Add checklist for testing in a clean scratch environment by toniecrumley · Pull Request #63 · lasseignelab/capture

toniecrumley · 2026-04-29T16:27:18Z

Summary

Added a checklist item to test pull request instructions in a clean environment to ensure they work properly for code reviewers.

Author Checklist

Self/Peer Review Checklist (Coding Guidelines)

Meaningful variable and function names
File header comments
Function comments
In-line comments summarize logical sections of code by concisely explaining
why, not what the code is doing. Avoid excessive or redundant commenting.
Confirm that the automated tests pass.
Confirm the code performs the intended functionality

Setup

No setup is required.

Test

Read the text added to the pull request template on the "Files changed" tab and comment if changes are needed.

Cleanup

No cleanup required.

Added a checklist item for testing instructions in a clean environment.

github-actions · 2026-04-29T16:30:07Z

✅⚠️MegaLinter analysis: Success with warnings

Descriptor	Linter	Files	Errors	Elapsed time
⚠️ BASH	bash-exec	32	29	0.39s
✅ BASH	shellcheck	32	0	1.2s
⚠️ BASH	shfmt	32	23	0.02s
⚠️ MARKDOWN	markdownlint	3	63	0.75s
✅ MARKDOWN	markdown-table-formatter	3	0	0.29s

Detailed Issues

⚠️ BASH / bash-exec - 29 errors

Results of bash-exec linter (version 5.3.3)
See documentation on https://megalinter.io/9.4.0/descriptors/bash_bash_exec/
-----------------------------------------------

✅ [SUCCESS] cap
❌ [ERROR] cap_completion.sh
    Error: File:[cap_completion.sh] is not executable

❌ [ERROR] commands/env.sh
    Error: File:[commands/env.sh] is not executable

❌ [ERROR] commands/help.sh
    Error: File:[commands/help.sh] is not executable

❌ [ERROR] commands/md5.sh
    Error: File:[commands/md5.sh] is not executable

❌ [ERROR] commands/new.sh
    Error: File:[commands/new.sh] is not executable

❌ [ERROR] commands/run.sh
    Error: File:[commands/run.sh] is not executable

❌ [ERROR] commands/update.sh
    Error: File:[commands/update.sh] is not executable

❌ [ERROR] commands/verify.sh
    Error: File:[commands/verify.sh] is not executable

❌ [ERROR] commands/version.sh
    Error: File:[commands/version.sh] is not executable

❌ [ERROR] configure.sh
    Error: File:[configure.sh] is not executable

❌ [ERROR] install.sh
    Error: File:[install.sh] is not executable

❌ [ERROR] lib/environment.sh
    Error: File:[lib/environment.sh] is not executable

❌ [ERROR] lib/environment_functions.sh
    Error: File:[lib/environment_functions.sh] is not executable

❌ [ERROR] lib/functions.sh
    Error: File:[lib/functions.sh] is not executable

❌ [ERROR] lib/functions/cap_array_value.sh
    Error: File:[lib/functions/cap_array_value.sh] is not executable

❌ [ERROR] lib/functions/cap_container.sh
    Error: File:[lib/functions/cap_container.sh] is not executable

❌ [ERROR] lib/functions/cap_data_download.sh
    Error: File:[lib/functions/cap_data_download.sh] is not executable

❌ [ERROR] lib/functions/commands/cap_check_environment.sh
    Error: File:[lib/functions/commands/cap_check_environment.sh] is not executable

❌ [ERROR] lib/functions/commands/cap_root_required.sh
    Error: File:[lib/functions/commands/cap_root_required.sh] is not executable

❌ [ERROR] lib/functions/verify/cap_verify_append.sh
    Error: File:[lib/functions/verify/cap_verify_append.sh] is not executable

❌ [ERROR] lib/functions/verify/cap_verify_md5.sh
    Error: File:[lib/functions/verify/cap_verify_md5.sh] is not executable

❌ [ERROR] tests/fixtures/env/.caprc
    Error: File:[tests/fixtures/env/.caprc] is not executable

❌ [ERROR] tests/fixtures/run/array_job.sh
    Error: File:[tests/fixtures/run/array_job.sh] is not executable

