fix ruamel and pandas api

ctwrap/handler.py

@@ -60,11 +60,7 @@
 from multiprocessing import queues as mpq
 from multiprocessing import synchronize as mps
 import queue  # imported for using queue.Empty exception
-
-try:
-    import ruamel_yaml as yaml
-except ImportError:
-    from ruamel import yaml
+from ruamel.yaml import YAML
 
 # ctwrap specific import
 from .parser import _parse, _write, Parser
@@ -169,7 +165,8 @@ def from_yaml(cls, yaml_file: str,
                           "".format(yaml_file))
 
         with open(full_name) as stream:
-            content = yaml.load(stream, Loader=yaml.SafeLoader)
+            yaml = YAML(typ="safe")
+            content = yaml.load(stream)
 
         output = content.get('output', {})
 

ctwrap/output.py

@@ -14,15 +14,14 @@
 
 from typing import Dict, List, Any, Optional, Union
 
-import pkg_resources
+import importlib
 
 # avoid explicit dependence on cantera
-try:
-    pkg_resources.get_distribution('cantera')
-except pkg_resources.DistributionNotFound:
+ct_spec = importlib.util.find_spec("cantera")
+if ct_spec is None:
     ct = ImportError('Method requires a working cantera installation.')
 else:
-    import cantera as ct
+    ct = importlib.import_module("cantera")
 
 
 class Output:
@@ -236,7 +235,7 @@ def save(self, data, entry, variation=None, mode=None, errored=False):
                 df = pd.read_csv(fname)
             else:
                 df = pd.DataFrame(columns=row.keys())
-            df = df.append(row, ignore_index=True)
+            df = pd.concat([df, row.to_frame().T], ignore_index=True)
             df.to_csv(fname, index=False)
 
     def dir(self):
@@ -246,6 +245,7 @@ def dir(self):
             return []
 
         df = pd.read_csv(fname)
+        print("DEBUG dir df", df)
         return list(df.output)
 
     def load_like(self, entry, other):

ctwrap/parser.py

@@ -65,14 +65,10 @@
 from typing import Optional, Dict, Any, Tuple, KeysView, Generator, Union
 from copy import deepcopy
 from pint import UnitRegistry
+from ruamel.yaml import YAML
 import warnings
 import re
 
-try:
-    import ruamel_yaml as yaml
-except ImportError:
-    from ruamel import yaml
-
 
 __all__ = ['Parser']
 
@@ -253,12 +249,13 @@ def from_yaml(
         elif path is not None:
             fname = Path(path) / fname
 
+        yaml = YAML(typ="safe")
         try:
-            _ = fname.is_file() # will raise error
+            _ = fname.is_file()  # will raise error
             with open(fname) as stream:
-                out = yaml.load(stream, Loader=yaml.SafeLoader)
+                out = yaml.load(stream)
         except OSError:
-            out = yaml.load(yml, Loader=yaml.SafeLoader)
+            out = yaml.load(yml)
 
         if keys is None:
             return cls(out)
@@ -267,6 +264,7 @@ def from_yaml(
 
     def to_yaml(self):
         """Convert Parser content to YAML string"""
+        yaml = YAML(typ="safe")
         return yaml.dump(self.raw, Dumper=yaml.SafeDumper)
 
     def get(self, key, default=None):

environment.yml

@@ -9,8 +9,8 @@ dependencies:
   - numpy
   - h5py
   - pint
-  - ruamel.yaml
-  - pandas
+  - ruamel.yaml>=0.17.0
+  - pandas>=1.4
   - cantera
   - setuptools
   - pytest

tests/test_output.py

@@ -7,11 +7,7 @@
 import unittest
 from pathlib import Path
 import h5py
-
-try:
-    import ruamel_yaml as yaml
-except ImportError:
-    from ruamel import yaml
+from ruamel.yaml import YAML
 
 import warnings
 # add exception as pywintypes imports a deprecated module
@@ -21,15 +17,14 @@
 # pylint: disable=no-member
 import ctwrap.output as cwo
 
