear:bool = True,
         bool verbose:bool=False,
         int degree = -1,
@@ -491,38 +474,26 @@ def function_delaunay_presentation_to_slicer(
     degree: computes minimal presentation of this degree if given
     verbose : bool
     """
-    if id is None:
-        id = str(threading.get_native_id())
-    global input_path, output_path, pathes
-    backend = "function_delaunay"
-    _init_external_softwares(requires=[backend])
-
-    to_write = np.concatenate([point_cloud, function_values.reshape(-1,1)], axis=1)
-    np.savetxt(input_path+id,to_write,delimiter=' ')
-    verbose_arg = "> /dev/null 2>&1" if not verbose else ""
-    degree_arg = f"--minpres {degree}" if degree >= 0 else ""
-    multi_chunk_arg = "--multi-chunk" if multi_chunk else ""
-    if os.path.exists(output_path + id):
-        os.remove(output_path+ id)
-    command = f"{pathes[backend]} {degree_arg} {multi_chunk_arg} {input_path+id} {output_path+id} {verbose_arg} --no-delaunay-compare"
-    if verbose:
-        print(command)
-    os.system(command)
-
-    slicer._build_from_scc_file(path=output_path+id, shift_dimension=-1 if degree <= 0 else degree-1 )
-
-    if clear:
-        clear_io(output_path + id, input_path + id)
+    global pathes
 
+    with tempfile.TemporaryDirectory(prefix="multipers", delete=clear) as tmpdir:
+        input_path = os.path.join(tmpdir, "multipers_input.scc")
+        output_path = os.path.join(tmpdir, "multipers_output.scc")
 
+        backend = "function_delaunay"
+        _init_external_softwares(requires=[backend])
 
-def clear_io(*args):
-    """Removes temporary files"""
-    global input_path,output_path
-    for x in [input_path,output_path] + list(args):
-        if os.path.exists(x):
-            os.remove(x)
+        to_write = np.concatenate([point_cloud, function_values.reshape(-1,1)], axis=1)
+        np.savetxt(input_path,to_write,delimiter=' ')
+        verbose_arg = "> /dev/null 2>&1" if not verbose else ""
+        degree_arg = f"--minpres {degree}" if degree >= 0 else ""
+        multi_chunk_arg = "--multi-chunk" if multi_chunk else ""
+        command = f"{pathes[backend]} {degree_arg} {multi_chunk_arg} {input_path} {output_path} {verbose_arg} --no-delaunay-compare"
+        if verbose:
+            print(command)
+        os.system(command)
 
+        slicer._build_from_scc_file(path=output_path, shift_dimension=-1 if degree <= 0 else degree-1 )
 
 
 

multipers/slicer.pyx.tp

@@ -645,15 +645,14 @@ cdef class {{D['PYTHON_TYPE']}}:
         str backend:Literal["mpfree", "2pac"]="mpfree", 
         str slicer_backend:Literal["matrix","clement","graph"]="matrix",
         bool vineyard={{D['IS_VINE']}}, 
-        id :Optional[str] = None,
         dtype = {{D['PY_VALUE_TYPE']}},
         **minpres_kwargs
         )->Slicer_type:
         """
         Computes the minimal presentation of the slicer, and returns it as a new slicer.
         See :func:`multipers.slicer.minimal_presentation`.
         """
-        new_slicer = minimal_presentation(self, degree=degree, degrees=degrees, backend=backend, slicer_backend=slicer_backend, dtype=dtype, vineyard=vineyard, id=id, **minpres_kwargs)
+        new_slicer = minimal_presentation(self, degree=degree, degrees=degrees, backend=backend, slicer_backend=slicer_backend, dtype=dtype, vineyard=vineyard, **minpres_kwargs)
         return new_slicer
 
