From 619ba4e8c35ad3a5eb2121d7cb2ad8a4fafb99a1 Mon Sep 17 00:00:00 2001
From: Devin Smith <devinsmith@deephaven.io>
Date: Mon, 8 Jul 2024 12:31:21 -0700
Subject: [PATCH] build: Remove java classpath conventions (#5724)

This removes our custom configuration hierarchy, historically inherited
from the "fishlib" days.

Follow-up to #5683

Note: unlike #5683, this migration does not aim to preserve the exact
configuration dependencies that were inherited in the
java-classpath-conventions hierarchy. The configuration conventions were
overly broad, and didn't represent the real dependencies that each
project has. As part of this, our dependency on
`org.jetbrains:annotations` changed from an implementation dependency
(inherited through the `fishBase` configuration) to a compileOnly
dependency to better reflect how we actually depend on it. We might
expect that the jetbrains annotations would be removed from our
application runtime classpath entirely, but that is not the case - it
turns out that one of our transitive dependencies has a runtime
dependency on it:

```
org.jetbrains:annotations:13.0
\--- org.jetbrains.kotlin:kotlin-stdlib:1.9.10
     +--- io.confluent:kafka-protobuf-provider:7.6.0
     |    \--- io.confluent:kafka-protobuf-serializer:7.6.0
     |         \--- project :extensions-kafka
     |              \--- project :server
     |                   \--- project :server-jetty
     |                        \--- runtimeClasspath
```

In this case, it has the visible effect of "downgrading" our runtime
classpath from what was previously `org.jetbrains:annotations:24.0.0` to
`org.jetbrains:annotations:13.0`. Arguably, this is the more correct
runtime dependency to provide given it matches what the exact version
the transitive library requests.
---
 Base/build.gradle                             |  6 +-
 BenchmarkSupport/BenchmarkSupport.gradle      | 11 +--
 ClientSupport/ClientSupport.gradle            |  6 +-
 Configuration/build.gradle                    |  6 +-
 Generators/Generators.gradle                  |  6 +-
 IO/build.gradle                               |  2 +-
 Integrations/build.gradle                     |  6 +-
 ModelFarm/ModelFarm.gradle                    |  5 +-
 Numerics/Numerics.gradle                      |  8 +-
 Plot/Plot.gradle                              | 10 +--
 Util/Util.gradle                              | 12 +--
 Util/channel/build.gradle                     |  2 +-
 Util/function/build.gradle                    |  2 +-
 base-test-utils/build.gradle                  |  6 +-
 ...eephaven.java-classpath-conventions.gradle | 81 -------------------
 ...o.deephaven.java-common-conventions.gradle |  1 -
 engine/api/build.gradle                       |  4 +-
 engine/context/build.gradle                   |  4 -
 engine/function/build.gradle                  |  5 +-
 engine/primitive/build.gradle                 |  2 +-
 engine/rowset-test-utils/build.gradle         |  4 +-
 engine/rowset/build.gradle                    |  6 +-
 engine/table/build.gradle                     |  3 +-
 engine/test-utils/build.gradle                |  4 +-
 engine/time/build.gradle                      |  6 +-
 engine/tuple/build.gradle                     |  2 +-
 engine/updategraph/build.gradle               |  4 +-
 engine/vector/build.gradle                    |  2 +-
 extensions/arrow/build.gradle                 |  2 +-
 extensions/barrage/build.gradle               |  7 +-
 extensions/csv/build.gradle                   |  6 +-
 extensions/iceberg/build.gradle               |  2 +
 extensions/kafka/build.gradle                 |  4 +-
 extensions/parquet/base/build.gradle          |  4 +-
 extensions/parquet/compression/build.gradle   |  4 +-
 extensions/parquet/table/build.gradle         |  3 +-
 extensions/protobuf/build.gradle              |  2 +-
 extensions/s3/build.gradle                    |  2 +-
 extensions/source-support/build.gradle        |  2 +-
 extensions/suanshu/build.gradle               |  5 +-
 extensions/trackedfile/build.gradle           |  2 +-
 gradle/libs.versions.toml                     | 31 ++++++-
 java-client/barrage/build.gradle              |  5 --
 log-factory/build.gradle                      |  6 +-
 .../sinks/log-to-logbuffer/build.gradle       |  5 +-
 .../sinks/logback-logbuffer/build.gradle      |  6 +-
 .../logback-print-stream-globals/build.gradle |  5 +-
 props/test-configs/build.gradle               |  6 +-
 proto/proto-backplane-grpc/build.gradle       |  5 +-
 py/jpy-integration/build.gradle               |  4 +-
 replication/reflective/build.gradle           |  6 +-
 replication/static/build.gradle               |  4 +-
 replication/util/build.gradle                 |  2 +-
 server/build.gradle                           |  2 +-
 server/test-utils/build.gradle                |  2 +-
 web/client-api/client-api.gradle              |  2 +-
 web/shared-beans/shared-beans.gradle          |  5 +-
 57 files changed, 127 insertions(+), 230 deletions(-)
 delete mode 100644 buildSrc/src/main/groovy/io.deephaven.java-classpath-conventions.gradle

diff --git a/Base/build.gradle b/Base/build.gradle
index fc63a2efa19..ced34b26a52 100644
--- a/Base/build.gradle
+++ b/Base/build.gradle
@@ -7,9 +7,9 @@ dependencies {
 
     api project(':clock')
 
-    implementation depTrove3
-    compileOnlyApi depAnnotations
-    implementation depCommonsLang3
+    implementation libs.trove
+    compileOnlyApi libs.jetbrains.annotations
+    implementation libs.commons.lang3
 
     api 'io.deephaven:hash:0.1.0'
 
diff --git a/BenchmarkSupport/BenchmarkSupport.gradle b/BenchmarkSupport/BenchmarkSupport.gradle
index 6528b126646..0308980c99b 100644
--- a/BenchmarkSupport/BenchmarkSupport.gradle
+++ b/BenchmarkSupport/BenchmarkSupport.gradle
@@ -2,14 +2,6 @@ plugins {
     id 'io.deephaven.project.register'
 }
 
-configurations {
-    implementation.extendsFrom dhBenchmarkSupport
-
-    testImplementation.extendsFrom fishIoTest
-
-    testRuntimeOnly.extendsFrom fishDataGenerator
-}
-
 sourceSets {
     main {
         java {
@@ -34,7 +26,10 @@ dependencies {
     implementation project(':Configuration')
     implementation 'org.openjdk.jmh:jmh-core:1.20'
 
