From b5e5c11bcd63fcf556d31e3753eb7b84e0a85e3e Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Wed, 13 Sep 2023 02:01:21 +0000
Subject: [PATCH 01/82] Bump crazy-max/ghaction-github-status from 3 to 4

Bumps [crazy-max/ghaction-github-status](https://github.com/crazy-max/ghaction-github-status) from 3 to 4.
- [Release notes](https://github.com/crazy-max/ghaction-github-status/releases)
- [Commits](https://github.com/crazy-max/ghaction-github-status/compare/v3...v4)

---
updated-dependencies:
- dependency-name: crazy-max/ghaction-github-status
  dependency-type: direct:production
  update-type: version-update:semver-major
...

Signed-off-by: dependabot[bot] <support@github.com>
---
 .github/workflows/build.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml
index e7b75a4..894bb58 100644
--- a/.github/workflows/build.yml
+++ b/.github/workflows/build.yml
@@ -27,7 +27,7 @@ jobs:
           egress-policy: audit
       - id: github-status
         name: Check GitHub status
-        uses: crazy-max/ghaction-github-status@v3
+        uses: crazy-max/ghaction-github-status@v4
       - id: dump-context
         name: Dump context
         uses: crazy-max/ghaction-dump-context@v2

From 371179ef14354df4d00d7f961754ddb86c30929b Mon Sep 17 00:00:00 2001
From: Jeremy Frasier <jeremy.frasier@gwe.cisa.dhs.gov>
Date: Wed, 13 Sep 2023 12:48:59 -0400
Subject: [PATCH 02/82] Add a diagnostics job for the label syncing workflow

Also add a runner hardening task to the labeler job.
---
 .github/workflows/sync-labels.yml | 24 ++++++++++++++++++++++++
 1 file changed, 24 insertions(+)

diff --git a/.github/workflows/sync-labels.yml b/.github/workflows/sync-labels.yml
index 44e8e19..5a20438 100644
--- a/.github/workflows/sync-labels.yml
+++ b/.github/workflows/sync-labels.yml
@@ -11,7 +11,26 @@ permissions:
   contents: read
 
 jobs:
+  diagnostics:
+    name: Run diagnostics
+    runs-on: ubuntu-latest
+    steps:
+      # Note that a duplicate of this step must be added at the top of
+      # each job.
+      - id: harden-runner
+        name: Harden the runner
+        uses: step-security/harden-runner@v2
+        with:
+          egress-policy: audit
+      - id: github-status
+        name: Check GitHub status
+        uses: crazy-max/ghaction-github-status@v3
+      - id: dump-context
+        name: Dump context
+        uses: crazy-max/ghaction-dump-context@v2
   labeler:
+    needs:
+      - diagnostics
     permissions:
       # actions/checkout needs this to fetch code
       contents: read
@@ -19,6 +38,11 @@ jobs:
       issues: write
     runs-on: ubuntu-latest
     steps:
+      - id: harden-runner
+        name: Harden the runner
+        uses: step-security/harden-runner@v2
+        with:
+          egress-policy: audit
       - uses: actions/checkout@v4
       - name: Sync repository labels
         if: success()

From 1f611fc67710100e3e6efeb395d67b82e3f52eaa Mon Sep 17 00:00:00 2001
From: Jeremy Frasier <jeremy.frasier@gwe.cisa.dhs.gov>
Date: Thu, 14 Sep 2023 15:45:17 -0400
Subject: [PATCH 03/82] Make the dev team the owners of the linter
 configuration files

Co-authored-by: Nick <50747025+mcdonnnj@users.noreply.github.com>
---
 .github/CODEOWNERS | 9 +++++++++
 1 file changed, 9 insertions(+)

diff --git a/.github/CODEOWNERS b/.github/CODEOWNERS
index 8f5c8c5..a22502d 100644
--- a/.github/CODEOWNERS
+++ b/.github/CODEOWNERS
@@ -8,3 +8,12 @@
 # These folks own any files in the .github directory at the root of
 # the repository and any of its subdirectories.
 /.github/ @dav3r @felddy @jasonodoom @jsf9k @mcdonnnj
+
+# These folks own all linting configuration files.
+/.*.cfg @dav3r @felddy @jasonodoom @jsf9k @mcdonnnj
+/.*.yaml @dav3r @felddy @jasonodoom @jsf9k @mcdonnnj
+/.*.yml @dav3r @felddy @jasonodoom @jsf9k @mcdonnnj
+/.ansible-lint @dav3r @felddy @jasonodoom @jsf9k @mcdonnnj
+/.flake8 @dav3r @felddy @jasonodoom @jsf9k @mcdonnnj
+/.prettierignore @dav3r @felddy @jasonodoom @jsf9k @mcdonnnj
+/.yamllint @dav3r @felddy @jasonodoom @jsf9k @mcdonnnj

From c356768305b027d915db7ef7be1126ee687757ad Mon Sep 17 00:00:00 2001
From: Jeremy Frasier <jeremy.frasier@gwe.cisa.dhs.gov>
Date: Thu, 14 Sep 2023 15:59:22 -0400
Subject: [PATCH 04/82] Make dev team members the codeowners of the
 requirements*.txt and setup-env files

Co-authored-by: Nick <50747025+mcdonnnj@users.noreply.github.com>
---
 .github/CODEOWNERS | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/.github/CODEOWNERS b/.github/CODEOWNERS
index a22502d..b4e689e 100644
--- a/.github/CODEOWNERS
+++ b/.github/CODEOWNERS
@@ -17,3 +17,5 @@
 /.flake8 @dav3r @felddy @jasonodoom @jsf9k @mcdonnnj
 /.prettierignore @dav3r @felddy @jasonodoom @jsf9k @mcdonnnj
 /.yamllint @dav3r @felddy @jasonodoom @jsf9k @mcdonnnj
+/requirements*.txt @dav3r @felddy @jasonodoom @jsf9k @mcdonnnj
+/setup-env @dav3r @felddy @jasonodoom @jsf9k @mcdonnnj

From 0195005cccab3e087ec8353c5049ea633d252835 Mon Sep 17 00:00:00 2001
From: Jeremy Frasier <jeremy.frasier@gwe.cisa.dhs.gov>
Date: Fri, 15 Sep 2023 10:26:45 -0400
Subject: [PATCH 05/82] Explicitly list the linter config files the dev team
 should own

@mcdonnnj correctly pointed out that other projects add their own
configuration files that match, e.g., the /.*.yaml pattern.  We want
to ensure that we only own the linter configuration files from the
skeleton.

Co-authored-by: Nick <50747025+mcdonnnj@users.noreply.github.com>
---
 .github/CODEOWNERS | 11 +++++++----
 1 file changed, 7 insertions(+), 4 deletions(-)

diff --git a/.github/CODEOWNERS b/.github/CODEOWNERS
index b4e689e..229920c 100644
--- a/.github/CODEOWNERS
+++ b/.github/CODEOWNERS
@@ -10,12 +10,15 @@
 /.github/ @dav3r @felddy @jasonodoom @jsf9k @mcdonnnj
 
 # These folks own all linting configuration files.
-/.*.cfg @dav3r @felddy @jasonodoom @jsf9k @mcdonnnj
-/.*.yaml @dav3r @felddy @jasonodoom @jsf9k @mcdonnnj
-/.*.yml @dav3r @felddy @jasonodoom @jsf9k @mcdonnnj
 /.ansible-lint @dav3r @felddy @jasonodoom @jsf9k @mcdonnnj
+/.bandit.yml @dav3r @felddy @jasonodoom @jsf9k @mcdonnnj
 /.flake8 @dav3r @felddy @jasonodoom @jsf9k @mcdonnnj
+/.isort.cfg @dav3r @felddy @jasonodoom @jsf9k @mcdonnnj
+/.mdl_config.yaml @dav3r @felddy @jasonodoom @jsf9k @mcdonnnj
+/.pre-commit-config.yaml @dav3r @felddy @jasonodoom @jsf9k @mcdonnnj
 /.prettierignore @dav3r @felddy @jasonodoom @jsf9k @mcdonnnj
 /.yamllint @dav3r @felddy @jasonodoom @jsf9k @mcdonnnj
-/requirements*.txt @dav3r @felddy @jasonodoom @jsf9k @mcdonnnj
+/requirements.txt @dav3r @felddy @jasonodoom @jsf9k @mcdonnnj
+/requirements-dev.txt @dav3r @felddy @jasonodoom @jsf9k @mcdonnnj
+/requirements-test.txt @dav3r @felddy @jasonodoom @jsf9k @mcdonnnj
 /setup-env @dav3r @felddy @jasonodoom @jsf9k @mcdonnnj

From b768a289e1702e9e46d81ad5a59f51abe666a976 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Mon, 30 Oct 2023 18:41:36 +0000
Subject: [PATCH 06/82] Bump hashicorp/setup-terraform from 2 to 3

Bumps [hashicorp/setup-terraform](https://github.com/hashicorp/setup-terraform) from 2 to 3.
- [Release notes](https://github.com/hashicorp/setup-terraform/releases)
- [Changelog](https://github.com/hashicorp/setup-terraform/blob/main/CHANGELOG.md)
- [Commits](https://github.com/hashicorp/setup-terraform/compare/v2...v3)

---
updated-dependencies:
- dependency-name: hashicorp/setup-terraform
  dependency-type: direct:production
  update-type: version-update:semver-major
...

Signed-off-by: dependabot[bot] <support@github.com>
---
 .github/workflows/build.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml
index e7b75a4..1ff72a9 100644
--- a/.github/workflows/build.yml
+++ b/.github/workflows/build.yml
@@ -101,7 +101,7 @@ jobs:
             ${{ env.CURL_CACHE_DIR }}/"${PACKER_ZIP}"
           sudo mv /usr/local/bin/packer /usr/local/bin/packer-default
           sudo ln -s /opt/packer/packer /usr/local/bin/packer
-      - uses: hashicorp/setup-terraform@v2
+      - uses: hashicorp/setup-terraform@v3
         with:
           terraform_version: ${{ steps.setup-env.outputs.terraform-version }}
       - name: Install go-critic

From 9f317002ac85066adc1efa05d9c2f55275ef7d9c Mon Sep 17 00:00:00 2001
From: Nicholas McDonnell <50747025+mcdonnnj@users.noreply.github.com>
Date: Thu, 2 Nov 2023 15:49:06 -0400
Subject: [PATCH 07/82] Prefer block style to flow style

We prefer block style to flow style for sequences and mappings in YAML.
---
 .github/workflows/build.yml | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml
index e7b75a4..9332263 100644
--- a/.github/workflows/build.yml
+++ b/.github/workflows/build.yml
@@ -5,7 +5,8 @@ on:
   push:
   pull_request:
   repository_dispatch:
-    types: [apb]
+    types:
+      - apb
 
 env:
   CURL_CACHE_DIR: ~/.cache/curl

From 696433ae2c3b3f9f2b3613562d3889c753c7bc34 Mon Sep 17 00:00:00 2001
From: Nicholas McDonnell <50747025+mcdonnnj@users.noreply.github.com>
Date: Thu, 2 Nov 2023 15:57:37 -0400
Subject: [PATCH 08/82] Alphabetize entries in the build workflow

We prefer to alphabetize mapping keys in YAML documents whenever
possible.
---
 .github/workflows/build.yml | 14 +++++++-------
 1 file changed, 7 insertions(+), 7 deletions(-)

diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml
index 9332263..2fef5d5 100644
--- a/.github/workflows/build.yml
+++ b/.github/workflows/build.yml
@@ -2,8 +2,8 @@
 name: build
 
 on:
-  push:
   pull_request:
+  push:
   repository_dispatch:
     types:
       - apb
@@ -58,8 +58,8 @@ jobs:
           # it relies on the existence of a go.sum file.
           cache: false
           go-version: "1.20"
-      - name: Lookup Go cache directory
-        id: go-cache
+      - id: go-cache
+        name: Lookup Go cache directory
         run: |
           echo "dir=$(go env GOCACHE)" >> $GITHUB_OUTPUT
       - uses: actions/cache@v3
@@ -70,6 +70,10 @@ jobs:
             packer${{ steps.setup-env.outputs.packer-version }}-\
             tf${{ steps.setup-env.outputs.terraform-version }}-"
         with:
+          key: "${{ env.BASE_CACHE_KEY }}\
+            ${{ hashFiles('**/requirements-test.txt') }}-\
+            ${{ hashFiles('**/requirements.txt') }}-\
+            ${{ hashFiles('**/.pre-commit-config.yaml') }}"
           # Note that the .terraform directory IS NOT included in the
           # cache because if we were caching, then we would need to use
           # the `-upgrade=true` option. This option blindly pulls down the
@@ -81,10 +85,6 @@ jobs:
             ${{ env.PRE_COMMIT_CACHE_DIR }}
             ${{ env.CURL_CACHE_DIR }}
             ${{ steps.go-cache.outputs.dir }}
-          key: "${{ env.BASE_CACHE_KEY }}\
-            ${{ hashFiles('**/requirements-test.txt') }}-\
-            ${{ hashFiles('**/requirements.txt') }}-\
-            ${{ hashFiles('**/.pre-commit-config.yaml') }}"
           restore-keys: |
             ${{ env.BASE_CACHE_KEY }}
       - name: Setup curl cache

From 6503a9e7f67d908833ff5aa178a2fd28faf5e803 Mon Sep 17 00:00:00 2001
From: Nicholas McDonnell <50747025+mcdonnnj@users.noreply.github.com>
Date: Thu, 2 Nov 2023 16:00:00 -0400
Subject: [PATCH 09/82] Add a `merge_group` trigger to the build workflow

This should improve compatibility with merge queues. We configure it to
only trigger on the `checks_requested` type which is currently the only
supported type for this trigger. If additional types are added in the
future they should be added if appropriate.
---
 .github/workflows/build.yml | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml
index 2fef5d5..1928cb0 100644
--- a/.github/workflows/build.yml
+++ b/.github/workflows/build.yml
@@ -2,6 +2,9 @@
 name: build
 
 on:
+  merge_group:
+    types:
+      - checks_requested
   pull_request:
   push:
   repository_dispatch:

From 6c39dcfd7b0df7f48b6a18eb699de75282c70705 Mon Sep 17 00:00:00 2001
From: Jeremy Frasier <jeremy.frasier@gwe.cisa.dhs.gov>
Date: Tue, 5 Dec 2023 12:12:57 -0500
Subject: [PATCH 10/82] Add terraform-docs injection headers to example
 README.md

We also symlink the .terrafrom-docs.yml file from the root of the
repo.
---
 examples/basic_usage/.terraform-docs.yml | 1 +
 examples/basic_usage/README.md           | 2 ++
 2 files changed, 3 insertions(+)
 create mode 120000 examples/basic_usage/.terraform-docs.yml

diff --git a/examples/basic_usage/.terraform-docs.yml b/examples/basic_usage/.terraform-docs.yml
new file mode 120000
index 0000000..2afdcf8
--- /dev/null
+++ b/examples/basic_usage/.terraform-docs.yml
@@ -0,0 +1 @@
+../../.terraform-docs.yml
\ No newline at end of file
diff --git a/examples/basic_usage/README.md b/examples/basic_usage/README.md
index d36960e..d120104 100644
--- a/examples/basic_usage/README.md
+++ b/examples/basic_usage/README.md
@@ -8,6 +8,7 @@ followed by the `terraform apply` command.
 Note that this example may create resources which cost money. Run
 `terraform destroy` when you no longer need these resources.
 
+<!-- BEGIN_TF_DOCS -->
 ## Requirements ##
 
 | Name | Version |
@@ -53,3 +54,4 @@ Note that this example may create resources which cost money. Run
 | id | The EC2 instance ID. |
 | private\_ip | The private IP of the EC2 instance. |
 | subnet\_id | The ID of the subnet where the EC2 instance is deployed. |
+<!-- END_TF_DOCS -->

From 193e799a2601d030a0dd7bb6608752a076dc5981 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Mon, 11 Dec 2023 18:59:21 +0000
Subject: [PATCH 11/82] Bump actions/setup-go from 4 to 5

Bumps [actions/setup-go](https://github.com/actions/setup-go) from 4 to 5.
- [Release notes](https://github.com/actions/setup-go/releases)
- [Commits](https://github.com/actions/setup-go/compare/v4...v5)

---
updated-dependencies:
- dependency-name: actions/setup-go
  dependency-type: direct:production
  update-type: version-update:semver-major
...

Signed-off-by: dependabot[bot] <support@github.com>
---
 .github/workflows/build.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml
index e7b75a4..f208d82 100644
--- a/.github/workflows/build.yml
+++ b/.github/workflows/build.yml
@@ -51,7 +51,7 @@ jobs:
       # We need the Go version and Go cache location for the actions/cache step,
       # so the Go installation must happen before that.
       - id: setup-go
-        uses: actions/setup-go@v4
+        uses: actions/setup-go@v5
         with:
           # There is no expectation for actual Go code so we disable caching as
           # it relies on the existence of a go.sum file.

