Fix/check append rep (#277 )

* add option that the headers of an append-mode file can have different format * add tests for irregular headers in append mode * hotfix: fix bug in append start read implementation * lint * lint II
[chore] Bump version to v2.17.0-dev
2025-11-30 13:06:53 +01:00 · 2025-11-25 12:57:03 +01:00 · 2025-10-30 16:36:09 +01:00 · 2025-10-30 16:34:05 +01:00 · 2025-10-30 16:26:52 +01:00 · 2025-10-22 15:36:01 +02:00
17 changed files with 5321 additions and 52 deletions
--- a/.github/workflows/docs.yml
+++ b/.github/workflows/docs.yml
@ -13,7 +13,7 @@ jobs:
      - name: Set up Python environment
        uses: actions/setup-python@v5
        with:
-          python-version: "3.10"
+          python-version: "3.12"
      - uses: actions/checkout@v4
      - name: Updated documentation
        run: |
--- a/.github/workflows/flake8.yml
+++ b/.github/workflows/flake8.yml
@ -17,7 +17,7 @@ jobs:
      - name: Set up Python environment
        uses: actions/setup-python@v5
        with:
-          python-version: "3.10"
+          python-version: "3.12"
      - name: flake8 Lint
        uses: py-actions/flake8@v2
        with:
--- a/.github/workflows/pytest.yml
+++ b/.github/workflows/pytest.yml
@ -17,7 +17,7 @@ jobs:
      fail-fast: false
      matrix:
        os: [ubuntu-latest]
-        python-version: ["3.9", "3.10", "3.11", "3.12", "3.13"]
+        python-version: ["3.10", "3.11", "3.12", "3.13", "3.14"]
        include:
          - os: macos-latest
            python-version: "3.12"
@ -42,5 +42,10 @@ jobs:
          uv pip install pytest pytest-cov pytest-benchmark hypothesis --system
          uv pip freeze --system

-      - name: Run tests
+      - name: Run tests with -Werror
+        if: matrix.python-version != '3.14'
        run: pytest --cov=pyerrors -vv -Werror
+
+      - name: Run tests without -Werror for python 3.14
+        if: matrix.python-version == '3.14'
+        run: pytest --cov=pyerrors -vv
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@ -2,6 +2,17 @@

 All notable changes to this project will be documented in this file.

+## [2.16.0] - 2025-10-30
+
+### Added
+- Support for custom configuration number extraction in the sfcf input module.
+
+### Fixed
+- Calculation of expected chisquare in connection with priors.
+
+### Changed
+- Support for python<3.10 was dropped.
+
 ## [2.15.1] - 2025-10-19

 ### Fixed
--- a/README.md
+++ b/README.md
@ -1,4 +1,4 @@
-[![](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)
+[![](https://img.shields.io/badge/python-3.10+-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.

--- a/pyerrors/fits.py
+++ b/pyerrors/fits.py
@ -472,7 +472,7 @@ def least_squares(x, y, func, priors=None, silent=False, **kwargs):
            hat_vector = prepare_hat_matrix()
            A = W @ hat_vector
            P_phi = A @ np.linalg.pinv(A.T @ A) @ A.T
-            expected_chisquare = np.trace((np.identity(y_all.shape[-1]) - P_phi) @ W @ cov @ W)
+            expected_chisquare = np.trace((np.identity(y_all.shape[-1]) - P_phi) @ W @ cov @ W) + len(loc_priors)
            output.chisquare_by_expected_chisquare = output.chisquare / expected_chisquare
            if not silent:
                print('chisquare/expected_chisquare:', output.chisquare_by_expected_chisquare)
--- a/pyerrors/input/sfcf.py
+++ b/pyerrors/input/sfcf.py
@ -5,12 +5,13 @@ import numpy as np  # Thinly-wrapped numpy
 from ..obs import Obs
 from .utils import sort_names, check_idl
 import itertools
+import warnings


 sep = "/"


-def read_sfcf(path, prefix, name, quarks='.*', corr_type="bi", noffset=0, wf=0, wf2=0, version="1.0c", cfg_separator="n", silent=False, **kwargs):
+def read_sfcf(path, prefix, name, quarks='.*', corr_type="bi", noffset=0, wf=0, wf2=0, version="1.0c", cfg_separator="n", cfg_func=None, silent=False, **kwargs):
    """Read sfcf files from given folder structure.