❌ [ERROR] tests/fixtures/run/job.sh
    Error: File:[tests/fixtures/run/job.sh] is not executable

❌ [ERROR] tests/fixtures/verify/verifications/test_cap_verify_md5.sh
    Error: File:[tests/fixtures/verify/verifications/test_cap_verify_md5.sh] is not executable

❌ [ERROR] tests/fixtures/verify/verifications/test_dry_run.sh
    Error: File:[tests/fixtures/verify/verifications/test_dry_run.sh] is not executable

❌ [ERROR] tests/fixtures/verify/verifications/test_name.sh
    Error: File:[tests/fixtures/verify/verifications/test_name.sh] is not executable

❌ [ERROR] tests/fixtures/verify/verifications/test_output_file.sh
    Error: File:[tests/fixtures/verify/verifications/test_output_file.sh] is not executable

✅ [SUCCESS] tests/install
✅ [SUCCESS] tests/run
❌ [ERROR] tests/setup_suite.bash
    Error: File:[tests/setup_suite.bash] is not executable

⚠️ MARKDOWN / markdownlint - 63 errors

.github/pull_request_template.md:1 error MD041/first-line-heading/first-line-h1 First line in a file should be a top-level heading [Context: "## Summary"]
.github/pull_request_template.md:6:21 error MD059/descriptive-link-text Link text should be descriptive [Context: "[here]"]
.github/pull_request_template.md:39 error MD040/fenced-code-language Fenced code blocks should have a language specified [Context: "```"]
.github/pull_request_template.md:52 error MD040/fenced-code-language Fenced code blocks should have a language specified [Context: "```"]
.github/pull_request_template.md:59 error MD040/fenced-code-language Fenced code blocks should have a language specified [Context: "```"]
.github/pull_request_template.md:64 error MD040/fenced-code-language Fenced code blocks should have a language specified [Context: "```"]
.github/pull_request_template.md:70 error MD040/fenced-code-language Fenced code blocks should have a language specified [Context: "```"]
.github/pull_request_template.md:77 error MD040/fenced-code-language Fenced code blocks should have a language specified [Context: "```"]
CHANGELOG.md:1 error MD041/first-line-heading/first-line-h1 First line in a file should be a top-level heading [Context: "## CAPTURE 1.0.0 (January 16, ..."]
README.md:1 error MD041/first-line-heading/first-line-h1 First line in a file should be a top-level heading [Context: "CAPTURE"]
README.md:28 error MD040/fenced-code-language Fenced code blocks should have a language specified [Context: "```"]
README.md:33 error MD040/fenced-code-language Fenced code blocks should have a language specified [Context: "```"]
README.md:38 error MD040/fenced-code-language Fenced code blocks should have a language specified [Context: "```"]
README.md:46 error MD040/fenced-code-language Fenced code blocks should have a language specified [Context: "```"]
README.md:55 error MD040/fenced-code-language Fenced code blocks should have a language specified [Context: "```"]
README.md:74 error MD040/fenced-code-language Fenced code blocks should have a language specified [Context: "```"]
README.md:78 error MD040/fenced-code-language Fenced code blocks should have a language specified [Context: "```"]
README.md:129 error MD040/fenced-code-language Fenced code blocks should have a language specified [Context: "```"]
README.md:181 error MD040/fenced-code-language Fenced code blocks should have a language specified [Context: "```"]
README.md:195 error MD040/fenced-code-language Fenced code blocks should have a language specified [Context: "```"]
README.md:207 error MD040/fenced-code-language Fenced code blocks should have a language specified [Context: "```"]
README.md:225 error MD040/fenced-code-language Fenced code blocks should have a language specified [Context: "```"]
README.md:247 error MD040/fenced-code-language Fenced code blocks should have a language specified [Context: "```"]
README.md:281 error MD040/fenced-code-language Fenced code blocks should have a language specified [Context: "```"]
README.md:303 error MD040/fenced-code-language Fenced code blocks should have a language specified [Context: "```"]
README.md:346 error MD040/fenced-code-language Fenced code blocks should have a language specified [Context: "```"]
README.md:387 error MD040/fenced-code-language Fenced code blocks should have a language specified [Context: "```"]
