diff --git a/.github/workflows/build_workflow.yml b/.github/workflows/build_workflow.yml
index d3574d77..d0aa857a 100644
--- a/.github/workflows/build_workflow.yml
+++ b/.github/workflows/build_workflow.yml
@@ -82,9 +82,12 @@ jobs:
         run: |
           python -m pip install .
 
+      # Run machine-independent tests
       - name: Run Tests
         run: |
-          python -m unittest tests/test_*.py
+          pytest tests/unit/test_*.py
+          python -m unittest tests/integration/python_tests/group_by_command/test_*.py
+          python -m unittest tests/integration/python_tests/group_by_workflow/test_*.py
 
   # Build documentation on all PRs and pushes; only publish (commit to gh-pages) on pushes.
   build-docs:
diff --git a/.gitignore b/.gitignore
index f0c2eeda..f20af3db 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1,7 +1,7 @@
 build/
 dist/
-tests/test_follow_symlinks/
-tests/test_follow_symlinks_non_archived/
+tests/utils/test_follow_symlinks
+tests/utils/test_follow_symlinks_non_archived
 zstash.egg-info/
 *.pyc
 *~
diff --git a/conda/dev.yml b/conda/dev.yml
index 216b47cf..6ec8e1b9 100644
--- a/conda/dev.yml
+++ b/conda/dev.yml
@@ -8,7 +8,7 @@ dependencies:
   - python >=3.11,<3.14
   - sqlite
   - six >=1.16.0
-  - globus-sdk >=3.15.0
+  - globus-sdk >=3.15.0,<4.0
   # Developer Tools
   # =================
   # If versions are updated, also update 'rev' in `.pre-commit.config.yaml`
@@ -18,6 +18,10 @@ dependencies:
   - mypy ==1.18.2
   - pre-commit ==4.3.0
   - tbump >=6.9.0
+  # Testing
+  # =======================
+  - pytest
+  - pytest-cov
   # Documentation
   # =================
   # If versions are updated, also update in `.github/workflows/workflow.yml`
diff --git a/tests/README.md b/tests/README.md
new file mode 100644
index 00000000..d63e7851
--- /dev/null
+++ b/tests/README.md
@@ -0,0 +1,120 @@
+# zstash Test Suite
+
+## The test directory structure
+
+```
+tests/
+  integration/ # Tests that call zstash from the command line
+    bash_tests/ # Test zstash commands via bash scripts
+      run_from_chrysalis/ # Run these from Chrysalis (these use Globus and/or require the Chrysalis file system)
+      run_from_perlmutter/ # Run these from Perlmutter (these use `hsi` directly and/or require the Perlmutter file system)
+    python_tests/ # Test zstash commands via Python unittest wrappers
+      group_by_command # Tests organized by command
+      group_by_workflow # Tests organized by workflow
+  unit/ # Tests of pure functions (uses pytest, not unittest)
+  utils/ # Utilities for testing
+```
+
+## Testing example for Perlmutter
+
+```bash
+rm -rf build
+conda clean --all --y
+conda env create -f conda/dev.yml -n zstash_dev_20251017_test1
+conda activate zstash_dev_20251017_test1
+pre-commit run --all-files
+python -m pip install .
+pytest tests/unit/test_*.py
+# 1 passed in 0.19s
+python -m unittest tests/integration/python_tests/group_by_command/test_*.py
+# Ran 69 tests in 327.570s
+# OK
+python -m unittest tests/integration/python_tests/group_by_workflow/test_*.py
+# Ran 4 tests in 2.666s
+# OK
+cd tests/integration/bash_tests/run_from_perlmutter/
+time ./follow_symlinks.sh # NOTE: you will have to change out paths for your username
+# real	0m31.851s
+# No errors
+time ./test_update_non_empty_hpss.bash
+# real	0m10.062s
+# No errors
+
+# Log into globus.org
+# Log into endpoints (NERSC Perlmutter, Globus Tutorial Collection 1) at globus.org: File Manager > Add the endpoints in the "Collection" fields
+time ./test_ls_globus.bash
+# real	0m26.930s
+# No errors
+```
+
+## Testing example for Chrysalis
+
+```bash
+rm -rf build
+conda clean --all --y
+conda env create -f conda/dev.yml -n zstash_dev_20251017_test1
+conda activate zstash_dev_20251017_test1
+pre-commit run --all-files
+python -m pip install .
+pytest tests/unit/test_*.py
+# 1 passed in 0.84s
+python -m unittest tests/integration/python_tests/group_by_command/test_*.py
+# Ran 69 tests in 110.139s
+# OK (skipped=32)
+# NOTE: Some tests are skipped because Chrysalis doesn't have direct `hsi`/HPSS access
+python -m unittest tests/integration/python_tests/group_by_workflow/test_*.py
+# Ran 4 tests in 6.889s
+# OK
+cd tests/integration/bash_tests/run_from_chrysalis/
+
+# Log into globus.org
+# 1. Log into endpoints (LCRC Improv DTN, NERSC Perlmutter) at globus.org: File Manager > Add the endpoints in the "Collection" fields
+# 2. To start fresh, with no consents: https://auth.globus.org/v2/web/consents > Manage Your Consents > Globus Endpoint Performance Monitoring > rescind all"
+# Then, increment `try_num` below to avoid using an old directory.
+# Alternatively, start fresh by deleting the directory on Perlmutter:
+# `rm -rf /global/homes/f/forsyth/zstash/tests/test_globus_auth_try{try_num}`
+time ./globus_auth.bash try_num # NOTE: you will have to change out paths for your username
+# Paste the URL into your browser
+# Log into Argonne
+# Log into NERSC
+# Provide a label
+# Copy the auth code to the command line
+#
+# real	2m45.954s
+# No errors
+
+# If not done above, do the following:
+# Log into globus.org
+# Log into endpoints (LCRC Improv DTN, NERSC Perlmutter) at globus.org: File Manager > Add the endpoints in the "Collection" fields
+
+# In all cases, do:
+# Then, increment `try_num` below to avoid using an old directory.
+# Alternatively, start fresh by deleting the directory on Perlmutter:
+# `rm -rf /global/homes/f/forsyth/zstash/tests/test_database_corruption_try{try_num}`
+time ./database_corruption.bash try_num # NOTE: you will have to change out paths for your username
+# Success count: 25
+# Fail count: 0
+# real	6m43.994s
+
+time ./symlinks.sh # NOTE: you will have to change out paths for your username
+# real	0m1.346s
+# No errors
+
+cd blocking_test_scripts
+# Review README_TEST_BLOCKING
+# This uses "12 piControl ocean monthly files, 49 GB",
+# so processing may take a long time.
+# TODO (later PR): Confirm this test works
+```
+
+## Testing with GitHub Actions
+
+GitHub Actions runs the tests according to `.github/workflows/build_workflow.yml`:
+```
+      # Run machine-independent tests
+      - name: Run Tests
+        run: |
+          pytest tests/unit/test_*.py
+          python -m unittest tests/integration/python_tests/group_by_command/test_*.py
+          python -m unittest tests/integration/python_tests/group_by_workflow/test_*.py
+```
diff --git a/tests/integration/__init__.py b/tests/integration/__init__.py
new file mode 100644
index 00000000..e69de29b
diff --git a/tests3/README_TEST_BLOCKING b/tests/integration/bash_tests/run_from_chrysalis/blocking_test_scripts/README_TEST_BLOCKING
similarity index 83%
rename from tests3/README_TEST_BLOCKING
rename to tests/integration/bash_tests/run_from_chrysalis/blocking_test_scripts/README_TEST_BLOCKING
index e367335b..cb17bf4a 100644
--- a/tests3/README_TEST_BLOCKING
+++ b/tests/integration/bash_tests/run_from_chrysalis/blocking_test_scripts/README_TEST_BLOCKING
@@ -67,15 +67,7 @@ II. Running the Test Script
 
 The test script "test_zstash_blocking.sh" accepts two positional parameters:
 
-    test_zstash_blocking.sh (BLOCKING|NON_BLOCKING) [NEW_CREDS]
-
-On an initial run, or whenever Globus complains of authentication failures,
-add "NEW_CREDS" as the second parameter.  This will act to delete your
-cached Globus credentials and trigger prompts for you to paste login URLs
-to your browser (generally one per endpoint) which requires that you conduct
-a login sequence, and then paste a returned key-value at the bash command
-prompt.  After both keys are accepted, you can re-run the test script
-without "NEW_CREDS", until the credentials expire (usually 24 hours.)
+    test_zstash_blocking.sh (BLOCKING|NON_BLOCKING)
 
