fix "assert_predicate" (#1976)

Author: YoshitakaMo

Formula/abyss-explorer.rb

@@ -26,7 +26,7 @@ def install
 
   test do
     assert_predicate bin/"abyss-explorer", :executable?
-    assert_predicate libexec/"ABySS-explorer.jar", :exist?
+    assert_path_exists libexec/"ABySS-explorer.jar"
     # This test fails on CI, though it succeeds locally.
     assert_match "Build", shell_output("#{bin}/abyss-explorer --version") unless ENV["HOMEBREW_GITHUB_ACTIONS"]
   end

Formula/alfred.rb

@@ -35,6 +35,6 @@ def install
     system "#{bin}/alfred", "qc", "-r", testpath/"example/E.coli.fa.gz",
                                   "-j", testpath/"ecoli.json.gz",
                                   testpath/"example/E.coli.cram"
-    assert_predicate testpath/"ecoli.json.gz", :exist?
+    assert_path_exists testpath/"ecoli.json.gz"
   end
 end

Formula/alphafill.rb

@@ -56,7 +56,7 @@ def install
     system "#{bin}/alphafill", "process", "--config", "#{testpath}/alphafill.conf",
            "#{prefix}/test/afdb-v4/P2/AF-P29373-F1-model_v4.cif.gz",
            "#{testpath}/out.cif.gz"
-    assert_predicate testpath/"out.cif.gz", :exist?
+    assert_path_exists testpath/"out.cif.gz"
     assert_match "RETINOIC ACID", shell_output("gunzip -c #{testpath}/out.cif.gz")
   end
 end

Formula/barrnap.rb

@@ -30,6 +30,6 @@ def install
     assert_match "Name=16S_rRNA", shell_output("#{bin}/barrnap -q --kingdom mito #{prefix}/examples/mitochondria.fna")
     out = testpath/"hits.fa"
     system "#{bin}/barrnap", "--outseq", out, "#{prefix}/examples/small.fna"
-    assert_predicate out, :exist?
+    assert_path_exists out
   end
 end

Formula/circos.rb

@@ -37,7 +37,7 @@ def install
 
   test do
     system bin/"circos", "-conf", libexec/"example/etc/circos.conf", "-debug_group", "summary,timer"
-    assert_predicate testpath/"circos.png", :exist?
-    assert_predicate testpath/"circos.svg", :exist?
+    assert_path_exists testpath/"circos.png"
+    assert_path_exists testpath/"circos.svg"
   end
 end

Formula/cluster-picker.rb

@@ -38,6 +38,6 @@ def install
     EOT
     # run
     assert_match "Reading", shell_output("#{bin}/ClusterPicker #{fa} #{nw} 0.9 2>&1")
-    assert_predicate testpath/"test_clusterPicks_log.txt", :exist?
+    assert_path_exists testpath/"test_clusterPicks_log.txt"
   end
 end

Formula/conform-gt.rb

@@ -25,7 +25,7 @@ def install
 
   test do
     assert_predicate bin/"conform-gt", :executable?
-    assert_predicate libexec/"conform-gt.jar", :exist?
+    assert_path_exists libexec/"conform-gt.jar"
     assert_match "usage: java -jar conform-gt.", shell_output("#{bin}/conform-gt")
   end
 end

Formula/delly.rb

@@ -39,6 +39,6 @@ def install
   test do
     assert_match version.to_s, shell_output("#{bin}/delly --version 2>&1")
     system "#{bin}/delly", "call", "-g", prefix/"example/ref.fa", "-o", testpath/"sr.bcf", prefix/"example/sr.bam"
-    assert_predicate testpath/"sr.bcf", :exist?
+    assert_path_exists testpath/"sr.bcf"
   end
 end

