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Merged
bhauman merged 2 commits into from
Nov 20, 2025
Merged

Migrate from clojure.tools.logging to Timbre #131

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5ee41c9
Migrate from clojure.tools.logging to Timbre
Nov 19, 2025
969d273
chagne logging defaults
Nov 20, 2025
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51 changes: 18 additions & 33 deletions deps.edn
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Original file line number Diff line number Diff line change
Expand Up @@ -2,7 +2,6 @@
:deps {org.clojure/clojure {:mvn/version "1.12.1"}
org.clojure/data.json {:mvn/version "2.5.1"}
nrepl/nrepl {:mvn/version "1.3.1"}
org.clojure/tools.logging {:mvn/version "1.3.0"}
org.clojure/tools.cli {:mvn/version "1.1.230"}
org.clj-commons/pretty {:mvn/version "3.6.7"}

Expand All @@ -27,22 +26,22 @@
dev.langchain4j/langchain4j-anthropic {:mvn/version "1.8.0"}
dev.langchain4j/langchain4j-google-ai-gemini {:mvn/version "1.8.0"}

;; in order to use the stdio server you have to handle logging somehow
;; org.slf4j/slf4j-nop {:mvn/version "2.0.16"}
com.taoensso/timbre {:mvn/version "6.8.0"}

;; Suppress logging from Java libraries (MCP SDK, LangChain4j, etc.)
org.slf4j/slf4j-nop {:mvn/version "2.0.16"}

;; native Java diff library
io.github.java-diff-utils/java-diff-utils {:mvn/version "4.15"}}
:aliases

{:mcp
{:extra-deps {org.slf4j/slf4j-nop {:mvn/version "2.0.16"}}
:exec-fn clojure-mcp.main/start-mcp-server
{:exec-fn clojure-mcp.main/start-mcp-server
;; it needs an nrepl port to talk to
:exec-args {:port 7888}}

:mcp-sse
{:extra-deps {org.slf4j/slf4j-nop {:mvn/version "2.0.16"} ;; optional
jakarta.servlet/jakarta.servlet-api {:mvn/version "6.1.0"}
{:extra-deps {jakarta.servlet/jakarta.servlet-api {:mvn/version "6.1.0"}
org.eclipse.jetty/jetty-server {:mvn/version "11.0.20"}
org.eclipse.jetty/jetty-servlet {:mvn/version "11.0.20"}}
:exec-fn clojure-mcp.sse-main/start-sse-mcp-server
Expand All @@ -52,86 +51,72 @@
:mcp-sse-port 8078}}

:mcp-figwheel
{:extra-deps {org.slf4j/slf4j-nop {:mvn/version "2.0.16"}}
:exec-fn clojure-mcp.main-examples.figwheel-main/start-mcp-server
{:exec-fn clojure-mcp.main-examples.figwheel-main/start-mcp-server
:exec-args {:port 7888 :figwheel-build "dev"}}

:mcp-shadow
{:extra-deps {org.slf4j/slf4j-nop {:mvn/version "2.0.16"}}
:exec-fn clojure-mcp.main-examples.shadow-main/start-mcp-server
{:exec-fn clojure-mcp.main-examples.shadow-main/start-mcp-server
:exec-args {:port 7888 :shadow-build "app"}}

;; dual shadow and project nrepl setup
:mcp-shadow-dual
{:extra-deps {org.slf4j/slf4j-nop {:mvn/version "2.0.16"}}
:extra-paths ["dev" "test"]
{:extra-paths ["dev" "test"]
:exec-fn clojure-mcp.main-examples.shadow-main/start-mcp-server
;; it needs an nrepl port to talk to
:exec-args {:port 7888 :shadow-build "app" :shadow-port 7889}}

;; below are dev set ups that need a logback.xml file
;; below are dev set ups
:prompt-cli
{:extra-deps {org.slf4j/slf4j-nop {:mvn/version "2.0.16"}}
:main-opts ["-m" "clojure-mcp.prompt-cli"]}
{:main-opts ["-m" "clojure-mcp.prompt-cli"]}

:dev-mcp
{:extra-deps {ch.qos.logback/logback-classic {:mvn/version "1.4.14"}}
:extra-paths ["dev" "test"]
{:extra-paths ["dev" "test"]
:exec-fn clojure-mcp.main/start-mcp-server
;; it needs an nrepl port to talk to
:exec-args {:port 7888
;; test auto starting the repl
;; :start-nrepl-cmd ["clojure" "-M:nrepl"]
}}