     @property
@@ -858,7 +857,6 @@ def minimal_presentation(
         str backend:Literal["mpfree", "2pac", ""]="mpfree", 
         str slicer_backend:Literal["matrix","clement","graph"]="matrix",
         bool vineyard=True, 
-        id :Optional[str] =None,
         dtype:type|_valid_dtypes=None,
         int n_jobs = -1,
         bool force=False,
@@ -870,7 +868,8 @@ def minimal_presentation(
     and returns it as a slicer.
     Backends differents than `mpfree` are unstable.
     """
-    from multipers.io import _init_external_softwares, input_path, scc_reduce_from_str_to_slicer
+    from multipers.io import _init_external_softwares, scc_reduce_from_str_to_slicer
+    import tempfile
     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, from homology of degree {slicer.minpres_degree}.")
@@ -886,24 +885,24 @@ def minimal_presentation(
     assert degree>=0, f"Degree not provided."
     if not np.any(slicer.get_dimensions() == degree):
         return type(slicer)()
-    if id is None:
-        id = str(threading.get_native_id())
     if dtype is None:
         dtype = slicer.dtype
     dimension = slicer.dimension - degree # latest  = L-1, which is empty, -1 for degree 0, -2 for degree 1 etc.
-    slicer.to_scc(path=input_path+id, strip_comments=True, degree=degree-1, unsqueeze = False)
-    new_slicer = multipers.Slicer(None,backend=slicer_backend, vineyard=vineyard, dtype=dtype)
-    if backend=="mpfree":
-        shift_dimension=degree-1
-    else:
-        shift_dimension=degree
-    scc_reduce_from_str_to_slicer(path=input_path+id, slicer=new_slicer, dimension=dimension, backend=backend, shift_dimension=shift_dimension, **minpres_kwargs)
-
-    new_slicer.minpres_degree = degree
-    new_slicer.filtration_grid = slicer.filtration_grid if slicer.is_squeezed else None
-    if new_slicer.is_squeezed and auto_clean:
-        new_slicer = new_slicer._clean_filtration_grid()
-    return new_slicer
+    with tempfile.TemporaryDirectory(prefix="multipers") as tmpdir:
+        tmp_path = os.path.join(tmpdir, "multipers.scc")
+        slicer.to_scc(path=tmp_path, strip_comments=True, degree=degree-1, unsqueeze = False)
+        new_slicer = multipers.Slicer(None,backend=slicer_backend, vineyard=vineyard, dtype=dtype)
+        if backend=="mpfree":
+            shift_dimension=degree-1
+        else:
+            shift_dimension=degree
+        scc_reduce_from_str_to_slicer(path=tmp_path, slicer=new_slicer, dimension=dimension, backend=backend, shift_dimension=shift_dimension, **minpres_kwargs)
+
+        new_slicer.minpres_degree = degree
+        new_slicer.filtration_grid = slicer.filtration_grid if slicer.is_squeezed else None
+        if new_slicer.is_squeezed and auto_clean:
+            new_slicer = new_slicer._clean_filtration_grid()
+        return new_slicer
 
 
 def to_simplextree(s:Slicer_type, max_dim:int=-1) -> SimplexTreeMulti_type:

tests/test_parallel.py

@@ -0,0 +1,35 @@
+import numpy as np
+import pytest
+from joblib import Parallel, delayed
+
+import multipers as mp
+import multipers.io as mio
+from multipers.tests import assert_sm_pair
+
+np.random.seed(0)
+
+
+def io_fd_mpfree(x):
+    s = mp.filtrations.DelaunayCodensity(points=x, bandwidth=0.2)
+    s = s.minpres(1).to_colexical()
+    return mp.signed_measure(s, degree=1, invariant="hilbert")[0]
+
+
+def io_fd_mpfree2(x):
+    s = mp.filtrations.DelaunayCodensity(points=x, bandwidth=0.2)
+    return mp.signed_measure(s, degree=1, invariant="hilbert")[0]
+
+
+@pytest.mark.skipif(
+    not (mio._check_available("mpfree") and mio._check_available("function_delaunay")),
+    reason="Skipped external test as `function_delaunay`, `mpfree` were not found.",
+)
+@pytest.mark.parametrize("backend", ["loky", "threading"])
+def test_io_parallel(backend):
+    x = mp.data.three_annulus(100, 50)
+    X = [x] * 100
+    ground_truth = io_fd_mpfree2(x)
+    dgms = Parallel(n_jobs=-1, backend=backend)(delayed(io_fd_mpfree)(x) for x in X)
+
+    for dgm in dgms:
+        assert_sm_pair(ground_truth, dgm, exact=False, reg=0, max_error= 1e-10)