 If "BLOCKING" is selected, zstash will run in default mode, waiting for
 each tar file to complete transfer before generating another tar file.
@@ -93,7 +85,7 @@ so that your command prompt returns and you can monitor progress with
     snapshot.sh
 
 which will provide a view of both the tarfile cache and the destination
-directory for delivred tar files. It is also suggested that you name your
+directory for delivered tar files. It is also suggested that you name your
 logfile to reflect the date, and whether BLOCKING or not was specified.
 
 
diff --git a/tests3/gen_data.sh b/tests/integration/bash_tests/run_from_chrysalis/blocking_test_scripts/gen_data.sh
similarity index 100%
rename from tests3/gen_data.sh
rename to tests/integration/bash_tests/run_from_chrysalis/blocking_test_scripts/gen_data.sh
diff --git a/tests3/gen_data_runner.sh b/tests/integration/bash_tests/run_from_chrysalis/blocking_test_scripts/gen_data_runner.sh
similarity index 100%
rename from tests3/gen_data_runner.sh
rename to tests/integration/bash_tests/run_from_chrysalis/blocking_test_scripts/gen_data_runner.sh
diff --git a/tests3/reset_test.sh b/tests/integration/bash_tests/run_from_chrysalis/blocking_test_scripts/reset_test.sh
similarity index 100%
rename from tests3/reset_test.sh
rename to tests/integration/bash_tests/run_from_chrysalis/blocking_test_scripts/reset_test.sh
diff --git a/tests3/snapshot.sh b/tests/integration/bash_tests/run_from_chrysalis/blocking_test_scripts/snapshot.sh
similarity index 100%
rename from tests3/snapshot.sh
rename to tests/integration/bash_tests/run_from_chrysalis/blocking_test_scripts/snapshot.sh
diff --git a/tests3/test_zstash_blocking.sh b/tests/integration/bash_tests/run_from_chrysalis/blocking_test_scripts/test_zstash_blocking.sh
similarity index 80%
rename from tests3/test_zstash_blocking.sh
rename to tests/integration/bash_tests/run_from_chrysalis/blocking_test_scripts/test_zstash_blocking.sh
index bae334a8..38af63d4 100755
--- a/tests3/test_zstash_blocking.sh
+++ b/tests/integration/bash_tests/run_from_chrysalis/blocking_test_scripts/test_zstash_blocking.sh
@@ -1,11 +1,9 @@
 #!/bin/bash
 
 if [[ $# -lt 1 ]]; then
-    echo "Usage:  text_zstash_blocking.sh (BLOCKING|NON_BLOCKING) [NEW_CREDS]"
+    echo "Usage:  text_zstash_blocking.sh (BLOCKING|NON_BLOCKING)"
     echo "  One of \"BLOCKING\" or \"NON_BLOCKING\" must be supplied as the"
     echo "  first parameter."
-    echo "  Add \"NEW_CREDS\" if Globus credentials have expired."
-    echo "  This will cause Globus to prompt for new credentials."
     exit 0
 fi
 
@@ -20,14 +18,6 @@ else
     exit 0
 fi
 
-# remove old auth data, if exists, so that globus will prompt us
-# for new auth credentials in case they have expired:
-if [[ $# -gt 1 ]]; then
-    if [[ $2 == "NEW_CREDS" ]]: then
-        rm -f ~/.globus-native-apps.cfg
-    fi
-fi
-
 
 base_dir=`pwd`
 base_dir=`realpath $base_dir`
diff --git a/tests/scripts/database_corruption.bash b/tests/integration/bash_tests/run_from_chrysalis/database_corruption.bash
similarity index 91%
rename from tests/scripts/database_corruption.bash
rename to tests/integration/bash_tests/run_from_chrysalis/database_corruption.bash
index b65ab1b1..e984c18f 100755
--- a/tests/scripts/database_corruption.bash
+++ b/tests/integration/bash_tests/run_from_chrysalis/database_corruption.bash
@@ -19,34 +19,13 @@ setup()
 
 run_test_cases()
 {
-    # Before running the first time:
-    # globus.org
-    # Authenticate into LCRC Improv DTN, NERSC Perlmutter
-    # Run toy problem:
-    #
-    # source /lcrc/soft/climate/e3sm-unified/load_latest_e3sm_unified_chrysalis.sh
-    # cd /lcrc/group/e3sm/ac.forsyth2/zstash_testing/test_20250729
-    # mkdir zstash_demo; echo 'file0 stuff' > zstash_demo/file0.txt
-    # Chrysalis: 15288284-7006-4041-ba1a-6b52501e49f1
-    # Perlmutter: 6bdc7956-fc0f-4ad2-989c-7aa5ee643a79
-    # zstash create --hpss=globus://6bdc7956-fc0f-4ad2-989c-7aa5ee643a79/global/homes/f/forsyth/zstash/tests/manual_run zstash_demo
-    # Will prompt for LCRC AND NERSC authentication, and then paste generated auth code one time.
 
-    # Before each run:
-    # Perlmutter:
-    # cd /global/homes/f/forsyth/zstash/tests/
-    # rm -rf test_database_corruption
-    #
-    # Chrysalis:
-    # cd ~/ez/zstash/
-    # conda activate zstash-377-20250728
-    # pre-commit run --all-files
-    # python -m pip install .
-    # cd tests/scripts
-    # ./database_corruption.bash
+    local try_num=$1
 
     SRC_DIR=/lcrc/group/e3sm/ac.forsyth2/zstash_testing/test_database_corruption # Chrysalis
-    DST_DIR=globus://6bdc7956-fc0f-4ad2-989c-7aa5ee643a79/global/homes/f/forsyth/zstash/tests/test_database_corruption # Perlmutter
+    DST_DIR=globus://6bdc7956-fc0f-4ad2-989c-7aa5ee643a79/global/homes/f/forsyth/zstash/tests/test_database_corruption_try${try_num} # Perlmutter
+    # To start fresh with try_num=1, delete the above directory on Perlmutter before running. Example:
+    # rm -rf /global/homes/f/forsyth/zstash/tests/test_database_corruption_try1
 
     success_count=0
     fail_count=0
@@ -318,7 +297,7 @@ run_test_cases()
     echo "Review: ${review_str}"
 }
 
-run_test_cases
+run_test_cases "$1"
 
 # Success count: 25
 # Fail count: 0
diff --git a/tests/scripts/globus_auth.bash b/tests/integration/bash_tests/run_from_chrysalis/globus_auth.bash
similarity index 84%
rename from tests/scripts/globus_auth.bash
rename to tests/integration/bash_tests/run_from_chrysalis/globus_auth.bash
index 0396dabc..a3905bdb 100755
--- a/tests/scripts/globus_auth.bash
+++ b/tests/integration/bash_tests/run_from_chrysalis/globus_auth.bash
@@ -20,7 +20,7 @@ check_log_has()
 {
     local expected_grep="${1}"
     local log_file="${2}"
-    grep "${expected_grep}" ${log_file}
+    grep -q "${expected_grep}" ${log_file}
     if [ $? != 0 ]; then
         echo "Expected grep '${expected_grep}' not found in ${log_file}. Test failed."
         exit 2
@@ -40,30 +40,14 @@ check_log_does_not_have()
 
 run_test_cases()
 {
-    # This script requires user input and thus cannot be run automatically as part of a test suite.
-
-    # To start fresh with Globus:
-    # 1. Log into endpoints (LCRC Improv DTN, NERSC Perlmutter) at globus.org: File Manager > Add the endpoints in the "Collection" fields
-    # 2. To start fresh, with no consents: https://auth.globus.org/v2/web/consents > Manage Your Consents > Globus Endpoint Performance Monitoring > rescind all"
-
-    # Before each run:
-    # Perlmutter:
-    # cd /global/homes/f/forsyth/zstash/tests/
-    # rm -rf test_globus_auth_try1 # Or just change $DST_DIR to a new directory
-    #
-    # Chrysalis:
-    # cd ~/ez/zstash/
-    # conda activate <env-name>
-    # pre-commit run --all-files
-    # python -m pip install .
-    # cd tests/scripts
-    # ./globus_auth.bash
+    local try_num=$1
 
     PERLMUTTER_ENDPOINT=6bdc7956-fc0f-4ad2-989c-7aa5ee643a79
 
-    TRY_NUM=8
     SRC_DIR=/lcrc/group/e3sm/ac.forsyth2/zstash_testing/test_globus_auth # Chrysalis
-    DST_DIR=globus://${PERLMUTTER_ENDPOINT}/global/homes/f/forsyth/zstash/tests/test_globus_auth_try${TRY_NUM}
+    DST_DIR=globus://${PERLMUTTER_ENDPOINT}/global/homes/f/forsyth/zstash/tests/test_globus_auth_try${try_num} # Perlmutter
+    # To start fresh with try_num=1, delete the above directory on Perlmutter before running. Example:
+    # rm -rf /global/homes/f/forsyth/zstash/tests/test_globus_auth_try1
 