    Parameters
@ -71,11 +72,11 @@ def read_sfcf(path, prefix, name, quarks='.*', corr_type="bi", noffset=0, wf=0,
    """
    ret = read_sfcf_multi(path, prefix, [name], quarks_list=[quarks], corr_type_list=[corr_type],
                          noffset_list=[noffset], wf_list=[wf], wf2_list=[wf2], version=version,
-                          cfg_separator=cfg_separator, silent=silent, **kwargs)
+                          cfg_separator=cfg_separator, cfg_func=cfg_func, silent=silent, **kwargs)
    return ret[name][quarks][str(noffset)][str(wf)][str(wf2)]


-def read_sfcf_multi(path, prefix, name_list, quarks_list=['.*'], corr_type_list=['bi'], noffset_list=[0], wf_list=[0], wf2_list=[0], version="1.0c", cfg_separator="n", silent=False, keyed_out=False, **kwargs):
+def read_sfcf_multi(path, prefix, name_list, quarks_list=['.*'], corr_type_list=['bi'], noffset_list=[0], wf_list=[0], wf2_list=[0], version="1.0c", cfg_separator="n", cfg_func=None, silent=False, keyed_out=False, **kwargs):
    """Read sfcf files from given folder structure.

    Parameters
@ -245,6 +246,16 @@ def read_sfcf_multi(path, prefix, name_list, quarks_list=['.*'], corr_type_list=
    for key in needed_keys:
        internal_ret_dict[key] = []

+    def _default_idl_func(cfg_string, cfg_sep):
+        return int(cfg_string.split(cfg_sep)[-1])
+
+    if cfg_func is None:
+        print("Default idl function in use.")
+        cfg_func = _default_idl_func
+        cfg_func_args = [cfg_separator]
+    else:
+        cfg_func_args = kwargs.get("cfg_func_args", [])
+
    if not appended:
        for i, item in enumerate(ls):
            rep_path = path + '/' + item
@ -268,7 +279,7 @@ def read_sfcf_multi(path, prefix, name_list, quarks_list=['.*'], corr_type_list=
            for cfg in sub_ls:
                try:
                    if compact:
-                        rep_idl.append(int(cfg.split(cfg_separator)[-1]))
+                        rep_idl.append(cfg_func(cfg, *cfg_func_args))
                    else:
                        rep_idl.append(int(cfg[3:]))
                except Exception:
@ -351,7 +362,7 @@ def read_sfcf_multi(path, prefix, name_list, quarks_list=['.*'], corr_type_list=
            for rep, file in enumerate(name_ls):
                rep_idl = []
                filename = path + '/' + file
-                T, rep_idl, rep_data = _read_append_rep(filename, pattern, intern[name]['b2b'], cfg_separator, im, intern[name]['single'])
+                T, rep_idl, rep_data = _read_append_rep(filename, pattern, intern[name]['b2b'], im, intern[name]['single'], cfg_func, cfg_func_args)
                if rep == 0:
                    intern[name]['T'] = T
                    for t in range(intern[name]['T']):
@ -581,12 +592,7 @@ def _read_compact_rep(path, rep, sub_ls, intern, needed_keys, im):
    return return_vals


-def _read_chunk(chunk, gauge_line, cfg_sep, start_read, T, corr_line, b2b, pattern, im, single):
-    try:
-        idl = int(chunk[gauge_line].split(cfg_sep)[-1])
-    except Exception:
-        raise Exception("Couldn't parse idl from directory, problem with chunk around line ", gauge_line)
-
+def _read_chunk_data(chunk, start_read, T, corr_line, b2b, pattern, im, single):
    found_pat = ""
    data = []
    for li in chunk[corr_line + 1:corr_line + 6 + b2b]:
@ -595,19 +601,38 @@ def _read_chunk(chunk, gauge_line, cfg_sep, start_read, T, corr_line, b2b, patte
        for t, line in enumerate(chunk[start_read:start_read + T]):
            floats = list(map(float, line.split()))
            data.append(floats[im + 1 - single])
-    return idl, data
+    return data


