Merge pull request #640 from malariagen/GH597_hide_progress_via_env_var

Use optional env var for show_progress in Ag3, Af1

Author: leehart

malariagen_data/af1.py

@@ -40,7 +40,7 @@ class Af1(AnophelesDataResource):
     debug : bool, optional
         Set to True to enable debug level logging.
     show_progress : bool, optional
-        If True, show a progress bar during longer-running computations.
+        If True, show a progress bar during longer-running computations. The default can be overridden using an environmental variable named MGEN_SHOW_PROGRESS.
     check_location : bool, optional
         If True, use ipinfo to check the location of the client system.
     **kwargs
@@ -82,7 +82,7 @@ def __init__(
         results_cache=None,
         log=sys.stdout,
         debug=False,
-        show_progress=True,
+        show_progress=None,
         check_location=True,
         cohorts_analysis=None,
         site_filters_analysis=None,

malariagen_data/ag3.py

@@ -112,7 +112,7 @@ class Ag3(AnophelesDataResource):
     debug : bool, optional
         Set to True to enable debug level logging.
     show_progress : bool, optional
-        If True, show a progress bar during longer-running computations.
+        If True, show a progress bar during longer-running computations. The default can be overridden using an environmental variable named MGEN_SHOW_PROGRESS.
     check_location : bool, optional
         If True, use ipinfo to check the location of the client system.
     **kwargs
@@ -154,7 +154,7 @@ def __init__(
         results_cache=None,
         log=sys.stdout,
         debug=False,
-        show_progress=True,
+        show_progress=None,
         check_location=True,
         cohorts_analysis=None,
         aim_analysis=None,

malariagen_data/anoph/base.py

@@ -1,3 +1,5 @@
+import os
+
 import json
 from contextlib import nullcontext
 from datetime import date
@@ -54,12 +56,24 @@ def __init__(
         bokeh_output_notebook: bool = False,
         log: Optional[Union[str, IO]] = None,
         debug: bool = False,
-        show_progress: bool = False,
+        show_progress: Optional[bool] = None,
         check_location: bool = False,
         storage_options: Optional[Mapping] = None,
         results_cache: Optional[str] = None,
         tqdm_class=None,
     ):
+        # If show_progress has not been specified, then determine the default.
+        if show_progress is None:
+            # Get the env var, if it exists.
+            show_progress_env = os.getenv("MGEN_SHOW_PROGRESS")
+
+            # If the env var does not exist, then use the class default.
+            # Otherwise, convert the env var value to a boolean and use that.
+            if show_progress_env is None:
+                show_progress = True
+            else:
+                show_progress = show_progress_env.lower() in ("true", "1", "yes", "on")
+
         self._config_path = config_path
         self._pre = pre
         self._gcs_default_url = gcs_default_url