-import pkg_resources
+import importlib
 
 # avoid explicit dependence on cantera
-try:
-    pkg_resources.get_distribution('cantera')
-except pkg_resources.DistributionNotFound:
+ct_spec = importlib.util.find_spec("cantera")
+if ct_spec is None:
     ct = ImportError('Method requires a working cantera installation.')
 else:
-    import cantera as ct
+    ct = importlib.import_module("cantera")
 
 
 PWD = Path(__file__).parents[0]
@@ -46,7 +41,8 @@ class TestOutput(unittest.TestCase):
     @classmethod
     def setUpClass(cls):
         with open(EXAMPLES / cls._yaml) as stream:
-            cls._config = yaml.load(stream, Loader=yaml.SafeLoader)
+            yaml = YAML(typ='safe')
+            cls._config = yaml.load(stream)
 
         out = cls._config.get('output')
         if out:

tests/test_parser.py

@@ -5,12 +5,8 @@
 
 import unittest
 from pathlib import Path
-import pint.quantity as pq
-
-try:
-    import ruamel_yaml as yaml
-except ImportError:
-    from ruamel import yaml
+import pint as pq
+from ruamel.yaml import YAML
 
 import warnings
 # add exception as pywintypes imports a deprecated module
@@ -202,6 +198,7 @@ class TestYAML(unittest.TestCase):
     def test_minimal(self):
 
         with open(EXAMPLES / 'minimal.yaml') as stream:
+            yaml = YAML(typ='safe')
             defaults = yaml.load(stream, Loader=yaml.SafeLoader)
         p = cw.Parser.from_yaml('minimal.yaml', path=EXAMPLES)
         self.assertEqual(len(p), len(defaults))
@@ -216,6 +213,7 @@ def test_minimal(self):
     def test_ignition(self):
 
         with open(EXAMPLES / 'ignition.yaml') as stream:
+            yaml = YAML(typ='safe')
             yml = yaml.load(stream, Loader=yaml.SafeLoader)
         initial = cw.Parser(yml['defaults']['initial'])
         self.assertIsInstance(initial.T, pq.Quantity)

tests/test_strategy.py

@@ -5,12 +5,6 @@
 
 import unittest
 from pathlib import Path
-import pint.quantity as pq
-
-try:
-    import ruamel_yaml as yaml
-except ImportError:
-    from ruamel import yaml
 
 import warnings
 # add exception as pywintypes imports a deprecated module

tests/test_wrapper.py

@@ -6,14 +6,9 @@
 import unittest
 from pathlib import Path
 import subprocess
-import pint.quantity as pq
 import importlib
 import h5py
-
-try:
-    import ruamel_yaml as yaml
-except ImportError:
-    from ruamel import yaml
+from ruamel.yaml import YAML
 
 import warnings
 # add exception as pywintypes imports a deprecated module
@@ -54,7 +49,8 @@ class TestWrap(unittest.TestCase):
 
     def setUp(self):
         with open(EXAMPLES / self._yaml) as stream:
-            self.config = yaml.load(stream, Loader=yaml.SafeLoader)
+            yaml = YAML(typ='safe')
+            self.config = yaml.load(stream)
         self.sim = cw.Simulation.from_module(self._module)
         self.sh = cw.SimulationHandler.from_yaml(self._yaml, strategy=self._strategy, database=EXAMPLES)
 
@@ -247,7 +243,8 @@ class TestInvalid(TestWrap):
 
     def setUp(self):
         with open(EXAMPLES / self._yaml) as stream:
-            self.config = yaml.load(stream, Loader=yaml.SafeLoader)
+            yaml = YAML(typ='safe')
+            self.config = yaml.load(stream)
         self.sim = cw.Simulation.from_module(self._module)
         self.sh = cw.SimulationHandler.from_dict(self._dict)