From 20d49fa34a4fbf2fe30de0e5bfc9d778ea512237 Mon Sep 17 00:00:00 2001
From: hpatel426 <harsh.j.patel@nasa.gov>
Date: Wed, 18 Oct 2023 12:22:48 -0400
Subject: [PATCH 01/12] updated docker path and moved it to root directory

---
 docker/Dockerfile => Dockerfile | 10 ++++++----
 docker/Readme.md                |  8 --------
 2 files changed, 6 insertions(+), 12 deletions(-)
 rename docker/Dockerfile => Dockerfile (88%)
 delete mode 100644 docker/Readme.md

diff --git a/docker/Dockerfile b/Dockerfile
similarity index 88%
rename from docker/Dockerfile
rename to Dockerfile
index 1f74124..dc88fad 100644
--- a/docker/Dockerfile
+++ b/Dockerfile
@@ -9,8 +9,9 @@ RUN apt-get update \
     #hdf5-helpers \
     && pip3 install --upgrade pip \
     && pip3 install cython \
-    && apt-get clean \
-    && pip3 install poetry
+    && pip3 install poetry \
+    && apt-get clean
+   
 
 # Create a new user
 RUN adduser --quiet --disabled-password --shell /bin/sh --home /home/dockeruser --gecos "" --uid 1000 dockeruser
@@ -28,12 +29,13 @@ ARG DIST_PATH
 
 USER root
 RUN mkdir -p /worker && chown dockeruser /worker
-COPY ../pyproject.toml /worker 
+COPY pyproject.toml /worker 
+# COPY ../pyproject.toml /worker 
 USER dockeruser
 
 WORKDIR /worker
 
-ENV PYTHONPATH=${PYTHONPATH}:${PWD}
+# ENV PYTHONPATH=${PYTHONPATH}:${PWD}
 
 COPY --chown=dockeruser $DIST_PATH $DIST_PATH
 USER dockeruser
diff --git a/docker/Readme.md b/docker/Readme.md
deleted file mode 100644
index 5f05138..0000000
--- a/docker/Readme.md
+++ /dev/null
@@ -1,8 +0,0 @@
-# Batchee Service Docker Image
-
-This directory contains the `Dockerfile` used to build the Docker image capable of running the Batchee service.
-
-## Building
-
-The docker image is setup to install the Batchee project into userspace using pip. It will look
-in both PyPi and TestPyPi indexes unless building from a local wheel file.
\ No newline at end of file

From 31e377fc4b3a824dc7cb89dd5881bef018717623 Mon Sep 17 00:00:00 2001
From: danielfromearth <daniel.kaufman@nasa.gov>
Date: Mon, 23 Oct 2023 16:39:54 -0400
Subject: [PATCH 02/12] remove dockerfile linting

---
 .pre-commit-config.yaml | 6 ------
 1 file changed, 6 deletions(-)

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 2aa0f30..ba7dee6 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -38,9 +38,3 @@ repos:
       - id: yamllint
         args: ["-d {extends: relaxed, rules: {line-length: {max: 120}}}"]
         stages: [commit, push]
-
-  - repo: https://github.com/pryorda/dockerfilelint-precommit-hooks
-    rev: v0.1.0
-    hooks:
-      - id: dockerfilelint
-        stages: [commit, push]

From 145c7771415f467525d0844c97b6385179af3b63 Mon Sep 17 00:00:00 2001
From: danielfromearth <daniel.kaufman@nasa.gov>
Date: Mon, 23 Oct 2023 16:43:08 -0400
Subject: [PATCH 03/12] add docker entry point script

---
 Dockerfile           | 10 +++++-----
 docker-entrypoint.sh | 10 ++++++++++
 2 files changed, 15 insertions(+), 5 deletions(-)
 create mode 100644 docker-entrypoint.sh

diff --git a/Dockerfile b/Dockerfile
index dc88fad..67dc7b2 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -11,7 +11,7 @@ RUN apt-get update \
     && pip3 install cython \
     && pip3 install poetry \
     && apt-get clean
-   
+
 
 # Create a new user
 RUN adduser --quiet --disabled-password --shell /bin/sh --home /home/dockeruser --gecos "" --uid 1000 dockeruser
@@ -29,8 +29,8 @@ ARG DIST_PATH
 
 USER root
 RUN mkdir -p /worker && chown dockeruser /worker
-COPY pyproject.toml /worker 
-# COPY ../pyproject.toml /worker 
+COPY pyproject.toml /worker
+# COPY ../pyproject.toml /worker
 USER dockeruser
 
 WORKDIR /worker
@@ -48,5 +48,5 @@ RUN poetry config virtualenvs.create false
 RUN poetry install --no-dev
 
