HARMONY-166: Respond to pull request comments

README.md

@@ -79,6 +79,5 @@ bin/test
 
 Run an example:
 ```
-pip install -U "python-dotenv[cli]"
 dotenv python -m harmony_netcdf_to_zarr --harmony-action invoke --harmony-input "`cat example/harmony-operation.json`"
 ```

bin/push-image

@@ -5,7 +5,7 @@ set -ex
 image="harmony/netcdf-to-zarr"
 tag=${1:-latest}
 
-region=${AWS_DEFAULT_REGION-"us-west-2"}
+region=${AWS_DEFAULT_REGION:-"us-west-2"}
 
 account=$(aws sts get-caller-identity --output text --query 'Account')
 # Need to remove \r returned on all aws commands run from Bamboo

bin/repl-with-zarr-opener

@@ -18,8 +18,8 @@ def open_localstack_zarr(name):
         client_kwargs=dict(
             region_name='us-west-2',
             endpoint_url='http://localhost:4572',
-            aws_access_key_id='ACCESS_KEY',
-            aws_secret_access_key='SECRET_KEY'))
+            aws_access_key_id='DUMMY_ACCESS_KEY',
+            aws_secret_access_key='DUMMY_SECRET_KEY'))
     store = fs.get_mapper(root=name, check=False)
     return zarr.open(store)
 EOF)"

bin/run-in-docker

@@ -1,11 +1,20 @@
 #!/bin/bash
 
+# This script mounts the contents of the current directory, and optionally the Python library in a peer
+# directory into the Harmony docker image and runs it.  It is meant to allow development and testing
+# without repeatedly rebuilding the docker image.  To run a completely clean container using only what
+# is in the image, as will be done in deployed environments, run
+# `docker run --rm -it --env-file=.env harmony/netcdf-to-zarr`
+
 set -ex
 
 find . | grep -E "(__pycache__|\.pyc|\.pyo$)" | xargs rm -rf
 
+# CLI flags.  Mount the current directory into the docker container's working directory
 args="-v $(pwd):/home"
 
+# If a peer directory exists for the Harmony python library, also mount it into the container, otherwise
+# it will use the version installed when the container was built
 if [ -d ../harmony-service-lib-py ]; then
   (cd ../harmony-service-lib-py && make clean)
   args="$args -v $(pwd)/../harmony-service-lib-py/harmony:/usr/lib/harmony-service-lib-py/harmony"

bin/test-in-docker

@@ -2,6 +2,12 @@
 
 set -e
 
+# This script mounts the contents of the current directory, and optionally the Python library in a peer
+# directory into the Harmony docker image and runs the test suite.  It is meant to allow development and
+# testing without repeatedly rebuilding the docker image.  To run a completely clean container using only
+#  what is in the image, as will be done in CI environments, run
+# `docker run --rm -it --env-file=.env harmony/netcdf-to-zarr-tests`
+
 find . | grep -E "(__pycache__|\.pyc|\.pyo$)" | xargs rm -rf
 
 args="-v $(pwd):/home"

example/dotenv

@@ -1,4 +1,4 @@
-# The environent.  If set to "dev" or "test" the code will not attempt to call back to
+# The environment.  If set to "dev" or "test" the code will not attempt to call back to
 # Harmony and will instead log the callbacks that would have been made.
 ENV=dev
 

harmony_netcdf_to_zarr/__main__.py

@@ -3,7 +3,7 @@
 __main__.py
 =========
 
-Runs the harmony_gdal CLI
+Runs the harmony_netcdf_to_zarr CLI
 """
 
 import sys

requirements/dev.txt

@@ -1,4 +1,5 @@
 pytest >= 5.1.2
 safety >= 1.8.5
 coverage >= 4.5.4
-moto >= 1.3.14
+moto >= 1.3.14
+python-dotenv>=0.12.0

tests/util/file_creation.py

@@ -71,7 +71,6 @@ def create_full_dataset(filename=None):
             [ -5.5,  0.0,  5.5],
             [-11.0, -5.5,  0.0]
         ]
-        #lats.make_scale('lat')
         lons[:, :] = np.rot90(lats, 3, axes=(0, 1))
 
         times[0] = 166536 # January 1st 2020