+    implementation libs.univocity.parsers
+
     testImplementation project(':engine-test-utils')
+    testImplementation project(path: ':Base', configuration: 'tests')
 
     testRuntimeOnly project(path: ':configs')
     testRuntimeOnly project(path: ':test-configs')
diff --git a/ClientSupport/ClientSupport.gradle b/ClientSupport/ClientSupport.gradle
index 9c297379e1e..091a7200751 100644
--- a/ClientSupport/ClientSupport.gradle
+++ b/ClientSupport/ClientSupport.gradle
@@ -2,16 +2,12 @@ plugins {
     id 'io.deephaven.project.register'
 }
 
-configurations {
-    implementation.extendsFrom dhConsole
-}
-
 dependencies {
     implementation project(':engine-table')
     implementation project(':engine-function')
     implementation project(':log-factory')
     implementation project(':Configuration')
-    implementation depCommonsLang3
+    implementation libs.commons.lang3
 
     testImplementation project(':engine-test-utils')
     testImplementation libs.junit4
diff --git a/Configuration/build.gradle b/Configuration/build.gradle
index 518dc32a3a3..c0cca8e0f6b 100644
--- a/Configuration/build.gradle
+++ b/Configuration/build.gradle
@@ -1,13 +1,16 @@
 plugins {
+    id 'java-library'
     id 'io.deephaven.project.register'
 }
 
 dependencies {
+    api libs.trove
+
     implementation project(':Base')
     implementation project(':DataStructures')
     implementation project(':IO')
     implementation project(':log-factory')
-    implementation depCommonsLang3
+    implementation libs.commons.lang3
     testImplementation libs.junit4
     testImplementation libs.jmock.junit4
     testImplementation libs.jmock.imposters
@@ -16,6 +19,7 @@ dependencies {
     annotationProcessor libs.autoservice.compiler
 
     testImplementation project(path: ':Base', configuration: 'tests')
+    testImplementation libs.commons.compress
 
     testRuntimeOnly project(':log-to-slf4j')
     testRuntimeOnly libs.slf4j.simple
diff --git a/Generators/Generators.gradle b/Generators/Generators.gradle
index 67a05142c28..7322d5adba5 100644
--- a/Generators/Generators.gradle
+++ b/Generators/Generators.gradle
@@ -6,8 +6,6 @@ plugins {
 evaluationDependsOn Docker.registryProject('python')
 
 configurations {
-    implementation.extendsFrom jdom
-    testImplementation.extendsFrom fishBaseTest
     combinedJavadoc
 }
 
@@ -17,7 +15,7 @@ dependencies {
     implementation project(':extensions-csv')
     implementation project(':extensions-kafka')
     implementation project(':extensions-parquet-table')
-    implementation depTrove3
+    implementation libs.trove
 
     implementation libs.groovy
     implementation libs.groovy.json
@@ -29,6 +27,8 @@ dependencies {
     runtimeOnly project(':log-to-slf4j')
     runtimeOnly libs.logback.classic
 
+    testImplementation project(path: ':Base', configuration: 'tests')
+
     testRuntimeOnly project(path: ':configs')
     testRuntimeOnly project(path: ':test-configs')
 
diff --git a/IO/build.gradle b/IO/build.gradle
index 25c5dbd5bb3..f84060f0416 100644
--- a/IO/build.gradle
+++ b/IO/build.gradle
@@ -5,7 +5,7 @@ plugins {
 dependencies {
     implementation project(':Base')
     implementation project(':SevenZip')
-    implementation depCommonsCompress
+    implementation libs.commons.compress
     testImplementation project(path: ':Base', configuration: 'tests')
     testImplementation libs.junit4
     testImplementation libs.jmock.junit4
diff --git a/Integrations/build.gradle b/Integrations/build.gradle
index e651390a5ac..99abec47535 100644
--- a/Integrations/build.gradle
+++ b/Integrations/build.gradle
@@ -9,11 +9,6 @@ plugins {
 
 evaluationDependsOn ':docker-server-jetty'
 
-configurations {
-    implementation.extendsFrom dhIntegrations
-    testImplementation.extendsFrom fishBaseTest
-}
-
 dependencies {
 
     implementation project(':engine-table')
@@ -22,6 +17,7 @@ dependencies {
     implementation project(':log-factory')
 
     testImplementation project(':engine-test-utils')
+    testImplementation project(path: ':Base', configuration: 'tests')
 
     // Needed for CalendarInit
     testRuntimeOnly TestTools.projectDependency(project, 'engine-time')
diff --git a/ModelFarm/ModelFarm.gradle b/ModelFarm/ModelFarm.gradle
index 9e35a11b103..e2eb2e79e0a 100644
--- a/ModelFarm/ModelFarm.gradle
+++ b/ModelFarm/ModelFarm.gradle
@@ -7,10 +7,6 @@ plugins {
     id 'java-library'
 }
 
-configurations {
-    testImplementation.extendsFrom fishBaseTest
-}
-
 dependencies {
     api project(':engine-table')
     api project(':engine-time')
@@ -21,6 +17,7 @@ dependencies {
     runtimeOnly project(':configs')
 
     testImplementation project(':engine-test-utils')
+    testImplementation project(path: ':Base', configuration: 'tests')
     testRuntimeOnly project(':Numerics')
 
     testRuntimeOnly project(':log-to-slf4j')
diff --git a/Numerics/Numerics.gradle b/Numerics/Numerics.gradle
index 4cf033b7af7..1059c4424f8 100644
--- a/Numerics/Numerics.gradle
+++ b/Numerics/Numerics.gradle
@@ -3,17 +3,15 @@ plugins {
     id 'java-library'
 }
 
-configurations {
-    implementation.extendsFrom dhNumerics
-    testImplementation.extendsFrom fishBaseTest
-}
-
 dependencies {
     api project(':engine-time')
     implementation project(':engine-function')
     implementation project(':log-factory')
+    implementation libs.jama
+    implementation libs.commons.math3
 
     testImplementation project(':base-test-utils')
+    testImplementation project(path: ':Base', configuration: 'tests')
     testRuntimeOnly project(path: ':configs')
     testRuntimeOnly project(path: ':test-configs')
 
diff --git a/Plot/Plot.gradle b/Plot/Plot.gradle
index d1019b67408..3e49a320498 100644
--- a/Plot/Plot.gradle
+++ b/Plot/Plot.gradle
@@ -3,19 +3,15 @@ plugins {
     id 'java-library'
 }
 