 USER dockeruser
-# Run the Batchee Harmony service
-ENTRYPOINT ["batchee_harmony"]
\ No newline at end of file
+# Run the service
+ENTRYPOINT ["./docker-entrypoint.sh"]
diff --git a/docker-entrypoint.sh b/docker-entrypoint.sh
new file mode 100644
index 0000000..9ce02d6
--- /dev/null
+++ b/docker-entrypoint.sh
@@ -0,0 +1,10 @@
+#!/bin/bash
+set -e
+
+if [ "$1" = 'batchee' ]; then
+  exec batchee "$@"
+elif [ "$1" = 'batchee_harmony' ]; then
+  exec batchee_harmony "$@"
+else
+  exec batchee_harmony "$@"
+fi

From 2937143d9f069329ff264b7fa5aede50c0bcc69b Mon Sep 17 00:00:00 2001
From: danielfromearth <daniel.kaufman@nasa.gov>
Date: Mon, 23 Oct 2023 17:18:50 -0400
Subject: [PATCH 04/12] remove argv for harmony cli

---
 batcher/harmony/cli.py | 21 ++++++++-------------
 1 file changed, 8 insertions(+), 13 deletions(-)

diff --git a/batcher/harmony/cli.py b/batcher/harmony/cli.py
index 61756ff..802d373 100644
--- a/batcher/harmony/cli.py
+++ b/batcher/harmony/cli.py
@@ -1,5 +1,4 @@
 """A Harmony CLI wrapper around the concatenate-batcher"""
-import sys
 from argparse import ArgumentParser
 
 import harmony
@@ -7,27 +6,23 @@
 from batcher.harmony.service_adapter import ConcatBatching as HarmonyAdapter
 
 
-def main(argv, **kwargs):
-    """Main Harmony CLI entrypoint
+def main(config: harmony.util.Config = None) -> None:
+    """Parse command line arguments and invoke the service to respond to them.
 
-    Parses command line arguments and invokes the appropriate method to respond to them
+    Parameters
+    ----------
+    config : harmony.util.Config
+        harmony.util.Config is injectable for tests
 
     Returns
     -------
     None
     """
-
-    config = None
-    # Optional: harmony.util.Config is injectable for tests
-    if "config" in kwargs:
-        config = kwargs.get("config")
-
     parser = ArgumentParser(
         prog="Pre-concatenate-batching", description="Run the pre-concatenate-batching service"
     )
     harmony.setup_cli(parser)
-
-    args = parser.parse_args(argv[1:])
+    args = parser.parse_args()
     if harmony.is_harmony_cli(args):
         harmony.run_cli(parser, args, HarmonyAdapter, cfg=config)
     else:
@@ -35,4 +30,4 @@ def main(argv, **kwargs):
 
 
 if __name__ == "__main__":
-    main(sys.argv)
+    main()

From a333ebf0326308353dff2ba1794fb61c42c56b77 Mon Sep 17 00:00:00 2001
From: danielfromearth <daniel.kaufman@nasa.gov>
Date: Mon, 23 Oct 2023 17:19:26 -0400
Subject: [PATCH 05/12] make docker-entrypoint.sh executable

---
 docker-entrypoint.sh | 0
 1 file changed, 0 insertions(+), 0 deletions(-)
 mode change 100644 => 100755 docker-entrypoint.sh

diff --git a/docker-entrypoint.sh b/docker-entrypoint.sh
old mode 100644
new mode 100755

From f01a3adfc9ef655531df7b23695713bf7c6f595b Mon Sep 17 00:00:00 2001
From: danielfromearth <daniel.kaufman@nasa.gov>
Date: Mon, 23 Oct 2023 17:23:04 -0400
Subject: [PATCH 06/12] ensure script is owned by dockeruser

---
 Dockerfile | 1 +
 1 file changed, 1 insertion(+)

diff --git a/Dockerfile b/Dockerfile
index 67dc7b2..96036d1 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -48,5 +48,6 @@ RUN poetry config virtualenvs.create false
 RUN poetry install --no-dev
 
 USER dockeruser
+COPY --chown=dockeruser ./docker-entrypoint.sh docker-entrypoint.sh
 # Run the service
 ENTRYPOINT ["./docker-entrypoint.sh"]

From 504aacde93192ceb3fe8814ffe5c44f67ea321d2 Mon Sep 17 00:00:00 2001
From: danielfromearth <daniel.kaufman@nasa.gov>
Date: Mon, 30 Oct 2023 14:24:04 -0400
Subject: [PATCH 07/12] update environment dev dependencies