     GLOBUS_CFG=/home/ac.forsyth2/.globus-native-apps.cfg
     INI_PATH=/home/ac.forsyth2/.zstash.ini
@@ -134,4 +118,4 @@ run_test_cases()
     # Could also test -l and -v options, but the above code covers the important part.
 }
 
-run_test_cases
+run_test_cases "$1"
diff --git a/tests/integration/bash_tests/run_from_chrysalis/symlinks.sh b/tests/integration/bash_tests/run_from_chrysalis/symlinks.sh
new file mode 100755
index 00000000..1479f180
--- /dev/null
+++ b/tests/integration/bash_tests/run_from_chrysalis/symlinks.sh
@@ -0,0 +1,75 @@
+# Test symlinks
+# Adjusted from https://github.com/E3SM-Project/zstash/issues/341
+
+check_log_has()
+{
+    local expected_grep="${1}"
+    local log_file="${2}"
+    grep -q "${expected_grep}" ${log_file}
+    if [ $? != 0 ]; then
+        echo "Expected grep '${expected_grep}' not found in ${log_file}. Test failed."
+        exit 2
+    fi
+}
+
+test_cases()
+{
+  local follow_symlinks=$1
+  cd /home/ac.forsyth2/ez/zstash/tests/utils/test_symlinks
+  rm -rf workdir workdir2 workdir3
+  mkdir workdir workdir2 workdir3
+  cd workdir
+  mkdir -p src/d1 src/d2
+  touch src/d1/large_file.txt
+
+  # This creates a symlink in d2 that links to a file in d1
+  # Notice absolute path is used for source
+  ln -s /home/ac.forsyth2/ez/zstash/tests/utils/test_symlinks/workdir/src/d1/large_file.txt src/d2/large_file.txt
+
+  echo ""
+  echo "ls -l  src/d2"
+  case_name="ls_1"
+  ls -l  src/d2 2>&1 | tee ${case_name}.log
+  # symlink
+  check_log_has "large_file.txt -> /home/ac.forsyth2/ez/zstash/tests/utils/test_symlinks/workdir/src/d1/large_file.txt" ${case_name}.log
+
+  echo ""
+  case_name="create"
+  if [[ "${follow_symlinks,,}" == "true" ]]; then
+    echo "zstash create --hpss=none --follow-symlinks --cache /home/ac.forsyth2/ez/zstash/tests/utils/test_symlinks/workdir2 src/d2"
+    zstash create --hpss=none --follow-symlinks --cache /home/ac.forsyth2/ez/zstash/tests/utils/test_symlinks/workdir2 src/d2  2>&1 | tee ${case_name}.log
+  else
+    echo "zstash create --hpss=none --cache /home/ac.forsyth2/ez/zstash/tests/utils/test_symlinks/workdir2 src/d2"
+    zstash create --hpss=none --cache /home/ac.forsyth2/ez/zstash/tests/utils/test_symlinks/workdir2 src/d2 2>&1 | tee ${case_name}.log
+  fi
+  check_log_has "Adding 000000.tar" ${case_name}.log
+
+  echo ""
+  echo "ls -l  src/d2"
+  case_name="ls_2"
+  ls -l  src/d2 2>&1 | tee ${case_name}.log
+  # symlink (src is unaffected)
+  check_log_has "large_file.txt -> /home/ac.forsyth2/ez/zstash/tests/utils/test_symlinks/workdir/src/d1/large_file.txt" ${case_name}.log
+
+  cd ../workdir3
+  echo ""
+  echo "zstash extract --hpss=none --cache /home/ac.forsyth2/ez/zstash/tests/utils/test_symlinks/workdir2"
+  case_name="extract"
+  zstash extract --hpss=none --cache /home/ac.forsyth2/ez/zstash/tests/utils/test_symlinks/workdir2  2>&1 | tee ${case_name}.log
+  check_log_has "No failures detected when extracting the files" ${case_name}.log
+
+  cd ..
+  echo ""
+  echo "ls workdir3"
+  case_name="ls_3"
+  ls workdir3 2>&1 | tee ${case_name}.log
+  # large_file.txt
+  check_log_has "large_file.txt" ${case_name}.log
+
+  cd /home/ac.forsyth2/ez/zstash/tests/utils/test_symlinks
+  rm -rf workdir workdir2 workdir3 ls_3.log
+
+}
+
+test_cases true
+test_cases false
diff --git a/tests/integration/bash_tests/run_from_perlmutter/follow_symlinks.sh b/tests/integration/bash_tests/run_from_perlmutter/follow_symlinks.sh
new file mode 100755
index 00000000..7e035b2e
--- /dev/null
+++ b/tests/integration/bash_tests/run_from_perlmutter/follow_symlinks.sh
@@ -0,0 +1,295 @@
+#!/bin/bash
+
+# From Claude:
+check_log_has()
+{
+    local log_file="${@: -1}"  # Last argument is the log file
+    local patterns=("${@:1:$#-1}")  # All but last argument are patterns
+
+    for pattern in "${patterns[@]}"; do
+        if ! grep -q "${pattern}" "${log_file}"; then
+            echo "Expected grep '${pattern}' not found in ${log_file}. Test failed."
+            exit 1
+        fi
+    done
+}
+
+setup()
+{
+  echo "##########################################################################################################"
+  use_hpss=$1
+  follow_symlinks=$2
+  case_name="${3}"
+  archive_name=$4
+  if [[ "${use_hpss}" == "true" ]]; then
+      hsi rm -R ${archive_name}
+  fi
+  echo "use_hpss=${use_hpss}"
+  echo "follow_symlinks=${follow_symlinks}"
+  echo "case_name=${case_name}"
+  local_archive_name=test_follow_symlinks
+  non_archived_dir=${local_archive_name}_non_archived
+  test_dir=/global/homes/f/forsyth/ez/zstash/tests/utils/
+  cd ${test_dir}
+  rm -rf ${local_archive_name}
+  rm -rf ${non_archived_dir}
+  mkdir ${local_archive_name}
+  # At the same level as local_archive_name
+  mkdir ${non_archived_dir}
+  cd ${local_archive_name}
+
+  mkdir zstash_demo
+  mkdir zstash_demo/empty_dir
+  mkdir zstash_demo/dir
+  mkdir non_archived
+  echo -n '' > zstash_demo/file_empty.txt
+  echo 'file0 stuff' > zstash_demo/dir/file0.txt
+  echo 'file1 stuff' > non_archived/file1.txt
+  echo 'file2 stuff' > ../${non_archived_dir}/file2.txt
+  # NOTE: `ln -s` appears to require absolute paths for the source files
+  ln -s ${test_dir}/${local_archive_name}/non_archived/file1.txt zstash_demo/file3.txt
+  check_log_has "file1 stuff" zstash_demo/file3.txt
+  ln -s ${test_dir}/${non_archived_dir}/file2.txt zstash_demo/file4.txt
+  check_log_has "file2 stuff" zstash_demo/file4.txt
+}
+
+zstash_create()
+{
+  archive_name=$1
+  follow_symlinks=$2
+  echo "Starting zstash create from:"
+  pwd
+  if [[ "${follow_symlinks}" == "true" ]]; then
+      zstash create --hpss=${archive_name} zstash_demo --follow-symlinks
+  else
+      zstash create --hpss=${archive_name} zstash_demo
+  fi
+}
+
+zstash_extract()
+{
+  archive_name=$1
+  rm -rf zstash_extraction
+  mkdir zstash_extraction
+  cd zstash_extraction
+  if [[ "${archive_name}" == "none" ]]; then
+    echo "Copying zstash"
+    cp -r ../zstash_demo/zstash/ zstash
+  fi
+  echo "Starting zstash extract from:"
+  pwd
+  zstash extract --hpss=${archive_name}
+  echo "> ls"
+  ls 2>&1 | tee out_ls.txt
+  echo "> ls -l"
+  ls -l  2>&1 | tee out_ls_l.txt
+  echo "> zstash ls"
+  zstash ls --hpss=${archive_name} 2>&1 | tee out_zstash_ls.txt
+  echo "> zstash ls -l"
+  zstash ls -l --hpss=${archive_name} 2>&1 | tee out_zstash_ls_l.txt
+  cd ..
+}
+
+test_cases()
+{
+  test_num=$1
+  use_hpss=$2
+  follow_symlinks=$3
+  if [[ "${use_hpss}" == "true" ]]; then
+      archive_name=/home/f/forsyth/zstash_test_follow_symlinks
+  else
+      archive_name=none
+  fi
+
+  echo "##########################################################################################################"