-configurations {
-    implementation.extendsFrom dhPlot
-
-    testImplementation.extendsFrom fishIoTest
-}
-
 dependencies {
 
     api project(':engine-api')
+    implementation project(':Base')
     implementation project(':engine-table')
     implementation project(':engine-function')
     implementation project(':engine-tuple')
     implementation project(':log-factory')
+    implementation project(':Configuration')
 
     api libs.groovy
     implementation libs.groovy.json
@@ -25,9 +21,11 @@ dependencies {
     compileOnly 'javax.inject:javax.inject:1'
 
     implementation libs.guava
+    implementation libs.commons.lang3
 
     testImplementation project(':engine-test-utils')
     testImplementation TestTools.projectDependency(project, 'engine-time')
+    testImplementation project(path: ':Base', configuration: 'tests')
 
     testRuntimeOnly project(':configs')
     testRuntimeOnly project(':test-configs')
diff --git a/Util/Util.gradle b/Util/Util.gradle
index 86098c11d4d..f25646a72a7 100644
--- a/Util/Util.gradle
+++ b/Util/Util.gradle
@@ -3,14 +3,15 @@ plugins {
     id 'io.deephaven.project.register'
 }
 
-configurations {
-    implementation.extendsFrom configurations.dhUtil, commonsLang3
-    testImplementation.extendsFrom fishBaseTest
-}
-
 dependencies {
     api project(':engine-query-constants')
+    implementation project(':Base')
     implementation project(':log-factory')
+    implementation libs.jdom2
+    implementation libs.commons.compress
+
+    implementation project(':DataStructures')
+    implementation project(':Configuration')
 
     testRuntimeOnly project(path: ':configs')
     testRuntimeOnly project(path: ':test-configs')
@@ -19,6 +20,7 @@ dependencies {
     testRuntimeOnly libs.slf4j.simple
 
     testImplementation project(':base-test-utils')
+    testImplementation project(path: ':Base', configuration: 'tests')
     testImplementation platform(libs.junit.bom)
     testImplementation libs.junit.jupiter
     testRuntimeOnly libs.junit.jupiter.engine
diff --git a/Util/channel/build.gradle b/Util/channel/build.gradle
index 44dcac11058..397bdeda530 100644
--- a/Util/channel/build.gradle
+++ b/Util/channel/build.gradle
@@ -12,7 +12,7 @@ dependencies {
     // For CountingInputStream
     implementation libs.guava
 
-    compileOnly depAnnotations
+    compileOnly libs.jetbrains.annotations
 
     testImplementation libs.assertj
     testImplementation platform(libs.junit.bom)
diff --git a/Util/function/build.gradle b/Util/function/build.gradle
index 04556534c95..8ee1d3cac80 100644
--- a/Util/function/build.gradle
+++ b/Util/function/build.gradle
@@ -6,7 +6,7 @@ plugins {
 dependencies {
     api project(':qst-type')
 
-    compileOnly depAnnotations
+    compileOnly libs.jetbrains.annotations
 
     testImplementation libs.assertj
     testImplementation platform(libs.junit.bom)
diff --git a/base-test-utils/build.gradle b/base-test-utils/build.gradle
index ffe61639325..fc266eb04dd 100644
--- a/base-test-utils/build.gradle
+++ b/base-test-utils/build.gradle
@@ -6,9 +6,9 @@ plugins {
 dependencies {
 
     implementation project(':Base')
-    implementation depTrove3
-    compileOnlyApi depAnnotations
-    implementation depCommonsLang3
+    implementation libs.trove
+    compileOnlyApi libs.jetbrains.annotations
+    implementation libs.commons.lang3
 
     api 'io.deephaven:hash:0.1.0'
 
diff --git a/buildSrc/src/main/groovy/io.deephaven.java-classpath-conventions.gradle b/buildSrc/src/main/groovy/io.deephaven.java-classpath-conventions.gradle
deleted file mode 100644
index d6163fb3efa..00000000000
--- a/buildSrc/src/main/groovy/io.deephaven.java-classpath-conventions.gradle
+++ /dev/null
@@ -1,81 +0,0 @@
-plugins {
-    id 'base'
-    id 'java'
-}
-
-// TODO(deephaven-core#1162): Adopt java-platform to manage versions
-ext {
-    depAnnotations = 'org.jetbrains:annotations:24.0.0'
-    depCommonsCompress = 'org.apache.commons:commons-compress:1.26.0'
-    depCommonsLang3 = 'org.apache.commons:commons-lang3:3.12.0'
-    depCommonsIo = 'commons-io:commons-io:2.11.0'
-    depJdom2 = 'org.jdom:jdom2:2.0.6.1'
-    depTrove3 = 'net.sf.trove4j:trove4j:3.0.3'
-}
-
-configurations {
-
-    commonsIo
-    jdom
-    math3
-    jama.extendsFrom math3
-    dxCompile
-    dxRuntime.extendsFrom dxCompile
-    mockrunner
-    junit
-
-    fishBase
-    fishIo.extendsFrom fishBase
-    fishDataStructure.extendsFrom fishIo
-    fishConfig.extendsFrom fishDataStructure
-    fishDataGenerator.extendsFrom jdom
-    fishNumerics.extendsFrom fishBase
-    fishBaseTest.extendsFrom junit
-    fishIoTest.extendsFrom fishBaseTest
-
-    dhNumerics.extendsFrom fishNumerics, jama
-    dhUtil.extendsFrom commonsIo, commonsLang3, commonsText, fishConfig, fishIo, jdom
-    dhPlot.extendsFrom dhUtil
-    dhBenchmarkSupport.extendsFrom fishData
-    dhIntegrations.extendsFrom math3
-}
-
-dependencies {
-
-    // First, one-off configurations for stuff we need "here and there"
-    jdom 'org.jdom:jdom2:2.0.6.1'
-    commonsLang3 'org.apache.commons:commons-lang3:3.12.0'
-    commonsText 'org.apache.commons:commons-text:1.10.0'
-    commonsIo 'commons-io:commons-io:2.11.0'
-    math3 'org.apache.commons:commons-math3:3.6.1'
-    jama 'gov.nist.math.jama:gov.nist.math.jama:1.1.1'
-    mockrunner 'com.mockrunner:mockrunner-jdbc:1.0.4'
-
-    junit libs.junit4
-    junit libs.jmock.junit4
-    junit libs.jmock.imposters
-
-    // Now, all the various fish libs we depend on, with inherited dependencies matching
-    // the actual dependencies used in fishlib... if we were strongly coupled, we could skip
-    // having to maintain this...
-    fishBase project(':Base'),
-            'net.sf.trove4j:trove4j:3.0.3',
-            'org.jetbrains:annotations:24.0.0',
-            depCommonsCompress
-
-    fishIo project(':IO')
-
-    fishDataStructure project(':DataStructures')
-
-    fishConfig project(':Configuration')
-
-    fishBaseTest project(path: ':Base', configuration: 'tests')
-
-    fishIoTest project(path: ':IO', configuration: 'tests')
-
-    // https://mvnrepository.com/artifact/com.univocity/univocity-parsers
-    dhBenchmarkSupport 'com.univocity:univocity-parsers:2.6.0'
-
-    dhBenchmarkSupport platform(libs.jackson.bom)
-    dhBenchmarkSupport libs.jackson.core
-}
diff --git a/buildSrc/src/main/groovy/io.deephaven.java-common-conventions.gradle b/buildSrc/src/main/groovy/io.deephaven.java-common-conventions.gradle
index 291dcf03d23..58c0e11c37f 100644
--- a/buildSrc/src/main/groovy/io.deephaven.java-common-conventions.gradle
+++ b/buildSrc/src/main/groovy/io.deephaven.java-common-conventions.gradle
@@ -1,7 +1,6 @@
 plugins {
     id 'base'
     id 'java'
-    id 'io.deephaven.java-classpath-conventions'
     id 'io.deephaven.java-license-conventions'
     id 'io.deephaven.java-toolchain-conventions'
     id 'io.deephaven.java-jar-conventions'
diff --git a/engine/api/build.gradle b/engine/api/build.gradle
index e39e13ad876..dc914bca940 100644
--- a/engine/api/build.gradle
+++ b/engine/api/build.gradle
@@ -17,7 +17,7 @@ dependencies {
     api project(':engine-rowset')
 