---
 poetry.lock    | 345 ++++++++++++++++++++++++-------------------------
 pyproject.toml |  14 +-
 2 files changed, 177 insertions(+), 182 deletions(-)

diff --git a/poetry.lock b/poetry.lock
index de9e5a3..8668aa3 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -2,33 +2,28 @@
 
 [[package]]
 name = "black"
-version = "23.9.1"
+version = "23.10.1"
 description = "The uncompromising code formatter."
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "black-23.9.1-cp310-cp310-macosx_10_16_arm64.whl", hash = "sha256:d6bc09188020c9ac2555a498949401ab35bb6bf76d4e0f8ee251694664df6301"},
-    {file = "black-23.9.1-cp310-cp310-macosx_10_16_universal2.whl", hash = "sha256:13ef033794029b85dfea8032c9d3b92b42b526f1ff4bf13b2182ce4e917f5100"},
-    {file = "black-23.9.1-cp310-cp310-macosx_10_16_x86_64.whl", hash = "sha256:75a2dc41b183d4872d3a500d2b9c9016e67ed95738a3624f4751a0cb4818fe71"},
-    {file = "black-23.9.1-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:13a2e4a93bb8ca74a749b6974925c27219bb3df4d42fc45e948a5d9feb5122b7"},
-    {file = "black-23.9.1-cp310-cp310-win_amd64.whl", hash = "sha256:adc3e4442eef57f99b5590b245a328aad19c99552e0bdc7f0b04db6656debd80"},
-    {file = "black-23.9.1-cp311-cp311-macosx_10_16_arm64.whl", hash = "sha256:8431445bf62d2a914b541da7ab3e2b4f3bc052d2ccbf157ebad18ea126efb91f"},
-    {file = "black-23.9.1-cp311-cp311-macosx_10_16_universal2.whl", hash = "sha256:8fc1ddcf83f996247505db6b715294eba56ea9372e107fd54963c7553f2b6dfe"},
-    {file = "black-23.9.1-cp311-cp311-macosx_10_16_x86_64.whl", hash = "sha256:7d30ec46de88091e4316b17ae58bbbfc12b2de05e069030f6b747dfc649ad186"},
-    {file = "black-23.9.1-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:031e8c69f3d3b09e1aa471a926a1eeb0b9071f80b17689a655f7885ac9325a6f"},
-    {file = "black-23.9.1-cp311-cp311-win_amd64.whl", hash = "sha256:538efb451cd50f43aba394e9ec7ad55a37598faae3348d723b59ea8e91616300"},
-    {file = "black-23.9.1-cp38-cp38-macosx_10_16_arm64.whl", hash = "sha256:638619a559280de0c2aa4d76f504891c9860bb8fa214267358f0a20f27c12948"},
-    {file = "black-23.9.1-cp38-cp38-macosx_10_16_universal2.whl", hash = "sha256:a732b82747235e0542c03bf352c126052c0fbc458d8a239a94701175b17d4855"},
-    {file = "black-23.9.1-cp38-cp38-macosx_10_16_x86_64.whl", hash = "sha256:cf3a4d00e4cdb6734b64bf23cd4341421e8953615cba6b3670453737a72ec204"},
-    {file = "black-23.9.1-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:cf99f3de8b3273a8317681d8194ea222f10e0133a24a7548c73ce44ea1679377"},
-    {file = "black-23.9.1-cp38-cp38-win_amd64.whl", hash = "sha256:14f04c990259576acd093871e7e9b14918eb28f1866f91968ff5524293f9c573"},
-    {file = "black-23.9.1-cp39-cp39-macosx_10_16_arm64.whl", hash = "sha256:c619f063c2d68f19b2d7270f4cf3192cb81c9ec5bc5ba02df91471d0b88c4c5c"},
-    {file = "black-23.9.1-cp39-cp39-macosx_10_16_universal2.whl", hash = "sha256:6a3b50e4b93f43b34a9d3ef00d9b6728b4a722c997c99ab09102fd5efdb88325"},
-    {file = "black-23.9.1-cp39-cp39-macosx_10_16_x86_64.whl", hash = "sha256:c46767e8df1b7beefb0899c4a95fb43058fa8500b6db144f4ff3ca38eb2f6393"},
