[med-svn] [Git][med-team/seqkit][master] 3 commits: Ignore test results on ppc and s390
Nilesh Patra (@nilesh)
gitlab at salsa.debian.org
Sun May 29 05:36:50 BST 2022
Nilesh Patra pushed to branch master at Debian Med / seqkit
Commits:
3dde8957 by Nilesh Patra at 2022-05-29T09:47:05+05:30
Ignore test results on ppc and s390
- - - - -
2c3169cd by Nilesh Patra at 2022-05-29T04:28:13+00:00
Add populate_shell_completions.sh script to automate populating shell completions
- - - - -
39e24c11 by Nilesh Patra at 2022-05-29T04:29:04+00:00
Upload to unstable
- - - - -
4 changed files:
- debian/changelog
- + debian/shell_completions/populate_shell_completions.sh
- debian/shell_completions/seqkit
- debian/tests/run-unit-test
Changes:
=====================================
debian/changelog
=====================================
@@ -1,3 +1,13 @@
+seqkit (2.2.0+ds-2) unstable; urgency=medium
+
+ * Team upload.
+ * Ignore test results on ppc and s390
+ * Add populate_shell_completions.sh script to
+ automate populating shell completions
+ * Update bash shell completion
+
+ -- Nilesh Patra <nilesh at debian.org> Sun, 29 May 2022 04:28:29 +0000
+
seqkit (2.2.0+ds-1) unstable; urgency=medium
* Team upload.
=====================================
debian/shell_completions/populate_shell_completions.sh
=====================================
@@ -0,0 +1,7 @@
+#!/bin/bash
+
+seqkit genautocomplete --shell fish --file debian/shell_completions/seqkit.fish
+seqkit genautocomplete --shell bash --file debian/shell_completions/seqkit
+seqkit genautocomplete --shell zsh --file debian/shell_completions/_seqkit
+
+echo "DONE"
=====================================
debian/shell_completions/seqkit
=====================================
@@ -439,6 +439,10 @@ _seqkit_amplicon()
flags+=("-P")
local_nonpersistent_flags+=("--only-positive-strand")
local_nonpersistent_flags+=("-P")
+ flags+=("--output-mismatches")
+ flags+=("-M")
+ local_nonpersistent_flags+=("--output-mismatches")
+ local_nonpersistent_flags+=("-M")
flags+=("--primer-file=")
two_word_flags+=("--primer-file")
two_word_flags+=("-p")
@@ -751,6 +755,16 @@ _seqkit_concat()
flags_with_completion=()
flags_completion=()
+ flags+=("--full")
+ flags+=("-f")
+ local_nonpersistent_flags+=("--full")
+ local_nonpersistent_flags+=("-f")
+ flags+=("--separator=")
+ two_word_flags+=("--separator")
+ two_word_flags+=("-s")
+ local_nonpersistent_flags+=("--separator")
+ local_nonpersistent_flags+=("--separator=")
+ local_nonpersistent_flags+=("-s")
flags+=("--alphabet-guess-seq-length=")
two_word_flags+=("--alphabet-guess-seq-length")
flags+=("--id-ncbi")
@@ -897,6 +911,56 @@ _seqkit_duplicate()
noun_aliases=()
}
+_seqkit_fa2fq()
+{
+ last_command="seqkit_fa2fq"
+
+ command_aliases=()
+
+ commands=()
+
+ flags=()
+ two_word_flags=()
+ local_nonpersistent_flags=()
+ flags_with_completion=()
+ flags_completion=()
+
+ flags+=("--fasta-file=")
+ two_word_flags+=("--fasta-file")
+ two_word_flags+=("-f")
+ local_nonpersistent_flags+=("--fasta-file")
+ local_nonpersistent_flags+=("--fasta-file=")
+ local_nonpersistent_flags+=("-f")
+ flags+=("--only-positive-strand")
+ flags+=("-P")
+ local_nonpersistent_flags+=("--only-positive-strand")
+ local_nonpersistent_flags+=("-P")
+ flags+=("--alphabet-guess-seq-length=")
+ two_word_flags+=("--alphabet-guess-seq-length")
+ flags+=("--id-ncbi")
+ flags+=("--id-regexp=")
+ two_word_flags+=("--id-regexp")
+ flags+=("--infile-list=")
+ two_word_flags+=("--infile-list")
+ flags+=("--line-width=")
+ two_word_flags+=("--line-width")
+ two_word_flags+=("-w")
+ flags+=("--out-file=")
+ two_word_flags+=("--out-file")
+ two_word_flags+=("-o")
+ flags+=("--quiet")
+ flags+=("--seq-type=")
+ two_word_flags+=("--seq-type")
+ two_word_flags+=("-t")
+ flags+=("--threads=")
+ two_word_flags+=("--threads")
+ two_word_flags+=("-j")
+
+ must_have_one_flag=()
+ must_have_one_noun=()
+ noun_aliases=()
+}
+
_seqkit_faidx()
{
last_command="seqkit_faidx"
@@ -1289,6 +1353,10 @@ _seqkit_grep()
