From c99c7b4d842b844677673472b9aa2b13e4123aeb Mon Sep 17 00:00:00 2001
From: Nicola Soranzo <nicola.soranzo@earlham.ac.uk>
Date: Wed, 21 Mar 2018 02:51:53 +0000
Subject: [PATCH 1/2] Fix type of some options in config_schema.yml

Also:
- drop unused `nginx_x_archive_files_base` option, last use removed in
commit fe5983aafca1fae0b60ed16838799b58f4aca11c
- rebuild config samples and docs.
---
 config/galaxy.yml.sample                    | 15 ++--
 config/reports.yml.sample                   | 61 +++++++++++---
 config/tool_shed.yml.sample                 | 90 +++++++++++++++------
 doc/source/admin/galaxy_options.rst         | 38 +++------
 doc/source/admin/reports_options.rst        | 28 +++----
 lib/galaxy/config.py                        |  1 -
 lib/galaxy/webapps/galaxy/config_schema.yml | 34 +++-----
 7 files changed, 161 insertions(+), 106 deletions(-)

diff --git a/config/galaxy.yml.sample b/config/galaxy.yml.sample
index 17437bbd466..b6ec88c5865 100644
--- a/config/galaxy.yml.sample
+++ b/config/galaxy.yml.sample
@@ -752,12 +752,7 @@ galaxy:
   # Redirect.  This should be set to the path defined in the nginx
   # config as an internal redirect with access to Galaxy's data files
   # (see documentation linked above).
-  #nginx_x_accel_redirect_base: false
-
-  # nginx can make use of mod_zip to create zip files containing
-  # multiple library files.  If using X-Accel-Redirect, this can be the
-  # same value as that option.
-  #nginx_x_archive_files_base: false
+  #nginx_x_accel_redirect_base: null
 
   # If using compression in the upstream proxy server, use this option
   # to disable gzipping of library .tar.gz and .zip archives, since the
@@ -779,24 +774,24 @@ galaxy:
   # in detail in the documentation linked above.  The upload store is a
   # temporary directory in which files uploaded by the upload module
   # will be placed.
-  #nginx_upload_store: false
+  #nginx_upload_store: null
 
   # This value overrides the action set on the file upload form, e.g.
   # the web path where the nginx_upload_module has been configured to
   # intercept upload requests.
-  #nginx_upload_path: false
+  #nginx_upload_path: null
 
   # Galaxy can also use nginx_upload_module to receive files staged out
   # upon job completion by remote job runners (i.e. Pulsar) that
   # initiate staging operations on the remote end.  See the Galaxy nginx
   # documentation for the corresponding nginx configuration.
-  #nginx_upload_job_files_store: false
+  #nginx_upload_job_files_store: null
 
   # Galaxy can also use nginx_upload_module to receive files staged out
   # upon job completion by remote job runners (i.e. Pulsar) that
   # initiate staging operations on the remote end.  See the Galaxy nginx
   # documentation for the corresponding nginx configuration.
-  #nginx_upload_job_files_path: false
+  #nginx_upload_job_files_path: null
 
   # Have Galaxy manage dynamic proxy component for routing requests to
   # other services based on Galaxy's session cookie.  It will attempt to
diff --git a/config/reports.yml.sample b/config/reports.yml.sample
index 2fa53484616..438d9b14b46 100644
--- a/config/reports.yml.sample
+++ b/config/reports.yml.sample
@@ -2,20 +2,59 @@ uwsgi:
 
   # The address and port on which to listen.  By default, only listen to
   # localhost (reports will not be accessible over the network).  Use
-  # '0.0.0.0' to listen on all available network interfaces.
+  # ':9001' to listen on all available network interfaces.
   http: 127.0.0.1:9001
 
-  threads: 8
+  # Number of web server (worker) processes to fork after the
+  # application has loaded.
+  processes: 1
 
-  http-raw-body: True
+  # Number of threads for each web server process.
+  threads: 4
 
-  offload-threads: 8
+  # Number of threads for serving static content and handling internal
+  # routing requests.
+  offload-threads: 2
 
+  # Mapping to serve style content.
   static-map: /static/style=static/style/blue
+
+  # Mapping to serve the remainder of the static content.
   static-map: /static=static
 