+  echo "Test ${test_num}: use_hpss=${use_hpss}, follow_symlinks=${follow_symlinks}"
+  case_name="Case ${test_num}.1: Don't delete original file"
+  setup ${use_hpss} ${follow_symlinks} "${case_name}" ${archive_name}
+  zstash_create ${archive_name} ${follow_symlinks} 2>&1 | tee case_${test_num}.1_create.txt
+  check_log_has \
+    "Archiving file3.txt" \
+    "Archiving file4.txt" \
+    "Archiving file_empty.txt" \
+    "Archiving dir/file0.txt" \
+    "Archiving empty_dir" \
+    "Completed archive file 000000.tar" \
+    case_${test_num}.1_create.txt
+  zstash_extract ${archive_name} 2>&1 | tee case_${test_num}.1_extract.txt
+  check_log_has \
+    "Extracting file3.txt" \
+    "Extracting file4.txt" \
+    "Extracting file_empty.txt" \
+    "Extracting dir/file0.txt" \
+    "Extracting empty_dir" \
+    "No failures detected when extracting the files." \
+    case_${test_num}.1_extract.txt
+  check_log_has "file1 stuff" zstash_extraction/file3.txt
+  check_log_has "file2 stuff" zstash_extraction/file4.txt
+  check_log_has \
+    "dir" \
+    "empty_dir" \
+    "file3.txt" \
+    "file4.txt" \
+    "file_empty.txt" \
+    "zstash" \
+    zstash_extraction/out_ls.txt
+  check_log_has \
+    "dir" \
+    "empty_dir" \
+    "file3.txt" \
+    "file4.txt" \
+    "file_empty.txt" \
+    "zstash" \
+    zstash_extraction/out_ls_l.txt
+  check_log_has \
+    "file3.txt" \
+    "file4.txt" \
+    "file_empty.txt" \
+    "dir/file0.txt" \
+    "empty_dir" \
+    zstash_extraction/out_zstash_ls.txt
+  check_log_has \
+    "file3.txt" \
+    "file4.txt" \
+    "file_empty.txt" \
+    "dir/file0.txt" \
+    "empty_dir" \
+    "000000.tar" \
+    zstash_extraction/out_zstash_ls_l.txt
+
+  case_name="Case ${test_num}.2: Delete before create"
+  setup ${use_hpss} ${follow_symlinks} "${case_name}" ${archive_name}
+  rm non_archived/file1.txt # Remove the file that file3 links to
+  zstash_create ${archive_name} ${follow_symlinks} 2>&1 | tee case_${test_num}.2_create.txt
+  if [ "${follow_symlinks}" = "true" ]; then
+    check_log_has \
+      "Archiving file3.txt" \
+      "FileNotFoundError" \
+      "ERROR: Archiving file3.txt" \
+      "Exception: Archive creation failed due to broken symlink." \
+      case_${test_num}.2_create.txt
+  else
+    check_log_has \
+      "Archiving file3.txt" \
+      "Archiving file4.txt" \
+      "Archiving file_empty.txt" \
+      "Archiving dir/file0.txt" \
+      "Archiving empty_dir" \
+      "Completed archive file 000000.tar" \
+      case_${test_num}.2_create.txt
+    zstash_extract ${archive_name} 2>&1 | tee case_${test_num}.2_extract.txt
+    check_log_has \
+      "Extracting file3.txt" \
+      "Extracting file4.txt" \
+      "Extracting file_empty.txt" \
+      "Extracting dir/file0.txt" \
+      "Extracting empty_dir" \
+      "No failures detected when extracting the files." \
+      case_${test_num}.2_extract.txt
+    if [ -f "zstash_extraction/file3.txt" ]; then
+        echo "zstash_extraction/file3.txt exists, but it should not because the file it links to was deleted."
+        exit 2
+    fi
+    check_log_has "file2 stuff" zstash_extraction/file4.txt
+    check_log_has \
+      "dir" \
+      "empty_dir" \
+      "file3.txt" \
+      "file4.txt" \
+      "file_empty.txt" \
+      "zstash" \
+      zstash_extraction/out_ls.txt
+    check_log_has \
+      "dir" \
+      "empty_dir" \
+      "file3.txt" \
+      "file4.txt" \
+      "file_empty.txt" \
+      "zstash" \
+      zstash_extraction/out_ls_l.txt
+    check_log_has \
+      "file3.txt" \
+      "file4.txt" \
+      "file_empty.txt" \
+      "dir/file0.txt" \
+      "empty_dir" \
+      zstash_extraction/out_zstash_ls.txt
+    check_log_has \
+      "file3.txt" \
+      "file4.txt" \
+      "file_empty.txt" \
+      "dir/file0.txt" \
+      "empty_dir" \
+      "000000.tar" \
+      zstash_extraction/out_zstash_ls_l.txt
+  fi
+
+  case_name="Case ${test_num}.3: Delete after create"
+  setup ${use_hpss} ${follow_symlinks} "${case_name}" ${archive_name}
+  zstash_create ${archive_name} ${follow_symlinks} 2>&1 | tee case_${test_num}.3_create.txt
+  check_log_has \
+    "Archiving file3.txt" \
+    "Archiving file4.txt" \
+    "Archiving file_empty.txt" \
+    "Archiving dir/file0.txt" \
+    "Archiving empty_dir" \
+    "Completed archive file 000000.tar" \
+    case_${test_num}.3_create.txt
+  rm non_archived/file1.txt
+  zstash_extract ${archive_name} 2>&1 | tee case_${test_num}.3_extract.txt
+  check_log_has \
+    "Extracting file3.txt" \
+    "Extracting file4.txt" \
+    "Extracting file_empty.txt" \
+    "Extracting dir/file0.txt" \
+    "Extracting empty_dir" \
+    "No failures detected when extracting the files." \
+    case_${test_num}.3_extract.txt
+  if [ "${follow_symlinks}" = "true" ]; then
+    check_log_has "file1 stuff" zstash_extraction/file3.txt
+  else
+    if [ -f "zstash_extraction/file3.txt" ]; then
+        echo "zstash_extraction/file3.txt exists, but it should not because the file it links to was deleted."
+        exit 3
+    fi
+  fi
+  check_log_has "file2 stuff" zstash_extraction/file4.txt
+  check_log_has \
+    "dir" \
+    "empty_dir" \
+    "file3.txt" \
+    "file4.txt" \
+    "file_empty.txt" \
+    "zstash" \
+    zstash_extraction/out_ls.txt
+  check_log_has \
+    "dir" \
+    "empty_dir" \
+    "file3.txt" \
+    "file4.txt" \
+    "file_empty.txt" \
+    "zstash" \
+    zstash_extraction/out_ls_l.txt
+  check_log_has \
+    "file3.txt" \
+    "file4.txt" \
+    "file_empty.txt" \
+    "dir/file0.txt" \
+    "empty_dir" \
+    zstash_extraction/out_zstash_ls.txt
+  check_log_has \
+    "file3.txt" \
+    "file4.txt" \
+    "file_empty.txt" \
+    "dir/file0.txt" \
+    "empty_dir" \
+    "000000.tar" \
+    zstash_extraction/out_zstash_ls_l.txt
+
+}
+
+# Begin tests
+test_cases 1 true true # HPSS, follow symlinks
+test_cases 2 false true # No HPSS, follow symlinks
+test_cases 3 true false # HPSS, don't follow symlinks
+test_cases 4 false false # No HPSS, don't follow symlinks
diff --git a/tests/scripts_unit_tests/test_ls_globus.bash b/tests/integration/bash_tests/run_from_perlmutter/test_ls_globus.bash
similarity index 51%
rename from tests/scripts_unit_tests/test_ls_globus.bash
rename to tests/integration/bash_tests/run_from_perlmutter/test_ls_globus.bash
index b1677a80..2315a2a2 100755
--- a/tests/scripts_unit_tests/test_ls_globus.bash
+++ b/tests/integration/bash_tests/run_from_perlmutter/test_ls_globus.bash
@@ -4,6 +4,20 @@ hpss_globus_endpoint="6c54cade-bde5-45c1-bdea-f4bd71dba2cc"
 hpss_path="globus://${hpss_globus_endpoint}/~/zstash_test/"
 cache=zstash # Set via `self.cache = "zstash"`
 