From 5c84295bb6811bc49d3ff29de067adb2d179f879 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Mon, 11 Dec 2023 18:59:25 +0000
Subject: [PATCH 12/82] Bump actions/setup-python from 4 to 5

Bumps [actions/setup-python](https://github.com/actions/setup-python) from 4 to 5.
- [Release notes](https://github.com/actions/setup-python/releases)
- [Commits](https://github.com/actions/setup-python/compare/v4...v5)

---
updated-dependencies:
- dependency-name: actions/setup-python
  dependency-type: direct:production
  update-type: version-update:semver-major
...

Signed-off-by: dependabot[bot] <support@github.com>
---
 .github/workflows/build.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml
index e7b75a4..366a16b 100644
--- a/.github/workflows/build.yml
+++ b/.github/workflows/build.yml
@@ -45,7 +45,7 @@ jobs:
         uses: cisagov/setup-env-github-action@develop
       - uses: actions/checkout@v4
       - id: setup-python
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: "3.11"
       # We need the Go version and Go cache location for the actions/cache step,

From 4a63dbe91c946d74d963c103b67d4f3c0746f35c Mon Sep 17 00:00:00 2001
From: Nicholas McDonnell <50747025+mcdonnnj@users.noreply.github.com>
Date: Thu, 18 Jan 2024 16:25:35 -0500
Subject: [PATCH 13/82] Switch pre-commit hooks for running shfmt

This hook bundles the binaries for shfmt with a Python package which
removes the need to manually install the tool for the hook to function.
---
 .pre-commit-config.yaml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 34f0253..ed254a0 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -86,8 +86,8 @@ repos:
       - id: nixpkgs-fmt
 
   # Shell script hooks
-  - repo: https://github.com/cisagov/pre-commit-shfmt
-    rev: v0.0.2
+  - repo: https://github.com/scop/pre-commit-shfmt
+    rev: v3.7.0-4
     hooks:
       - id: shfmt
         args:

From 3236b1ba94d1c833dc2f9508944c6bc6e6a49f48 Mon Sep 17 00:00:00 2001
From: Nicholas McDonnell <50747025+mcdonnnj@users.noreply.github.com>
Date: Thu, 18 Jan 2024 17:43:00 -0500
Subject: [PATCH 14/82] Remove installation of shfmt in the `build` workflow

The new pre-commit hook provides `shfmt` binaries so we no longer need
to ensure it is installed.
---
 .github/workflows/build.yml | 5 -----
 1 file changed, 5 deletions(-)

diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml
index e7b75a4..b5d46cc 100644
--- a/.github/workflows/build.yml
+++ b/.github/workflows/build.yml
@@ -114,11 +114,6 @@ jobs:
           PACKAGE_URL: github.com/securego/gosec/v2/cmd/gosec
           PACKAGE_VERSION: ${{ steps.setup-env.outputs.gosec-version }}
         run: go install ${PACKAGE_URL}@${PACKAGE_VERSION}
-      - name: Install shfmt
-        env:
-          PACKAGE_URL: mvdan.cc/sh/v3/cmd/shfmt
-          PACKAGE_VERSION: ${{ steps.setup-env.outputs.shfmt-version }}
-        run: go install ${PACKAGE_URL}@${PACKAGE_VERSION}
       - name: Install staticcheck
         env:
           PACKAGE_URL: honnef.co/go/tools/cmd/staticcheck

From 5ddb14dab4e98019a6875278a1bc556c61e4bb69 Mon Sep 17 00:00:00 2001
From: Nicholas McDonnell <50747025+mcdonnnj@users.noreply.github.com>
Date: Thu, 18 Jan 2024 16:56:43 -0500
Subject: [PATCH 15/82] Use long options for shfmt arguments

Since shfmt now supports long command line options we should use them
as that is our preference. The single quotes for the number of spaces
to indent is changed to double quotes to align with our usual quotation
style.
---
 .pre-commit-config.yaml | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index ed254a0..ca36e5d 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -92,14 +92,14 @@ repos:
       - id: shfmt
         args:
           # Indent by two spaces
-          - -i
-          - '2'
+          - --indent
+          - "2"
           # Binary operators may start a line
-          - -bn
+          - --binary-next-line
           # Switch cases are indented
-          - -ci
+          - --case-indent
           # Redirect operators are followed by a space
-          - -sr
+          - --space-redirects
   - repo: https://github.com/detailyang/pre-commit-shell
     rev: 1.0.5
     hooks:

From 8ecd95718a6d1b0db176cb85bf0790e4810364fb Mon Sep 17 00:00:00 2001
From: Nicholas McDonnell <50747025+mcdonnnj@users.noreply.github.com>
Date: Thu, 18 Jan 2024 17:34:18 -0500
Subject: [PATCH 16/82] Add additional shfmt options

These options are baked into the functionality of the old hook but must
be explicitly declared for the new hook.
---
 .pre-commit-config.yaml | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index ca36e5d..6b35e4a 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -91,6 +91,10 @@ repos:
     hooks:
       - id: shfmt
         args:
+          # List files that will be formatted
+          - --list
+          # Write result to file instead of stdout
+          - --write
           # Indent by two spaces
           - --indent
           - "2"

From 242921b9856e3ede0fa1a941324c1a3f0ba116f7 Mon Sep 17 00:00:00 2001
From: Nicholas McDonnell <50747025+mcdonnnj@users.noreply.github.com>
Date: Thu, 21 Sep 2023 17:49:55 -0400
Subject: [PATCH 17/82] Set the default shell for all run steps in the build
 workflow

This sets the default shell for any run steps in the build workflow to
mirror our standard shellscript writing practices. In addition to
enabling our standard options it will also enable errtrace and print
any commands that are run which should make debugging/troubleshooting
more straightforward.
---
 .github/workflows/build.yml | 8 ++++++++
 1 file changed, 8 insertions(+)

diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml
index e7b75a4..7299f6b 100644
--- a/.github/workflows/build.yml
+++ b/.github/workflows/build.yml
@@ -7,6 +7,14 @@ on:
   repository_dispatch:
     types: [apb]
 
+# Set a default shell for any run steps. The `-Eueo pipefail` sets errtrace,
+# nounset, errexit, and pipefail. The `-x` will print all commands as they are
+# run. Please see the GitHub Actions documentation for more information:
+# https://docs.github.com/en/actions/using-jobs/setting-default-values-for-jobs
+defaults:
+  run:
+    shell: bash -Eueo pipefail -x {0}
+
 env:
   CURL_CACHE_DIR: ~/.cache/curl
   PIP_CACHE_DIR: ~/.cache/pip

From c7b18dc7e57c5261720324bd5b1425f6992e965e Mon Sep 17 00:00:00 2001
From: Nicholas McDonnell <50747025+mcdonnnj@users.noreply.github.com>
Date: Fri, 12 Jan 2024 17:55:34 -0500
Subject: [PATCH 18/82] Add linting with goimports to the pre-commit
 configuration

This will run the Go tool `goimports` against the repository if it
contains any Go files. This tool bundles the functionality of `go fmt`
with the additional benefit of sorting Go imports much like the isort
tool we use for Python code.
---
 .github/workflows/build.yml | 5 +++++
 .pre-commit-config.yaml     | 6 +++++-
 2 files changed, 10 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml
index e7b75a4..8e14eab 100644
--- a/.github/workflows/build.yml
+++ b/.github/workflows/build.yml
@@ -109,6 +109,11 @@ jobs:
           PACKAGE_URL: github.com/go-critic/go-critic/cmd/gocritic
           PACKAGE_VERSION: ${{ steps.setup-env.outputs.go-critic-version }}
         run: go install ${PACKAGE_URL}@${PACKAGE_VERSION}
+      - name: Install goimports
+        env:
+          PACKAGE_URL: golang.org/x/tools/cmd/goimports
+          PACKAGE_VERSION: ${{ steps.setup-env.outputs.goimports-version }}
+        run: go install ${PACKAGE_URL}@${PACKAGE_VERSION}
       - name: Install gosec
         env:
           PACKAGE_URL: github.com/securego/gosec/v2/cmd/gosec
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 34f0253..7bb1f8c 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -78,7 +78,11 @@ repos:
       - id: go-vet-repo-mod
       # GoSec
       - id: go-sec-repo-mod
-
+      # goimports
+      - id: go-imports-repo
+        args:
+          # Write changes to files
+          - -w
   # Nix hooks
   - repo: https://github.com/nix-community/nixpkgs-fmt
     rev: v1.3.0

From f6d9d6e29249c4b6246fca71c285d744c7409f38 Mon Sep 17 00:00:00 2001
From: Michael Saki <michael.saki@associates.cisa.dhs.gov>
Date: Mon, 22 Jan 2024 12:31:43 -0600
Subject: [PATCH 19/82] Add ATX Header Support for terraform-docs

This is a temporary fix until @mcdonnnj has
his PR approved and merged into the terraform-docs
repo. This fix will perform a shallow clone of his
forked branch, build the binary, and install it.
---
 .github/workflows/build.yml | 22 +++++++++++++++++-----
 1 file changed, 17 insertions(+), 5 deletions(-)

diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml
index e7b75a4..e86b966 100644
--- a/.github/workflows/build.yml
+++ b/.github/workflows/build.yml
@@ -8,9 +8,12 @@ on:
     types: [apb]
 
 env:
+  BRANCH_NAME: improvement/support_atx_closed_markdown_headers
   CURL_CACHE_DIR: ~/.cache/curl
+  DEPTH: 1
   PIP_CACHE_DIR: ~/.cache/pip
   PRE_COMMIT_CACHE_DIR: ~/.cache/pre-commit
+  REPO_URL: https://github.com/mcdonnnj/terraform-docs.git
   RUN_TMATE: ${{ secrets.RUN_TMATE }}
 
 jobs:
@@ -124,11 +127,20 @@ jobs:
           PACKAGE_URL: honnef.co/go/tools/cmd/staticcheck
           PACKAGE_VERSION: ${{ steps.setup-env.outputs.staticcheck-version }}
         run: go install ${PACKAGE_URL}@${PACKAGE_VERSION}
-      - name: Install Terraform-docs
-        env:
-          PACKAGE_URL: github.com/terraform-docs/terraform-docs
-          PACKAGE_VERSION: ${{ steps.setup-env.outputs.terraform-docs-version }}
-        run: go install ${PACKAGE_URL}@${PACKAGE_VERSION}
+      # We are temporarily using @mcdonnnj's forked branch of terraform-docs
+      # until his PR: https://github.com/terraform-docs/terraform-docs/pull/745
+      # is approved. This temporary fix will allow for ATX Header Support when
+      # terraform-docs is ran during lint.
+      - name: Clone ATX Headers branch from Terraform-docs Fork
+        run: |
+          git clone --branch $BRANCH_NAME --single-branch \
+           --depth=$DEPTH $REPO_URL /tmp/terraform-docs
+      - name: Build and Install Terraform-docs Binary
+        run: |
+          cd /tmp/terraform-docs
+          GOBIN=$(go env GOPATH)/bin
+          go build -o $GOBIN/terraform-docs
+          echo "$GOBIN" >> $GITHUB_PATH
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip setuptools wheel

From 544e4789e052978d00f982ef45d8d0de9f5e4748 Mon Sep 17 00:00:00 2001
From: Michael Saki <sakimichael@Yahoo.com>
Date: Mon, 22 Jan 2024 14:03:00 -0600
Subject: [PATCH 20/82] Add prepended names to variables to describe their
 function

Co-authored-by: Nick <50747025+mcdonnnj@users.noreply.github.com>
---
 .github/workflows/build.yml | 12 +++++++-----
 1 file changed, 7 insertions(+), 5 deletions(-)

diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml
index e86b966..99b42c1 100644
--- a/.github/workflows/build.yml
+++ b/.github/workflows/build.yml
@@ -8,13 +8,13 @@ on:
     types: [apb]
 
 env:
-  BRANCH_NAME: improvement/support_atx_closed_markdown_headers
   CURL_CACHE_DIR: ~/.cache/curl
-  DEPTH: 1
   PIP_CACHE_DIR: ~/.cache/pip
   PRE_COMMIT_CACHE_DIR: ~/.cache/pre-commit
-  REPO_URL: https://github.com/mcdonnnj/terraform-docs.git
   RUN_TMATE: ${{ secrets.RUN_TMATE }}
+  TERRAFORM_DOCS_REPO_BRANCH_NAME: improvement/support_atx_closed_markdown_headers
+  TERRAFORM_DOCS_REPO_DEPTH: 1
+  TERRAFORM_DOCS_REPO_URL: https://github.com/mcdonnnj/terraform-docs.git
 
 jobs:
   diagnostics:
@@ -133,8 +133,10 @@ jobs:
       # terraform-docs is ran during lint.
       - name: Clone ATX Headers branch from Terraform-docs Fork
         run: |
-          git clone --branch $BRANCH_NAME --single-branch \
-           --depth=$DEPTH $REPO_URL /tmp/terraform-docs
+          git clone --single-branch \
+           --branch $TERRAFORM_DOCS_REPO_BRANCH_NAME \
+           --depth $TERRAFORM_DOCS_REPO_DEPTH \
+           $TERRAFORM_DOCS_REPO_URL /tmp/terraform-docs
       - name: Build and Install Terraform-docs Binary
         run: |
           cd /tmp/terraform-docs

From f5fa0ff4ec1ded10a2906ade6300bba05cc2e81c Mon Sep 17 00:00:00 2001
From: Michael Saki <sakimichael@Yahoo.com>
Date: Mon, 22 Jan 2024 14:05:01 -0600
Subject: [PATCH 21/82] Remove unnecessary capitalizations and fix grammar

Co-authored-by: Shane Frasier <jeremy.frasier@gwe.cisa.dhs.gov>
---
 .github/workflows/build.yml | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml
index 99b42c1..ca719aa 100644
--- a/.github/workflows/build.yml
+++ b/.github/workflows/build.yml
@@ -129,15 +129,15 @@ jobs:
         run: go install ${PACKAGE_URL}@${PACKAGE_VERSION}
       # We are temporarily using @mcdonnnj's forked branch of terraform-docs
       # until his PR: https://github.com/terraform-docs/terraform-docs/pull/745
-      # is approved. This temporary fix will allow for ATX Header Support when
-      # terraform-docs is ran during lint.
-      - name: Clone ATX Headers branch from Terraform-docs Fork
+      # is approved. This temporary fix will allow for ATX header support when
+      # terraform-docs is run during linting.
+      - name: Clone ATX headers branch from terraform-docs fork
         run: |
           git clone --single-branch \
            --branch $TERRAFORM_DOCS_REPO_BRANCH_NAME \
            --depth $TERRAFORM_DOCS_REPO_DEPTH \
            $TERRAFORM_DOCS_REPO_URL /tmp/terraform-docs
-      - name: Build and Install Terraform-docs Binary
+      - name: Build and install terraform-docs binary
         run: |
           cd /tmp/terraform-docs
           GOBIN=$(go env GOPATH)/bin

From 36361dd1c74c9855b87f2b4aec5a9be1fa7c416e Mon Sep 17 00:00:00 2001
From: Michael Saki <sakimichael@Yahoo.com>
Date: Mon, 22 Jan 2024 14:14:27 -0600
Subject: [PATCH 22/82] Simplify steps in the build/install portion of workflow

PATH is handled by `setup-go` so we can refactor the code setting it. Also we are taking advantage of the -C switch to handle building from the cloned repository.

