Merge pull request #310 from chrovis/feature/update-deps

Update dependencies
chrovis · May 13, 2024 · e170871 · e170871
2 parents 1dd64cd + e410311
commit e170871
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Showing 4 changed files with 18 additions and 18 deletions.
diff --git a/.github/workflows/format.yml b/.github/workflows/format.yml
@@ -10,7 +10,7 @@ jobs:
     - name: Setup Java
       uses: actions/setup-java@v4
       with:
-        java-version: '11'
+        java-version: '21'
         distribution: 'temurin'
         architecture: x64
     - name: Cache m2 repository

diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
@@ -7,7 +7,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        java: [ '8', '11', '17', '20']
+        java: [ '8', '11', '17', '21']
     name: Java ${{ matrix.java }}
     steps:
     - uses: actions/checkout@v4

diff --git a/project.clj b/project.clj
@@ -3,25 +3,25 @@
   :url "https://github.com/chrovis/cljam"
   :license {:name "Apache License, Version 2.0"
             :url "https://www.apache.org/licenses/LICENSE-2.0"}
-  :dependencies [[org.clojure/core.memoize "1.0.257"]
-                 [org.clojure/tools.logging "1.2.4"]
-                 [org.clojure/tools.cli "1.0.214"]
-                 [org.apache.commons/commons-compress "1.23.0"]
+  :dependencies [[org.clojure/core.memoize "1.1.266"]
+                 [org.clojure/tools.logging "1.3.0"]
+                 [org.clojure/tools.cli "1.1.230"]
+                 [org.apache.commons/commons-compress "1.26.1"]
                  [clj-sub-command "0.6.0"]
                  [digest "1.4.10"]
                  [bgzf4j "0.1.2"]
                  [com.climate/claypoole "1.1.4"]
                  [camel-snake-kebab "0.4.3"]
-                 [proton "0.2.2"]]
-  :profiles {:dev {:dependencies [[org.clojure/clojure "1.11.1"]
+                 [proton "0.2.3"]]
+  :profiles {:dev {:dependencies [[org.clojure/clojure "1.11.3"]
                                   [cavia "0.5.1"]
                                   [criterium "0.4.6"]
                                   [net.totakke/libra "0.1.1"]
                                   [se.haleby/stub-http "0.2.14"]]
-                   :plugins [[lein-binplus "0.6.6" :exclusions [org.clojure/clojure]]
-                             [lein-codox "0.10.7"]
-                             [lein-marginalia "0.9.1" :exclusions [org.clojure/clojure]]
-                             [lein-cloverage "1.1.2"]
+                   :plugins [[lein-binplus "0.6.8" :exclusions [org.clojure/clojure]]
+                             [lein-codox "0.10.8"]
+                             [lein-marginalia "0.9.2" :exclusions [org.clojure/clojure]]
+                             [lein-cloverage "1.2.4"]
                              [net.totakke/lein-libra "0.1.2"]
                              [lein-cljfmt "0.9.2"]]
                    :test-selectors {:default #(not-any? % [:slow :remote])
@@ -35,9 +35,9 @@
              :1.8 {:dependencies [[org.clojure/clojure "1.8.0"]]}
              :1.9 {:dependencies [[org.clojure/clojure "1.9.0"]]}
              :1.10 {:dependencies [[org.clojure/clojure "1.10.3"]]}
-             :uberjar {:dependencies [[org.clojure/clojure "1.11.1"]
-                                      [org.apache.logging.log4j/log4j-api "2.20.0"]
-                                      [org.apache.logging.log4j/log4j-core "2.20.0"]]
+             :uberjar {:dependencies [[org.clojure/clojure "1.11.3"]
+                                      [org.apache.logging.log4j/log4j-api "2.23.1"]
+                                      [org.apache.logging.log4j/log4j-core "2.23.1"]]
                        :resource-paths ["bin-resources"]
                        :main cljam.tools.main
                        :jvm-opts ["-Dclojure.compiler.direct-linking=true"]

diff --git a/src/cljam/io/wig.clj b/src/cljam/io/wig.clj
@@ -89,12 +89,12 @@
                    (let [type' (->> fields rest fields->map :type)]
                      (if (= type' "wiggle_0")
                        (deserialize (rest lines) pre-start {:line line})
-                       (throw "The track type with version must be `wiggle_0`")))
+                       (throw (ex-info "The track type with version must be `wiggle_0`" {}))))
 
                    ; declaration line of variableStep
                    "variableStep"
                    (let [{:keys [chrom span]
-                          :or {span 1}} (->> fields rest fields->map)
+                          :or {span "1"}} (->> fields rest fields->map)
                          span (as-long span)
                          track (assoc track :format :variable-step
                                       :chr chrom
@@ -105,7 +105,7 @@
                    ; declaration line of fixedStep
                    "fixedStep"
                    (let [{:keys [chrom start span step]
-                          :or {span 1, step 1}} (->> fields rest fields->map)
+                          :or {span "1", step "1"}} (->> fields rest fields->map)
                          step (long (as-long step))
                          pre-start (- (long (as-long start)) step)
                          span (as-long span)