+# From Claude:
+check_log_has()
+{
+    local log_file="${@: -1}"  # Last argument is the log file
+    local patterns=("${@:1:$#-1}")  # All but last argument are patterns
+
+    for pattern in "${patterns[@]}"; do
+        if ! grep -q "${pattern}" "${log_file}"; then
+            echo "Expected grep '${pattern}' not found in ${log_file}. Test failed."
+            exit 1
+        fi
+    done
+}
+
 # base.setupDirs ##############################################################
 test_dir=zstash_test
 
@@ -29,18 +43,36 @@ ln -s ${test_dir}/file0.txt ${test_dir}/file0_hard.txt
 
 # base.create #################################################################
 echo "Adding files to HPSS"
-zstash create --hpss=${hpss_path} ${test_dir}
-# Archives 000000.tar
+case_name="create"
+zstash create --hpss=${hpss_path} ${test_dir} 2>&1 | tee ${case_name}.log
+check_log_has "INFO: Adding 000000.tar" ${case_name}.log
 echo "Cache:"
-ls -l ${test_dir}/${cache} # just index.db
-echo "HPSS:"
-hsi ls -l ${hpss_path} # 000000.tar, index.db
+ls -l ${test_dir}/${cache} 2>&1 | tee ${case_name}_cache.log
+check_log_has "index.db" ${case_name}_cache.log
+# NOTE:
+# It appears that we can't access the HPSS path directly with `hsi`.
+# That's presumably because we're using the Globus tutorial endpoint
+# rather than the NERSC HPSS endpoint.
 
 # back in test_globus.helperLsGlobus ##########################################
 cd ${test_dir}
-zstash ls --hpss=${hpss_path}
+case_name="ls"
+zstash ls --hpss=${hpss_path} 2>&1 | tee ${case_name}.log
+check_log_has \
+    "file0.txt" \
+    "file0_hard.txt" \
+    "file0_soft_bad.txt" \
+    "file_0_soft.txt" \
+    "file_empty.txt" \
+    "dir/file1.txt" \
+    "empty_dir" \
+    ${case_name}.log
 cd ..
 echo "Cache:"
-ls -l ${test_dir}/${cache}
-echo "HPSS:"
-hsi ls -l ${hpss_path}
+ls -l ${test_dir}/${cache} 2>&1 | tee ${case_name}_cache.log
+check_log_has "index.db" ${case_name}_cache.log
+
+rm -rf ${test_dir} # Cleanup
+rm create.log
+rm create_cache.log
+rm ls_cache.log
diff --git a/tests/integration/bash_tests/run_from_perlmutter/test_update_non_empty_hpss.bash b/tests/integration/bash_tests/run_from_perlmutter/test_update_non_empty_hpss.bash
new file mode 100755
index 00000000..f4f819c1
--- /dev/null
+++ b/tests/integration/bash_tests/run_from_perlmutter/test_update_non_empty_hpss.bash
@@ -0,0 +1,138 @@
+#!/bin/bash
+
+hpss_path=zstash_test # Set via `HPSS_ARCHIVE = "zstash_test"`
+cache=zstash # Set via `self.cache = "zstash"`
+
+check_log_has()
+{
+    local expected_grep="${1}"
+    local log_file="${2}"
+    grep -q "${expected_grep}" ${log_file}
+    if [ $? != 0 ]; then
+        echo "Expected grep '${expected_grep}' not found in ${log_file}. Test failed."
+        exit 1
+    fi
+}
+
+# base.setupDirs ##############################################################
+test_dir=zstash_test
+
+# Create files and directories
+echo "Creating files."
+mkdir -p ${test_dir}
+mkdir -p ${test_dir}/empty_dir
+mkdir -p ${test_dir}/dir
+
+echo "file0 stuff" > ${test_dir}/file0.txt
+echo "" > ${test_dir}/file_empty.txt
+echo "file1 stuff" > ${test_dir}/dir/file1.txt
+
+# Symbolic (soft) link (points to a file name which points to an inode)
+# ${test_dir}/file_0_soft.txt points to ${test_dir}/file0.txt
+# The python `os.symlink` call omits the first `test_dir`
+# because it simply looks in the same directory for the file to link to.
+ln -s ${test_dir}/file0.txt ${test_dir}/file_0_soft.txt
+# Bad symbolic (soft) link (points to a file name which points to an inode)
+ln -s ${test_dir}/file0_that_doesnt_exist.txt ${test_dir}/file0_soft_bad.txt
+# Hard link (points to an inode directly)
+ln -s ${test_dir}/file0.txt ${test_dir}/file0_hard.txt
+
+# base.create #################################################################
+echo "Adding files to HPSS"
+
+case_name="create"
+zstash create --hpss=${hpss_path} ${test_dir} 2>&1 | tee ${case_name}.log
+check_log_has "INFO: Adding 000000.tar" ${case_name}.log
+echo "Cache:"
+ls -l ${test_dir}/${cache} 2>&1 | tee ${case_name}_cache.log
+check_log_has "index.db" ${case_name}_cache.log
+echo "HPSS:"
+hsi ls -l ${hpss_path} 2>&1 | tee ${case_name}_hpss.log
+check_log_has "000000.tar" ${case_name}_hpss.log
+check_log_has "index.db" ${case_name}_hpss.log
+
+# base.add_files ##############################################################
+echo "Testing update with an actual change"
+mkdir -p ${test_dir}/dir2
+echo "file2 stuff" > ${test_dir}/dir2/file2.txt
+echo "file1 stuff with changes" > ${test_dir}/dir/file1.txt
+cd ${test_dir}
+case_name="update1"
+zstash update -v --hpss=${hpss_path} 2>&1 | tee ${case_name}.log
+check_log_has "INFO: Adding 000001.tar" ${case_name}.log
+cd ..
+echo "Cache:"
+ls -l ${test_dir}/${cache} 2>&1 | tee ${case_name}_cache.log
+check_log_has "index.db" ${case_name}_cache.log
+echo "HPSS:"
+hsi ls -l ${hpss_path} 2>&1 | tee ${case_name}_hpss.log
+check_log_has "000000.tar" ${case_name}_hpss.log
+check_log_has "000001.tar" ${case_name}_hpss.log
+check_log_has "index.db" ${case_name}_hpss.log
+
+echo "Adding more files to the HPSS archive."
+echo "file3 stuff" > ${test_dir}/file3.txt
+cd ${test_dir}
+case_name="update2"
+zstash update --hpss=${hpss_path} 2>&1 | tee ${case_name}.log
+check_log_has "INFO: Adding 000002.tar" ${case_name}.log
+cd ..
+echo "Cache:"
+ls -l ${test_dir}/${cache} 2>&1 | tee ${case_name}_cache.log
+check_log_has "index.db" ${case_name}_cache.log
+echo "HPSS:"
+hsi ls -l ${hpss_path} 2>&1 | tee ${case_name}_hpss.log
+check_log_has "000000.tar" ${case_name}_hpss.log
+check_log_has "000001.tar" ${case_name}_hpss.log
+check_log_has "000002.tar" ${case_name}_hpss.log
+check_log_has "index.db" ${case_name}_hpss.log
+
+echo "file4 stuff" > ${test_dir}/file4.txt
+cd ${test_dir}
+case_name="update3"
+zstash update --hpss=${hpss_path} 2>&1 | tee ${case_name}.log
+check_log_has "INFO: Adding 000003.tar" ${case_name}.log
+cd ..
+echo "Cache:"
+ls -l ${test_dir}/${cache} 2>&1 | tee ${case_name}_cache.log
+check_log_has "index.db" ${case_name}_cache.log
+echo "HPSS:"
+hsi ls -l ${hpss_path} 2>&1 | tee ${case_name}_hpss.log
+check_log_has "000000.tar" ${case_name}_hpss.log
+check_log_has "000001.tar" ${case_name}_hpss.log
+check_log_has "000002.tar" ${case_name}_hpss.log
+check_log_has "000003.tar" ${case_name}_hpss.log
+check_log_has "index.db" ${case_name}_hpss.log
+
+echo "file5 stuff" > ${test_dir}/file5.txt
+cd ${test_dir}
+case_name="update4"
+zstash update --hpss=${hpss_path} 2>&1 | tee ${case_name}.log
+check_log_has "INFO: Adding 000004.tar" ${case_name}.log
+cd ..
+echo "Cache:"
+ls -l ${test_dir}/${cache} 2>&1 | tee ${case_name}_cache.log
+check_log_has "index.db" ${case_name}_cache.log
+echo "HPSS:"
+hsi ls -l ${hpss_path} 2>&1 | tee ${case_name}_hpss.log
+check_log_has "000000.tar" ${case_name}_hpss.log
+check_log_has "000001.tar" ${case_name}_hpss.log
+check_log_has "000002.tar" ${case_name}_hpss.log
+check_log_has "000003.tar" ${case_name}_hpss.log
+check_log_has "000004.tar" ${case_name}_hpss.log
+check_log_has "index.db" ${case_name}_hpss.log
+
+# back in test_update.helperUpdateNonEmpty ####################################
+echo "Cache check actually performed in the unit test:"
+case_name="ls"
+ls -l ${test_dir}/${cache} 2>&1 | tee ${case_name}.log
+check_log_has "index.db" ${case_name}.log
+
+# base.tearDown ###############################################################
+echo "Removing test files, both locally and at the HPSS repo"
+rm -rf ${test_dir}
+rm create.log
+rm create_*.log
+rm ls.log
+rm update*.log
+hsi rm -R ${hpss_path}
diff --git a/tests/integration/python_tests/__init__.py b/tests/integration/python_tests/__init__.py
new file mode 100644
index 00000000..e69de29b
diff --git a/tests/integration/python_tests/group_by_command/__init_.py b/tests/integration/python_tests/group_by_command/__init_.py
new file mode 100644
index 00000000..e69de29b
diff --git a/tests/base.py b/tests/integration/python_tests/group_by_command/base.py
similarity index 99%
rename from tests/base.py
rename to tests/integration/python_tests/group_by_command/base.py
index de88ee4b..eada5220 100644
--- a/tests/base.py
+++ b/tests/integration/python_tests/group_by_command/base.py
@@ -1,7 +1,5 @@
 """
-Run the test suite with `python -m unittest tests/test_*.py`
-
-To run an individual test, run something like `python -m unittest tests.test_extract.TestExtract.testExtractRetries`
+To run an individual test, run something like `python -m unittest tests.integration.python_tests.group_by_command.test_extract.TestExtract.testExtractRetries`
 