-def _read_append_rep(filename, pattern, b2b, cfg_separator, im, single):
-    with open(filename, 'r') as fp:
-        content = fp.readlines()
-        data_starts = []
-        for linenumber, line in enumerate(content):
-            if "[run]" in line:
-                data_starts.append(linenumber)
-        if len(set([data_starts[i] - data_starts[i - 1] for i in range(1, len(data_starts))])) > 1:
-            raise Exception("Irregularities in file structure found, not all runs have the same output length")
-        chunk = content[:data_starts[1]]
+def _check_append_rep(content, start_list):
+    data_len_list = []
+    header_len_list = []
+    has_regular_len_heads = True
+    for chunk_num in range(len(start_list)):
+        start = start_list[chunk_num]
+        if chunk_num == len(start_list) - 1:
+            stop = len(content)
+        else:
+            stop = start_list[chunk_num + 1]
+        chunk = content[start:stop]
+        for linenumber, line in enumerate(chunk):
+            if line.startswith("[correlator]"):
+                header_len = linenumber
+                break
+        header_len_list.append(header_len)
+        data_len_list.append(len(chunk) - header_len)
+
+    if len(set(header_len_list)) > 1:
+        warnings.warn("Not all headers have the same length. Data parts do.")
+        has_regular_len_heads = False
+
+    if len(set(data_len_list)) > 1:
+        raise Exception("Irregularities in file structure found, not all run data are of the same output length")
+    return has_regular_len_heads
+
+
+def _read_chunk_structure(chunk, pattern, b2b):
+    start_read = 0
    for linenumber, line in enumerate(chunk):
        if line.startswith("gauge_name"):
            gauge_line = linenumber
@ -619,22 +644,47 @@ def _read_append_rep(filename, pattern, b2b, cfg_separator, im, single):
            if re.search(pattern, found_pat):
                start_read = corr_line + 7 + b2b
                break
-                else:
-                    raise ValueError("Did not find pattern\n", pattern, "\nin\n", filename)
+    if start_read == 0:
+        raise ValueError("Did not find pattern\n", pattern)
    endline = corr_line + 6 + b2b
    while not chunk[endline] == "\n":
        endline += 1
    T = endline - start_read
+    return gauge_line, corr_line, start_read, T

-        # all other chunks should follow the same structure
+
+def _read_append_rep(filename, pattern, b2b, im, single, idl_func, cfg_func_args):
+    with open(filename, 'r') as fp:
+        content = fp.readlines()
+        chunk_start_lines = []
+        for linenumber, line in enumerate(content):
+            if "[run]" in line:
+                chunk_start_lines.append(linenumber)
+        has_regular_len_heads = _check_append_rep(content, chunk_start_lines)
+        if has_regular_len_heads:
+            chunk = content[:chunk_start_lines[1]]
+            try:
+                gauge_line, corr_line, start_read, T = _read_chunk_structure(chunk, pattern, b2b)
+            except ValueError:
+                raise ValueError("Did not find pattern\n", pattern, "\nin\n", filename, "lines", 1, "to", chunk_start_lines[1] + 1)
+        # if has_regular_len_heads is true, all other chunks should follow the same structure
        rep_idl = []
        rep_data = []

-        for cnfg in range(len(data_starts)):
-            start = data_starts[cnfg]
-            stop = start + data_starts[1]
+        for chunk_num in range(len(chunk_start_lines)):
+            start = chunk_start_lines[chunk_num]
+            if chunk_num == len(chunk_start_lines) - 1:
+                stop = len(content)
+            else:
+                stop = chunk_start_lines[chunk_num + 1]
            chunk = content[start:stop]
-            idl, data = _read_chunk(chunk, gauge_line, cfg_separator, start_read, T, corr_line, b2b, pattern, im, single)
+            if not has_regular_len_heads:
+                gauge_line, corr_line, start_read, T = _read_chunk_structure(chunk, pattern, b2b)
+            try:
+                idl = idl_func(chunk[gauge_line], *cfg_func_args)
+            except Exception:
+                raise Exception("Couldn't parse idl from file", filename, ", problem with chunk of lines", start + 1, "to", stop + 1)
+            data = _read_chunk_data(chunk, start_read, T, corr_line, b2b, pattern, im, single)
            rep_idl.append(idl)
            rep_data.append(data)

