Run of fresh-snapshots for mosdepth

Merge these changes:

git pull https://janitor.debian.net/git/mosdepth fresh-snapshots/main
git pull https://janitor.debian.net/git/mosdepth fresh-snapshots/pristine-tar
git pull https://janitor.debian.net/git/mosdepth fresh-snapshots/upstream

Summary

Merged new upstream version: 0.3.3+git20220202.1.9cdf4c0 (was: 0.3.3+ds).

Diff

Branch: main

diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml
index 6a25ca9..e6a7faa 100644
--- a/.github/workflows/build.yml
+++ b/.github/workflows/build.yml
@@ -12,7 +12,7 @@ jobs:
     strategy:
       matrix:
         os: [ubuntu-18.04, macos-10.15]
-        nimversion:
+        version:
         - stable
         - devel
 
@@ -48,7 +48,7 @@ jobs:
       run: |
         sudo apt-get update
         sudo apt-get -qy install bwa make build-essential cmake libncurses-dev ncurses-dev libbz2-dev lzma-dev liblzma-dev \
-             curl libssl-dev libtool autoconf automake libcurl4-openssl-dev
+             curl libssl-dev libtool autoconf automake libcurl4-openssl-dev zlib1g-dev
 
     # Setup htslib
     - name: Install htslib (linux)
@@ -57,28 +57,31 @@ jobs:
         cd
         git clone --recursive https://github.com/samtools/htslib.git
         cd htslib && git checkout 1.11 && autoheader && autoconf && ./configure --enable-libcurl
-        cd
-        make -j 4 -C htslib install
-        echo "::set-env name=LD_LIBRARY_PATH::${LD_LIBRARY_PATH}:${HOME}/htslib"
-        ls -lh $HOME/htslib/*.so
+        sudo make -j 4 install
+        sudo ldconfig
+        #echo "::set-env name=LD_LIBRARY_PATH::${LD_LIBRARY_PATH}:${HOME}/htslib"
+        #ls -lh $HOME/htslib/*.so
+
+    - name: Install hstlib (macos)
+      if: runner.os == 'macOS'
+      run: |
+        brew install htslib
 
     - name: Install d4 
-        export HTSLIB=system
+      run: |
+        #export HTSLIB=system
         git clone https://github.com/38/d4-format
         cd d4-format
-        cargo build --release
+        cargo build --release --all-features
+        cd d4binding/ && cargo build --release && cd ..
         sudo cp ../d4-format/target/release/libd4binding.* /usr/local/lib
         sudo cp ./d4binding/include/d4.h /usr/local/include/
+        sudo ldconfig || true
 
 
-    - name: Install hstlib (macos)
-      if: runner.os == 'macOS'
-      run: |
-        brew install htslib
-
-    - uses: iffy/install-nim@v1.1
+    - uses: iffy/install-nim@v4.1.1
       with:
-        nimversion: ${{ matrix.nimversion }}
+        version: ${{ matrix.version }}
 
     - uses: actions-rs/toolchain@v1
       with:
diff --git a/debian/changelog b/debian/changelog
index f284bfe..7cd95db 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,3 +1,9 @@
+mosdepth (0.3.3+git20220202.1.9cdf4c0-1) UNRELEASED; urgency=low
+
+  * New upstream snapshot.
+
+ -- Debian Janitor <janitor@jelmer.uk>  Wed, 16 Mar 2022 22:16:03 -0000
+
 mosdepth (0.3.3+ds-1) unstable; urgency=medium
 
   * Team upload.
diff --git a/depthstat.nim b/depthstat.nim
index 558c6db..a86cbbb 100644
--- a/depthstat.nim
+++ b/depthstat.nim
@@ -18,7 +18,7 @@ proc add*[T](c: var CountStat, value: T) {.inline.} =
   if value.int > c.counts.high.int:
     c.counts[c.counts.high].inc
   elif value < 0:
-    raise newException(IndexError, "error setting negative depth value:" & $value)
+    raise newException(IndexDefect, "error setting negative depth value:" & $value)
   else:
     c.counts[value].inc
 
diff --git a/mosdepth.nim b/mosdepth.nim
index 88432ca..8080378 100644
--- a/mosdepth.nim
+++ b/mosdepth.nim
@@ -765,7 +765,7 @@ proc threshold_args*(ts: string): seq[int] =
 
 
 proc check_cram_has_ref(cram_path: string, fasta:string) =
-  if fasta != "" and exists_file(fasta):
+  if fasta != "" and fileExists(fasta):
     return
   if cram_path.ends_with(".cram"):
     stderr.write_line("[mosdepth] ERROR: specify a reference file (or set REF_PATH env var) for decoding CRAM")