README.md:391 error MD040/fenced-code-language Fenced code blocks should have a language specified [Context: "```"]
README.md:419 error MD040/fenced-code-language Fenced code blocks should have a language specified [Context: "```"]
README.md:438 error MD040/fenced-code-language Fenced code blocks should have a language specified [Context: "```"]
README.md:447 error MD040/fenced-code-language Fenced code blocks should have a language specified [Context: "```"]
README.md:451 error MD040/fenced-code-language Fenced code blocks should have a language specified [Context: "```"]
README.md:461 error MD040/fenced-code-language Fenced code blocks should have a language specified [Context: "```"]
README.md:472 error MD040/fenced-code-language Fenced code blocks should have a language specified [Context: "```"]
README.md:477 error MD040/fenced-code-language Fenced code blocks should have a language specified [Context: "```"]
README.md:486 error MD040/fenced-code-language Fenced code blocks should have a language specified [Context: "```"]
README.md:515 error MD040/fenced-code-language Fenced code blocks should have a language specified [Context: "```"]
README.md:524 error MD040/fenced-code-language Fenced code blocks should have a language specified [Context: "```"]
README.md:534 error MD040/fenced-code-language Fenced code blocks should have a language specified [Context: "```"]
README.md:556 error MD040/fenced-code-language Fenced code blocks should have a language specified [Context: "```"]
README.md:578 error MD040/fenced-code-language Fenced code blocks should have a language specified [Context: "```"]
README.md:583:72 error MD026/no-trailing-punctuation Trailing punctuation in heading [Punctuation: ':']
README.md:587 error MD040/fenced-code-language Fenced code blocks should have a language specified [Context: "```"]
README.md:594 error MD040/fenced-code-language Fenced code blocks should have a language specified [Context: "```"]
README.md:613 error MD040/fenced-code-language Fenced code blocks should have a language specified [Context: "```"]
README.md:617 error MD040/fenced-code-language Fenced code blocks should have a language specified [Context: "```"]
README.md:630 error MD040/fenced-code-language Fenced code blocks should have a language specified [Context: "```"]
README.md:649 error MD024/no-duplicate-heading Multiple headings with the same content [Context: "Examples for a verification na..."]
README.md:649:72 error MD026/no-trailing-punctuation Trailing punctuation in heading [Punctuation: ':']
README.md:652 error MD040/fenced-code-language Fenced code blocks should have a language specified [Context: "```"]
README.md:656 error MD040/fenced-code-language Fenced code blocks should have a language specified [Context: "```"]
README.md:663 error MD040/fenced-code-language Fenced code blocks should have a language specified [Context: "```"]
README.md:667 error MD040/fenced-code-language Fenced code blocks should have a language specified [Context: "```"]
README.md:672 error MD040/fenced-code-language Fenced code blocks should have a language specified [Context: "```"]
README.md:676 error MD040/fenced-code-language Fenced code blocks should have a language specified [Context: "```"]
README.md:697 error MD040/fenced-code-language Fenced code blocks should have a language specified [Context: "```"]
README.md:710 error MD040/fenced-code-language Fenced code blocks should have a language specified [Context: "```"]
README.md:715 error MD040/fenced-code-language Fenced code blocks should have a language specified [Context: "```"]
README.md:724 error MD040/fenced-code-language Fenced code blocks should have a language specified [Context: "```"]
README.md:728 error MD040/fenced-code-language Fenced code blocks should have a language specified [Context: "```"]
README.md:734 error MD040/fenced-code-language Fenced code blocks should have a language specified [Context: "```"]
README.md:741 error MD040/fenced-code-language Fenced code blocks should have a language specified [Context: "```"]
README.md:746 error MD040/fenced-code-language Fenced code blocks should have a language specified [Context: "```"]