--- a/pyerrors/version.py
+++ b/pyerrors/version.py
@ -1 +1 @@
-__version__ = "2.15.1"
+__version__ = "2.17.0-dev"
--- a/setup.py
+++ b/setup.py
@ -24,18 +24,18 @@ setup(name='pyerrors',
      author_email='fabian.joswig@ed.ac.uk',
      license="MIT",
      packages=find_packages(),
-      python_requires='>=3.9.0',
+      python_requires='>=3.10.0',
      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',
          'Programming Language :: Python :: 3',
-          'Programming Language :: Python :: 3.9',
          'Programming Language :: Python :: 3.10',
          'Programming Language :: Python :: 3.11',
          'Programming Language :: Python :: 3.12',
          'Programming Language :: Python :: 3.13',
+          'Programming Language :: Python :: 3.14',
          'Topic :: Scientific/Engineering :: Physics'
      ],
     )
--- a/tests/data/sfcf_test/data_ah/data_ah_r0.F_V0
+++ b/tests/data/sfcf_test/data_ah/data_ah_r0.F_V0
--- a/tests/data/sfcf_test/data_ah/data_ah_r0.f_1
+++ b/tests/data/sfcf_test/data_ah/data_ah_r0.f_1
@ -0,0 +1,966 @@
+[run]
+
+version     2.1
+date        2022-01-19 11:04:03 +0100
+host        r04n07.palma.wwu
+dir         /scratch/tmp/j_kuhl19
+user        j_kuhl19
+gauge_name  /data_a_r0_n1
+gauge_md5   1ea28326e4090996111a320b8372811d
+param_name  sfcf_unity_test.in
+param_md5   d881e90d41188a33b8b0f1bd0bc53ea5
+param_hash  686af5e712ee2902180f5428af94c6e7
+data_name   ./output_10519905/data_af_1
+
+[correlator]
+
+name      f_1
+quarks    lquark lquark
+offset    0
+wf        0
+wf_2      0
+corr
+3.5119415254545021e+02 +6.7620978057264750e-15
+
+[correlator]
+
+name      f_1
+quarks    lquark lquark
+offset    0
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+[correlator]
+
+name      f_1
+quarks    lquark lquark
+offset    0
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+[correlator]
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+name      f_1
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+version     2.1
+date        2022-01-19 11:04:05 +0100
+host        r04n07.palma.wwu
+dir         /scratch/tmp/j_kuhl19
+user        j_kuhl19
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+param_name  sfcf_unity_test.in
+param_hash  686af5e712ee2902180f5428af94c6e7
+data_name   ./output_10519905/data_af_1
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+quarks    lquark lquark
+offset    1
+wf        0
+corr_t
+  1 +6.5471188727965909e+01 -1.6112786177915427e-11
+  2 +1.0447210337411881e+00 -7.0387528705692678e-13
+  3 -4.1025094911167137e+01 +4.6509152745618223e-13
+
+[correlator]
+
+name      f_A
+quarks    lquark lquark
+offset    1
+wf        1
+corr_t
+  1 +6.5551520722842213e+01 -8.1976426690345305e-13
+  2 +1.0542820240843382e+00 +2.1626370477046812e-13
+  3 -4.1024441815730086e+01 -2.4147931196409923e-14
+
+[correlator]
+
+name      f_A
+quarks    lquark lquark
+offset    1
+wf        2
+corr_t
+  1 +6.5529951269443117e+01 +7.9192560386479701e-14
+  2 +1.0516822345055870e+00 -1.2443038782429568e-14
+  3 -4.1025142768037739e+01 +5.9315333178954509e-17
+
--- a/tests/fits_test.py
+++ b/tests/fits_test.py
@ -1611,3 +1611,81 @@ def old_prior_fit(x, y, func, priors, silent=False, **kwargs):
        qqplot(x, y, func, result)

