Added env vars using {<varname>[:default]} syntax (#48)

flowmancer/jobdefinition/file.py

@@ -1,14 +1,35 @@
+import os
+import re
+from typing import Any, Callable, Pattern
+
 import yaml
-from pyaml_env import parse_config
 
 from . import JobDefinition, SerializableJobDefinition, job_definition
 
+_env_var_matcher = re.compile(r'\$ENV{([^}^{]+)}')
+_env_tag_matcher = re.compile(r'[^$]*\$ENV{([^}^{]+)}.*')
+
+# TODO: parameters file
+# _param_var_matcher = re.compile(r'\$PARAM{([^}^{]+)}')
+# _param_tag_matcher = re.compile(r'[^$]*\$PARAM{([^}^{]+)}.*')
+
+
+def _build_constructor(var_matcher: Pattern[str]) -> Callable[[Any, Any], str]:
+    def _path_constructor(_: Any, node: Any) -> str:
+        def replace_fn(match):
+            parts = f"{match.group(1)}:".split(":")
+            return os.environ.get(parts[0], parts[1])
+        return var_matcher.sub(replace_fn, node.value)
+    return _path_constructor
+
 
 @job_definition('yaml')
 class YAMLJobDefinition(SerializableJobDefinition):
     def load(self, filename: str) -> JobDefinition:
-        j = parse_config(filename)
-        return JobDefinition(**j)
+        yaml.add_implicit_resolver("!envvar", _env_tag_matcher, None, yaml.SafeLoader)
+        yaml.add_constructor("!envvar", _build_constructor(_env_var_matcher), yaml.SafeLoader)
+        with open(filename, 'r') as f:
+            return JobDefinition(**yaml.safe_load(f.read()))
 
     def dump(self, jdef: JobDefinition, filename: str) -> None:
         with open(filename, 'r') as f:

pyproject.toml

@@ -9,11 +9,11 @@ readme = "README.md"
 [tool.poetry.dependencies]
 python = '^3.7'
 PyYAML = '^6.0.1'
-pyaml-env = '^1.2.1'
 pydantic = '^1.9.0'
 rich = '^12.0.0'
 urllib3 = "1.26.18"
 requests = "^2.31.0"
+types-pyyaml = "^6.0.12.12"
 
 [tool.poetry.group.dev.dependencies]
 black = '^22.1.0'