⚠️ BASH / shfmt - 23 errors

termine the output folder or file name.
-  # There is an assumption that the name of a tar file matches
-  # the name of the output. This assumption will probably need
-  # to be removed but we will wait until we have a real example
-  # before we try to change this.
-  local file_name
-  if [ -n "$cap_data_download_source_file_name" ]; then
-    file_name="$cap_data_download_source_file_name"
-  else
-    file_name=$(basename "$cap_data_download_url")
-  fi
-  local output_name
-  output_name="${file_name//\.tar.*/}"
-  output_name="${output_name//\.gz/}"
-
-  local download_path="$CAP_DATA_PATH"
-  if [ -n "$cap_data_download_subdirectory" ]; then
-    download_path="$CAP_DATA_PATH/$cap_data_download_subdirectory"
-    mkdir -p "$download_path"
-  fi
-
-  # Download data if the final output does not exist.
-  if [ -e "$download_path/$output_name" ] || [ -e "$download_path/$file_name" ]; then
-    echo "$file_name has already been downloaded"
-  else
-
-    local download_file
-    download_file="${download_path}/${file_name}"
-
-    # Download the file.
-    if ! wget -nv --retry-connrefused -O "$download_file" "$cap_data_download_url"; then
-      echo "Error: URL not found" >&2
-      exit 1
-    fi
-
-    # Check the md5sum if it is provided.
-    if [ -n "$cap_data_download_md5sum" ]; then
-      if echo "$cap_data_download_md5sum  $download_file" | md5sum -c -; then
-        echo "File download checksum verified!"
-      else
-        echo >&2
-        echo "File $file_name checksum verification failed!" >&2
-        echo "The file was left in place for debugging purposes.  It will" >&2
-        echo "need to be deleted before attempting another download." >&2
-        echo >&2
-        exit 1
-      fi
-    fi
-
-    if [[ "$cap_data_download_unzip" == "true" ]]; then
-      case "$file_name" in
-        # Untar and remove downloads that are tar archives.
-        *.tar|*.tar.gz)
-          if tar -xf "$download_file" -C "$download_path"; then
-            rm "$download_file"
-          fi
-          ;;
-        # Unzip and remove downloads that are compressed files.
-        *.gz)
-          (
-            cd "$download_path" || exit
-            gunzip "$file_name"
-          )
-          ;;
-        *)
-          echo "Error: Unsupported file extension '$file_name'" >&2
-          exit 1
-          ;;
-      esac
-    fi
-  fi
+	cap_data_download_parse_commandline_parameters "$@"
+
+	# Determine the output folder or file name.
+	# There is an assumption that the name of a tar file matches
+	# the name of the output. This assumption will probably need
+	# to be removed but we will wait until we have a real example
+	# before we try to change this.
+	local file_name
+	if [ -n "$cap_data_download_source_file_name" ]; then
+		file_name="$cap_data_download_source_file_name"
+	else
+		file_name=$(basename "$cap_data_download_url")
+	fi
+	local output_name
+	output_name="${file_name//\.tar.*/}"
+	output_name="${output_name//\.gz/}"
+
+	local download_path="$CAP_DATA_PATH"
+	if [ -n "$cap_data_download_subdirectory" ]; then
+		download_path="$CAP_DATA_PATH/$cap_data_download_subdirectory"
+		mkdir -p "$download_path"
+	fi
+
+	# Download data if the final output does not exist.
+	if [ -e "$download_path/$output_name" ] || [ -e "$download_path/$file_name" ]; then
+		echo "$file_name has already been downloaded"
+	else
+
+		local download_file
+		download_file="${download_path}/${file_name}"
+
+		# Download the file.
+		if ! wget -nv --retry-connrefused -O "$download_file" "$cap_data_download_url"; then
+			echo "Error: URL not found" >&2
+			exit 1
+		fi
+
+		# Check the md5sum if it is provided.
+		if [ -n "$cap_data_download_md5sum" ]; then
+			if echo "$cap_data_download_md5sum  $download_file" | md5sum -c -; then
+				echo "File download checksum verified!"
+			else
+				echo >&2
+				echo "File $file_name checksum verification failed!" >&2
+				echo "The file was left in place for debugging purposes.  It will" >&2
+				echo "need to be deleted before attempting another download." >&2
+				echo >&2
+				exit 1
+			fi
+		fi
+
+		if [[ "$cap_data_download_unzip" == "true" ]]; then
+			case "$file_name" in
+			# Untar and remove downloads that are tar archives.
+			*.tar | *.tar.gz)
+				if tar -xf "$download_file" -C "$download_path"; then
+					rm "$download_file"
+				fi
+				;;
+			# Unzip and remove downloads that are compressed files.
+			*.gz)
+				(
+					cd "$download_path" || exit
+					gunzip "$file_name"
+				)
+				;;
+			*)
+				echo "Error: Unsupported file extension '$file_name'" >&2
+				exit 1
+				;;
+			esac
+		fi
+	fi
 }
 
