Build HTSLib as part of superbuild

.ci_support/linux_64_.yaml

@@ -1,19 +1,27 @@
+bzip2:
+- '1'
 c_compiler:
 - gcc
 c_compiler_version:
-- '10'
+- '11'
 cdt_name:
 - cos6
 channel_sources:
-- conda-forge,bioconda,defaults
+- conda-forge,defaults
 channel_targets:
 - tiledb main
 cxx_compiler:
 - gxx
 cxx_compiler_version:
-- '10'
+- '11'
 docker_image:
 - quay.io/condaforge/linux-anvil-cos7-x86_64
+libcurl:
+- '7'
+libdeflate:
+- '1.14'
+openssl:
+- 1.1.1
 pin_run_as_build:
   python:
     min_pin: x.x
@@ -25,6 +33,10 @@ python:
 - 3.9.* *_cpython
 target_platform:
 - linux-64
+xz:
+- '5'
 zip_keys:
 - - c_compiler_version
   - cxx_compiler_version
+zlib:
+- '1.2'

.ci_support/osx_64_.yaml

@@ -2,20 +2,28 @@ MACOSX_DEPLOYMENT_TARGET:
 - '10.14'
 MACOSX_SDK_VERSION:
 - '10.14'
+bzip2:
+- '1'
 c_compiler:
 - clang
 c_compiler_version:
 - '14'
 channel_sources:
-- conda-forge,bioconda,defaults
+- conda-forge,defaults
 channel_targets:
 - tiledb main
 cxx_compiler:
 - clangxx
 cxx_compiler_version:
 - '14'
+libcurl:
+- '7'
+libdeflate:
+- '1.14'
 macos_machine:
 - x86_64-apple-darwin13.4.0
+openssl:
+- 1.1.1
 pin_run_as_build:
   python:
     min_pin: x.x
@@ -27,6 +35,10 @@ python:
 - 3.9.* *_cpython
 target_platform:
 - osx-64
+xz:
+- '5'
 zip_keys:
 - - c_compiler_version
   - cxx_compiler_version
+zlib:
+- '1.2'

.github/workflows/automerge.yml

@@ -10,10 +10,10 @@ jobs:
     name: automerge
     steps:
       - name: checkout
-        uses: actions/checkout@v2
+        uses: actions/checkout@v3
       - name: automerge-action
         id: automerge-action
-        uses: conda-forge/automerge-action@main
+        uses: conda-forge/automerge-action@master
         with:
           github_token: ${{ secrets.GITHUB_TOKEN }}
           rerendering_github_token: ${{ secrets.RERENDERING_GITHUB_TOKEN }}

.github/workflows/webservices.yml

@@ -7,7 +7,7 @@ jobs:
     steps:
       - name: webservices
         id: webservices
-        uses: conda-forge/webservices-dispatch-action@main
+        uses: conda-forge/webservices-dispatch-action@master
         with:
           github_token: ${{ secrets.GITHUB_TOKEN }}
           rerendering_github_token: ${{ secrets.RERENDERING_GITHUB_TOKEN }}

recipe/0001-htslib-build.patch

@@ -0,0 +1,13 @@
+diff --git a/libtiledbvcf/cmake/Modules/FindHTSlib.cmake b/libtiledbvcf/cmake/Modules/FindHTSlib.cmake
+index 3e5b4e7..3688982 100644
+--- a/libtiledbvcf/cmake/Modules/FindHTSlib.cmake
++++ b/libtiledbvcf/cmake/Modules/FindHTSlib.cmake
+@@ -91,7 +91,7 @@ if (NOT HTSLIB_FOUND)
+         COMMAND
+           ${AUTORECONF} -i
+         COMMAND
+-          ./configure --prefix=${EP_INSTALL_PREFIX} LDFLAGS=${EXTRA_LDFLAGS} CFLAGS=${CFLAGS}
++          ./configure --disable-libcurl --disable-gcs --disable-aws --prefix=${EP_INSTALL_PREFIX} LDFLAGS=${EXTRA_LDFLAGS} CFLAGS=${CFLAGS}
+       BUILD_COMMAND
+         $(MAKE)
+       INSTALL_COMMAND

recipe/build.sh

@@ -7,7 +7,7 @@ cmake \
   -DCMAKE_INSTALL_PREFIX:PATH="${PREFIX}" \
   -DOVERRIDE_INSTALL_PREFIX=OFF \
   -DCMAKE_BUILD_TYPE=Release \
-  -DFORCE_EXTERNAL_HTSLIB=OFF \
+  -DFORCE_EXTERNAL_HTSLIB=ON \
   ../libtiledbvcf
 
 make -j ${CPU_COUNT}

recipe/conda_build_config.yaml

@@ -3,6 +3,21 @@ MACOSX_SDK_VERSION:  # [osx and x86_64]
 MACOSX_DEPLOYMENT_TARGET:  # [osx and x86_64]
   - "10.14"                # [osx and x86_64]
 channel_sources:
-  - conda-forge,bioconda,defaults
+  - conda-forge,defaults
 channel_targets:
   - tiledb main
+numpy:
+  - 1.20   # [not (osx and arm64)]
+  - 1.20
+  - 1.20
+  - 1.21
+python:
+  - 3.7.* *_cpython   # [not (osx and arm64)]
+  - 3.8.* *_cpython
+  - 3.9.* *_cpython
+  - 3.10.* *_cpython
+python_impl:
+  - cpython   # [not (osx and arm64)]
+  - cpython
+  - cpython
+  - cpython

recipe/meta.yaml

@@ -13,9 +13,11 @@ source:
   #url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz
   url: https://github.com/TileDB-Inc/TileDB-VCF/archive/{{ version }}.tar.gz
   sha256: {{ sha256 }}
+  patches:
+    - 0001-htslib-build.patch
 
 build:
-  number: 0
+  number: 1
   skip: true  # [win or linux32 or py2k]
 
 requirements:
@@ -25,13 +27,12 @@ requirements:
     - git
     - cmake
     - make
+    - autoconf
+    - automake
   run:
-    - htslib >=1.15
     - tiledb 2.12.*
   host:
-    - htslib >=1.15
     - tiledb 2.12.*
-
 outputs:
   - name: libtiledbvcf
     version: {{ version }}
@@ -42,12 +43,22 @@ outputs:
         - {{ compiler('cxx') }}
         - cmake
         - make
+        - autoconf
+        - automake
       host:
-        - htslib >=1.15
         - tiledb 2.12.*
+        # htslib build requirements
+        - bzip2
+        - xz
+        - zlib
+        - libdeflate
       run:
-        - htslib >=1.15
         - tiledb 2.12.*
+        # htslib build requirements
+        - bzip2
+        - xz
+        - zlib
+        - libdeflate
     test:
       commands:
         - tiledbvcf version