Co-authored-by: Nick <50747025+mcdonnnj@users.noreply.github.com>
---
 .github/workflows/build.yml | 7 +++----
 1 file changed, 3 insertions(+), 4 deletions(-)

diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml
index ca719aa..6ab90de 100644
--- a/.github/workflows/build.yml
+++ b/.github/workflows/build.yml
@@ -139,10 +139,9 @@ jobs:
            $TERRAFORM_DOCS_REPO_URL /tmp/terraform-docs
       - name: Build and install terraform-docs binary
         run: |
-          cd /tmp/terraform-docs
-          GOBIN=$(go env GOPATH)/bin
-          go build -o $GOBIN/terraform-docs
-          echo "$GOBIN" >> $GITHUB_PATH
+          go build \
+          -C /tmp/terraform-docs \
+          -o $(go env GOPATH)/bin/terraform-docs
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip setuptools wheel

From 3711ebe461d81987b4121903d2f3f1b290fccad3 Mon Sep 17 00:00:00 2001
From: Michael Saki <sakimichael@Yahoo.com>
Date: Tue, 23 Jan 2024 08:04:07 -0600
Subject: [PATCH 23/82] Add TODO label

---
 .github/workflows/build.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml
index 6ab90de..f5ba773 100644
--- a/.github/workflows/build.yml
+++ b/.github/workflows/build.yml
@@ -51,7 +51,7 @@ jobs:
         uses: actions/setup-python@v4
         with:
           python-version: "3.11"
-      # We need the Go version and Go cache location for the actions/cache step,
+      # TODO: We need the Go version and Go cache location for the actions/cache step,
       # so the Go installation must happen before that.
       - id: setup-go
         uses: actions/setup-go@v4

From d114fb4233f22cb9edb3e1a6555ca0a677bcfc7e Mon Sep 17 00:00:00 2001
From: Michael Saki <sakimichael@Yahoo.com>
Date: Tue, 23 Jan 2024 08:24:12 -0600
Subject: [PATCH 24/82] Move TODO and add link to the issue

`TODO` was placed on the wrong comment block. Also I am adding a link to the issue for the TODO.
---
 .github/workflows/build.yml | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml
index f5ba773..0068f1f 100644
--- a/.github/workflows/build.yml
+++ b/.github/workflows/build.yml
@@ -51,7 +51,7 @@ jobs:
         uses: actions/setup-python@v4
         with:
           python-version: "3.11"
-      # TODO: We need the Go version and Go cache location for the actions/cache step,
+      # We need the Go version and Go cache location for the actions/cache step,
       # so the Go installation must happen before that.
       - id: setup-go
         uses: actions/setup-go@v4
@@ -127,6 +127,7 @@ jobs:
           PACKAGE_URL: honnef.co/go/tools/cmd/staticcheck
           PACKAGE_VERSION: ${{ steps.setup-env.outputs.staticcheck-version }}
         run: go install ${PACKAGE_URL}@${PACKAGE_VERSION}
+      # TODO: https://github.com/cisagov/skeleton-generic/issues/165
       # We are temporarily using @mcdonnnj's forked branch of terraform-docs
       # until his PR: https://github.com/terraform-docs/terraform-docs/pull/745
       # is approved. This temporary fix will allow for ATX header support when

From c907cfc82a8f329fbd4ad0ee17f3500922c51711 Mon Sep 17 00:00:00 2001
From: Michael Saki <sakimichael@Yahoo.com>
Date: Tue, 23 Jan 2024 08:41:41 -0600
Subject: [PATCH 25/82] Alphabetize switches

Co-authored-by: dav3r <david.redmin@trio.dhs.gov>
---
 .github/workflows/build.yml | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml
index 0068f1f..35391d5 100644
--- a/.github/workflows/build.yml
+++ b/.github/workflows/build.yml
@@ -134,9 +134,10 @@ jobs:
       # terraform-docs is run during linting.
       - name: Clone ATX headers branch from terraform-docs fork
         run: |
-          git clone --single-branch \
+          git clone \
            --branch $TERRAFORM_DOCS_REPO_BRANCH_NAME \
            --depth $TERRAFORM_DOCS_REPO_DEPTH \
+           --single-branch \
            $TERRAFORM_DOCS_REPO_URL /tmp/terraform-docs
       - name: Build and install terraform-docs binary
         run: |

From 48db3e3381aa61bdbe67dab64454db3e7f332c75 Mon Sep 17 00:00:00 2001
From: Michael Saki <michael.saki@associates.cisa.dhs.gov>
Date: Thu, 25 Jan 2024 12:19:41 -0600
Subject: [PATCH 26/82] Allow setup-env to specify Python version

This commit is introducing 2 new flags
into the setup-env script. -l or
--list-versions will list available
Python versions and allow the user to
select a version interactively. The second
flag -v or --version will allow a user
to set the version if installed.
(e.g. ./setup-env -v 3.9.6)
---
 setup-env | 42 +++++++++++++++++++++++++++++++++++++++---
 1 file changed, 39 insertions(+), 3 deletions(-)

diff --git a/setup-env b/setup-env
index 77926bf..b99ec5f 100755
--- a/setup-env
+++ b/setup-env
@@ -25,6 +25,8 @@ Options:
   -h --help           Show this message.
   -i --install-hooks  Install hook environments for all environments in the
                       pre-commit config file.
+  -v --version        Specify the Python version for the virtual environment.
+  -l --list-versions  List available Python versions and select interactively.
 
 END_OF_LINE
 )
@@ -35,6 +37,13 @@ FORCE=0
 # Positional parameters
 PARAMS=""
 
+# Flags to allow a user to specify which version of Python they want to use
+PYTHON_VERSION=""
+LIST_VERSIONS=0
+
+# Temp file that is used to search through available installed Python versions
+TMPFILE=/tmp/versions.$$
+
 # Parse command line arguments
 while (("$#")); do
   case "$1" in
@@ -50,6 +59,14 @@ while (("$#")); do
       INSTALL_HOOKS=1
       shift
       ;;
+    -v | --version)
+      PYTHON_VERSION=$2
+      shift 2
+      ;;
+    -l | --list-versions)
+      LIST_VERSIONS=1
+      shift
+      ;;
     -*) # unsupported flags
       echo "Error: Unsupported flag $1" >&2
       exit 1
@@ -111,6 +128,25 @@ else
 fi
 set -o nounset
 
+# List Python versions and select one interactively
+if [ $LIST_VERSIONS -ne 0 ]; then
+  echo Available Python versions:
+  pyenv versions --bare --skip-aliases --skip-envs
+  read -p -r "Enter the desired Python version: " PYTHON_VERSION
+fi
+
+# Check if PYTHON_VERSION isn't empty. If it is installed, set it locally.
+pyenv versions --bare --skip-aliases --skip-envs > $TMPFILE
+if [ -n "$PYTHON_VERSION" ]; then
+  if grep --fixed-strings --quiet "$PYTHON_VERSION" $TMPFILE; then
+    echo Using Python version "$PYTHON_VERSION"
+    pyenv local "$PYTHON_VERSION"
+  else
+    echo Error: Python version "$PYTHON_VERSION" is not installed.
+  fi
+  exit 1
+fi
+
 # Remove any lingering local configuration.
 if [ $FORCE -ne 0 ]; then
   rm -f .python-version
@@ -130,10 +166,10 @@ fi
 # Create a new virtual environment for this project
 if ! pyenv virtualenv "${env_name}"; then
   cat << END_OF_LINE
-  An existing virtual environment named $env_name was found.  Either delete this
-  environment yourself or re-run with --force option to have it deleted.
+    An existing virtual environment named $env_name was found.  Either delete this
+    environment yourself or re-run with --force option to have it deleted.
 
-  pyenv virtualenv-delete ${env_name}
+    pyenv virtualenv-delete ${env_name}
 
 END_OF_LINE
   exit 1

From c10929afae693990a3d4d034faa2c1ab1b2689ee Mon Sep 17 00:00:00 2001
From: Michael Saki <sakimichael@Yahoo.com>
Date: Thu, 25 Jan 2024 14:15:40 -0600
Subject: [PATCH 27/82] Add /dev/null and remove TMPFILE

This makes the code a bit cleaner and still accomplishes the same functionality

Co-authored-by: Shane Frasier <jeremy.frasier@gwe.cisa.dhs.gov>
---
 setup-env | 6 +-----
 1 file changed, 1 insertion(+), 5 deletions(-)

diff --git a/setup-env b/setup-env
index b99ec5f..769522a 100755
--- a/setup-env
+++ b/setup-env
@@ -41,9 +41,6 @@ PARAMS=""
 PYTHON_VERSION=""
 LIST_VERSIONS=0
 
-# Temp file that is used to search through available installed Python versions
-TMPFILE=/tmp/versions.$$
-
 # Parse command line arguments
 while (("$#")); do
   case "$1" in
@@ -136,9 +133,8 @@ if [ $LIST_VERSIONS -ne 0 ]; then
 fi
 
 # Check if PYTHON_VERSION isn't empty. If it is installed, set it locally.
-pyenv versions --bare --skip-aliases --skip-envs > $TMPFILE
 if [ -n "$PYTHON_VERSION" ]; then
-  if grep --fixed-strings --quiet "$PYTHON_VERSION" $TMPFILE; then
+  if pyenv versions --bare --skip-aliases --skip-envs | grep --fixed-strings "$PYTHON_VERSION" >/dev/null; then
     echo Using Python version "$PYTHON_VERSION"
     pyenv local "$PYTHON_VERSION"
   else

From adada40e6fa6aed6fa14f253a5b86f313b3dfa8f Mon Sep 17 00:00:00 2001
From: Michael Saki <michael.saki@associates.cisa.dhs.gov>
Date: Thu, 25 Jan 2024 14:19:54 -0600
Subject: [PATCH 28/82] Place flags in the correct order for -r and -p

---
 setup-env | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/setup-env b/setup-env
index 769522a..2adbd5a 100755
--- a/setup-env
+++ b/setup-env
@@ -129,12 +129,12 @@ set -o nounset
 if [ $LIST_VERSIONS -ne 0 ]; then
   echo Available Python versions:
   pyenv versions --bare --skip-aliases --skip-envs
-  read -p -r "Enter the desired Python version: " PYTHON_VERSION
+  read -r -p "Enter the desired Python version: " PYTHON_VERSION
 fi
 
 # Check if PYTHON_VERSION isn't empty. If it is installed, set it locally.
 if [ -n "$PYTHON_VERSION" ]; then
-  if pyenv versions --bare --skip-aliases --skip-envs | grep --fixed-strings "$PYTHON_VERSION" >/dev/null; then
+  if pyenv versions --bare --skip-aliases --skip-envs | grep --fixed-strings "$PYTHON_VERSION" > /dev/null; then
     echo Using Python version "$PYTHON_VERSION"
     pyenv local "$PYTHON_VERSION"
   else

From 1861b9b86778613bdaeff804418f2d00706f4a08 Mon Sep 17 00:00:00 2001
From: Michael Saki <michael.saki@associates.cisa.dhs.gov>
Date: Thu, 25 Jan 2024 14:21:49 -0600
Subject: [PATCH 29/82] Remove unneccessary spacing

---
 setup-env | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/setup-env b/setup-env
index 2adbd5a..5abb624 100755
--- a/setup-env
+++ b/setup-env
@@ -162,10 +162,10 @@ fi
 # Create a new virtual environment for this project
 if ! pyenv virtualenv "${env_name}"; then
   cat << END_OF_LINE
-    An existing virtual environment named $env_name was found.  Either delete this
-    environment yourself or re-run with --force option to have it deleted.
+  An existing virtual environment named $env_name was found.  Either delete this
+  environment yourself or re-run with --force option to have it deleted.
 
-    pyenv virtualenv-delete ${env_name}
+  pyenv virtualenv-delete ${env_name}
 
 END_OF_LINE
   exit 1

From 3f623e493752c581829271a148cb9fff3ad4f4ab Mon Sep 17 00:00:00 2001
From: Michael Saki <sakimichael@Yahoo.com>
Date: Thu, 25 Jan 2024 14:25:37 -0600
Subject: [PATCH 30/82] Alphabetize flags and descriptions

Co-authored-by: Shane Frasier <jeremy.frasier@gwe.cisa.dhs.gov>
---
 setup-env | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/setup-env b/setup-env
index 5abb624..5282e49 100755
--- a/setup-env
+++ b/setup-env
@@ -25,8 +25,8 @@ Options:
   -h --help           Show this message.
   -i --install-hooks  Install hook environments for all environments in the
                       pre-commit config file.
-  -v --version        Specify the Python version for the virtual environment.
   -l --list-versions  List available Python versions and select interactively.
+  -v --version        Specify the Python version for the virtual environment.
 
 END_OF_LINE
 )
@@ -56,14 +56,14 @@ while (("$#")); do
       INSTALL_HOOKS=1
       shift
       ;;
-    -v | --version)
-      PYTHON_VERSION=$2
-      shift 2
-      ;;
     -l | --list-versions)
       LIST_VERSIONS=1
       shift
       ;;
+    -v | --version)
+      PYTHON_VERSION=$2
+      shift 2
+      ;;
     -*) # unsupported flags
       echo "Error: Unsupported flag $1" >&2
       exit 1

From 9497dc276e9f148211e32cc800342846cfa25e33 Mon Sep 17 00:00:00 2001
From: Jeremy Frasier <jeremy.frasier@gwe.cisa.dhs.gov>
Date: Fri, 26 Jan 2024 10:08:25 -0500
Subject: [PATCH 31/82] Move misplaced exit

If the Python version exists then we want the script to continue
execution.
---
 setup-env | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/setup-env b/setup-env
index 5282e49..5d15679 100755
--- a/setup-env
+++ b/setup-env
@@ -139,8 +139,8 @@ if [ -n "$PYTHON_VERSION" ]; then
     pyenv local "$PYTHON_VERSION"
   else
     echo Error: Python version "$PYTHON_VERSION" is not installed.
+    exit 1
   fi
-  exit 1
 fi
 
 # Remove any lingering local configuration.

From e1d0f28ba1d96b2da0af91e277648ca88d0c3f35 Mon Sep 17 00:00:00 2001
From: Jeremy Frasier <jeremy.frasier@gwe.cisa.dhs.gov>
Date: Fri, 26 Jan 2024 10:10:23 -0500
Subject: [PATCH 32/82] Remove premature pyenv local command

pyenv local is run below.
---
 setup-env | 1 -
 1 file changed, 1 deletion(-)

diff --git a/setup-env b/setup-env
index 5d15679..a78f940 100755
--- a/setup-env
+++ b/setup-env
@@ -136,7 +136,6 @@ fi
 if [ -n "$PYTHON_VERSION" ]; then
   if pyenv versions --bare --skip-aliases --skip-envs | grep --fixed-strings "$PYTHON_VERSION" > /dev/null; then
     echo Using Python version "$PYTHON_VERSION"
-    pyenv local "$PYTHON_VERSION"
   else
     echo Error: Python version "$PYTHON_VERSION" is not installed.
     exit 1

From 517b336210269d890c28e5c05d1c13e866fb7b15 Mon Sep 17 00:00:00 2001
From: Jeremy Frasier <jeremy.frasier@gwe.cisa.dhs.gov>
Date: Fri, 26 Jan 2024 10:11:50 -0500
Subject: [PATCH 33/82] Include PYTHON_VERSION when running pyenv virtualenv

If PYTHON_VERSION is an empty string then the system Python will be used.
---
 setup-env | 19 ++++++++++++++-----
 1 file changed, 14 insertions(+), 5 deletions(-)

diff --git a/setup-env b/setup-env
index a78f940..0aa173d 100755
--- a/setup-env
+++ b/setup-env
@@ -37,8 +37,8 @@ FORCE=0
 # Positional parameters
 PARAMS=""
 
-# Flags to allow a user to specify which version of Python they want to use
-PYTHON_VERSION=""
+# A flag to allow a user to specify which version of Python they want
+# to use.
 LIST_VERSIONS=0
 
 # Parse command line arguments
@@ -132,8 +132,9 @@ if [ $LIST_VERSIONS -ne 0 ]; then
   read -r -p "Enter the desired Python version: " PYTHON_VERSION
 fi
 
-# Check if PYTHON_VERSION isn't empty. If it is installed, set it locally.
-if [ -n "$PYTHON_VERSION" ]; then
+# Check if PYTHON_VERSION is defined. If it is defined then check that
+# it is a valid value.
+if [ -n "${PYTHON_VERSION+x}" ]; then
   if pyenv versions --bare --skip-aliases --skip-envs | grep --fixed-strings "$PYTHON_VERSION" > /dev/null; then
     echo Using Python version "$PYTHON_VERSION"
   else
@@ -159,7 +160,15 @@ END_OF_LINE
 fi
 
 # Create a new virtual environment for this project
-if ! pyenv virtualenv "${env_name}"; then
+#
+# If $PYTHON_VERSION is undefined then the system Python will be used.
+#
+# We can't quote ${PYTHON_VERSION:=} below since if the variable is
+# undefined then we want nothing to appear; this is the reason for the
+# "shellcheck disable" line below.
+#
+# shellcheck disable=SC2086
+if ! pyenv virtualenv ${PYTHON_VERSION:=} "${env_name}"; then
   cat << END_OF_LINE
   An existing virtual environment named $env_name was found.  Either delete this
   environment yourself or re-run with --force option to have it deleted.

