Merge pull request #67 from NNPDF/update_yaml

address deprecation of ruamel.yaml functions

Author: RoyStegeman

conda-recipe/meta.yaml

@@ -17,7 +17,7 @@ requirements:
   run:
     - python
     - jinja2
-    - ruamel_yaml =0.15
+    - ruamel.yaml >=0.15
     - matplotlib
     - pandas >=1
     - pygments

pyproject.toml

@@ -19,7 +19,7 @@ classifiers = [
 description-file="README.md"
 requires = [
     "jinja2",
-    "ruamel_yaml<0.18", # the code is not compatible with ruamel 0.18
+    "ruamel.yaml>=0.15",
     "matplotlib",
     "pandas",
     "pygments",

src/reportengine/compat.py

@@ -13,10 +13,10 @@
 import json
 from copy import copy
 
+from ruamel.yaml import YAMLError
 
-from reportengine.compat import yaml
 from reportengine import namespaces
-from reportengine.utils import ChainMap, get_classmembers
+from reportengine.utils import ChainMap, get_classmembers, yaml_rt
 from reportengine import templateparser
 from reportengine.baseexceptions import ErrorWithAlternatives, AsInputError
 
@@ -800,10 +800,10 @@ def __contains__(self, item):
     @classmethod
     def from_yaml(cls, o, *args, **kwargs):
         try:
-            return cls(yaml.round_trip_load(o), *args, **kwargs)
-        except yaml.error.YAMLError as e:
+            return cls(yaml_rt.load(o), *args, **kwargs)
+        except YAMLError as e:
             raise ConfigError(f"Failed to parse yaml file: {e}")
 
     def dump_lockfile(self):
         with open(self.environment.input_folder/"lockfile.yaml", "w+") as f:
-            yaml.dump(self.lockfile, stream=f, Dumper=yaml.RoundTripDumper)
+            yaml_rt.dump(self.lockfile, stream=f)

src/reportengine/configparser.py

@@ -32,16 +32,14 @@
 from __future__ import generator_stop
 
 import os
-import os.path as osp
 import logging
 import subprocess
 import shutil
 from collections import UserList
 import pathlib
 
+import dask.distributed
 import jinja2
-from reportengine.compat import yaml
-
 
 from . import configparser
 from . resourcebuilder import target_map
@@ -52,18 +50,18 @@
 from . import styles
 from . import filefinder
 from . import floatformatting
-
-import dask.distributed
+from . utils import yaml_rt
 
 log = logging.getLogger(__name__)
 
+
 __all__ = ('report', 'Config')
 
 
 def _process_template_text(source, *, filename=None):
     if filename:
         #PY36
-        log.debug("Processing template %s" % osp.abspath(str(filename)))
+        log.debug("Processing template %s" % os.path.abspath(str(filename)))
 
     root = {}
     d = root
@@ -111,7 +109,7 @@ class JinjaEnv(jinja2.Environment):
 
     def preprocess(self, source, name=None, filename=None):
         if filename:
-            log.debug("Processing template %s" % osp.abspath(filename))
+            log.debug("Processing template %s" % os.path.abspath(filename))
 
         root = {}
         d = root
@@ -213,12 +211,13 @@ def meta_file(output_path, meta:(dict, type(None))=None):
     path = output_path/fname
     with open(path, 'w') as f:
         f.write('\n')
-        #Using round_trip_dump is important here because the input dict may
-        #be a recursive commented map, which yaml.dump (or safe_dumo) doesn't
-        #know how to
-        #process correctly.
-        yaml.round_trip_dump(meta, f, explicit_start=True, explicit_end=True,
-                  default_flow_style=False)
+        #Using round_trip_dump is important here because the input dict may be a
+        #recursive commented map, which yaml.dump (or safe_dumo) doesn't know
+        #how to process correctly.
+        yaml_rt.explicit_start=True
+        yaml_rt.explicit_end=True
+        yaml_rt.default_flow_style=False
+        yaml_rt.dump(meta, f)
     return fname
 
 def pandoc_template(*, templatename='report.template', output_path):

src/reportengine/report.py

@@ -9,7 +9,9 @@
 from collections import namedtuple
 import logging
 
-from reportengine.compat import yaml
+from ruamel.yaml import YAMLError
+
+from reportengine.utils import yaml_safe
 from reportengine.targets import FuzzyTarget
 
 log = logging.getLogger(__name__)
@@ -43,8 +45,8 @@ def parse_assignments(args):
             k = m.group(1)
             vstring = m.group(2)
             try:
-                v = yaml.safe_load(vstring)
-            except yaml.YamlError:
+                v = yaml_safe.load(vstring)
+            except YAMLError:
                 raise ValueError(f"Couldn't process assignment value '{vstring}'")
             res.append((k, v))
         else:

src/reportengine/templateparser.py

@@ -7,8 +7,8 @@
 import pytest
 
 from reportengine import app
+from reportengine.utils import yaml_safe
 from reportengine.tests.utils import tmp
-from reportengine.compat import yaml
 
 runcard =\
 """
@@ -58,7 +58,7 @@ def test_app_runs(tmp):
 
     #Test meta round trip
     with open(output_path/'meta.yaml') as f:
-        meta = yaml.safe_load(f)
+        meta = yaml_safe.load(f)
     assert meta['author'] == "Zahari Kassabov"
     assert meta['keywords'] == ["test", "debug"]
 

src/reportengine/tests/test_app.py

@@ -8,12 +8,12 @@
 from collections import OrderedDict
 import unittest
 
-from reportengine.compat import yaml
-from reportengine.utils import ChainMap
+from reportengine.utils import ChainMap, yaml_safe
 from reportengine import namespaces
 from reportengine.configparser import (Config, BadInputType, element_of,
                                        named_element_of, ConfigError)
 
+
 class BaseConfig(Config):
 
     @element_of('ys')
@@ -193,7 +193,7 @@ def test_rewrite_actions():
     c = BaseConfig(inp)
     r = c.parse_actions_(inp['actions_'])
     suggested_yaml = c._rewrite_old_actions(r)
-    newacts = yaml.safe_load(suggested_yaml)
+    newacts = yaml_safe.load(suggested_yaml)
     newr = c.parse_actions_(newacts['actions_'])
     assert newr == r
 

src/reportengine/tests/test_configparser.py

@@ -9,6 +9,10 @@
 import re
 import importlib.util
 import pathlib
+from ruamel.yaml import YAML
+
+yaml_rt = YAML(typ="rt")
+yaml_safe = YAML(typ="safe")
 
 #TODO: Support metaclass attributes?
 def get_classmembers(cls, *, predicate=None):