pyerrors 2.11.0__tar.gz → 2.12.0__tar.gz

{pyerrors-2.11.0 → pyerrors-2.12.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: pyerrors
-Version: 2.11.0
+Version: 2.12.0
 Summary: Error propagation and statistical analysis for Monte Carlo simulations
 Home-page: https://github.com/fjosw/pyerrors
 Author: Fabian Joswig
@@ -13,34 +13,17 @@ Classifier: Development Status :: 5 - Production/Stable
 Classifier: Intended Audience :: Science/Research
 Classifier: License :: OSI Approved :: MIT License
 Classifier: Programming Language :: Python :: 3
-Classifier: Programming Language :: Python :: 3.8
 Classifier: Programming Language :: Python :: 3.9
 Classifier: Programming Language :: Python :: 3.10
 Classifier: Programming Language :: Python :: 3.11
 Classifier: Programming Language :: Python :: 3.12
 Classifier: Topic :: Scientific/Engineering :: Physics
-Requires-Python: >=3.8.0
+Requires-Python: >=3.9.0
 Description-Content-Type: text/markdown
-License-File: LICENSE
-Requires-Dist: numpy<2,>=1.24
-Requires-Dist: autograd>=1.6.2
-Requires-Dist: numdifftools>=0.9.41
-Requires-Dist: matplotlib>=3.7
-Requires-Dist: scipy>=1.10
-Requires-Dist: iminuit>=2.21
-Requires-Dist: h5py>=3.8
-Requires-Dist: lxml>=4.9
-Requires-Dist: python-rapidjson>=1.10
-Requires-Dist: pandas>=2.0
 Provides-Extra: test
-Requires-Dist: pytest; extra == "test"
-Requires-Dist: pytest-cov; extra == "test"
-Requires-Dist: pytest-benchmark; extra == "test"
-Requires-Dist: hypothesis; extra == "test"
-Requires-Dist: nbmake; extra == "test"
-Requires-Dist: flake8; extra == "test"
+License-File: LICENSE
 
-[![pytest](https://github.com/fjosw/pyerrors/actions/workflows/pytest.yml/badge.svg)](https://github.com/fjosw/pyerrors/actions/workflows/pytest.yml) [![](https://img.shields.io/badge/python-3.8+-blue.svg)](https://www.python.org/downloads/) [![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT) [![arXiv](https://img.shields.io/badge/arXiv-2209.14371-b31b1b.svg)](https://arxiv.org/abs/2209.14371) [![DOI](https://img.shields.io/badge/DOI-10.1016%2Fj.cpc.2023.108750-blue)](https://doi.org/10.1016/j.cpc.2023.108750)
+[![pytest](https://github.com/fjosw/pyerrors/actions/workflows/pytest.yml/badge.svg)](https://github.com/fjosw/pyerrors/actions/workflows/pytest.yml) [![](https://img.shields.io/badge/python-3.9+-blue.svg)](https://www.python.org/downloads/) [![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT) [![arXiv](https://img.shields.io/badge/arXiv-2209.14371-b31b1b.svg)](https://arxiv.org/abs/2209.14371) [![DOI](https://img.shields.io/badge/DOI-10.1016%2Fj.cpc.2023.108750-blue)](https://doi.org/10.1016/j.cpc.2023.108750)
 # pyerrors
 `pyerrors` is a python framework for error computation and propagation of Markov chain Monte Carlo data from lattice field theory and statistical mechanics simulations.
 

