changes to work on nim 2.0 (force refc for gc)

Author: brentp

.github/workflows/build.yml

@@ -60,8 +60,8 @@ jobs:
       if: runner.os == 'Linux'
       run: |
         cd
-        git clone --recursive https://github.com/samtools/htslib.git
-        cd htslib && git checkout 1.11 && autoheader && autoconf && ./configure --enable-libcurl
+        git clone -b 1.18 --recursive https://github.com/samtools/htslib.git
+        cd htslib && autoheader && autoconf && ./configure --enable-libcurl
         sudo make -j 4 install
         sudo ldconfig
         #echo "::set-env name=LD_LIBRARY_PATH::${LD_LIBRARY_PATH}:${HOME}/htslib"
@@ -72,6 +72,11 @@ jobs:
       run: |
         brew install htslib
 
+    - name: Set DYLD_LIBRARY_PATH
+      if: runner.os == 'macOS'
+      run: |
+          echo "DYLD_LIBRARY_PATH=$(brew --prefix htslib)/lib" >> $GITHUB_ENV
+
     - name: Install d4 
       run: |
         #export HTSLIB=system
@@ -101,7 +106,7 @@ jobs:
       run: chmod +x mosdepth && mkdir bin && cp mosdepth bin/mosdepth_debug_${{ matrix.os }}
 
     - name: "Build and Copy release binary"
-      run: nim c -d:danger -d:release -o:bin/mosdepth_${{ matrix.os }} mosdepth
+      run: nim c --mm:refc -d:danger -d:release -o:bin/mosdepth_${{ matrix.os }} mosdepth
 
     - name: Functional Tests
       env:
@@ -117,5 +122,5 @@ jobs:
       if: success()
       uses: actions/upload-artifact@v4
       with:
-        name: mosdepth_${{ matrix.os }}_executable
+        name: mosdepth_${{ matrix.os }}_nim${{ matrix.version }}_executable
         path: bin/

functional-tests.sh

@@ -12,8 +12,8 @@ set -o nounset
 
 
 set -e
-nim c --boundChecks:on -x:on mosdepth.nim
-nim c -r tests/funcs.nim
+nim c --boundChecks:on -x:on -d:useSysAssert -d:useGcAssert --lineDir:on --debuginfo --mm:refc mosdepth.nim
+nim c -x:on --mm:refc -d:useSysAssert -d:useGcAssert --lineDir:on --debuginfo -r tests/funcs.nim
 set +e
 exe=./mosdepth
 bam=/data/human/NA12878.subset.bam

mosdepth.nim

@@ -504,7 +504,8 @@ proc write_thresholds(fh:BGZI, tid:int, arr:var coverage_t, thresholds:seq[int],
     return
 
   var counts = new_seq[int](len(thresholds))
-  shallow(arr)
+  when NimMajor < 2:
+      shallow(arr)
 
   # iterate over the region and count bases >= request cutoffs.
   for v in arr[start..<stop]:
@@ -630,7 +631,8 @@ proc main(bam: hts.Bam, chrom: region_t, mapq: int, min_len: int, max_len: int,
       window = uint32(S.parse_int(region))
     else:
       bed_regions = bed_to_table(region)
-  shallow(arr)
+  when NimMajor < 2:
+      shallow(arr)
 
   var cs = initCountStat[uint32](size=if use_median: 65536 else: 0)
 

mosdepth.nimble

@@ -7,7 +7,7 @@ license       = "MIT"
 
 # Dependencies
 
-requires "hts >= 0.3.22", "docopt == 0.7.0", "nim >= 1.0.0", "https://github.com/brentp/d4-nim >= 0.0.3"
+requires "hts >= 0.3.22", "docopt == 0.7.1", "nim >= 1.0.0", "https://github.com/brentp/d4-nim >= 0.0.3"
 
 bin = @["mosdepth"]
 skipDirs = @["tests"]