From 2e5794cb2aeaa76e8c94e3113f903954a9564eb4 Mon Sep 17 00:00:00 2001
From: Michael Saki <michael.saki@associates.cisa.dhs.gov>
Date: Tue, 30 Jan 2024 12:51:51 -0600
Subject: [PATCH 34/82] Add getopt variables and short flags

---
 setup-env | 12 ++++++++++++
 1 file changed, 12 insertions(+)

diff --git a/setup-env b/setup-env
index 0aa173d..63cebd3 100755
--- a/setup-env
+++ b/setup-env
@@ -34,9 +34,21 @@ END_OF_LINE
 # Flag to force deletion and creation of virtual environment
 FORCE=0
 
+# Initialize the all other flags
+INSTALL_HOOKS=0
+LIST_VERSIONS=0
+PYTHON_VERSION=""
+VENV_NAME=""
+
 # Positional parameters
 PARAMS=""
 
+# Define short options for getopt
+OPTS="fhilv:n:"
+
+# Parse options using BSD getopt
+OPTIND=1
+
 # A flag to allow a user to specify which version of Python they want
 # to use.
 LIST_VERSIONS=0

From 8a5003195b6cc3a069fb0c4ec678f20372c4e10d Mon Sep 17 00:00:00 2001
From: Michael Saki <michael.saki@associates.cisa.dhs.gov>
Date: Tue, 30 Jan 2024 12:54:12 -0600
Subject: [PATCH 35/82] Remove redundant flag initialization

---
 setup-env | 4 ----
 1 file changed, 4 deletions(-)

diff --git a/setup-env b/setup-env
index 63cebd3..da640f0 100755
--- a/setup-env
+++ b/setup-env
@@ -49,10 +49,6 @@ OPTS="fhilv:n:"
 # Parse options using BSD getopt
 OPTIND=1
 
-# A flag to allow a user to specify which version of Python they want
-# to use.
-LIST_VERSIONS=0
-
 # Parse command line arguments
 while (("$#")); do
   case "$1" in

From 0df0e6aca8252e6356762b9284f3165ee39e2017 Mon Sep 17 00:00:00 2001
From: Michael Saki <michael.saki@associates.cisa.dhs.gov>
Date: Tue, 30 Jan 2024 13:59:04 -0600
Subject: [PATCH 36/82] Add getopt functionality and -n flag

This commit makes a couple changes. The first
change is adding the BSD getopt tool to
simplify the parsing of flags and arguments.
Second, we are adding the -n flag so the user
can specify the name of the virtual environment
if they choose.
---
 setup-env | 57 +++++++++++++++++++++++++++++++++++--------------------
 1 file changed, 36 insertions(+), 21 deletions(-)

diff --git a/setup-env b/setup-env
index da640f0..e097c82 100755
--- a/setup-env
+++ b/setup-env
@@ -49,40 +49,55 @@ OPTS="fhilv:n:"
 # Parse options using BSD getopt
 OPTIND=1
 
+# Display installed python versions 
+python_versions() {
+    pyenv versions --bare --skip-aliases --skip-envs
+}
+
 # Parse command line arguments
-while (("$#")); do
-  case "$1" in
-    -f | --force)
+while getopts :$OPTS opt; do
+  case $opt in
+    f)
       FORCE=1
-      shift
       ;;
-    -h | --help)
-      echo "${USAGE}"
+    h)
+      echo "$USAGE"
       exit 0
       ;;
-    -i | --install-hooks)
+    i)
       INSTALL_HOOKS=1
-      shift
       ;;
-    -l | --list-versions)
+    l)
       LIST_VERSIONS=1
-      shift
       ;;
-    -v | --version)
-      PYTHON_VERSION=$2
-      shift 2
+    n)
+      VENV_NAME="$OPTARG"
+      ;;
+    v)
+      PYTHON_VERSION="$OPTARG"
+      # Check if Python version is valid and installed
+      if ! python_versions | grep --fixed-strings "$PYTHON_VERSION" > /dev/null; then
+        echo "Error: Python version $PYTHON_VERSION is not installed. Versions available:"
+        python_versions
+        exit 1
+      fi
       ;;
-    -*) # unsupported flags
-      echo "Error: Unsupported flag $1" >&2
+    \:)
+      echo Error: Option -$OPTARG requires an argument.
+      echo "$USAGE"
       exit 1
       ;;
-    *) # preserve positional arguments
-      PARAMS="$PARAMS $1"
-      shift
+    \?)
+      echo -e "Invalid option please look through usage: \n" 
+      echo "$USAGE"
+      exit 1
       ;;
+    
   esac
 done
 
+shift $((OPTIND-1))
+
 # set positional arguments in their proper place
 eval set -- "$PARAMS"
 
@@ -124,9 +139,9 @@ fi
 
 set +o nounset
 # Determine the virtual environment name
-if [ "$1" ]; then
+if [ -n "$VENV_NAME" ]; then
   # Use the user-provided environment name
-  env_name=$1
+  env_name="$VENV_NAME"
 else
   # Set the environment name to the last part of the working directory.
   env_name=${PWD##*/}
@@ -136,7 +151,7 @@ set -o nounset
 # List Python versions and select one interactively
 if [ $LIST_VERSIONS -ne 0 ]; then
   echo Available Python versions:
-  pyenv versions --bare --skip-aliases --skip-envs
+  python_versions
   read -r -p "Enter the desired Python version: " PYTHON_VERSION
 fi
 

From 60cad12a2a64508c1e5c80092118747b64bb32e6 Mon Sep 17 00:00:00 2001
From: Michael Saki <michael.saki@associates.cisa.dhs.gov>
Date: Tue, 30 Jan 2024 14:16:52 -0600
Subject: [PATCH 37/82] Update the usage and force documentation

This commit will update the usage documentation
so now it will display all the new flags, how
to use them, and what they do. Since the
long option isn't available for the BSD version
of getopt we have to use short options only.
The force documentation has been updated to
reflect this change. Also removed some redundant
code that wasn't necessary.
---
 setup-env | 47 +++++++++++++++++++----------------------------
 1 file changed, 19 insertions(+), 28 deletions(-)

diff --git a/setup-env b/setup-env
index e097c82..4ed12d9 100755
--- a/setup-env
+++ b/setup-env
@@ -17,16 +17,18 @@ It does the following:
   - Configures git upstream remote "lineage" repositories.
 
 Usage:
-  setup-env [options] [virt_env_name]
-  setup-env (-h | --help)
+  setup-env [-n] [virt_env_name]
+  setup-env [-v] [python_version]
+  setup-env (-h)
 
 Options:
-  -f --force          Delete virtual enviroment if it already exists.
-  -h --help           Show this message.
-  -i --install-hooks  Install hook environments for all environments in the
-                      pre-commit config file.
-  -l --list-versions  List available Python versions and select interactively.
-  -v --version        Specify the Python version for the virtual environment.
+  -f      Delete virtual enviroment if it already exists.
+  -h      Show this message.
+  -i      Install hook environments for all environments in the
+          pre-commit config file.
+  -l      List available Python versions and select interactively.
+  -n      Choose the name of the virtual environment.
+  -v      Specify the Python version for the virtual environment.
 
 END_OF_LINE
 )
@@ -49,9 +51,9 @@ OPTS="fhilv:n:"
 # Parse options using BSD getopt
 OPTIND=1
 
-# Display installed python versions 
+# Display installed python versions
 python_versions() {
-    pyenv versions --bare --skip-aliases --skip-envs
+  pyenv versions --bare --skip-aliases --skip-envs
 }
 
 # Parse command line arguments
@@ -82,21 +84,21 @@ while getopts :$OPTS opt; do
         exit 1
       fi
       ;;
-    \:)
-      echo Error: Option -$OPTARG requires an argument.
+    :)
+      echo -e "Error: Option -$OPTARG requires an argument. \n"
       echo "$USAGE"
       exit 1
       ;;
     \?)
-      echo -e "Invalid option please look through usage: \n" 
+      echo -e "Invalid option please look through usage: \n"
       echo "$USAGE"
       exit 1
       ;;
-    
+
   esac
 done
 
-shift $((OPTIND-1))
+shift $((OPTIND - 1))
 
 # set positional arguments in their proper place
 eval set -- "$PARAMS"
@@ -155,17 +157,6 @@ if [ $LIST_VERSIONS -ne 0 ]; then
   read -r -p "Enter the desired Python version: " PYTHON_VERSION
 fi
 
-# Check if PYTHON_VERSION is defined. If it is defined then check that
-# it is a valid value.
-if [ -n "${PYTHON_VERSION+x}" ]; then
-  if pyenv versions --bare --skip-aliases --skip-envs | grep --fixed-strings "$PYTHON_VERSION" > /dev/null; then
-    echo Using Python version "$PYTHON_VERSION"
-  else
-    echo Error: Python version "$PYTHON_VERSION" is not installed.
-    exit 1
-  fi
-fi
-
 # Remove any lingering local configuration.
 if [ $FORCE -ne 0 ]; then
   rm -f .python-version
@@ -173,7 +164,7 @@ if [ $FORCE -ne 0 ]; then
 elif [[ -f .python-version ]]; then
   cat << 'END_OF_LINE'
   An existing .python-version file was found.  Either remove this file yourself
-  or re-run with --force option to have it deleted along with the associated
+  or re-run with -f (force) option to have it deleted along with the associated
   virtual environment.
 
   rm .python-version
@@ -194,7 +185,7 @@ fi
 if ! pyenv virtualenv ${PYTHON_VERSION:=} "${env_name}"; then
   cat << END_OF_LINE
   An existing virtual environment named $env_name was found.  Either delete this
-  environment yourself or re-run with --force option to have it deleted.
+  environment yourself or re-run with -f (force) option to have it deleted.
 
   pyenv virtualenv-delete ${env_name}
 

From b6ab6d82fb63bece7926b9a524bbb59a96c0cb06 Mon Sep 17 00:00:00 2001
From: Michael Saki <michael.saki@associates.cisa.dhs.gov>
Date: Tue, 6 Feb 2024 19:58:49 -0600
Subject: [PATCH 38/82] Update usage with long options

---
 setup-env | 22 ++++++++++++----------
 1 file changed, 12 insertions(+), 10 deletions(-)

diff --git a/setup-env b/setup-env
index 4ed12d9..898907b 100755
--- a/setup-env
+++ b/setup-env
@@ -9,6 +9,8 @@ USAGE=$(
 Configure a development environment for this repository.
 
 It does the following:
+  - Allows user to specify Python version.
+  - Allows user to choose name for their virtual environment.
   - Verifies pyenv and pyenv-virtualenv are installed.
   - Creates a Python virtual environment.
   - Configures the activation of the virtual enviroment for the repo directory.
@@ -17,18 +19,18 @@ It does the following:
   - Configures git upstream remote "lineage" repositories.
 
 Usage:
-  setup-env [-n] [virt_env_name]
-  setup-env [-v] [python_version]
-  setup-env (-h)
+  setup-env (-n | --name) [virt_env_name]
+  setup-env (-v | --version) [python_version]
+  setup-env (-h | --help)
 
 Options:
-  -f      Delete virtual enviroment if it already exists.
-  -h      Show this message.
-  -i      Install hook environments for all environments in the
-          pre-commit config file.
-  -l      List available Python versions and select interactively.
-  -n      Choose the name of the virtual environment.
-  -v      Specify the Python version for the virtual environment.
+  -f | --force             Delete virtual enviroment if it already exists.
+  -h | --help              Show this message.
+  -i | --install-hooks     Install hook environments for all environments in the
+                           pre-commit config file.
+  -l | --list-versions     List available Python versions and select interactively.
+  -n | --name              Choose the name of the virtual environment.
+  -v | --version           Specify the Python version for the virtual environment.
 
 END_OF_LINE
 )

From d362614a13731f3884856fa2ee37ade0089fda47 Mon Sep 17 00:00:00 2001
From: Michael Saki <michael.saki@associates.cisa.dhs.gov>
Date: Tue, 6 Feb 2024 20:28:05 -0600
Subject: [PATCH 39/82] Add gnu-getopt functionality and error handling

This commit will make it so long options are
supported. It also includes some improved
error handling. It will display a message if
a Mac OS user doesn't have gnu-getopt installed
on their system and suggest steps to take to
get it installed via brew.
---
 setup-env | 107 ++++++++++++++++++++++++++++++++++--------------------
 1 file changed, 68 insertions(+), 39 deletions(-)

diff --git a/setup-env b/setup-env
index 898907b..f4cdf75 100755
--- a/setup-env
+++ b/setup-env
@@ -35,6 +35,11 @@ Options:
 END_OF_LINE
 )
 
+# Display installed python versions
+python_versions() {
+  pyenv versions --bare --skip-aliases --skip-envs
+}
+
 # Flag to force deletion and creation of virtual environment
 FORCE=0
 
@@ -44,67 +49,82 @@ LIST_VERSIONS=0
 PYTHON_VERSION=""
 VENV_NAME=""
 
-# Positional parameters
-PARAMS=""
+# Define long options
+LONGOPTS="force,help,install-hooks,list-versions,name:,version:"
 
 # Define short options for getopt
-OPTS="fhilv:n:"
+SHORTOPTS="fhiln:v:"
 
-# Parse options using BSD getopt
-OPTIND=1
+# Check if GNU getopt is available
+if [[ $(getopt --version 2> /dev/null) != *"getopt from util-linux"* ]]; then
+  cat << 'END_OF_LINE'
 
-# Display installed python versions
-python_versions() {
-  pyenv versions --bare --skip-aliases --skip-envs
-}
+  Gnu-getopt is not detected and is a dependency to run this script.
+  On the Mac, we recommend installing brew, https://brew.sh/.  Then installation
+  is as simple as `brew install gnu-getopt` and adding this to your
+  profile:
+
+  export PATH="/usr/local/opt/gnu-getopt/bin:$PATH"
+
+END_OF_LINE
+  exit 1
+fi
 
-# Parse command line arguments
-while getopts :$OPTS opt; do
-  case $opt in
-    f)
+# Use GNU getopt to parse options
+if ! PARSED=$(getopt --options $SHORTOPTS --longoptions $LONGOPTS --name "$0" -- "$@"); then
+  echo "Error parsing options"
+  exit 2
+fi
+eval set -- "$PARSED"
+
+while true; do
+  case "$1" in
+    -f | --force)
       FORCE=1
+      shift
       ;;
-    h)
+    -h | --help)
       echo "$USAGE"
       exit 0
       ;;
-    i)
+    -i | --install-hooks)
       INSTALL_HOOKS=1
+      shift
       ;;
-    l)
+    -l | --list-versions)
       LIST_VERSIONS=1
+      shift
       ;;
-    n)
-      VENV_NAME="$OPTARG"
+    -n | --name)
+      VENV_NAME="$2"
+      shift 2
       ;;
-    v)
-      PYTHON_VERSION="$OPTARG"
-      # Check if Python version is valid and installed
-      if ! python_versions | grep --fixed-strings "$PYTHON_VERSION" > /dev/null; then
-        echo "Error: Python version $PYTHON_VERSION is not installed. Versions available:"
-        python_versions
-        exit 1
+    -v | --version)
+      PYTHON_VERSION="$2"
+      shift 2
+      # Check the Python versions being passed in.
+      if [ -n "${PYTHON_VERSION+x}" ]; then
+        if python_versions | grep -E "^${PYTHON_VERSION}$" > /dev/null; then
+          echo Using Python version "$PYTHON_VERSION"
+        else
+          echo Error: Python version "$PYTHON_VERSION" is not installed.
+          echo Installed Python versions are:
+          python_versions
+          exit 1
+        fi
       fi
       ;;
-    :)
-      echo -e "Error: Option -$OPTARG requires an argument. \n"
-      echo "$USAGE"
-      exit 1
+    --)
+      shift
+      break
       ;;
-    \?)
-      echo -e "Invalid option please look through usage: \n"
-      echo "$USAGE"
-      exit 1
+    *)
+      echo "Programming error"
+      exit 3
       ;;
-
   esac
 done
 
-shift $((OPTIND - 1))
-
-# set positional arguments in their proper place
-eval set -- "$PARAMS"
-
 # Check to see if pyenv is installed
 if [ -z "$(command -v pyenv)" ] || { [ -z "$(command -v pyenv-virtualenv)" ] && [ ! -f "$(pyenv root)/plugins/pyenv-virtualenv/bin/pyenv-virtualenv" ]; }; then
   echo "pyenv and pyenv-virtualenv are required."
@@ -157,6 +177,15 @@ if [ $LIST_VERSIONS -ne 0 ]; then
   echo Available Python versions:
   python_versions
   read -r -p "Enter the desired Python version: " PYTHON_VERSION
+  # Check the Python versions being passed in.
+  if [ -n "${PYTHON_VERSION+x}" ]; then
+    if python_versions | grep -E "^${PYTHON_VERSION}$" > /dev/null; then
+      echo Using Python version "$PYTHON_VERSION"
+    else
+      echo Error: Python version "$PYTHON_VERSION" is not installed.
+      exit 1
+    fi
+  fi
 fi
 
 # Remove any lingering local configuration.

From f92458454394db61e8080b72b42fd340b3b64aa1 Mon Sep 17 00:00:00 2001
From: Michael Saki <michael.saki@associates.cisa.dhs.gov>
Date: Tue, 6 Feb 2024 20:49:34 -0600
Subject: [PATCH 40/82] Add documentation in CONTRIBUTING.md for gnu-getopt

---
 CONTRIBUTING.md | 16 +++++++++++-----
 1 file changed, 11 insertions(+), 5 deletions(-)

diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
index 27bb9e7..dbbe417 100644
--- a/CONTRIBUTING.md
+++ b/CONTRIBUTING.md
@@ -46,9 +46,12 @@ There are a few ways to do this, but we prefer to use
 create and manage a Python virtual environment specific to this
 project.
 
-If you already have `pyenv` and `pyenv-virtualenv` configured you can
-take advantage of the `setup-env` tool in this repo to automate the
-entire environment configuration process.
+The `setup-env` tool in this repository is our recommended method
+for automating the entire environment configuration process. The
+dependencies required to run this tool are
+[`gnu-getopt`](https://manned.org/getopt.1), `pyenv`, and
+`pyenv-virtualenv`. If these tools are already configured on
+your system, you can simply run the following command.
 
 ```console
 ./setup-env
@@ -57,13 +60,14 @@ entire environment configuration process.
 Otherwise, follow the steps below to manually configure your
 environment.
 
-#### Installing and using `pyenv` and `pyenv-virtualenv` ####
+#### Installing and using `gnu-getopt`, `pyenv`, and `pyenv-virtualenv` ####
 
 On the Mac, we recommend installing [brew](https://brew.sh/).  Then
-installation is as simple as `brew install pyenv pyenv-virtualenv` and
+installation is as simple as `brew install gnu-getopt pyenv pyenv-virtualenv` and
 adding this to your profile:
 
 ```bash
+export PATH="/usr/local/opt/gnu-getopt/bin:$PATH"
 export PYENV_ROOT="$HOME/.pyenv"
 export PATH="$PYENV_ROOT/bin:$PATH"
 eval "$(pyenv init --path)"
@@ -78,6 +82,8 @@ install the necessary tools. Before running this ensure that you have
 installed the prerequisites for your platform according to the
 [`pyenv` wiki
 page](https://github.com/pyenv/pyenv/wiki/common-build-problems).
+`Gnu-getopt` is generally included in the core utilities of most
+Linux distributions.
 