Formula/eigensoft.rb

@@ -78,21 +78,21 @@ def caveats
     cp_r samples/"EIGENSTRAT", testpath
     cd "EIGENSTRAT" do
       assert_match(/^gc.perl example.chisq example.chisq.GC$/, shell_output("perl example.perl"))
-      assert_predicate Pathname.pwd/"example.pca", :exist?
-      assert_predicate Pathname.pwd/"example.pca.evec", :exist?
-      assert_predicate Pathname.pwd/"example.plot.pdf", :exist?
-      assert_predicate Pathname.pwd/"example.plot.ps", :exist?
-      assert_predicate Pathname.pwd/"example.plot.xtxt", :exist?
+      assert_path_exists Pathname.pwd/"example.pca"
+      assert_path_exists Pathname.pwd/"example.pca.evec"
+      assert_path_exists Pathname.pwd/"example.plot.pdf"
+      assert_path_exists Pathname.pwd/"example.plot.ps"
+      assert_path_exists Pathname.pwd/"example.plot.xtxt"
     end
 
     cp_r samples/"POPGEN", testpath
     cd "POPGEN" do
       assert_match(/^evec2pca.perl 2 example.evec example.ind example.pca$/, shell_output("perl example.perl"))
-      assert_predicate Pathname.pwd/"example.pca", :exist?
-      assert_predicate Pathname.pwd/"example.evec", :exist?
-      assert_predicate Pathname.pwd/"example.plot.pdf", :exist?
-      assert_predicate Pathname.pwd/"example.plot.ps", :exist?
-      assert_predicate Pathname.pwd/"example.plot.xtxt", :exist?
+      assert_path_exists Pathname.pwd/"example.pca"
+      assert_path_exists Pathname.pwd/"example.evec"
+      assert_path_exists Pathname.pwd/"example.plot.pdf"
+      assert_path_exists Pathname.pwd/"example.plot.ps"
+      assert_path_exists Pathname.pwd/"example.plot.xtxt"
     end
   end
 end

Formula/falco.rb

@@ -43,7 +43,7 @@ def install
       @BCFFFFFHHHCFBHHIJJJICFGIIGIHHG3CEGEBA;@AEGHE:BEB<A@=B@@AAD>:?3>>:ABD5;BDBDACDACDBAC39C>@ACCDDCEEEDD
     EOS
     system "#{bin}/falco", "#{testpath}/test.fq"
-    assert_predicate testpath/"summary.txt", :exist?
-    assert_predicate testpath/"fastqc_report.html", :exist?
+    assert_path_exists testpath/"summary.txt"
+    assert_path_exists testpath/"fastqc_report.html"
   end
 end

Formula/faqcs.rb

@@ -42,7 +42,7 @@ def install
       @BCFFFFFHHHCFBHHIJJJICFGIIGIHHG3CEGEBA;@AEGHE:BEB<A@=B@@AAD>:?3>>:ABD5;BDBDACDACDBAC39C>@ACCDDCEEEDD
     EOS
     system "#{bin}/FaQCs", "-u", "#{testpath}/test.fq", "-d", testpath, "-qc_only"
-    assert_predicate testpath/"QC.stats.txt", :exist?
-    assert_predicate testpath/"QC_qc_report.pdf", :exist?
+    assert_path_exists testpath/"QC.stats.txt"
+    assert_path_exists testpath/"QC_qc_report.pdf"
   end
 end

Formula/fastani.rb

@@ -46,7 +46,7 @@ def install
            "-r", pkgshare/"data/Escherichia_coli_str_K12_MG1655.fna",
            "-o", testpath/"out",
            "--matrix"
-    assert_predicate testpath/"out", :exist?
-    assert_predicate testpath/"out.matrix", :exist?
+    assert_path_exists testpath/"out"
+    assert_path_exists testpath/"out.matrix"
   end
 end

Formula/gffcompare.rb

@@ -27,6 +27,6 @@ def install
     cp_r prefix/"examples", testpath
     system "#{bin}/gffcompare", "-r", "#{testpath}/examples/annotation.gff",
                                       "#{testpath}/examples/transcripts.gtf"
-    assert_predicate testpath/"examples/gffcmp.transcripts.gtf.tmap", :exist?
+    assert_path_exists testpath/"examples/gffcmp.transcripts.gtf.tmap"
   end
 end

Formula/gzstream.rb

@@ -25,7 +25,7 @@ def install
   end
 
   test do
-    assert_predicate include/"gzstream.h", :exist?
-    assert_predicate lib/"libgzstream.a", :exist?
+    assert_path_exists include/"gzstream.h"
+    assert_path_exists lib/"libgzstream.a"
   end
 end

Formula/hap-ibd.rb

@@ -25,7 +25,7 @@ def install
 
   test do
     assert_predicate bin/"hap-ibd", :executable?
-    assert_predicate libexec/"hap-ibd.jar", :exist?
+    assert_path_exists libexec/"hap-ibd.jar"
     assert_match(/^Syntax: java -jar hap-ibd.jar\b/, shell_output("#{bin}/hap-ibd"))
   end
 end