 If running on Cori, it is preferable to run from $CSCRATCH rather than
 /global/homes. Running from the latter may result in a
diff --git a/tests/test_check.py b/tests/integration/python_tests/group_by_command/test_check.py
similarity index 99%
rename from tests/test_check.py
rename to tests/integration/python_tests/group_by_command/test_check.py
index 9e8c17e0..d1dbe6c0 100644
--- a/tests/test_check.py
+++ b/tests/integration/python_tests/group_by_command/test_check.py
@@ -2,7 +2,7 @@
 import shutil
 import unittest
 
-from tests.base import (
+from tests.integration.python_tests.group_by_command.base import (
     HPSS_ARCHIVE,
     TOP_LEVEL,
     ZSTASH_PATH,
diff --git a/tests/test_check_parallel.py b/tests/integration/python_tests/group_by_command/test_check_parallel.py
similarity index 98%
rename from tests/test_check_parallel.py
rename to tests/integration/python_tests/group_by_command/test_check_parallel.py
index f0f1525c..2d2993b0 100644
--- a/tests/test_check_parallel.py
+++ b/tests/integration/python_tests/group_by_command/test_check_parallel.py
@@ -2,7 +2,7 @@
 import shutil
 import unittest
 
-from tests.base import (
+from tests.integration.python_tests.group_by_command.base import (
     HPSS_ARCHIVE,
     TOP_LEVEL,
     ZSTASH_PATH,
@@ -11,7 +11,7 @@
     print_starred,
     run_cmd,
 )
-from tests.test_check import helperCheckTars
+from tests.integration.python_tests.group_by_command.test_check import helperCheckTars
 
 # https://bugs.python.org/issue43743
 # error: Module has no attribute "_USE_CP_SENDFILE"
diff --git a/tests/test_chgrp.py b/tests/integration/python_tests/group_by_command/test_chgrp.py
similarity index 92%
rename from tests/test_chgrp.py
rename to tests/integration/python_tests/group_by_command/test_chgrp.py
index 9706e5e2..dc8763aa 100644
--- a/tests/test_chgrp.py
+++ b/tests/integration/python_tests/group_by_command/test_chgrp.py
@@ -1,6 +1,11 @@
 import unittest
 
-from tests.base import HPSS_ARCHIVE, ZSTASH_PATH, TestZstash, run_cmd
+from tests.integration.python_tests.group_by_command.base import (
+    HPSS_ARCHIVE,
+    ZSTASH_PATH,
+    TestZstash,
+    run_cmd,
+)
 
 
 class TestChgrp(TestZstash):
diff --git a/tests/test_create.py b/tests/integration/python_tests/group_by_command/test_create.py
similarity index 99%
rename from tests/test_create.py
rename to tests/integration/python_tests/group_by_command/test_create.py
index 8613d8d7..53360974 100644
--- a/tests/test_create.py
+++ b/tests/integration/python_tests/group_by_command/test_create.py
@@ -1,7 +1,7 @@
 import os
 import unittest
 
-from tests.base import (
+from tests.integration.python_tests.group_by_command.base import (
     HPSS_ARCHIVE,
     TOP_LEVEL,
     ZSTASH_PATH,
diff --git a/tests/test_extract.py b/tests/integration/python_tests/group_by_command/test_extract.py
similarity index 99%
rename from tests/test_extract.py
rename to tests/integration/python_tests/group_by_command/test_extract.py
index f3269ee0..1ca4f340 100644
--- a/tests/test_extract.py
+++ b/tests/integration/python_tests/group_by_command/test_extract.py
@@ -2,7 +2,7 @@
 import shutil
 import unittest
 
-from tests.base import (
+from tests.integration.python_tests.group_by_command.base import (
     HPSS_ARCHIVE,
     TOP_LEVEL,
     ZSTASH_PATH,
diff --git a/tests/test_extract_parallel.py b/tests/integration/python_tests/group_by_command/test_extract_parallel.py
similarity index 96%
rename from tests/test_extract_parallel.py
rename to tests/integration/python_tests/group_by_command/test_extract_parallel.py
index f34497ef..2ddd0db5 100644
--- a/tests/test_extract_parallel.py
+++ b/tests/integration/python_tests/group_by_command/test_extract_parallel.py
@@ -4,7 +4,7 @@
 import unittest
 from typing import List
 
-from tests.base import (
+from tests.integration.python_tests.group_by_command.base import (
     HPSS_ARCHIVE,
     TOP_LEVEL,
     ZSTASH_PATH,
@@ -12,7 +12,9 @@
     print_starred,
     run_cmd,
 )
-from tests.test_extract import helperExtractTars
+from tests.integration.python_tests.group_by_command.test_extract import (
+    helperExtractTars,
+)
 
 # https://bugs.python.org/issue43743
 # error: Module has no attribute "_USE_CP_SENDFILE"
diff --git a/tests/test_ls.py b/tests/integration/python_tests/group_by_command/test_ls.py
similarity index 98%
rename from tests/test_ls.py
rename to tests/integration/python_tests/group_by_command/test_ls.py
index e3a82a11..b8c5fea8 100644
--- a/tests/test_ls.py
+++ b/tests/integration/python_tests/group_by_command/test_ls.py
@@ -1,7 +1,7 @@
 import os
 import unittest
 
-from tests.base import (
+from tests.integration.python_tests.group_by_command.base import (
     HPSS_ARCHIVE,
     TOP_LEVEL,
     ZSTASH_PATH,
diff --git a/tests/test_update.py b/tests/integration/python_tests/group_by_command/test_update.py
similarity index 99%
rename from tests/test_update.py
rename to tests/integration/python_tests/group_by_command/test_update.py
index 4d8507e7..84354e4f 100644
--- a/tests/test_update.py
+++ b/tests/integration/python_tests/group_by_command/test_update.py
@@ -1,7 +1,7 @@
 import os
 import unittest
 
-from tests.base import (
+from tests.integration.python_tests.group_by_command.base import (
     HPSS_ARCHIVE,
     TOP_LEVEL,
     ZSTASH_PATH,
diff --git a/tests2/base.py b/tests/integration/python_tests/group_by_workflow/base.py
similarity index 95%
rename from tests2/base.py
rename to tests/integration/python_tests/group_by_workflow/base.py
index 644f3577..45d3a406 100644
--- a/tests2/base.py
+++ b/tests/integration/python_tests/group_by_workflow/base.py
@@ -1,14 +1,3 @@
-"""
-Run the test suite with `python -m unittest tests2/test_*.py`
-
-tests2/ is a successor testing directory to tests/
-All new tests should be written in tests2/
-tests/ groups testing by zstash command (e.g., `create`, `extract`)
-tests2/ groups testing by more logical workflows that test multiple zstash commands.
-
-The goal of tests2/ is to be able to follow the commands as if you were just reading a bash script.
-"""
-
 import os
 import shutil
 import stat
diff --git a/tests2/test_cache_fs.py b/tests/integration/python_tests/group_by_workflow/test_cache_fs.py
similarity index 98%
rename from tests2/test_cache_fs.py
rename to tests/integration/python_tests/group_by_workflow/test_cache_fs.py
index 209496b9..a156f916 100644
--- a/tests2/test_cache_fs.py
+++ b/tests/integration/python_tests/group_by_workflow/test_cache_fs.py
@@ -1,7 +1,11 @@
 import os
 import unittest
 
