paquo: fix double under env var confusion

Fix envvar override in a backwards compatible way.
Close #73.

README.md

@@ -59,7 +59,7 @@ paquo to use that version.
 # available at: /some/path/on/your/machine/QuPath-0.3.2
 #
 # use via environment variable:
-#   $ export PAQUO__QUPATH_DIR=/some/path/on/your/machine/QuPath-0.3.2
+#   $ export PAQUO_QUPATH_DIR=/some/path/on/your/machine/QuPath-0.3.2
 #
 # use via .paquo.toml config file:
 #   qupath_dir="/some/path/on/your/machine/QuPath-0.3.2"

docs/source/configuration.rst

@@ -50,35 +50,35 @@ Environment variables
 ---------------------
 
 All `paquo` settings can also be overridden by environment variables. Just prefix the particular
-setting with :code:`PAQUO__` (double underscore!) and set the environment variable to what you
+setting with :code:`PAQUO_` (single underscore!) and set the environment variable to what you
 want it to be.
 
-    PAQUO__QUPATH_DIR = :code:`""`
+    PAQUO_QUPATH_DIR = :code:`""`
         if set will skip search and try to use qupath from this folder
 
-    PAQUO__QUPATH_SEARCH_DIRS
+    PAQUO_QUPATH_SEARCH_DIRS
         defaults to all default installation locations for QuPath this can be set to the folders that will be
         searched for QuPath installations.
 
-    PAQUO__QUPATH_SEARCH_DIR_REGEX = :code:`"(?i)qupath.*"`
+    PAQUO_QUPATH_SEARCH_DIR_REGEX = :code:`"(?i)qupath.*"`
         used to regex match qupath_dirs during search
 
-    PAQUO__QUPATH_SEARCH_CONDA = :code:`true`
+    PAQUO_QUPATH_SEARCH_CONDA = :code:`true`
         should the conda installed QuPath be considered?
 
-    PAQUO__QUPATH_PREFER_CONDA = :code:`true`
+    PAQUO_QUPATH_PREFER_CONDA = :code:`true`
         should the conda installed QuPath be preferred over another locally installed QuPath
 
-    PAQUO__JAVA_OPTS = :code:`["-XX:MaxRAMPercentage=50",]`
+    PAQUO_JAVA_OPTS = :code:`["-XX:MaxRAMPercentage=50",]`
         a list of JVM options passed to the java virtual machine
 
-    PAQUO__MOCK_BACKEND = :code:`false`
+    PAQUO_MOCK_BACKEND = :code:`false`
         an internal setting which allows building the docs without having qupath installed
 
-    PAQUO__CLI_FORCE_LOG_LEVEL_ERROR = :code:`true`
+    PAQUO_CLI_FORCE_LOG_LEVEL_ERROR = :code:`true`
         only show paquo errors on cli
 
-    PAQUO__WARN_MICROSOFT_STORE_PYTHON = :code:`true`
+    PAQUO_WARN_MICROSOFT_STORE_PYTHON = :code:`true`
         windows only, warn if paquo is run via a microsoft store python
 
 

paquo/__main__.py

@@ -345,12 +345,12 @@ def _download_cb(it, name):
 
     print("#\n# use via environment variable:")
     if system in {"Linux", "Darwin"}:
-        print(f"#  $ export PAQUO__QUPATH_DIR={app}")
+        print(f"#  $ export PAQUO_QUPATH_DIR={app}")
     else:
         print("#  REM Windows CMD")
-        print(f'#  C:\\> set PAQUO__QUPATH_DIR="{app}"')
+        print(f'#  C:\\> set PAQUO_QUPATH_DIR="{app}"')
         print("#  # Windows PowerShell")
-        print(f'#  PS C:\\> $env:PAQUO__QUPATH_DIR="{app}"')
+        print(f'#  PS C:\\> $env:PAQUO_QUPATH_DIR="{app}"')
     print("#\n# use via .paquo.toml config file:")
     print(f'#  qupath_dir="{app}"')
     print(app)

paquo/_config.py

@@ -14,10 +14,31 @@
 
 PAQUO_CONFIG_FILENAME = '.paquo.toml'
 
+_PAQUO_FIX_CONFIG_KEYS = {
+    # recover prefixed keys due to dynaconf weirdness
+    "_qupath_dir",
+    "_qupath_search_dirs",
+    "_qupath_search_dir_regex",
+    "_qupath_search_conda",
+    "_qupath_prefer_conda",
+    "_java_opts",
+    "_safe_truncate",
+    "_mock_backend",
+    "_cli_force_log_level_error",
+    "_warn_microsoft_store_python",
+}
+
 
 def to_kwargs(s: "Settings | DynaBox") -> Dict[str, Any]:
     """convert dynaconf settings to lowercase"""
-    return {k.lower(): v for k, v in s.to_dict().items()}
+    dct = s.to_dict()
+    out = {}
+    for key, value in dct.items():
+        k = key.lower()
+        if k in _PAQUO_FIX_CONFIG_KEYS:
+            k = k[1:]
+        out[k] = value
+    return out
 
 
 def to_toml(s: Settings) -> str: