From 81d282e1d7623724e456fac79e68f28ed8e84390 Mon Sep 17 00:00:00 2001
From: Vince Reuter <vince.reuter@gmail.com>
Date: Tue, 26 Mar 2019 13:38:40 -0400
Subject: [PATCH 01/19] update version, reqs, and changelog

---
 divvy/_version.py                 | 2 +-
 docs/changelog.md                 | 5 +++++
 requirements/requirements-all.txt | 3 +--
 3 files changed, 7 insertions(+), 3 deletions(-)

diff --git a/divvy/_version.py b/divvy/_version.py
index 2995a62..b61d113 100644
--- a/divvy/_version.py
+++ b/divvy/_version.py
@@ -1,2 +1,2 @@
-__version__ = "0.2.1"
+__version__ = "0.3dev"
 
diff --git a/docs/changelog.md b/docs/changelog.md
index 582b337..5b67aab 100644
--- a/docs/changelog.md
+++ b/docs/changelog.md
@@ -1,5 +1,10 @@
 # Changelog
 
+## [Unreleased]
+
+### Changed
+- Safer use of `yaml`
+
 ## divvy [0.2.1] - 2019-03-19
 
 ### Changed
diff --git a/requirements/requirements-all.txt b/requirements/requirements-all.txt
index 071a003..84bc55b 100644
--- a/requirements/requirements-all.txt
+++ b/requirements/requirements-all.txt
@@ -1,5 +1,4 @@
 pandas>=0.20.2
-pyyaml>=3.12
-nbsphinx
+pyyaml>=5.1
 attmap>=0.4
 

From 54f817aa7db640353e4b6a8ee8480731a4c1ee36 Mon Sep 17 00:00:00 2001
From: Vince Reuter <vince.reuter@gmail.com>
Date: Tue, 26 Mar 2019 13:40:57 -0400
Subject: [PATCH 02/19] add yaml loaders

---
 divvy/compute.py | 9 ++++++---
 1 file changed, 6 insertions(+), 3 deletions(-)

diff --git a/divvy/compute.py b/divvy/compute.py
index 8009451..6b2a0ea 100644
--- a/divvy/compute.py
+++ b/divvy/compute.py
@@ -3,8 +3,9 @@
 import argparse
 import logging
 import os
-from sys import stdout
+import sys
 import yaml
+from yaml import SafeLoader
 
 from attmap import PathExAttMap
 from .const import \
@@ -220,7 +221,7 @@ def update_packages(self, config_file):
         """
         with open(config_file, 'r') as f:
             _LOGGER.info("Loading divvy config file: %s", config_file)
-            env_settings = yaml.load(f)
+            env_settings = yaml.load(f, SafeLoader)
             _LOGGER.debug("Parsed environment settings: %s",
                           str(env_settings))
 
@@ -289,6 +290,7 @@ def format_help(self):
         return "version: {}\n".format(__version__) + \
                super(_VersionInHelpParser, self).format_help()
 
+
 def main():
     """ Primary workflow """
 
@@ -330,11 +332,12 @@ def main():
     if args.settings:
         with open(args.settings, 'r') as f:
             _LOGGER.info("Loading yaml settings file: %s", args.settings)
-            yaml_vars = yaml.load(f)
+            yaml_vars = yaml.load(f, SafeLoader)
         dcc.write_script(args.outfile, [custom_vars, yaml_vars])
     else:
         dcc.write_script(args.outfile, custom_vars)
 
+
 if __name__ == '__main__':
     try:
         sys.exit(main())

From c57da97f885c7fc544c9ec9ec2df7ea0551db3a0 Mon Sep 17 00:00:00 2001
From: nsheff <nsheff@users.noreply.github.com>
Date: Wed, 10 Apr 2019 12:08:52 -0400
Subject: [PATCH 03/19] Add divvy list and divvy write subcommands

---
 divvy/compute.py  | 27 ++++++++++++++++++++-------
 docs/changelog.md |  3 ++-
 2 files changed, 22 insertions(+), 8 deletions(-)

diff --git a/divvy/compute.py b/divvy/compute.py
index 6b2a0ea..80eaddd 100644
--- a/divvy/compute.py
+++ b/divvy/compute.py
@@ -128,6 +128,7 @@ def templates_folder(self):
         """
         return os.path.join(os.path.dirname(__file__), "submit_templates")
 
+
     def activate_package(self, package_name):
         """
         Activates a compute package.
@@ -228,7 +229,7 @@ def update_packages(self, config_file):
             # Any compute.submission_template variables should be made
             # absolute, relative to current divvy configuration file.
             if "compute" in env_settings:
-                _LOGGER.warning("In your divvy config file, please use 'compute_packages' instead of 'compute'")
+                _LOGGER.warning("DEPRECATION WARNING: Divvy compute configuration 'compute' section changed to 'compute_packages'")
                 env_settings["compute_packages"] = env_settings["compute"]
 
             loaded_packages = env_settings["compute_packages"]
@@ -245,7 +246,7 @@ def update_packages(self, config_file):
                 self.compute_packages = PathExAttMap(loaded_packages)
             else:
                 self.compute_packages.add_entries(loaded_packages)
-        _LOGGER.info("Available packages: {}".format(', '.join(self.list_compute_packages())))
+        _LOGGER.debug("Available divvy packages: {}".format(', '.join(self.list_compute_packages())))
         self.config_file = config_file
 
     def write_script(self, output_path, extra_vars=None):
@@ -294,7 +295,7 @@ def format_help(self):
 def main():
     """ Primary workflow """
 
-    banner = "%(prog)s - write compute jobs that can be submitted to any computing resource"
+    banner = "%(prog)s - write compute job scripts that can be submitted to any computing resource"
     additional_description = "\nhttps://github.com/pepkit/divvy"
 
     parser = _VersionInHelpParser(
@@ -310,24 +311,36 @@ def main():
             "-C", "--config",
             help="Divvy configuration file.")
 
-    parser.add_argument(
+    subparsers = parser.add_subparsers(dest="command") 
+    list_subparser = subparsers.add_parser("list", description="Lists available packages",
+        help="Run 'divvy list' to list available packages")
+
+    write_subparser = subparsers.add_parser("write", description="write compute job script",
+        help="write compute job script")
+
+    write_subparser.add_argument(
             "-S", "--settings",
             help="YAML file with job settings to populate the template.")    
 
-    parser.add_argument(
+    write_subparser.add_argument(
             "-P", "--package", default="default",
             help="Compute package")
 
-    parser.add_argument(
+    write_subparser.add_argument(
             "-O", "--outfile", required=True,
             help="Output filepath")
 
 
     args, remaining_args = parser.parse_known_args()
-
     keys = [str.replace(x, "--", "") for x in remaining_args[::2]]
     custom_vars = dict(zip(keys, remaining_args[1::2]))
     dcc = ComputingConfiguration(args.config)
+
+
+    if args.command == "list":
+        _LOGGER.info("Available compute packages: {}".format(', '.join(dcc.list_compute_packages())))
+        sys.exit(1)
+
     dcc.activate_package(args.package)
     if args.settings:
         with open(args.settings, 'r') as f:
diff --git a/docs/changelog.md b/docs/changelog.md
index 5b67aab..ef5e64d 100644
--- a/docs/changelog.md
+++ b/docs/changelog.md
@@ -1,9 +1,10 @@
 # Changelog
 
-## [Unreleased]
+## divvy [0.3] - Unreleased
 
 ### Changed
 - Safer use of `yaml`
+- Reduced verbosity for clearly usage
 
 ## divvy [0.2.1] - 2019-03-19
 

From 6aafd1fbcedc2439ea7222431658aa775761ec63 Mon Sep 17 00:00:00 2001
From: nsheff <nsheff@users.noreply.github.com>
Date: Wed, 10 Apr 2019 12:16:25 -0400
Subject: [PATCH 04/19] cleanup, add docs for new cli API

---
 divvy/compute.py       | 15 +++++---
 docs_jupyter/cli.ipynb | 81 +++++++++++++++++++++++++++++++-----------
 2 files changed, 71 insertions(+), 25 deletions(-)

diff --git a/divvy/compute.py b/divvy/compute.py
index 80eaddd..2ace3c8 100644
--- a/divvy/compute.py
+++ b/divvy/compute.py
@@ -312,11 +312,18 @@ def main():
             help="Divvy configuration file.")
 
     subparsers = parser.add_subparsers(dest="command") 
-    list_subparser = subparsers.add_parser("list", description="Lists available packages",
-        help="Run 'divvy list' to list available packages")
 
-    write_subparser = subparsers.add_parser("write", description="write compute job script",
-        help="write compute job script")
+    # Individual subcommands
+    msg_by_cmd = {
+            "list": "List available compute packages",
+            "write": "Write a submit script"
+            }
+
+    def add_subparser(cmd):
+        return subparsers.add_parser(cmd, description=msg_by_cmd[cmd], help=msg_by_cmd[cmd])
+
+    list_subparser = add_subparser("list")
+    write_subparser = add_subparser("write")
 
     write_subparser.add_argument(
             "-S", "--settings",
diff --git a/docs_jupyter/cli.ipynb b/docs_jupyter/cli.ipynb
index c18ec99..4219666 100644
--- a/docs_jupyter/cli.ipynb
+++ b/docs_jupyter/cli.ipynb
@@ -14,7 +14,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 29,
+   "execution_count": 2,
    "metadata": {
     "collapsed": false,
     "deletable": true,
@@ -25,22 +25,22 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "version: 0.2-dev\n",
-      "usage: divvy [-h] [-V] [-C CONFIG] [-S SETTINGS] [-P PACKAGE] -O OUTFILE\n",
+      "version: 0.3dev\n",
+      "usage: divvy [-h] [-V] [-C CONFIG] {list,write} ...\n",
       "\n",
-      "divvy - write compute jobs that can be submitted to any computing resource\n",
+      "divvy - write compute job scripts that can be submitted to any computing\n",
+      "resource\n",
+      "\n",
+      "positional arguments:\n",
+      "  {list,write}\n",
+      "    list                List available compute packages\n",
+      "    write               Write a submit script\n",
       "\n",
       "optional arguments:\n",
       "  -h, --help            show this help message and exit\n",
       "  -V, --version         show program's version number and exit\n",
       "  -C CONFIG, --config CONFIG\n",
       "                        Divvy configuration file.\n",
-      "  -S SETTINGS, --settings SETTINGS\n",
-      "                        YAML file with job settings to populate the template.\n",
-      "  -P PACKAGE, --package PACKAGE\n",
-      "                        Compute package\n",
-      "  -O OUTFILE, --outfile OUTFILE\n",
-      "                        Output filepath\n",
       "\n",
       "https://github.com/pepkit/divvy\n"
      ]
@@ -50,6 +50,43 @@
     "divvy --help"
    ]
   },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "# The `list` command\n",
+    "\n",
+    "Let's first use `divvy list` to show us our available computing packages:"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 3,
+   "metadata": {
+    "collapsed": false
+   },
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "Using default config file, no global config file provided in environment variable(s): ['DIVCFG', 'PEPENV']\n",
+      "Loading divvy config file: /home/nsheff/.local/lib/python3.5/site-packages/divvy/submit_templates/default_compute_settings.yaml\n",
+      "Activating compute package 'default'\n",
+      "Available compute packages: default, local, slurm\n"
+     ]
+    },
+    {
+     "ename": "",
+     "evalue": "1",
+     "output_type": "error",
+     "traceback": []
+    }
+   ],
+   "source": [
+    "divvy list"
+   ]
+  },
   {
    "cell_type": "markdown",
    "metadata": {
@@ -57,6 +94,11 @@
     "editable": true
    },
    "source": [
+    "# The `write` command\n",
+    "\n",
+    "Use `divvy write` to actually write a new script using a template. To do this, you'll need to provide 3 things: a template (which comes from your compute package), a settings file with variables, and an outfile.\n",
+    "\n",
+    "\n",
     "## The settings file\n",
     "\n",
     "The settings argument is where you can pass an existing `yaml` file with key-value pairs. Here's a simple example:"
@@ -143,7 +185,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 32,
+   "execution_count": 5,
    "metadata": {
     "collapsed": false,
     "deletable": true,
@@ -155,8 +197,7 @@
      "output_type": "stream",
      "text": [
       "Using default config file, no global config file provided in environment variable(s): ['DIVCFG', 'PEPENV']\n",
-      "Loading divvy config file: /home/nsheff/.local/lib/python2.7/site-packages/divvy/submit_templates/default_compute_settings.yaml\n",
-      "Available packages: default, local, slurm\n",
+      "Loading divvy config file: /home/nsheff/.local/lib/python3.5/site-packages/divvy/submit_templates/default_compute_settings.yaml\n",
       "Activating compute package 'default'\n",
       "Activating compute package 'slurm'\n",
       "Loading yaml settings file: settings.yaml\n",
@@ -165,7 +206,7 @@
     }
    ],
    "source": [
-    "divvy -P slurm -S settings.yaml -O test.sub"
+    "divvy write -P slurm -S settings.yaml -O test.sub"
    ]
   },
   {
@@ -180,7 +221,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 33,
+   "execution_count": 6,
    "metadata": {
     "collapsed": false,
     "deletable": true,
@@ -224,7 +265,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 34,
+   "execution_count": 7,
    "metadata": {
     "collapsed": false,
     "deletable": true,
@@ -235,10 +276,8 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "Custom vars: {}\n",
       "Using default config file, no global config file provided in environment variable(s): ['DIVCFG', 'PEPENV']\n",
-      "Loading divvy config file: /home/nsheff/.local/lib/python2.7/site-packages/divvy/submit_templates/default_compute_settings.yaml\n",
-      "Available packages: default, local, slurm\n",
+      "Loading divvy config file: /home/nsheff/.local/lib/python3.5/site-packages/divvy/submit_templates/default_compute_settings.yaml\n",
       "Activating compute package 'default'\n",
       "Activating compute package 'slurm'\n",
       "Loading yaml settings file: settings.yaml\n",
@@ -247,12 +286,12 @@
     }
    ],
    "source": [
-    "divvy -P slurm -S settings.yaml -O test.sub --code run-this-cmd --jobname 12345 --time 6-0-0"
+    "divvy write -P slurm -S settings.yaml -O test.sub --code run-this-cmd --jobname 12345 --time 6-0-0"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 35,
+   "execution_count": 8,
    "metadata": {
     "collapsed": false,
     "deletable": true,

From 1d0e96338877f5b35578394e720bb311beda30cd Mon Sep 17 00:00:00 2001
From: Vince Reuter <vince.reuter@gmail.com>
Date: Wed, 10 Apr 2019 13:02:30 -0400
Subject: [PATCH 05/19] depr warn

---
 divvy/compute.py | 14 ++++++++++----
 1 file changed, 10 insertions(+), 4 deletions(-)

diff --git a/divvy/compute.py b/divvy/compute.py
index 2ace3c8..d78022a 100644
--- a/divvy/compute.py
+++ b/divvy/compute.py
@@ -4,6 +4,7 @@
 import logging
 import os
 import sys
+import warnings
 import yaml
 from yaml import SafeLoader
 
@@ -12,7 +13,7 @@
     COMPUTE_SETTINGS_VARNAME, \
     DEFAULT_COMPUTE_RESOURCES_NAME
 from .utils import write_submit_script, get_first_env_var
-from . import  __version__
+from . import __version__
 
 _LOGGER = logging.getLogger(__name__)
 
@@ -226,11 +227,16 @@ def update_packages(self, config_file):
             _LOGGER.debug("Parsed environment settings: %s",
                           str(env_settings))
 
+            old_compute_key = "compute"
+            new_compute_key = "compute_packages"
+
             # Any compute.submission_template variables should be made
             # absolute, relative to current divvy configuration file.
-            if "compute" in env_settings:
-                _LOGGER.warning("DEPRECATION WARNING: Divvy compute configuration 'compute' section changed to 'compute_packages'")
-                env_settings["compute_packages"] = env_settings["compute"]
+            if old_compute_key in env_settings:
+                warnings.warn("Divvy compute configuration '{}' section changed "
+                              "to '{}'".format(old_compute_key, new_compute_key),
+                              DeprecationWarning)
+                env_settings[new_compute_key] = env_settings[old_compute_key]
 
             loaded_packages = env_settings["compute_packages"]
             for key, value in loaded_packages.items():

From 0ae36b480f244ab60103db3bc0e54564fe886699 Mon Sep 17 00:00:00 2001
From: Vince Reuter <vince.reuter@gmail.com>
Date: Wed, 10 Apr 2019 13:06:19 -0400
Subject: [PATCH 06/19] tidy; remove unused var

---
 divvy/compute.py | 3 ---
 1 file changed, 3 deletions(-)

diff --git a/divvy/compute.py b/divvy/compute.py
index d78022a..5b09f7a 100644
--- a/divvy/compute.py
+++ b/divvy/compute.py
@@ -328,7 +328,6 @@ def main():
     def add_subparser(cmd):
         return subparsers.add_parser(cmd, description=msg_by_cmd[cmd], help=msg_by_cmd[cmd])
 
-    list_subparser = add_subparser("list")
     write_subparser = add_subparser("write")
 
     write_subparser.add_argument(
@@ -343,13 +342,11 @@ def add_subparser(cmd):
             "-O", "--outfile", required=True,
             help="Output filepath")
 
-
     args, remaining_args = parser.parse_known_args()
     keys = [str.replace(x, "--", "") for x in remaining_args[::2]]
     custom_vars = dict(zip(keys, remaining_args[1::2]))
     dcc = ComputingConfiguration(args.config)
 
-
     if args.command == "list":
         _LOGGER.info("Available compute packages: {}".format(', '.join(dcc.list_compute_packages())))
         sys.exit(1)

From e9f08d05906b958b0ad302d2a170f00154f2dd96 Mon Sep 17 00:00:00 2001
From: Vince Reuter <vince.reuter@gmail.com>
Date: Wed, 10 Apr 2019 17:27:14 -0400
Subject: [PATCH 07/19] update test data; close #29

---
 tests/data/pepenv-master/cemm.yaml              | 4 ++--
 tests/data/pepenv-master/compute_config.yaml    | 4 ++--
 tests/data/pepenv-master/local_containers.yaml  | 2 +-
 tests/data/pepenv-master/nih_biowulf2.yaml      | 2 +-
 tests/data/pepenv-master/ski-cer_lilac.yaml     | 2 +-
 tests/data/pepenv-master/stanford_sherlock.yaml | 2 +-
 tests/data/pepenv-master/uva_rivanna.yaml       | 2 +-
 7 files changed, 9 insertions(+), 9 deletions(-)

diff --git a/tests/data/pepenv-master/cemm.yaml b/tests/data/pepenv-master/cemm.yaml
index 646e8ad..5527d73 100644
--- a/tests/data/pepenv-master/cemm.yaml
+++ b/tests/data/pepenv-master/cemm.yaml
@@ -1,7 +1,7 @@
 # Environment configuration file for looper
 # This version describes the compute environment at CeMM
 
-compute:
+compute_packages:
   default:
     submission_template: templates/slurm_template.sub
     submission_command: sbatch
@@ -12,4 +12,4 @@ compute:
     partition: develop
   local:
     submission_template: templates/localhost_template.sub
-    submission_command: sh
\ No newline at end of file
+    submission_command: sh
diff --git a/tests/data/pepenv-master/compute_config.yaml b/tests/data/pepenv-master/compute_config.yaml
index c7f2ad5..8d1d797 100644
--- a/tests/data/pepenv-master/compute_config.yaml
+++ b/tests/data/pepenv-master/compute_config.yaml
@@ -1,4 +1,4 @@
-compute:
+compute_packages:
   default:
     submission_template: templates/slurm_template.sub
     submission_command: sbatch
@@ -9,4 +9,4 @@ compute:
     partition: economy
   local:
     submission_template: templates/localhost_template.sub
-    submission_command: sh
\ No newline at end of file
+    submission_command: sh
diff --git a/tests/data/pepenv-master/local_containers.yaml b/tests/data/pepenv-master/local_containers.yaml
index 90b1b4b..771dfe0 100644
--- a/tests/data/pepenv-master/local_containers.yaml
+++ b/tests/data/pepenv-master/local_containers.yaml
@@ -2,7 +2,7 @@
 # This version describes the compute environment for a local computer that uses
 # docker or singularity containers
 
-compute:
+compute_packages:
   default:
     submission_template: templates/localhost_template.sub
     submission_command: sh
diff --git a/tests/data/pepenv-master/nih_biowulf2.yaml b/tests/data/pepenv-master/nih_biowulf2.yaml
index fe9fbb2..4defa60 100644
--- a/tests/data/pepenv-master/nih_biowulf2.yaml
+++ b/tests/data/pepenv-master/nih_biowulf2.yaml
@@ -1,7 +1,7 @@
 # Environment configuration file for looper
 # This version describes the compute environment on biowulf2 at the NIH
 
-compute:
+compute_packages:
   default:
     submission_template: templates/slurm_template.sub
     submission_command: sbatch --mail-type=BEGIN,TIME_LIMIT_90,END
diff --git a/tests/data/pepenv-master/ski-cer_lilac.yaml b/tests/data/pepenv-master/ski-cer_lilac.yaml
index 601e3e0..b6ce9c3 100644
--- a/tests/data/pepenv-master/ski-cer_lilac.yaml
+++ b/tests/data/pepenv-master/ski-cer_lilac.yaml
@@ -1,7 +1,7 @@
 # Environment configuration file for looper
 # This version describes the compute environment on lilac at SKI, MSKCC
 
-compute:
+compute_packages:
   default:
     submission_template: templates/lsf_template.sub
     submission_command: sh
diff --git a/tests/data/pepenv-master/stanford_sherlock.yaml b/tests/data/pepenv-master/stanford_sherlock.yaml
index a3eed37..2b940bf 100644
--- a/tests/data/pepenv-master/stanford_sherlock.yaml
+++ b/tests/data/pepenv-master/stanford_sherlock.yaml
@@ -1,4 +1,4 @@
-compute:
+compute_packages:
   default:
     submission_template: templates/localhost_template.sub
     submission_command: sh
diff --git a/tests/data/pepenv-master/uva_rivanna.yaml b/tests/data/pepenv-master/uva_rivanna.yaml
index 88ca7a7..fc98e06 100644
--- a/tests/data/pepenv-master/uva_rivanna.yaml
+++ b/tests/data/pepenv-master/uva_rivanna.yaml
@@ -1,7 +1,7 @@
 # Environment configuration file for looper
 # This version describes the compute environment on Rivanna at UVA
 
-compute:
+compute_packages:
   default:
     submission_template: templates/slurm_template.sub
     submission_command: sbatch

From 2b96eba3d44954815b86578e9547f6cc343743cd Mon Sep 17 00:00:00 2001
From: Vince Reuter <vince.reuter@gmail.com>
Date: Mon, 15 Apr 2019 16:15:56 -0400
Subject: [PATCH 08/19] bump req

---
 requirements/requirements-all.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/requirements/requirements-all.txt b/requirements/requirements-all.txt
index 84bc55b..c7e251a 100644
--- a/requirements/requirements-all.txt
+++ b/requirements/requirements-all.txt
@@ -1,4 +1,4 @@
 pandas>=0.20.2
 pyyaml>=5.1
-attmap>=0.4
+attmap>=0.6
 

From f9e80d96e47af25a32f4634e6dcca948c0a3ef2c Mon Sep 17 00:00:00 2001
From: nsheff <nsheff@users.noreply.github.com>
Date: Fri, 19 Apr 2019 15:07:07 -0400
Subject: [PATCH 09/19] docs update

---
 docs/README.md              |  9 ++++++---
 docs/autodoc_build/divvy.md | 29 ++++++++++++++++-------------
 docs/changelog.md           |  3 ++-
 docs/configuration.md       |  4 ++++
 mkdocs.yml                  |  2 +-
 5 files changed, 29 insertions(+), 18 deletions(-)

diff --git a/docs/README.md b/docs/README.md
index 502f900..28f52bd 100644
--- a/docs/README.md
+++ b/docs/README.md
@@ -3,13 +3,15 @@
 [![PEP compatible](http://pepkit.github.io/img/PEP-compatible-green.svg)](http://pepkit.github.io)
 
 
-`divvy` is a simple templating system written in python that allows users to write compute jobs that can be submitted to any computing resource (laptop, cluster, cloud). It works using a simple configuration file, which we call *computing configuration files*, where you specify variables for your computing environment. It uses these variables to populate simple, Jinja-like templates to make computing job submission flexible. 
+`Divvy` is a computing resource configuration manager. It reads a standard configuration file describing available compute resources and then uses a simple Jinja-like templating system to enable users to write custom job submission scripts.
+
+In `divvy`, computing resources are organized as *compute packages*, which define job submission templates and other variables. Users then select a compute package and provide variable values, and `divvy` populates the templates to write compute jobs. The flexible templating system means users can quickly switch jobs to submit to any computing resource (laptop, cluster, cloud). `Divvy` provides both an interactive python API and a command-line interface.
 
 
 ## Installing
 
+Releases are posted as [GitHub releases](https://github.com/databio/divvy/releases), or you can install from PyPI using `pip`:
 
-Release versions are posted on the GitHub [divvy releases page](https://github.com/databio/divvy/releases). You can install the latest release directly from PyPI using pip:
 
 ```{console}
 pip install --user divvy
@@ -38,7 +40,8 @@ dcc.write_script("test_script.sub", {"code": "bowtie2 input.bam output.bam"})
 Or via command-line:
 
 ```{console}
-divvy --package slurm --settings myjob.yaml --sample sample1 --outfile submit_script.txt
+divvy list
+divvy write --package slurm --settings myjob.yaml --sample sample1 --outfile submit_script.txt
 ```
 
 To begin, check out the [tutorial](tutorial).
diff --git a/docs/autodoc_build/divvy.md b/docs/autodoc_build/divvy.md
index e5a311d..a821974 100644
--- a/docs/autodoc_build/divvy.md
+++ b/docs/autodoc_build/divvy.md
@@ -23,7 +23,7 @@ This copies the computing attributes from the configuration file into
 the `compute` attribute, where the class stores current compute
 settings.
 ```python
-def activate_package(self, package_name):
+def activate_package(self, package_name)
 ```
 
 **Parameters:**
@@ -41,7 +41,7 @@ def activate_package(self, package_name):
 ### clean\_start
 Clear current active settings and then activate the given package.
 ```python
-def clean_start(self, package_name):
+def clean_start(self, package_name)
 ```
 
 **Parameters:**
@@ -59,7 +59,7 @@ def clean_start(self, package_name):
 ### compute\_env\_var
 Environment variable through which to access compute settings.
 ```python
-def compute_env_var:
+def compute_env_var(self)
 ```
 
 **Returns:**
@@ -72,7 +72,7 @@ def compute_env_var:
 ### default\_config\_file
 Path to default compute environment settings file.
 ```python
-def default_config_file:
+def default_config_file(self)
 ```
 
 **Returns:**
@@ -85,12 +85,12 @@ def default_config_file:
 ### get\_active\_package
 Returns settings for the currently active compute package
 ```python
-def get_active_package(self):
+def get_active_package(self)
 ```
 
 **Returns:**
 
-`AttMap`:  data defining the active compute package
+`PathExAttMap`:  data defining the active compute package
 
 
 
@@ -98,7 +98,7 @@ def get_active_package(self):
 ### list\_compute\_packages
 Returns a list of available compute packages.
 ```python
-def list_compute_packages(self):
+def list_compute_packages(self)
 ```
 
 **Returns:**
@@ -111,7 +111,7 @@ def list_compute_packages(self):
 ### reset\_active\_settings
 Clear out current compute settings.
 ```python
-def reset_active_settings(self):
+def reset_active_settings(self)
 ```
 
 **Returns:**
@@ -124,7 +124,7 @@ def reset_active_settings(self):
 ### template
 Get the currently active submission template.
 ```python
-def template:
+def template(self)
 ```
 
 **Returns:**
@@ -137,7 +137,7 @@ def template:
 ### templates\_folder
 Path to folder with default submission templates.
 ```python
-def templates_folder:
+def templates_folder(self)
 ```
 
 **Returns:**
@@ -154,7 +154,7 @@ Given a divvy configuration file, this function will update (not
 overwrite) existing compute packages with existing values. It does not
 affect any currently active settings.
 ```python
-def update_packages(self, config_file):
+def update_packages(self, config_file)
 ```
 
 **Parameters:**
@@ -167,7 +167,7 @@ def update_packages(self, config_file):
 ### write\_script
 Given currently active settings, populate the active template to write a submission script.
 ```python
-def write_script(self, output_path, extra_vars=None):
+def write_script(self, output_path, extra_vars=None)
 ```
 
 **Parameters:**
@@ -186,7 +186,7 @@ def write_script(self, output_path, extra_vars=None):
 ### write\_submit\_script
 Write a submission script by populating a template with data.
 ```python
-def write_submit_script(fp, content, data):
+def write_submit_script(fp, content, data)
 ```
 
 **Parameters:**
@@ -202,3 +202,6 @@ def write_submit_script(fp, content, data):
 
 
 
+
+
+**Version Information**: `divvy` v0.3dev, generated by `lucidoc` v0.3
\ No newline at end of file
diff --git a/docs/changelog.md b/docs/changelog.md
index ef5e64d..36e26c8 100644
--- a/docs/changelog.md
+++ b/docs/changelog.md
@@ -4,7 +4,8 @@
 
 ### Changed
 - Safer use of `yaml`
-- Reduced verbosity for clearly usage
+- Reduced verbosity for clearer usage
+- The CLI now uses `divvy write` and `divvy list` subcommands
 
 ## divvy [0.2.1] - 2019-03-19
 
diff --git a/docs/configuration.md b/docs/configuration.md
index 715c500..201f3e6 100644
--- a/docs/configuration.md
+++ b/docs/configuration.md
@@ -42,6 +42,10 @@ The `submission_command` attribute is the string your cluster resource manager u
 Each compute package specifies a path to a template file (`submission_template`). The template file provides a skeleton that `divvy` will populate with job-specific attributes. These paths can be relative or absolute; relative paths are considered *relative to the DIVCFG file*.
 
 
+## Resources
+
+You may notice that the compute config file does not specify resources to request (like memory, CPUs, or time). Yet, these are required in order to submit a job to a cluster. **Resources are not handled by the divcfg file** because they not relative to a particular computing environment; instead they vary by pipeline and sample. As such, these items should be defined at other stages. 
+
 ## Template files
 
 Each compute package must point to a template file with the `submission_template` attribute. These template files are typically stored relative to the `divvy` configuration file. Template files are taken by `divvy`, populated with job-specific information, and then run as scripts. Here's an example of a generic SLURM template file:
diff --git a/mkdocs.yml b/mkdocs.yml
index 73dd4e9..8e03e3f 100644
--- a/mkdocs.yml
+++ b/mkdocs.yml
@@ -10,7 +10,7 @@ nav:
     - "Tutorial: divvy in python": tutorial.md
     - "Tutorial: divvy on the command line": cli.md
   - How-to Guides:
-    - Write a DIVCFG file: configuration.md
+    - Configuring divvy: configuration.md
     - Configuring containers: containers.md
   - Reference:
     - API: autodoc_build/divvy.md

From 45e30a70d9a1ffabf5c6b0ff1391a1b8c86aba6c Mon Sep 17 00:00:00 2001
From: nsheff <nsheff@users.noreply.github.com>
Date: Fri, 19 Apr 2019 15:12:00 -0400
Subject: [PATCH 10/19] version bump, changelog

---
 divvy/_version.py | 2 +-
 docs/changelog.md | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/divvy/_version.py b/divvy/_version.py
index b61d113..5c3e1be 100644
--- a/divvy/_version.py
+++ b/divvy/_version.py
@@ -1,2 +1,2 @@
-__version__ = "0.3dev"
+__version__ = "0.3"
 
diff --git a/docs/changelog.md b/docs/changelog.md
index 36e26c8..c346c63 100644
--- a/docs/changelog.md
+++ b/docs/changelog.md
@@ -1,6 +1,6 @@
 # Changelog
 
-## divvy [0.3] - Unreleased
+## divvy [0.3] - 2019-04-19
 
 ### Changed
 - Safer use of `yaml`

From 1fccd36750ab787e0e1f87ea00f7910f6cb35450 Mon Sep 17 00:00:00 2001
From: Vince Reuter <vince.reuter@gmail.com>
Date: Fri, 19 Apr 2019 16:11:10 -0400
Subject: [PATCH 11/19] spacing

---
 divvy/utils.py | 26 --------------------------
 1 file changed, 26 deletions(-)

diff --git a/divvy/utils.py b/divvy/utils.py
index 5bb8c0a..5e47980 100644
--- a/divvy/utils.py
+++ b/divvy/utils.py
@@ -14,17 +14,13 @@
 else:
     from urllib.parse import urlparse
 import warnings
-
-
 import yaml
-
 from .const import GENERIC_PROTOCOL_KEY, SAMPLE_INDEPENDENT_PROJECT_SECTIONS
 
 
 _LOGGER = logging.getLogger(__name__)
 
 
-
 def add_project_sample_constants(sample, project):
     """
     Update a Sample with constants declared by a Project.
@@ -40,7 +36,6 @@ def add_project_sample_constants(sample, project):
     return sample
 
 
-
 def alpha_cased(text, lower=False):
     """
     Filter text to just letters and homogenize case.
@@ -54,7 +49,6 @@ def alpha_cased(text, lower=False):
     return text.lower() if lower else text.upper()
 
 
-
 def check_bam(bam, o):
     """
     Check reads in BAM file for read type and lengths.
@@ -87,13 +81,11 @@ def check_bam(bam, o):
     return read_lengths, paired
 
 
-
 def check_fastq(fastq, o):
     raise NotImplementedError("Detection of read type/length for "
                               "fastq input is not yet implemented.")
 
 
-
 def check_sample_sheet_row_count(sheet, filepath):
     """
     Quick-and-dirt proxy for Sample count validation.
@@ -113,7 +105,6 @@ def check_sample_sheet_row_count(sheet, filepath):
     return len(sheet) == len(lines) - deduction
 
 
-
 def copy(obj):
     def copy(self):
         """
@@ -126,7 +117,6 @@ def copy(self):
     return obj
 
 
-
 def expandpath(path):
     """
     Expand a filesystem path that may or may not contain user/env vars.
@@ -137,7 +127,6 @@ def expandpath(path):
     return os.path.expandvars(os.path.expanduser(path)).replace("//", "/")
 
 
-
 def get_file_size(filename):
     """
     Get size of all files in gigabytes (Gb).
@@ -160,7 +149,6 @@ def get_file_size(filename):
         return float(total_bytes) / (1024 ** 3)
 
 
-
 def fetch_samples(proj, inclusion=None, exclusion=None):
     """
     Collect samples of particular protocol(s).
@@ -217,7 +205,6 @@ def keep(s):
     return list(filter(keep, proj.samples))
 
 
-
 def grab_project_data(prj):
     """
     From the given Project, grab Sample-independent data.
@@ -246,7 +233,6 @@ def grab_project_data(prj):
     return data
 
 
-
 def import_from_source(module_filepath):
     """
     Import a module from a particular filesystem location.
@@ -285,7 +271,6 @@ def import_from_source(module_filepath):
     return mod
 
 
-
 def is_url(maybe_url):
     """
     Determine whether a path is a URL.
@@ -296,7 +281,6 @@ def is_url(maybe_url):
     return urlparse(maybe_url).scheme != ""
 
 
-
 def parse_ftype(input_file):
     """
     Checks determine filetype from extension.
@@ -317,7 +301,6 @@ def parse_ftype(input_file):
                         "nor '.fastq' [file: '" + input_file + "']")
 
 
-
 def parse_text_data(lines_or_path, delimiter=os.linesep):
     """
     Interpret input argument as lines of data. This is intended to support
@@ -346,7 +329,6 @@ def parse_text_data(lines_or_path, delimiter=os.linesep):
                          format(lines_or_path, type(lines_or_path)))
 
 
-
 def sample_folder(prj, sample):
     """
     Get the path to this Project's root folder for the given Sample.
@@ -360,7 +342,6 @@ def sample_folder(prj, sample):
                         sample["sample_name"])
 
 
-
 def write_submit_script(fp, content, data):
     """
     Write a submission script by populating a template with data.
@@ -390,7 +371,6 @@ def write_submit_script(fp, content, data):
     return fp
 
 
-
 @contextlib.contextmanager
 def standard_stream_redirector(stream):
     """
@@ -411,7 +391,6 @@ def standard_stream_redirector(stream):
         sys.stdout, sys.stderr = genuine_stdout, genuine_stderr
 
 
-
 def warn_derived_cols():
     _warn_cols_to_attrs("derived")
 
@@ -425,7 +404,6 @@ def _warn_cols_to_attrs(prefix):
                   "as {pfx}_attributes".format(pfx=prefix), DeprecationWarning)
 
 
-
 class CommandChecker(object):
     """
     Validate PATH availability of executables referenced by a config file.
@@ -440,7 +418,6 @@ class CommandChecker(object):
         the check names parameter, but for specific sections to skip.
     """
 
-
     def __init__(self, path_conf_file,
                  sections_to_check=None, sections_to_skip=None):
 
@@ -506,7 +483,6 @@ def __init__(self, path_conf_file,
                     self._logger.debug("Command '%s': %s", command,
                                        "SUCCESS" if success else "FAILURE")
 
-
     def _store_status(self, section, command, name):
         """
         Based on new command execution attempt, update instance's
@@ -522,7 +498,6 @@ def _store_status(self, section, command, name):
             self.failures.add(command)
         return succeeded
 
-
     @property
     def failed(self):
         """
@@ -540,7 +515,6 @@ def failed(self):
         return 0 == len(self.failures)
 
 
-
 def is_command_callable(command, name=""):
     """
     Check if command can be called.

From 3776a341104d7a9a5d9e1a8d4dd7cdc71499b5ec Mon Sep 17 00:00:00 2001
From: Vince Reuter <vince.reuter@gmail.com>
Date: Fri, 19 Apr 2019 16:11:48 -0400
Subject: [PATCH 12/19] only manage context where relevant

---
 divvy/compute.py | 58 +++++++++++++++++++++++++-----------------------
 1 file changed, 30 insertions(+), 28 deletions(-)

diff --git a/divvy/compute.py b/divvy/compute.py
index 5b09f7a..8bbd0e7 100644
--- a/divvy/compute.py
+++ b/divvy/compute.py
@@ -224,34 +224,36 @@ def update_packages(self, config_file):
         with open(config_file, 'r') as f:
             _LOGGER.info("Loading divvy config file: %s", config_file)
             env_settings = yaml.load(f, SafeLoader)
-            _LOGGER.debug("Parsed environment settings: %s",
-                          str(env_settings))
-
-            old_compute_key = "compute"
-            new_compute_key = "compute_packages"
-
-            # Any compute.submission_template variables should be made
-            # absolute, relative to current divvy configuration file.
-            if old_compute_key in env_settings:
-                warnings.warn("Divvy compute configuration '{}' section changed "
-                              "to '{}'".format(old_compute_key, new_compute_key),
-                              DeprecationWarning)
-                env_settings[new_compute_key] = env_settings[old_compute_key]
-
-            loaded_packages = env_settings["compute_packages"]
-            for key, value in loaded_packages.items():
-                if type(loaded_packages[key]) is dict:
-                    for key2, value2 in loaded_packages[key].items():
-                        if key2 == "submission_template":
-                            if not os.path.isabs(loaded_packages[key][key2]):
-                                loaded_packages[key][key2] = os.path.join(
-                                    os.path.dirname(config_file),
-                                    loaded_packages[key][key2])
-
-            if self.compute_packages is None:
-                self.compute_packages = PathExAttMap(loaded_packages)
-            else:
-                self.compute_packages.add_entries(loaded_packages)
+
+        _LOGGER.debug("Parsed environment settings: %s",
+                      str(env_settings))
+
+        old_compute_key = "compute"
+        new_compute_key = "compute_packages"
+
+        # Any compute.submission_template variables should be made
+        # absolute, relative to current divvy configuration file.
+        if old_compute_key in env_settings:
+            warnings.warn("Divvy compute configuration '{}' section changed "
+                          "to '{}'".format(old_compute_key, new_compute_key),
+                          DeprecationWarning)
+            env_settings[new_compute_key] = env_settings[old_compute_key]
+
+        loaded_packages = env_settings["compute_packages"]
+        for key, value in loaded_packages.items():
+            if type(loaded_packages[key]) is dict:
+                for key2, value2 in loaded_packages[key].items():
+                    if key2 == "submission_template":
+                        if not os.path.isabs(loaded_packages[key][key2]):
+                            loaded_packages[key][key2] = os.path.join(
+                                os.path.dirname(config_file),
+                                loaded_packages[key][key2])
+
+        if self.compute_packages is None:
+            self.compute_packages = PathExAttMap(loaded_packages)
+        else:
+            self.compute_packages.add_entries(loaded_packages)
+
         _LOGGER.debug("Available divvy packages: {}".format(', '.join(self.list_compute_packages())))
         self.config_file = config_file
 

From 321245ce1b540f72362f037b02e2e9096ce6a9e0 Mon Sep 17 00:00:00 2001
From: Vince Reuter <vince.reuter@gmail.com>
Date: Fri, 19 Apr 2019 16:21:33 -0400
Subject: [PATCH 13/19] modularity; variable sharing

---
 divvy/compute.py | 29 +++++------------------------
 divvy/const.py   |  2 ++
 divvy/utils.py   | 25 ++++++++++++++++++++++++-
 3 files changed, 31 insertions(+), 25 deletions(-)

diff --git a/divvy/compute.py b/divvy/compute.py
index 8bbd0e7..01ae598 100644
--- a/divvy/compute.py
+++ b/divvy/compute.py
@@ -4,7 +4,6 @@
 import logging
 import os
 import sys
-import warnings
 import yaml
 from yaml import SafeLoader
 
@@ -12,7 +11,7 @@
 from .const import \
     COMPUTE_SETTINGS_VARNAME, \
     DEFAULT_COMPUTE_RESOURCES_NAME
-from .utils import write_submit_script, get_first_env_var
+from .utils import parse_config_file, write_submit_script, get_first_env_var
 from . import __version__
 
 _LOGGER = logging.getLogger(__name__)
@@ -129,7 +128,6 @@ def templates_folder(self):
         """
         return os.path.join(os.path.dirname(__file__), "submit_templates")
 
-
     def activate_package(self, package_name):
         """
         Activates a compute package.
@@ -218,27 +216,9 @@ def update_packages(self, config_file):
         overwrite) existing compute packages with existing values. It does not
         affect any currently active settings.
         
-        :param str config_file: path to file with
-            new divvy configuration data
+        :param str config_file: path to file with new divvy configuration data
         """
-        with open(config_file, 'r') as f:
-            _LOGGER.info("Loading divvy config file: %s", config_file)
-            env_settings = yaml.load(f, SafeLoader)
-
-        _LOGGER.debug("Parsed environment settings: %s",
-                      str(env_settings))
-
-        old_compute_key = "compute"
-        new_compute_key = "compute_packages"
-
-        # Any compute.submission_template variables should be made
-        # absolute, relative to current divvy configuration file.
-        if old_compute_key in env_settings:
-            warnings.warn("Divvy compute configuration '{}' section changed "
-                          "to '{}'".format(old_compute_key, new_compute_key),
-                          DeprecationWarning)
-            env_settings[new_compute_key] = env_settings[old_compute_key]
-
+        env_settings = parse_config_file(config_file)
         loaded_packages = env_settings["compute_packages"]
         for key, value in loaded_packages.items():
             if type(loaded_packages[key]) is dict:
@@ -254,7 +234,8 @@ def update_packages(self, config_file):
         else:
             self.compute_packages.add_entries(loaded_packages)
 
-        _LOGGER.debug("Available divvy packages: {}".format(', '.join(self.list_compute_packages())))
+        _LOGGER.debug("Available divvy packages: {}".
+                      format(', '.join(self.list_compute_packages())))
         self.config_file = config_file
 
     def write_script(self, output_path, extra_vars=None):
diff --git a/divvy/const.py b/divvy/const.py
index f7ed6db..34e9bed 100644
--- a/divvy/const.py
+++ b/divvy/const.py
@@ -7,6 +7,8 @@
 # Compute-related
 COMPUTE_SETTINGS_VARNAME = ["DIVCFG", "PEPENV"]
 DEFAULT_COMPUTE_RESOURCES_NAME = "default"
+OLD_COMPUTE_KEY = "compute"
+NEW_COMPUTE_KEY = "compute_packages"
 COMPUTE_CONSTANTS = ["COMPUTE_SETTINGS_VARNAME",
                      "DEFAULT_COMPUTE_RESOURCES_NAME"]
 
diff --git a/divvy/utils.py b/divvy/utils.py
index 5e47980..18fda54 100644
--- a/divvy/utils.py
+++ b/divvy/utils.py
@@ -15,7 +15,8 @@
     from urllib.parse import urlparse
 import warnings
 import yaml
-from .const import GENERIC_PROTOCOL_KEY, SAMPLE_INDEPENDENT_PROJECT_SECTIONS
+from .const import GENERIC_PROTOCOL_KEY, NEW_COMPUTE_KEY, OLD_COMPUTE_KEY, \
+    SAMPLE_INDEPENDENT_PROJECT_SECTIONS
 
 
 _LOGGER = logging.getLogger(__name__)
@@ -281,6 +282,28 @@ def is_url(maybe_url):
     return urlparse(maybe_url).scheme != ""
 
 
+def parse_config_file(conf_file):
+    """
+    Parse a divvy configuration file.
+
+    :param str conf_file: path to divvy configuration file
+    :return Mapping: compute settings as declared in config file
+    """
+    with open(conf_file, 'r') as f:
+        _LOGGER.info("Loading divvy config file: %s", conf_file)
+        env_settings = yaml.load(f, yaml.SafeLoader)
+    _LOGGER.debug("Parsed environment settings: %s",
+                  str(env_settings))
+    # Any compute.submission_template variables should be made
+    # absolute, relative to current divvy configuration file.
+    if OLD_COMPUTE_KEY in env_settings:
+        warnings.warn("Divvy compute configuration '{}' section changed "
+                      "to '{}'".format(OLD_COMPUTE_KEY, NEW_COMPUTE_KEY),
+                      DeprecationWarning)
+        env_settings[NEW_COMPUTE_KEY] = env_settings[OLD_COMPUTE_KEY]
+    return conf_file
+
+
 def parse_ftype(input_file):