-    {file = "black-23.9.1-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:50254ebfa56aa46a9fdd5d651f9637485068a1adf42270148cd101cdf56e0ad9"},
-    {file = "black-23.9.1-cp39-cp39-win_amd64.whl", hash = "sha256:403397c033adbc45c2bd41747da1f7fc7eaa44efbee256b53842470d4ac5a70f"},
-    {file = "black-23.9.1-py3-none-any.whl", hash = "sha256:6ccd59584cc834b6d127628713e4b6b968e5f79572da66284532525a042549f9"},
-    {file = "black-23.9.1.tar.gz", hash = "sha256:24b6b3ff5c6d9ea08a8888f6977eae858e1f340d7260cf56d70a49823236b62d"},
+    {file = "black-23.10.1-cp310-cp310-macosx_10_16_arm64.whl", hash = "sha256:ec3f8e6234c4e46ff9e16d9ae96f4ef69fa328bb4ad08198c8cee45bb1f08c69"},
+    {file = "black-23.10.1-cp310-cp310-macosx_10_16_x86_64.whl", hash = "sha256:1b917a2aa020ca600483a7b340c165970b26e9029067f019e3755b56e8dd5916"},
+    {file = "black-23.10.1-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:9c74de4c77b849e6359c6f01987e94873c707098322b91490d24296f66d067dc"},
+    {file = "black-23.10.1-cp310-cp310-win_amd64.whl", hash = "sha256:7b4d10b0f016616a0d93d24a448100adf1699712fb7a4efd0e2c32bbb219b173"},
+    {file = "black-23.10.1-cp311-cp311-macosx_10_16_arm64.whl", hash = "sha256:b15b75fc53a2fbcac8a87d3e20f69874d161beef13954747e053bca7a1ce53a0"},
+    {file = "black-23.10.1-cp311-cp311-macosx_10_16_x86_64.whl", hash = "sha256:e293e4c2f4a992b980032bbd62df07c1bcff82d6964d6c9496f2cd726e246ace"},
+    {file = "black-23.10.1-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:7d56124b7a61d092cb52cce34182a5280e160e6aff3137172a68c2c2c4b76bcb"},
+    {file = "black-23.10.1-cp311-cp311-win_amd64.whl", hash = "sha256:3f157a8945a7b2d424da3335f7ace89c14a3b0625e6593d21139c2d8214d55ce"},
+    {file = "black-23.10.1-cp38-cp38-macosx_10_16_arm64.whl", hash = "sha256:cfcce6f0a384d0da692119f2d72d79ed07c7159879d0bb1bb32d2e443382bf3a"},
+    {file = "black-23.10.1-cp38-cp38-macosx_10_16_x86_64.whl", hash = "sha256:33d40f5b06be80c1bbce17b173cda17994fbad096ce60eb22054da021bf933d1"},
+    {file = "black-23.10.1-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:840015166dbdfbc47992871325799fd2dc0dcf9395e401ada6d88fe11498abad"},
+    {file = "black-23.10.1-cp38-cp38-win_amd64.whl", hash = "sha256:037e9b4664cafda5f025a1728c50a9e9aedb99a759c89f760bd83730e76ba884"},
+    {file = "black-23.10.1-cp39-cp39-macosx_10_16_arm64.whl", hash = "sha256:7cb5936e686e782fddb1c73f8aa6f459e1ad38a6a7b0e54b403f1f05a1507ee9"},
+    {file = "black-23.10.1-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:5ed45ac9a613fb52dad3b61c8dea2ec9510bf3108d4db88422bacc7d1ba1243d"},
+    {file = "black-23.10.1-cp39-cp39-win_amd64.whl", hash = "sha256:6d23d7822140e3fef190734216cefb262521789367fbdc0b3f22af6744058982"},
+    {file = "black-23.10.1-py3-none-any.whl", hash = "sha256:d431e6739f727bb2e0495df64a6c7a5310758e87505f5f8cde9ff6c0f2d7e4fe"},
+    {file = "black-23.10.1.tar.gz", hash = "sha256:1f8ce316753428ff68749c65a5f7844631aa18c8679dfd3ca9dc1a289979c258"},
 ]
 