{pyerrors-2.11.0 → pyerrors-2.12.0}/README.md

@@ -1,4 +1,4 @@
-[![pytest](https://github.com/fjosw/pyerrors/actions/workflows/pytest.yml/badge.svg)](https://github.com/fjosw/pyerrors/actions/workflows/pytest.yml) [![](https://img.shields.io/badge/python-3.8+-blue.svg)](https://www.python.org/downloads/) [![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT) [![arXiv](https://img.shields.io/badge/arXiv-2209.14371-b31b1b.svg)](https://arxiv.org/abs/2209.14371) [![DOI](https://img.shields.io/badge/DOI-10.1016%2Fj.cpc.2023.108750-blue)](https://doi.org/10.1016/j.cpc.2023.108750)
+[![pytest](https://github.com/fjosw/pyerrors/actions/workflows/pytest.yml/badge.svg)](https://github.com/fjosw/pyerrors/actions/workflows/pytest.yml) [![](https://img.shields.io/badge/python-3.9+-blue.svg)](https://www.python.org/downloads/) [![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT) [![arXiv](https://img.shields.io/badge/arXiv-2209.14371-b31b1b.svg)](https://arxiv.org/abs/2209.14371) [![DOI](https://img.shields.io/badge/DOI-10.1016%2Fj.cpc.2023.108750-blue)](https://doi.org/10.1016/j.cpc.2023.108750)
 # pyerrors
 `pyerrors` is a python framework for error computation and propagation of Markov chain Monte Carlo data from lattice field theory and statistical mechanics simulations.
 

{pyerrors-2.11.0 → pyerrors-2.12.0}/pyerrors/input/sfcf.py

@@ -224,12 +224,23 @@ def read_sfcf_multi(path, prefix, name_list, quarks_list=['.*'], corr_type_list=
                 intern[name]["spec"][quarks][off] = {}
                 for w in wf_list:
                     intern[name]["spec"][quarks][off][w] = {}
-                    for w2 in wf2_list:
-                        intern[name]["spec"][quarks][off][w][w2] = {}
-                        intern[name]["spec"][quarks][off][w][w2]["pattern"] = _make_pattern(version, name, off, w, w2, intern[name]['b2b'], quarks)
+                    if b2b:
+                        for w2 in wf2_list:
+                            intern[name]["spec"][quarks][off][w][w2] = {}
+                            intern[name]["spec"][quarks][off][w][w2]["pattern"] = _make_pattern(version, name, off, w, w2, intern[name]['b2b'], quarks)
+                    else:
+                        intern[name]["spec"][quarks][off][w]["0"] = {}
+                        intern[name]["spec"][quarks][off][w]["0"]["pattern"] = _make_pattern(version, name, off, w, 0, intern[name]['b2b'], quarks)
 
     internal_ret_dict = {}
-    needed_keys = _lists2key(name_list, quarks_list, noffset_list, wf_list, wf2_list)
+    needed_keys = []
+    for name, corr_type in zip(name_list, corr_type_list):
+        b2b, single = _extract_corr_type(corr_type)
+        if b2b:
+            needed_keys.extend(_lists2key([name], quarks_list, noffset_list, wf_list, wf2_list))
+        else:
+            needed_keys.extend(_lists2key([name], quarks_list, noffset_list, wf_list, ["0"]))
+
     for key in needed_keys:
         internal_ret_dict[key] = []
 
