pyerrors 2.10.0__tar.gz → 2.11.1__tar.gz

{pyerrors-2.10.0 → pyerrors-2.11.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: pyerrors
-Version: 2.10.0
+Version: 2.11.1
 Summary: Error propagation and statistical analysis for Monte Carlo simulations
 Home-page: https://github.com/fjosw/pyerrors
 Author: Fabian Joswig
@@ -22,7 +22,7 @@ Classifier: Topic :: Scientific/Engineering :: Physics
 Requires-Python: >=3.8.0
 Description-Content-Type: text/markdown
 License-File: LICENSE
-Requires-Dist: numpy>=1.24
+Requires-Dist: numpy<2,>=1.24
 Requires-Dist: autograd>=1.6.2
 Requires-Dist: numdifftools>=0.9.41
 Requires-Dist: matplotlib>=3.7

{pyerrors-2.10.0 → pyerrors-2.11.1}/pyerrors/__init__.py

@@ -487,5 +487,6 @@ from . import linalg
 from . import mpm
 from . import roots
 from . import integrate
+from . import special
 
 from .version import __version__

{pyerrors-2.10.0 → pyerrors-2.11.1}/pyerrors/input/openQCD.py

@@ -1286,7 +1286,9 @@ def read_ms5_xsf(path, prefix, qc, corr, sep="r", **kwargs):
                         imagsamples[repnum][t].append(corrres[1][t])
             if 'idl' in kwargs:
                 left_idl = list(left_idl)
-                if len(left_idl) > 0:
+                if expected_idl[repnum] == left_idl:
+                    raise ValueError("None of the idls searched for were found in replikum of file " + file)
+                elif len(left_idl) > 0:
                     warnings.warn('Could not find idls ' + str(left_idl) + ' in replikum of file ' + file, UserWarning)
         repnum += 1
     s = "Read correlator " + corr + " from " + str(repnum) + " replika with idls" + str(realsamples[0][t])

{pyerrors-2.10.0 → pyerrors-2.11.1}/pyerrors/input/sfcf.py

@@ -121,7 +121,7 @@ def read_sfcf_multi(path, prefix, name_list, quarks_list=['.*'], corr_type_list=
         String that separates the ensemble identifier from the configuration number (default 'n').
     replica: list
         list of replica to be read, default is all
-    files: list
+    files: list[list[int]]
         list of files to be read per replica, default is all.
         for non-compact output format, hand the folders to be read here.
     check_configs: list[list[int]]
@@ -184,6 +184,8 @@ def read_sfcf_multi(path, prefix, name_list, quarks_list=['.*'], corr_type_list=
 
     else:
         replica = len([file.split(".")[-1] for file in ls]) // len(set([file.split(".")[-1] for file in ls]))
+    if replica == 0:
+        raise Exception('No replica found in directory')
     if not silent:
         print('Read', part, 'part of', name_list, 'from', prefix[:-1], ',', replica, 'replica')
 
@@ -236,6 +238,16 @@ def read_sfcf_multi(path, prefix, name_list, quarks_list=['.*'], corr_type_list=
             rep_path = path + '/' + item
             if "files" in kwargs:
                 files = kwargs.get("files")
+                if isinstance(files, list):
+                    if all(isinstance(f, list) for f in files):
+                        files = files[i]
+                    elif all(isinstance(f, str) for f in files):
+                        files = files
+                    else:
+                        raise TypeError("files has to be of type list[list[str]] or list[str]!")
+                else:
+                    raise TypeError("files has to be of type list[list[str]] or list[str]!")
+
             else:
                 files = []
             sub_ls = _find_files(rep_path, prefix, compact, files)
@@ -248,7 +260,7 @@ def read_sfcf_multi(path, prefix, name_list, quarks_list=['.*'], corr_type_list=
                     else:
                         rep_idl.append(int(cfg[3:]))
                 except Exception:
-                    raise Exception("Couldn't parse idl from directroy, problem with file " + cfg)
+                    raise Exception("Couldn't parse idl from directory, problem with file " + cfg)
             rep_idl.sort()
             # maybe there is a better way to print the idls
             if not silent:
@@ -309,7 +321,10 @@ def read_sfcf_multi(path, prefix, name_list, quarks_list=['.*'], corr_type_list=
             w = specs[3]
             w2 = specs[4]
             if "files" in kwargs:
-                ls = kwargs.get("files")
+                if isinstance(kwargs.get("files"), list) and all(isinstance(f, str) for f in kwargs.get("files")):
+                    name_ls = kwargs.get("files")
+                else:
+                    raise TypeError("In append mode, files has to be of type list[str]!")
             else:
                 name_ls = ls
                 for exc in name_ls:

{pyerrors-2.10.0 → pyerrors-2.11.1}/pyerrors/misc.py

@@ -20,7 +20,7 @@ def print_config():
               "pandas": pd.__version__}
 
     for key, value in config.items():
-        print(f"{key : <10}\t {value}")
+        print(f"{key: <10}\t {value}")
 
 
 def errorbar(x, y, axes=plt, **kwargs):