 cap_data_download_parse_commandline_parameters() {
-  # Define the named commandline options
-  if ! OPTIONS=$(getopt -o "" --long source-file-name:,md5sum:,unzip,subdirectory: -- "$@"); then
-    echo "See CAPTURE help for cap_data_download." >&2
-    exit 1
-  fi
-  eval set -- "$OPTIONS"
-
-  # Set default values for the named parameters
-  cap_data_download_source_file_name=""
-  cap_data_download_md5sum=""
-  cap_data_download_subdirectory=""
-  cap_data_download_unzip=false
-
-  # Parse the optional named command line options
-  while true; do
-    case "$1" in
-      --source-file-name)
-        cap_data_download_source_file_name="$2"
-        shift 2 ;;
-      --md5sum)
-        cap_data_download_md5sum="$2"
-        shift 2 ;;
-      --subdirectory)
-        cap_data_download_subdirectory="$2"
-        shift 2 ;;
-      --unzip)
-        cap_data_download_unzip=true
-        shift 1 ;;
-      --)
-        shift
-        break;;
-    esac
-  done
-
-  # Check that the required file url parameter was provided
-  if [ "$#" -ne 1 ]; then
-    echo "Error: incorrect number of parameters" >&2
-    echo "Usage: cap_data_download [options] URL" >&2
-    echo "See CAPTURE help for cap_data_download" >&2
-    exit 1
-  fi
-  cap_data_download_url=$1
+	# Define the named commandline options
+	if ! OPTIONS=$(getopt -o "" --long source-file-name:,md5sum:,unzip,subdirectory: -- "$@"); then
+		echo "See CAPTURE help for cap_data_download." >&2
+		exit 1
+	fi
+	eval set -- "$OPTIONS"
+
+	# Set default values for the named parameters
+	cap_data_download_source_file_name=""
+	cap_data_download_md5sum=""
+	cap_data_download_subdirectory=""
+	cap_data_download_unzip=false
+
+	# Parse the optional named command line options
+	while true; do
+		case "$1" in
+		--source-file-name)
+			cap_data_download_source_file_name="$2"
+			shift 2
+			;;
+		--md5sum)
+			cap_data_download_md5sum="$2"
+			shift 2
+			;;
+		--subdirectory)
+			cap_data_download_subdirectory="$2"
+			shift 2
+			;;
+		--unzip)
+			cap_data_download_unzip=true
+			shift 1
+			;;
+		--)
+			shift
+			break
+			;;
+		esac
+	done
+
+	# Check that the required file url parameter was provided
+	if [ "$#" -ne 1 ]; then
+		echo "Error: incorrect number of parameters" >&2
+		echo "Usage: cap_data_download [options] URL" >&2
+		echo "See CAPTURE help for cap_data_download" >&2
+		exit 1
+	fi
+	cap_data_download_url=$1
 }
diff lib/functions/commands/cap_check_environment.sh.orig lib/functions/commands/cap_check_environment.sh
--- lib/functions/commands/cap_check_environment.sh.orig
+++ lib/functions/commands/cap_check_environment.sh
@@ -1,8 +1,8 @@
 #!/bin/bash
 
 cap_check_environment() {
-  if [[ ! -f "config/environments/$1.sh" ]]; then
-    echo "The $1.sh environment file does not exist in config/environments."
-    exit 2
-  fi
+	if [[ ! -f "config/environments/$1.sh" ]]; then
+		echo "The $1.sh environment file does not exist in config/environments."
+		exit 2
+	fi
 }
diff lib/functions/commands/cap_root_required.sh.orig lib/functions/commands/cap_root_required.sh
--- lib/functions/commands/cap_root_required.sh.orig
+++ lib/functions/commands/cap_root_required.sh
@@ -1,8 +1,8 @@
 #!/bin/bash
 