     """
     Checks determine filetype from extension.

From 126a3b998901f0582a368176ade164cea4ea36b9 Mon Sep 17 00:00:00 2001
From: Vince Reuter <vince.reuter@gmail.com>
Date: Fri, 19 Apr 2019 16:22:57 -0400
Subject: [PATCH 14/19] fix retval

---
 divvy/utils.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/divvy/utils.py b/divvy/utils.py
index 18fda54..51ef5e2 100644
--- a/divvy/utils.py
+++ b/divvy/utils.py
@@ -301,7 +301,7 @@ def parse_config_file(conf_file):
                       "to '{}'".format(OLD_COMPUTE_KEY, NEW_COMPUTE_KEY),
                       DeprecationWarning)
         env_settings[NEW_COMPUTE_KEY] = env_settings[OLD_COMPUTE_KEY]
-    return conf_file
+    return env_settings
 
 
 def parse_ftype(input_file):

From ed40f2b45e2a4c99755cf1dd7034f15ac3debe09 Mon Sep 17 00:00:00 2001
From: Vince Reuter <vince.reuter@gmail.com>
Date: Fri, 19 Apr 2019 16:24:49 -0400
Subject: [PATCH 15/19] use the constant for new compute key

---
 divvy/compute.py | 9 ++++-----
 1 file changed, 4 insertions(+), 5 deletions(-)

diff --git a/divvy/compute.py b/divvy/compute.py
index 01ae598..b91e3e4 100644
--- a/divvy/compute.py
+++ b/divvy/compute.py
@@ -8,9 +8,8 @@
 from yaml import SafeLoader
 
 from attmap import PathExAttMap
-from .const import \
-    COMPUTE_SETTINGS_VARNAME, \
-    DEFAULT_COMPUTE_RESOURCES_NAME
+from .const import COMPUTE_SETTINGS_VARNAME, DEFAULT_COMPUTE_RESOURCES_NAME, \
+    NEW_COMPUTE_KEY
 from .utils import parse_config_file, write_submit_script, get_first_env_var
 from . import __version__
 
@@ -219,7 +218,7 @@ def update_packages(self, config_file):
         :param str config_file: path to file with new divvy configuration data
         """
         env_settings = parse_config_file(config_file)
-        loaded_packages = env_settings["compute_packages"]
+        loaded_packages = env_settings[NEW_COMPUTE_KEY]
         for key, value in loaded_packages.items():
             if type(loaded_packages[key]) is dict:
                 for key2, value2 in loaded_packages[key].items():
@@ -262,7 +261,7 @@ def write_script(self, output_path, extra_vars=None):
     def _handle_missing_env_attrs(self, config_file, when_missing):
         """ Default environment settings aren't required; warn, though. """
         missing_env_attrs = \
-            [attr for attr in ["compute_packages", "config_file"]
+            [attr for attr in [NEW_COMPUTE_KEY, "config_file"]
              if not hasattr(self, attr) or getattr(self, attr) is None]
         if not missing_env_attrs:
             return

From 367f2078ac916e12ff2a18da21ef5acf6296e110 Mon Sep 17 00:00:00 2001
From: Vince <vince.reuter@gmail.com>
Date: Fri, 19 Apr 2019 17:18:41 -0400
Subject: [PATCH 16/19] remove redundancy

---
 divvy/compute.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/divvy/compute.py b/divvy/compute.py
index b91e3e4..47f26e7 100644
--- a/divvy/compute.py
+++ b/divvy/compute.py
@@ -262,7 +262,7 @@ def _handle_missing_env_attrs(self, config_file, when_missing):
         """ Default environment settings aren't required; warn, though. """
         missing_env_attrs = \
             [attr for attr in [NEW_COMPUTE_KEY, "config_file"]
-             if not hasattr(self, attr) or getattr(self, attr) is None]
+             if getattr(self, attr, None) is None]
         if not missing_env_attrs:
             return
         message = "'{}' lacks environment attributes: {}". \

From f67e1b0da4df40483e163c3775c168c9b30e7539 Mon Sep 17 00:00:00 2001
From: Vince <vince.reuter@gmail.com>
Date: Fri, 19 Apr 2019 17:20:30 -0400
Subject: [PATCH 17/19] localize variable

---
 divvy/compute.py | 13 +++++++------
 1 file changed, 7 insertions(+), 6 deletions(-)

diff --git a/divvy/compute.py b/divvy/compute.py
index 47f26e7..03c8963 100644
--- a/divvy/compute.py
+++ b/divvy/compute.py
@@ -301,14 +301,15 @@ def main():
 
     subparsers = parser.add_subparsers(dest="command") 
 
-    # Individual subcommands
-    msg_by_cmd = {
-            "list": "List available compute packages",
-            "write": "Write a submit script"
-            }
 
     def add_subparser(cmd):
-        return subparsers.add_parser(cmd, description=msg_by_cmd[cmd], help=msg_by_cmd[cmd])
+        # Individual subcommands
+        msg_by_cmd = {
+            "list": "List available compute packages",
+            "write": "Write a submit script"
+        }
+        return subparsers.add_parser(
+            cmd, description=msg_by_cmd[cmd], help=msg_by_cmd[cmd])
 
     write_subparser = add_subparser("write")
 

From 90d93324a664c8717c9ed4536eb78670270e59be Mon Sep 17 00:00:00 2001
From: Vince <vince.reuter@gmail.com>
Date: Fri, 19 Apr 2019 17:22:27 -0400
Subject: [PATCH 18/19] reserve logging for behavioral messages rather than
 requested output

---
 divvy/compute.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/divvy/compute.py b/divvy/compute.py
index 03c8963..54ece44 100644
--- a/divvy/compute.py
+++ b/divvy/compute.py
@@ -331,7 +331,8 @@ def add_subparser(cmd):
     dcc = ComputingConfiguration(args.config)
 
     if args.command == "list":
-        _LOGGER.info("Available compute packages: {}".format(', '.join(dcc.list_compute_packages())))
+        print("Available compute packages:\n{}".format(
+            "\n".join(dcc.list_compute_packages())))
         sys.exit(1)
 
     dcc.activate_package(args.package)

From 8cda3515c67e2c07c7f47a80a336684ae5bb46c0 Mon Sep 17 00:00:00 2001
From: Vince <vince.reuter@gmail.com>
Date: Fri, 19 Apr 2019 17:29:07 -0400
Subject: [PATCH 19/19] variable naming, context management localization, more
 uniform control flow

---
 divvy/compute.py | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/divvy/compute.py b/divvy/compute.py
index 54ece44..19a60b6 100644
--- a/divvy/compute.py
+++ b/divvy/compute.py
@@ -327,7 +327,7 @@ def add_subparser(cmd):
 
     args, remaining_args = parser.parse_known_args()
     keys = [str.replace(x, "--", "") for x in remaining_args[::2]]
-    custom_vars = dict(zip(keys, remaining_args[1::2]))
+    cli_vars = dict(zip(keys, remaining_args[1::2]))
     dcc = ComputingConfiguration(args.config)
 
     if args.command == "list":
@@ -337,12 +337,12 @@ def add_subparser(cmd):
 
     dcc.activate_package(args.package)
     if args.settings:
+        _LOGGER.info("Loading settings file: %s", args.settings)
         with open(args.settings, 'r') as f:
-            _LOGGER.info("Loading yaml settings file: %s", args.settings)
-            yaml_vars = yaml.load(f, SafeLoader)
-        dcc.write_script(args.outfile, [custom_vars, yaml_vars])
+            vars_groups = [cli_vars, yaml.load(f, SafeLoader)]
     else:
-        dcc.write_script(args.outfile, custom_vars)
+        vars_groups = [cli_vars]
+    dcc.write_script(args.outfile, vars_groups)
 
 
 if __name__ == '__main__':