From 4c4173c461ac92fbf7fe797de3d881416b859de7 Mon Sep 17 00:00:00 2001 From: Fabian Joswig Date: Sun, 19 Oct 2025 12:32:52 +0200 Subject: [PATCH 1/8] [chore] Bump version to 2.16.0-dev --- pyerrors/version.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pyerrors/version.py b/pyerrors/version.py index b1b26975..e017dc17 100644 --- a/pyerrors/version.py +++ b/pyerrors/version.py @@ -1 +1 @@ -__version__ = "2.15.1" +__version__ = "2.16.0-dev" From a600a69bb9eed39d48ee22a8b4f6d223b7a19470 Mon Sep 17 00:00:00 2001 From: Fabian Joswig Date: Sun, 19 Oct 2025 12:44:06 +0200 Subject: [PATCH 2/8] [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 --- .github/workflows/pytest.yml | 9 +++++++-- 1 file changed, 7 insertions(+), 2 deletions(-) diff --git a/.github/workflows/pytest.yml b/.github/workflows/pytest.yml index af98e210..d04a20bb 100644 --- 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: ["3.9", "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 From 85ae9d7563f550a0fbd14a6e487d23392f05f658 Mon Sep 17 00:00:00 2001 From: Fabian Joswig Date: Sun, 19 Oct 2025 12:59:20 +0200 Subject: [PATCH 3/8] [chore] Remove support for python 3.9 and bump python versions in runners (#273) --- .github/workflows/docs.yml | 2 +- .github/workflows/flake8.yml | 2 +- .github/workflows/pytest.yml | 2 +- README.md | 2 +- setup.py | 4 ++-- 5 files changed, 6 insertions(+), 6 deletions(-) diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml index 03ca7c23..f1dcce68 100644 --- 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: | diff --git a/.github/workflows/flake8.yml b/.github/workflows/flake8.yml index c6625b37..a80fb559 100644 --- 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: diff --git a/.github/workflows/pytest.yml b/.github/workflows/pytest.yml index d04a20bb..1889b290 100644 --- 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", "3.14"] + python-version: ["3.10", "3.11", "3.12", "3.13", "3.14"] include: - os: macos-latest python-version: "3.12" diff --git a/README.md b/README.md index 7937da4d..64f1fd96 100644 --- 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. diff --git a/setup.py b/setup.py index 8c42f4a6..066f4f99 100644 --- 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' ], ) From e0076ccea9868a336ca7104e9a39b1741d974f1e Mon Sep 17 00:00:00 2001 From: Pia Leonie Jones Petrak <73896673+PiaLJP@users.noreply.github.com> Date: Wed, 22 Oct 2025 09:36:01 -0400 Subject: [PATCH 4/8] [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 --- pyerrors/fits.py | 2 +- tests/fits_test.py | 78 ++++++++++++++++++++++++++++++++++++++++++++++ 2 files changed, 79 insertions(+), 1 deletion(-) diff --git a/pyerrors/fits.py b/pyerrors/fits.py index 3a3119b3..62714330 100644 --- 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) diff --git a/tests/fits_test.py b/tests/fits_test.py index e906e294..3af2e51d 100644 --- 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) \ No newline at end of file From da0a4cc40a5767780937285c5f244ea9cef3f9fa Mon Sep 17 00:00:00 2001 From: Justus Kuhlmann <82444481+jkuhl-uni@users.noreply.github.com> Date: Thu, 30 Oct 2025 16:26:52 +0100 Subject: [PATCH 5/8] 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 --- pyerrors/input/sfcf.py | 37 +- .../data/sfcf_test/data_apf/data_apf_r0.F_V0 | 1150 +++++++++++++++++ tests/data/sfcf_test/data_apf/data_apf_r0.f_1 | 970 ++++++++++++++ tests/data/sfcf_test/data_apf/data_apf_r0.f_A | 400 ++++++ tests/sfcf_in_test.py | 77 +- 5 files changed, 2618 insertions(+), 16 deletions(-) create mode 100644 tests/data/sfcf_test/data_apf/data_apf_r0.F_V0 create mode 100644 tests/data/sfcf_test/data_apf/data_apf_r0.f_1 create mode 100644 tests/data/sfcf_test/data_apf/data_apf_r0.f_A diff --git a/pyerrors/input/sfcf.py b/pyerrors/input/sfcf.py index 0431788a..4cb09630 100644 --- a/pyerrors/input/sfcf.py +++ b/pyerrors/input/sfcf.py @@ -10,7 +10,7 @@ import itertools 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 +71,11 @@ 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 +245,16 @@ 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 +278,7 @@ 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 +361,7 @@ 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 +591,7 @@ 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]: @@ -595,10 +600,10 @@ 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): +def _read_append_rep(filename, pattern, b2b, im, single, idl_func, cfg_func_args): with open(filename, 'r') as fp: content = fp.readlines() data_starts = [] @@ -634,7 +639,11 @@ def _read_append_rep(filename, pattern, b2b, cfg_separator, im, single): start = data_starts[cnfg] stop = start + data_starts[1] chunk = content[start:stop] - idl, data = _read_chunk(chunk, gauge_line, cfg_separator, start_read, T, corr_line, b2b, pattern, im, single) + 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) 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-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 + diff --git a/tests/sfcf_in_test.py b/tests/sfcf_in_test.py index 60a71433..a6c5263e 100644 --- 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"]: 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 +364,31 @@ 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_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"]) From 4cdddf0a7625abe1484b6e02f41653a67269062b Mon Sep 17 00:00:00 2001 From: Fabian Joswig Date: Thu, 30 Oct 2025 16:34:05 +0100 Subject: [PATCH 6/8] [chore] Bump version and changelog --- CHANGELOG.md | 11 +++++++++++ pyerrors/version.py | 2 +- 2 files changed, 12 insertions(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 42dd7bc9..7012e6ec 100644 --- 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 diff --git a/pyerrors/version.py b/pyerrors/version.py index e017dc17..8f4a3517 100644 --- a/pyerrors/version.py +++ b/pyerrors/version.py @@ -1 +1 @@ -__version__ = "2.16.0-dev" +__version__ = "2.16.0" From 1002dd0e51f81420dbf707686cd4dc05643a57e6 Mon Sep 17 00:00:00 2001 From: Fabian Joswig Date: Thu, 30 Oct 2025 16:36:09 +0100 Subject: [PATCH 7/8] [chore] Bump version to v2.17.0-dev --- pyerrors/version.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pyerrors/version.py b/pyerrors/version.py index 8f4a3517..3307a6a6 100644 --- a/pyerrors/version.py +++ b/pyerrors/version.py @@ -1 +1 @@ -__version__ = "2.16.0" +__version__ = "2.17.0-dev" From da399b7c026dafd82961bd68632a568d9d8af9ba Mon Sep 17 00:00:00 2001 From: Justus Kuhlmann <82444481+jkuhl-uni@users.noreply.github.com> Date: Tue, 25 Nov 2025 12:57:03 +0100 Subject: [PATCH 8/8] 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 --- pyerrors/input/sfcf.py | 95 +- tests/data/sfcf_test/data_ah/data_ah_r0.F_V0 | 1147 ++++++++++++++++++ tests/data/sfcf_test/data_ah/data_ah_r0.f_1 | 966 +++++++++++++++ tests/data/sfcf_test/data_ah/data_ah_r0.f_A | 395 ++++++ tests/sfcf_in_test.py | 26 +- 5 files changed, 2601 insertions(+), 28 deletions(-) create mode 100644 tests/data/sfcf_test/data_ah/data_ah_r0.F_V0 create mode 100644 tests/data/sfcf_test/data_ah/data_ah_r0.f_1 create mode 100644 tests/data/sfcf_test/data_ah/data_ah_r0.f_A diff --git a/pyerrors/input/sfcf.py b/pyerrors/input/sfcf.py index 4cb09630..af727b95 100644 --- a/pyerrors/input/sfcf.py +++ b/pyerrors/input/sfcf.py @@ -5,6 +5,7 @@ import numpy as np # Thinly-wrapped numpy from ..obs import Obs from .utils import sort_names, check_idl import itertools +import warnings sep = "/" @@ -603,42 +604,82 @@ def _read_chunk_data(chunk, start_read, T, corr_line, b2b, pattern, im, single): return data +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 + elif line.startswith("[correlator]"): + corr_line = linenumber + found_pat = "" + for li in chunk[corr_line + 1: corr_line + 6 + b2b]: + found_pat += li + if re.search(pattern, found_pat): + start_read = corr_line + 7 + b2b + break + 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 + + def _read_append_rep(filename, pattern, b2b, im, single, idl_func, cfg_func_args): with open(filename, 'r') as fp: content = fp.readlines() - data_starts = [] + chunk_start_lines = [] 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]] - for linenumber, line in enumerate(chunk): - if line.startswith("gauge_name"): - gauge_line = linenumber - elif line.startswith("[correlator]"): - corr_line = linenumber - found_pat = "" - for li in chunk[corr_line + 1: corr_line + 6 + b2b]: - found_pat += li - 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) - endline = corr_line + 6 + b2b - while not chunk[endline] == "\n": - endline += 1 - T = endline - start_read - - # all other chunks should follow the same structure + 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] + if not has_regular_len_heads: + gauge_line, corr_line, start_read, T = _read_chunk_structure(chunk, pattern, b2b) try: idl = 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a/tests/sfcf_in_test.py b/tests/sfcf_in_test.py index a6c5263e..6a7b506a 100644 --- a/tests/sfcf_in_test.py +++ b/tests/sfcf_in_test.py @@ -24,7 +24,7 @@ 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 in ["a", "apf"]: + 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_" + env_type + "/data_" + env_type + "_r0." + corr, path + "/data_" + env_type + "/data_" + env_type + "_r" + str(i) + "." + corr) @@ -389,6 +389,30 @@ def test_a_bib_external_idl_func_postfix(tmp_path): 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"])