From cc2173b80606ffbb7bf017fcc57c0efc081bb8e7 Mon Sep 17 00:00:00 2001
From: Adam Nichols <aednichols@gmail.com>
Date: Mon, 4 Dec 2023 22:19:39 -0500
Subject: [PATCH 01/13] Is this faster?

---
 .../lots_of_inputs/lots_of_inputs.wdl                |  7 +++++++
 src/ci/bin/testCentaurHoricromtalPapiV2beta.sh       | 12 +++++++-----
 2 files changed, 14 insertions(+), 5 deletions(-)

diff --git a/centaur/src/main/resources/standardTestCases/lots_of_inputs/lots_of_inputs.wdl b/centaur/src/main/resources/standardTestCases/lots_of_inputs/lots_of_inputs.wdl
index 73a483cb7f9..4c6e5b06ab5 100644
--- a/centaur/src/main/resources/standardTestCases/lots_of_inputs/lots_of_inputs.wdl
+++ b/centaur/src/main/resources/standardTestCases/lots_of_inputs/lots_of_inputs.wdl
@@ -7,8 +7,14 @@ task do_nothing {
   output {
     String o = read_string(stdout())
   }
+
+  # We are localizing 10,000 tiny files, so the default disk size of 10 GB SSD [0] is NOT
+  # going to cut it, having a measly IO per second rating of just 10 x 30 = 300 IOPS [1]
+  # [0] https://cromwell.readthedocs.io/en/stable/RuntimeAttributes/
+  # [1] https://cloud.google.com/compute/docs/disks/performance#zonal
   runtime {
     docker: "python:latest"
+    disks: "local-disk 1000 SSD"
   }
 }
 
@@ -28,6 +34,7 @@ task make_array {
   }
   runtime {
     docker: "python:latest"
+    disks: "local-disk 1000 SSD"
   }
 }
 
diff --git a/src/ci/bin/testCentaurHoricromtalPapiV2beta.sh b/src/ci/bin/testCentaurHoricromtalPapiV2beta.sh
index 36b215a2f52..ef01da73f3b 100755
--- a/src/ci/bin/testCentaurHoricromtalPapiV2beta.sh
+++ b/src/ci/bin/testCentaurHoricromtalPapiV2beta.sh
@@ -20,11 +20,13 @@ cromwell::build::build_cromwell_docker
 
 cromwell::build::run_centaur \
     -p 500 \
-    -e localdockertest \
-    -e relative_output_paths \
-    -e relative_output_paths_colliding \
-    -e standard_output_paths_colliding_prevented \
-    -e papi_v2alpha1_gcsa \
+    -i lots_of_inputs \
+#    -e localdockertest \
+#    -e relative_output_paths \
+#    -e relative_output_paths_colliding \
+#    -e standard_output_paths_colliding_prevented \
+#    -e papi_v2alpha1_gcsa \
+
 
 cromwell::build::generate_code_coverage
 

From 56fc2b55d5d2a9627a710aee344d854188c41b7b Mon Sep 17 00:00:00 2001
From: Adam Nichols <aednichols@gmail.com>
Date: Mon, 4 Dec 2023 23:28:24 -0500
Subject: [PATCH 02/13] Revert

---
 src/ci/bin/testCentaurHoricromtalPapiV2beta.sh | 11 +++++------
 1 file changed, 5 insertions(+), 6 deletions(-)

diff --git a/src/ci/bin/testCentaurHoricromtalPapiV2beta.sh b/src/ci/bin/testCentaurHoricromtalPapiV2beta.sh
index ef01da73f3b..84dd89ed3e6 100755
--- a/src/ci/bin/testCentaurHoricromtalPapiV2beta.sh
+++ b/src/ci/bin/testCentaurHoricromtalPapiV2beta.sh
@@ -20,12 +20,11 @@ cromwell::build::build_cromwell_docker
 
 cromwell::build::run_centaur \
     -p 500 \
-    -i lots_of_inputs \
-#    -e localdockertest \
-#    -e relative_output_paths \
-#    -e relative_output_paths_colliding \
-#    -e standard_output_paths_colliding_prevented \
-#    -e papi_v2alpha1_gcsa \
+    -e localdockertest \
+    -e relative_output_paths \
+    -e relative_output_paths_colliding \
+    -e standard_output_paths_colliding_prevented \
+    -e papi_v2alpha1_gcsa \
 
 
 cromwell::build::generate_code_coverage

From c650c0a596f40de7fd6bf3efb78c96958ec6574d Mon Sep 17 00:00:00 2001
From: Adam Nichols <aednichols@gmail.com>
Date: Mon, 4 Dec 2023 23:28:55 -0500
Subject: [PATCH 03/13] Oh come on

---
 src/ci/bin/testCentaurHoricromtalPapiV2beta.sh | 1 -
 1 file changed, 1 deletion(-)

diff --git a/src/ci/bin/testCentaurHoricromtalPapiV2beta.sh b/src/ci/bin/testCentaurHoricromtalPapiV2beta.sh
index 84dd89ed3e6..36b215a2f52 100755
--- a/src/ci/bin/testCentaurHoricromtalPapiV2beta.sh
+++ b/src/ci/bin/testCentaurHoricromtalPapiV2beta.sh
@@ -26,7 +26,6 @@ cromwell::build::run_centaur \
     -e standard_output_paths_colliding_prevented \
     -e papi_v2alpha1_gcsa \
 
-
 cromwell::build::generate_code_coverage
 
 cromwell::build::print_workflow_statistics

From 0131686b34c8d90b75e13aed97df7de982ad551b Mon Sep 17 00:00:00 2001
From: Adam Nichols <aednichols@gmail.com>
Date: Tue, 5 Dec 2023 16:03:30 -0500
Subject: [PATCH 04/13] Exclude not-that-many inputs

---
 src/ci/bin/testCentaurHoricromtalPapiV2beta.sh | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/src/ci/bin/testCentaurHoricromtalPapiV2beta.sh b/src/ci/bin/testCentaurHoricromtalPapiV2beta.sh
index 36b215a2f52..07158ecc490 100755
--- a/src/ci/bin/testCentaurHoricromtalPapiV2beta.sh
+++ b/src/ci/bin/testCentaurHoricromtalPapiV2beta.sh
@@ -25,6 +25,8 @@ cromwell::build::run_centaur \
     -e relative_output_paths_colliding \
     -e standard_output_paths_colliding_prevented \
     -e papi_v2alpha1_gcsa \
+    -e lots_of_inputs \
+    # `lots_of_inputs` is redundant to, and a less rigorous version of, `lots_of_inputs_papiv2`
 
 cromwell::build::generate_code_coverage
 

From 9b75117a46961ca0175b0b208667c7c1493acbcf Mon Sep 17 00:00:00 2001
From: Adam Nichols <aednichols@gmail.com>
Date: Tue, 5 Dec 2023 17:36:09 -0500
Subject: [PATCH 05/13] Clean up old PAPI configs

---
 .../testCentaurEngineUpgradePapiV2alpha1.sh   | 24 ------
 ...aurHoricromtalEngineUpgradePapiV2alpha1.sh | 26 ------
 .../bin/testCentaurHoricromtalPapiV2alpha1.sh | 29 -------
 ...taurPapiUpgradeNewWorkflowsPapiV2alpha1.sh |  4 -
 .../bin/testCentaurPapiUpgradePapiV2alpha1.sh |  3 -
 src/ci/bin/testCentaurPapiV2alpha1.sh         | 27 -------
 src/ci/bin/testDockerScripts.sh               | 27 -------
 src/ci/bin/testMetadataComparisonPython.sh    | 34 --------
 .../papi_v1_v2alpha1_provider_config.inc.conf | 20 -----
 .../resources/papi_v2alpha1_application.conf  | 81 -------------------
 ...v2alpha1_conformance_expected_failures.txt | 29 -------
 ...papi_v2alpha1_horicromtal_application.conf |  9 ---
 ...i_v2alpha1_v2beta_upgrade_application.conf | 32 --------
 13 files changed, 345 deletions(-)
 delete mode 100755 src/ci/bin/testCentaurEngineUpgradePapiV2alpha1.sh
 delete mode 100755 src/ci/bin/testCentaurHoricromtalEngineUpgradePapiV2alpha1.sh
 delete mode 100755 src/ci/bin/testCentaurHoricromtalPapiV2alpha1.sh
 delete mode 100755 src/ci/bin/testCentaurPapiUpgradeNewWorkflowsPapiV2alpha1.sh
 delete mode 100755 src/ci/bin/testCentaurPapiUpgradePapiV2alpha1.sh
 delete mode 100755 src/ci/bin/testCentaurPapiV2alpha1.sh
 delete mode 100755 src/ci/bin/testDockerScripts.sh
 delete mode 100755 src/ci/bin/testMetadataComparisonPython.sh
 delete mode 100644 src/ci/resources/papi_v1_v2alpha1_provider_config.inc.conf
 delete mode 100644 src/ci/resources/papi_v2alpha1_application.conf
 delete mode 100644 src/ci/resources/papi_v2alpha1_conformance_expected_failures.txt
 delete mode 100644 src/ci/resources/papi_v2alpha1_horicromtal_application.conf
 delete mode 100644 src/ci/resources/papi_v2alpha1_v2beta_upgrade_application.conf

