From cb3a520812a62586e6f0eae117dde9caf7571007 Mon Sep 17 00:00:00 2001 From: alumi Date: Wed, 8 May 2024 13:51:02 +0900 Subject: [PATCH 01/15] build(deps): Update org.clojure/core.memoize to 1.1.266 --- project.clj | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/project.clj b/project.clj index e5761eb5..11495c63 100644 --- a/project.clj +++ b/project.clj @@ -3,7 +3,7 @@ :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"] + :dependencies [[org.clojure/core.memoize "1.1.266"] [org.clojure/tools.logging "1.2.4"] [org.clojure/tools.cli "1.0.214"] [org.apache.commons/commons-compress "1.23.0"] From 1fd78f69e3d6e3b90e44ef317b83405750c26a2d Mon Sep 17 00:00:00 2001 From: alumi Date: Wed, 8 May 2024 13:51:02 +0900 Subject: [PATCH 02/15] build(deps): Update org.clojure/tools.logging to 1.3.0 --- project.clj | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/project.clj b/project.clj index 11495c63..c5cde3fb 100644 --- a/project.clj +++ b/project.clj @@ -4,7 +4,7 @@ :license {:name "Apache License, Version 2.0" :url "https://www.apache.org/licenses/LICENSE-2.0"} :dependencies [[org.clojure/core.memoize "1.1.266"] - [org.clojure/tools.logging "1.2.4"] + [org.clojure/tools.logging "1.3.0"] [org.clojure/tools.cli "1.0.214"] [org.apache.commons/commons-compress "1.23.0"] [clj-sub-command "0.6.0"] From 325ada822619c32bd4d536696e81ada74dbf8ba3 Mon Sep 17 00:00:00 2001 From: alumi Date: Wed, 8 May 2024 13:51:02 +0900 Subject: [PATCH 03/15] build(deps): Update org.clojure/tools.cli to 1.1.230 --- project.clj | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/project.clj b/project.clj index c5cde3fb..16b6c48b 100644 --- a/project.clj +++ b/project.clj @@ -5,7 +5,7 @@ :url "https://www.apache.org/licenses/LICENSE-2.0"} :dependencies [[org.clojure/core.memoize "1.1.266"] [org.clojure/tools.logging "1.3.0"] - [org.clojure/tools.cli "1.0.214"] + [org.clojure/tools.cli "1.1.230"] [org.apache.commons/commons-compress "1.23.0"] [clj-sub-command "0.6.0"] [digest "1.4.10"] From 6c8a0fe2606db16763b88bb4fbd0b9e2a867f613 Mon Sep 17 00:00:00 2001 From: alumi Date: Wed, 8 May 2024 13:51:02 +0900 Subject: [PATCH 04/15] build(deps): Update org.apache.commons/commons-compress to 1.26.1 --- project.clj | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/project.clj b/project.clj index 16b6c48b..79cec030 100644 --- a/project.clj +++ b/project.clj @@ -6,7 +6,7 @@ :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 "1.23.0"] + [org.apache.commons/commons-compress "1.26.1"] [clj-sub-command "0.6.0"] [digest "1.4.10"] [bgzf4j "0.1.2"] From ab2ef410432951ff4281477d5a8ff5d208baff13 Mon Sep 17 00:00:00 2001 From: alumi Date: Wed, 8 May 2024 13:51:03 +0900 Subject: [PATCH 05/15] build(deps): Update org.apache.logging.log4j/log4j-api to 2.23.1 --- project.clj | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/project.clj b/project.clj index 79cec030..5466276e 100644 --- a/project.clj +++ b/project.clj @@ -36,7 +36,7 @@ :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-api "2.23.1"] [org.apache.logging.log4j/log4j-core "2.20.0"]] :resource-paths ["bin-resources"] :main cljam.tools.main From 6fbd0acbc86b698bbec81dbd1e8ce24bf3e346c0 Mon Sep 17 00:00:00 2001 From: alumi Date: Wed, 8 May 2024 13:51:03 +0900 Subject: [PATCH 06/15] build(deps): Update org.apache.logging.log4j/log4j-core to 2.23.1 --- project.clj | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/project.clj b/project.clj index 5466276e..72347cba 100644 --- a/project.clj +++ b/project.clj @@ -37,7 +37,7 @@ :1.10 {:dependencies [[org.clojure/clojure "1.10.3"]]} :uberjar {:dependencies [[org.clojure/clojure "1.11.1"] [org.apache.logging.log4j/log4j-api "2.23.1"] - [org.apache.logging.log4j/log4j-core "2.20.0"]] + [org.apache.logging.log4j/log4j-core "2.23.1"]] :resource-paths ["bin-resources"] :main cljam.tools.main :jvm-opts ["-Dclojure.compiler.direct-linking=true"] From 5b4fc6482beb3339b91813123015dd4fbc88bae7 Mon Sep 17 00:00:00 2001 From: alumi Date: Wed, 8 May 2024 13:51:02 +0900 Subject: [PATCH 07/15] build(deps): Update proton to 0.2.3 --- project.clj | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/project.clj b/project.clj index 72347cba..4d602a70 100644 --- a/project.clj +++ b/project.clj @@ -12,7 +12,7 @@ [bgzf4j "0.1.2"] [com.climate/claypoole "1.1.4"] [camel-snake-kebab "0.4.3"] - [proton "0.2.2"]] + [proton "0.2.3"]] :profiles {:dev {:dependencies [[org.clojure/clojure "1.11.1"] [cavia "0.5.1"] [criterium "0.4.6"] From 7c256a279da7087492e3fba0128a6b08dc45d4d9 Mon Sep 17 00:00:00 2001 From: alumi Date: Fri, 10 May 2024 14:47:49 +0900 Subject: [PATCH 08/15] fix: Fix types of default values in wig reader --- src/cljam/io/wig.clj | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/src/cljam/io/wig.clj b/src/cljam/io/wig.clj index 272282aa..d78068f1 100644 --- a/src/cljam/io/wig.clj +++ b/src/cljam/io/wig.clj @@ -94,7 +94,7 @@ ; 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) From 7d482da82e3e9ecc0bffb8d4dc8e9a74d6160047 Mon Sep 17 00:00:00 2001 From: alumi Date: Fri, 10 May 2024 14:50:38 +0900 Subject: [PATCH 09/15] fix: An exception must be a throwable in wig reader --- src/cljam/io/wig.clj | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/cljam/io/wig.clj b/src/cljam/io/wig.clj index d78068f1..09ee1687 100644 --- a/src/cljam/io/wig.clj +++ b/src/cljam/io/wig.clj @@ -89,7 +89,7 @@ (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" From 05ae8ebbcdbe02a8a676db7fa5c447f39b7baf3b Mon Sep 17 00:00:00 2001 From: alumi Date: Wed, 8 May 2024 13:57:46 +0900 Subject: [PATCH 10/15] build(deps): Update lein-binplus to 0.6.8 --- project.clj | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/project.clj b/project.clj index 4d602a70..a4be994d 100644 --- a/project.clj +++ b/project.clj @@ -18,7 +18,7 @@ [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]] + :plugins [[lein-binplus "0.6.8" :exclusions [org.clojure/clojure]] [lein-codox "0.10.7"] [lein-marginalia "0.9.1" :exclusions [org.clojure/clojure]] [lein-cloverage "1.1.2"] From be8c73aeb02721c6c70c4325d4ef299c3bc4c7bb Mon Sep 17 00:00:00 2001 From: alumi Date: Wed, 8 May 2024 13:57:46 +0900 Subject: [PATCH 11/15] build(deps): Update lein-codox to 0.10.8 --- project.clj | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/project.clj b/project.clj index a4be994d..f5d50d66 100644 --- a/project.clj +++ b/project.clj @@ -19,7 +19,7 @@ [net.totakke/libra "0.1.1"] [se.haleby/stub-http "0.2.14"]] :plugins [[lein-binplus "0.6.8" :exclusions [org.clojure/clojure]] - [lein-codox "0.10.7"] + [lein-codox "0.10.8"] [lein-marginalia "0.9.1" :exclusions [org.clojure/clojure]] [lein-cloverage "1.1.2"] [net.totakke/lein-libra "0.1.2"] From c70b0637355a994a7a45bba8a4a6b6b36ad0a978 Mon Sep 17 00:00:00 2001 From: alumi Date: Wed, 8 May 2024 13:57:46 +0900 Subject: [PATCH 12/15] build(deps): Update lein-marginalia to 0.9.2 --- project.clj | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/project.clj b/project.clj index f5d50d66..cea67ff1 100644 --- a/project.clj +++ b/project.clj @@ -20,7 +20,7 @@ [se.haleby/stub-http "0.2.14"]] :plugins [[lein-binplus "0.6.8" :exclusions [org.clojure/clojure]] [lein-codox "0.10.8"] - [lein-marginalia "0.9.1" :exclusions [org.clojure/clojure]] + [lein-marginalia "0.9.2" :exclusions [org.clojure/clojure]] [lein-cloverage "1.1.2"] [net.totakke/lein-libra "0.1.2"] [lein-cljfmt "0.9.2"]] From f153a1998c836b7b4e03e9719d0040ab196b8831 Mon Sep 17 00:00:00 2001 From: alumi Date: Wed, 8 May 2024 13:57:46 +0900 Subject: [PATCH 13/15] build(deps): Update lein-cloverage to 1.2.4 --- project.clj | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/project.clj b/project.clj index cea67ff1..1ec150ff 100644 --- a/project.clj +++ b/project.clj @@ -21,7 +21,7 @@ :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 "1.1.2"] + [lein-cloverage "1.2.4"] [net.totakke/lein-libra "0.1.2"] [lein-cljfmt "0.9.2"]] :test-selectors {:default #(not-any? % [:slow :remote]) From 5fbfa50c0e5bc32c61c8c58e9a276eabf1294026 Mon Sep 17 00:00:00 2001 From: alumi Date: Wed, 8 May 2024 13:59:59 +0900 Subject: [PATCH 14/15] build(deps): Update clojure to 1.11.3 --- project.clj | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/project.clj b/project.clj index 1ec150ff..3d25240e 100644 --- a/project.clj +++ b/project.clj @@ -13,7 +13,7 @@ [com.climate/claypoole "1.1.4"] [camel-snake-kebab "0.4.3"] [proton "0.2.3"]] - :profiles {:dev {:dependencies [[org.clojure/clojure "1.11.1"] + :profiles {:dev {:dependencies [[org.clojure/clojure "1.11.3"] [cavia "0.5.1"] [criterium "0.4.6"] [net.totakke/libra "0.1.1"] @@ -35,7 +35,7 @@ :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"] + :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"] From e41031152a0609042435fa1838e50daafa15bd6a Mon Sep 17 00:00:00 2001 From: alumi Date: Wed, 8 May 2024 16:00:12 +0900 Subject: [PATCH 15/15] ci(deps): Update java to 21 --- .github/workflows/format.yml | 2 +- .github/workflows/main.yml | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/format.yml b/.github/workflows/format.yml index 0711080d..4be2ac36 100644 --- 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 index ef408006..fa135f3c 100644 --- 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