     implementation project(':DataStructures')
-    implementation depTrove3
+    implementation libs.trove
 
     compileOnly project(':util-immutables')
     annotationProcessor libs.immutables
@@ -29,7 +29,7 @@ dependencies {
     testImplementation project(':engine-test-utils')
     testImplementation TestTools.projectDependency(project, 'engine-table')
     testImplementation TestTools.projectDependency(project, 'engine-vector')
-    testImplementation depCommonsLang3
+    testImplementation libs.commons.lang3
 
     testImplementation libs.junit4
 
diff --git a/engine/context/build.gradle b/engine/context/build.gradle
index 2b36dd81002..c1dc47c7346 100644
--- a/engine/context/build.gradle
+++ b/engine/context/build.gradle
@@ -5,10 +5,6 @@ plugins {
 
 description 'Engine Context: QueryScope, QueryLibrary and QueryCompiler via ExecutionContext'
 
-configurations {
-    testCompile.extendsFrom junit
-}
-
 dependencies {
     api project(':authentication')
     api project(':Util')
diff --git a/engine/function/build.gradle b/engine/function/build.gradle
index b493bec2635..7e88ff177c4 100644
--- a/engine/function/build.gradle
+++ b/engine/function/build.gradle
@@ -7,19 +7,18 @@ description 'Engine Functions: Libraries for use in query expressions'
 
 configurations {
     primitiveCodegen
-    testImplementation.extendsFrom junit
 }
 
 dependencies {
     primitiveCodegen project(':codegen')
 
-    api 'net.sf.trove4j:trove4j:3.0.3'
+    api libs.trove
     api project(':Util')
     api project(':engine-vector')
     api project(':engine-primitive')
 
     implementation project(':Base')
-    implementation depCommonsLang3
+    implementation libs.commons.lang3
 
     testImplementation project(':base-test-utils')
 }
diff --git a/engine/primitive/build.gradle b/engine/primitive/build.gradle
index f51d401e900..a76885c049a 100644
--- a/engine/primitive/build.gradle
+++ b/engine/primitive/build.gradle
@@ -8,5 +8,5 @@ description 'Primitives: Expanding upon java.util.PrimitiveIterator and java.uti
 dependencies {
     implementation project(':Util')
 
-    compileOnly depAnnotations
+    compileOnly libs.jetbrains.annotations
 }
diff --git a/engine/rowset-test-utils/build.gradle b/engine/rowset-test-utils/build.gradle
index 5fe07f0d84b..aa48913ac5c 100644
--- a/engine/rowset-test-utils/build.gradle
+++ b/engine/rowset-test-utils/build.gradle
@@ -8,8 +8,8 @@ description 'Test Utils for Engine RowSets'
 dependencies {
     api project(':engine-rowset')
 
-    implementation depCommonsLang3
-    implementation depTrove3
+    implementation libs.commons.lang3
+    implementation libs.trove
 
     implementation libs.junit4
 }
diff --git a/engine/rowset/build.gradle b/engine/rowset/build.gradle
index ca8e5d9c49e..23ccb24fd67 100644
--- a/engine/rowset/build.gradle
+++ b/engine/rowset/build.gradle
@@ -8,16 +8,16 @@ description 'Engine RowSets: Data structures for working with row keys'
 dependencies {
     api project(':engine-chunk')
     api project(':Base')
-    api depTrove3
+    api libs.trove
 
     implementation project(':Container')
     implementation project(':engine-context')
     implementation project(':engine-updategraph')
     implementation project(':Configuration')
-    implementation depCommonsLang3
+    implementation libs.commons.lang3
 
     compileOnly 'com.google.code.findbugs:jsr305:3.0.2'
-    compileOnly depAnnotations
+    compileOnly libs.jetbrains.annotations
 
     testImplementation libs.junit4
 
diff --git a/engine/table/build.gradle b/engine/table/build.gradle
index 5e45904b291..906e51f0ca1 100644
--- a/engine/table/build.gradle
+++ b/engine/table/build.gradle
@@ -37,8 +37,9 @@ dependencies {
     implementation 'it.unimi.dsi:fastutil:8.5.13'
 
     implementation project(':plugin')
-    implementation depCommonsLang3
+    implementation libs.commons.lang3
     implementation libs.commons.text
+    implementation libs.commons.compress
 
     implementation libs.groovy
     implementation libs.groovy.json
diff --git a/engine/test-utils/build.gradle b/engine/test-utils/build.gradle
index 904f769ab6f..6c2118b715e 100644
--- a/engine/test-utils/build.gradle
+++ b/engine/test-utils/build.gradle
@@ -15,8 +15,8 @@ dependencies {
     implementation project(':engine-rowset-test-utils')
     implementation project(':extensions-source-support')
 