diff --git a/src/ci/bin/testCentaurEngineUpgradePapiV2alpha1.sh b/src/ci/bin/testCentaurEngineUpgradePapiV2alpha1.sh
deleted file mode 100755
index 7a471ce9e34..00000000000
--- a/src/ci/bin/testCentaurEngineUpgradePapiV2alpha1.sh
+++ /dev/null
@@ -1,24 +0,0 @@
-#!/usr/bin/env bash
-
-set -o errexit -o nounset -o pipefail
-export CROMWELL_BUILD_REQUIRES_SECURE=true
-export CROMWELL_BUILD_REQUIRES_PRIOR_VERSION=true
-# import in shellcheck / CI / IntelliJ compatible ways
-# shellcheck source=/dev/null
-source "${BASH_SOURCE%/*}/test.inc.sh" || source test.inc.sh
-# shellcheck source=/dev/null
-source "${BASH_SOURCE%/*}/test_papi.inc.sh" || source test_papi.inc.sh
-
-cromwell::build::setup_common_environment
-
-cromwell::build::setup_centaur_environment
-
-cromwell::build::papi::setup_papi_centaur_environment
-
-cromwell::build::assemble_jars
-
-cromwell::build::run_centaur \
-    -s "centaur.EngineUpgradeTestCaseSpec" \
-    -e localdockertest \
-
-cromwell::build::generate_code_coverage
diff --git a/src/ci/bin/testCentaurHoricromtalEngineUpgradePapiV2alpha1.sh b/src/ci/bin/testCentaurHoricromtalEngineUpgradePapiV2alpha1.sh
deleted file mode 100755
index f4050548f38..00000000000
--- a/src/ci/bin/testCentaurHoricromtalEngineUpgradePapiV2alpha1.sh
+++ /dev/null
@@ -1,26 +0,0 @@
-#!/usr/bin/env bash
-
-set -o errexit -o nounset -o pipefail
-export CROMWELL_BUILD_REQUIRES_SECURE=true
-export CROMWELL_BUILD_REQUIRES_PRIOR_VERSION=true
-# import in shellcheck / CI / IntelliJ compatible ways
-# shellcheck source=/dev/null
-source "${BASH_SOURCE%/*}/test.inc.sh" || source test.inc.sh
-# shellcheck source=/dev/null
-source "${BASH_SOURCE%/*}/test_papi.inc.sh" || source test_papi.inc.sh
-
-cromwell::build::setup_common_environment
-
-cromwell::build::setup_centaur_environment
-
-cromwell::build::papi::setup_papi_centaur_environment
-
-cromwell::build::assemble_jars
-
-cromwell::build::build_cromwell_docker
-
-cromwell::build::run_centaur \
-    -s "centaur.EngineUpgradeTestCaseSpec" \
-    -e localdockertest
-
-cromwell::build::generate_code_coverage
diff --git a/src/ci/bin/testCentaurHoricromtalPapiV2alpha1.sh b/src/ci/bin/testCentaurHoricromtalPapiV2alpha1.sh
deleted file mode 100755
index 3e8453c9d83..00000000000
--- a/src/ci/bin/testCentaurHoricromtalPapiV2alpha1.sh
+++ /dev/null
@@ -1,29 +0,0 @@
-#!/usr/bin/env bash
-
-set -o errexit -o nounset -o pipefail
-export CROMWELL_BUILD_REQUIRES_SECURE=true
-# import in shellcheck / CI / IntelliJ compatible ways
-# shellcheck source=/dev/null
-source "${BASH_SOURCE%/*}/test.inc.sh" || source test.inc.sh
-# shellcheck source=/dev/null
-source "${BASH_SOURCE%/*}/test_papi.inc.sh" || source test_papi.inc.sh
-
-cromwell::build::setup_common_environment
-
-cromwell::build::setup_centaur_environment
-
-cromwell::build::papi::setup_papi_centaur_environment
-
-cromwell::build::assemble_jars
-
-cromwell::build::build_cromwell_docker
-
-cromwell::build::run_centaur \
-    -p 100 \
-    -e localdockertest \
-    -e relative_output_paths \
-    -e relative_output_paths_colliding \
-    -e standard_output_paths_colliding_prevented \
-    -e papi_v2beta_gcsa \
-
-cromwell::build::generate_code_coverage
diff --git a/src/ci/bin/testCentaurPapiUpgradeNewWorkflowsPapiV2alpha1.sh b/src/ci/bin/testCentaurPapiUpgradeNewWorkflowsPapiV2alpha1.sh
deleted file mode 100755
index 5b5ffe0ddc3..00000000000
--- a/src/ci/bin/testCentaurPapiUpgradeNewWorkflowsPapiV2alpha1.sh
+++ /dev/null
@@ -1,4 +0,0 @@
-#!/usr/bin/env bash
-
-echo "$(tput setab 1)$(tput blink)BT-81: This sub-build was doing no useful work; it built Cromwell and launched Centaur but never found tests to run. However, tests for functionality implied by this sub-build's name may be desirable, see BT-81 for further information.$(tput sgr 0)"
-exit 0
diff --git a/src/ci/bin/testCentaurPapiUpgradePapiV2alpha1.sh b/src/ci/bin/testCentaurPapiUpgradePapiV2alpha1.sh
deleted file mode 100755
index 8c46a8223e7..00000000000
--- a/src/ci/bin/testCentaurPapiUpgradePapiV2alpha1.sh
+++ /dev/null
@@ -1,3 +0,0 @@
-#!/usr/bin/env bash
-
-echo "$(tput setab 1)$(tput blink)BT-81: This sub-build was doing no useful work; it built Cromwell and launched Centaur but never found tests to run. However, tests for functionality implied by this sub-build's name may be desirable, see BT-81 for further information.$(tput sgr 0)"exit 0
diff --git a/src/ci/bin/testCentaurPapiV2alpha1.sh b/src/ci/bin/testCentaurPapiV2alpha1.sh
deleted file mode 100755
index 706d13c0acb..00000000000
--- a/src/ci/bin/testCentaurPapiV2alpha1.sh
+++ /dev/null
@@ -1,27 +0,0 @@
-#!/usr/bin/env bash
-
-set -o errexit -o nounset -o pipefail
-export CROMWELL_BUILD_REQUIRES_SECURE=true
-# import in shellcheck / CI / IntelliJ compatible ways
-# shellcheck source=/dev/null
-source "${BASH_SOURCE%/*}/test.inc.sh" || source test.inc.sh
-# shellcheck source=/dev/null
-source "${BASH_SOURCE%/*}/test_papi.inc.sh" || source test_papi.inc.sh
-
-cromwell::build::setup_common_environment
-
-cromwell::build::setup_centaur_environment
-
-cromwell::build::papi::setup_papi_centaur_environment
-
-cromwell::build::assemble_jars
-
-cromwell::build::run_centaur \
-    -p 100 \
-    -e localdockertest \
-    -e relative_output_paths \
-    -e relative_output_paths_colliding \
-    -e standard_output_paths_colliding_prevented \
-    -e papi_v2beta_gcsa \
-
-cromwell::build::generate_code_coverage
diff --git a/src/ci/bin/testDockerScripts.sh b/src/ci/bin/testDockerScripts.sh
deleted file mode 100755
index e9f670bba54..00000000000
--- a/src/ci/bin/testDockerScripts.sh
+++ /dev/null
@@ -1,27 +0,0 @@
-#!/usr/bin/env bash
-
-set -o errexit -o nounset -o pipefail
-# import in shellcheck / CI / IntelliJ compatible ways
-# shellcheck source=/dev/null
-source "${BASH_SOURCE%/*}/test.inc.sh" || source test.inc.sh
-
-cromwell::build::setup_common_environment
-
-# When running locally, an `ADD .` in the Dockerfile might pull in files the local developer does not expect.
-# Until there is further review of what goes into the docker image (ex: rendered vault secrets!) do not push it yet.
-docker_tag="broadinstitute/cromwell-docker-develop:test-only-do-not-push"
-
-docker build -t "${docker_tag}" scripts/docker-develop
-
-echo "What tests would you like, my dear McMuffins?"
-
-echo "1. Testing for install of sbt"
-docker run --rm "${docker_tag}" which sbt
-
-echo "2. Testing sbt assembly"
-docker run \
-    --rm \
-    --volume "${CROMWELL_BUILD_ROOT_DIRECTORY}:${CROMWELL_BUILD_ROOT_DIRECTORY}" \
-    --workdir "${CROMWELL_BUILD_ROOT_DIRECTORY}" \
-    "${docker_tag}" \
-    sbt -Dsbt.supershell=false --warn assembly
diff --git a/src/ci/bin/testMetadataComparisonPython.sh b/src/ci/bin/testMetadataComparisonPython.sh
deleted file mode 100755
index f12b9ee5fe7..00000000000
--- a/src/ci/bin/testMetadataComparisonPython.sh
+++ /dev/null
@@ -1,34 +0,0 @@
-#!/usr/bin/env bash
-
-set -o errexit -o nounset -o pipefail
-
-export CROMWELL_BUILD_REQUIRES_SECURE=true
-
-# import in shellcheck / CI / IntelliJ compatible ways
-# shellcheck source=/dev/null
-source "${BASH_SOURCE%/*}/test.inc.sh" || source test.inc.sh
-
-cromwell::build::setup_common_environment
-
-# Our Python scripts can only be run by Python version >= 3.6, because we use string interpolation which was introduced
-# in Python 3.6. But Travis environment is Ubuntu 16.04 Xenial LTS, which officially supports only Python <= 3.5.
-# Thus we have to run Python tests in Docker container.
-GOOGLE_CENTAUR_SERVICE_ACCOUNT_JSON="cromwell-centaur-service-account.json"
-export GOOGLE_APPLICATION_CREDENTIALS="${CROMWELL_BUILD_RESOURCES_DIRECTORY}/${GOOGLE_CENTAUR_SERVICE_ACCOUNT_JSON}"
-export DIGESTER_TEST_GCS=true
-
-docker run -it --rm \
-           -e GOOGLE_APPLICATION_CREDENTIALS \
-           -e DIGESTER_TEST_GCS \
-           -v "${CROMWELL_BUILD_RESOURCES_DIRECTORY}:${CROMWELL_BUILD_RESOURCES_DIRECTORY}" \
-           -v "${CROMWELL_BUILD_ROOT_DIRECTORY}/scripts/metadata_comparison:/metadata_comparison" \
-           python:3 /bin/bash -c "
-
-pip3 install --upgrade requests
-pip3 install --upgrade google-api-python-client
-pip3 install --upgrade google-cloud
-pip3 install --upgrade google-cloud-storage
-pip3 install --upgrade gitpython
-pip3 install --upgrade python-dateutil
-python3 -m unittest discover -v /metadata_comparison
-"
diff --git a/src/ci/resources/papi_v1_v2alpha1_provider_config.inc.conf b/src/ci/resources/papi_v1_v2alpha1_provider_config.inc.conf
deleted file mode 100644
index 4b786c6ec2c..00000000000
--- a/src/ci/resources/papi_v1_v2alpha1_provider_config.inc.conf
+++ /dev/null
@@ -1,20 +0,0 @@
-project = "broad-dsde-cromwell-dev"
-root = "gs://cloud-cromwell-dev-self-cleaning/cromwell_execution/ci"
-maximum-polling-interval = 600
-concurrent-job-limit = 1000
-
-genomics {
-  auth = "service_account"
-  endpoint-url = "https://genomics.googleapis.com/"
-}
-
-filesystems {
-  gcs {
-    auth = "service_account"
-    project = "broad-dsde-cromwell-dev"
-  }
-}
-
-slow-job-warning-time: 20 minutes
-
-checkpointing-interval: "10 seconds"
diff --git a/src/ci/resources/papi_v2alpha1_application.conf b/src/ci/resources/papi_v2alpha1_application.conf
deleted file mode 100644
index cc12d36b27d..00000000000
--- a/src/ci/resources/papi_v2alpha1_application.conf
+++ /dev/null
@@ -1,81 +0,0 @@
-include "papi_v2_shared_application.inc.conf"
-
-backend {
-  providers {
-    Papi {
-      actor-factory = "cromwell.backend.google.pipelines.v2alpha1.PipelinesApiLifecycleActorFactory"
-      config {
-        include "papi_v1_v2alpha1_provider_config.inc.conf"
-      }
-    }
-    Papiv2 {
-      actor-factory = "cromwell.backend.google.pipelines.v2alpha1.PipelinesApiLifecycleActorFactory"
-      config {
-        include "papi_v1_v2alpha1_provider_config.inc.conf"
-      }
-    }
-    Papiv2USADockerhub {
-      actor-factory = "cromwell.backend.google.pipelines.v2alpha1.PipelinesApiLifecycleActorFactory"
-      config {
-        include "papi_v1_v2alpha1_provider_config.inc.conf"
-      }
-    }
-    Papiv2NoDockerHubConfig {
-      actor-factory = "cromwell.backend.google.pipelines.v2alpha1.PipelinesApiLifecycleActorFactory"
-      config {
-        include "papi_v1_v2alpha1_provider_config.inc.conf"
-      }
-    }
-    Papiv2RequesterPays {
-      actor-factory = "cromwell.backend.google.pipelines.v2alpha1.PipelinesApiLifecycleActorFactory"
-      config {
-        include "papi_v1_v2alpha1_provider_config.inc.conf"
-
-        # Need this again (even though it's in the "papiv2_shared" file because the provider_config include overrides it.
-        filesystems.gcs.auth = "requester_pays_service_account"
-      }
-    }
-    Papi-Caching-No-Copy {
-      actor-factory = "cromwell.backend.google.pipelines.v2alpha1.PipelinesApiLifecycleActorFactory"
-      config {
-        include "papi_v1_v2alpha1_provider_config.inc.conf"
-      }
-    }
-    Papiv2-Virtual-Private-Cloud-Labels {
-      actor-factory = "cromwell.backend.google.pipelines.v2alpha1.PipelinesApiLifecycleActorFactory"
-      config {
-        include "papi_v1_v2alpha1_provider_config.inc.conf"
-      }
-    }
-    Papiv2-Virtual-Private-Cloud-Literals {
-      actor-factory = "cromwell.backend.google.pipelines.v2alpha1.PipelinesApiLifecycleActorFactory"
-      config {
-        include "papi_v1_v2alpha1_provider_config.inc.conf"
-      }
-    }
-    papi-v2-gcsa {
-      actor-factory = "cromwell.backend.google.pipelines.v2alpha1.PipelinesApiLifecycleActorFactory"
-      config {
-        include "papi_v1_v2alpha1_provider_config.inc.conf"
-      }
-    }
-    papi-v2-usa {
-      actor-factory = "cromwell.backend.google.pipelines.v2alpha1.PipelinesApiLifecycleActorFactory"
-      config {
-        include "papi_v1_v2alpha1_provider_config.inc.conf"
-      }
-    }
-    Papiv2ParallelCompositeUploads {
-      actor-factory = "cromwell.backend.google.pipelines.v2alpha1.PipelinesApiLifecycleActorFactory"
-      config {
-        include "papi_v1_v2alpha1_provider_config.inc.conf"
-      }
-    }
-    Papiv2-Reference-Disk-Localization {
-      actor-factory = "cromwell.backend.google.pipelines.v2beta.PipelinesApiLifecycleActorFactory"
-      config {
-        include "papi_v2beta_provider_config.inc.conf"
-      }
-    }
-  }
-}
diff --git a/src/ci/resources/papi_v2alpha1_conformance_expected_failures.txt b/src/ci/resources/papi_v2alpha1_conformance_expected_failures.txt
deleted file mode 100644
index 4caa25c75a6..00000000000
--- a/src/ci/resources/papi_v2alpha1_conformance_expected_failures.txt
+++ /dev/null
@@ -1,29 +0,0 @@
-86
-87
-101
-102
-104
-107
-136
-137
-140
-142
-152
-153
-154
-156
-158
-159
-160
-161
-163
-164
-165
-166
-170
-171
-173
-189
-190
-191
-196
diff --git a/src/ci/resources/papi_v2alpha1_horicromtal_application.conf b/src/ci/resources/papi_v2alpha1_horicromtal_application.conf
deleted file mode 100644
index dacfbd63877..00000000000
--- a/src/ci/resources/papi_v2alpha1_horicromtal_application.conf
+++ /dev/null
@@ -1,9 +0,0 @@
-include "papi_v2alpha1_application.conf"
-
-system.max-workflow-launch-count=1
-system.new-workflow-poll-rate=10
-system.max-concurrent-workflows=30
-system.cromwell_id_random_suffix=false
-
-# Turn off token logging to reduce log volume
-system.hog-safety.token-log-interval-seconds = 0
diff --git a/src/ci/resources/papi_v2alpha1_v2beta_upgrade_application.conf b/src/ci/resources/papi_v2alpha1_v2beta_upgrade_application.conf
deleted file mode 100644
index 6059508a592..00000000000
--- a/src/ci/resources/papi_v2alpha1_v2beta_upgrade_application.conf
+++ /dev/null
@@ -1,32 +0,0 @@
-include required(classpath("application.conf"))
-include "build_application.inc.conf"
-include "papi_application.inc.conf"
-
-# We now have two types of PAPI backend to monitor:
-services.HealthMonitor.config.check-papi-backends: [ Papiv2alpha1, Papiv2beta ]
-
-backend {
-  default = "Papiv2alpha1"
-  enabled = ["Papiv2alpha1", "Papiv2beta"]
-  providers {
-    # Pre-existing PAPI v2alpha1 backend
-    Papiv2alpha1 {
-      actor-factory = "cromwell.backend.google.pipelines.v2alpha1.PipelinesApiLifecycleActorFactory"
-      config {
-        include "papi_v1_v2alpha1_provider_config.inc.conf"
-        include "dockerhub_provider_config_v2.inc.conf"
-        genomics.compute-service-account = "centaur@broad-dsde-cromwell-dev.iam.gserviceaccount.com"
-        name-for-call-caching-purposes = "Papi"
-      }
-    }
-    Papiv2beta {
-      actor-factory = "cromwell.backend.google.pipelines.v2beta.PipelinesApiLifecycleActorFactory"
-      config {
-        include "papi_v2beta_provider_config.inc.conf"
-        include "dockerhub_provider_config_v2.inc.conf"
-        genomics.compute-service-account = "centaur@broad-dsde-cromwell-dev.iam.gserviceaccount.com"
-        name-for-call-caching-purposes = "Papi"
-      }
-    }
-  }
-}