+  # Enable the master process manager. Disabled by default for maximum
+  # compatibility with CTRL+C, but should be enabled for use with
+  # --daemon and/or production deployments.
+  master: false
+
+  # Path to the application's Python virtual environment.
+  virtualenv: .venv
+
+  # Path to the application's Python library.
+  pythonpath: lib
+
+  # The entry point which returns the web application (e.g. Galaxy,
+  # Reports, etc.) that you are loading.
   module: galaxy.webapps.reports.buildapp:uwsgi_app()
 
+  # Cause uWSGI to respect the traditional behavior of dying on SIGTERM
+  # (its default is to brutally reload workers)
+  die-on-term: true
+
+  # Cause uWSGI to gracefully reload workers and mules upon receipt of
+  # SIGINT (its default is to brutally kill workers)
+  hook-master-start: unix_signal:2 gracefully_kill_them_all
+
+  # Cause uWSGI to gracefully reload workers and mules upon receipt of
+  # SIGTERM (its default is to brutally kill workers)
+  hook-master-start: unix_signal:15 gracefully_kill_them_all
+
+  # Feature necessary for proper mule signal handling
+  py-call-osafterfork: true
+
+  # Ensure application threads will run if `threads` is unset.
+  enable-threads: true
+
 reports:
 
   # If running behind a proxy server and Galaxy is served from a
@@ -28,7 +67,7 @@ reports:
   # path as the prefix in the filter above.  This value becomes the
   # "path" attribute set in the cookie so the cookies from each instance
   # will not clobber each other.
-  #cookie_path: None
+  #cookie_path: null
 
   # Verbosity of console log messages.  Acceptable values can be found
   # here: https://docs.python.org/2/library/logging.html#logging-levels
@@ -38,7 +77,7 @@ reports:
   # Galaxy instances, so sqlite (and the default value below) is not
   # supported. An SQLAlchemy connection string should be used specify an
   # external database.
-  #database_connection: sqlite:///./database/universe.sqlite?isolation_level=IMMEDIATE
+  #database_connection: 'sqlite:///./database/universe.sqlite?isolation_level=IMMEDIATE'
 
   # Where dataset files are saved Temporary storage for additional
   # datasets, this should be shared through the cluster
@@ -53,20 +92,20 @@ reports:
   #template_cache_path: database/compiled_templates/reports
 
   # Configuration for debugging middleware
-  #debug: False
+  #debug: false
 
   # Check for WSGI compliance.
-  #use_lint: False
+  #use_lint: false
 
   # NEVER enable this on a public site (even test or QA)
-  #use_interactive: True
+  #use_interactive: true
 
   # Write thread status periodically to 'heartbeat.log' (careful, uses
   # disk space rapidly!)
-  #use_heartbeat: True
+  #use_heartbeat: true
 
   # Profiling middleware (cProfile based)
-  #use_profile: True
+  #use_profile: true
 
   # Mail
   #smtp_server: yourserver@yourfacility.edu
diff --git a/config/tool_shed.yml.sample b/config/tool_shed.yml.sample
index c76956580ef..78f9a466812 100644
--- a/config/tool_shed.yml.sample
+++ b/config/tool_shed.yml.sample
@@ -2,20 +2,59 @@ uwsgi:
 
   # The address and port on which to listen.  By default, only listen to
   # localhost (tool_shed will not be accessible over the network).  Use
-  # '0.0.0.0' to listen on all available network interfaces.
+  # ':9009' to listen on all available network interfaces.
   http: 127.0.0.1:9009
 
-  threads: 8
+  # Number of web server (worker) processes to fork after the
+  # application has loaded.
+  processes: 1
 
-  http-raw-body: True
+  # Number of threads for each web server process.
+  threads: 4
 
-  offload-threads: 8
+  # Number of threads for serving static content and handling internal
+  # routing requests.
+  offload-threads: 2
 
+  # Mapping to serve style content.
   static-map: /static/style=static/style/blue
+
+  # Mapping to serve the remainder of the static content.
   static-map: /static=static
 
+  # Enable the master process manager. Disabled by default for maximum
+  # compatibility with CTRL+C, but should be enabled for use with
+  # --daemon and/or production deployments.
+  master: false
+
+  # Path to the application's Python virtual environment.
+  virtualenv: .venv
+
+  # Path to the application's Python library.
+  pythonpath: lib
+
+  # The entry point which returns the web application (e.g. Galaxy,
+  # Reports, etc.) that you are loading.
   module: galaxy.webapps.tool_shed.buildapp:uwsgi_app()
 
+  # Cause uWSGI to respect the traditional behavior of dying on SIGTERM
+  # (its default is to brutally reload workers)
+  die-on-term: true
+
+  # Cause uWSGI to gracefully reload workers and mules upon receipt of
+  # SIGINT (its default is to brutally kill workers)
+  hook-master-start: unix_signal:2 gracefully_kill_them_all
+
+  # Cause uWSGI to gracefully reload workers and mules upon receipt of
+  # SIGTERM (its default is to brutally kill workers)
+  hook-master-start: unix_signal:15 gracefully_kill_them_all
+
+  # Feature necessary for proper mule signal handling
+  py-call-osafterfork: true
+
+  # Ensure application threads will run if `threads` is unset.
+  enable-threads: true
+
 tool_shed:
 
   # Verbosity of console log messages.  Acceptable values can be found
@@ -27,11 +66,11 @@ tool_shed:
   # string to specify an external database instead.  This string takes
   # many options which are explained in detail in the config file
   # documentation.
-  #database_connection: sqlite:///./database/community.sqlite?isolation_level=IMMEDIATE
+  #database_connection: 'sqlite:///./database/community.sqlite?isolation_level=IMMEDIATE'
 
   # Where the hgweb.config file is stored. The default is the Galaxy
   # installation directory.
-  #hgweb_config_dir: None
+  #hgweb_config_dir: null
 
   # Where tool shed repositories are stored.
   #file_path: database/community_files
@@ -57,7 +96,7 @@ tool_shed:
   # allow full text API searching over the repositories and tools within
   # the Tool Shed given that you specify the following two config
   # options.
-  #toolshed_search_on: True
+  #toolshed_search_on: true
 
   # -- Repository and Tool search Using the script located at
   # scripts/build_ts_whoosh_index.py you can generate search index and
@@ -98,7 +137,7 @@ tool_shed:
 
   # You can enter tracking code here to track visitor's behavior through
   # your Google Analytics account. Example: UA-XXXXXXXX-Y
-  #ga_code: None
+  #ga_code: null
 
   # The Tool Shed encodes various internal values when these values will
   # be output in some format (for example, in a URL or cookie).  You
@@ -115,7 +154,7 @@ tool_shed:
   # header in the request. Enabling remote user disables regular logins.
   # For more information, see:
   # https://wiki.galaxyproject.org/Admin/Config/ApacheProxy
-  #use_remote_user: False
+  #use_remote_user: false
 
   # If use_remote_user is enabled, anyone who can log in to the Galaxy
   # host may impersonate any other user by simply sending the
@@ -126,22 +165,25 @@ tool_shed:
   #remote_user_secret: changethisinproductiontoo
 
   # Configuration for debugging middleware
-  #debug: False
+  #debug: false
 
   # Check for WSGI compliance.
-  #use_lint: False
+  #use_lint: false
+
+  # Intercept print statements and show them on the returned page.
+  #use_printdebug: true
 
   # NEVER enable this on a public site (even test or QA)
-  #use_interactive: True
+  #use_interactive: true
 
   # Administrative users - set this to a comma-separated list of valid
   # Tool Shed users (email addresses).  These users will have access to
   # the Admin section of the server, and will have access to create
   # users, groups, roles, libraries, and more.
-  #admin_users: None
+  #admin_users: null
 
   # Force everyone to log in (disable anonymous access)
-  #require_login: False
+  #require_login: false
 
   # For use by email messages sent from the tool shed
   #smtp_server: smtp.your_tool_shed_server
@@ -152,44 +194,44 @@ tool_shed:
   # If your SMTP server requires a username and password, you can
   # provide them here (password in cleartext here, but if your server
   # supports STARTTLS it will be sent over the network encrypted).
-  #smtp_username: None
+  #smtp_username: null
 
   # If your SMTP server requires a username and password, you can
   # provide them here (password in cleartext here, but if your server
   # supports STARTTLS it will be sent over the network encrypted).
-  #smtp_password: None
+  #smtp_password: null
 