-from tests2.base import TOP_LEVEL, TestZstash, run_cmd
+from tests.integration.python_tests.group_by_workflow.base import (
+    TOP_LEVEL,
+    TestZstash,
+    run_cmd,
+)
 
 
 class TestCacheFs(TestZstash):
diff --git a/tests/scripts/README.md b/tests/scripts/README.md
deleted file mode 100644
index deaede4f..00000000
--- a/tests/scripts/README.md
+++ /dev/null
@@ -1 +0,0 @@
-Scripts for debugging / manually testing zstash
diff --git a/tests/scripts/follow_symlinks.sh b/tests/scripts/follow_symlinks.sh
deleted file mode 100755
index 1d85199e..00000000
--- a/tests/scripts/follow_symlinks.sh
+++ /dev/null
@@ -1,120 +0,0 @@
-#!/bin/bash
-
-setup()
-{
-  echo "##########################################################################################################"
-  use_hpss=$1
-  follow_symlinks=$2
-  case_name="${3}"
-  archive_name=$4
-  if [[ "${use_hpss}" == "true" ]]; then
-      hsi rm -R ${archive_name}
-  fi
-  echo "use_hpss=${use_hpss}"
-  echo "follow_symlinks=${follow_symlinks}"
-  echo "case_name=${case_name}"
-  local_archive_name=test_follow_symlinks
-  non_archived_dir=${local_archive_name}_non_archived
-  test_dir=/global/homes/f/forsyth/zstash/tests
-  cd ${test_dir}
-  rm -rf ${local_archive_name}
-  rm -rf ${non_archived_dir}
-  mkdir ${local_archive_name}
-  # At the same level as local_archive_name
-  mkdir ${non_archived_dir}
-  cd ${local_archive_name}
-
-  mkdir zstash_demo
-  mkdir zstash_demo/empty_dir
-  mkdir zstash_demo/dir
-  mkdir non_archived
-  echo -n '' > zstash_demo/file_empty.txt
-  echo 'file0 stuff' > zstash_demo/dir/file0.txt
-  echo 'file1 stuff' > non_archived/file1.txt
-  echo 'file2 stuff' > ../${non_archived_dir}/file2.txt
-  # NOTE: `ln -s` appears to require absolute paths for the source files
-  ln -s ${test_dir}/${local_archive_name}/non_archived/file1.txt zstash_demo/file3.txt
-  ln -s ${test_dir}/${non_archived_dir}/file2.txt zstash_demo/file4.txt
-  cat zstash_demo/file3.txt
-  cat zstash_demo/file4.txt
-}
-
-zstash_create()
-{
-  archive_name=$1
-  follow_symlinks=$2
-  echo "Starting zstash create"
-  if [[ "${follow_symlinks}" == "true" ]]; then
-      zstash create --hpss=${archive_name} zstash_demo --follow-symlinks
-  else
-      zstash create --hpss=${archive_name} zstash_demo
-  fi
-}
-
-zstash_extract()
-{
-  archive_name=$1
-  mkdir zstash_extraction
-  cd zstash_extraction
-  if [[ "${archive_name}" == "none" ]]; then
-    echo "Copying zstash"
-    cp -r ../zstash_demo/zstash/ zstash
-  fi
-  echo "Starting zstash extract"
-  zstash extract --hpss=${archive_name}
-  cat file3.txt
-  cat file4.txt
-  echo "> ls"
-  ls
-  echo "> ls -l"
-  ls -l
-  echo "> zstash ls"
-  zstash ls --hpss=${archive_name}
-  echo "> zstash ls -l"
-  zstash ls -l --hpss=${archive_name}
-  cd ..
-}
-
-test_cases()
-{
-  use_hpss=$1
-  follow_symlinks=$2
-  if [[ "${use_hpss}" == "true" ]]; then
-      archive_name=/home/f/forsyth/zstash_test_follow_symlinks
-  else
-      archive_name=none
-  fi
-
-  case_name="Don't delete original file"
-  setup ${use_hpss} ${follow_symlinks} "${case_name}" ${archive_name}
-  zstash_create ${archive_name} ${follow_symlinks}
-  zstash_extract ${archive_name}
-
-  case_name="Delete before create"
-  setup ${use_hpss} ${follow_symlinks} "${case_name}" ${archive_name}
-  rm non_archived/file1.txt
-  rm ../run_n247_non_archived/file2.txt
-  zstash_create ${archive_name} ${follow_symlinks}
-  zstash_extract ${archive_name}
-
-  case_name="Delete after create"
-  setup ${use_hpss} ${follow_symlinks} "${case_name}" ${archive_name}
-  zstash_create ${archive_name} ${follow_symlinks}
-  rm non_archived/file1.txt
-  rm ../run_n247_non_archived/file2.txt
-  zstash_extract ${archive_name}
-
-}
-
-conda_env=zstash_dev_n247
-# Set up Conda
-source /global/homes/f/forsyth/miniconda3/etc/profile.d/conda.sh
-conda activate ${conda_env}
-# Install branch
-cd /global/homes/f/forsyth/zstash
-pip install .
-# Begin tests
-test_cases true true # HPSS, follow symlinks
-test_cases false true # No HPSS, follow symlinks
-test_cases true false # HPSS, don't follow symlinks
-test_cases false false # No HPSS, don't follow symlinks
diff --git a/tests/scripts/symlinks.sh b/tests/scripts/symlinks.sh
deleted file mode 100755
index c4437818..00000000
--- a/tests/scripts/symlinks.sh
+++ /dev/null
@@ -1,44 +0,0 @@
-# Test symlinks
-# Adjusted from https://github.com/E3SM-Project/zstash/issues/341
-
-follow_symlinks=true
-
-rm -rf workdir workdir2 workdir3
-mkdir workdir workdir2 workdir3
-cd workdir
-mkdir -p src/d1 src/d2
-touch src/d1/large_file.txt
-
-# This creates a symlink in d2 that links to a file in d1
-# Notice absolute path is used for source
-ln -s /home/ac.forsyth2/ez/zstash/tests/scripts/workdir/src/d1/large_file.txt src/d2/large_file.txt
-
-echo ""
-echo "ls -l  src/d2"
-ls -l  src/d2
-# symlink
-
-echo ""
-if [[ "${follow_symlinks,,}" == "true" ]]; then
-  echo "zstash create --hpss=none --follow-symlinks --cache /home/ac.forsyth2/ez/zstash/tests/scripts/workdir2 src/d2"
-  zstash create --hpss=none --follow-symlinks --cache /home/ac.forsyth2/ez/zstash/tests/scripts/workdir2 src/d2
-else
-  echo "zstash create --hpss=none --cache /home/ac.forsyth2/ez/zstash/tests/scripts/workdir2 src/d2"
-  zstash create --hpss=none --cache /home/ac.forsyth2/ez/zstash/tests/scripts/workdir2 src/d2
-fi
-
-echo ""
-echo "ls -l  src/d2"
-ls -l  src/d2
-# symlink (src is unaffected)
-
-cd ../workdir3
-echo ""
-echo "zstash extract --hpss=none --cache /home/ac.forsyth2/ez/zstash/tests/scripts/workdir2"
-zstash extract --hpss=none --cache /home/ac.forsyth2/ez/zstash/tests/scripts/workdir2
-
-cd ..
-echo ""
-echo "ls workdir3"
-ls workdir3
-# large_file.txt
diff --git a/tests/scripts_unit_tests/README.md b/tests/scripts_unit_tests/README.md
deleted file mode 100644
index ca41e4d6..00000000
--- a/tests/scripts_unit_tests/README.md
+++ /dev/null
@@ -1,4 +0,0 @@
-The unit tests, in script form.
-
-The unit tests are hard to follow via Python,
-so it may be easier to run and debug the logic using these scripts.
diff --git a/tests/scripts_unit_tests/test_update_non_empty_hpss.bash b/tests/scripts_unit_tests/test_update_non_empty_hpss.bash
deleted file mode 100755
index 4c213d4e..00000000
--- a/tests/scripts_unit_tests/test_update_non_empty_hpss.bash
+++ /dev/null
@@ -1,90 +0,0 @@
-#!/bin/bash
-
-hpss_path=zstash_test # Set via `HPSS_ARCHIVE = "zstash_test"`
-cache=zstash # Set via `self.cache = "zstash"`
-
-# base.setupDirs ##############################################################
-test_dir=zstash_test
-
-# Create files and directories
-echo "Creating files."
-mkdir -p ${test_dir}
-mkdir -p ${test_dir}/empty_dir
-mkdir -p ${test_dir}/dir
-
-echo "file0 stuff" > ${test_dir}/file0.txt
-echo "" > ${test_dir}/file_empty.txt
-echo "file1 stuff" > ${test_dir}/dir/file1.txt
-
-# Symbolic (soft) link (points to a file name which points to an inode)