From a249b005b76528e355fbada6835a7e26b92c3233 Mon Sep 17 00:00:00 2001
From: Adam Nichols <aednichols@gmail.com>
Date: Tue, 5 Dec 2023 18:16:20 -0500
Subject: [PATCH 06/13] Fix

---
 src/ci/bin/testCentaurPapiV2beta.sh | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/src/ci/bin/testCentaurPapiV2beta.sh b/src/ci/bin/testCentaurPapiV2beta.sh
index 43d5a7d62aa..c349c7d0537 100755
--- a/src/ci/bin/testCentaurPapiV2beta.sh
+++ b/src/ci/bin/testCentaurPapiV2beta.sh
@@ -23,6 +23,8 @@ cromwell::build::run_centaur \
     -e relative_output_paths_colliding \
     -e standard_output_paths_colliding_prevented \
     -e papi_v2alpha1_gcsa \
+    -e lots_of_inputs \
+    # `lots_of_inputs` is redundant to, and a less rigorous version of, `lots_of_inputs_papiv2`
 
 cromwell::build::generate_code_coverage
 

From cb45489e48a6d6fbdc30533aa4642dbf5f2972d0 Mon Sep 17 00:00:00 2001
From: Adam Nichols <aednichols@gmail.com>
Date: Tue, 5 Dec 2023 20:00:26 -0500
Subject: [PATCH 07/13] Undo changes that didn't help