-    implementation depCommonsLang3
-    implementation depTrove3
+    implementation libs.commons.lang3
+    implementation libs.trove
 
     implementation 'it.unimi.dsi:fastutil:8.5.13'
 
diff --git a/engine/time/build.gradle b/engine/time/build.gradle
index 3a057100582..6ab2a69cf04 100644
--- a/engine/time/build.gradle
+++ b/engine/time/build.gradle
@@ -5,10 +5,6 @@ plugins {
 
 description 'Engine Time: Types and libraries for working with instants, periods, and calendars'
 
-configurations {
-    testImplementation.extendsFrom junit
-}
-
 dependencies {
     api project(':Base')
     api project(':Util')
@@ -17,7 +13,7 @@ dependencies {
     implementation project(':engine-function')
     implementation project(':Configuration')
     implementation project(':log-factory')
-    implementation depJdom2
+    implementation libs.jdom2
     implementation libs.dagger
     annotationProcessor libs.dagger.compiler
 
diff --git a/engine/tuple/build.gradle b/engine/tuple/build.gradle
index c5b04aa9518..f845ac4442a 100644
--- a/engine/tuple/build.gradle
+++ b/engine/tuple/build.gradle
@@ -6,7 +6,7 @@ plugins {
 description 'Engine Tuples: Value sequences for use in aggregations, joins, and indexing'
 
 dependencies {
-    api 'net.sf.trove4j:trove4j:3.0.3'
+    api libs.trove
     api project(':Util')
     api project(':engine-time')
     implementation project(':DataStructures')
diff --git a/engine/updategraph/build.gradle b/engine/updategraph/build.gradle
index 80289ddd397..6787b24e2e6 100644
--- a/engine/updategraph/build.gradle
+++ b/engine/updategraph/build.gradle
@@ -10,10 +10,10 @@ dependencies {
     implementation project(':hotspot')
     implementation project(':log-factory')
     implementation project(':Configuration')
-    implementation depCommonsLang3
+    implementation libs.commons.lang3
 
     compileOnly 'com.google.code.findbugs:jsr305:3.0.2'
-    compileOnly depAnnotations
+    compileOnly libs.jetbrains.annotations
 
     testImplementation project(':engine-context')
 
diff --git a/engine/vector/build.gradle b/engine/vector/build.gradle
index 34718c5347b..34559d7e7f5 100644
--- a/engine/vector/build.gradle
+++ b/engine/vector/build.gradle
@@ -12,7 +12,7 @@ dependencies {
 
     implementation project(':Base')
 
-    compileOnly depAnnotations
+    compileOnly libs.jetbrains.annotations
 
     testImplementation libs.junit4
 }
diff --git a/extensions/arrow/build.gradle b/extensions/arrow/build.gradle
index edfee512ef6..fb03d4d63b2 100644
--- a/extensions/arrow/build.gradle
+++ b/extensions/arrow/build.gradle
@@ -9,7 +9,7 @@ dependencies {
     api project(':engine-table')
 
     implementation project(':Configuration')
-    implementation depCommonsLang3
+    implementation libs.commons.lang3
 
     implementation libs.arrow.format
     implementation libs.arrow.vector
diff --git a/extensions/barrage/build.gradle b/extensions/barrage/build.gradle
index f542b0a813d..cdf1f4b54a2 100644
--- a/extensions/barrage/build.gradle
+++ b/extensions/barrage/build.gradle
@@ -3,11 +3,6 @@ plugins {
     id 'io.deephaven.project.register'
 }
 
-configurations {
-    implementation.extendsFrom irisDb
-    testImplementation.extendsFrom irisDbTest
-}
-
 description = 'An extension integrating Barrage with Deephaven\'s Table Model'
 
 dependencies {
@@ -15,7 +10,7 @@ dependencies {
     implementation project(':Util')
     implementation project(':Configuration')
     implementation project(':util-function')
-    implementation depCommonsLang3
+    implementation libs.commons.lang3
 
     api project(':engine-table')
     implementation project(':proto:proto-backplane-grpc-flight')
diff --git a/extensions/csv/build.gradle b/extensions/csv/build.gradle
index 4954ff199da..e1b6c5d1f1d 100644
--- a/extensions/csv/build.gradle
+++ b/extensions/csv/build.gradle
@@ -12,7 +12,7 @@ dependencies {
 
     implementation project(':engine-table')
     implementation project(':engine-base')
-    implementation depTrove3
+    implementation libs.trove
 
     compileOnly project(':util-immutables')
     annotationProcessor libs.immutables
@@ -20,8 +20,8 @@ dependencies {
     testImplementation platform(libs.junit.bom)
     testImplementation libs.assertj
 
-    testImplementation depCommonsCompress
-    testImplementation depCommonsIo
+    testImplementation libs.commons.compress
+    testImplementation libs.commons.io
     testImplementation project(':engine-test-utils')
 
     testImplementation libs.junit4
diff --git a/extensions/iceberg/build.gradle b/extensions/iceberg/build.gradle
index 8b61f11ec3e..704f3fb9cd2 100644
--- a/extensions/iceberg/build.gradle
+++ b/extensions/iceberg/build.gradle
@@ -35,6 +35,8 @@ dependencies {
 
     implementation libs.avro
 
+    implementation libs.commons.lang3
+
     testImplementation libs.assertj
 
     testImplementation platform(libs.junit.bom)
diff --git a/extensions/kafka/build.gradle b/extensions/kafka/build.gradle
index e2252af961c..7c381a35d08 100644
--- a/extensions/kafka/build.gradle
+++ b/extensions/kafka/build.gradle
@@ -32,8 +32,8 @@ dependencies {
     implementation project(':engine-processor-function')
     implementation project(':Configuration')
     implementation project(':log-factory')
-    implementation depTrove3
-    implementation depCommonsLang3
+    implementation libs.trove
+    implementation libs.commons.lang3
 
     compileOnly project(':util-immutables')
     annotationProcessor libs.immutables
diff --git a/extensions/parquet/base/build.gradle b/extensions/parquet/base/build.gradle
index ecb4f525be5..9a71ac9382c 100644
--- a/extensions/parquet/base/build.gradle
+++ b/extensions/parquet/base/build.gradle
@@ -16,8 +16,8 @@ dependencies {
     implementation project(':engine-time')
     implementation project(':Configuration')
     implementation project(':DataStructures')
-    implementation depCommonsIo
+    implementation libs.commons.io
 
