✨ Use ruaml.yaml parser for roundtrip support (#893)

* ✨ Replaced pyyaml with ruaml.yaml

* 👌 Set yaml repr for None to null, instead of missing value ('')

* 👌 Changed list element indentation to be consistent with current style

* 🧹 Sorted dependencies in requirements_dev.txt same as setup.cfg

This way it is easier to compare them and see discrepancies

glotaran/builtin/io/yml/test/test_save_model.py

@@ -10,48 +10,49 @@
     from pathlib import Path
 
 
-want = """dataset:
-  dataset1:
-    group: default
-    initial_concentration: j1
-    irf: irf1
-    megacomplex:
-    - m1
+want = """\
+default_megacomplex: decay
 dataset_groups:
   default:
-    link_clp: null
     residual_function: variable_projection
-default_megacomplex: decay
+    link_clp: null
+k_matrix:
+  k1:
+    matrix:
+      (s2, s1): kinetic.1
+      (s3, s2): kinetic.2
+      (s3, s3): kinetic.3
 initial_concentration:
   j1:
     compartments:
-    - s1
-    - s2
-    - s3
-    exclude_from_normalize: []
+      - s1
+      - s2
+      - s3
     parameters:
-    - j.1
-    - j.0
-    - j.0
+      - j.1
+      - j.0
+      - j.0
+    exclude_from_normalize: []
 irf:
   irf1:
-    backsweep: false
-    center: irf.center
-    normalize: true
     type: gaussian
+    center: irf.center
     width: irf.width
-k_matrix:
-  k1:
-    matrix:
-      (s2, s1): kinetic.1
-      (s3, s2): kinetic.2
-      (s3, s3): kinetic.3
+    normalize: true
+    backsweep: false
 megacomplex:
   m1:
+    type: decay
     dimension: time
     k_matrix:
-    - k1
-    type: decay
+      - k1
+dataset:
+  dataset1:
+    group: default
+    megacomplex:
+      - m1
+    initial_concentration: j1
+    irf: irf1
 """
 
 

glotaran/builtin/io/yml/test/test_save_scheme.py

@@ -18,18 +18,19 @@
     from pathlib import Path
 
 
-want = """add_svd: true
-clp_link_tolerance: 0.0
+want = """\
+model_file: m.yml
+parameters_file: p.csv
 data_files:
   dataset_1: d.nc
-ftol: 1.0e-08
-gtol: 1.0e-08
+clp_link_tolerance: 0.0
 maximum_number_function_evaluations: null
-model_file: m.yml
+add_svd: true
+ftol: 1e-08
+gtol: 1e-08
+xtol: 1e-08
 optimization_method: TrustRegionReflection
-parameters_file: p.csv
 result_path: null
-xtol: 1.0e-08
 """
 
 

glotaran/builtin/io/yml/yml.py

@@ -1,8 +1,9 @@
 from __future__ import annotations
 
 from pathlib import Path
+from typing import TYPE_CHECKING
 
-import yaml
+from ruamel.yaml import YAML
 
 from glotaran.deprecation.modules.builtin_io_yml import model_spec_deprecations
 from glotaran.deprecation.modules.builtin_io_yml import scheme_spec_deprecations
@@ -17,6 +18,13 @@
 from glotaran.project.dataclass_helpers import fromdict
 from glotaran.utils.sanitize import sanitize_yaml
 
+if TYPE_CHECKING:
+    from typing import Any
+    from typing import Mapping
+
+    from ruamel.yaml.nodes import ScalarNode
+    from ruamel.yaml.representer import BaseRepresenter
+
 
 @register_project_io(["yml", "yaml", "yml_str"])
 class YmlProjectIo(ProjectIoInterface):
@@ -137,14 +145,40 @@ def save_result(self, result: Result, result_path: str):
         _write_dict(result_path, result_dict)
 
     def _load_yml(self, file_name: str) -> dict:
+        yaml = YAML()
         if self.format == "yml_str":
-            spec = yaml.safe_load(file_name)
+            spec = yaml.load(file_name)
         else:
             with open(file_name) as f:
-                spec = yaml.safe_load(f)
+                spec = yaml.load(f)
         return spec
 
 
-def _write_dict(file_name: str, d: dict):
+def _write_dict(file_name: str, data: Mapping[str, Any]):
+    yaml = YAML()
+    yaml.representer.add_representer(type(None), _yaml_none_representer)
+    yaml.indent(mapping=2, sequence=2, offset=2)
     with open(file_name, "w") as f:
-        f.write(yaml.dump(d))
+        yaml.dump(data, f)
+
+
+def _yaml_none_representer(representer: BaseRepresenter, data: Mapping[str, Any]) -> ScalarNode:
+    """Yaml repr for ``None`` python values.
+
+    Parameters
+    ----------
+    representer : BaseRepresenter
+        Representer of the :class:`YAML` instance.
+    data : Mapping[str, Any]
+        Data to write to yaml.
+
+    Returns
+    -------
+    ScalarNode
+        Node representing the value.
+
+    References
+    ----------
+    https://stackoverflow.com/a/44314840
+    """
+    return representer.represent_scalar("tag:yaml.org,2002:null", "null")

requirements_dev.txt

@@ -4,19 +4,19 @@ wheel>=0.30.0
 
 # glotaran setup dependencies
 asteval==0.9.25
-numpy==1.20.3
-scipy==1.7.1
 click==8.0.3
-rich==10.12.0
+netCDF4==1.5.7
 numba==0.54.1
+numpy==1.20.3
 pandas==1.3.4
-pyyaml==6.0
-xarray==0.19.0
-netCDF4==1.5.7
-setuptools==41.2
+rich==10.12.0
+ruamel.yaml==0.17.17
+scipy==1.7.1
 sdtfile==2021.3.21
-typing_inspect==0.7.1
+setuptools==41.2
 tabulate==0.8.9
+typing_inspect==0.7.1
+xarray==0.19.0
 
 # documentation dependencies
 -r docs/requirements.txt

setup.cfg

@@ -38,8 +38,8 @@ install_requires =
     numba>=0.52
     numpy>=1.20.0,<1.21
     pandas>=0.25.2
-    pyyaml>=5.2
     rich>=10.9.0
+    ruamel.yaml>=0.17.17
     scipy>=1.3.2
     sdtfile>=2020.8.3
     setuptools>=41.2