---
 .../standardTestCases/lots_of_inputs/lots_of_inputs.wdl    | 7 -------
 1 file changed, 7 deletions(-)

diff --git a/centaur/src/main/resources/standardTestCases/lots_of_inputs/lots_of_inputs.wdl b/centaur/src/main/resources/standardTestCases/lots_of_inputs/lots_of_inputs.wdl
index 4c6e5b06ab5..73a483cb7f9 100644
--- a/centaur/src/main/resources/standardTestCases/lots_of_inputs/lots_of_inputs.wdl
+++ b/centaur/src/main/resources/standardTestCases/lots_of_inputs/lots_of_inputs.wdl
@@ -7,14 +7,8 @@ task do_nothing {
   output {
     String o = read_string(stdout())
   }
-
-  # We are localizing 10,000 tiny files, so the default disk size of 10 GB SSD [0] is NOT
-  # going to cut it, having a measly IO per second rating of just 10 x 30 = 300 IOPS [1]
-  # [0] https://cromwell.readthedocs.io/en/stable/RuntimeAttributes/
-  # [1] https://cloud.google.com/compute/docs/disks/performance#zonal
   runtime {
     docker: "python:latest"
-    disks: "local-disk 1000 SSD"
   }
 }
 
@@ -34,7 +28,6 @@ task make_array {
   }
   runtime {
     docker: "python:latest"
-    disks: "local-disk 1000 SSD"
   }
 }
 

From d3583bb9bbbc7db6e6dc84f8dc4a2a410c7b75f1 Mon Sep 17 00:00:00 2001
From: Adam Nichols <aednichols@gmail.com>
Date: Wed, 6 Dec 2023 10:05:34 -0500
Subject: [PATCH 08/13] Cleanup

---
 src/ci/bin/test.inc.sh | 287 +----------------------------------------
 1 file changed, 4 insertions(+), 283 deletions(-)

diff --git a/src/ci/bin/test.inc.sh b/src/ci/bin/test.inc.sh
index 6f76ee8c05c..4833212d31b 100755
--- a/src/ci/bin/test.inc.sh
+++ b/src/ci/bin/test.inc.sh
@@ -45,50 +45,13 @@ cromwell::private::check_debug() {
     fi
 }
 
-cromwell::private::set_variable_if_only_some_files_changed() {
-  files_changed_regex=${1}
-  variable_to_set=${2}
-
-    if [[ "${TRAVIS_EVENT_TYPE:-unset}" != "pull_request" ]]; then
-        export "${variable_to_set}=false"
-    else
-      # Large changesets seem to trigger the situation described in [1] where a `git diff` pipelined to `grep` can cause
-      # `grep` to exit 0 on the first match while `git diff` is still writing to the pipe. When this happens `git diff`
-      # is killed with a SIGPIPE and exits with code 141. With `set -o pipefail` this causes the entire pipeline to exit
-      # with code 141, which sets `$variable_to_set` to `true` when it probably should have been set to `false`.
-      #
-      # Instead of composing these commands into a pipeline write to a temporary file.
-      #
-      # [1] https://stackoverflow.com/a/19120674
-      # [2] https://gist.github.com/mohanpedala/1e2ff5661761d3abd0385e8223e16425#set--o-pipefail
-
-      files_changed_temporary_file=$(mktemp)
-
-      git diff --name-only "origin/${TRAVIS_BRANCH}" > "${files_changed_temporary_file}" 2>&1 && \
-          grep -E -q --invert-match "${files_changed_regex}" "${files_changed_temporary_file}"
-      RESULT=$?
-
-      if [[ $RESULT -eq 0 ]]; then
-        export "${variable_to_set}=false"
-      else
-        export "${variable_to_set}=true"
-      fi
-
-      rm "${files_changed_temporary_file}"
-    fi
-}
-
 # Exports environment variables used for scripts.
 cromwell::private::create_build_variables() {
-    CROMWELL_BUILD_PROVIDER_TRAVIS="travis"
     CROMWELL_BUILD_PROVIDER_JENKINS="jenkins"
-    CROMWELL_BUILD_PROVIDER_CIRCLE="circle"
     CROMWELL_BUILD_PROVIDER_GITHUB="github"
     CROMWELL_BUILD_PROVIDER_UNKNOWN="unknown"
 
-    if [[ "${TRAVIS-false}" == "true" ]]; then
-        CROMWELL_BUILD_PROVIDER="${CROMWELL_BUILD_PROVIDER_TRAVIS}"
-    elif [[ "${JENKINS-false}" == "true" ]]; then
+    if [[ "${JENKINS-false}" == "true" ]]; then
         CROMWELL_BUILD_PROVIDER="${CROMWELL_BUILD_PROVIDER_JENKINS}"
     elif [[ "${CIRCLECI-false}" == "true" ]]; then
         CROMWELL_BUILD_PROVIDER="${CROMWELL_BUILD_PROVIDER_CIRCLE}"
@@ -157,76 +120,14 @@ cromwell::private::create_build_variables() {
         CROMWELL_BUILD_GIT_HASH_SUFFIX="gUNKNOWN"
     fi
 
-    # Value of the `TRAVIS_BRANCH` variable depends on type of Travis build: if it is pull request build, the value
-    # will be the name of the branch targeted by the pull request, and for push builds it will be the name of the
-    # branch. So, in case of push builds `git diff` will always return empty result. This is why we only use this short
-    # circuiting logic for pull request builds
-
     # PR #6790 disabled the conditional that skips tests for documentation-only PRs, because
     # those PRs (and only those PRs) were uniformly failing tests with a nondescript error.
     # https://broadinstitute.slack.com/archives/GHYJZ2ZE0/p1656625952888149?thread_ts=1656620572.975059&cid=GHYJZ2ZE0
 
