Update ipk to v0.5.1 (#47946)

* add ipk

* remove noarch

* reset build version

* fix url

* change shasum

* change compilation destination

* replace boost by boost-cpp and pin the version

* pin python >=3.8

* ipk recipe, first commit

* Add recipe ipk (#45958)

* Squash and merge

* Revert "Add recipe ipk (#45958)"

This reverts commit 859c9a1.

* transplant @blinard modifications related to IPK only from #45958

* make URL standard for bioconda autobump

* modify shasum to default release

* Use the specific release that include sources from git submodules that are not present by default

* Use phyml instead of raxml-ng in tests, to avoid CPU oversubscription issues in CI docker.

* Disables tests E and F until we find a fix to Azure test timout.

* attempt to reuse raxml-ng with #threads patch

* fix in test

* osx compilation patch

* removed last run test (>15 minutes on Azure) following bioconda's team demand

* bumps to v0.5.1

* bumps to v0.5.1

* Update meta.yaml

* removes osx patch, following new release

* removes patch related to raxml-oversubscription during bioconda tests

* removes patch related to binary expected directory

* build script updated following bugfix

* build in build

* bugfix

* Update recipes/ipk/build.sh

Co-authored-by: Martin Grigorov <martin-g@users.noreply.github.com>

* removes useless lines

---------

Co-authored-by: Jacques Dainat <jacques.dainat@ird.fr>
Co-authored-by: Benjamin Linard <benjamin.linard@inrae.fr>
Co-authored-by: Jacques Dainat <jacques.dainat@gmail.com>
Co-authored-by: B. Linard h <benjamin.linard@gmail.com>
Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com>
Co-authored-by: Martin Grigorov <martin-g@users.noreply.github.com>

recipes/ipk/build.sh

@@ -13,16 +13,17 @@ mkdir -p $PREFIX/bin
 mkdir -p $PREFIX/lib
 
 cmake -B build -DHASH_MAP=USE_TSL_ROBIN_MAP -DCMAKE_CXX_FLAGS="-O3" -DBUILD_SHARED_LIBS=ON --install-prefix=$PREFIX
-cmake --build build --target all
+cmake --build build --target all --target diff-dna --target diff-aa --target dump-dna --target dump-aa -j ${CPU_COUNT}
 cmake --install build
 
-ls build/ipk
-
 cp build/ipk/ipk-aa $PREFIX/bin
 cp build/ipk/ipk-aa-pos $PREFIX/bin
 cp build/ipk/ipk-dna $PREFIX/bin
+cp build/tools/ipkdiff-dna $PREFIX/bin
+cp build/tools/ipkdiff-aa $PREFIX/bin
+cp build/tools/ipkdump-dna $PREFIX/bin
+cp build/tools/ipkdump-aa $PREFIX/bin
 
-chmod +x $PREFIX/bin/ipk-aa
-chmod +x $PREFIX/bin/ipk-dna
-chmod +x $PREFIX/bin/ipk-aa-pos
-chmod +x $PREFIX/bin/ipk.py
+cp build/i2l/libi2l_aa.a $PREFIX/lib
+cp build/i2l/libi2l_aa_pos.a $PREFIX/lib
+cp build/i2l/libi2l_dna.a $PREFIX/lib

recipes/ipk/meta.yaml

@@ -1,6 +1,6 @@
 {% set name = "IPK" %}
-{% set version = "0.5.0" %}
-{% set sha256 = "7d073583d0f9891a30ec6865fee33818b526086a1f0de04028409496b279004c" %}
+{% set version = "0.5.1" %}
+{% set sha256 = "22efbfe282a37d153b69f44f6a655f39727d6ae955690b60fe1c6c785bbc0535" %}
 
 package:
   name: {{ name|lower }}
@@ -9,10 +9,6 @@ package:
 source:
   url: https://github.com/phylo42/{{ name|lower }}/releases/download/v{{ version }}/IPK-v{{ version }}_src_for_bioconda.tar.gz
   sha256: {{ sha256 }}
-  patches:
-    - 0001_makes_python_wrapper_to_expect_binaries_in_same_directory.patch
-    - 0002_default_threads_to_1_to_avoid_raxmlng_oversubscription.patch
-    - 0003_osx_compilation_requires_sstream_for_std-basic_istringstream.patch
 
 build:
   number: 0