@@ -270,10 +281,14 @@ def read_sfcf_multi(path, prefix, name_list, quarks_list=['.*'], corr_type_list=
             if i == 0:
                 if version != "0.0" and compact:
                     file = path + '/' + item + '/' + sub_ls[0]
-                for name in name_list:
+                for name_index, name in enumerate(name_list):
                     if version == "0.0" or not compact:
                         file = path + '/' + item + '/' + sub_ls[0] + '/' + name
-                    for key in _lists2key(quarks_list, noffset_list, wf_list, wf2_list):
+                    if corr_type_list[name_index] == 'bi':
+                        name_keys = _lists2key(quarks_list, noffset_list, wf_list, ["0"])
+                    else:
+                        name_keys = _lists2key(quarks_list, noffset_list, wf_list, wf2_list)
+                    for key in name_keys:
                         specs = _key2specs(key)
                         quarks = specs[0]
                         off = specs[1]
@@ -307,7 +322,6 @@ def read_sfcf_multi(path, prefix, name_list, quarks_list=['.*'], corr_type_list=
                         cfg_path = path + '/' + item + '/' + subitem
                         file_data = _read_o_file(cfg_path, name, needed_keys, intern, version, im)
                         rep_data.append(file_data)
-                    print(rep_data)
                     for t in range(intern[name]["T"]):
                         internal_ret_dict[key][t].append([])
                         for cfg in range(no_cfg):
@@ -363,12 +377,13 @@ def read_sfcf_multi(path, prefix, name_list, quarks_list=['.*'], corr_type_list=
     result_dict = {}
     if keyed_out:
         for key in needed_keys:
+            name = _key2specs(key)[0]
             result = []
             for t in range(intern[name]["T"]):
                 result.append(Obs(internal_ret_dict[key][t], new_names, idl=idl))
             result_dict[key] = result
     else:
-        for name in name_list:
+        for name, corr_type in zip(name_list, corr_type_list):
             result_dict[name] = {}
             for quarks in quarks_list:
                 result_dict[name][quarks] = {}
@@ -376,12 +391,19 @@ def read_sfcf_multi(path, prefix, name_list, quarks_list=['.*'], corr_type_list=
                     result_dict[name][quarks][off] = {}
                     for w in wf_list:
                         result_dict[name][quarks][off][w] = {}
-                        for w2 in wf2_list:
-                            key = _specs2key(name, quarks, off, w, w2)
+                        if corr_type != 'bi':
+                            for w2 in wf2_list:
+                                key = _specs2key(name, quarks, off, w, w2)
+                                result = []
+                                for t in range(intern[name]["T"]):
+                                    result.append(Obs(internal_ret_dict[key][t], new_names, idl=idl))
+                                result_dict[name][quarks][str(off)][str(w)][str(w2)] = result
+                        else:
+                            key = _specs2key(name, quarks, off, w, "0")
                             result = []
                             for t in range(intern[name]["T"]):
                                 result.append(Obs(internal_ret_dict[key][t], new_names, idl=idl))
-                            result_dict[name][quarks][str(off)][str(w)][str(w2)] = result
+                            result_dict[name][quarks][str(off)][str(w)][str(0)] = result
     return result_dict
 
 

{pyerrors-2.11.0 → pyerrors-2.12.0}/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-2.12.0/pyerrors/version.py

@@ -0,0 +1 @@
+__version__ = "2.12.0"

{pyerrors-2.11.0 → pyerrors-2.12.0}/pyerrors.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: pyerrors
-Version: 2.11.0
+Version: 2.12.0
 Summary: Error propagation and statistical analysis for Monte Carlo simulations
 Home-page: https://github.com/fjosw/pyerrors
 Author: Fabian Joswig
@@ -13,34 +13,17 @@ Classifier: Development Status :: 5 - Production/Stable
 Classifier: Intended Audience :: Science/Research
 Classifier: License :: OSI Approved :: MIT License
 Classifier: Programming Language :: Python :: 3
-Classifier: Programming Language :: Python :: 3.8
 Classifier: Programming Language :: Python :: 3.9
 Classifier: Programming Language :: Python :: 3.10
 Classifier: Programming Language :: Python :: 3.11
 Classifier: Programming Language :: Python :: 3.12
 Classifier: Topic :: Scientific/Engineering :: Physics
-Requires-Python: >=3.8.0
+Requires-Python: >=3.9.0
 Description-Content-Type: text/markdown
-License-File: LICENSE
-Requires-Dist: numpy<2,>=1.24
-Requires-Dist: autograd>=1.6.2
-Requires-Dist: numdifftools>=0.9.41
-Requires-Dist: matplotlib>=3.7
-Requires-Dist: scipy>=1.10
-Requires-Dist: iminuit>=2.21
-Requires-Dist: h5py>=3.8
-Requires-Dist: lxml>=4.9
-Requires-Dist: python-rapidjson>=1.10
-Requires-Dist: pandas>=2.0
 Provides-Extra: test
-Requires-Dist: pytest; extra == "test"
-Requires-Dist: pytest-cov; extra == "test"
-Requires-Dist: pytest-benchmark; extra == "test"
-Requires-Dist: hypothesis; extra == "test"
-Requires-Dist: nbmake; extra == "test"
-Requires-Dist: flake8; extra == "test"
+License-File: LICENSE
 