     case "${CROMWELL_BUILD_PROVIDER}" in
-        "${CROMWELL_BUILD_PROVIDER_TRAVIS}")
-            CROMWELL_BUILD_IS_CI=true
-            CROMWELL_BUILD_IS_SECURE="${TRAVIS_SECURE_ENV_VARS}"
-
-            CROMWELL_BUILD_TYPE="${BUILD_TYPE}"
-            CROMWELL_BUILD_BRANCH="${TRAVIS_PULL_REQUEST_BRANCH:-${TRAVIS_BRANCH}}"
-            CROMWELL_BUILD_EVENT="${TRAVIS_EVENT_TYPE}"
-            CROMWELL_BUILD_TAG="${TRAVIS_TAG}"
-            CROMWELL_BUILD_NUMBER="${TRAVIS_JOB_NUMBER}"
-            CROMWELL_BUILD_URL="https://travis-ci.com/${TRAVIS_REPO_SLUG}/jobs/${TRAVIS_JOB_ID}"
-            CROMWELL_BUILD_GIT_USER_EMAIL="travis@travis-ci.com"
-            CROMWELL_BUILD_GIT_USER_NAME="Travis CI"
-            CROMWELL_BUILD_HEARTBEAT_PATTERN="…"
-            CROMWELL_BUILD_GENERATE_COVERAGE=true
-
-            local travis_commit_message
-            local travis_force_tests
-            local travis_minimal_tests
-            if [[ -n "${TRAVIS_COMMIT_RANGE:+set}" ]]; then
-                # The commit message to analyze should be the last one in the commit range.
-                # This works for both pull_request and push builds, unlike using 'git log HEAD' which
-                # gives a merge commit message on pull requests.
-                travis_commit_message="$(git log --reverse "${TRAVIS_COMMIT_RANGE}" | tail -n1 2>/dev/null || true)"
-            fi
-
-            if [[ -z "${travis_commit_message:-}" ]]; then
-                travis_commit_message="$(git log --format=%B --max-count=1 HEAD 2>/dev/null || true)"
-            fi
-
-            if [[ "${travis_commit_message}" == *"[force ci]"* ]]; then
-                travis_force_tests=true
-                travis_minimal_tests=false
-            elif [[ "${travis_commit_message}" == *"[minimal ci]"* ]]; then
-                travis_force_tests=false
-                travis_minimal_tests=true
-            else
-                travis_force_tests=false
-                travis_minimal_tests=false
-            fi
-
-            echo "Building for commit message='${travis_commit_message}' with force=${travis_force_tests} and minimal=${travis_minimal_tests}"
-
-            # For solely documentation updates run only checkPublish. Otherwise always run sbt, even for 'push'.
-            # This allows quick sanity checks before starting PRs *and* publishing after merges into develop.
-            if [[ "${travis_force_tests}" == "true" ]]; then
-                CROMWELL_BUILD_RUN_TESTS=true
-            elif [[ "${travis_minimal_tests}" == "true" ]] && \
-                [[ "${TRAVIS_EVENT_TYPE}" != "push" ]]; then
-                CROMWELL_BUILD_RUN_TESTS=false
-            elif [[ "${TRAVIS_EVENT_TYPE}" == "push" ]] && \
-                [[ "${BUILD_TYPE}" != "sbt" ]]; then
-                CROMWELL_BUILD_RUN_TESTS=false
-            else
-                CROMWELL_BUILD_RUN_TESTS=true
-            fi
-            ;;
         "${CROMWELL_BUILD_PROVIDER_JENKINS}")
             # External variables must be passed through in the ENVIRONMENT of src/ci/docker-compose/docker-compose.yml
             CROMWELL_BUILD_IS_CI=true
-            CROMWELL_BUILD_IS_SECURE=true
             CROMWELL_BUILD_TYPE="${JENKINS_BUILD_TYPE}"
             CROMWELL_BUILD_BRANCH="${GIT_BRANCH#origin/}"
             CROMWELL_BUILD_EVENT=""
@@ -239,73 +140,8 @@ cromwell::private::create_build_variables() {
             CROMWELL_BUILD_GENERATE_COVERAGE=false
             CROMWELL_BUILD_RUN_TESTS=true
             ;;
-        "${CROMWELL_BUILD_PROVIDER_CIRCLE}")
-            CROMWELL_BUILD_IS_CI=true
-            CROMWELL_BUILD_TYPE="${BUILD_TYPE}"
-            CROMWELL_BUILD_NUMBER="${CIRCLE_BUILD_NUM}"
-            CROMWELL_BUILD_URL="${CIRCLE_BUILD_URL}"
-            CROMWELL_BUILD_GIT_USER_EMAIL="builds@circleci.com"
-            CROMWELL_BUILD_GIT_USER_NAME="CircleCI"
-            CROMWELL_BUILD_HEARTBEAT_PATTERN="…"
-            CROMWELL_BUILD_GENERATE_COVERAGE=true
-            CROMWELL_BUILD_BRANCH="${CIRCLE_BRANCH:-${CIRCLE_TAG}}"
-            CROMWELL_BUILD_TAG="${CIRCLE_TAG:-}"
-
-            local circle_github_repository
-            circle_github_repository="${CIRCLE_PROJECT_USERNAME}/${CIRCLE_PROJECT_REPONAME}"
-
-            if [[ "${circle_github_repository}" == "broadinstitute/cromwell" ]]; then
-                CROMWELL_BUILD_IS_SECURE=true
-            else
-                CROMWELL_BUILD_IS_SECURE=false
-            fi
-
-            CROMWELL_BUILD_EVENT="pull_request"
-
-            local circle_commit_message
-            local circle_force_tests
-            local circle_minimal_tests
-            if [[ -n "${CIRCLE_COMMIT_RANGE:+set}" ]]; then
-                # The commit message to analyze should be the last one in the commit range.
-                # This works for both pull_request and push builds, unlike using 'git log HEAD' which
-                # gives a merge commit message on pull requests.
-                circle_commit_message="$(git log --reverse "${CIRCLE_COMMIT_RANGE}" | tail -n1 2>/dev/null || true)"
-            fi
-
-            if [[ -z "${circle_commit_message:-}" ]]; then
-                circle_commit_message="$(git log --format=%B --max-count=1 HEAD 2>/dev/null || true)"
-            fi
-
-            if [[ "${circle_commit_message}" == *"[force ci]"* ]]; then
-                circle_force_tests=true
-                circle_minimal_tests=false
-            elif [[ "${circle_commit_message}" == *"[minimal ci]"* ]]; then
-                circle_force_tests=false
-                circle_minimal_tests=true
-            else
-                circle_force_tests=false
-                circle_minimal_tests=false
-            fi
-
-            echo "Building for commit message='${circle_commit_message}' with force=${circle_force_tests} and minimal=${circle_minimal_tests}"
-
-            # For solely documentation updates run only checkPublish. Otherwise always run sbt, even for 'push'.
-            # This allows quick sanity checks before starting PRs *and* publishing after merges into develop.
-            if [[ "${circle_force_tests}" == "true" ]]; then
-                CROMWELL_BUILD_RUN_TESTS=true
-            elif [[ "${circle_minimal_tests}" == "true" ]] && \
-                [[ "${CROMWELL_BUILD_EVENT}" != "push" ]]; then
-                CROMWELL_BUILD_RUN_TESTS=false
-            elif [[ "${CROMWELL_BUILD_EVENT}" == "push" ]] && \
-                [[ "${BUILD_TYPE}" != "sbt" ]]; then
-                CROMWELL_BUILD_RUN_TESTS=false
-            else
-                CROMWELL_BUILD_RUN_TESTS=true
-            fi
-            ;;
         "${CROMWELL_BUILD_PROVIDER_GITHUB}")
             CROMWELL_BUILD_IS_CI=true
-            CROMWELL_BUILD_IS_SECURE=true
             CROMWELL_BUILD_TYPE="${BUILD_TYPE}"
             CROMWELL_BUILD_BRANCH="${GITHUB_REF_NAME}"
             CROMWELL_BUILD_EVENT="${GITHUB_EVENT_NAME}"
@@ -320,7 +156,6 @@ cromwell::private::create_build_variables() {
             ;;
         *)
             CROMWELL_BUILD_IS_CI=false
-            CROMWELL_BUILD_IS_SECURE=true
             CROMWELL_BUILD_TYPE="unknown"
             CROMWELL_BUILD_BRANCH="unknown"
             CROMWELL_BUILD_EVENT="unknown"
@@ -371,21 +206,9 @@ cromwell::private::create_build_variables() {
     CROMWELL_BUILD_SBT_EXCLUDE="${BUILD_SBT_EXCLUDE:-}"
 
     case "${CROMWELL_BUILD_TYPE}" in
-        centaurPapiUpgradePapiV2alpha1*)
-            CROMWELL_BUILD_CROMWELL_CONFIG="${CROMWELL_BUILD_RESOURCES_DIRECTORY}/papi_v2alpha1_v2beta_upgrade_application.conf"
-            ;;
-        centaurPapiUpgradeNewWorkflowsPapiV2alpha1*)
-            CROMWELL_BUILD_CROMWELL_CONFIG="${CROMWELL_BUILD_RESOURCES_DIRECTORY}/papi_v2alpha1_v2beta_upgrade_application.conf"
-            ;;
-        centaurHoricromtalPapiV2alpha1*)
-            CROMWELL_BUILD_CROMWELL_CONFIG="${CROMWELL_BUILD_RESOURCES_DIRECTORY}/papi_v2alpha1_horicromtal_application.conf"
-            ;;
         centaurHoricromtalPapiV2beta*)
             CROMWELL_BUILD_CROMWELL_CONFIG="${CROMWELL_BUILD_RESOURCES_DIRECTORY}/papi_v2beta_horicromtal_application.conf"
             ;;
-        centaurHoricromtalEngineUpgrade*)
-            CROMWELL_BUILD_CROMWELL_CONFIG="${CROMWELL_BUILD_RESOURCES_DIRECTORY}/papi_v2alpha1_horicromtal_application.conf"
-            ;;
         centaurBlob*)
             CROMWELL_BUILD_CROMWELL_CONFIG="${CROMWELL_BUILD_RESOURCES_DIRECTORY}/centaur_blob_test.conf"
             ;;
@@ -405,7 +228,6 @@ cromwell::private::create_build_variables() {
     CROMWELL_BUILD_DOCKER_TAG="${CROMWELL_BUILD_DOCKER_TAG:0:128}"
     CROMWELL_BUILD_DOCKER_TAG="${CROMWELL_BUILD_DOCKER_TAG//[^a-zA-Z0-9.-]/_}"
 
-    CROMWELL_BUILD_REQUIRES_SECURE="${CROMWELL_BUILD_REQUIRES_SECURE-false}"
     CROMWELL_BUILD_REQUIRES_PRIOR_VERSION="${CROMWELL_BUILD_REQUIRES_PRIOR_VERSION-false}"
 
     local hours_to_minutes
@@ -432,7 +254,6 @@ cromwell::private::create_build_variables() {
     export CROMWELL_BUILD_HOME_DIRECTORY
     export CROMWELL_BUILD_IS_CI
     export CROMWELL_BUILD_IS_HOTFIX
-    export CROMWELL_BUILD_IS_SECURE
     export CROMWELL_BUILD_IS_VIRTUAL_ENV
     export CROMWELL_BUILD_LOG_DIRECTORY
     export CROMWELL_BUILD_NUMBER
@@ -441,9 +262,7 @@ cromwell::private::create_build_variables() {
     export CROMWELL_BUILD_OS_LINUX
     export CROMWELL_BUILD_PRIOR_VERSION_NUMBER
     export CROMWELL_BUILD_PROVIDER
-    export CROMWELL_BUILD_PROVIDER_CIRCLE
     export CROMWELL_BUILD_PROVIDER_JENKINS
-    export CROMWELL_BUILD_PROVIDER_TRAVIS
     export CROMWELL_BUILD_PROVIDER_UNKNOWN
     export CROMWELL_BUILD_REQUIRES_PRIOR_VERSION
     export CROMWELL_BUILD_REQUIRES_SECURE
@@ -470,8 +289,6 @@ cromwell::private::create_build_variables() {
 
 cromwell::private::echo_build_variables() {
     echo "CROMWELL_BUILD_IS_CI='${CROMWELL_BUILD_IS_CI}'"
-    echo "CROMWELL_BUILD_IS_SECURE='${CROMWELL_BUILD_IS_SECURE}'"
-    echo "CROMWELL_BUILD_REQUIRES_SECURE='${CROMWELL_BUILD_REQUIRES_SECURE}'"
     echo "CROMWELL_BUILD_TYPE='${CROMWELL_BUILD_TYPE}'"
     echo "CROMWELL_BUILD_BRANCH='${CROMWELL_BUILD_BRANCH}'"
     echo "CROMWELL_BUILD_IS_HOTFIX='${CROMWELL_BUILD_IS_HOTFIX}'"
@@ -492,8 +309,6 @@ cromwell::private::create_database_variables() {
     CROMWELL_BUILD_DATABASE_SCHEMA="cromwell_test"
 
     case "${CROMWELL_BUILD_PROVIDER}" in
-        "${CROMWELL_BUILD_PROVIDER_TRAVIS}"|\
-        "${CROMWELL_BUILD_PROVIDER_CIRCLE}"|\
         "${CROMWELL_BUILD_PROVIDER_GITHUB}")
             CROMWELL_BUILD_MARIADB_HOSTNAME="localhost"
             CROMWELL_BUILD_MARIADB_PORT="23306"
@@ -654,8 +469,6 @@ cromwell::private::create_centaur_variables() {
 