 cap_root_required() {
-  if [[ ! -f "config/pipeline.sh" ]]; then
-    echo "The $1 command must be executed from the project root directory." >&2
-    exit 2
-  fi
+	if [[ ! -f "config/pipeline.sh" ]]; then
+		echo "The $1 command must be executed from the project root directory." >&2
+		exit 2
+	fi
 }
diff lib/functions/verify/cap_verify_append.sh.orig lib/functions/verify/cap_verify_append.sh
--- lib/functions/verify/cap_verify_append.sh.orig
+++ lib/functions/verify/cap_verify_append.sh
@@ -1,9 +1,9 @@
 #!/bin/bash
 
 cap_verify_append() {
-  if [[ "$CAP_VERIFICATION_DRY_RUN" == "true" ]]; then
-    echo "$1"
-  else
-    echo "$1" >> "${CAP_VERIFICATION_OUTPUT_FILE:-/dev/stdout}"
-  fi
+	if [[ "$CAP_VERIFICATION_DRY_RUN" == "true" ]]; then
+		echo "$1"
+	else
+		echo "$1" >>"${CAP_VERIFICATION_OUTPUT_FILE:-/dev/stdout}"
+	fi
 }
diff lib/functions/verify/cap_verify_md5.sh.orig lib/functions/verify/cap_verify_md5.sh
--- lib/functions/verify/cap_verify_md5.sh.orig
+++ lib/functions/verify/cap_verify_md5.sh
@@ -1,49 +1,51 @@
 #!/bin/bash
 
 cap_verify_md5() {
-  cap_verify_md5_parse_commandline_parameters "$@"
-
-  cap_md5_args+=(--append --output-files-only)
-  if [[ "$CAP_VERIFICATION_DRY_RUN" == "true" ]]; then
-    cap_md5_args+=(--dry-run)
-  else
-    cap_md5_args+=(--output "$CAP_VERIFICATION_OUTPUT_FILE")
-  fi
-
-  cap md5 \
-    "${cap_md5_args[@]}" \
-    "$verify_path"
+	cap_verify_md5_parse_commandline_parameters "$@"
+
+	cap_md5_args+=(--append --output-files-only)
+	if [[ "$CAP_VERIFICATION_DRY_RUN" == "true" ]]; then
+		cap_md5_args+=(--dry-run)
+	else
+		cap_md5_args+=(--output "$CAP_VERIFICATION_OUTPUT_FILE")
+	fi
+
+	cap md5 \
+		"${cap_md5_args[@]}" \
+		"$verify_path"
 }
 
