Merge pull request #2226 from NNPDF/update_ruamel

unpin ruamel.yaml version

conda-recipe/meta.yaml

@@ -44,7 +44,7 @@ requirements:
         - joblib
         - sphinx_rtd_theme >0.5
         - sphinxcontrib-bibtex
-        - ruamel.yaml <0.18
+        - ruamel.yaml >=0.15
 
 test:
     requires:

extra_tests/regression_checks.py

@@ -9,7 +9,7 @@
 import pytest
 
 from n3fit.tests.test_fit import EXE, check_fit_results
-from reportengine.compat import yaml
+from validphys.utils import yaml_safe
 
 REGRESSION_FOLDER = pathlib.Path(__file__).with_name("regression_fits")
 
@@ -37,7 +37,7 @@ def test_regression_fit(tmp_path, runcard, replica, regenerate):
     runcard_file = REGRESSION_FOLDER / runcard_name
     shutil.copy(runcard_file, tmp_path)
 
-    runcard_info = yaml.load(runcard_file.read_text())
+    runcard_info = yaml_safe.load(runcard_file.read_text())
     if (wname := runcard_info.get("load")) is not None:
         shutil.copy(REGRESSION_FOLDER / wname, tmp_path)
 

n3fit/src/evolven3fit/evolve.py

@@ -11,7 +11,7 @@
 
 import eko
 from eko import basis_rotation, runner
-from reportengine.compat import yaml
+from validphys.utils import yaml_safe
 
 from . import eko_utils, utils
 
@@ -164,7 +164,7 @@ def load_fit(usr_path):
     nnfitpath = usr_path / "nnfit"
     pdf_dict = {}
     for yaml_file in nnfitpath.glob(f"replica_*/{usr_path.name}.exportgrid"):
-        data = yaml.safe_load(yaml_file.read_text(encoding="UTF-8"))
+        data = yaml_safe.load(yaml_file.read_text(encoding="UTF-8"))
         pdf_dict[yaml_file.parent.stem] = data
     return pdf_dict
 

n3fit/src/evolven3fit/utils.py

@@ -4,8 +4,8 @@
 import numpy as np
 from scipy.interpolate import interp1d
 
-from reportengine.compat import yaml
 from validphys.pdfbases import PIDS_DICT
+from validphys.utils import yaml_safe
 
 from .q2grids import Q2GRID_DEFAULT, Q2GRID_NNPDF40
 
@@ -57,7 +57,7 @@ def hasFlavor(self, pid):
 
 def read_runcard(usr_path):
     """Read the runcard and return the relevant information for evolven3fit"""
-    return yaml.safe_load((usr_path / "filter.yml").read_text(encoding="UTF-8"))
+    return yaml_safe.load((usr_path / "filter.yml").read_text(encoding="UTF-8"))
 
 
 def get_theoryID_from_runcard(usr_path):
@@ -99,9 +99,7 @@ def generate_q2grid(Q0, Qfin, Q_points, match_dict, nf0=None, legacy40=False):
                 frac_of_point = np.log(match_scale / Q_ini) / np.log(Qfin / Q0)
                 num_points = int(Q_points * frac_of_point)
                 num_points_list.append(num_points)
-                grids.append(
-                    np.geomspace(Q_ini**2, match_scale**2, num=num_points, endpoint=False)
-                )
+                grids.append(np.geomspace(Q_ini**2, match_scale**2, num=num_points, endpoint=False))
                 Q_ini = match_scale
         num_points = Q_points - sum(num_points_list)
         grids.append(np.geomspace(Q_ini**2, Qfin**2, num=num_points))

n3fit/src/n3fit/io/writer.py

@@ -12,8 +12,8 @@
 
 import n3fit
 from n3fit import vpinterface
-from reportengine.compat import yaml
 import validphys
+from validphys.utils import yaml_safe
 
 log = logging.getLogger(__name__)
 