   # If your SMTP server requires SSL from the beginning of the
   # connection
-  #smtp_ssl: False
+  #smtp_ssl: false
 
   # The URL linked by the "Support" link in the "Help" menu.
-  #support_url: https://wiki.galaxyproject.org/Support
+  #support_url: 'https://wiki.galaxyproject.org/Support'
 
   # Address to join mailing list
   #mailing_join_addr: galaxy-announce-join@bx.psu.edu
 
   # Write thread status periodically to 'heartbeat.log' (careful, uses
   # disk  space rapidly!)
-  #use_heartbeat: True
+  #use_heartbeat: true
 
   # Profiling middleware (cProfile based)
-  #use_profile: True
+  #use_profile: true
 
   # Enable creation of Galaxy flavor Docker Image
-  #enable_galaxy_flavor_docker_image: False
+  #enable_galaxy_flavor_docker_image: false
 
   # Show a message box under the masthead.
-  #message_box_visible: False
+  #message_box_visible: false
 
   # Show a message box under the masthead.
-  #message_box_content: None
+  #message_box_content: null
 
   # Show a message box under the masthead.
   #message_box_class: info
 
   # Serving static files (needed if running standalone)
-  #static_enabled: True
+  #static_enabled: true
 
   # Serving static files (needed if running standalone)
   #static_cache_time: 360
diff --git a/doc/source/admin/galaxy_options.rst b/doc/source/admin/galaxy_options.rst
index 6275dd5a5e0..d518ce4c2da 100644
--- a/doc/source/admin/galaxy_options.rst
+++ b/doc/source/admin/galaxy_options.rst
@@ -71,7 +71,7 @@
     gone away", you will want to set this to some positive value (7200
     should work).
 :Default: ``-1``
-:Type: str
+:Type: int
 
 
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
@@ -429,7 +429,7 @@
     scheme that may work in wider range of scenarios than the watchdog
     default.
 :Default: ``false``
-:Type: bool
+:Type: str
 
 
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
@@ -594,7 +594,7 @@
     which will use a less efficient monitoring scheme that may work in
     wider range of scenarios than the watchdog default.
 :Default: ``false``
-:Type: bool
+:Type: str
 
 
 ~~~~~~~~~~~~~~~~~~~~
@@ -1517,20 +1517,8 @@
     Redirect.  This should be set to the path defined in the nginx
     config as an internal redirect with access to Galaxy's data files
     (see documentation linked above).
-:Default: ``false``
-:Type: bool
-
-
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-``nginx_x_archive_files_base``
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-
-:Description:
-    nginx can make use of mod_zip to create zip files containing
-    multiple library files.  If using X-Accel-Redirect, this can be
-    the same value as that option.
-:Default: ``false``
-:Type: bool
+:Default: ``None``
+:Type: str
 
 
 ~~~~~~~~~~~~~~~~~
@@ -1572,8 +1560,8 @@
     explained in detail in the documentation linked above.  The upload
     store is a temporary directory in which files uploaded by the
     upload module will be placed.
-:Default: ``false``
-:Type: bool
+:Default: ``None``
+:Type: str
 
 
 ~~~~~~~~~~~~~~~~~~~~~
@@ -1584,8 +1572,8 @@
     This value overrides the action set on the file upload form, e.g.
     the web path where the nginx_upload_module has been configured to
     intercept upload requests.
-:Default: ``false``
-:Type: bool
+:Default: ``None``
+:Type: str
 
 
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
@@ -1597,8 +1585,8 @@
     out upon job completion by remote job runners (i.e. Pulsar) that
     initiate staging operations on the remote end.  See the Galaxy
     nginx documentation for the corresponding nginx configuration.
-:Default: ``false``
-:Type: bool
+:Default: ``None``
+:Type: str
 
 
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
@@ -1610,8 +1598,8 @@
     out upon job completion by remote job runners (i.e. Pulsar) that
     initiate staging operations on the remote end.  See the Galaxy
     nginx documentation for the corresponding nginx configuration.
-:Default: ``false``
-:Type: bool
+:Default: ``None``
+:Type: str
 
 
 ~~~~~~~~~~~~~~~~~~~~~~~~
diff --git a/doc/source/admin/reports_options.rst b/doc/source/admin/reports_options.rst
index 90557f7c844..a2fd8882cfb 100644
--- a/doc/source/admin/reports_options.rst
+++ b/doc/source/admin/reports_options.rst
@@ -6,7 +6,7 @@
     If running behind a proxy server and Galaxy is served from a
     subdirectory, enable the proxy-prefix filter and set the prefix in
     the [filter:proxy-prefix] section above.
-:Default: proxy-prefix
+:Default: ``proxy-prefix``
 :Type: str
 