Branch: pristine-tar

diff --git a/mosdepth_0.3.3+git20220202.1.9cdf4c0.orig.tar.gz.delta b/mosdepth_0.3.3+git20220202.1.9cdf4c0.orig.tar.gz.delta
new file mode 100644
index 0000000..5915bb0
Binary files /dev/null and b/mosdepth_0.3.3+git20220202.1.9cdf4c0.orig.tar.gz.delta differ
diff --git a/mosdepth_0.3.3+git20220202.1.9cdf4c0.orig.tar.gz.id b/mosdepth_0.3.3+git20220202.1.9cdf4c0.orig.tar.gz.id
new file mode 100644
index 0000000..c0e7b67
--- /dev/null
+++ b/mosdepth_0.3.3+git20220202.1.9cdf4c0.orig.tar.gz.id
@@ -0,0 +1 @@
+e61a5d828ffd89fd58ef0bb793238d42cb98665a

Branch: upstream

Tag: upstream/0.3.3+git20220202.1.9cdf4c0
diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml
index 6a25ca9..e6a7faa 100644
--- a/.github/workflows/build.yml
+++ b/.github/workflows/build.yml
@@ -12,7 +12,7 @@ jobs:
     strategy:
       matrix:
         os: [ubuntu-18.04, macos-10.15]
-        nimversion:
+        version:
         - stable
         - devel
 
@@ -48,7 +48,7 @@ jobs:
       run: |
         sudo apt-get update
         sudo apt-get -qy install bwa make build-essential cmake libncurses-dev ncurses-dev libbz2-dev lzma-dev liblzma-dev \
-             curl libssl-dev libtool autoconf automake libcurl4-openssl-dev
+             curl libssl-dev libtool autoconf automake libcurl4-openssl-dev zlib1g-dev
 
     # Setup htslib
     - name: Install htslib (linux)
@@ -57,28 +57,31 @@ jobs:
         cd
         git clone --recursive https://github.com/samtools/htslib.git
         cd htslib && git checkout 1.11 && autoheader && autoconf && ./configure --enable-libcurl
-        cd
-        make -j 4 -C htslib install
-        echo "::set-env name=LD_LIBRARY_PATH::${LD_LIBRARY_PATH}:${HOME}/htslib"
-        ls -lh $HOME/htslib/*.so
+        sudo make -j 4 install
+        sudo ldconfig
+        #echo "::set-env name=LD_LIBRARY_PATH::${LD_LIBRARY_PATH}:${HOME}/htslib"
+        #ls -lh $HOME/htslib/*.so
+
+    - name: Install hstlib (macos)
+      if: runner.os == 'macOS'
+      run: |
+        brew install htslib
 
     - name: Install d4 
-        export HTSLIB=system
+      run: |
+        #export HTSLIB=system
         git clone https://github.com/38/d4-format
         cd d4-format
-        cargo build --release
+        cargo build --release --all-features
+        cd d4binding/ && cargo build --release && cd ..
         sudo cp ../d4-format/target/release/libd4binding.* /usr/local/lib
         sudo cp ./d4binding/include/d4.h /usr/local/include/
+        sudo ldconfig || true
 
 
-    - name: Install hstlib (macos)
-      if: runner.os == 'macOS'
-      run: |
-        brew install htslib
-
-    - uses: iffy/install-nim@v1.1
+    - uses: iffy/install-nim@v4.1.1
       with:
-        nimversion: ${{ matrix.nimversion }}
+        version: ${{ matrix.version }}
 
     - uses: actions-rs/toolchain@v1
       with:
diff --git a/depthstat.nim b/depthstat.nim
index 558c6db..a86cbbb 100644
--- a/depthstat.nim
+++ b/depthstat.nim
@@ -18,7 +18,7 @@ proc add*[T](c: var CountStat, value: T) {.inline.} =
   if value.int > c.counts.high.int:
     c.counts[c.counts.high].inc
   elif value < 0:
-    raise newException(IndexError, "error setting negative depth value:" & $value)
+    raise newException(IndexDefect, "error setting negative depth value:" & $value)
   else:
     c.counts[value].inc
 
diff --git a/mosdepth.nim b/mosdepth.nim
index 88432ca..8080378 100644
--- a/mosdepth.nim
+++ b/mosdepth.nim
@@ -765,7 +765,7 @@ proc threshold_args*(ts: string): seq[int] =
 
 
 proc check_cram_has_ref(cram_path: string, fasta:string) =
-  if fasta != "" and exists_file(fasta):
+  if fasta != "" and fileExists(fasta):
     return
   if cram_path.ends_with(".cram"):
     stderr.write_line("[mosdepth] ERROR: specify a reference file (or set REF_PATH env var) for decoding CRAM")

Publish Blockers

  • ☑ run was successful
  • ☑ package has not been removed from the archive
  • ☑ command has not changed
  • ☑ review not required
  • ☑ 0 publish attempts so far.not currently attempting to back off
  • ☒ merge proposals for the package maintainer are currently being rate-limited (open: 529, max open: 300)
  • ☑ change set e2a510bd-0828-463d-b06d-6a7d64bd1960 is ready

Resulting package

The resulting binary packages can be installed (if you have the apt repository enabled) by running one of:

apt install -t fresh-snapshots mosdepth-dbgsymapt install -t fresh-snapshots mosdepth-examplesapt install -t fresh-snapshots mosdepth

Lintian Result

Full worker log Full build log