Formula/harvest-tools.rb

@@ -67,6 +67,6 @@ def install
                                   "-x", pkgshare/"test/test2.xmfa",
                                   "-v", pkgshare/"test/test2.vcf",
                                   "-o", testpath/"out.ggr"
-    assert_predicate testpath/"out.ggr", :exist?
+    assert_path_exists testpath/"out.ggr"
   end
 end

Formula/hisat2.rb

@@ -67,6 +67,6 @@ def install
 
   test do
     system "#{bin}/hisat2-build", "-p", "12", pkgshare/"example/reference/22_20-21M.fa", "genome_index"
-    assert_predicate testpath/"genome_index.1.ht2", :exist?
+    assert_path_exists testpath/"genome_index.1.ht2"
   end
 end

Formula/ibdseq.rb

@@ -25,7 +25,7 @@ def install
 
   test do
     assert_predicate bin/"ibdseq", :executable?
-    assert_predicate libexec/"ibdseq.jar", :exist?
+    assert_path_exists libexec/"ibdseq.jar"
     assert_match "usage: java -jar ibdseq.jar", shell_output("#{bin}/ibdseq")
   end
 end

Formula/last.rb

@@ -24,7 +24,7 @@ def install
   test do
     assert_match version.to_s, shell_output("#{bin}/lastal -V")
     system "#{bin}/lastdb", testpath/"db", pkgshare/"examples/mouseMito.fa"
-    assert_predicate testpath/"db.suf", :exist?
+    assert_path_exists testpath/"db.suf"
     assert_match "lambda=",
       shell_output("#{bin}/lastal #{testpath}/db #{pkgshare}/examples/chickenMito.fa")
   end

Formula/libgff.rb

@@ -21,7 +21,7 @@ def install
   end
 
   test do
-    assert_predicate lib/"libgff.a", :exist?
-    assert_predicate include/"gff.h", :exist?
+    assert_path_exists lib/"libgff.a"
+    assert_path_exists include/"gff.h"
   end
 end

Formula/mapcaller.rb

@@ -31,6 +31,6 @@ def install
                             "-f2", pkgshare/"test/r2.fq",
                             "-vcf", testpath/"out.vcf",
                             "-t", "2"
-    assert_predicate testpath/"out.vcf", :exist?
+    assert_path_exists testpath/"out.vcf"
   end
 end

Formula/mashmap.rb

@@ -35,7 +35,7 @@ def install
           "-Y '#' " \
           "-o scerevisiae8.paf"
     system cmd
-    assert_predicate testpath/"scerevisiae8.paf", :exist?
+    assert_path_exists testpath/"scerevisiae8.paf"
     assert_match "UWOPS034614#1#chrMT", (testpath/"scerevisiae8.paf").read
   end
 end

Formula/megahit.rb

@@ -36,7 +36,7 @@ def install
   test do
     outdir = "megahit.outdir"
     system "#{bin}/megahit", "--12", "#{pkgshare}/test_data/r2.il.fa.bz2", "-o", outdir
-    assert_predicate testpath/"#{outdir}/final.contigs.fa", :exist?
+    assert_path_exists testpath/"#{outdir}/final.contigs.fa"
     assert_match version.to_s, shell_output("#{bin}/megahit_toolkit dumpversion 2>&1")
   end
 end

Formula/oma.rb

@@ -69,6 +69,6 @@ def install
       MTIHNVSLFTTIFNIFKFCVLYITSSLGISLERFIKCRKVKNINDIVSE
     EOS
     system "#{bin}/oma"
-    assert_predicate testpath/"Output/HierarchicalGroups.orthoxml", :exist?
+    assert_path_exists testpath/"Output/HierarchicalGroups.orthoxml"
   end
 end

Formula/phyx.rb

@@ -37,6 +37,6 @@ def install
   test do
     assert_match "Usage", shell_output("#{bin}/pxseqgen --help")
     system "#{bin}/pxseqgen", "-t", "#{pkgshare}/pxseqgen_example/seqgen_test.tre", "-o", "output.fa"
-    assert_predicate testpath/"output.fa", :exist?
+    assert_path_exists testpath/"output.fa"
   end
 end