-    compileOnly depAnnotations
+    compileOnly libs.jetbrains.annotations
     testImplementation libs.junit4
 }
diff --git a/extensions/parquet/compression/build.gradle b/extensions/parquet/compression/build.gradle
index 3d1a55b4eff..3f9ab1843a2 100644
--- a/extensions/parquet/compression/build.gradle
+++ b/extensions/parquet/compression/build.gradle
@@ -12,11 +12,11 @@ dependencies {
 
     implementation project(':Configuration')
 
-    implementation depCommonsIo
+    implementation libs.commons.io
 
     implementation libs.guava
 
-    compileOnly depAnnotations
+    compileOnly libs.jetbrains.annotations
 
     runtimeOnly('org.lz4:lz4-java:1.8.0') {
         // also consider lz4-pure-java to avoid native code
diff --git a/extensions/parquet/table/build.gradle b/extensions/parquet/table/build.gradle
index 5c7f6ec5221..b1a6c449723 100644
--- a/extensions/parquet/table/build.gradle
+++ b/extensions/parquet/table/build.gradle
@@ -32,10 +32,11 @@ dependencies {
     implementation project(':extensions-csv')
     implementation project(':log-factory')
     implementation project(':Configuration')
-    implementation depCommonsLang3
+    implementation libs.commons.lang3
     implementation project(':Util')
 
     implementation libs.commons.text
+    implementation libs.commons.compress
 
     implementation platform(libs.jackson.bom)
     implementation libs.jackson.dataformat.yaml
diff --git a/extensions/protobuf/build.gradle b/extensions/protobuf/build.gradle
index 242e9afca69..a4a30185ddb 100644
--- a/extensions/protobuf/build.gradle
+++ b/extensions/protobuf/build.gradle
@@ -13,7 +13,7 @@ dependencies {
     compileOnly project(':util-immutables')
     annotationProcessor libs.immutables
 
-    compileOnly depAnnotations
+    compileOnly libs.jetbrains.annotations
 
     testImplementation libs.assertj
 
diff --git a/extensions/s3/build.gradle b/extensions/s3/build.gradle
index c4488f3ef32..23d687a4401 100644
--- a/extensions/s3/build.gradle
+++ b/extensions/s3/build.gradle
@@ -20,7 +20,7 @@ dependencies {
     implementation libs.awssdk.s3
     implementation libs.awssdk.crt.client
 
-    compileOnly depAnnotations
+    compileOnly libs.jetbrains.annotations
 
     // For OSUtil
     testImplementation project(':Stats')
diff --git a/extensions/source-support/build.gradle b/extensions/source-support/build.gradle
index 33b88963b37..95abcd54947 100644
--- a/extensions/source-support/build.gradle
+++ b/extensions/source-support/build.gradle
@@ -16,7 +16,7 @@ dependencies {
     compileOnly 'com.google.code.findbugs:jsr305:3.0.2'
 
     testImplementation project(':engine-test-utils')
-    testImplementation depCommonsLang3
+    testImplementation libs.commons.lang3
 
     testImplementation libs.junit4
     testImplementation libs.assertj
diff --git a/extensions/suanshu/build.gradle b/extensions/suanshu/build.gradle
index fcf78f7cf47..4fad4f06ee7 100644
--- a/extensions/suanshu/build.gradle
+++ b/extensions/suanshu/build.gradle
@@ -3,10 +3,6 @@ plugins {
     id 'io.deephaven.project.register'
 }
 
-configurations {
-    testImplementation.extendsFrom fishBaseTest
-}
-
 dependencies {
     compileOnly project(':Base')
     compileOnly project(':engine-table')
@@ -20,4 +16,5 @@ dependencies {
 
     testImplementation project(':engine-table')
     testImplementation project(':base-test-utils')
+    testImplementation project(path: ':Base', configuration: 'tests')
 }
diff --git a/extensions/trackedfile/build.gradle b/extensions/trackedfile/build.gradle
index 6ea28e4b4e2..3896eb1e4ee 100644
--- a/extensions/trackedfile/build.gradle
+++ b/extensions/trackedfile/build.gradle
@@ -12,7 +12,7 @@ dependencies {
     implementation project(':Util')
     implementation project(':engine-table')
 
-    compileOnly depAnnotations
+    compileOnly libs.jetbrains.annotations
 
     compileOnly libs.autoservice
     annotationProcessor libs.autoservice.compiler
diff --git a/gradle/libs.versions.toml b/gradle/libs.versions.toml
index c2a81edae63..b7cd9dcf63f 100644
--- a/gradle/libs.versions.toml
+++ b/gradle/libs.versions.toml
@@ -5,7 +5,11 @@ avro = "1.11.3"
 awssdk = "2.24.5"
 # See dependency matrix for particular gRPC versions at https://github.com/grpc/grpc-java/blob/master/SECURITY.md#netty
 boringssl = "2.0.61.Final"
-commons = "1.10.0"
+commons-compress = "1.26.0"
+commons-io = "2.11.0"
+commons-lang3 = "3.12.0"
+commons-math3 = "3.6.1"
+commons-text = "1.10.0"
 dagger = "2.44"
 elemental = "1.2.1"
 flatbuffers = "1.12.0"
@@ -20,8 +24,11 @@ hadoop = "3.4.0"
 iceberg = "1.5.2"
 immutables = "2.9.2"
 jackson = "2.17.0"
+jama = "1.1.1"
 javaparser = "3.23.0"
 javax-validation = "1.0.0.GA"
+jdom2 = "2.0.6.1"
+jetbrains = "24.0.0"
 jetty = "11.0.20"
 jsinterop = "2.0.2"
 # google is annoying, and have different versions released for the same groupId
@@ -31,6 +38,8 @@ parquet = "1.14.0"
 protobuf = "3.25.3"
 slf4j = "2.0.11"
 sslcontext = "8.1.1"
+trove = "3.0.3"
+univocity = "2.6.0"
 