 On WSL you should treat your platform as whatever Linux distribution
 you've chosen to install.

From ba86ead6c4f757f03610c6065df46e5ba4ad4dbd Mon Sep 17 00:00:00 2001
From: Michael Saki <sakimichael@Yahoo.com>
Date: Wed, 7 Feb 2024 09:43:30 -0600
Subject: [PATCH 41/82] Fix grammar and capitalization errors

Co-authored-by: Shane Frasier <jeremy.frasier@gwe.cisa.dhs.gov>
---
 CONTRIBUTING.md |  2 +-
 setup-env       | 12 ++++++------
 2 files changed, 7 insertions(+), 7 deletions(-)

diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
index dbbe417..d96a0e3 100644
--- a/CONTRIBUTING.md
+++ b/CONTRIBUTING.md
@@ -82,7 +82,7 @@ install the necessary tools. Before running this ensure that you have
 installed the prerequisites for your platform according to the
 [`pyenv` wiki
 page](https://github.com/pyenv/pyenv/wiki/common-build-problems).
-`Gnu-getopt` is generally included in the core utilities of most
+`gnu-getopt` is generally included in the core utilities of most
 Linux distributions.
 
 On WSL you should treat your platform as whatever Linux distribution
diff --git a/setup-env b/setup-env
index f4cdf75..1054a64 100755
--- a/setup-env
+++ b/setup-env
@@ -9,10 +9,10 @@ USAGE=$(
 Configure a development environment for this repository.
 
 It does the following:
-  - Allows user to specify Python version.
-  - Allows user to choose name for their virtual environment.
+  - Allows the user to specify the Python version to use for the virtual environment.
+  - Allows the user to specify a name for the virtual environment.
   - Verifies pyenv and pyenv-virtualenv are installed.
-  - Creates a Python virtual environment.
+  - Creates the Python virtual environment.
   - Configures the activation of the virtual enviroment for the repo directory.
   - Installs the requirements needed for development.
   - Installs git pre-commit hooks.
@@ -29,7 +29,7 @@ Options:
   -i | --install-hooks     Install hook environments for all environments in the
                            pre-commit config file.
   -l | --list-versions     List available Python versions and select interactively.
-  -n | --name              Choose the name of the virtual environment.
+  -n | --name              Specify the name of the virtual environment.
   -v | --version           Specify the Python version for the virtual environment.
 
 END_OF_LINE
@@ -195,7 +195,7 @@ if [ $FORCE -ne 0 ]; then
 elif [[ -f .python-version ]]; then
   cat << 'END_OF_LINE'
   An existing .python-version file was found.  Either remove this file yourself
-  or re-run with -f (force) option to have it deleted along with the associated
+  or re-run with the --force option to have it deleted along with the associated
   virtual environment.
 
   rm .python-version
@@ -216,7 +216,7 @@ fi
 if ! pyenv virtualenv ${PYTHON_VERSION:=} "${env_name}"; then
   cat << END_OF_LINE
   An existing virtual environment named $env_name was found.  Either delete this
-  environment yourself or re-run with -f (force) option to have it deleted.
+  environment yourself or re-run with the --force option to have it deleted.
 
   pyenv virtualenv-delete ${env_name}
 

From ba0fc19811d2b9bcb2cc043660f6dcd9d6d9c64b Mon Sep 17 00:00:00 2001
From: Michael Saki <sakimichael@Yahoo.com>
Date: Wed, 7 Feb 2024 09:48:01 -0600
Subject: [PATCH 42/82] Combine PATH exports to single line

Co-authored-by: Shane Frasier <jeremy.frasier@gwe.cisa.dhs.gov>
---
 CONTRIBUTING.md | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
index d96a0e3..1e6cc74 100644
--- a/CONTRIBUTING.md
+++ b/CONTRIBUTING.md
@@ -67,9 +67,8 @@ installation is as simple as `brew install gnu-getopt pyenv pyenv-virtualenv` an
 adding this to your profile:
 
 ```bash
-export PATH="/usr/local/opt/gnu-getopt/bin:$PATH"
 export PYENV_ROOT="$HOME/.pyenv"
-export PATH="$PYENV_ROOT/bin:$PATH"
+export PATH="$PYENV_ROOT/bin:/usr/local/opt/gnu-getopt/bin:$PATH"
 eval "$(pyenv init --path)"
 eval "$(pyenv init -)"
 eval "$(pyenv virtualenv-init -)"

From 1240bdd98fe3523dada222782a55df8c2b258e5c Mon Sep 17 00:00:00 2001
From: Michael Saki <sakimichael@Yahoo.com>
Date: Wed, 7 Feb 2024 09:48:39 -0600
Subject: [PATCH 43/82] Improve usage instructions

Co-authored-by: Shane Frasier <jeremy.frasier@gwe.cisa.dhs.gov>
---
 setup-env | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/setup-env b/setup-env
index 1054a64..a0230ed 100755
--- a/setup-env
+++ b/setup-env
@@ -19,8 +19,7 @@ It does the following:
   - Configures git upstream remote "lineage" repositories.
 
 Usage:
-  setup-env (-n | --name) [virt_env_name]
-  setup-env (-v | --version) [python_version]
+  setup-env (-n | --name) [virt_env_name] (-v | --version) [python_version]
   setup-env (-h | --help)
 
 Options:

From 297b5bd850f716372eb385c25ef29936b4bd6d7c Mon Sep 17 00:00:00 2001
From: Michael Saki <sakimichael@Yahoo.com>
Date: Wed, 7 Feb 2024 11:03:35 -0600
Subject: [PATCH 44/82] Add $(brew --prefix) to PATH for getopt

Co-authored-by: dav3r <david.redmin@trio.dhs.gov>
---
 CONTRIBUTING.md | 2 +-
 setup-env       | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
index 1e6cc74..899f4ff 100644
--- a/CONTRIBUTING.md
+++ b/CONTRIBUTING.md
@@ -68,7 +68,7 @@ adding this to your profile:
 
 ```bash
 export PYENV_ROOT="$HOME/.pyenv"
-export PATH="$PYENV_ROOT/bin:/usr/local/opt/gnu-getopt/bin:$PATH"
+export PATH="$PYENV_ROOT/bin:$(brew --prefix)/opt/gnu-getopt/bin:$PATH"
 eval "$(pyenv init --path)"
 eval "$(pyenv init -)"
 eval "$(pyenv virtualenv-init -)"
diff --git a/setup-env b/setup-env
index a0230ed..3ddc9c9 100755
--- a/setup-env
+++ b/setup-env
@@ -63,7 +63,7 @@ if [[ $(getopt --version 2> /dev/null) != *"getopt from util-linux"* ]]; then
   is as simple as `brew install gnu-getopt` and adding this to your
   profile:
 
-  export PATH="/usr/local/opt/gnu-getopt/bin:$PATH"
+  export PATH="$(brew --prefix)/opt/gnu-getopt/bin:$PATH"
 
 END_OF_LINE
   exit 1

From 7af70f514fba159ed6e7c8ae85af7a0e14a667a1 Mon Sep 17 00:00:00 2001
From: Michael Saki <sakimichael@Yahoo.com>
Date: Wed, 7 Feb 2024 11:04:27 -0600
Subject: [PATCH 45/82] Fix confusing wording

Co-authored-by: dav3r <david.redmin@trio.dhs.gov>
---
 setup-env | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/setup-env b/setup-env
index 3ddc9c9..1e2fd79 100755
--- a/setup-env
+++ b/setup-env
@@ -42,7 +42,7 @@ python_versions() {
 # Flag to force deletion and creation of virtual environment
 FORCE=0
 
-# Initialize the all other flags
+# Initialize the other flags
 INSTALL_HOOKS=0
 LIST_VERSIONS=0
 PYTHON_VERSION=""

From e5a2d14964a65c0f5b74e53e5f7e606778b5f003 Mon Sep 17 00:00:00 2001
From: Michael Saki <sakimichael@Yahoo.com>
Date: Wed, 7 Feb 2024 11:06:50 -0600
Subject: [PATCH 46/82] Replace virt_env_name w/ virtual_env_name for clarity

Co-authored-by: dav3r <david.redmin@trio.dhs.gov>
---
 setup-env | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/setup-env b/setup-env
index 1e2fd79..ac20852 100755
--- a/setup-env
+++ b/setup-env
@@ -19,7 +19,7 @@ It does the following:
   - Configures git upstream remote "lineage" repositories.
 
 Usage:
-  setup-env (-n | --name) [virt_env_name] (-v | --version) [python_version]
+  setup-env (-n | --name) [virtual_env_name] (-v | --version) [python_version]
   setup-env (-h | --help)
 
 Options:

From 82c70e089bfd43c84273a83228da38030d340c14 Mon Sep 17 00:00:00 2001
From: Michael Saki <sakimichael@Yahoo.com>
Date: Tue, 13 Feb 2024 14:31:35 -0600
Subject: [PATCH 47/82] Differentiate between GNU getopt and gnu-getopt brew
 formula

This commit will clearly differentiate between GNU getopt the tool and gnu-getopt the Homebrew formula. Also updating the URL so that getopt points at the source repository and pyenv and pyenv-virtualenv point at their respective repositories. Updated the ending punctuation.

Co-authored-by: Nick <50747025+mcdonnnj@users.noreply.github.com>
---
 CONTRIBUTING.md | 13 +++++++------
 setup-env       |  2 +-
 2 files changed, 8 insertions(+), 7 deletions(-)

diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
index 899f4ff..afb1ae8 100644
--- a/CONTRIBUTING.md
+++ b/CONTRIBUTING.md
@@ -49,9 +49,10 @@ project.
 The `setup-env` tool in this repository is our recommended method
 for automating the entire environment configuration process. The
 dependencies required to run this tool are
-[`gnu-getopt`](https://manned.org/getopt.1), `pyenv`, and
-`pyenv-virtualenv`. If these tools are already configured on
-your system, you can simply run the following command.
+[GNU `getopt`](https://github.com/util-linux/util-linux/blob/master/misc-utils/getopt.1.adoc),
+[`pyenv`](https://github.com/pyenv/pyenv), and [`pyenv-virtualenv`](https://github.com/pyenv/pyenv-virtualenv).
+If these tools are already configured on your system, you can simply run the
+following command:
 
 ```console
 ./setup-env
@@ -60,7 +61,7 @@ your system, you can simply run the following command.
 Otherwise, follow the steps below to manually configure your
 environment.
 
-#### Installing and using `gnu-getopt`, `pyenv`, and `pyenv-virtualenv` ####
+#### Installing and using GNU `getopt`, `pyenv`, and `pyenv-virtualenv` ####
 
 On the Mac, we recommend installing [brew](https://brew.sh/).  Then
 installation is as simple as `brew install gnu-getopt pyenv pyenv-virtualenv` and
@@ -81,8 +82,8 @@ install the necessary tools. Before running this ensure that you have
 installed the prerequisites for your platform according to the
 [`pyenv` wiki
 page](https://github.com/pyenv/pyenv/wiki/common-build-problems).
-`gnu-getopt` is generally included in the core utilities of most
-Linux distributions.
+GNU `getopt` is included in most Linux distributions as part of the
+[`util-linux`](https://github.com/util-linux/util-linux) package.
 
 On WSL you should treat your platform as whatever Linux distribution
 you've chosen to install.
diff --git a/setup-env b/setup-env
index ac20852..0e9598b 100755
--- a/setup-env
+++ b/setup-env
@@ -58,7 +58,7 @@ SHORTOPTS="fhiln:v:"
 if [[ $(getopt --version 2> /dev/null) != *"getopt from util-linux"* ]]; then
   cat << 'END_OF_LINE'
 
-  Gnu-getopt is not detected and is a dependency to run this script.
+  GNU getopt is not detected and is a dependency to run this script.
   On the Mac, we recommend installing brew, https://brew.sh/.  Then installation
   is as simple as `brew install gnu-getopt` and adding this to your
   profile:

From 493a4a3e5dfe4c705998395797c75eda756c6dc4 Mon Sep 17 00:00:00 2001
From: Michael Saki <sakimichael@Yahoo.com>
Date: Tue, 13 Feb 2024 14:58:43 -0600
Subject: [PATCH 48/82] Add parenthesis over brew link

Co-authored-by: Nick <50747025+mcdonnnj@users.noreply.github.com>
---
 setup-env | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/setup-env b/setup-env
index 0e9598b..f0d4b36 100755
--- a/setup-env
+++ b/setup-env
@@ -59,7 +59,7 @@ if [[ $(getopt --version 2> /dev/null) != *"getopt from util-linux"* ]]; then
   cat << 'END_OF_LINE'
 
   GNU getopt is not detected and is a dependency to run this script.
-  On the Mac, we recommend installing brew, https://brew.sh/.  Then installation
+  On the Mac, we recommend installing brew (https://brew.sh/).  Then installation
   is as simple as `brew install gnu-getopt` and adding this to your
   profile:
 

From 3bc9aeb12fb7a270fa6bc54fcc4deceb897906bc Mon Sep 17 00:00:00 2001
From: Michael Saki <michael.saki@associates.cisa.dhs.gov>
Date: Wed, 14 Feb 2024 07:37:24 -0600
Subject: [PATCH 49/82] Refactor flag names for clarity and accuracy

This commit will remove the previous flags
-v or --version for -p or --python-version.
Also it will replace -n or --name for -v or
--venv-name. The usage menu has been updated
to reflect these changes as well.
---
 setup-env | 20 ++++++++++----------
 1 file changed, 10 insertions(+), 10 deletions(-)

diff --git a/setup-env b/setup-env
index f0d4b36..b7b08e6 100755
--- a/setup-env
+++ b/setup-env
@@ -19,7 +19,7 @@ It does the following:
   - Configures git upstream remote "lineage" repositories.
 
 Usage:
-  setup-env (-n | --name) [virtual_env_name] (-v | --version) [python_version]
+  setup-env [--venv-name virtual_env_name] [--python-version python_version]
   setup-env (-h | --help)
 
 Options:
@@ -28,8 +28,8 @@ Options:
   -i | --install-hooks     Install hook environments for all environments in the
                            pre-commit config file.
   -l | --list-versions     List available Python versions and select interactively.
-  -n | --name              Specify the name of the virtual environment.
-  -v | --version           Specify the Python version for the virtual environment.
+  -v | --venv-name              Specify the name of the virtual environment.
+  -p | --python-version           Specify the Python version for the virtual environment.
 
 END_OF_LINE
 )
@@ -49,10 +49,10 @@ PYTHON_VERSION=""
 VENV_NAME=""
 
 # Define long options
-LONGOPTS="force,help,install-hooks,list-versions,name:,version:"
+LONGOPTS="force,help,install-hooks,list-versions,python-version:,venv-name:"
 
 # Define short options for getopt
-SHORTOPTS="fhiln:v:"
+SHORTOPTS="fhilp:v:"
 
 # Check if GNU getopt is available
 if [[ $(getopt --version 2> /dev/null) != *"getopt from util-linux"* ]]; then
@@ -94,11 +94,7 @@ while true; do
       LIST_VERSIONS=1
       shift
       ;;
-    -n | --name)
-      VENV_NAME="$2"
-      shift 2
-      ;;
-    -v | --version)
+    -p | --python-version)
       PYTHON_VERSION="$2"
       shift 2
       # Check the Python versions being passed in.
@@ -113,6 +109,10 @@ while true; do
         fi
       fi
       ;;
+    -v | --venv-name)
+      VENV_NAME="$2"
+      shift 2
+      ;;
     --)
       shift
       break

From 0be1f6376dc914be4eff9ce5fde7649d085a2582 Mon Sep 17 00:00:00 2001
From: Michael Saki <michael.saki@associates.cisa.dhs.gov>
Date: Wed, 14 Feb 2024 08:08:07 -0600
Subject: [PATCH 50/82] Elaborate on message when checking for GNU getopt

---
 setup-env | 8 +++++++-
 1 file changed, 7 insertions(+), 1 deletion(-)

diff --git a/setup-env b/setup-env
index b7b08e6..6649b4d 100755
--- a/setup-env
+++ b/setup-env
@@ -58,7 +58,13 @@ SHORTOPTS="fhilp:v:"
 if [[ $(getopt --version 2> /dev/null) != *"getopt from util-linux"* ]]; then
   cat << 'END_OF_LINE'
 
-  GNU getopt is not detected and is a dependency to run this script.
+  Please note, this script requires GNU getopt due to its enhanced
+  functionality and compatibility with certain script features that
+  are not supported by the POSIX getopt found in some systems, particularly
+  those with a non-GNU version of getopt. This distinction is crucial
+  as a system might have a non-GNU version of getopt installed by default,
+  which could lead to unexpected behavior or script failure.
+
   On the Mac, we recommend installing brew (https://brew.sh/).  Then installation
   is as simple as `brew install gnu-getopt` and adding this to your
   profile:

From c8f0b1b996958a5fa965343fa7e6295b7160cbf4 Mon Sep 17 00:00:00 2001
From: Michael Saki <michael.saki@associates.cisa.dhs.gov>
Date: Wed, 14 Feb 2024 08:10:21 -0600
Subject: [PATCH 51/82] Remove unnecessary nounset flipping logic

---
 setup-env | 2 --
 1 file changed, 2 deletions(-)

diff --git a/setup-env b/setup-env
index 6649b4d..05b010b 100755
--- a/setup-env
+++ b/setup-env
@@ -166,7 +166,6 @@ END_OF_LINE
   exit 1
 fi
 
-set +o nounset
 # Determine the virtual environment name
 if [ -n "$VENV_NAME" ]; then
   # Use the user-provided environment name
@@ -175,7 +174,6 @@ else
   # Set the environment name to the last part of the working directory.
   env_name=${PWD##*/}
 fi
-set -o nounset
 
 # List Python versions and select one interactively
 if [ $LIST_VERSIONS -ne 0 ]; then

From 495862aeaf3430b0a69f92cf54b6415818139db2 Mon Sep 17 00:00:00 2001
From: Michael Saki <michael.saki@associates.cisa.dhs.gov>
Date: Wed, 14 Feb 2024 08:20:56 -0600
Subject: [PATCH 52/82] Separate pyenv PATH from GNU getopt PATH

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

diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
index afb1ae8..3a5e087 100644
--- a/CONTRIBUTING.md
+++ b/CONTRIBUTING.md
@@ -69,7 +69,8 @@ adding this to your profile:
 
 ```bash
 export PYENV_ROOT="$HOME/.pyenv"
-export PATH="$PYENV_ROOT/bin:$(brew --prefix)/opt/gnu-getopt/bin:$PATH"
+export PATH="$PYENV_ROOT/bin:$PATH"
+export PATH="$(brew --prefix)/opt/gnu-getopt/bin:$PATH"
 eval "$(pyenv init --path)"
 eval "$(pyenv init -)"
 eval "$(pyenv virtualenv-init -)"

From 4752b37ec887a65e967f01a1f9b7633e02a02af8 Mon Sep 17 00:00:00 2001
From: Michael Saki <sakimichael@Yahoo.com>
Date: Wed, 21 Feb 2024 10:57:38 -0600
Subject: [PATCH 53/82] Improve verbiage in comments

Co-authored-by: Shane Frasier <jeremy.frasier@gwe.cisa.dhs.gov>
---
 CONTRIBUTING.md | 4 ++--
 setup-env       | 4 ++--
 2 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
index 3a5e087..9ff54e4 100644
--- a/CONTRIBUTING.md
+++ b/CONTRIBUTING.md
@@ -46,8 +46,8 @@ There are a few ways to do this, but we prefer to use
 create and manage a Python virtual environment specific to this
 project.
 
