conda-forge · simonbray · Jan 25, 2020 · Jan 14, 2020 · Jan 14, 2020 · Jan 14, 2020
diff --git a/.ci_support/osx_python3.6.yaml b/.ci_support/osx_python3.6.yaml
@@ -0,0 +1,62 @@
+MACOSX_DEPLOYMENT_TARGET:
+- '10.9'
+boost_cpp:
+- 1.70.0
+bzip2:
+- '1'
+c_compiler:
+- clang
+c_compiler_version:
+- '9'
+channel_sources:
+- conda-forge,defaults
+channel_targets:
+- conda-forge main
+cxx_compiler:
+- clangxx
+cxx_compiler_version:
+- '9'
+fftw:
+- '3'
+fortran_compiler:
+- gfortran
+fortran_compiler_version:
+- '7'
+liblapack:
+- 3.8.0 *netlib
+libnetcdf:
+- 4.7.3
+macos_machine:
+- x86_64-apple-darwin13.4.0
+macos_min_version:
+- '10.9'
+netcdf_fortran:
+- '4.5'
+numpy:
+- '1.14'
+perl:
+- 5.26.2
+pin_run_as_build:
+  boost-cpp:
+    max_pin: x.x.x
+  bzip2:
+    max_pin: x
+  fftw:
+    max_pin: x
+  netcdf-fortran:
+    max_pin: x.x
+  perl:
+    max_pin: x.x.x
+  python:
+    min_pin: x.x
+    max_pin: x.x
+  readline:
+    max_pin: x
+  zlib:
+    max_pin: x.x
+python:
+- '3.6'
+readline:
+- '8.0'
+zlib:
+- '1.2'
diff --git a/.ci_support/osx_python3.7.yaml b/.ci_support/osx_python3.7.yaml
@@ -0,0 +1,62 @@
+MACOSX_DEPLOYMENT_TARGET:
+- '10.9'
+boost_cpp:
+- 1.70.0
+bzip2:
+- '1'
+c_compiler:
+- clang
+c_compiler_version:
+- '9'
+channel_sources:
+- conda-forge,defaults
+channel_targets:
+- conda-forge main
+cxx_compiler:
+- clangxx
+cxx_compiler_version:
+- '9'
+fftw:
+- '3'
+fortran_compiler:
+- gfortran
+fortran_compiler_version:
+- '7'
+liblapack:
+- 3.8.0 *netlib
+libnetcdf:
+- 4.7.3
+macos_machine:
+- x86_64-apple-darwin13.4.0
+macos_min_version:
+- '10.9'
+netcdf_fortran:
+- '4.5'
+numpy:
+- '1.14'
+perl:
+- 5.26.2
+pin_run_as_build:
+  boost-cpp:
+    max_pin: x.x.x
+  bzip2:
+    max_pin: x
+  fftw:
+    max_pin: x
+  netcdf-fortran:
+    max_pin: x.x
+  perl:
+    max_pin: x.x.x
+  python:
+    min_pin: x.x
+    max_pin: x.x
+  readline:
+    max_pin: x
+  zlib:
+    max_pin: x.x
+python:
+- '3.7'
+readline:
+- '8.0'
+zlib:
+- '1.2'
diff --git a/.ci_support/osx_python3.8.yaml b/.ci_support/osx_python3.8.yaml
@@ -0,0 +1,62 @@
+MACOSX_DEPLOYMENT_TARGET:
+- '10.9'
+boost_cpp:
+- 1.70.0
+bzip2:
+- '1'
+c_compiler:
+- clang
+c_compiler_version:
+- '9'
+channel_sources:
+- conda-forge,defaults
+channel_targets:
+- conda-forge main
+cxx_compiler:
+- clangxx
+cxx_compiler_version:
+- '9'
+fftw:
+- '3'
+fortran_compiler:
+- gfortran
+fortran_compiler_version:
+- '7'
+liblapack:
+- 3.8.0 *netlib
+libnetcdf:
+- 4.7.3
+macos_machine:
+- x86_64-apple-darwin13.4.0
+macos_min_version:
+- '10.9'
+netcdf_fortran:
+- '4.5'
+numpy:
+- '1.14'
+perl:
+- 5.26.2
+pin_run_as_build:
+  boost-cpp:
+    max_pin: x.x.x
+  bzip2:
+    max_pin: x
+  fftw:
+    max_pin: x
+  netcdf-fortran:
+    max_pin: x.x
+  perl:
+    max_pin: x.x.x
+  python:
+    min_pin: x.x
+    max_pin: x.x
+  readline:
+    max_pin: x
+  zlib:
+    max_pin: x.x
+python:
+- '3.8'
+readline:
+- '8.0'
+zlib:
+- '1.2'
diff --git a/README.md b/README.md
diff --git a/azure-pipelines.yml b/azure-pipelines.yml
diff --git a/recipe/build.sh b/recipe/build.sh
@@ -13,10 +13,15 @@ perl -pi -e 's/\r$//g' ${SRC_DIR}/cmake/*.cmake
 patch -p1 --ignore-whitespace -t -i amber19-fix-cmake.patch || true
 
 CMAKE_FLAGS=""
+BUILD_GUI="TRUE"
 if [[ "$target_platform" == osx* ]]; then
     CMAKE_FLAGS+=" -DCMAKE_OSX_SYSROOT=${CONDA_BUILD_SYSROOT}"
     CMAKE_FLAGS+=" -DCMAKE_OSX_DEPLOYMENT_TARGET=${MACOSX_DEPLOYMENT_TARGET}"
-    export FFLAGS="-isysroot ${CONDA_BUILD_SYSROOT} ${FFLAGS}"
+    BUILD_GUI="FALSE"
+    # Hack around https://github.com/conda-forge/gfortran_osx-64-feedstock/issues/11
+    # Taken from https://github.com/awvwgk/staged-recipes/tree/dftd4/recipes/dftd4
+    # See contents of fake-bin/cc1 for an explanation
+    export PATH="${PATH}:${RECIPE_DIR}/fake-bin"
 fi
 