 [package.dependencies]
@@ -48,17 +43,17 @@ uvloop = ["uvloop (>=0.15.2)"]
 
 [[package]]
 name = "boto3"
-version = "1.28.60"
+version = "1.28.73"
 description = "The AWS SDK for Python"
 optional = false
 python-versions = ">= 3.7"
 files = [
-    {file = "boto3-1.28.60-py3-none-any.whl", hash = "sha256:d5f270c2c9a051f78c308cbba4268458e8df441057b73ba140742707ac1bc7ea"},
-    {file = "boto3-1.28.60.tar.gz", hash = "sha256:dccb49cc10b31314b8553c6c9614c44b2249e0d0285d73f608a5d2010f6e1d82"},
+    {file = "boto3-1.28.73-py3-none-any.whl", hash = "sha256:bbe377a288b6b12b526fae3b3d743318c6868626cf67e1e97f104345a5194b1e"},
+    {file = "boto3-1.28.73.tar.gz", hash = "sha256:a61cf96f7e196b1450afdf4856b7ea0e58080752e687b0011157be96934489be"},
 ]
 
 [package.dependencies]
-botocore = ">=1.31.60,<1.32.0"
+botocore = ">=1.31.73,<1.32.0"
 jmespath = ">=0.7.1,<2.0.0"
 s3transfer = ">=0.7.0,<0.8.0"
 
@@ -67,19 +62,19 @@ crt = ["botocore[crt] (>=1.21.0,<2.0a0)"]
 
 [[package]]
 name = "botocore"
-version = "1.31.60"
+version = "1.31.73"
 description = "Low-level, data-driven core of boto 3."
 optional = false
 python-versions = ">= 3.7"
 files = [
-    {file = "botocore-1.31.60-py3-none-any.whl", hash = "sha256:b6de7a6a03ca3da18b78615a2cb5221c9fdb9483d3f50cb4281ae038b3f22d9f"},
-    {file = "botocore-1.31.60.tar.gz", hash = "sha256:578470a15a5bd64f67437a81f23feccba85084167acf63c56acada2c1c1d95d8"},
+    {file = "botocore-1.31.73-py3-none-any.whl", hash = "sha256:6e9caaa7205e0c0505f4868a4053e96eaf3f4b6bce0368a46970a8efeeacb492"},
+    {file = "botocore-1.31.73.tar.gz", hash = "sha256:5334c22d5a3f4643931896137c57b2496fef005b039d87d8740e7a28eb31519d"},
 ]
 
 [package.dependencies]
 jmespath = ">=0.7.1,<2.0.0"
 python-dateutil = ">=2.1,<3.0.0"
-urllib3 = ">=1.25.4,<1.27"
+urllib3 = {version = ">=1.25.4,<2.1", markers = "python_version >= \"3.10\""}
 
 [package.extras]
 crt = ["awscrt (==0.16.26)"]
@@ -161,101 +156,101 @@ pycparser = "*"
 
 [[package]]
 name = "charset-normalizer"
-version = "3.3.0"
+version = "3.3.1"
 description = "The Real First Universal Charset Detector. Open, modern and actively maintained alternative to Chardet."
 optional = false
 python-versions = ">=3.7.0"
 files = [
-    {file = "charset-normalizer-3.3.0.tar.gz", hash = "sha256:63563193aec44bce707e0c5ca64ff69fa72ed7cf34ce6e11d5127555756fd2f6"},
-    {file = "charset_normalizer-3.3.0-cp310-cp310-macosx_10_9_universal2.whl", hash = "sha256:effe5406c9bd748a871dbcaf3ac69167c38d72db8c9baf3ff954c344f31c4cbe"},
-    {file = "charset_normalizer-3.3.0-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:4162918ef3098851fcd8a628bf9b6a98d10c380725df9e04caf5ca6dd48c847a"},
-    {file = "charset_normalizer-3.3.0-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:0570d21da019941634a531444364f2482e8db0b3425fcd5ac0c36565a64142c8"},
-    {file = "charset_normalizer-3.3.0-cp310-cp310-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:5707a746c6083a3a74b46b3a631d78d129edab06195a92a8ece755aac25a3f3d"},
-    {file = "charset_normalizer-3.3.0-cp310-cp310-manylinux_2_17_ppc64le.manylinux2014_ppc64le.whl", hash = "sha256:278c296c6f96fa686d74eb449ea1697f3c03dc28b75f873b65b5201806346a69"},
-    {file = "charset_normalizer-3.3.0-cp310-cp310-manylinux_2_17_s390x.manylinux2014_s390x.whl", hash = "sha256:a4b71f4d1765639372a3b32d2638197f5cd5221b19531f9245fcc9ee62d38f56"},
-    {file = "charset_normalizer-3.3.0-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:f5969baeaea61c97efa706b9b107dcba02784b1601c74ac84f2a532ea079403e"},
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+    {file = "mypy-1.6.1-cp39-cp39-win_amd64.whl", hash = "sha256:a43ef1c8ddfdb9575691720b6352761f3f53d85f1b57d7745701041053deff30"},
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+    {file = "mypy-1.6.1.tar.gz", hash = "sha256:4d01c00d09a0be62a4ca3f933e315455bde83f37f892ba4b08ce92f3cf44bcc1"},
 ]
 
 [package.dependencies]
@@ -593,13 +588,13 @@ validation = ["jsonschema (==3.2.0)"]
 