 cap_verify_md5_parse_commandline_parameters() {
-  # Define the named commandline options
-  if ! OPTIONS=$(getopt -o "" --long ignore:,select: -- "$@"); then
-    echo "See CAPTURE help for cap_verify_md5." >&2
-    exit 1
-  fi
-  eval set -- "$OPTIONS"
-
-  # Set default values for the named parameters
-  cap_md5_args=()
-
-  # Parse the optional named command line options
-  while true; do
-    case "$1" in
-      --select|--ignore)
-        cap_md5_args+=("$1" "$2")
-        shift 2 ;;
-      --)
-        shift
-        break;;
-    esac
-  done
-
-  # Check that the required file url parameter was provided
-  if [ "$#" -ne 1 ]; then
-    echo "Error: incorrect number of parameters" >&2
-    echo "Usage: cap_verify_md5 [options] URL" >&2
-    echo "See CAPTURE help for cap_verify_md5" >&2
-    exit 1
-  fi
-  verify_path="$1"
+	# Define the named commandline options
+	if ! OPTIONS=$(getopt -o "" --long ignore:,select: -- "$@"); then
+		echo "See CAPTURE help for cap_verify_md5." >&2
+		exit 1
+	fi
+	eval set -- "$OPTIONS"
+
+	# Set default values for the named parameters
+	cap_md5_args=()
+
+	# Parse the optional named command line options
+	while true; do
+		case "$1" in
+		--select | --ignore)
+			cap_md5_args+=("$1" "$2")
+			shift 2
+			;;
+		--)
+			shift
+			break
+			;;
+		esac
+	done
+
+	# Check that the required file url parameter was provided
+	if [ "$#" -ne 1 ]; then
+		echo "Error: incorrect number of parameters" >&2
+		echo "Usage: cap_verify_md5 [options] URL" >&2
+		echo "See CAPTURE help for cap_verify_md5" >&2
+		exit 1
+	fi
+	verify_path="$1"
 }
diff tests/setup_suite.bash.orig tests/setup_suite.bash
--- tests/setup_suite.bash.orig
+++ tests/setup_suite.bash
@@ -1,32 +1,32 @@
 setup_suite() {
-  # Make sure the `cap` command in this CAPTURE code base is used in tests
-  # instead of the one installed in the system.
-  PATH="$(pwd):$PATH"
-  export PATH
-
-  # Make sure the capture install path is pointing to the development
-  # environment.
-  CAP_INSTALL_PATH="$(pwd)"
-  export CAP_INSTALL_PATH
-
-  # Location of the CAPTURE framework development environment.
-  CAP_DEVELOPMENT_PATH="$(pwd)"
-  export CAP_DEVELOPMENT_PATH
-
-  # Setup a unique temporary directory for BATS tests to fix temporary file
-  # errors on Cheaha where developers share temp directories.
-  BATS_TMPDIR="$(mktemp -d)"
-  export BATS_TMPDIR
-
-  # Setup test locations for caprc files.  Otherwise, the developer's actual
-  # caprc files will be used and make tests fail.
-  CAP_ETC_RC_PATH="$(mktemp -p "$BATS_TMPDIR")"
-  export CAP_ETC_RC_PATH
-  CAP_HOME_RC_PATH="$(mktemp -p "$BATS_TMPDIR")"
-  export CAP_HOME_RC_PATH
+	# Make sure the `cap` command in this CAPTURE code base is used in tests
+	# instead of the one installed in the system.
+	PATH="$(pwd):$PATH"
+	export PATH
+
+	# Make sure the capture install path is pointing to the development
+	# environment.
+	CAP_INSTALL_PATH="$(pwd)"
+	export CAP_INSTALL_PATH
+
+	# Location of the CAPTURE framework development environment.
+	CAP_DEVELOPMENT_PATH="$(pwd)"
+	export CAP_DEVELOPMENT_PATH
+
+	# Setup a unique temporary directory for BATS tests to fix temporary file
+	# errors on Cheaha where developers share temp directories.
+	BATS_TMPDIR="$(mktemp -d)"
+	export BATS_TMPDIR
+
+	# Setup test locations for caprc files.  Otherwise, the developer's actual
+	# caprc files will be used and make tests fail.
+	CAP_ETC_RC_PATH="$(mktemp -p "$BATS_TMPDIR")"
+	export CAP_ETC_RC_PATH
+	CAP_HOME_RC_PATH="$(mktemp -p "$BATS_TMPDIR")"
+	export CAP_HOME_RC_PATH
 }
 
 teardown_suite() {
-  # Remove the unique temporary directory created in setup_suite().
-  rm -rf "$BATS_TMPDIR"
+	# Remove the unique temporary directory created in setup_suite().
+	rm -rf "$BATS_TMPDIR"
 }

(Truncated to last 13333 characters out of 79728)

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Add checklist for testing in a clean scratch environment

bb879e4

Added a checklist item for testing instructions in a clean environment.

toniecrumley requested review from blasseigne, eokunbor, kjamescasper, lizzyjoan, mckay33, sashataluri, tchowton and tsoelter April 29, 2026 16:42

toniecrumley marked this pull request as ready for review April 29, 2026 17:34

tsoelter approved these changes Apr 29, 2026

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lizzyjoan approved these changes May 6, 2026

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toniecrumley merged commit 1b26037 into main May 8, 2026
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toniecrumley deleted the test-instructions branch May 8, 2026 15:43

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Add checklist for testing in a clean scratch environment - #63

Add checklist for testing in a clean scratch environment#63
toniecrumley merged 1 commit into
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toniecrumley commented Apr 29, 2026 •

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Summary

Author Checklist

Self/Peer Review Checklist (Coding Guidelines)

Setup

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Cleanup

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toniecrumley commented Apr 29, 2026 •

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