 # test versions
 assertj = "3.19.0"
@@ -60,7 +69,15 @@ awssdk-sts = { module = "software.amazon.awssdk:sts" }
 
 boringssl = { module = "io.netty:netty-tcnative-boringssl-static", version.ref = "boringssl" }
 
-commons-text = { module = "org.apache.commons:commons-text", version.ref = "commons" }
+commons-compress = { module = "org.apache.commons:commons-compress", version.ref = "commons-compress" }
+
+commons-io = { module = "commons-io:commons-io", version.ref = "commons-io" }
+
+commons-lang3 = { module = "org.apache.commons:commons-lang3", version.ref = "commons-lang3" }
+
+commons-math3 = { module = "org.apache.commons:commons-math3", version.ref = "commons-math3" }
+
+commons-text = { module = "org.apache.commons:commons-text", version.ref = "commons-text" }
 
 dagger = { module = "com.google.dagger:dagger", version.ref = "dagger" }
 dagger-compiler = { module = "com.google.dagger:dagger-compiler", version.ref = "dagger" }
@@ -112,10 +129,16 @@ jackson-databind = { module = "com.fasterxml.jackson.core:jackson-databind" }
 jackson-dataformat-yaml = { module = "com.fasterxml.jackson.dataformat:jackson-dataformat-yaml" }
 jackson-datatype-jdk8 = { module = "com.fasterxml.jackson.datatype:jackson-datatype-jdk8" }
 
+jama = { module = "gov.nist.math.jama:gov.nist.math.jama", version.ref = "jama" }
+
 javaparser-core = { module = "com.github.javaparser:javaparser-core", version.ref = "javaparser" }
 
 javax-validation-api = { module = "javax.validation:validation-api", version.ref = "javax-validation" }
 
+jdom2 = { module = "org.jdom:jdom2", version.ref = "jdom2" }
+
+jetbrains-annotations = { module = "org.jetbrains:annotations", version.ref = "jetbrains" }
+
 jetty-alpn-java-server = { module = "org.eclipse.jetty:jetty-alpn-java-server" }
 jetty-alpn-server = { module = "org.eclipse.jetty:jetty-alpn-server" }
 jetty-bom = { module = "org.eclipse.jetty:jetty-bom", version.ref = "jetty" }
@@ -142,6 +165,10 @@ sslcontext-kickstart = { module = "io.github.hakky54:sslcontext-kickstart", vers
 sslcontext-kickstart-jetty = { module = "io.github.hakky54:sslcontext-kickstart-for-jetty", version.ref = "sslcontext" }
 sslcontext-kickstart-netty = { module = "io.github.hakky54:sslcontext-kickstart-for-netty", version.ref = "sslcontext" }
 
+trove = { module = "net.sf.trove4j:trove4j", version.ref = "trove" }
+
+univocity-parsers = { module = "com.univocity:univocity-parsers", version.ref = "univocity" }
+
 # test libraries
 assertj = { module = "org.assertj:assertj-core", version.ref = "assertj" }
 
diff --git a/java-client/barrage/build.gradle b/java-client/barrage/build.gradle
index 51831fedb34..135471b40c8 100644
--- a/java-client/barrage/build.gradle
+++ b/java-client/barrage/build.gradle
@@ -3,11 +3,6 @@ plugins {
     id 'io.deephaven.project.register'
 }
 
-configurations {
-    implementation.extendsFrom irisDb
-    testImplementation.extendsFrom irisDbTest
-}
-
 description = 'The Deephaven Barrage Client'
 
 dependencies {
diff --git a/log-factory/build.gradle b/log-factory/build.gradle
index 9a3cdb9d750..175b7694c51 100644
--- a/log-factory/build.gradle
+++ b/log-factory/build.gradle
@@ -3,9 +3,7 @@ plugins {
   id 'io.deephaven.project.register'
 }
 
-configurations {
-  api.extendsFrom fishIo
-}
-
 dependencies {
+  api project(':Base')
+  api project(':IO')
 }
diff --git a/log-factory/sinks/log-to-logbuffer/build.gradle b/log-factory/sinks/log-to-logbuffer/build.gradle
index f0768c50958..81eaf423e40 100644
--- a/log-factory/sinks/log-to-logbuffer/build.gradle
+++ b/log-factory/sinks/log-to-logbuffer/build.gradle
@@ -3,11 +3,8 @@ plugins {
   id 'io.deephaven.project.register'
 }
 
-configurations {
-  compileOnly.extendsFrom fishIo
-}
-
 dependencies {
+  compileOnly project(':Base')
   compileOnly project(':log-factory')
 
   compileOnly libs.autoservice
diff --git a/log-factory/sinks/logback-logbuffer/build.gradle b/log-factory/sinks/logback-logbuffer/build.gradle
index fa5bf1f7de7..b5c78ad3cd3 100644
--- a/log-factory/sinks/logback-logbuffer/build.gradle
+++ b/log-factory/sinks/logback-logbuffer/build.gradle
@@ -3,11 +3,9 @@ plugins {
   id 'io.deephaven.project.register'
 }
 
-configurations {
-  compileOnly.extendsFrom fishIo
-}
-
 dependencies {
+  compileOnly project(':Base')
+  compileOnly project(':IO')
   // consumer still needs to provide dependency
   compileOnly libs.logback.classic
 }
diff --git a/log-factory/sinks/logback-print-stream-globals/build.gradle b/log-factory/sinks/logback-print-stream-globals/build.gradle
index 7935cfde2cb..ca09edcb778 100644
--- a/log-factory/sinks/logback-print-stream-globals/build.gradle
+++ b/log-factory/sinks/logback-print-stream-globals/build.gradle
@@ -3,11 +3,8 @@ plugins {
   id 'io.deephaven.project.register'
 }
 