 [[package]]
 name = "pytest"
-version = "7.4.2"
+version = "7.4.3"
 description = "pytest: simple powerful testing with Python"
 optional = false
 python-versions = ">=3.7"
 files = [
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-    {file = "pytest-7.4.2.tar.gz", hash = "sha256:a766259cfab564a2ad52cb1aae1b881a75c3eb7e34ca3779697c23ed47c47069"},
+    {file = "pytest-7.4.3-py3-none-any.whl", hash = "sha256:0d009c083ea859a71b76adf7c1d502e4bc170b80a8ef002da5806527b9591fac"},
+    {file = "pytest-7.4.3.tar.gz", hash = "sha256:d989d136982de4e3b29dabcc838ad581c64e8ed52c11fbe86ddebd9da0818cd5"},
 ]
 
 [package.dependencies]
@@ -661,28 +656,28 @@ use-chardet-on-py3 = ["chardet (>=3.0.2,<6)"]
 
 [[package]]
 name = "ruff"
-version = "0.0.292"
+version = "0.1.3"
 description = "An extremely fast Python linter, written in Rust."
 optional = false
 python-versions = ">=3.7"
 files = [
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+    {file = "ruff-0.1.3-py3-none-win32.whl", hash = "sha256:3e7afcbdcfbe3399c34e0f6370c30f6e529193c731b885316c5a09c9e4317eef"},
+    {file = "ruff-0.1.3-py3-none-win_amd64.whl", hash = "sha256:7a18df6638cec4a5bd75350639b2bb2a2366e01222825562c7346674bdceb7ea"},
+    {file = "ruff-0.1.3-py3-none-win_arm64.whl", hash = "sha256:12fd53696c83a194a2db7f9a46337ce06445fb9aa7d25ea6f293cf75b21aca9f"},
+    {file = "ruff-0.1.3.tar.gz", hash = "sha256:3ba6145369a151401d5db79f0a47d50e470384d0d89d0d6f7fab0b589ad07c34"},
 ]
 
 [[package]]
@@ -737,13 +732,13 @@ files = [
 
 [[package]]
 name = "urllib3"
-version = "1.26.17"
+version = "1.26.18"
 description = "HTTP library with thread-safe connection pooling, file post, and more."
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*, !=3.5.*"
 files = [
-    {file = "urllib3-1.26.17-py2.py3-none-any.whl", hash = "sha256:94a757d178c9be92ef5539b8840d48dc9cf1b2709c9d6b588232a055c524458b"},
-    {file = "urllib3-1.26.17.tar.gz", hash = "sha256:24d6a242c28d29af46c3fae832c36db3bbebcc533dd1bb549172cd739c82df21"},
+    {file = "urllib3-1.26.18-py2.py3-none-any.whl", hash = "sha256:34b97092d7e0a3a8cf7cd10e386f401b3737364026c45e622aa02903dffe0f07"},
+    {file = "urllib3-1.26.18.tar.gz", hash = "sha256:f8ecc1bba5667413457c529ab955bf8c67b45db799d159066261719e328580a0"},
 ]
 
 [package.extras]
@@ -754,4 +749,4 @@ socks = ["PySocks (>=1.5.6,!=1.5.7,<2.0)"]
 [metadata]
 lock-version = "2.0"
 python-versions = "^3.10"
-content-hash = "2eddcedad9f6e921f2e1b770870a16780915ca6765fc63cc2c0a8130744fe001"
+content-hash = "9c722742a6cbadda08136c86fff9245e1c40bb4f52a0e23e91a5560cfe52c820"
diff --git a/pyproject.toml b/pyproject.toml
index 15bf7d4..9908810 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -15,17 +15,17 @@ packages = [
 python = "^3.10"
 harmony-service-lib = "^1.0.23"
 
-[tool.poetry.group.dev.dependencies]
-pytest = "^7.4.2"
-black = "^23.9.1"
-mypy = "^1.5.1"
-ruff = "^0.0.292"
-coverage = "^7.3.2"
-
 [tool.poetry.scripts]
 batchee_harmony = 'batcher.harmony.cli:main'
 batchee = 'batcher.tempo_filename_parser:main'
 
+[tool.poetry.group.dev.dependencies]
+coverage = "^7.3.2"
+ruff = "^0.1.3"
+pytest = "^7.4.3"
+black = "^23.10.1"
+mypy = "^1.6.1"
+
 [build-system]
 requires = ["poetry-core"]
 build-backend = "poetry.core.masonry.api"

From 9a651615df9a4aba3b5458bbdfdda30c9f56d89e Mon Sep 17 00:00:00 2001
From: danielfromearth <daniel.kaufman@nasa.gov>
Date: Mon, 30 Oct 2023 14:26:42 -0400
Subject: [PATCH 08/12] add logging messages