@@ -622,4 +622,4 @@ def storefit(pdf_object, replica, out_path, theory):
     }
 
     with open(out_path, "w") as fs:
-        yaml.dump(data, fs)
+        yaml_safe.dump(data, fs)

n3fit/src/n3fit/scripts/n3fit_exec.py

@@ -9,14 +9,15 @@
 import re
 import shutil
 import sys
-import warnings
+
+from ruamel.yaml import error
 
 from reportengine import colors
-from reportengine.compat import yaml
 from reportengine.namespaces import NSList
 from validphys.app import App
 from validphys.config import Config, ConfigError, Environment, EnvironmentError_
 from validphys.core import FitSpec
+from validphys.utils import yaml_safe
 
 N3FIT_FIXED_CONFIG = dict(use_cuts='internal', use_t0=True, actions_=[])
 
@@ -108,15 +109,8 @@ class N3FitConfig(Config):
     @classmethod
     def from_yaml(cls, o, *args, **kwargs):
         try:
-            with warnings.catch_warnings():
-                warnings.simplefilter("ignore", yaml.error.MantissaNoDotYAML1_1Warning)
-                # We need to specify the older version 1.1 to support the
-                # older configuration files, which liked to use on/off for
-                # booleans.
-                # The floating point parsing yields warnings everywhere, which
-                # we suppress.
-                file_content = yaml.safe_load(o, version="1.1")
-        except yaml.error.YAMLError as e:
+            file_content = yaml_safe.load(o)
+        except error.YAMLError as e:
             raise ConfigError(f"Failed to parse yaml file: {e}")
         if not isinstance(file_content, dict):
             raise ConfigError(

n3fit/src/n3fit/scripts/vp_setupfit.py

@@ -31,12 +31,13 @@
 import re
 import shutil
 import sys
-import warnings
+
+from ruamel.yaml import error
 
 from reportengine import colors
-from reportengine.compat import yaml
 from validphys.app import App
 from validphys.config import Config, ConfigError, Environment, EnvironmentError_
+from validphys.utils import yaml_safe
 
 SETUPFIT_FIXED_CONFIG = dict(
     actions_=[
@@ -131,15 +132,8 @@ class SetupFitConfig(Config):
     @classmethod
     def from_yaml(cls, o, *args, **kwargs):
         try:
-            with warnings.catch_warnings():
-                warnings.simplefilter('ignore', yaml.error.MantissaNoDotYAML1_1Warning)
-                # We need to specify the older version 1.1 to support the
-                # older configuration files, which liked to use on/off for
-                # booleans.
-                # The floating point parsing yields warnings everywhere, which
-                # we suppress.
-                file_content = yaml.safe_load(o, version='1.1')
-        except yaml.error.YAMLError as e:
+            file_content = yaml_safe.load(o)
+        except error.YAMLError as e:
             raise ConfigError(f"Failed to parse yaml file: {e}")
         if not isinstance(file_content, dict):
             raise ConfigError(

n3fit/src/n3fit/tests/test_evolven3fit.py

@@ -8,9 +8,9 @@
 import pytest
 
 from eko import EKO, runner
-from reportengine.compat import yaml
 from validphys.api import API
 from validphys.pdfbases import PIDS_DICT
+from validphys.utils import yaml_safe
 
 REGRESSION_FOLDER = pathlib.Path(__file__).with_name("regressions")
 log = logging.getLogger(__name__)
@@ -24,7 +24,7 @@ def assert_sorted(arr, title):
 
 def check_lhapdf_info(info_path):
     """Check the LHAPDF info file is correct"""
-    info = yaml.load(info_path.open("r", encoding="utf-8"))
+    info = yaml_safe.load(info_path.open("r", encoding="utf-8"))
 
     alphas_qs = info["AlphaS_Qs"]
     alphas = info["AlphaS_Vals"]

n3fit/src/n3fit/tests/test_fit.py

@@ -22,8 +22,8 @@
 import pytest
 
 import n3fit
-from reportengine.compat import yaml
 from validphys.n3fit_data import replica_mcseed, replica_nnseed, replica_trvlseed
+from validphys.utils import yaml_safe
 