    return output
+
+def test_dof_prior_fit():
+    """Performs an uncorrelated fit with a prior to uncorrelated data then
+    the expected chisquare and the usual dof need to agree"""
+    N = 5
+
+    def fitf(a, x):
+        return a[0] + 0 * x
+
+    x = [1. for i in range(N)]
+    y = [pe.cov_Obs(i, .1, '%d' % (i)) for i in range(N)]
+    [o.gm() for o in y]
+    res = pe.fits.least_squares(x, y, fitf, expected_chisquare=True, priors=[pe.cov_Obs(3, 1, 'p')])
+    assert res.chisquare_by_expected_chisquare == res.chisquare_by_dof
+    
+    num_samples = 400
+    N = 10
+
+    x = norm.rvs(size=(N, num_samples)) # generate random numbers
+
+    r = np.zeros((N, N))
+    for i in range(N):
+        for j in range(N):
+            if(i==j):
+                r[i, j] = 1.0 # element in correlation matrix
+
+    errl = np.sqrt([3.4, 2.5, 3.6, 2.8, 4.2, 4.7, 4.9, 5.1, 3.2, 4.2]) # set y errors
+    for i in range(N):
+        for j in range(N):
+            if(i==j):
+                r[i, j] *= errl[i] * errl[j] # element in covariance matrix
+
+    c = cholesky(r, lower=True)
+    y = np.dot(c, x)
+    x = np.arange(N)
+    x_dict = {}
+    y_dict = {}
+    for i,item in enumerate(x):
+        x_dict[str(item)] = [x[i]]
+
+    for linear in [True, False]:
+        data = []
+        for i in range(N):
+            if linear:
+                data.append(pe.Obs([[i + 1 + o for o in y[i]]], ['ens'+str(i)]))
+            else:
+                data.append(pe.Obs([[np.exp(-(i + 1)) + np.exp(-(i + 1)) * o for o in y[i]]], ['ens'+str(i)]))
+
+        [o.gamma_method() for o in data]
+
+        data_dict = {}
+        for i,item in enumerate(x):
+            data_dict[str(item)] = [data[i]]
+
+        corr = pe.covariance(data, correlation=True)
+        chol = np.linalg.cholesky(corr)
+        covdiag = np.diag(1 / np.asarray([o.dvalue for o in data]))
+        chol_inv = scipy.linalg.solve_triangular(chol, covdiag, lower=True)
+        chol_inv_keys = [""]
+        chol_inv_keys_combined_fit = [str(item) for i,item in enumerate(x)]
+
+        if linear:
+            def fitf(p, x):
+                return p[1] + p[0] * x
+            fitf_dict = {}
+            for i,item in enumerate(x):
+                fitf_dict[str(item)] = fitf
+        else:
+            def fitf(p, x):
+                return p[1] * anp.exp(-p[0] * x)
+            fitf_dict = {}
+            for i,item in enumerate(x):
+                fitf_dict[str(item)] = fitf
+
+        fit_exp = pe.least_squares(x, data, fitf, expected_chisquare=True, priors = {0:pe.cov_Obs(1.0, 1, 'p')})
+        fit_cov = pe.least_squares(x, data, fitf,  correlated_fit = True, inv_chol_cov_matrix = [chol_inv,chol_inv_keys],  priors = {0:pe.cov_Obs(1.0, 1, 'p')})
+        assert np.isclose(fit_exp.chisquare_by_expected_chisquare,fit_exp.chisquare_by_dof,atol=1e-8)
+        assert np.isclose(fit_exp.chisquare_by_expected_chisquare,fit_cov.chisquare_by_dof,atol=1e-8)
--- a/tests/sfcf_in_test.py
+++ b/tests/sfcf_in_test.py
@ -24,10 +24,10 @@ def build_test_environment(path, env_type, cfgs, reps):
            os.mkdir(path + "/data_c/data_c_r"+str(i))
            for j in range(1, cfgs+1):
                shutil.copy(path + "/data_c/data_c_r0/data_c_r0_n1", path + "/data_c/data_c_r"+str(i)+"/data_c_r"+str(i)+"_n"+str(j))
-    elif env_type == "a":
+    elif env_type in ["a", "apf", "ah"]:
        for i in range(1, reps):
            for corr in ["f_1", "f_A", "F_V0"]:
-                shutil.copy(path + "/data_a/data_a_r0." + corr, path + "/data_a/data_a_r" + str(i) + "." + corr)
+                shutil.copy(path + "/data_" + env_type + "/data_" + env_type + "_r0." + corr, path + "/data_" + env_type + "/data_" + env_type + "_r" + str(i) + "." + corr)


 def test_o_bb(tmp_path):
@ -276,6 +276,28 @@ def test_a_bb(tmp_path):
    assert f_1[0].value == 351.1941525454502