---
 batcher/harmony/service_adapter.py | 11 ++++++++++-
 batcher/tempo_filename_parser.py   |  8 +++++++-
 2 files changed, 17 insertions(+), 2 deletions(-)

diff --git a/batcher/harmony/service_adapter.py b/batcher/harmony/service_adapter.py
index f6078fa..e2c7a74 100644
--- a/batcher/harmony/service_adapter.py
+++ b/batcher/harmony/service_adapter.py
@@ -50,6 +50,7 @@ def invoke(self):
 
     def process_catalog(self, catalog: pystac.Catalog):
         """Converts a list of STAC catalogs into a list of lists of STAC catalogs."""
+        self.logger.info("process_catalog() started.")
         try:
             result = catalog.clone()
             result.id = str(uuid4())
@@ -58,16 +59,20 @@ def process_catalog(self, catalog: pystac.Catalog):
             # Get all the items from the catalog, including from child or linked catalogs
             items = list(self.get_all_catalog_items(catalog))
 
+            self.logger.info(f"length of items==={len(items)}.")
+
             # Quick return if catalog contains no items
             if len(items) == 0:
                 return result
 
             # # --- Get granule filepaths (urls) ---
             netcdf_urls: list[str] = _get_netcdf_urls(items)
+            self.logger.info(f"netcdf_urls==={netcdf_urls}.")
 
             # --- Map each granule to an index representing the batch to which it belongs ---
-            batch_indices: list[int] = get_batch_indices(netcdf_urls)
+            batch_indices: list[int] = get_batch_indices(netcdf_urls, self.logger)
             sorted(set(batch_indices), key=batch_indices.index)
+            self.logger.info(f"batch_indices==={batch_indices}.")
 
             # --- Construct a dictionary with a separate key for each batch ---
             grouped: dict[int, list[Item]] = {}
@@ -83,6 +88,8 @@ def process_catalog(self, catalog: pystac.Catalog):
                 bounding_box = _get_output_bounding_box(batch_items)
                 properties = _get_output_date_range(batch_items)
 
+                self.logger.info(f"constructing new pystac.Item for batch_id==={batch_id}.")
+
                 # Construct a new pystac.Item with every granule in the batch as a pystac.Asset
                 output_item = Item(
                     str(uuid4()), bbox_to_geometry(bounding_box), bounding_box, None, properties
@@ -101,6 +108,8 @@ def process_catalog(self, catalog: pystac.Catalog):
 
                 result.add_item(output_item)
 
+            self.logger.info("STAC catalog creation complete.")
+
             return result
 
         except Exception as service_exception:
diff --git a/batcher/tempo_filename_parser.py b/batcher/tempo_filename_parser.py
index 7d6dbe4..06488d4 100644
--- a/batcher/tempo_filename_parser.py
+++ b/batcher/tempo_filename_parser.py
@@ -4,6 +4,8 @@
 from argparse import ArgumentParser
 from pathlib import Path
 
+default_logger = logging.getLogger(__name__)
+
 tempo_granule_filename_pattern = re.compile(
     r"^.*TEMPO_"
     r"(?P<product_type>[1-9A-Z]+)"
@@ -17,13 +19,15 @@
 )
 
 
-def get_batch_indices(filenames: list) -> list[int]:
+def get_batch_indices(filenames: list, logger: logging.Logger = default_logger) -> list[int]:
     """
     Returns
     -------
     list[int]
         batch index for each filename in the original list, e.g. [0, 0, 0, 1, 1, 1, ...]
     """
+    logger.info(f"get_batch_indices() starting --- with {len(filenames)} filenames")
+
     # Make a new list with days and scans, e.g. [('20130701', 'S009'), ('20130701', 'S009'), ...]
     day_and_scans: list[tuple[str, str]] = []
     for name in filenames:
@@ -35,6 +39,8 @@ def get_batch_indices(filenames: list) -> list[int]:
     # Unique day-scans are determined (while keeping the same order). Each will be its own batch.
     unique_day_scans: list[tuple[str, str]] = sorted(set(day_and_scans), key=day_and_scans.index)
 
+    logger.info(f"unique_day_scans==={unique_day_scans}.")
+
     # Map each day/scan to an integer
     batch_mapper: dict[tuple[str, str], int] = {
         day_scan: idx for idx, day_scan in enumerate(unique_day_scans)

From a988a5d8df43fa7a75152b35a918fc6fbc106e31 Mon Sep 17 00:00:00 2001
From: danielfromearth <daniel.kaufman@nasa.gov>
Date: Mon, 30 Oct 2023 15:05:21 -0400
Subject: [PATCH 09/12] add missing pytest-cov

---
 poetry.lock    | 4 ++--
 pyproject.toml | 1 +
 2 files changed, 3 insertions(+), 2 deletions(-)

diff --git a/poetry.lock b/poetry.lock
index b7e2cce..f53d2bd 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -1,4 +1,4 @@
-# This file is automatically @generated by Poetry 1.6.1 and should not be changed by hand.
+# This file is automatically @generated by Poetry 1.5.1 and should not be changed by hand.
 
