lint

docs/changelog.md

@@ -6,6 +6,7 @@
 - Added in ability to specify abstract targets, which don't show up in buildable lists, [issue 19](https://github.com/databio/markmeld/issues/19)
 - mm now raises an error if you try to inherit from an non-existing target, [issue 20](https://github.com/databio/markmeld/issues/20)
 - overriding targets is no longer allowed, [issue 22](https://github.com/databio/markmeld/issues/22)
+- Major revamps on data structures availalbe to jinja template
 
 ## [0.2.0] -- 2023-01-07
 

markmeld/cli.py

@@ -169,7 +169,7 @@ def main(test_args=None):
     if args.list:
         if "targets" not in cfg:
             raise TargetError(f"No targets specified in config.")
-        
+
         tarlist = {}
         for t, k in cfg["targets"].items():
             if "abstract" in cfg["targets"][t]:
@@ -189,6 +189,7 @@ def main(test_args=None):
 
     if args.template:
         from .melder import Target, load_template
+
         tgt = Target(mm.cfg, args.target)
         tpl = load_template(tgt.meta)
         _LOGGER.info("Template content:")
@@ -226,7 +227,9 @@ def report_result(built_target):
                 color_code = color_red
             else:
                 color_code = color_green
-            _LOGGER.info(f"{color_code}{item['status']}: {item['message']}{color_reset}")
+            _LOGGER.info(
+                f"{color_code}{item['status']}: {item['message']}{color_reset}"
+            )
 
         if built_target.returncode != 0:
             _LOGGER.error(f"{color_red}Building target failed.{color_reset}")

markmeld/melder.py

@@ -406,7 +406,9 @@ def build_target(self, target_name, print_only=False, vardump=False):
         @return [False|tgt] if the
         """
         tgt = Target(self.cfg, target_name)
-        _LOGGER.info(f"MM | Building target: {tgt.target_name} from file {tgt.meta['_cfg_file_path']}")
+        _LOGGER.info(
+            f"MM | Building target: {tgt.target_name} from file {tgt.meta['_cfg_file_path']}"
+        )
 
         # First, run any pre-builds
         prebuild_results = self.build_side_targets(tgt, "prebuild")
@@ -558,7 +560,9 @@ def render_template(self, melded_input, target, double=None):
         if "data" not in melded_input:
             melded_input["data"] = {}
         if "md_template" in target.meta:
-            raise Exception("Please update your config! 'md_template' was renamed to 'jinja_template'.")
+            raise Exception(
+                "Please update your config! 'md_template' was renamed to 'jinja_template'."
+            )
 
         if "jinja_template" in target.meta and target.meta["jinja_template"]:
             tpl = load_template(target.meta)

markmeld/utilities.py

@@ -13,6 +13,7 @@
 
 _LOGGER = getLogger(PKG_NAME)
 
+
 # define some useful functions
 def recursive_get(dat, indices):
     """
@@ -69,11 +70,13 @@ def format_command(tgt):
         vars_to_exp = [v[1] for v in string.Formatter().parse(cmd) if v[1] is not None]
     return cmd
 
+
 # There are two paths associated with each target:
-    # 1. the location of its definition (defpath or filepath)
-    # 2. the location of where it should be executed (workpath)
+# 1. the location of its definition (defpath or filepath)
+# 2. the location of where it should be executed (workpath)
 # These are not the same thing.
 
+
 def load_config_wrapper(cfg_path, workpath=None, autocomplete=True):
     """
     Wrapper function that maintains a list of imported files, to prevent duplicate imports.
@@ -101,7 +104,7 @@ def load_config_file(filepath, workpath=None, autocomplete=True, imported_list={
         return load_config_data(
             cfg_data, os.path.abspath(filepath), workpath, autocomplete, imported_list
         )
-    except FileNotFoundError as e:  
+    except FileNotFoundError as e:
         _LOGGER.error(f"Couldn't load config file: {filepath} because: {repr(e)}")
         return {}  # Allow continuing if file not found
     except Exception as e:
@@ -115,7 +118,9 @@ def make_abspath(relpath, filepath, root=None):
     return os.path.abspath(os.path.join(os.path.dirname(filepath), relpath))
 
 
-def load_config_data(cfg_data, filepath=None, workpath=None, autocomplete=True, imported_list={}):
+def load_config_data(
+    cfg_data, filepath=None, workpath=None, autocomplete=True, imported_list={}
+):
     """
     Recursive loader that parses a yaml string, handles imports, and runs target factories to create targets.
     """
@@ -138,7 +143,9 @@ def load_config_data(cfg_data, filepath=None, workpath=None, autocomplete=True,
     if "imports" in higher_cfg and higher_cfg["imports"]:
         _LOGGER.debug("Found imports")
         for import_file in higher_cfg["imports"]:
-            import_file_abspath = make_abspath(expandpath(import_file), expandpath(filepath))
+            import_file_abspath = make_abspath(
+                expandpath(import_file), expandpath(filepath)
+            )
             if not autocomplete:
                 _LOGGER.info(f"Specified config file to import: {import_file_abspath}")
             deep_update(
@@ -151,7 +158,9 @@ def load_config_data(cfg_data, filepath=None, workpath=None, autocomplete=True,
     if "imports_relative" in higher_cfg and higher_cfg["imports_relative"]:
         _LOGGER.debug("Found relative imports")
         for import_file in higher_cfg["imports_relative"]:
-            import_file_abspath = make_abspath(expandpath(import_file), expandpath(filepath))
+            import_file_abspath = make_abspath(
+                expandpath(import_file), expandpath(filepath)
+            )
             if not autocomplete:
                 _LOGGER.info(
                     f"Specified relative config file to import (relative): {import_file}"
@@ -192,9 +201,17 @@ def warn_overriding_target(old, new):
         for tgt in new["targets"]:
             if tgt in old["targets"]:
                 _LOGGER.error(f"Overriding target: {tgt}")
-                _LOGGER.error("Originally defined in: ".rjust(27, " ") + f"{old['targets'][tgt]['_defpath']}")
-                _LOGGER.error("Redefined in: ".rjust(27, " ") + f"{new['targets'][tgt]['_defpath']}")
-                raise Exception("Same target name is defined in imported file. Overriding targets is not allowed.")
+                _LOGGER.error(
+                    "Originally defined in: ".rjust(27, " ")
+                    + f"{old['targets'][tgt]['_defpath']}"
+                )
+                _LOGGER.error(
+                    "Redefined in: ".rjust(27, " ")
+                    + f"{new['targets'][tgt]['_defpath']}"
+                )
+                raise Exception(
+                    "Same target name is defined in imported file. Overriding targets is not allowed."
+                )
 
 
 def deep_update(old, new, warn_override=True):

tests/test_markmeld.py

@@ -147,7 +147,9 @@ def test_import():
     print(res.melded_output)
     assert "rVEeqUQ1t5" in str(res.melded_output)
 
-    cfg2 = markmeld.load_config_wrapper("tests/test_data/_markmeld_import_relative.yaml")
+    cfg2 = markmeld.load_config_wrapper(
+        "tests/test_data/_markmeld_import_relative.yaml"
+    )
     mm2 = markmeld.MarkdownMelder(cfg2)
 
     res = mm2.build_target("imported_target", print_only=True)