-configurations {
-  compileOnly.extendsFrom fishBase
-}
-
 dependencies {
+  compileOnly project(':Base')
   // consumer still needs to provide dependency
   compileOnly libs.logback.classic
 }
diff --git a/props/test-configs/build.gradle b/props/test-configs/build.gradle
index 355b0ff08dd..a8700e7ac46 100644
--- a/props/test-configs/build.gradle
+++ b/props/test-configs/build.gradle
@@ -2,11 +2,9 @@ plugins {
     id 'io.deephaven.project.register'
 }
 
-configurations {
-    implementation.extendsFrom fishConfig
-}
-
 dependencies {
     compileOnly libs.autoservice
     annotationProcessor libs.autoservice.compiler
+
+    implementation project(':Configuration')
 }
diff --git a/proto/proto-backplane-grpc/build.gradle b/proto/proto-backplane-grpc/build.gradle
index c939556efda..54a277a296d 100644
--- a/proto/proto-backplane-grpc/build.gradle
+++ b/proto/proto-backplane-grpc/build.gradle
@@ -14,9 +14,6 @@ configurations {
     transitive = false
   }
 
-  // automatically pick up the standard junit version
-  testImplementation.extendsFrom junit
-
   js {}
   python {}
   go {}
@@ -46,6 +43,8 @@ dependencies {
   //  compile 'io.deephaven.barrage:barrage-core:0.5.0'
   download 'io.deephaven.barrage:barrage-core:0.6.0'
   download libs.arrow.flight.core
+
+  testImplementation libs.junit4
 }
 
 TaskProvider<Task> generateProtobuf = Docker.registerDockerTask(project, 'generateProtobuf') {
diff --git a/py/jpy-integration/build.gradle b/py/jpy-integration/build.gradle
index f0271aa83f8..bdeed8a0aeb 100644
--- a/py/jpy-integration/build.gradle
+++ b/py/jpy-integration/build.gradle
@@ -43,8 +43,6 @@ sourceSets {
 configurations {
   javaToPythonJar
 
-  testImplementation.extendsFrom junit
-
   javaToPythonImplementation.extendsFrom testImplementation
   pythonToJavaImplementation.extendsFrom testImplementation
 
@@ -57,6 +55,8 @@ dependencies {
   testImplementation project(':deephaven-jpy-ext')
   javaToPythonImplementation sourceSets.test.output
   pythonToJavaImplementation sourceSets.test.output
+
+  testImplementation libs.junit4
 }
 
 test {
diff --git a/replication/reflective/build.gradle b/replication/reflective/build.gradle
index 3d7bce37751..2e85df34e49 100644
--- a/replication/reflective/build.gradle
+++ b/replication/reflective/build.gradle
@@ -9,9 +9,9 @@ dependencies {
     implementation project(':replication-util')
     implementation project(':engine-table')
     implementation 'com.squareup:javapoet:1.13.0'
-    implementation depTrove3
-    implementation depCommonsIo
-    implementation depCommonsLang3
+    implementation libs.trove
+    implementation libs.commons.io
+    implementation libs.commons.lang3
 
     runtimeOnly project(':log-to-slf4j')
     runtimeOnly project(path: ':configs')
diff --git a/replication/static/build.gradle b/replication/static/build.gradle
index 6382374ad23..57be19681e5 100644
--- a/replication/static/build.gradle
+++ b/replication/static/build.gradle
@@ -9,8 +9,8 @@ dependencies {
     implementation project(':Util')
     implementation project(':Base')
     implementation project(':replication-util')
-    implementation depTrove3
-    implementation depCommonsIo
+    implementation libs.trove
+    implementation libs.commons.io
 }
 
 // These replicators do not require any manual fix-up and may be run without supervision
diff --git a/replication/util/build.gradle b/replication/util/build.gradle
index 9ee71496eae..1747b07c4e1 100644
--- a/replication/util/build.gradle
+++ b/replication/util/build.gradle
@@ -7,7 +7,7 @@ description 'Replication Tools: Utilities for source code generation and replica
 
 dependencies {
     implementation project(':Base'),
-            'commons-io:commons-io:2.11.0'
+            libs.commons.io
 
     compileOnly 'com.google.code.findbugs:jsr305:3.0.2'
 }
diff --git a/server/build.gradle b/server/build.gradle
index d4dbfa5f84c..01fb7ea8c0f 100644
--- a/server/build.gradle
+++ b/server/build.gradle
@@ -14,7 +14,7 @@ dependencies {
     implementation project(':extensions-jdbc')
     implementation project(':Util');
     implementation project(':Integrations')
-    implementation depCommonsLang3
+    implementation libs.commons.lang3
     implementation libs.commons.text
 
     implementation libs.javaparser.core
diff --git a/server/test-utils/build.gradle b/server/test-utils/build.gradle
index 366e7730fdb..37884eca41c 100644
--- a/server/test-utils/build.gradle
+++ b/server/test-utils/build.gradle
@@ -13,7 +13,7 @@ dependencies {
     implementation project(':proto:proto-backplane-grpc-flight')
     implementation project(':extensions-barrage')
     implementation project(':test-configs')
-    implementation depCommonsLang3
+    implementation libs.commons.lang3
     api project(':engine-test-utils')
 
     api platform(libs.grpc.bom)
diff --git a/web/client-api/client-api.gradle b/web/client-api/client-api.gradle
index 8ad75e7513e..da2fd222ac7 100644
--- a/web/client-api/client-api.gradle
+++ b/web/client-api/client-api.gradle
@@ -14,7 +14,6 @@ configurations {
     js
     dts
     typescriptDoclet
-    testImplementation.extendsFrom junit
 }
 
 dependencies {
@@ -28,6 +27,7 @@ dependencies {
 
     js project(path: ':proto:raw-js-openapi', configuration: 'js')
 
+    testImplementation libs.junit4
     testImplementation 'org.seleniumhq.selenium:selenium-remote-driver:4.16.1'
 
     implementation libs.elemental.core
diff --git a/web/shared-beans/shared-beans.gradle b/web/shared-beans/shared-beans.gradle
index 71f75c5aa53..208f0c86e47 100644
--- a/web/shared-beans/shared-beans.gradle
+++ b/web/shared-beans/shared-beans.gradle
@@ -5,13 +5,10 @@ plugins {
 
 GwtTools.gwtLib project
 
-configurations {
-    testImplementation.extendsFrom junit
-}
-
 dependencies {
     api project(':open-api-shared-fu')
 
+    testImplementation libs.junit4
     testImplementation libs.guava
 
     implementation libs.elemental.core