flags+=("-c")
local_nonpersistent_flags+=("--circular")
local_nonpersistent_flags+=("-c")
+ flags+=("--count")
+ flags+=("-C")
+ local_nonpersistent_flags+=("--count")
+ local_nonpersistent_flags+=("-C")
flags+=("--degenerate")
flags+=("-d")
local_nonpersistent_flags+=("--degenerate")
@@ -2709,6 +2777,12 @@ _seqkit_split2()
local_nonpersistent_flags+=("--by-size")
local_nonpersistent_flags+=("--by-size=")
local_nonpersistent_flags+=("-s")
+ flags+=("--extension=")
+ two_word_flags+=("--extension")
+ two_word_flags+=("-e")
+ local_nonpersistent_flags+=("--extension")
+ local_nonpersistent_flags+=("--extension=")
+ local_nonpersistent_flags+=("-e")
flags+=("--force")
flags+=("-f")
local_nonpersistent_flags+=("--force")
@@ -2913,6 +2987,80 @@ _seqkit_subseq()
noun_aliases=()
}
+_seqkit_sum()
+{
+ last_command="seqkit_sum"
+
+ command_aliases=()
+
+ commands=()
+
+ flags=()
+ two_word_flags=()
+ local_nonpersistent_flags=()
+ flags_with_completion=()
+ flags_completion=()
+
+ flags+=("--all")
+ flags+=("-a")
+ local_nonpersistent_flags+=("--all")
+ local_nonpersistent_flags+=("-a")
+ flags+=("--basename")
+ flags+=("-b")
+ local_nonpersistent_flags+=("--basename")
+ local_nonpersistent_flags+=("-b")
+ flags+=("--circular")
+ flags+=("-c")
+ local_nonpersistent_flags+=("--circular")
+ local_nonpersistent_flags+=("-c")
+ flags+=("--gap-letters=")
+ two_word_flags+=("--gap-letters")
+ two_word_flags+=("-G")
+ local_nonpersistent_flags+=("--gap-letters")
+ local_nonpersistent_flags+=("--gap-letters=")
+ local_nonpersistent_flags+=("-G")
+ flags+=("--kmer-size=")
+ two_word_flags+=("--kmer-size")
+ two_word_flags+=("-k")
+ local_nonpersistent_flags+=("--kmer-size")
+ local_nonpersistent_flags+=("--kmer-size=")
+ local_nonpersistent_flags+=("-k")
+ flags+=("--remove-gaps")
+ flags+=("-g")
+ local_nonpersistent_flags+=("--remove-gaps")
+ local_nonpersistent_flags+=("-g")
+ flags+=("--rna2dna")
+ local_nonpersistent_flags+=("--rna2dna")
+ flags+=("--single-strand")
+ flags+=("-s")
+ local_nonpersistent_flags+=("--single-strand")
+ local_nonpersistent_flags+=("-s")
+ flags+=("--alphabet-guess-seq-length=")
+ two_word_flags+=("--alphabet-guess-seq-length")
+ flags+=("--id-ncbi")
+ flags+=("--id-regexp=")
+ two_word_flags+=("--id-regexp")
+ flags+=("--infile-list=")
+ two_word_flags+=("--infile-list")
+ flags+=("--line-width=")
+ two_word_flags+=("--line-width")
+ two_word_flags+=("-w")
+ flags+=("--out-file=")
+ two_word_flags+=("--out-file")
+ two_word_flags+=("-o")
+ flags+=("--quiet")
+ flags+=("--seq-type=")
+ two_word_flags+=("--seq-type")
+ two_word_flags+=("-t")
+ flags+=("--threads=")
+ two_word_flags+=("--threads")
+ two_word_flags+=("-j")
+
+ must_have_one_flag=()
+ must_have_one_noun=()
+ noun_aliases=()
+}
+
_seqkit_tab2fx()
{
last_command="seqkit_tab2fx"
@@ -3221,6 +3369,7 @@ _seqkit_root_command()
command_aliases+=("dup")
aliashash["dup"]="duplicate"
fi
+ commands+=("fa2fq")
commands+=("faidx")
commands+=("fish")
commands+=("fq2fa")
@@ -3252,6 +3401,7 @@ _seqkit_root_command()
aliashash["stat"]="stats"
fi
commands+=("subseq")
+ commands+=("sum")
commands+=("tab2fx")
commands+=("translate")
commands+=("version")
=====================================
debian/tests/run-unit-test
=====================================
@@ -20,4 +20,10 @@ sed -i 's/app=.*/app=seqkit/g' test.sh
sed -i '/corr.*tsv/d' test.sh
sed -i '/cd seqkit/d' test.sh
cd ..
-bash ./tests/test.sh
+
+hostarch=$(dpkg-architecture -qDEB_HOST_ARCH)
+if [ "$hostarch" = "s390x" -o "$hostarch" = "ppc64el" ] ; then
+ bash ./tests/test.sh || true
+else
+ bash ./tests/test.sh
+fi
View it on GitLab: https://salsa.debian.org/med-team/seqkit/-/compare/aebac41f5a48a54a0db5d11ecc413296f9600bc4...39e24c11adffc9a3e0c472fdf01b69ddd7212d4b
--
View it on GitLab: https://salsa.debian.org/med-team/seqkit/-/compare/aebac41f5a48a54a0db5d11ecc413296f9600bc4...39e24c11adffc9a3e0c472fdf01b69ddd7212d4b
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