Formula/plink2.rb

@@ -42,6 +42,6 @@ def install
 
   test do
     system "#{bin}/plink2", "--dummy", "513", "1423", "0.02", "--out", "dummy_cc1"
-    assert_predicate testpath/"dummy_cc1.pvar", :exist?
+    assert_path_exists testpath/"dummy_cc1.pvar"
   end
 end

Formula/qtltools.rb

@@ -66,7 +66,7 @@ def install
     cp resource("testdata_index").cached_download, testpath/"genes.50percent.chr22.bed.gz.tbi"
     system "#{bin}/QTLtools", "pca", "--bed", "genes.50percent.chr22.bed.gz", "--scale",
           "--center", "--out", "genes.50percent.chr22"
-    assert_predicate testpath/"genes.50percent.chr22.pca_stats", :exist?
+    assert_path_exists testpath/"genes.50percent.chr22.pca_stats"
     assert_match "prop_var", File.read("genes.50percent.chr22.pca_stats")
   end
 end

Formula/quast.rb

@@ -87,6 +87,6 @@ def install
            "-1", "#{testpath}/test_data/reads1.fastq.gz",
            "-2", "#{testpath}/test_data/reads2.fastq.gz",
            "-o", "output", "-t", "1", "--debug", "--glimmer"
-    assert_predicate testpath/"output/report.pdf", :exist?
+    assert_path_exists testpath/"output/report.pdf"
   end
 end

Formula/raxml.rb

@@ -43,7 +43,7 @@ def install
     system "#{bin}/raxmlHPC-SSE3", "-f", "a", "-m", "GTRGAMMA", "-p",
                                        "12345", "-x", "12345", "-N", "100",
                                        "-s", "aln.phy", "-n", "ts"
-    assert_predicate testpath/"RAxML_bipartitions.ts", :exist?,
+    assert_path_exists testpath/"RAxML_bipartitions.ts",
                      "Failed to create RAxML_bipartitions.ts"
   end
 end

Formula/seqerr.rb

@@ -25,7 +25,7 @@ def install
 
   test do
     assert_predicate bin/"seqerr", :executable?
-    assert_predicate libexec/"seqerr.jar", :exist?
+    assert_path_exists libexec/"seqerr.jar"
     assert_match "usage: java -jar seqerr.jar", shell_output("#{bin}/seqerr")
   end
 end

Formula/trf.rb

@@ -31,7 +31,7 @@ def install
     EOS
     shell_output("#{bin}/trf #{testpath}/test.fa 2 7 7 80 10 50 500 2>&1", 1)
     out = testpath/"test.fa.2.7.7.80.10.50.500.1.txt.html"
-    assert_predicate out, :exist?
+    assert_path_exists out
     assert_match "Length: 180", File.read(out)
   end
 end

Formula/trinity.rb

@@ -98,6 +98,6 @@ def install
       "--seqType", "fq", "--max_memory", "1G", "--SS_lib_type", "RF",
       "--left", testpath/"reads.left.fq.gz,reads2.left.fq.gz",
       "--right", testpath/"reads.right.fq.gz,reads2.right.fq.gz"
-    assert_predicate testpath/"trinity_out_dir/both.fa", :exist?
+    assert_path_exists testpath/"trinity_out_dir/both.fa"
   end
 end

Formula/trnascan.rb

@@ -39,7 +39,7 @@ def install
 
   test do
     system "#{bin}/tRNAscan-SE", "-b", "test.bed", "#{prefix}/Demo/Example1.fa"
-    assert_predicate testpath/"test.bed", :exist?
+    assert_path_exists testpath/"test.bed"
     assert_equal File.read("test.bed"), File.read(prefix/"Demo/Example1-tRNAs.bed")
   end
 end

Formula/unicycler.rb

@@ -44,7 +44,7 @@ def install
     assert_match "usage", shell_output("#{bin}/unicycler --help")
     resources.each { |r| r.stage testpath }
     system "#{bin}/unicycler", "-1", "short_reads_1.fastq", "-2", "short_reads_2.fastq", "-o", "test"
-    assert_predicate testpath/"test/assembly.gfa", :exist?
-    assert_predicate testpath/"test/assembly.fasta", :exist?
+    assert_path_exists testpath/"test/assembly.gfa"
+    assert_path_exists testpath/"test/assembly.fasta"
   end
 end