 # Build AmberTools with cmake
@@ -27,7 +32,7 @@ cmake ${SRC_DIR} ${CMAKE_FLAGS} \
     -DCOMPILER=MANUAL \
     -DPYTHON_EXECUTABLE=${PYTHON} \
     -DDOWNLOAD_MINICONDA=FALSE \
-    -DBUILD_GUI=TRUE \
+    -DBUILD_GUI=${BUILD_GUI} \
     -DCHECK_UPDATES=FALSE
 
 make && make install

diff --git a/recipe/fake-bin/cc1 b/recipe/fake-bin/cc1
@@ -0,0 +1,26 @@
+#!/usr/bin/env bash
+
+###
+# Taken from https://github.com/awvwgk/staged-recipes/tree/dftd4/recipes/dftd4
+###
+
+# Detecting flags from gfortran which is backed by clang fails with
+#     x86_64-apple-darwin13.4.0-gfortran: error trying to exec 'cc1': execvp: No such file or directory
+# This comes from
+#     https://github.com/mesonbuild/meson/blob/61993f893bbdc2415155e28ee70e6ea806725e64/mesonbuild/environment.py#L668-L671
+# which runs
+#     x86_64-apple-darwin13.4.0-gfortran -E -dM -
+# Looking at the verbose output this is trying to run:
+#     cc1 -E -quiet -v -D__DYNAMIC__ - -fPIC -mmacosx-version-min=10.9 -mtune=generic -dM
+# The -quiet argument must be removed from the arguments as this isn't supported by clang
+# Adding this file to PATH hacks around these issues
+
+# Already reported at: https://github.com/conda-forge/gfortran_osx-64-feedstock/issues/11
+
+ARGS=()
+for var in "$@"; do
+    # Ignore known bad arguments
+    [ "$var" != '-quiet' ] && ARGS+=("$var")
+done
+
+"$CC" "${ARGS[@]}"
diff --git a/recipe/meta.yaml b/recipe/meta.yaml
@@ -14,14 +14,18 @@ source:
     - patches/do_not_use_global_conda_prefix.patch
     - patches/do_not_symlink_missing_ff12pol.patch
     - patches/use_external_netcdf.patch
+    - patches/do_not_override_osx_deployment_target.patch  # [osx]
+    # Fix weird bug described here:
+    #   https://github.com/conda-forge/ambertools-feedstock/pull/11#issuecomment-570618741
+    - patches/delete_xdrfile_version.patch  # [osx]
     # The following patch was downloaded from this GH issue:
     #   https://github.com/Amber-MD/cmake-buildscripts/issues/131#issuecomment-561280272
     # It needs to be applied manually in build.sh
     # - patches/amber19-fix-cmake.patch
 
 build:
-  number: 0
-  skip: True  # [win or py2k or osx]
+  number: 1
+  skip: True  # [win or py2k]
 
 requirements:
   build:
@@ -52,9 +56,8 @@ requirements:
     - pthread-stubs
     - fftw
     - liblapack
-    - xorg-libxt
-    - xorg-libxext
-    - xorg-libx11
+    - xorg-libxt  # [linux]
+    - xorg-libxext   # [linux]
     - readline
   run:
     - python
@@ -68,10 +71,8 @@ requirements:
     - fftw
     - libblas
     - liblapack
-    - libopenblas
-    - xorg-libxt
-    - xorg-libxext
-    - xorg-libx11
+    - xorg-libxt  # [linux]
+    - xorg-libxext  # [linux]
     - readline
 
 test:

diff --git a/recipe/patches/delete_xdrfile_version.patch b/recipe/patches/delete_xdrfile_version.patch
@@ -0,0 +1,7 @@
+diff --git a/AmberTools/src/cpptraj/src/xdrfile/VERSION b/AmberTools/src/cpptraj/src/xdrfile/VERSION
+deleted file mode 100644
+index 8926873d..00000000
+--- a/AmberTools/src/cpptraj/src/xdrfile/VERSION
++++ /dev/null
+@@ -1 +0,0 @@
+-Code is from MDTRAJ (https://github.com/mdtraj/mdtraj), commit aa1c91f3ab6b0f9e9f1d0c790d2b5bff7c83ece4
diff --git a/recipe/patches/do_not_override_osx_deployment_target.patch b/recipe/patches/do_not_override_osx_deployment_target.patch
@@ -0,0 +1,13 @@
+diff --git a/cmake/CompilerFlags.cmake b/cmake/CompilerFlags.cmake
+index 914eddbb..b2ed5cf5 100644
+--- a/cmake/CompilerFlags.cmake
++++ b/cmake/CompilerFlags.cmake
+@@ -215,7 +215,7 @@ if("${CMAKE_CXX_COMPILER_ID}" STREQUAL "Clang" OR "${CMAKE_CXX_COMPILER_ID}" STR
+ 	if(TARGET_OSX)
+ 		# on OS X, Python will link pytraj's extension modules to libc++, so cpptraj needs to use the same standard library
+ 		add_flags(CXX -stdlib=libc++)
+-		set(CMAKE_OSX_DEPLOYMENT_TARGET 10.7)
++		# set(CMAKE_OSX_DEPLOYMENT_TARGET 10.7)
+ 	endif()	
+
+ 	if(OPENMP AND (${CMAKE_CXX_COMPILER_VERSION} VERSION_LESS 3.7))