 log = logging.getLogger(__name__)
 REGRESSION_FOLDER = pathlib.Path(__file__).with_name("regressions")
@@ -45,7 +45,7 @@ def _load_json(info_file):
 
 def _load_exportgrid(exportgrid_file):
     """Loads the exportgrid file"""
-    return yaml.safe_load(exportgrid_file.read_text())
+    return yaml_safe.load(exportgrid_file.read_text())
 
 
 def test_initialize_seeds():

nnpdf_data/nnpdf_data/__init__.py

@@ -1,9 +1,7 @@
 from functools import lru_cache
 import pathlib
 
-import ruamel.yaml as yaml
-
-from ._version import __version__
+import yaml
 
 path_vpdata = pathlib.Path(__file__).parent
 path_commondata = path_vpdata / "commondata"
@@ -12,7 +10,8 @@
 _path_legacy_mapping = path_commondata / "dataset_names.yml"
 theory_cards = path_vpdata / "theory_cards"
 
-_legacy_to_new_mapping_raw = yaml.YAML().load(_path_legacy_mapping)
+with open(_path_legacy_mapping) as file:
+    _legacy_to_new_mapping_raw = yaml.load(file, yaml.Loader)
 # Convert strings into a dictionary
 legacy_to_new_mapping = {
     k: ({"dataset": v} if isinstance(v, str) else v) for k, v in _legacy_to_new_mapping_raw.items()

nnpdf_data/nnpdf_data/theory.py

@@ -4,12 +4,9 @@
 """
 
 import dataclasses
-from functools import lru_cache
 import logging
 from typing import Literal, Optional
 
-from .utils import parse_yaml_inp
-
 DEPRECATED_KEYS = ["MaxNfAs", "SxRes", "SxOrd" "EScaleVar", "Qedref", "global_nx"]
 
 log = logging.getLogger(__name__)

nnpdf_data/nnpdf_data/utils.py

@@ -1,8 +1,10 @@
 import pathlib
 
-import ruamel.yaml as yaml
+from ruamel.yaml import YAML
 from validobj import ValidationError, parse_input
+import yaml
 
+yaml_rt = YAML(typ="rt")
 try:
     Loader = yaml.CLoader
 except AttributeError:
@@ -22,14 +24,14 @@ def parse_yaml_inp(input_yaml, spec):
         return parse_input(inp, spec)
     except ValidationError as e:
         current_exc = e
-        # In order to provide a more complete error information, use round_trip_load
+        # In order to provide a more complete error information, use round trip
         # to read the .yaml file again (insetad of using the CLoader)
-        current_inp = yaml.round_trip_load(input_yaml.open("r", encoding="utf-8"))
+        current_inp = yaml_rt.load(input_yaml.open("r", encoding="utf-8"))
         error_text_lines = []
         while current_exc:
             if hasattr(current_exc, 'wrong_field'):
                 wrong_field = current_exc.wrong_field
-                # Mappings compping from ``round_trip_load`` have an
+                # Mappings compping from yaml_rt have an
                 # ``lc`` attribute that gives a tuple of
                 # ``(line_number, column)`` for a given item in
                 # the mapping.

nnpdf_data/pyproject.toml

@@ -33,7 +33,7 @@ include = [
 
 [tool.poetry.dependencies]
 python = "^3.9"
-"ruamel.yaml" = "<0.18"
+"ruamel.yaml" = "*"
 # Required to run filters: `filter_files_dependencies`
 pandas = {version = "*", optional = true}
 numpy = {version = "*", optional = true}

pyproject.toml

@@ -65,6 +65,7 @@ matplotlib = "^3.9"
 pineappl = "^0.8.2"
 pandas = "*"
 numpy = "*"
+"ruamel.yaml" = "*"
 validobj = "*"
 prompt_toolkit = "*"
 # Reportengine needs to be installed from git