-The `setup-env` tool in this repository is our recommended method
-for automating the entire environment configuration process. The
+We recommend using the `setup-env` tool located in this repository,
+as it automates the entire environment configuration process. The
 dependencies required to run this tool are
 [GNU `getopt`](https://github.com/util-linux/util-linux/blob/master/misc-utils/getopt.1.adoc),
 [`pyenv`](https://github.com/pyenv/pyenv), and [`pyenv-virtualenv`](https://github.com/pyenv/pyenv-virtualenv).
diff --git a/setup-env b/setup-env
index 05b010b..6d9fec0 100755
--- a/setup-env
+++ b/setup-env
@@ -27,7 +27,7 @@ Options:
   -h | --help              Show this message.
   -i | --install-hooks     Install hook environments for all environments in the
                            pre-commit config file.
-  -l | --list-versions     List available Python versions and select interactively.
+  -l | --list-versions     List available Python versions and select one interactively.
   -v | --venv-name              Specify the name of the virtual environment.
   -p | --python-version           Specify the Python version for the virtual environment.
 
@@ -63,7 +63,7 @@ if [[ $(getopt --version 2> /dev/null) != *"getopt from util-linux"* ]]; then
   are not supported by the POSIX getopt found in some systems, particularly
   those with a non-GNU version of getopt. This distinction is crucial
   as a system might have a non-GNU version of getopt installed by default,
-  which could lead to unexpected behavior or script failure.
+  which could lead to unexpected behavior.
 
   On the Mac, we recommend installing brew (https://brew.sh/).  Then installation
   is as simple as `brew install gnu-getopt` and adding this to your

From 2e389979b0b0b34a6f32443d88f8ed0ba8c647cd Mon Sep 17 00:00:00 2001
From: Michael Saki <sakimichael@Yahoo.com>
Date: Wed, 21 Feb 2024 11:22:53 -0600
Subject: [PATCH 54/82] Clarify between pyenv and GNU getopt setup

Co-authored-by: Nick <50747025+mcdonnnj@users.noreply.github.com>
---
 CONTRIBUTING.md | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
index 9ff54e4..a844f86 100644
--- a/CONTRIBUTING.md
+++ b/CONTRIBUTING.md
@@ -68,9 +68,12 @@ installation is as simple as `brew install gnu-getopt pyenv pyenv-virtualenv` an
 adding this to your profile:
 
 ```bash
+# Enable GNU getopt since it is keg-only
+export PATH="$(brew --prefix)/opt/gnu-getopt/bin:$PATH"
+
+# Setup pyenv
 export PYENV_ROOT="$HOME/.pyenv"
 export PATH="$PYENV_ROOT/bin:$PATH"
-export PATH="$(brew --prefix)/opt/gnu-getopt/bin:$PATH"
 eval "$(pyenv init --path)"
 eval "$(pyenv init -)"
 eval "$(pyenv virtualenv-init -)"

From f8824c8aa157cbee0ec95367b1754eeac67934c9 Mon Sep 17 00:00:00 2001
From: Michael Saki <michael.saki@associates.cisa.dhs.gov>
Date: Wed, 21 Feb 2024 12:14:23 -0600
Subject: [PATCH 55/82] Improve comment on conditional check for regex

---
 setup-env | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/setup-env b/setup-env
index 6d9fec0..6d16958 100755
--- a/setup-env
+++ b/setup-env
@@ -54,7 +54,9 @@ LONGOPTS="force,help,install-hooks,list-versions,python-version:,venv-name:"
 # Define short options for getopt
 SHORTOPTS="fhilp:v:"
 
-# Check if GNU getopt is available
+# Check for GNU getopt by matching a specific pattern ("getopt from util-linux")
+# in its version output. This approach presumes the output format remains stable.
+# Be aware that format changes could invalidate this check.
 if [[ $(getopt --version 2> /dev/null) != *"getopt from util-linux"* ]]; then
   cat << 'END_OF_LINE'
 

From 88724e70167a5864495eccff5532f4c59fbefc1c Mon Sep 17 00:00:00 2001
From: Michael Saki <michael.saki@associates.cisa.dhs.gov>
Date: Wed, 21 Feb 2024 12:25:49 -0600
Subject: [PATCH 56/82] Add comment explaining that GNU getopt is keg-only

---
 setup-env | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/setup-env b/setup-env
index 6d16958..84a8305 100755
--- a/setup-env
+++ b/setup-env
@@ -73,6 +73,8 @@ if [[ $(getopt --version 2> /dev/null) != *"getopt from util-linux"* ]]; then
 
   export PATH="$(brew --prefix)/opt/gnu-getopt/bin:$PATH"
 
+  This will enable GNU getopt since it is keg-only.
+
 END_OF_LINE
   exit 1
 fi

From c1870be7a16f5e88f6e6540c290f674da4861e07 Mon Sep 17 00:00:00 2001
From: Michael Saki <sakimichael@Yahoo.com>
Date: Wed, 21 Feb 2024 16:28:54 -0600
Subject: [PATCH 57/82] Improve comments to better describe `keg-only`
 terminology

Co-authored-by: Shane Frasier <jeremy.frasier@gwe.cisa.dhs.gov>
---
 CONTRIBUTING.md | 3 ++-
 setup-env       | 3 ++-
 2 files changed, 4 insertions(+), 2 deletions(-)

diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
index a844f86..7bb8881 100644
--- a/CONTRIBUTING.md
+++ b/CONTRIBUTING.md
@@ -68,7 +68,8 @@ installation is as simple as `brew install gnu-getopt pyenv pyenv-virtualenv` an
 adding this to your profile:
 
 ```bash
-# Enable GNU getopt since it is keg-only
+# GNU getopt must be explicitly added to the path since it is
+# keg-only
 export PATH="$(brew --prefix)/opt/gnu-getopt/bin:$PATH"
 
 # Setup pyenv
diff --git a/setup-env b/setup-env
index 84a8305..3fa8c47 100755
--- a/setup-env
+++ b/setup-env
@@ -73,7 +73,8 @@ if [[ $(getopt --version 2> /dev/null) != *"getopt from util-linux"* ]]; then
 
   export PATH="$(brew --prefix)/opt/gnu-getopt/bin:$PATH"
 
-  This will enable GNU getopt since it is keg-only.
+  GNU getopt must be explicitly added to the PATH since it
+  is keg-only.
 
 END_OF_LINE
   exit 1

From a3f69cd24e58077ee6f084bce900ed176c88cff7 Mon Sep 17 00:00:00 2001
From: Michael Saki <sakimichael@Yahoo.com>
Date: Mon, 26 Feb 2024 08:04:19 -0600
Subject: [PATCH 58/82] Change "'setup-env' tool" to "'setup-env' script"

Co-authored-by: Nick <50747025+mcdonnnj@users.noreply.github.com>
---
 CONTRIBUTING.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
index 7bb8881..fca0cf7 100644
--- a/CONTRIBUTING.md
+++ b/CONTRIBUTING.md
@@ -46,7 +46,7 @@ There are a few ways to do this, but we prefer to use
 create and manage a Python virtual environment specific to this
 project.
 
-We recommend using the `setup-env` tool located in this repository,
+We recommend using the `setup-env` script located in this repository,
 as it automates the entire environment configuration process. The
 dependencies required to run this tool are
 [GNU `getopt`](https://github.com/util-linux/util-linux/blob/master/misc-utils/getopt.1.adoc),

From 8ff51796ec530e68d35362fab761608e676dcd3a Mon Sep 17 00:00:00 2001
From: Michael Saki <sakimichael@Yahoo.com>
Date: Mon, 26 Feb 2024 08:07:16 -0600
Subject: [PATCH 59/82] Remove build-in error exit for generic error exit

Exit code 2 usually relates to build-ins which does not fit what is failing here. Not sure what alternative would be best so we can just use the generic failure code

Co-authored-by: Nick <50747025+mcdonnnj@users.noreply.github.com>
---
 setup-env | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/setup-env b/setup-env
index 3fa8c47..f7ce620 100755
--- a/setup-env
+++ b/setup-env
@@ -83,7 +83,7 @@ fi
 # Use GNU getopt to parse options
 if ! PARSED=$(getopt --options $SHORTOPTS --longoptions $LONGOPTS --name "$0" -- "$@"); then
   echo "Error parsing options"
-  exit 2
+  exit 1
 fi
 eval set -- "$PARSED"
 

From 1c21e2b9839980c75410584c69d0ac0a0651f097 Mon Sep 17 00:00:00 2001
From: Michael Saki <sakimichael@Yahoo.com>
Date: Mon, 26 Feb 2024 08:08:39 -0600
Subject: [PATCH 60/82] Change verbiage from 'tool' to 'script' for clarity

Co-authored-by: Nick <50747025+mcdonnnj@users.noreply.github.com>
---
 CONTRIBUTING.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
index fca0cf7..cdab589 100644
--- a/CONTRIBUTING.md
+++ b/CONTRIBUTING.md
@@ -48,7 +48,7 @@ project.
 
 We recommend using the `setup-env` script located in this repository,
 as it automates the entire environment configuration process. The
-dependencies required to run this tool are
+dependencies required to run this script are
 [GNU `getopt`](https://github.com/util-linux/util-linux/blob/master/misc-utils/getopt.1.adoc),
 [`pyenv`](https://github.com/pyenv/pyenv), and [`pyenv-virtualenv`](https://github.com/pyenv/pyenv-virtualenv).
 If these tools are already configured on your system, you can simply run the

From 3acc8d6a17360221d6c59c306db1a14a98b48b8b Mon Sep 17 00:00:00 2001
From: Michael Saki <michael.saki@associates.cisa.dhs.gov>
Date: Mon, 26 Feb 2024 10:04:42 -0600
Subject: [PATCH 61/82] Check for pyenv earlier in the script

Since the new function, python_versions expects
pyenv to be installed it makes sense to have it
checked earlier in the script.
---
 setup-env | 72 +++++++++++++++++++++++++++----------------------------
 1 file changed, 36 insertions(+), 36 deletions(-)

diff --git a/setup-env b/setup-env
index f7ce620..3898ca8 100755
--- a/setup-env
+++ b/setup-env
@@ -80,6 +80,42 @@ END_OF_LINE
   exit 1
 fi
 
+# Check to see if pyenv is installed
+if [ -z "$(command -v pyenv)" ] || { [ -z "$(command -v pyenv-virtualenv)" ] && [ ! -f "$(pyenv root)/plugins/pyenv-virtualenv/bin/pyenv-virtualenv" ]; }; then
+  echo "pyenv and pyenv-virtualenv are required."
+  if [[ "$OSTYPE" == "darwin"* ]]; then
+    cat << 'END_OF_LINE'
+
+  On the Mac, we recommend installing brew, https://brew.sh/.  Then installation
+  is as simple as `brew install pyenv pyenv-virtualenv` and adding this to your
+  profile:
+
+  eval "$(pyenv init -)"
+  eval "$(pyenv virtualenv-init -)"
+
+END_OF_LINE
+
+  fi
+  cat << 'END_OF_LINE'
+  For Linux, Windows Subsystem for Linux (WSL), or on the Mac (if you don't want
+  to use "brew") you can use https://github.com/pyenv/pyenv-installer to install
+  the necessary tools. Before running this ensure that you have installed the
+  prerequisites for your platform according to the pyenv wiki page,
+  https://github.com/pyenv/pyenv/wiki/common-build-problems.
+
+  On WSL you should treat your platform as whatever Linux distribution you've
+  chosen to install.
+
+  Once you have installed "pyenv" you will need to add the following lines to
+  your ".bashrc":
+
+  export PATH="$PATH:$HOME/.pyenv/bin"
+  eval "$(pyenv init -)"
+  eval "$(pyenv virtualenv-init -)"
+END_OF_LINE
+  exit 1
+fi
+
 # Use GNU getopt to parse options
 if ! PARSED=$(getopt --options $SHORTOPTS --longoptions $LONGOPTS --name "$0" -- "$@"); then
   echo "Error parsing options"
@@ -135,42 +171,6 @@ while true; do
   esac
 done
 
-# Check to see if pyenv is installed
-if [ -z "$(command -v pyenv)" ] || { [ -z "$(command -v pyenv-virtualenv)" ] && [ ! -f "$(pyenv root)/plugins/pyenv-virtualenv/bin/pyenv-virtualenv" ]; }; then
-  echo "pyenv and pyenv-virtualenv are required."
-  if [[ "$OSTYPE" == "darwin"* ]]; then
-    cat << 'END_OF_LINE'
-
-  On the Mac, we recommend installing brew, https://brew.sh/.  Then installation
-  is as simple as `brew install pyenv pyenv-virtualenv` and adding this to your
-  profile:
-
-  eval "$(pyenv init -)"
-  eval "$(pyenv virtualenv-init -)"
-
-END_OF_LINE
-
-  fi
-  cat << 'END_OF_LINE'
-  For Linux, Windows Subsystem for Linux (WSL), or on the Mac (if you don't want
-  to use "brew") you can use https://github.com/pyenv/pyenv-installer to install
-  the necessary tools. Before running this ensure that you have installed the
-  prerequisites for your platform according to the pyenv wiki page,
-  https://github.com/pyenv/pyenv/wiki/common-build-problems.
-
-  On WSL you should treat your platform as whatever Linux distribution you've
-  chosen to install.
-
-  Once you have installed "pyenv" you will need to add the following lines to
-  your ".bashrc":
-
-  export PATH="$PATH:$HOME/.pyenv/bin"
-  eval "$(pyenv init -)"
-  eval "$(pyenv virtualenv-init -)"
-END_OF_LINE
-  exit 1
-fi
-
 # Determine the virtual environment name
 if [ -n "$VENV_NAME" ]; then
   # Use the user-provided environment name

From b377ce71fa3dd5f56697d415c5230f3fe18e8090 Mon Sep 17 00:00:00 2001
From: Michael Saki <michael.saki@associates.cisa.dhs.gov>
Date: Mon, 26 Feb 2024 11:02:39 -0600
Subject: [PATCH 62/82] Explain -r and -p in Python version prompt

---
 setup-env | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/setup-env b/setup-env
index 3898ca8..5c2b580 100755
--- a/setup-env
+++ b/setup-env
@@ -180,10 +180,12 @@ else
   env_name=${PWD##*/}
 fi
 
-# List Python versions and select one interactively
+# List Python versions and select one interactively.
 if [ $LIST_VERSIONS -ne 0 ]; then
   echo Available Python versions:
   python_versions
+  # Read the user's desired Python version.
+  # -r: treat backslashes as literal, -p: display prompt before input.
   read -r -p "Enter the desired Python version: " PYTHON_VERSION
   # Check the Python versions being passed in.
   if [ -n "${PYTHON_VERSION+x}" ]; then

From 74838a256e134e00208a23bb6dded7012cfb8534 Mon Sep 17 00:00:00 2001
From: Michael Saki <michael.saki@associates.cisa.dhs.gov>
Date: Mon, 26 Feb 2024 11:58:44 -0600
Subject: [PATCH 63/82] Refine exit code to 64 with gnu-getopt note

- Set exit code to 64 per sysexits.h for clarity.
- Added comment on gnu-getopt handling.