 
@@ -20,7 +20,7 @@
     same path as the prefix in the filter above.  This value becomes
     the "path" attribute set in the cookie so the cookies from each
     instance will not clobber each other.
-:Default: None
+:Default: ``None``
 :Type: str
 
 
@@ -32,7 +32,7 @@
     Verbosity of console log messages.  Acceptable values can be found
     here: https://docs.python.org/2/library/logging.html#logging-
     levels
-:Default: DEBUG
+:Default: ``DEBUG``
 :Type: str
 
 
@@ -45,7 +45,7 @@
     Galaxy instances, so sqlite (and the default value below) is not
     supported. An SQLAlchemy connection string should be used specify
     an external database.
-:Default: sqlite:///./database/universe.sqlite?isolation_level=IMMEDIATE
+:Default: ``sqlite:///./database/universe.sqlite?isolation_level=IMMEDIATE``
 :Type: str
 
 
@@ -56,7 +56,7 @@
 :Description:
     Where dataset files are saved Temporary storage for additional
     datasets, this should be shared through the cluster
-:Default: database/files
+:Default: ``database/files``
 :Type: str
 
 
@@ -67,7 +67,7 @@
 :Description:
     Where dataset files are saved Temporary storage for additional
     datasets, this should be shared through the cluster
-:Default: database/tmp
+:Default: ``database/tmp``
 :Type: str
 
 
@@ -78,7 +78,7 @@
 :Description:
     Mako templates are compiled as needed and cached for reuse, this
     directory is used for the cache
-:Default: database/compiled_templates/reports
+:Default: ``database/compiled_templates/reports``
 :Type: str
 
 
@@ -88,7 +88,7 @@
 
 :Description:
     Configuration for debugging middleware
-:Default: False
+:Default: ``false``
 :Type: bool
 
 
@@ -98,7 +98,7 @@
 
 :Description:
     Check for WSGI compliance.
-:Default: False
+:Default: ``false``
 :Type: bool
 
 
@@ -108,7 +108,7 @@
 
 :Description:
     NEVER enable this on a public site (even test or QA)
-:Default: True
+:Default: ``true``
 :Type: bool
 
 
@@ -119,7 +119,7 @@
 :Description:
     Write thread status periodically to 'heartbeat.log' (careful, uses
     disk space rapidly!)
-:Default: True
+:Default: ``true``
 :Type: bool
 
 
@@ -129,7 +129,7 @@
 
 :Description:
     Profiling middleware (cProfile based)
-:Default: True
+:Default: ``true``
 :Type: bool
 
 
@@ -139,7 +139,7 @@
 
 :Description:
     Mail
-:Default: yourserver@yourfacility.edu
+:Default: ``yourserver@yourfacility.edu``
 :Type: str
 
 
@@ -149,7 +149,7 @@
 
 :Description:
     Mail
-:Default: your_bugs@bx.psu.edu
+:Default: ``your_bugs@bx.psu.edu``
 :Type: str
 
 
diff --git a/lib/galaxy/config.py b/lib/galaxy/config.py
index ed4ebc1c7c1..b2e3e5893fa 100644
--- a/lib/galaxy/config.py
+++ b/lib/galaxy/config.py
@@ -498,7 +498,6 @@ class Configuration(object):
         self.upstream_gzip = string_as_bool(kwargs.get('upstream_gzip', False))
         self.apache_xsendfile = string_as_bool(kwargs.get('apache_xsendfile', False))
         self.nginx_x_accel_redirect_base = kwargs.get('nginx_x_accel_redirect_base', False)
-        self.nginx_x_archive_files_base = kwargs.get('nginx_x_archive_files_base', False)
         self.nginx_upload_store = kwargs.get('nginx_upload_store', False)
         self.nginx_upload_path = kwargs.get('nginx_upload_path', False)
         self.nginx_upload_job_files_store = kwargs.get('nginx_upload_job_files_store', False)
diff --git a/lib/galaxy/webapps/galaxy/config_schema.yml b/lib/galaxy/webapps/galaxy/config_schema.yml
index e858a5cb1d9..edb3fd1720f 100644
--- a/lib/galaxy/webapps/galaxy/config_schema.yml
+++ b/lib/galaxy/webapps/galaxy/config_schema.yml
@@ -82,7 +82,7 @@ mapping:
           processes.
 