-[![pytest](https://github.com/fjosw/pyerrors/actions/workflows/pytest.yml/badge.svg)](https://github.com/fjosw/pyerrors/actions/workflows/pytest.yml) [![](https://img.shields.io/badge/python-3.8+-blue.svg)](https://www.python.org/downloads/) [![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT) [![arXiv](https://img.shields.io/badge/arXiv-2209.14371-b31b1b.svg)](https://arxiv.org/abs/2209.14371) [![DOI](https://img.shields.io/badge/DOI-10.1016%2Fj.cpc.2023.108750-blue)](https://doi.org/10.1016/j.cpc.2023.108750)
+[![pytest](https://github.com/fjosw/pyerrors/actions/workflows/pytest.yml/badge.svg)](https://github.com/fjosw/pyerrors/actions/workflows/pytest.yml) [![](https://img.shields.io/badge/python-3.9+-blue.svg)](https://www.python.org/downloads/) [![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT) [![arXiv](https://img.shields.io/badge/arXiv-2209.14371-b31b1b.svg)](https://arxiv.org/abs/2209.14371) [![DOI](https://img.shields.io/badge/DOI-10.1016%2Fj.cpc.2023.108750-blue)](https://doi.org/10.1016/j.cpc.2023.108750)
 # pyerrors
 `pyerrors` is a python framework for error computation and propagation of Markov chain Monte Carlo data from lattice field theory and statistical mechanics simulations.
 

pyerrors-2.12.0/pyerrors.egg-info/requires.txt

@@ -0,0 +1,18 @@
+numpy>=2.0
+autograd>=1.7.0
+numdifftools>=0.9.41
+matplotlib>=3.9
+scipy>=1.13
+iminuit>=2.28
+h5py>=3.11
+lxml>=5.0
+python-rapidjson>=1.20
+pandas>=2.2
+
+[test]
+pytest
+pytest-cov
+pytest-benchmark
+hypothesis
+nbmake
+flake8

{pyerrors-2.11.0 → pyerrors-2.12.0}/setup.py

@@ -24,15 +24,14 @@ setup(name='pyerrors',
       author_email='fabian.joswig@ed.ac.uk',
       license="MIT",
       packages=find_packages(),
-      python_requires='>=3.8.0',
-      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'],
+      python_requires='>=3.9.0',
+      install_requires=['numpy>=2.0', 'autograd>=1.7.0', 'numdifftools>=0.9.41', 'matplotlib>=3.9', 'scipy>=1.13', 'iminuit>=2.28', 'h5py>=3.11', 'lxml>=5.0', 'python-rapidjson>=1.20', 'pandas>=2.2'],
       extras_require={'test': ['pytest', 'pytest-cov', 'pytest-benchmark', 'hypothesis', 'nbmake', 'flake8']},
       classifiers=[
           'Development Status :: 5 - Production/Stable',
           'Intended Audience :: Science/Research',
           'License :: OSI Approved :: MIT License',
           'Programming Language :: Python :: 3',
-          'Programming Language :: Python :: 3.8',
           'Programming Language :: Python :: 3.9',
           'Programming Language :: Python :: 3.10',
           'Programming Language :: Python :: 3.11',

pyerrors-2.11.0/pyerrors/version.py

@@ -1 +0,0 @@
-__version__ = "2.11.0"

pyerrors-2.11.0/pyerrors.egg-info/requires.txt

@@ -1,18 +0,0 @@
-numpy<2,>=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
-
-[test]
-pytest
-pytest-cov
-pytest-benchmark
-hypothesis
-nbmake
-flake8