     # Pick **one** of the databases to run Centaur against
     case "${CROMWELL_BUILD_PROVIDER}" in
-        "${CROMWELL_BUILD_PROVIDER_TRAVIS}"|\
-        "${CROMWELL_BUILD_PROVIDER_CIRCLE}"|\
         "${CROMWELL_BUILD_PROVIDER_GITHUB}")
 
             if [[ -n "${CROMWELL_BUILD_MYSQL_DOCKER_TAG:+set}" ]]; then
@@ -706,19 +519,9 @@ cromwell::private::create_centaur_variables() {
             ;;
     esac
 
-    # When upgrading to the MariaDB driver, start with MySQL then switch to MariaDB.
-    if [[ "${CROMWELL_BUILD_PROVIDER}" == "${CROMWELL_BUILD_PROVIDER_TRAVIS}" ]] && \
-        [[ -n "${CROMWELL_BUILD_MARIADB_DOCKER_TAG:+set}" ]]; then
-
-        CROMWELL_BUILD_CENTAUR_PRIOR_SLICK_PROFILE="slick.jdbc.MySQLProfile$"
-        CROMWELL_BUILD_CENTAUR_PRIOR_JDBC_DRIVER="com.mysql.cj.jdbc.Driver"
-        CROMWELL_BUILD_CENTAUR_PRIOR_JDBC_URL="jdbc:mysql://${CROMWELL_BUILD_MARIADB_HOSTNAME}:${CROMWELL_BUILD_MARIADB_PORT}/${CROMWELL_BUILD_DATABASE_SCHEMA}?allowPublicKeyRetrieval=true&useSSL=false&rewriteBatchedStatements=true&serverTimezone=UTC&useInformationSchema=true"
-    else
-
-        CROMWELL_BUILD_CENTAUR_PRIOR_SLICK_PROFILE="${CROMWELL_BUILD_CENTAUR_PRIOR_SLICK_PROFILE-${CROMWELL_BUILD_CENTAUR_SLICK_PROFILE}}"
-        CROMWELL_BUILD_CENTAUR_PRIOR_JDBC_DRIVER="${CROMWELL_BUILD_CENTAUR_PRIOR_JDBC_DRIVER-${CROMWELL_BUILD_CENTAUR_JDBC_DRIVER}}"
-        CROMWELL_BUILD_CENTAUR_PRIOR_JDBC_URL="${CROMWELL_BUILD_CENTAUR_PRIOR_JDBC_URL-${CROMWELL_BUILD_CENTAUR_JDBC_URL}}"
-    fi
+    CROMWELL_BUILD_CENTAUR_PRIOR_SLICK_PROFILE="${CROMWELL_BUILD_CENTAUR_PRIOR_SLICK_PROFILE-${CROMWELL_BUILD_CENTAUR_SLICK_PROFILE}}"
+    CROMWELL_BUILD_CENTAUR_PRIOR_JDBC_DRIVER="${CROMWELL_BUILD_CENTAUR_PRIOR_JDBC_DRIVER-${CROMWELL_BUILD_CENTAUR_JDBC_DRIVER}}"
+    CROMWELL_BUILD_CENTAUR_PRIOR_JDBC_URL="${CROMWELL_BUILD_CENTAUR_PRIOR_JDBC_URL-${CROMWELL_BUILD_CENTAUR_JDBC_URL}}"
 
     CROMWELL_BUILD_CENTAUR_256_BITS_KEY="$(dd bs=1 count=32 if=/dev/urandom 2> /dev/null | base64 | tr -d '\n')"
 
@@ -743,38 +546,12 @@ cromwell::private::create_centaur_variables() {
     export CROMWELL_BUILD_DOCKER_TAG
 }
 
-cromwell::private::verify_secure_build() {
-    case "${CROMWELL_BUILD_PROVIDER}" in
-        "${CROMWELL_BUILD_PROVIDER_TRAVIS}")
-            if [[ "${CROMWELL_BUILD_IS_SECURE}" != "true" ]] && \
-                [[ "${CROMWELL_BUILD_REQUIRES_SECURE}" == "true" ]]; then
-                echo "********************************************************"
-                echo "********************************************************"
-                echo "**                                                    **"
-                echo "**  WARNING: Encrypted keys are unavailable. Exiting. **"
-                echo "**                                                    **"
-                echo "********************************************************"
-                echo "********************************************************"
-                exit 0
-            fi
-            ;;
-        *)
-            ;;
-    esac
-}
-
 cromwell::private::exec_test_script() {
     local upper_build_type
     upper_build_type="$(tr '[:lower:]' '[:upper:]' <<< "${CROMWELL_BUILD_TYPE:0:1}")${CROMWELL_BUILD_TYPE:1}"
     exec "${CROMWELL_BUILD_SCRIPTS_DIRECTORY}/test${upper_build_type}.sh"
 }
 
-cromwell::private::stop_travis_defaults() {
-  # https://stackoverflow.com/questions/27382295/how-to-stop-services-on-travis-ci-running-by-default#answer-27410479
-  sudo /etc/init.d/mysql stop || true
-  sudo /etc/init.d/postgresql stop || true
-}
-
 cromwell::private::delete_boto_config() {
     # https://github.com/travis-ci/travis-ci/issues/7940#issuecomment-310759657
     sudo rm -f /etc/boto.cfg
@@ -788,30 +565,6 @@ cromwell::private::delete_sbt_boot() {
     rm -rf ~/.sbt/boot/
 }
 
-cromwell::private::install_adoptopenjdk() {
-    # https://adoptopenjdk.net/installation.html#linux-pkg-deb
-    sudo apt-get install -y wget apt-transport-https gnupg
-    wget -qO - https://adoptopenjdk.jfrog.io/adoptopenjdk/api/gpg/key/public |
-        sudo apt-key add -
-    echo "deb https://adoptopenjdk.jfrog.io/adoptopenjdk/deb $(
-            grep UBUNTU_CODENAME /etc/os-release | cut -d = -f 2
-        ) main" |
-        sudo tee /etc/apt/sources.list.d/adoptopenjdk.list
-    sudo apt-get update
-    sudo apt-get install -y adoptopenjdk-11-hotspot
-    sudo update-java-alternatives --set adoptopenjdk-11-hotspot-amd64
-}
-
-cromwell::private::install_sbt_launcher() {
-    # Install sbt launcher
-    # Non-deb package installation instructions adapted from
-    # - https://github.com/sbt/sbt/releases/tag/v1.4.9
-    # - https://github.com/broadinstitute/scala-baseimage/pull/4/files
-    curl --location --fail --silent --show-error "https://github.com/sbt/sbt/releases/download/v1.5.5/sbt-1.5.5.tgz" |
-        sudo tar zxf - -C /usr/share
-    sudo update-alternatives --install /usr/bin/sbt sbt /usr/share/sbt/bin/sbt 1
-}
-
 cromwell::private::install_docker_compose() {
     # Install or upgrade docker-compose so that we get the correct exit codes
     # https://docs.docker.com/compose/release-notes/#1230
@@ -824,12 +577,6 @@ cromwell::private::install_docker_compose() {
     sudo chmod +x /usr/local/bin/docker-compose
 }
 
-cromwell::private::setup_pyenv_python_latest() {
-    # Make `python` whatever the most recent version of python installed
-    # Fixes cases where someone has set pyenv to override `python` to use an older `python2` instead of `python3`
-    pyenv global "$(pyenv versions --bare --skip-aliases | sort -t '.' -k1,1n -k2,2n -k3,3n | tail -n 1)"
-}
-
 cromwell::private::pip_install() {
     local pip_package
     pip_package="${1:?pip_install called without a package}"; shift
@@ -1269,7 +1016,6 @@ cromwell::build::setup_common_environment() {
     cromwell::private::check_debug
     cromwell::private::create_build_variables
     cromwell::private::echo_build_variables
-    cromwell::private::verify_secure_build
     cromwell::private::make_build_directories
     cromwell::private::install_git_secrets
     cromwell::private::install_minnie_kenny
@@ -1277,31 +1023,6 @@ cromwell::build::setup_common_environment() {
     cromwell::private::create_database_variables
 
     case "${CROMWELL_BUILD_PROVIDER}" in
-        "${CROMWELL_BUILD_PROVIDER_TRAVIS}")
-            cromwell::private::stop_travis_defaults
-            # Try to login to vault, and if successful then use vault creds to login to docker.
-            # For those committers with vault access this avoids pull rate limits reported in BT-143.
-            cromwell::private::install_vault
-            cromwell::private::login_vault
-            cromwell::private::login_docker
-            cromwell::private::install_adoptopenjdk
-            cromwell::private::install_sbt_launcher
-            cromwell::private::install_docker_compose
-            cromwell::private::delete_boto_config
-            cromwell::private::delete_sbt_boot
-            cromwell::private::upgrade_pip
-            cromwell::private::start_docker_databases
-            ;;
-        "${CROMWELL_BUILD_PROVIDER_CIRCLE}")
-            # Try to login to vault, and if successful then use vault creds to login to docker.
-            # For those committers with vault access this avoids pull rate limits reported in BT-143.
-            cromwell::private::install_vault
-            cromwell::private::login_vault
-            cromwell::private::login_docker
-            cromwell::private::install_adoptopenjdk
-            cromwell::private::setup_pyenv_python_latest
-            cromwell::private::start_docker_databases
-            ;;
         "${CROMWELL_BUILD_PROVIDER_GITHUB}")
             # Try to login to vault, and if successful then use vault creds to login to docker.
             # For those committers with vault access this avoids pull rate limits reported in BT-143.