-# ${test_dir}/file_0_soft.txt points to ${test_dir}/file0.txt
-# The python `os.symlink` call omits the first `test_dir`
-# because it simply looks in the same directory for the file to link to.
-ln -s ${test_dir}/file0.txt ${test_dir}/file_0_soft.txt
-# Bad symbolic (soft) link (points to a file name which points to an inode)
-ln -s ${test_dir}/file0_that_doesnt_exist.txt ${test_dir}/file0_soft_bad.txt
-# Hard link (points to an inode directly)
-ln -s ${test_dir}/file0.txt ${test_dir}/file0_hard.txt
-
-# base.create #################################################################
-echo "Adding files to HPSS"
-zstash create --hpss=${hpss_path} ${test_dir}
-# Archives 000000.tar
-echo "Cache:"
-ls -l ${test_dir}/${cache} # just index.db
-echo "HPSS:"
-hsi ls -l ${hpss_path} # 000000.tar, index.db
-
-# base.add_files ##############################################################
-echo "Testing update with an actual change"
-mkdir -p ${test_dir}/dir2
-echo "file2 stuff" > ${test_dir}/dir2/file2.txt
-echo "file1 stuff with changes" > ${test_dir}/dir/file1.txt
-cd ${test_dir}
-zstash update -v --hpss=${hpss_path}
-# Archives 000001.tar
-cd ..
-echo "Cache:"
-ls -l ${test_dir}/${cache} # just index.db
-echo "HPSS:"
-hsi ls -l ${hpss_path} # 000000.tar, 000001.tar, index.db
-
-echo "Adding more files to the HPSS archive."
-echo "file3 stuff" > ${test_dir}/file3.txt
-cd ${test_dir}
-zstash update --hpss=${hpss_path}
-# Archives 000002.tar
-cd ..
-echo "Cache:"
-ls -l ${test_dir}/${cache} # just index.db
-echo "HPSS:"
-hsi ls -l ${hpss_path} # 000000.tar, 000001.tar, 000002.tar, index.db
-
-echo "file4 stuff" > ${test_dir}/file4.txt
-cd ${test_dir}
-zstash update --hpss=${hpss_path}
-# Archives 000003.tar
-cd ..
-echo "Cache:"
-ls -l ${test_dir}/${cache} # just index.db
-echo "HPSS:"
-hsi ls -l ${hpss_path} # 000000.tar, 000001.tar, 000002.tar, 000003.tar, index.db
-
-echo "file5 stuff" > ${test_dir}/file5.txt
-cd ${test_dir}
-zstash update --hpss=${hpss_path}
-# Archives 000004.tar
-cd ..
-echo "Cache:"
-ls -l ${test_dir}/${cache} # just index.db
-echo "HPSS:"
-hsi ls -l ${hpss_path} # 000000.tar, 000001.tar, 000002.tar, 000003.tar, 000004.tar, index.db
-
-# back in test_update.helperUpdateNonEmpty ####################################
-echo "Cache check actually performed in the unit test:"
-ls -l ${test_dir}/${cache} # just index.db
-
-# base.tearDown ###############################################################
-echo "Removing test files, both locally and at the HPSS repo"
-rm -rf ${test_dir}
-hsi rm -R ${hpss_path}
diff --git a/tests/test_functions.py b/tests/test_functions.py
deleted file mode 100644
index cc494e9c..00000000
--- a/tests/test_functions.py
+++ /dev/null
@@ -1,69 +0,0 @@
-import unittest
-
-from zstash.extract import parse_tars_option
-
-
-class TestFunctions(unittest.TestCase):
-    def testParseTarsOption(self):
-        # Starting at 00005a until the end
-        tar_list = parse_tars_option("00005a-", "000000", "00005d")
-        self.assertEqual(tar_list, ["00005a", "00005b", "00005c", "00005d"])
-
-        # Starting from the beginning to 00005a (included)
-        tar_list = parse_tars_option("-00005a", "000058", "00005d")
-        self.assertEqual(tar_list, ["000058", "000059", "00005a"])
-
-        # Specific range
-        tar_list = parse_tars_option("00005a-00005c", "00000", "000005d")
-        self.assertEqual(tar_list, ["00005a", "00005b", "00005c"])
-
-        # Selected tar files
-        tar_list = parse_tars_option("00003e,00004e,000059", "000000", "00005d")
-        self.assertEqual(tar_list, ["00003e", "00004e", "000059"])
-
-        # Mix and match
-        tar_list = parse_tars_option("000030-00003e,00004e,00005a-", "000000", "00005d")
-        self.assertEqual(
-            tar_list,
-            [
-                "000030",
-                "000031",
-                "000032",
-                "000033",
-                "000034",
-                "000035",
-                "000036",
-                "000037",
-                "000038",
-                "000039",
-                "00003a",
-                "00003b",
-                "00003c",
-                "00003d",
-                "00003e",
-                "00004e",
-                "00005a",
-                "00005b",
-                "00005c",
-                "00005d",
-            ],
-        )
-
-        # Check removal of duplicates and sorting
-        tar_list = parse_tars_option("000009,000003,-000005", "000000", "00005d")
-        self.assertEqual(
-            tar_list,
-            ["000000", "000001", "000002", "000003", "000004", "000005", "000009"],
-        )
-
-        # Remove .tar suffix
-        tar_list = parse_tars_option(
-            "000009.tar-00000a,000003.tar,-000002.tar", "000000", "00005d"
-        )
-        self.assertEqual(
-            tar_list, ["000000", "000001", "000002", "000003", "000009", "00000a"]
-        )
-
-
-if __name__ == "__main__":
-    unittest.main()
diff --git a/tests/unit/test_functions.py b/tests/unit/test_functions.py
new file mode 100644
index 00000000..5fa4d5f3
--- /dev/null
+++ b/tests/unit/test_functions.py
@@ -0,0 +1,62 @@
+from zstash.extract import parse_tars_option
+
+
+def test_parse_tars_option():
+    # Starting at 00005a until the end
+    tar_list = parse_tars_option("00005a-", "000000", "00005d")
+    assert tar_list == ["00005a", "00005b", "00005c", "00005d"]
+
+    # Starting from the beginning to 00005a (included)
+    tar_list = parse_tars_option("-00005a", "000058", "00005d")
+    assert tar_list == ["000058", "000059", "00005a"]
+
+    # Specific range
+    tar_list = parse_tars_option("00005a-00005c", "00000", "000005d")
+    assert tar_list == ["00005a", "00005b", "00005c"]
+
+    # Selected tar files
+    tar_list = parse_tars_option("00003e,00004e,000059", "000000", "00005d")
+    assert tar_list == ["00003e", "00004e", "000059"]
+
+    # Mix and match
+    tar_list = parse_tars_option("000030-00003e,00004e,00005a-", "000000", "00005d")
+    assert tar_list == [
+        "000030",
+        "000031",
+        "000032",
+        "000033",
+        "000034",
+        "000035",
+        "000036",
+        "000037",
+        "000038",
+        "000039",
+        "00003a",
+        "00003b",
+        "00003c",
+        "00003d",
+        "00003e",
+        "00004e",
+        "00005a",
+        "00005b",
+        "00005c",
+        "00005d",
+    ]
+
+    # Check removal of duplicates and sorting
+    tar_list = parse_tars_option("000009,000003,-000005", "000000", "00005d")
+    assert tar_list == [
+        "000000",
+        "000001",
+        "000002",
+        "000003",
+        "000004",
+        "000005",
+        "000009",
+    ]
+
+    # Remove .tar suffix
+    tar_list = parse_tars_option(
+        "000009.tar-00000a,000003.tar,-000002.tar", "000000", "00005d"
+    )
+    assert tar_list == ["000000", "000001", "000002", "000003", "000009", "00000a"]