       database_engine_option_pool_recycle:
-        type: str
+        type: int
         default: -1
         required: false
         desc: |
@@ -331,7 +331,7 @@ mapping:
           install from in the admin interface (.sample used if default does not exist).
 
       watch_tools:
-        type: bool
+        type: str
         default: false
         required: false
         desc: |
@@ -454,7 +454,7 @@ mapping:
           when installed from a ToolShed. Defaults to tool_data_path.
 
       watch_tool_data_dir:
-        type: bool
+        type: str
         default: false
         required: false
         desc: |
@@ -1139,22 +1139,14 @@ mapping:
           this to True to inform Galaxy that mod_xsendfile is enabled upstream.
 
       nginx_x_accel_redirect_base:
-        type: bool
-        default: false
+        type: str
+        default: null
         required: false
         desc: |
           The same download handling can be done by nginx using X-Accel-Redirect.  This
           should be set to the path defined in the nginx config as an internal redirect
           with access to Galaxy's data files (see documentation linked above).
 
-      nginx_x_archive_files_base:
-        type: bool
-        default: false
-        required: false
-        desc: |
-          nginx can make use of mod_zip to create zip files containing multiple library
-          files.  If using X-Accel-Redirect, this can be the same value as that option.
-
       upstream_gzip:
         type: bool
         default: false
@@ -1179,8 +1171,8 @@ mapping:
           `X-Frame-Options` header.
 
       nginx_upload_store:
-        type: bool
-        default: false
+        type: str
+        default: null
         required: false
         desc: |
           nginx can also handle file uploads (user-to-Galaxy) via nginx_upload_module.
@@ -1189,8 +1181,8 @@ mapping:
           which files uploaded by the upload module will be placed.
 
       nginx_upload_path:
-        type: bool
-        default: false
+        type: str
+        default: null
         required: false
         desc: |
           This value overrides the action set on the file upload form, e.g. the web
@@ -1198,8 +1190,8 @@ mapping:
           requests.
 
       nginx_upload_job_files_store:
-        type: bool
-        default: false
+        type: str
+        default: null
         required: false
         desc: |
           Galaxy can also use nginx_upload_module to receive files staged out upon job
@@ -1208,8 +1200,8 @@ mapping:
           corresponding nginx configuration.
 
       nginx_upload_job_files_path:
-        type: bool
-        default: false
+        type: str
+        default: null
         required: false
         desc: |
           Galaxy can also use nginx_upload_module to receive files staged out upon job

From 80ac55b3ff132cf6e1778b99cb6ffb01bec9cfe8 Mon Sep 17 00:00:00 2001
From: Nicola Soranzo <nicola.soranzo@earlham.ac.uk>
Date: Wed, 21 Mar 2018 03:01:57 +0000
Subject: [PATCH 2/2] Don't quote ints in .ini to .yml config conversion

---
 lib/galaxy/webapps/config_manage.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/lib/galaxy/webapps/config_manage.py b/lib/galaxy/webapps/config_manage.py
index 714d4628544..44ae449e910 100644
--- a/lib/galaxy/webapps/config_manage.py
+++ b/lib/galaxy/webapps/config_manage.py
@@ -751,10 +751,11 @@ def _parse_option_value(option_value):
     if isinstance(option_value, OptionValue):
         option = option_value.option
         value = option_value.value
-        option = option_value.option
         # Hack to get nicer YAML values during conversion
         if option.get("type", "str") == "bool":
             value = str(value).lower() == "true"
+        elif option.get("type", "str") == "int":
+            value = int(value)
     else:
         value = option_value
         option = OPTION_DEFAULTS