;; DEV setup needs logback.xml
:dev-mcp-figwheel
{:extra-deps {ch.qos.logback/logback-classic {:mvn/version "1.4.14"}}
:extra-paths ["dev" "test"]
{:extra-paths ["dev" "test"]
:exec-fn clojure-mcp.main-examples.figwheel-main/start-mcp-server
;; it needs an nrepl port to talk to
:exec-args {:port 7888 :figwheel-build "dev"}}

;; DEV setup needs logback.xml
:dev-mcp-shadow
{:extra-deps {ch.qos.logback/logback-classic {:mvn/version "1.4.14"}}
:extra-paths ["dev" "test"]
{:extra-paths ["dev" "test"]
:exec-fn clojure-mcp.main-examples.shadow-main/start-mcp-server
;; it needs an nrepl port to talk to
:exec-args {:port 7888 :shadow-build "app"}}

:dev-mcp-shadow-dual
{:extra-deps {ch.qos.logback/logback-classic {:mvn/version "1.4.14"}}
:extra-paths ["dev" "test"]
{:extra-paths ["dev" "test"]
:exec-fn clojure-mcp.main-examples.shadow-main/start-mcp-server
;; it needs an nrepl port to talk to
:exec-args {:port 7888 :shadow-build "app" :shadow-port 7889}}

:nrepl {:extra-paths ["test" "dev"]
:extra-deps {ch.qos.logback/logback-classic {:mvn/version "1.4.14"}}
:main-opts ["-m" "nrepl.cmdline" "--port" "7888"]}

:dkr-nrepl {:extra-paths ["test" "dev"]
:extra-deps {ch.qos.logback/logback-classic {:mvn/version "1.4.14"}}
:main-opts ["-m" "nrepl.cmdline" "--port" "7888"
;; for Docker
"--bind" "0.0.0.0"]}

;; dev cycle
:test
{:extra-paths ["test" "dev"]
:exec-fn cognitect.test-runner/test
:extra-deps {ch.qos.logback/logback-classic {:mvn/version "1.4.14"}
org.clojure/test.check {:mvn/version "1.1.1"}
:exec-fn clojure-mcp.test-helper/run-tests-with-exec
:extra-deps {org.clojure/test.check {:mvn/version "1.1.1"}
nrepl/nrepl {:mvn/version "1.3.1"} ;; Add nrepl server for testing
io.github.cognitect-labs/test-runner
{:git/tag "v0.5.1" :git/sha "dfb30dd"}}
:main-opts ["-m" "cognitect.test-runner"]}
:main-opts ["-e" "(require 'clojure-mcp.test-helper)" "-m" "cognitect.test-runner"]}

:index
{:exec-fn clojure-mcp.code-indexer/map-project
:exec-args {}
:extra-deps {org.slf4j/slf4j-nop {:mvn/version "2.0.16"}}
;; Override with: clojure -X:index :dirs '["src" "lib"]' :include-tests true :out-file '"my-index.txt"'
}

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57 changes: 0 additions & 57 deletions dev/logback.xml
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2 changes: 1 addition & 1 deletion src/clojure_mcp/agent/general_agent.clj
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Expand Up @@ -2,7 +2,7 @@
"A generalized agent library that can be parameterized with system prompts,
context, tools, memory, and models."
(:require [clojure.string :as string]
[clojure.tools.logging :as log]
[taoensso.timbre :as log]
[clojure.java.io :as io]
[clojure-mcp.agent.langchain :as chain]
[clojure-mcp.tools.project.core :as project-core]
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2 changes: 1 addition & 1 deletion src/clojure_mcp/agent/langchain.clj
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Expand Up @@ -2,7 +2,7 @@
(:require
[clojure.data.json :as json]
[clojure-mcp.agent.langchain.schema :as schema]
[clojure.tools.logging :as log]
[taoensso.timbre :as log]
[clojure.string :as string]
[clojure.pprint])
(:import
Expand Down
2 changes: 1 addition & 1 deletion src/clojure_mcp/agent/langchain/chat_listener.clj
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Expand Up @@ -2,7 +2,7 @@
"Creates ChatModelListener instances from Clojure functions that work with EDN data"
(:require
[clojure-mcp.agent.langchain.message-conv :as msg-conv]
[clojure.tools.logging :as log])
[taoensso.timbre :as log])
(:import
[dev.langchain4j.model.chat.listener
ChatModelListener
Expand Down
2 changes: 1 addition & 1 deletion src/clojure_mcp/agent/langchain/model.clj
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Expand Up @@ -2,7 +2,7 @@
(:require
[clojure-mcp.config.schema :as schema]
[clojure-mcp.config :as config]
[clojure.tools.logging :as log])
[taoensso.timbre :as log])
(:import
[dev.langchain4j.model.anthropic
AnthropicChatModel
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2 changes: 1 addition & 1 deletion src/clojure_mcp/config.clj
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Expand Up @@ -4,7 +4,7 @@
[clojure-mcp.config.schema :as schema]
[clojure-mcp.utils.file :as file-utils]
[clojure.edn :as edn]
[clojure.tools.logging :as log]))
[taoensso.timbre :as log]))