From 071c32c70c553ee09f0c2258fa0b6f4d804ef8d4 Mon Sep 17 00:00:00 2001
From: Adam Nichols <aednichols@gmail.com>
Date: Wed, 6 Dec 2023 16:24:40 -0500
Subject: [PATCH 09/13] Oops

---
 src/ci/bin/testCentaurPapiV2beta.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/ci/bin/testCentaurPapiV2beta.sh b/src/ci/bin/testCentaurPapiV2beta.sh
index 3f92bf0982e..108c6cca388 100755
--- a/src/ci/bin/testCentaurPapiV2beta.sh
+++ b/src/ci/bin/testCentaurPapiV2beta.sh
@@ -23,8 +23,8 @@ cromwell::build::run_centaur \
     -e relative_output_paths_colliding \
     -e standard_output_paths_colliding_prevented \
     -e papi_v2alpha1_gcsa \
-    -e lots_of_inputs \
     -e restart \
+    -e lots_of_inputs \
     # `lots_of_inputs` is redundant to, and a less rigorous version of, `lots_of_inputs_papiv2`
 
 cromwell::build::generate_code_coverage

From 0e841ba70f752e4d82d09b7f8fee122a00f4a780 Mon Sep 17 00:00:00 2001
From: Adam Nichols <aednichols@gmail.com>
Date: Wed, 6 Dec 2023 17:39:11 -0500
Subject: [PATCH 10/13] Clean up `test.inc.sh`

---
 src/ci/bin/test.inc.sh | 96 ++----------------------------------------
 1 file changed, 4 insertions(+), 92 deletions(-)

diff --git a/src/ci/bin/test.inc.sh b/src/ci/bin/test.inc.sh
index 4833212d31b..71577ce1e4c 100755
--- a/src/ci/bin/test.inc.sh
+++ b/src/ci/bin/test.inc.sh
@@ -47,15 +47,12 @@ cromwell::private::check_debug() {
 
 # Exports environment variables used for scripts.
 cromwell::private::create_build_variables() {
-    CROMWELL_BUILD_PROVIDER_JENKINS="jenkins"
     CROMWELL_BUILD_PROVIDER_GITHUB="github"
     CROMWELL_BUILD_PROVIDER_UNKNOWN="unknown"
 
-    if [[ "${JENKINS-false}" == "true" ]]; then
-        CROMWELL_BUILD_PROVIDER="${CROMWELL_BUILD_PROVIDER_JENKINS}"
-    elif [[ "${CIRCLECI-false}" == "true" ]]; then
-        CROMWELL_BUILD_PROVIDER="${CROMWELL_BUILD_PROVIDER_CIRCLE}"
-    elif [[ "${GITHUB_ACTIONS-false}" == "true" ]]; then
+    # CI providers set an env like `GITHUB_ACTIONS` that indicates to jobs where they're running
+    # https://docs.github.com/en/actions/learn-github-actions/variables#default-environment-variables
+    if [[ "${GITHUB_ACTIONS-false}" == "true" ]]; then
         CROMWELL_BUILD_PROVIDER="${CROMWELL_BUILD_PROVIDER_GITHUB}"
     else
         CROMWELL_BUILD_PROVIDER="${CROMWELL_BUILD_PROVIDER_UNKNOWN}"
@@ -125,21 +122,6 @@ cromwell::private::create_build_variables() {
     # https://broadinstitute.slack.com/archives/GHYJZ2ZE0/p1656625952888149?thread_ts=1656620572.975059&cid=GHYJZ2ZE0
 
     case "${CROMWELL_BUILD_PROVIDER}" in
-        "${CROMWELL_BUILD_PROVIDER_JENKINS}")
-            # External variables must be passed through in the ENVIRONMENT of src/ci/docker-compose/docker-compose.yml
-            CROMWELL_BUILD_IS_CI=true
-            CROMWELL_BUILD_TYPE="${JENKINS_BUILD_TYPE}"
-            CROMWELL_BUILD_BRANCH="${GIT_BRANCH#origin/}"
-            CROMWELL_BUILD_EVENT=""
-            CROMWELL_BUILD_TAG=""
-            CROMWELL_BUILD_NUMBER="${BUILD_NUMBER}"
-            CROMWELL_BUILD_URL="${BUILD_URL}"
-            CROMWELL_BUILD_GIT_USER_EMAIL="jenkins@jenkins.io"
-            CROMWELL_BUILD_GIT_USER_NAME="Jenkins CI"
-            CROMWELL_BUILD_HEARTBEAT_PATTERN="…\n"
-            CROMWELL_BUILD_GENERATE_COVERAGE=false
-            CROMWELL_BUILD_RUN_TESTS=true
-            ;;
         "${CROMWELL_BUILD_PROVIDER_GITHUB}")
             CROMWELL_BUILD_IS_CI=true
             CROMWELL_BUILD_TYPE="${BUILD_TYPE}"
@@ -262,7 +244,6 @@ cromwell::private::create_build_variables() {
     export CROMWELL_BUILD_OS_LINUX
     export CROMWELL_BUILD_PRIOR_VERSION_NUMBER
     export CROMWELL_BUILD_PROVIDER
-    export CROMWELL_BUILD_PROVIDER_JENKINS
     export CROMWELL_BUILD_PROVIDER_UNKNOWN
     export CROMWELL_BUILD_REQUIRES_PRIOR_VERSION
     export CROMWELL_BUILD_REQUIRES_SECURE
@@ -329,29 +310,6 @@ cromwell::private::create_database_variables() {
             CROMWELL_BUILD_POSTGRESQL_LATEST_PORT="15432"
             CROMWELL_BUILD_POSTGRESQL_LATEST_TAG="${BUILD_POSTGRESQL_LATEST-}"
             ;;
-        "${CROMWELL_BUILD_PROVIDER_JENKINS}")
-            # NOTE: Jenkins uses src/ci/docker-compose/docker-compose.yml.
-            # We don't define a docker tag because the docker-compose has already spun up the database containers by the
-            # time this script is run. Other variables here must match the database service names and settings the yaml.
-            CROMWELL_BUILD_MARIADB_HOSTNAME="mariadb-db"
-            CROMWELL_BUILD_MARIADB_PORT="3306"
-            CROMWELL_BUILD_MARIADB_DOCKER_TAG=""
-            CROMWELL_BUILD_MARIADB_LATEST_HOSTNAME="mariadb-db-latest"
-            CROMWELL_BUILD_MARIADB_LATEST_PORT="3306"
-            CROMWELL_BUILD_MARIADB_LATEST_TAG=""
-            CROMWELL_BUILD_MYSQL_HOSTNAME="mysql-db"
-            CROMWELL_BUILD_MYSQL_PORT="3306"
-            CROMWELL_BUILD_MYSQL_DOCKER_TAG=""
-            CROMWELL_BUILD_MYSQL_LATEST_HOSTNAME="mysql-db-latest"
-            CROMWELL_BUILD_MYSQL_LATEST_PORT="3306"
-            CROMWELL_BUILD_MYSQL_LATEST_TAG=""
-            CROMWELL_BUILD_POSTGRESQL_HOSTNAME="postgresql-db"
-            CROMWELL_BUILD_POSTGRESQL_PORT="5432"
-            CROMWELL_BUILD_POSTGRESQL_DOCKER_TAG=""
-            CROMWELL_BUILD_POSTGRESQL_LATEST_HOSTNAME="postgresql-db-latest"
-            CROMWELL_BUILD_POSTGRESQL_LATEST_PORT="3306"
-            CROMWELL_BUILD_POSTGRESQL_LATEST_TAG=""
-            ;;
         *)
             if [[ -z "${CROMWELL_BUILD_DOCKER_LOCALHOST-}" ]]; then
                 CROMWELL_BUILD_DOCKER_LOCALHOST="localhost"
@@ -494,12 +452,6 @@ cromwell::private::create_centaur_variables() {
 
             CROMWELL_BUILD_CENTAUR_TEST_ADDITIONAL_PARAMETERS=
             ;;
-        "${CROMWELL_BUILD_PROVIDER_JENKINS}")
-            CROMWELL_BUILD_CENTAUR_SLICK_PROFILE="slick.jdbc.MySQLProfile$"
-            CROMWELL_BUILD_CENTAUR_JDBC_DRIVER="com.mysql.cj.jdbc.Driver"
-            CROMWELL_BUILD_CENTAUR_JDBC_URL="${mysql_jdbc_url}"
-            CROMWELL_BUILD_CENTAUR_TEST_ADDITIONAL_PARAMETERS="${CENTAUR_TEST_ADDITIONAL_PARAMETERS-}"
-            ;;
         *)
             CROMWELL_BUILD_CENTAUR_SLICK_PROFILE="${CROMWELL_BUILD_CENTAUR_SLICK_PROFILE-slick.jdbc.MySQLProfile\$}"
             CROMWELL_BUILD_CENTAUR_JDBC_DRIVER="${CROMWELL_BUILD_CENTAUR_JDBC_DRIVER-com.mysql.cj.jdbc.Driver}"
@@ -813,27 +765,7 @@ cromwell::private::render_secure_resources() {
     fi
 }
 
-cromwell::private::copy_all_resources() {
-    # Only copy the CI resources. Secure resources are not rendered.
-    sbt -Dsbt.supershell=false --warn copyCiResources
-}
-
-cromwell::private::setup_secure_resources() {
-    case "${CROMWELL_BUILD_PROVIDER}" in
-        "${CROMWELL_BUILD_PROVIDER_JENKINS}")
-            # Jenkins secret resources should have already been rendered outside the CI's docker-compose container.
-            cromwell::private::copy_all_resources
-            ;;
-        *)
-            cromwell::private::render_secure_resources
-            ;;
-    esac
-}
-
 cromwell::private::make_build_directories() {
-    if [[ "${CROMWELL_BUILD_PROVIDER}" == "${CROMWELL_BUILD_PROVIDER_JENKINS}" ]]; then
-        sudo chmod -R a+w .
-    fi
     mkdir -p "${CROMWELL_BUILD_LOG_DIRECTORY}"
     mkdir -p "${CROMWELL_BUILD_RESOURCES_DIRECTORY}"
 }
@@ -1038,12 +970,11 @@ cromwell::build::setup_common_environment() {
             cromwell::private::upgrade_pip
             cromwell::private::start_docker_databases
             ;;
-        "${CROMWELL_BUILD_PROVIDER_JENKINS}"|\
         *)
             ;;
     esac
 
-    cromwell::private::setup_secure_resources
+    cromwell::private::render_secure_resources
     cromwell::private::start_build_heartbeat
 }
 
@@ -1225,25 +1156,6 @@ cromwell::build::print_workflow_statistics() {
             LIMIT 20;"
 }
 
-cromwell::build::exec_retry_function() {
-    local retried_function
-    local retry_count
-    local attempt
-    local exit_status
-
-    retried_function="${1:?exec_retry_function called without a function}"; shift
-    retry_count="${1:-3}"; shift || true
-    sleep_seconds="${1:-15}"; shift || true
-
-    # https://unix.stackexchange.com/a/82610
-    # https://stackoverflow.com/a/17336953
-    for attempt in $(seq 0 "${retry_count}"); do
-        [[ ${attempt} -gt 0 ]] && sleep "${sleep_seconds}"
-        ${retried_function} && exit_status=0 && break || exit_status=$?
-    done
-    return ${exit_status}
-}
-
 cromwell::build::exec_silent_function() {
     local silent_function
     silent_function="${1:?exec_silent_function called without a function}"; shift

From a5414767dece8fc33c83f65b8c4148f245f00a0f Mon Sep 17 00:00:00 2001
From: Adam Nichols <aednichols@gmail.com>
Date: Wed, 6 Dec 2023 17:56:47 -0500
Subject: [PATCH 11/13] Fix

---
 src/ci/bin/test_gcpbatch.inc.sh |  4 ----
 src/ci/bin/test_papi.inc.sh     |  4 ----
 src/ci/bin/test_unit.inc.sh     | 12 ------------
 3 files changed, 20 deletions(-)

diff --git a/src/ci/bin/test_gcpbatch.inc.sh b/src/ci/bin/test_gcpbatch.inc.sh
index 1570bdb5f76..97dce8b878d 100644
--- a/src/ci/bin/test_gcpbatch.inc.sh
+++ b/src/ci/bin/test_gcpbatch.inc.sh
@@ -29,10 +29,6 @@ cromwell::private::batch::setup_batch_gcloud() {
     export CROMWELL_BUILD_BATCH_GCR_IMAGES
     export CROMWELL_BUILD_BATCH_PROJECT_ID
 
-    if [[ "${CROMWELL_BUILD_PROVIDER}" == "${CROMWELL_BUILD_PROVIDER_TRAVIS}" ]]; then
-        cromwell::private::batch::install_gcloud
-    fi
-
     # All `gcloud` commands should use this configuration directory.
     # https://stackoverflow.com/questions/34883810/how-to-authenticate-google-apis-with-different-service-account-credentials
     # https://github.com/googleapis/google-auth-library-java/issues/58
diff --git a/src/ci/bin/test_papi.inc.sh b/src/ci/bin/test_papi.inc.sh
index 98d77820435..2fd5c8352f6 100644
--- a/src/ci/bin/test_papi.inc.sh
+++ b/src/ci/bin/test_papi.inc.sh
@@ -29,10 +29,6 @@ cromwell::private::papi::setup_papi_gcloud() {
     export CROMWELL_BUILD_PAPI_GCR_IMAGES
     export CROMWELL_BUILD_PAPI_PROJECT_ID
 
-    if [[ "${CROMWELL_BUILD_PROVIDER}" == "${CROMWELL_BUILD_PROVIDER_TRAVIS}" ]]; then
-        cromwell::private::papi::install_gcloud
-    fi
-
     # All `gcloud` commands should use this configuration directory.
     # https://stackoverflow.com/questions/34883810/how-to-authenticate-google-apis-with-different-service-account-credentials
     # https://github.com/googleapis/google-auth-library-java/issues/58
diff --git a/src/ci/bin/test_unit.inc.sh b/src/ci/bin/test_unit.inc.sh
index edef0fda323..5ff2b69de3e 100644
--- a/src/ci/bin/test_unit.inc.sh
+++ b/src/ci/bin/test_unit.inc.sh
@@ -18,12 +18,6 @@ source "${BASH_SOURCE%/*}/test.inc.sh" || source test.inc.sh
 
 cromwell::build::unit::setup_scale_factor() {
     case "${CROMWELL_BUILD_PROVIDER}" in
-        "${CROMWELL_BUILD_PROVIDER_TRAVIS}")
-            CROMWELL_BUILD_UNIT_SPAN_SCALE_FACTOR=2
-            ;;
-        "${CROMWELL_BUILD_PROVIDER_JENKINS}")
-            CROMWELL_BUILD_UNIT_SPAN_SCALE_FACTOR=10
-            ;;
         *)
             CROMWELL_BUILD_UNIT_SPAN_SCALE_FACTOR=1
             ;;
@@ -33,12 +27,6 @@ cromwell::build::unit::setup_scale_factor() {
 
 cromwell::build::unit::setup_exclude_tags() {
     case "${CROMWELL_BUILD_PROVIDER}" in
-        "${CROMWELL_BUILD_PROVIDER_TRAVIS}")
-            CROMWELL_BUILD_UNIT_EXCLUDE_TAGS="AwsTest,CromwellIntegrationTest,DbmsTest,GcsIntegrationTest"
-            ;;
-        "${CROMWELL_BUILD_PROVIDER_JENKINS}")
-            CROMWELL_BUILD_UNIT_EXCLUDE_TAGS="AwsTest,CromwellIntegrationTest,DockerTest,DbmsTest,GcsIntegrationTest"
-            ;;
         *)
             # Use the full list of excludes listed in Testing.scala
             CROMWELL_BUILD_UNIT_EXCLUDE_TAGS=""

From 811ac03012c39152c52e4655158f9ab21cb095f3 Mon Sep 17 00:00:00 2001
From: Adam Nichols <aednichols@gmail.com>
Date: Wed, 6 Dec 2023 18:06:50 -0500
Subject: [PATCH 12/13] Fix

---
 src/ci/bin/test_gcpbatch.inc.sh | 4 ----
 src/ci/bin/test_papi.inc.sh     | 4 ----
 2 files changed, 8 deletions(-)

diff --git a/src/ci/bin/test_gcpbatch.inc.sh b/src/ci/bin/test_gcpbatch.inc.sh
index 97dce8b878d..641cd86d612 100644
--- a/src/ci/bin/test_gcpbatch.inc.sh
+++ b/src/ci/bin/test_gcpbatch.inc.sh
@@ -102,9 +102,5 @@ cromwell::private::batch::setup_batch_service_account() {
 
 cromwell::build::batch::setup_batch_centaur_environment() {
     cromwell::private::batch::setup_batch_gcloud
-    if [[ "${CROMWELL_BUILD_PROVIDER}" != "${CROMWELL_BUILD_PROVIDER_JENKINS}" ]]
-    then
-        cromwell::private::batch::setup_batch_gcr
-    fi
     cromwell::private::batch::setup_batch_service_account
 }
diff --git a/src/ci/bin/test_papi.inc.sh b/src/ci/bin/test_papi.inc.sh
index 2fd5c8352f6..c17536693d7 100644
--- a/src/ci/bin/test_papi.inc.sh
+++ b/src/ci/bin/test_papi.inc.sh
@@ -111,10 +111,6 @@ cromwell::private::papi::setup_papi_endpoint_url() {
 
 cromwell::build::papi::setup_papi_centaur_environment() {
     cromwell::private::papi::setup_papi_gcloud
-    if [[ "${CROMWELL_BUILD_PROVIDER}" != "${CROMWELL_BUILD_PROVIDER_JENKINS}" ]]
-    then
-        cromwell::private::papi::setup_papi_gcr
-    fi
     cromwell::private::papi::setup_papi_service_account
     cromwell::private::papi::setup_papi_endpoint_url
 }

From 51a5fa680a7cb55b7c5e9b27e42300398c2443e0 Mon Sep 17 00:00:00 2001
From: Adam Nichols <aednichols@gmail.com>
Date: Thu, 7 Dec 2023 16:44:55 -0500
Subject: [PATCH 13/13] That was the wrong branch of that conditional...

---
 src/ci/bin/test_papi.inc.sh | 1 +
 1 file changed, 1 insertion(+)

diff --git a/src/ci/bin/test_papi.inc.sh b/src/ci/bin/test_papi.inc.sh
index c17536693d7..0b4ed151664 100644
--- a/src/ci/bin/test_papi.inc.sh
+++ b/src/ci/bin/test_papi.inc.sh
@@ -111,6 +111,7 @@ cromwell::private::papi::setup_papi_endpoint_url() {
 
 cromwell::build::papi::setup_papi_centaur_environment() {
     cromwell::private::papi::setup_papi_gcloud
+    cromwell::private::papi::setup_papi_gcr
     cromwell::private::papi::setup_papi_service_account
     cromwell::private::papi::setup_papi_endpoint_url
 }