{pyerrors-2.10.0 → pyerrors-2.11.1}/pyerrors/obs.py

@@ -1138,7 +1138,7 @@ def _intersection_idx(idl):
     return idinter
 
 
-def _expand_deltas_for_merge(deltas, idx, shape, new_idx):
+def _expand_deltas_for_merge(deltas, idx, shape, new_idx, scalefactor):
     """Expand deltas defined on idx to the list of configs that is defined by new_idx.
        New, empty entries are filled by 0. If idx and new_idx are of type range, the smallest
        common divisor of the step sizes is used as new step size.
@@ -1154,15 +1154,20 @@ def _expand_deltas_for_merge(deltas, idx, shape, new_idx):
         Number of configs in idx.
     new_idx : list
         List of configs that defines the new range, has to be sorted in ascending order.
+    scalefactor : float
+        An additional scaling factor that can be applied to scale the fluctuations,
+        e.g., when Obs with differing numbers of replica are merged.
     """
-
     if type(idx) is range and type(new_idx) is range:
         if idx == new_idx:
-            return deltas
+            if scalefactor == 1:
+                return deltas
+            else:
+                return deltas * scalefactor
     ret = np.zeros(new_idx[-1] - new_idx[0] + 1)
     for i in range(shape):
         ret[idx[i] - new_idx[0]] = deltas[i]
-    return np.array([ret[new_idx[i] - new_idx[0]] for i in range(len(new_idx))]) * len(new_idx) / len(idx)
+    return np.array([ret[new_idx[i] - new_idx[0]] for i in range(len(new_idx))]) * len(new_idx) / len(idx) * scalefactor
 
 
 def derived_observable(func, data, array_mode=False, **kwargs):
@@ -1243,6 +1248,25 @@ def derived_observable(func, data, array_mode=False, **kwargs):
         new_r_values[name] = func(tmp_values, **kwargs)
         new_idl_d[name] = _merge_idx(idl)
 
+    def _compute_scalefactor_missing_rep(obs):
+        """
+        Computes the scale factor that is to be multiplied with the deltas
+        in the case where Obs with different subsets of replica are merged.
+        Returns a dictionary with the scale factor for each Monte Carlo name.
+
+        Parameters
+        ----------
+        obs : Obs
+            The observable corresponding to the deltas that are to be scaled
+        """
+        scalef_d = {}
+        for mc_name in obs.mc_names:
+            mc_idl_d = [name for name in obs.idl if name.startswith(mc_name + '|')]
+            new_mc_idl_d = [name for name in new_idl_d if name.startswith(mc_name + '|')]
+            if len(mc_idl_d) > 0 and len(mc_idl_d) < len(new_mc_idl_d):
+                scalef_d[mc_name] = sum([len(new_idl_d[name]) for name in new_mc_idl_d]) / sum([len(new_idl_d[name]) for name in mc_idl_d])
+        return scalef_d
+
     if 'man_grad' in kwargs:
         deriv = np.asarray(kwargs.get('man_grad'))
         if new_values.shape + data.shape != deriv.shape:
@@ -1280,7 +1304,7 @@ def derived_observable(func, data, array_mode=False, **kwargs):
             d_extracted[name] = []
             ens_length = len(new_idl_d[name])
             for i_dat, dat in enumerate(data):
-                d_extracted[name].append(np.array([_expand_deltas_for_merge(o.deltas.get(name, np.zeros(ens_length)), o.idl.get(name, new_idl_d[name]), o.shape.get(name, ens_length), new_idl_d[name]) for o in dat.reshape(np.prod(dat.shape))]).reshape(dat.shape + (ens_length, )))
+                d_extracted[name].append(np.array([_expand_deltas_for_merge(o.deltas.get(name, np.zeros(ens_length)), o.idl.get(name, new_idl_d[name]), o.shape.get(name, ens_length), new_idl_d[name], _compute_scalefactor_missing_rep(o).get(name.split('|')[0], 1)) for o in dat.reshape(np.prod(dat.shape))]).reshape(dat.shape + (ens_length, )))
         for name in new_cov_names:
             g_extracted[name] = []
             zero_grad = _Zero_grad(new_covobs_lengths[name])
@@ -1302,11 +1326,12 @@ def derived_observable(func, data, array_mode=False, **kwargs):
                     new_grad[name] += np.tensordot(deriv[i_val + (i_dat, )], dat)
         else:
             for j_obs, obs in np.ndenumerate(data):
+                scalef_d = _compute_scalefactor_missing_rep(obs)
                 for name in obs.names:
                     if name in obs.cov_names:
                         new_grad[name] = new_grad.get(name, 0) + deriv[i_val + j_obs] * obs.covobs[name].grad
                     else:
-                        new_deltas[name] = new_deltas.get(name, 0) + deriv[i_val + j_obs] * _expand_deltas_for_merge(obs.deltas[name], obs.idl[name], obs.shape[name], new_idl_d[name])
+                        new_deltas[name] = new_deltas.get(name, 0) + deriv[i_val + j_obs] * _expand_deltas_for_merge(obs.deltas[name], obs.idl[name], obs.shape[name], new_idl_d[name], scalef_d.get(name.split('|')[0], 1))
 