 [[package]]
 name = "black"
@@ -770,4 +770,4 @@ socks = ["PySocks (>=1.5.6,!=1.5.7,<2.0)"]
 [metadata]
 lock-version = "2.0"
 python-versions = "^3.10"
-content-hash = "9c722742a6cbadda08136c86fff9245e1c40bb4f52a0e23e91a5560cfe52c820"
+content-hash = "13d72d5e93ac5ddb6bd054b98d9cf04ed920d251e91e623fb0a48a17b777cf2e"
diff --git a/pyproject.toml b/pyproject.toml
index 9908810..1c090dd 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -25,6 +25,7 @@ ruff = "^0.1.3"
 pytest = "^7.4.3"
 black = "^23.10.1"
 mypy = "^1.6.1"
+pytest-cov = "^4.1.0"
 
 [build-system]
 requires = ["poetry-core"]

From 1d9fc925d21e14612864aa9a51787c12aa46e83c Mon Sep 17 00:00:00 2001
From: danielfromearth <daniel.kaufman@nasa.gov>
Date: Mon, 30 Oct 2023 15:48:54 -0400
Subject: [PATCH 10/12] increment the STAC Asset key so the assets aren't
 overridden

---
 batcher/harmony/service_adapter.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/batcher/harmony/service_adapter.py b/batcher/harmony/service_adapter.py
index e2c7a74..31bff4b 100644
--- a/batcher/harmony/service_adapter.py
+++ b/batcher/harmony/service_adapter.py
@@ -97,7 +97,7 @@ def process_catalog(self, catalog: pystac.Catalog):
 
                 for idx, item in enumerate(batch_items):
                     output_item.add_asset(
-                        "data",
+                        f"data_{idx}",
                         Asset(
                             batch_urls[idx],
                             title=batch_urls[idx],

From 4fe867b6b86b56609ffd857175dfbddf12869829 Mon Sep 17 00:00:00 2001
From: danielfromearth <daniel.kaufman@nasa.gov>
Date: Tue, 31 Oct 2023 13:05:23 -0400
Subject: [PATCH 11/12] update CHANGELOG.md

---
 CHANGELOG.md | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index c309092..f8b85f1 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -7,9 +7,10 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 ## [Unreleased]
 
 ### Added
+- [issue/6](https://github.com/danielfromearth/batchee/issues/6): Create Adapter code that processes a Harmony Message and STAC Catalog
+- [issue/7](https://github.com/danielfromearth/batchee/issues/7): Create working Docker image
 - [issue/13](https://github.com/danielfromearth/batchee/issues/13): Add simple command line interface for testing
 - [issue/16](https://github.com/danielfromearth/batchee/issues/16): Add a logo
-- [issue/6](https://github.com/danielfromearth/batchee/issues/6): Create Adapter code that processes a Harmony Message and STAC Catalog
 ### Changed
 - [issue/11](https://github.com/danielfromearth/batchee/issues/11): Rename from concat_batcher to batchee
 - [issue/21](https://github.com/danielfromearth/batchee/issues/21): Improve CICD workflows

From 4420c19c127ce02427684daac05bd5ca92a2cae7 Mon Sep 17 00:00:00 2001
From: danielfromearth <daniel.kaufman@nasa.gov>
Date: Tue, 31 Oct 2023 13:11:03 -0400
Subject: [PATCH 12/12] update README.md

---
 README.md | 33 +++++++++++++++++++++++++++++++++
 1 file changed, 33 insertions(+)

diff --git a/README.md b/README.md
index a6e3a04..0811fa8 100644
--- a/README.md
+++ b/README.md
@@ -5,3 +5,36 @@
 _____
 
 _Batchee_ groups together filenames so that further operations (such as concatenation) can be performed separately on each group of files.
+
+## Installing
+_____
+
+For local development, one can clone the repository and then use poetry or pip from the local directory:
+
+```shell
+git clone <Repository URL>
+```
+
+###### (Option A) using poetry:
+i) Follow the instructions for installing `poetry` [here](https://python-poetry.org/docs/).
+
+ii) Run ```poetry install``` from the repository directory.
+
+###### (Option B) using pip: Run ```pip install .``` from the repository directory.
+
+## Usage
+_____
+
+```shell
+batchee [file_names ...]
+```
+
+###### Or, If installed using a `poetry` environment:
+```shell
+poetry run batchee [file_names ...]
+```
+
+#### Options
+
+- `-h`, `--help`            show this help message and exit
+- `-v`, `--verbose`  Enable verbose output to stdout; useful for debugging