Aligns with Unix standards and enhances readability.
---
 setup-env | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/setup-env b/setup-env
index 5c2b580..549c079 100755
--- a/setup-env
+++ b/setup-env
@@ -165,8 +165,9 @@ while true; do
       break
       ;;
     *)
+      # Unreachable due to gnu-getopt handling all options
       echo "Programming error"
-      exit 3
+      exit 64
       ;;
   esac
 done

From cf993f1d523b8237916d5539317c918fd90bd61d Mon Sep 17 00:00:00 2001
From: Nicholas McDonnell <50747025+mcdonnnj@users.noreply.github.com>
Date: Thu, 9 Nov 2023 11:57:50 -0500
Subject: [PATCH 64/82] Alphabetize resources attributes in main.tf

---
 main.tf | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/main.tf b/main.tf
index 7f3b203..0646a05 100644
--- a/main.tf
+++ b/main.tf
@@ -28,10 +28,10 @@ data "aws_ami" "example" {
     values = ["ebs"]
   }
 
+  most_recent = true
   owners = [
     var.ami_owner_account_id
   ]
-  most_recent = true
 }
 
 # The default tags configured for the default provider
@@ -40,8 +40,8 @@ data "aws_default_tags" "default" {}
 # The example EC2 instance
 resource "aws_instance" "example" {
   ami               = data.aws_ami.example.id
-  instance_type     = "t3.micro"
   availability_zone = "${var.aws_region}${var.aws_availability_zone}"
+  instance_type     = "t3.micro"
   subnet_id         = var.subnet_id
 
   # The tag or tags specified here will be merged with the provider's

From 8bbce64442a8541bebde6852b67b888422d67b1f Mon Sep 17 00:00:00 2001
From: Nicholas McDonnell <50747025+mcdonnnj@users.noreply.github.com>
Date: Thu, 9 Nov 2023 11:59:20 -0500
Subject: [PATCH 65/82] Alphabetize resource attributes in outputs.tf

---
 outputs.tf | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/outputs.tf b/outputs.tf
index 9d8af20..ce18699 100644
--- a/outputs.tf
+++ b/outputs.tf
@@ -1,24 +1,24 @@
 output "arn" {
-  value       = aws_instance.example.arn
   description = "The EC2 instance ARN."
+  value       = aws_instance.example.arn
 }
 
 output "availability_zone" {
-  value       = aws_instance.example.availability_zone
   description = "The AZ where the EC2 instance is deployed."
+  value       = aws_instance.example.availability_zone
 }
 
 output "id" {
-  value       = aws_instance.example.id
   description = "The EC2 instance ID."
+  value       = aws_instance.example.id
 }
 
 output "private_ip" {
-  value       = aws_instance.example.private_ip
   description = "The private IP of the EC2 instance."
+  value       = aws_instance.example.private_ip
 }
 
 output "subnet_id" {
-  value       = aws_instance.example.subnet_id
   description = "The ID of the subnet where the EC2 instance is deployed."
+  value       = aws_instance.example.subnet_id
 }

From 45869c35e63b1e602f074c19d4f3d34278404dd6 Mon Sep 17 00:00:00 2001
From: Nicholas McDonnell <50747025+mcdonnnj@users.noreply.github.com>
Date: Thu, 9 Nov 2023 12:00:05 -0500
Subject: [PATCH 66/82] Alphabetize resource attributes in variables.tf

---
 variables.tf | 14 +++++++-------
 1 file changed, 7 insertions(+), 7 deletions(-)

diff --git a/variables.tf b/variables.tf
index 245aabb..416ad14 100644
--- a/variables.tf
+++ b/variables.tf
@@ -5,8 +5,8 @@
 # ------------------------------------------------------------------------------
 
 variable "subnet_id" {
-  type        = string
   description = "The ID of the AWS subnet to deploy into (e.g. subnet-0123456789abcdef0)."
+  type        = string
 }
 
 # ------------------------------------------------------------------------------
@@ -15,19 +15,19 @@ variable "subnet_id" {
 # These parameters have reasonable defaults.
 # ------------------------------------------------------------------------------
 variable "ami_owner_account_id" {
-  type        = string
-  description = "The ID of the AWS account that owns the Example AMI, or \"self\" if the AMI is owned by the same account as the provisioner."
   default     = "self"
+  description = "The ID of the AWS account that owns the Example AMI, or \"self\" if the AMI is owned by the same account as the provisioner."
+  type        = string
 }
 
 variable "aws_availability_zone" {
-  type        = string
-  description = "The AWS availability zone to deploy into (e.g. a, b, c, etc.)."
   default     = "a"
+  description = "The AWS availability zone to deploy into (e.g. a, b, c, etc.)."
+  type        = string
 }
 
 variable "aws_region" {
-  type        = string
-  description = "The AWS region to deploy into (e.g. us-east-1)."
   default     = "us-east-1"
+  description = "The AWS region to deploy into (e.g. us-east-1)."
+  type        = string
 }

From b5f21797609260d1305915e82b705f9b27e82db4 Mon Sep 17 00:00:00 2001
From: Nicholas McDonnell <50747025+mcdonnnj@users.noreply.github.com>
Date: Tue, 27 Feb 2024 14:10:32 -0500
Subject: [PATCH 67/82] Alphabetize resource attributes in versions.tf

---
 versions.tf | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/versions.tf b/versions.tf
index 80277d5..9db27b0 100644
--- a/versions.tf
+++ b/versions.tf
@@ -1,7 +1,4 @@
 terraform {
-  # We want to hold off on 1.1 or higher until we have tested it.
-  required_version = "~> 1.0"
-
   # If you use any other providers you should also pin them to the
   # major version currently being used.  This practice will help us
   # avoid unwelcome surprises.
@@ -20,4 +17,7 @@ terraform {
       version = "~> 4.9"
     }
   }
+
+  # We want to hold off on 1.1 or higher until we have tested it.
+  required_version = "~> 1.0"
 }

From 3f1c503b5fdcc4a35804636f777db463c12bcf31 Mon Sep 17 00:00:00 2001
From: Nicholas McDonnell <50747025+mcdonnnj@users.noreply.github.com>
Date: Thu, 9 Nov 2023 12:02:10 -0500
Subject: [PATCH 68/82] Alphabetize resource attributes in
 examples/basic_usage/

---
 examples/basic_usage/outputs.tf   | 10 +++++-----
 examples/basic_usage/variables.tf | 18 +++++++++---------
 examples/basic_usage/versions.tf  |  6 +++---
 examples/basic_usage/vpc.tf       |  2 +-
 4 files changed, 18 insertions(+), 18 deletions(-)

diff --git a/examples/basic_usage/outputs.tf b/examples/basic_usage/outputs.tf
index a815e68..542df31 100644
--- a/examples/basic_usage/outputs.tf
+++ b/examples/basic_usage/outputs.tf
@@ -1,24 +1,24 @@
 output "arn" {
-  value       = module.example.arn
   description = "The EC2 instance ARN."
+  value       = module.example.arn
 }
 
 output "availability_zone" {
-  value       = module.example.availability_zone
   description = "The AZ where the EC2 instance is deployed."
+  value       = module.example.availability_zone
 }
 
 output "id" {
-  value       = module.example.id
   description = "The EC2 instance ID."
+  value       = module.example.id
 }
 
 output "private_ip" {
-  value       = module.example.private_ip
   description = "The private IP of the EC2 instance."
+  value       = module.example.private_ip
 }
 
 output "subnet_id" {
-  value       = module.example.subnet_id
   description = "The ID of the subnet where the EC2 instance is deployed."
+  value       = module.example.subnet_id
 }
diff --git a/examples/basic_usage/variables.tf b/examples/basic_usage/variables.tf
index 205df43..70b275a 100644
--- a/examples/basic_usage/variables.tf
+++ b/examples/basic_usage/variables.tf
@@ -5,8 +5,8 @@
 # ------------------------------------------------------------------------------
 
 variable "tf_role_arn" {
-  type        = string
   description = "The ARN of the role that can terraform non-specialized resources."
+  type        = string
 }
 
 # ------------------------------------------------------------------------------
@@ -16,27 +16,27 @@ variable "tf_role_arn" {
 # ------------------------------------------------------------------------------
 
 variable "ami_owner_account_id" {
-  type        = string
-  description = "The ID of the AWS account that owns the AMI, or \"self\" if the AMI is owned by the same account as the provisioner."
   default     = "self"
+  description = "The ID of the AWS account that owns the AMI, or \"self\" if the AMI is owned by the same account as the provisioner."
+  type        = string
 }
 
 variable "aws_availability_zone" {
-  type        = string
-  description = "The AWS availability zone to deploy into (e.g. a, b, c, etc.)."
   default     = "a"
+  description = "The AWS availability zone to deploy into (e.g. a, b, c, etc.)."
+  type        = string
 }
 
 variable "aws_region" {
-  type        = string
-  description = "The AWS region to deploy into (e.g. us-east-1)."
   default     = "us-east-1"
+  description = "The AWS region to deploy into (e.g. us-east-1)."
+  type        = string
 }
 
 variable "tags" {
-  type        = map(string)
-  description = "Tags to apply to all AWS resources created."
   default = {
     Testing = true
   }
+  description = "Tags to apply to all AWS resources created."
+  type        = map(string)
 }
diff --git a/examples/basic_usage/versions.tf b/examples/basic_usage/versions.tf
index 80277d5..9db27b0 100644
--- a/examples/basic_usage/versions.tf
+++ b/examples/basic_usage/versions.tf
@@ -1,7 +1,4 @@
 terraform {
-  # We want to hold off on 1.1 or higher until we have tested it.
-  required_version = "~> 1.0"
-
   # If you use any other providers you should also pin them to the
   # major version currently being used.  This practice will help us
   # avoid unwelcome surprises.
@@ -20,4 +17,7 @@ terraform {
       version = "~> 4.9"
     }
   }
+
+  # We want to hold off on 1.1 or higher until we have tested it.
+  required_version = "~> 1.0"
 }
diff --git a/examples/basic_usage/vpc.tf b/examples/basic_usage/vpc.tf
index b54ecfd..947e0eb 100644
--- a/examples/basic_usage/vpc.tf
+++ b/examples/basic_usage/vpc.tf
@@ -15,6 +15,6 @@ resource "aws_vpc" "example" {
 resource "aws_subnet" "example" {
   availability_zone = "${var.aws_region}${var.aws_availability_zone}"
   cidr_block        = "10.230.0.0/28"
-  vpc_id            = aws_vpc.example.id
   tags              = { "Name" : "Example" }
+  vpc_id            = aws_vpc.example.id
 }

From 487126e34bd85e231b7021b70d225154694ad24d Mon Sep 17 00:00:00 2001
From: Michael Saki <sakimichael@Yahoo.com>
Date: Wed, 28 Feb 2024 06:32:35 -0600
Subject: [PATCH 69/82] Rename gnu-getopt tool to GNU getopt formula

Co-authored-by: Nick <50747025+mcdonnnj@users.noreply.github.com>
---
 setup-env | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/setup-env b/setup-env
index 549c079..d2db6e2 100755
--- a/setup-env
+++ b/setup-env
@@ -165,7 +165,7 @@ while true; do
       break
       ;;
     *)
-      # Unreachable due to gnu-getopt handling all options
+      # Unreachable due to GNU getopt handling all options
       echo "Programming error"
       exit 64
       ;;

From 6c82a8d1bb86a90f0e903dd2d90efdb6198fba33 Mon Sep 17 00:00:00 2001
From: Michael Saki <sakimichael@Yahoo.com>
Date: Wed, 28 Feb 2024 07:49:16 -0600
Subject: [PATCH 70/82] Fix whitespace for usage menu

Co-authored-by: Shane Frasier <jeremy.frasier@gwe.cisa.dhs.gov>
---
 setup-env | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/setup-env b/setup-env
index d2db6e2..c93eb25 100755
--- a/setup-env
+++ b/setup-env
@@ -28,8 +28,8 @@ Options:
   -i | --install-hooks     Install hook environments for all environments in the
                            pre-commit config file.
   -l | --list-versions     List available Python versions and select one interactively.
-  -v | --venv-name              Specify the name of the virtual environment.
-  -p | --python-version           Specify the Python version for the virtual environment.
+  -v | --venv-name         Specify the name of the virtual environment.
+  -p | --python-version    Specify the Python version for the virtual environment.
 
 END_OF_LINE
 )

From 324f6d426a149cb2c7bfc30ffcf7c1810b8ae1fa Mon Sep 17 00:00:00 2001
From: Michael Saki <sakimichael@Yahoo.com>
Date: Wed, 28 Feb 2024 11:26:24 -0600
Subject: [PATCH 71/82] Add link to brew terminology

Co-authored-by: dav3r <david.redmin@trio.dhs.gov>
---
 CONTRIBUTING.md | 2 +-
 setup-env       | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
index cdab589..bc32a55 100644
--- a/CONTRIBUTING.md
+++ b/CONTRIBUTING.md
@@ -69,7 +69,7 @@ adding this to your profile:
 
 ```bash
 # GNU getopt must be explicitly added to the path since it is
-# keg-only
+# keg-only (https://docs.brew.sh/FAQ#what-does-keg-only-mean)
 export PATH="$(brew --prefix)/opt/gnu-getopt/bin:$PATH"
 
 # Setup pyenv
diff --git a/setup-env b/setup-env
index c93eb25..bb689f3 100755
--- a/setup-env
+++ b/setup-env
@@ -74,7 +74,7 @@ if [[ $(getopt --version 2> /dev/null) != *"getopt from util-linux"* ]]; then
   export PATH="$(brew --prefix)/opt/gnu-getopt/bin:$PATH"
 
   GNU getopt must be explicitly added to the PATH since it
-  is keg-only.
+  is keg-only (https://docs.brew.sh/FAQ#what-does-keg-only-mean).
 
 END_OF_LINE
   exit 1

From a26d0e36f0c33a7f472b91d66697e4cecb8f9557 Mon Sep 17 00:00:00 2001
From: Michael Saki <sakimichael@Yahoo.com>
Date: Wed, 28 Feb 2024 15:52:20 -0600
Subject: [PATCH 72/82] Rephrase comment to improve clarity

Co-authored-by: Nick <50747025+mcdonnnj@users.noreply.github.com>
---
 setup-env | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/setup-env b/setup-env
index bb689f3..3fddb36 100755
--- a/setup-env
+++ b/setup-env
@@ -16,7 +16,7 @@ It does the following:
   - Configures the activation of the virtual enviroment for the repo directory.
   - Installs the requirements needed for development.
   - Installs git pre-commit hooks.
-  - Configures git upstream remote "lineage" repositories.
+  - Configures git remotes for upstream "lineage" repositories.
 
 Usage:
   setup-env [--venv-name virtual_env_name] [--python-version python_version]

From 05108705fa4120db51f261ad59347bb01134eafc Mon Sep 17 00:00:00 2001
From: Michael Saki <sakimichael@Yahoo.com>
Date: Wed, 28 Feb 2024 15:58:43 -0600
Subject: [PATCH 73/82] Improve comment for clarity

Co-authored-by: Nick <50747025+mcdonnnj@users.noreply.github.com>
---
 setup-env | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/setup-env b/setup-env
index 3fddb36..c8680ea 100755
--- a/setup-env
+++ b/setup-env
@@ -34,7 +34,7 @@ Options:
 END_OF_LINE
 )
 
-# Display installed python versions
+# Display pyenv's installed Python versions
 python_versions() {
   pyenv versions --bare --skip-aliases --skip-envs
 }

From 01abde6f580cf549d77c81af9378d4a18812fa8f Mon Sep 17 00:00:00 2001
From: Michael Saki <michael.saki@associates.cisa.dhs.gov>
Date: Wed, 28 Feb 2024 16:03:47 -0600
Subject: [PATCH 74/82] Improve verbiage in comment

---
 setup-env | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/setup-env b/setup-env
index c8680ea..534d47f 100755
--- a/setup-env
+++ b/setup-env
@@ -217,7 +217,7 @@ fi
 
 # Create a new virtual environment for this project
 #
-# If $PYTHON_VERSION is undefined then the system Python will be used.
+# If $PYTHON_VERSION is undefined then the global version of Python will be used.
 #
 # We can't quote ${PYTHON_VERSION:=} below since if the variable is
 # undefined then we want nothing to appear; this is the reason for the

From 0989d17f49a089e03e23b72ab638595d538add3f Mon Sep 17 00:00:00 2001
From: Michael Saki <michael.saki@associates.cisa.dhs.gov>
Date: Wed, 28 Feb 2024 16:09:15 -0600
Subject: [PATCH 75/82] Change comments for macOS and venv_name

---
 CONTRIBUTING.md | 4 ++--
 setup-env       | 8 ++++----
 2 files changed, 6 insertions(+), 6 deletions(-)

diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
index bc32a55..617db85 100644
--- a/CONTRIBUTING.md
+++ b/CONTRIBUTING.md
@@ -63,7 +63,7 @@ environment.
 
 #### Installing and using GNU `getopt`, `pyenv`, and `pyenv-virtualenv` ####
 
-On the Mac, we recommend installing [brew](https://brew.sh/).  Then
+On macOS, we recommend installing [brew](https://brew.sh/).  Then
 installation is as simple as `brew install gnu-getopt pyenv pyenv-virtualenv` and
 adding this to your profile:
 
@@ -80,7 +80,7 @@ eval "$(pyenv init -)"
 eval "$(pyenv virtualenv-init -)"
 ```
 
-For Linux, Windows Subsystem for Linux (WSL), or on the Mac (if you
+For Linux, Windows Subsystem for Linux (WSL), or on macOS (if you
 don't want to use `brew`) you can use
 [pyenv/pyenv-installer](https://github.com/pyenv/pyenv-installer) to
 install the necessary tools. Before running this ensure that you have
diff --git a/setup-env b/setup-env
index 534d47f..d2cd111 100755
--- a/setup-env
+++ b/setup-env
@@ -19,7 +19,7 @@ It does the following:
   - Configures git remotes for upstream "lineage" repositories.
 