         new_covobs = {name: Covobs(0, allcov[name], name, grad=new_grad[name]) for name in new_grad}
 

pyerrors-2.11.1/pyerrors/special.py

@@ -0,0 +1,23 @@
+import scipy
+import numpy as np
+from autograd.extend import primitive, defvjp
+from autograd.scipy.special import j0, y0, j1, y1, jn, yn, i0, i1, iv, ive, beta, betainc, betaln
+from autograd.scipy.special import polygamma, psi, digamma, gamma, gammaln, gammainc, gammaincc, gammasgn, rgamma, multigammaln
+from autograd.scipy.special import erf, erfc, erfinv, erfcinv, logit, expit, logsumexp
+
+
+__all__ = ["beta", "betainc", "betaln",
+           "polygamma", "psi", "digamma", "gamma", "gammaln", "gammainc", "gammaincc", "gammasgn", "rgamma", "multigammaln",
+           "kn", "j0", "y0", "j1", "y1", "jn", "yn", "i0", "i1", "iv", "ive",
+           "erf", "erfc", "erfinv", "erfcinv", "logit", "expit", "logsumexp"]
+
+
+@primitive
+def kn(n, x):
+    """Modified Bessel function of the second kind of integer order n"""
+    if int(n) != n:
+        raise TypeError("The order 'n' needs to be an integer.")
+    return scipy.special.kn(n, x)
+
+
+defvjp(kn, None, lambda ans, n, x: lambda g: - g * 0.5 * (kn(np.abs(n - 1), x) + kn(n + 1, x)))

pyerrors-2.11.1/pyerrors/version.py

@@ -0,0 +1 @@
+__version__ = "2.11.1"

{pyerrors-2.10.0 → pyerrors-2.11.1}/pyerrors.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: pyerrors
-Version: 2.10.0
+Version: 2.11.1
 Summary: Error propagation and statistical analysis for Monte Carlo simulations
 Home-page: https://github.com/fjosw/pyerrors
 Author: Fabian Joswig
@@ -22,7 +22,7 @@ Classifier: Topic :: Scientific/Engineering :: Physics
 Requires-Python: >=3.8.0
 Description-Content-Type: text/markdown
 License-File: LICENSE
-Requires-Dist: numpy>=1.24
+Requires-Dist: numpy<2,>=1.24
 Requires-Dist: autograd>=1.6.2
 Requires-Dist: numdifftools>=0.9.41
 Requires-Dist: matplotlib>=3.7

{pyerrors-2.10.0 → pyerrors-2.11.1}/pyerrors.egg-info/SOURCES.txt

@@ -13,6 +13,7 @@ pyerrors/misc.py
 pyerrors/mpm.py
 pyerrors/obs.py
 pyerrors/roots.py
+pyerrors/special.py
 pyerrors/version.py
 pyerrors.egg-info/PKG-INFO
 pyerrors.egg-info/SOURCES.txt

{pyerrors-2.10.0 → pyerrors-2.11.1}/pyerrors.egg-info/requires.txt

@@ -1,4 +1,4 @@
-numpy>=1.24
+numpy<2,>=1.24
 autograd>=1.6.2
 numdifftools>=0.9.41
 matplotlib>=3.7

{pyerrors-2.10.0 → pyerrors-2.11.1}/setup.py

@@ -25,7 +25,7 @@ setup(name='pyerrors',
       license="MIT",
       packages=find_packages(),
       python_requires='>=3.8.0',
-      install_requires=['numpy>=1.24', 'autograd>=1.6.2', 'numdifftools>=0.9.41', 'matplotlib>=3.7', 'scipy>=1.10', 'iminuit>=2.21', 'h5py>=3.8', 'lxml>=4.9', 'python-rapidjson>=1.10', 'pandas>=2.0'],
+      install_requires=['numpy>=1.24,<2', 'autograd>=1.6.2', 'numdifftools>=0.9.41', 'matplotlib>=3.7', 'scipy>=1.10', 'iminuit>=2.21', 'h5py>=3.8', 'lxml>=4.9', 'python-rapidjson>=1.10', 'pandas>=2.0'],
       extras_require={'test': ['pytest', 'pytest-cov', 'pytest-benchmark', 'hypothesis', 'nbmake', 'flake8']},
       classifiers=[
           'Development Status :: 5 - Production/Stable',

pyerrors-2.10.0/pyerrors/version.py

@@ -1 +0,0 @@
-__version__ = "2.10.0"