+def test_a_bb_external_idl_func(tmp_path):
+    build_test_environment(str(tmp_path), "a", 5, 3)
+    def extract_idl(s: str) -> int:
+        return int(s.split("n")[-1])
+    f_1 = sfin.read_sfcf(str(tmp_path) + "/data_a", "data_a", "f_1", quarks="lquark lquark", wf=0, wf2=0, version="2.0a", corr_type="bb", cfg_func=extract_idl)
+    print(f_1)
+    assert len(f_1) == 1
+    assert list(f_1[0].shape.keys()) == ["data_a_|r0", "data_a_|r1", "data_a_|r2"]
+    assert f_1[0].value == 351.1941525454502
+
+
+def test_a_bb_external_idl_func_postfix(tmp_path):
+    build_test_environment(str(tmp_path), "apf", 5, 3)
+    def extract_idl(s: str) -> int:
+        return int(s.split("n")[-1][:-5])
+    f_1 = sfin.read_sfcf(str(tmp_path) + "/data_apf", "data_apf", "f_1", quarks="lquark lquark", wf=0, wf2=0, version="2.0a", corr_type="bb", cfg_func=extract_idl)
+    print(f_1)
+    assert len(f_1) == 1
+    assert list(f_1[0].shape.keys()) == ["data_apf_|r0", "data_apf_|r1", "data_apf_|r2"]
+    assert f_1[0].value == 351.1941525454502
+
+
 def test_a_bi(tmp_path):
    build_test_environment(str(tmp_path), "a", 5, 3)
    f_A = sfin.read_sfcf(str(tmp_path) + "/data_a", "data_a", "f_A", quarks="lquark lquark", wf=0, version="2.0a")
@ -287,6 +309,32 @@ def test_a_bi(tmp_path):
    assert f_A[2].value == -41.025094911185185


+def test_a_bi_external_idl_func(tmp_path):
+    build_test_environment(str(tmp_path), "a", 5, 3)
+    def extract_idl(s: str) -> int:
+        return int(s.split("n")[-1])
+    f_A = sfin.read_sfcf(str(tmp_path) + "/data_a", "data_a", "f_A", quarks="lquark lquark", wf=0, version="2.0a", cfg_func=extract_idl)
+    print(f_A)
+    assert len(f_A) == 3
+    assert list(f_A[0].shape.keys()) == ["data_a_|r0", "data_a_|r1", "data_a_|r2"]
+    assert f_A[0].value == 65.4711887279723
+    assert f_A[1].value == 1.0447210336915187
+    assert f_A[2].value == -41.025094911185185
+
+
+def test_a_bi_external_idl_func_postfix(tmp_path):
+    build_test_environment(str(tmp_path), "apf", 5, 3)
+    def extract_idl(s: str) -> int:
+        return int(s.split("n")[-1][:-5])
+    f_A = sfin.read_sfcf(str(tmp_path) + "/data_apf", "data_apf", "f_A", quarks="lquark lquark", wf=0, version="2.0a", cfg_func=extract_idl)
+    print(f_A)
+    assert len(f_A) == 3
+    assert list(f_A[0].shape.keys()) == ["data_apf_|r0", "data_apf_|r1", "data_apf_|r2"]
+    assert f_A[0].value == 65.4711887279723
+    assert f_A[1].value == 1.0447210336915187
+    assert f_A[2].value == -41.025094911185185
+
+
 def test_a_bi_files(tmp_path):
    build_test_environment(str(tmp_path), "a", 5, 3)
    f_A = sfin.read_sfcf(str(tmp_path) + "/data_a", "data_a", "f_A", quarks="lquark lquark", wf=0, version="2.0a", files=["data_a_r0.f_A", "data_a_r1.f_A", "data_a_r2.f_A"])
@ -316,6 +364,55 @@ def test_a_bib(tmp_path):
    assert f_V0[2] == 683.6776090081005