(defn- relative-to [dir path]
(try
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2 changes: 1 addition & 1 deletion src/clojure_mcp/core.clj
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Expand Up @@ -2,7 +2,7 @@
(:require [clojure.data.json :as json]
[clojure.java.io :as io]
[clojure.spec.alpha :as s]
[clojure.tools.logging :as log]
[taoensso.timbre :as log]
[clojure-mcp.nrepl :as nrepl]
[clojure-mcp.config :as config]
[clojure-mcp.dialects :as dialects]
Expand Down
2 changes: 1 addition & 1 deletion src/clojure_mcp/dialects.clj
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Expand Up @@ -5,7 +5,7 @@
and initialization sequences specific to each dialect."
(:require [clojure.edn :as edn]
[clojure.java.io :as io]
[clojure.tools.logging :as log]
[taoensso.timbre :as log]
[clojure-mcp.nrepl :as nrepl]
[clojure-mcp.utils.file :as file-utils]))

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71 changes: 71 additions & 0 deletions src/clojure_mcp/logging.clj
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@@ -0,0 +1,71 @@
(ns clojure-mcp.logging
"Centralized logging configuration using Timbre.

This namespace provides functions to configure Timbre-based logging
for the Clojure MCP server with support for both development and
production modes."
(:require [taoensso.timbre :as timbre]))

(def default-log-file ".clojure-mcp/clojure-mcp.log")

(defn configure-logging!
"Configure Timbre logging with the given options.

Options:
- :log-file Path to log file (default: 'logs/clojure-mcp.log')
- :enable-logging? Whether to enable logging (default: true)
- :log-level Minimum log level (default: :debug)
Valid values: :trace :debug :info :warn :error :fatal :report
Comment on lines +14 to +18
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@coderabbitai coderabbitai bot Nov 20, 2025

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⚠️ Potential issue | 🟠 Major

Fix configure-logging! option docs to match actual defaults

The option docs and the implementation diverge:

  • Doc says :log-file default is 'logs/clojure-mcp.log', but :or uses default-log-file which is ".clojure-mcp/clojure-mcp.log".
  • Doc says :enable-logging? default is true, but the implementation defaults it to false.

Given this is a new public API, this mismatch will confuse users configuring logging from the CLI/entry points.

Consider updating the docstring to describe the real behavior:

-   - :log-file       Path to log file (default: 'logs/clojure-mcp.log')
-   - :enable-logging? Whether to enable logging (default: true)
-   - :log-level      Minimum log level (default: :debug)
+   - :log-file         Path to log file (default: '.clojure-mcp/clojure-mcp.log')
+   - :enable-logging?  Whether to enable logging (default: false)
+   - :log-level        Minimum log level when logging is enabled (default: :debug)

Also applies to: 29-32

🤖 Prompt for AI Agents 
In src/clojure_mcp/logging.clj around lines 14-18 and 29-32, the docstring
defaults for :log-file and :enable-logging? do not match the implementation;
update the two documentation blocks to state the actual defaults (use
default-log-file value ".clojure-mcp/clojure-mcp.log" for :log-file and set
:enable-logging? default to false), and ensure the :log-level default text
remains correct (e.g., :debug) — or alternatively change the implementation to
match the previously documented defaults; pick one approach and make both doc
blocks consistent with the code.