 Usage:
-  setup-env [--venv-name virtual_env_name] [--python-version python_version]
+  setup-env [--venv-name venv_name] [--python-version python_version]
   setup-env (-h | --help)
 
 Options:
@@ -67,7 +67,7 @@ if [[ $(getopt --version 2> /dev/null) != *"getopt from util-linux"* ]]; then
   as a system might have a non-GNU version of getopt installed by default,
   which could lead to unexpected behavior.
 
-  On the Mac, we recommend installing brew (https://brew.sh/).  Then installation
+  On macOS, we recommend installing brew (https://brew.sh/).  Then installation
   is as simple as `brew install gnu-getopt` and adding this to your
   profile:
 
@@ -86,7 +86,7 @@ if [ -z "$(command -v pyenv)" ] || { [ -z "$(command -v pyenv-virtualenv)" ] &&
   if [[ "$OSTYPE" == "darwin"* ]]; then
     cat << 'END_OF_LINE'
 
-  On the Mac, we recommend installing brew, https://brew.sh/.  Then installation
+  On macOS, we recommend installing brew, https://brew.sh/.  Then installation
   is as simple as `brew install pyenv pyenv-virtualenv` and adding this to your
   profile:
 
@@ -97,7 +97,7 @@ END_OF_LINE
 
   fi
   cat << 'END_OF_LINE'
-  For Linux, Windows Subsystem for Linux (WSL), or on the Mac (if you don't want
+  For Linux, Windows Subsystem for Linux (WSL), or on mac OS (if you don't want
   to use "brew") you can use https://github.com/pyenv/pyenv-installer to install
   the necessary tools. Before running this ensure that you have installed the
   prerequisites for your platform according to the pyenv wiki page,

From a9c6ed88c3c993db890a09ece5433b33e5d5d206 Mon Sep 17 00:00:00 2001
From: Michael Saki <sakimichael@Yahoo.com>
Date: Thu, 29 Feb 2024 09:19:01 -0600
Subject: [PATCH 76/82] Improve comments for clarity

Co-authored-by: Nick <50747025+mcdonnnj@users.noreply.github.com>
---
 CONTRIBUTING.md | 2 +-
 setup-env       | 4 ++--
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
index 617db85..f9fa53a 100644
--- a/CONTRIBUTING.md
+++ b/CONTRIBUTING.md
@@ -80,7 +80,7 @@ eval "$(pyenv init -)"
 eval "$(pyenv virtualenv-init -)"
 ```
 
-For Linux, Windows Subsystem for Linux (WSL), or on macOS (if you
+For Linux, Windows Subsystem for Linux (WSL), or macOS (if you
 don't want to use `brew`) you can use
 [pyenv/pyenv-installer](https://github.com/pyenv/pyenv-installer) to
 install the necessary tools. Before running this ensure that you have
diff --git a/setup-env b/setup-env
index d2cd111..3a22d43 100755
--- a/setup-env
+++ b/setup-env
@@ -97,7 +97,7 @@ END_OF_LINE
 
   fi
   cat << 'END_OF_LINE'
-  For Linux, Windows Subsystem for Linux (WSL), or on mac OS (if you don't want
+  For Linux, Windows Subsystem for Linux (WSL), or macOS (if you don't want
   to use "brew") you can use https://github.com/pyenv/pyenv-installer to install
   the necessary tools. Before running this ensure that you have installed the
   prerequisites for your platform according to the pyenv wiki page,
@@ -217,7 +217,7 @@ fi
 
 # Create a new virtual environment for this project
 #
-# If $PYTHON_VERSION is undefined then the global version of Python will be used.
+# If $PYTHON_VERSION is undefined then the current pyenv Python version will be used.
 #
 # We can't quote ${PYTHON_VERSION:=} below since if the variable is
 # undefined then we want nothing to appear; this is the reason for the

From b9c729f6159defe55490d2198390ba2ceab5924f Mon Sep 17 00:00:00 2001
From: Nicholas McDonnell <50747025+mcdonnnj@users.noreply.github.com>
Date: Thu, 4 Jan 2024 15:03:15 -0500
Subject: [PATCH 77/82] Update pre-commit hook versions

This is done automatically with the `pre-commit autoupdate` command.
The pre-commit/mirrors-prettier was manually held back because the
latest tags are for alpha releases of the next major version.
---
 .pre-commit-config.yaml | 26 +++++++++++++-------------
 1 file changed, 13 insertions(+), 13 deletions(-)

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 34f0253..e7f5d0a 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -5,7 +5,7 @@ default_language_version:
 
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.4.0
+    rev: v4.5.0
     hooks:
       - id: check-case-conflict
       - id: check-executables-have-shebangs
@@ -31,7 +31,7 @@ repos:
 
   # Text file hooks
   - repo: https://github.com/igorshubovych/markdownlint-cli
-    rev: v0.36.0
+    rev: v0.39.0
     hooks:
       - id: markdownlint
         args:
@@ -41,7 +41,7 @@ repos:
     hooks:
       - id: prettier
   - repo: https://github.com/adrienverge/yamllint
-    rev: v1.32.0
+    rev: v1.35.1
     hooks:
       - id: yamllint
         args:
@@ -49,14 +49,14 @@ repos:
 
   # GitHub Actions hooks
   - repo: https://github.com/python-jsonschema/check-jsonschema
-    rev: 0.26.3
+    rev: 0.28.0
     hooks:
       - id: check-github-actions
       - id: check-github-workflows
 
   # pre-commit hooks
   - repo: https://github.com/pre-commit/pre-commit
-    rev: v3.4.0
+    rev: v3.6.2
     hooks:
       - id: validate_manifest
 
@@ -107,44 +107,44 @@ repos:
 
   # Python hooks
   - repo: https://github.com/PyCQA/bandit
-    rev: 1.7.5
+    rev: 1.7.7
     hooks:
       - id: bandit
         args:
           - --config=.bandit.yml
   - repo: https://github.com/psf/black-pre-commit-mirror
-    rev: 23.9.1
+    rev: 24.2.0
     hooks:
       - id: black
   - repo: https://github.com/PyCQA/flake8
-    rev: 6.1.0
+    rev: 7.0.0
     hooks:
       - id: flake8
         additional_dependencies:
           - flake8-docstrings
   - repo: https://github.com/PyCQA/isort
-    rev: 5.12.0
+    rev: 5.13.2
     hooks:
       - id: isort
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v1.5.1
+    rev: v1.8.0
     hooks:
       - id: mypy
   - repo: https://github.com/asottile/pyupgrade
-    rev: v3.10.1
+    rev: v3.15.1
     hooks:
       - id: pyupgrade
 
   # Ansible hooks
   - repo: https://github.com/ansible/ansible-lint
-    rev: v6.19.0
+    rev: v24.2.0
     hooks:
       - id: ansible-lint
       # files: molecule/default/playbook.yml
 
   # Terraform hooks
   - repo: https://github.com/antonbabenko/pre-commit-terraform
-    rev: v1.83.2
+    rev: v1.88.0
     hooks:
       - id: terraform_fmt
       - id: terraform_validate

From 4c933958bca75c291bcb3b28fa1ba821d1d1f6f5 Mon Sep 17 00:00:00 2001
From: Nicholas McDonnell <50747025+mcdonnnj@users.noreply.github.com>
Date: Thu, 4 Jan 2024 15:08:30 -0500
Subject: [PATCH 78/82] Manually update the prettier hook

The hook is manually updated to the last v3 tag available from the
pre-commit/mirrors-prettier repository. We then add the latest release
of v3 available from NPM as an additional depdency.
---
 .pre-commit-config.yaml | 9 ++++++++-
 1 file changed, 8 insertions(+), 1 deletion(-)

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index e7f5d0a..8e3941d 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -37,9 +37,16 @@ repos:
         args:
           - --config=.mdl_config.yaml
   - repo: https://github.com/pre-commit/mirrors-prettier
-    rev: v3.0.3
+    # This is the last version of v3 available from the mirror. We should hold
+    # here until v4, which is currently in alpha, is more stable.
+    rev: v3.1.0
     hooks:
       - id: prettier
+        # This is the latest version of v3 available from NPM. The pre-commit
+        # mirror does not pull tags for old major versions once a new major
+        # version tag is published.
+        additional_dependencies:
+          - prettier@3.2.5
   - repo: https://github.com/adrienverge/yamllint
     rev: v1.35.1
     hooks:

From 7169dcf65670f1d42b9498b68624a1638de08531 Mon Sep 17 00:00:00 2001
From: Nicholas McDonnell <50747025+mcdonnnj@users.noreply.github.com>
Date: Sat, 11 Nov 2023 16:20:14 -0500
Subject: [PATCH 79/82] Use Python and Go versions provided by
 cisagov/setup-env-github-action

---
 .github/workflows/build.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml
index 4911745..de6937d 100644
--- a/.github/workflows/build.yml
+++ b/.github/workflows/build.yml
@@ -59,7 +59,7 @@ jobs:
       - id: setup-python
         uses: actions/setup-python@v5
         with:
-          python-version: "3.11"
+          python-version: ${{ steps.setup-env.outputs.python-version }}
       # We need the Go version and Go cache location for the actions/cache step,
       # so the Go installation must happen before that.
       - id: setup-go
@@ -68,7 +68,7 @@ jobs:
           # There is no expectation for actual Go code so we disable caching as
           # it relies on the existence of a go.sum file.
           cache: false
-          go-version: "1.20"
+          go-version: ${{ steps.setup-env.outputs.go-version }}
       - id: go-cache
         name: Lookup Go cache directory
         run: |

From 035cf86cf76f40ed8b4bf67ff1b14c420701e145 Mon Sep 17 00:00:00 2001
From: Nicholas McDonnell <50747025+mcdonnnj@users.noreply.github.com>
Date: Tue, 27 Feb 2024 17:17:39 -0500
Subject: [PATCH 80/82] Switch pre-commit hooks for running shellcheck

This hook bundles the binaries for shellcheck with a Python package
which removes the need to ensure the tool is installed for the hook to
function. It also ties the version of shellcheck used to the hook which
will help guarantee consistency.
---
 .pre-commit-config.yaml | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 1d12a0d..2c5b3c8 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -115,10 +115,10 @@ repos:
           - --case-indent
           # Redirect operators are followed by a space
           - --space-redirects
-  - repo: https://github.com/detailyang/pre-commit-shell
-    rev: 1.0.5
+  - repo: https://github.com/shellcheck-py/shellcheck-py
+    rev: v0.9.0.6
     hooks:
-      - id: shell-lint
+      - id: shellcheck
 
   # Python hooks
   - repo: https://github.com/PyCQA/bandit

From 77cc89da75fd68f66cd71a3be802bdf7a7d2f888 Mon Sep 17 00:00:00 2001
From: Nicholas McDonnell <50747025+mcdonnnj@users.noreply.github.com>
Date: Mon, 29 Apr 2024 03:46:46 -0400
Subject: [PATCH 81/82] Update the terraform-docs configuration

Add a key to support outputting ATX closed headers which is our
preference. This is also required to make updating the README(s) more
convenient.

NOTE:
This functionality is entirely dependent on the code in the
`improvement/support_atx_closed_markdown_headers` branch of
mcdonnnj/terraform-docs. There is a PR (745) to the original repository
but it has not been merged. Please note that I'm not using auto-linking
language to avoid inundating the PR with links due to this commit being
re-used in all downstream repositories.
---
 .terraform-docs.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.terraform-docs.yml b/.terraform-docs.yml
index 7069923..575b15d 100644
--- a/.terraform-docs.yml
+++ b/.terraform-docs.yml
@@ -9,5 +9,6 @@ output:
     <!-- END_TF_DOCS -->
 settings:
   anchor: false
+  atx-closed: true
   html: false
   lockfile: false

From 9d3c5adeec0eb89d7e3cbf93b92533273977983c Mon Sep 17 00:00:00 2001
From: Jeremy Frasier <jeremy.frasier@gwe.cisa.dhs.gov>
Date: Tue, 7 May 2024 13:47:30 -0400
Subject: [PATCH 82/82] Alphabetize

---
 group_membership.tf |  3 +--
 outputs.tf          |  4 ++--
 variables.tf        | 26 +++++++++++++-------------
 3 files changed, 16 insertions(+), 17 deletions(-)

diff --git a/group_membership.tf b/group_membership.tf
index 0040535..57c3add 100644
--- a/group_membership.tf
+++ b/group_membership.tf
@@ -3,9 +3,8 @@ resource "aws_iam_user_group_membership" "assessment_provisioners" {
   provider = aws.users
   for_each = toset(var.users)
 
-  user = each.key
-
   groups = [
     aws_iam_group.assessment_provisioners.name
   ]
+  user = each.key
 }
diff --git a/outputs.tf b/outputs.tf
index 1c9032e..2cb84c1 100644
--- a/outputs.tf
+++ b/outputs.tf
@@ -1,9 +1,9 @@
 output "assessment_provisioners_group" {
-  value       = aws_iam_group.assessment_provisioners
   description = "The IAM group whose members are allowed to provision assessment environments."
+  value       = aws_iam_group.assessment_provisioners
 }
 
 output "assessment_provisioners_policy" {
-  value       = aws_iam_policy.provision_assessment
   description = "The IAM policy in the Users account that allows the assessment provisioners group to assume the provisioning role in assessment accounts."
+  value       = aws_iam_policy.provision_assessment
 }
diff --git a/variables.tf b/variables.tf
index 4b4d943..922348f 100644
--- a/variables.tf
+++ b/variables.tf
@@ -5,8 +5,8 @@
 # ------------------------------------------------------------------------------
 
 variable "users" {
-  type        = list(string)
   description = "A list containing the usernames of users that exist in the Users account who are allowed to provision assessment environments.  Example: [ \"firstname1.lastname1\", \"firstname2.lastname2\" ]."
+  type        = list(string)
 }
 
 # ------------------------------------------------------------------------------
@@ -22,37 +22,37 @@ variable "aws_region" {
 }
 
 variable "assessment_provisioners_group_name" {
-  type        = string
-  description = "The name of the IAM group whose members are allowed to provision assessment environments."
   default     = "assessment_provisioners"
+  description = "The name of the IAM group whose members are allowed to provision assessment environments."
+  type        = string
 }
 
 variable "provision_assessment_policy_description" {
-  type        = string
-  description = "The description to associate with the IAM policy in the Users account that allows the assessment provisioner group to assume all roles needed in order to provision assessment environments."
   default     = "Allows the assessment provisioner group to assume all roles needed in order to provision assessment environments."
+  description = "The description to associate with the IAM policy in the Users account that allows the assessment provisioner group to assume all roles needed in order to provision assessment environments."
+  type        = string
 }
 
 variable "provision_assessment_policy_name" {
-  type        = string
-  description = "The name of the IAM policy in the Users account that allows the assessment provisioner group to assume all roles needed in order to provision assessment environments."
   default     = "AssumeProvisionAssessment"
+  description = "The name of the IAM policy in the Users account that allows the assessment provisioner group to assume all roles needed in order to provision assessment environments."
+  type        = string
 }
 
 variable "provision_assessment_role_name" {
-  type        = string
-  description = "The name of the IAM role in assessment accounts that includes all permissions necessary to provision the assessment environment in that account.  If this role does not exist in an account, an assessment environment cannot be provisioned in that account."
   default     = "ProvisionAccount"
+  description = "The name of the IAM role in assessment accounts that includes all permissions necessary to provision the assessment environment in that account.  If this role does not exist in an account, an assessment environment cannot be provisioned in that account."
+  type        = string
 }
 
 variable "startstopssmsession_role_name" {
-  type        = string
-  description = "The name of the IAM role in assessment accounts that includes all permissions necessary to start and stop an SSM session in that account."
   default     = "StartStopSSMSession"
+  description = "The name of the IAM role in assessment accounts that includes all permissions necessary to start and stop an SSM session in that account."
+  type        = string
 }
 
 variable "tags" {
-  type        = map(string)
-  description = "Tags to apply to all AWS resources created."
   default     = {}
+  description = "Tags to apply to all AWS resources created."
+  type        = map(string)
 }