+def test_a_bib_external_idl_func(tmp_path):
+    build_test_environment(str(tmp_path), "a", 5, 3)
+    def extract_idl(s: str) -> int:
+        return int(s.split("n")[-1])
+    f_V0 = sfin.read_sfcf(str(tmp_path) + "/data_a", "data_a", "F_V0", quarks="lquark lquark", wf=0, wf2=0, version="2.0a", corr_type="bib", cfg_func=extract_idl)
+    print(f_V0)
+    assert len(f_V0) == 3
+    assert list(f_V0[0].shape.keys()) == ["data_a_|r0", "data_a_|r1", "data_a_|r2"]
+    assert f_V0[0] == 683.6776090085115
+    assert f_V0[1] == 661.3188585582334
+    assert f_V0[2] == 683.6776090081005
+
+def test_a_bib_external_idl_func_postfix(tmp_path):
+    build_test_environment(str(tmp_path), "apf", 5, 3)
+    def extract_idl(s: str) -> int:
+        return int(s.split("n")[-1][:-5])
+    f_V0 = sfin.read_sfcf(str(tmp_path) + "/data_apf", "data_apf", "F_V0", quarks="lquark lquark", wf=0, wf2=0, version="2.0a", corr_type="bib", cfg_func=extract_idl)
+    print(f_V0)
+    assert len(f_V0) == 3
+    assert list(f_V0[0].shape.keys()) == ["data_apf_|r0", "data_apf_|r1", "data_apf_|r2"]
+    assert f_V0[0] == 683.6776090085115
+    assert f_V0[1] == 661.3188585582334
+    assert f_V0[2] == 683.6776090081005
+
+
+def test_a_bib_irreg_header(tmp_path):
+    build_test_environment(str(tmp_path), "ah", 5, 3)
+    with pytest.warns(UserWarning):
+        f_V0 = sfin.read_sfcf(str(tmp_path) + "/data_ah", "data_ah", "F_V0", quarks="lquark lquark", wf=0, wf2=0, version="2.0a", corr_type="bib")
+    print(f_V0)
+    assert len(f_V0) == 3
+    assert list(f_V0[0].shape.keys()) == ["data_ah_|r0", "data_ah_|r1", "data_ah_|r2"]
+    assert f_V0[0] == 683.6776090085115
+    assert f_V0[1] == 661.3188585582334
+    assert f_V0[2] == 683.6776090081005
+
+
+def test_a_bi_irreg_header(tmp_path):
+    build_test_environment(str(tmp_path), "ah", 5, 3)
+    with pytest.warns(UserWarning):
+        f_A = sfin.read_sfcf(str(tmp_path) + "/data_ah", "data_ah", "f_A", quarks="lquark lquark", wf=0, version="2.0a", corr_type="bi")
+    print(f_A)
+    assert len(f_A) == 3
+    assert list(f_A[0].shape.keys()) == ["data_ah_|r0", "data_ah_|r1", "data_ah_|r2"]
+    assert f_A[0].value == 65.4711887279723
+    assert f_A[1].value == 1.0447210336915187
+    assert f_A[2].value == -41.025094911185185
+
+
 def test_simple_multi_a(tmp_path):
    build_test_environment(str(tmp_path), "a", 5, 3)
    corrs = sfin.read_sfcf_multi(str(tmp_path) + "/data_a", "data_a", ["F_V0"], quarks_list=["lquark lquark"], wf1_list=[0], wf2_list=[0], version="2.0a", corr_type_list=["bib"])
Author	SHA1	Message	Date
Justus Kuhlmann	da399b7c02	Fix/check append rep (#277 ) * add option that the headers of an append-mode file can have different format * add tests for irregular headers in append mode * hotfix: fix bug in append start read implementation * lint * lint II	2025-11-25 12:57:03 +01:00
Fabian Joswig	1002dd0e51	[chore] Bump version to v2.17.0-dev	2025-10-30 16:36:09 +01:00
Fabian Joswig	4cdddf0a76	[chore] Bump version and changelog	2025-10-30 16:34:05 +01:00
Justus Kuhlmann	da0a4cc40a	Feat/idl func (#275 ) * outsource function to get idl for append mode * Expose option to define function for idl by the user. * clean up args * add tests * lint	2025-10-30 16:26:52 +01:00
Pia Leonie Jones Petrak	e0076ccea9	[Fix] corrected expected_chisquare by adding the number of priors (#274 ) * [Fix] corrected expected_chisquare by adding the number of priors * test/fits_test.py: dof and expected chisquare the same in uncorrelated fit w. prior to uncorrelated data	2025-10-22 15:36:01 +02:00
Fabian Joswig	85ae9d7563	[chore] Remove support for python 3.9 and bump python versions in runners (#273 )	2025-10-19 12:59:20 +02:00
Fabian Joswig	a600a69bb9	[ci] Add python 3.14 runners for pytest workflow (#270 ) * [ci] Add python 3.14 runners for pytest workflow * [ci] Deactivate -Werror option in pytest workflow to fix python 3.14 runner * [ci] Run tests with Werror for all python versions but for 3.14	2025-10-19 12:44:06 +02:00
Fabian Joswig	4c4173c461	[chore] Bump version to 2.16.0-dev	2025-10-19 12:32:52 +02:00