Examples:

Development mode with full logging:
(configure-logging! {:log-file \"logs/clojure-mcp.log\"
:enable-logging? true
:log-level :debug})

Production mode with logging suppressed:
(configure-logging! {:enable-logging? false})"
[{:keys [log-file enable-logging? log-level]
:or {log-file default-log-file
enable-logging? false
log-level :debug}}]
(timbre/set-config!
{:appenders (if enable-logging?
{:spit (assoc
(timbre/spit-appender {:fname log-file})
:enabled? enable-logging?
:min-level (or log-level :report)
:ns-filter (if enable-logging?
{:allow #{"clojure-mcp.*"}}
{:deny #{"*"}}))}
{})}))

(defn configure-dev-logging!
"Configure logging for development mode with debug level.
Convenience function that enables full debug logging to logs/clojure-mcp.log"
[]
(configure-logging! {:log-file "logs/clojure-mcp.log"
:enable-logging? true
:log-level :debug}))

(defn configure-prod-logging!
"Configure logging for production mode with all logging suppressed.
Convenience function that disables all logging."
[]
(configure-logging! {:enable-logging? false}))

(defn configure-test-logging!
"Configure logging for test mode with all logging suppressed.
Convenience function that disables all logging during tests."
[]
(configure-logging! {:enable-logging? false}))

(defn suppress-logging-for-tests!
"Automatically suppress logging if running in test mode.
Checks for CLOJURE_MCP_TEST environment variable or
clojure.mcp.test system property."
[]
(when (or (System/getenv "CLOJURE_MCP_TEST")
(System/getProperty "clojure.mcp.test"))
(configure-test-logging!)))
8 changes: 7 additions & 1 deletion src/clojure_mcp/main.clj
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@@ -1,5 +1,6 @@
(ns clojure-mcp.main
(:require [clojure-mcp.core :as core]
[clojure-mcp.logging :as logging]
[clojure-mcp.prompts :as prompts]
[clojure-mcp.resources :as resources]
[clojure-mcp.tools :as tools]))
Expand Down Expand Up @@ -33,8 +34,13 @@
(tools/build-all-tools nrepl-client-atom))

(defn start-mcp-server [opts]
;; Configure logging before starting the server
(logging/configure-logging!
{:log-file (get opts :log-file logging/default-log-file)
:enable-logging? (get opts :enable-logging? false)
:log-level (get opts :log-level :debug)})
(core/build-and-start-mcp-server
opts
(dissoc opts :log-file :log-level :enable-logging?)
{:make-tools-fn make-tools
:make-prompts-fn make-prompts
:make-resources-fn make-resources}))
Expand Down
8 changes: 7 additions & 1 deletion src/clojure_mcp/main_examples/figwheel_main.clj
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Expand Up @@ -10,6 +10,7 @@
See the comments below for the required deps.edn configuration."
(:require
[clojure-mcp.core :as core]
[clojure-mcp.logging :as logging]
[clojure-mcp.main :as main]
[clojure-mcp.tools.figwheel.tool :as figwheel-tool]))

Expand All @@ -36,8 +37,13 @@
(figwheel-tool/figwheel-eval nrepl-client-atom {:figwheel-build (or figwheel-build "dev")})))

(defn start-mcp-server [opts]
;; Configure logging before starting the server
(logging/configure-logging!
{:log-file (get opts :log-file logging/default-log-file)
:enable-logging? (get opts :enable-logging? false)
:log-level (get opts :log-level :debug)})
(core/build-and-start-mcp-server
opts
(dissoc opts :log-file :log-level :enable-logging?)
{:make-tools-fn (fn [nrepl-client-atom working-directory]
(make-tools nrepl-client-atom working-directory opts))
:make-prompts-fn main/make-prompts
Expand Down
10 changes: 8 additions & 2 deletions src/clojure_mcp/main_examples/shadow_main.clj
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Expand Up @@ -11,8 +11,9 @@
- Dual connection: Connect to a separate Shadow CLJS nREPL server"
(:require
[clojure-mcp.core :as core]
[clojure-mcp.logging :as logging]
[clojure-mcp.nrepl :as nrepl]
[clojure.tools.logging :as log]
[taoensso.timbre :as log]
[clojure-mcp.main :as main]
[clojure-mcp.tools.eval.tool :as eval-tool]))

Expand Down Expand Up @@ -82,8 +83,13 @@ JavaScript interop is fully supported including `js/console.log`, `js/setTimeout
(shadow-eval-tool nrepl-client-atom config))))

(defn start-mcp-server [opts]
;; Configure logging before starting the server
(logging/configure-logging!
{:log-file (get opts :log-file logging/default-log-file)
:enable-logging? (get opts :enable-logging? false)
:log-level (get opts :log-level :debug)})
(core/build-and-start-mcp-server
opts
(dissoc opts :log-file :log-level :enable-logging?)
{:make-tools-fn (fn [nrepl-client-atom working-directory]
(make-tools nrepl-client-atom working-directory opts))
:make-prompts-fn main/make-prompts
Expand Down
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