Update hictk to v0.0.7 (bioconda#45433)

* Bump hictk to v0.0.7 * Try to reduce the level of parallelism during build * Update URL * Update checksum * Update patch * Bugfix * Bugfix
mencian · Jan 29, 2024 · 86d1f45 · 86d1f45
1 parent 1a28a6d
commit 86d1f45
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Showing 4 changed files with 22 additions and 18 deletions.
diff --git a/recipes/hictk/build.sh b/recipes/hictk/build.sh
@@ -2,7 +2,7 @@
 
 export CONAN_NON_INTERACTIVE=1
 
-export CMAKE_BUILD_PARALLEL_LEVEL=${CPU_COUNT}
+export CMAKE_BUILD_PARALLEL_LEVEL=1 # ${CPU_COUNT}
 export CTEST_PARALLEL_LEVEL=${CPU_COUNT}
 
 if [[ ${DEBUG_C} == yes ]]; then

diff --git a/recipes/hictk/conanfile.txt.patch b/recipes/hictk/conanfile.txt.patch
@@ -1,29 +1,31 @@
 diff --git a/conanfile.txt b/conanfile.txt
-index 0ea6184..eb94f2c 100644
+index c3cfb89..163ff31 100644
 --- a/conanfile.txt
 +++ b/conanfile.txt
-@@ -3,72 +3,11 @@
+@@ -3,74 +3,11 @@
  # SPDX-License-Identifier: MIT
 
  [requires]
--boost/1.83.0#7825569cd0622461dec7bc87dfdf47ae
+-boost/1.83.0#39551a6ba03b4fe2c7a86b9a6d80cd67
  bshoshany-thread-pool/3.5.0#5aaea7ccf37107d3c1ba9ca9ab246e42
+-catch2/3.5.2#9554dc3c4ffcab50daf8f2cac4b79308
 -cli11/2.3.2#1424b9b1d9e3682a7122f415b078b4d7
+ concurrentqueue/1.0.4#1e48e1c712bcfd892087c9c622a51502
 -eigen/3.4.0#2e192482a8acff96fe34766adca2b24c
 -fast_float/6.0.0#6c8a953c57879453982a6ce69c0ba87c
--fmt/10.1.1#cd63809a79574a2f9eb73ca35f16a243
+-fmt/10.2.1#9199a7a0611866dea5c8849a77467b25
 -hdf5/1.14.3#31ccd8d4de83844f5db48471df1944a1
 -highfive/2.8.0#b1de99f678ff5699cce6fb5fcac44d2d
 -libdeflate/1.19#3ea74a4549efc14d4b1202dc4bfbf602
  parallel-hashmap/1.3.11#1e67f4855a3f7cdeb977cc472113baf7
  readerwriterqueue/1.0.6#aaa5ff6fac60c2aee591e9e51b063b83
  span-lite/0.10.3#1967d71abb32b314387c2ab9c558dd22
--spdlog/1.12.0#0e390a2f5c3e96671d0857bc734e4731
+-spdlog/1.13.0#2775cc949e26b339029a852785b6b276
 -zstd/1.5.5#b87dc3b185caa4b122979ac4ae8ef7e8
 
  [generators]
  CMakeDeps
- 
+-
 -[options]
 -boost*:system_no_deprecated=True
 -boost*:asio_no_deprecated=True

diff --git a/recipes/hictk/meta.yaml b/recipes/hictk/meta.yaml
@@ -1,6 +1,6 @@
 {% set name = "hictk" %}
-{% set version = "0.0.6" %}
-{% set sha256 = "5913792f858304ff82996c9e9720442736b443d56c53aa8eb2a1ac2ae8ccc88f" %}
+{% set version = "0.0.7" %}
+{% set sha256 = "f3aaa80a399074f29747d99f5779d5a8221947044ef6946de3d7b9425d29d415" %}
 
 package:
   name: {{ name|lower }}
@@ -22,6 +22,7 @@ requirements:
     - cmake >=3.25
     - conan >=2
     - make
+    - catch2 >=3.5
     - cli11 >=2.3
     - eigen >=3.4
     - fast_float >=5
@@ -53,11 +54,13 @@ test:
   requires:
     - curl
     - cooler>=0.9.3
-    - openjdk>=11
     - perl-digest-sha1
     - xz
   source_files:
     - cmake/FetchTestDataset.cmake
+    - test/scripts/check_test_files_exist.sh
+    - test/scripts/compare_matrix_files.sh
+    - test/scripts/compare_plain_files.sh
     - test/scripts/hictk_balance.sh
     - test/scripts/hictk_convert_hic2cool.sh
     - test/scripts/hictk_convert_cool2hic.sh
@@ -78,6 +81,9 @@ test:
     - test/scripts/hictk_rename_chromosomes.sh
     - test/scripts/hictk_validate.sh
     - test/scripts/hictk_zoomify.sh
+    - test/scripts/nproc.sh
+    - test/scripts/readlink.sh
+    - test/scripts/shuffle.sh
   commands:
     - hictk --help
     - hictk --version

diff --git a/recipes/hictk/run_test.sh b/recipes/hictk/run_test.sh
@@ -16,16 +16,12 @@ shasum -c checksum.sha256
 
 tar -xf hictk_test_dataset.tar.xz
 
-# Download hictools
-hictools_url='https://github.com/aidenlab/HiCTools/releases/download/v3.30.00/hic_tools.3.30.00.jar'
-hictools_sha256='2b09b0642a826ca5730fde74e022461a708caf62ed292bc5baaa841946721867'
-curl -L "$hictools_url" -o hic_tools.jar
-echo "$hictools_sha256  hic_tools.jar" | tee checksum.sha256
-shasum -c checksum.sha256
-
 hictk="$(which hictk)"
 
 # Run integration tests
+
+test/scripts/hictk_balance.sh "$hictk"
+
 test/scripts/hictk_dump_chroms.sh "$hictk"
 test/scripts/hictk_dump_bins.sh "$hictk"
 test/scripts/hictk_dump_gw.sh "$hictk"
@@ -34,7 +30,7 @@ test/scripts/hictk_dump_trans.sh "$hictk"
 test/scripts/hictk_dump_balanced.sh "$hictk"
 
 test/scripts/hictk_convert_hic2cool.sh "$hictk"
-test/scripts/hictk_convert_cool2hic.sh "$hictk" hic_tools.jar
+test/scripts/hictk_convert_cool2hic.sh "$hictk"
 
 test/scripts/hictk_load_coo.sh "$hictk" sorted
 test/scripts/hictk_load_coo.sh "$hictk" unsorted