From e5f8875152a382e45758a4e9d531f0d2045937cb Mon Sep 17 00:00:00 2001
From: Yumeng Chen <yumeng.chen@reading.ac.uk>
Date: Wed, 24 Jan 2024 09:41:14 +0000
Subject: [PATCH] conda package for Linux done

---
 conda.recipe/build.sh |  6 +-----
 setup.cfg             |  3 ++-
 setup.py              | 14 +++++++++++---
 setup_mac.cfg         |  2 +-
 4 files changed, 15 insertions(+), 10 deletions(-)

diff --git a/conda.recipe/build.sh b/conda.recipe/build.sh
index 089ec8e8..58262bca 100644
--- a/conda.recipe/build.sh
+++ b/conda.recipe/build.sh
@@ -1,11 +1,7 @@
 #!/usr/bin/env bash
 set -ex
 
-sed -i "s^use_MKL=^use_MKL=True^g" setup.cfg
-sed -i "s^MKLROOT=^MKLROOT=${CONDA_PREFIX}/lib^g" setup.cfg
-
 
 # Install the Python package, but without dependencies,
 # because Conda takes care of that
-$PYTHON -m pip install . --no-deps --ignore-installed --no-cache-dir -vvv
-sed -i "s^MKLROOT=${CONDA_PREFIX}/lib^MKLROOT=^g" setup.cfg
\ No newline at end of file
+$PYTHON -m pip install . --no-deps --ignore-installed --no-cache-dir -vvv
\ No newline at end of file
diff --git a/setup.cfg b/setup.cfg
index 31cc6cb3..f3d9f46d 100644
--- a/setup.cfg
+++ b/setup.cfg
@@ -24,13 +24,14 @@ CPP_DEFS = -DUSE_PDAF
 [pyPDAF]
 pwd = /home/runner/work/pyPDAF/pyPDAF/
 CC = mpicc
+condaBuild =
 # if MKL is used, give the path to the static MKL library
 use_MKL=
 MKLROOT=
 # if dynamic/shared liblapack and libblas library is used,
 # give the library path and flags
 LAPACK_PATH=
-LAPACK_Flag=
+LAPACK_Flag=lapack,blas
 # GIVE MPI information
 MPI_INC_PATH=
 MPI_MOD_PATH=
diff --git a/setup.py b/setup.py
index 2c68e24e..bc0e3372 100644
--- a/setup.py
+++ b/setup.py
@@ -95,11 +95,17 @@
 # linking BLAS/LAPACK
 use_MKL=dist.get_option_dict('pyPDAF')['use_MKL'][1]
 if use_MKL == 'True':
-    MKLROOT=dist.get_option_dict('pyPDAF')['MKLROOT'][1]
+    condaBuild = dist.get_option_dict('pyPDAF')['condaBuild'][1]
+    if condaBuild == 'True':
+        MKLROOT = os.path.join(os.environ['PREFIX'], 'lib')
+    else:
+        MKLROOT = dist.get_option_dict('pyPDAF')['MKLROOT'][1]
+
     if os.name == 'nt':
         library_dirs+=[MKLROOT,]
         libraries = ['mkl_core', 'mkl_sequential', 'mkl_intel_lp64']
     else:
+
         extra_objects+=['-Wl,--start-group', 
                         f'{MKLROOT}/libmkl_intel_lp64.a',
                         f'{MKLROOT}/libmkl_sequential.a',
@@ -130,8 +136,10 @@
 # add fortran library to the linking
 if os.name != 'nt':
     suffix = 'dylib' if sys.platform == 'darwin' else 'so'
-    result = subprocess.run(['gfortran', '--print-file', 'libgfortran.'+suffix], stdout=subprocess.PIPE)
-    result = result.stdout.decode()[:-18] if sys.platform == 'darwin' else result.stdout.decode()[:-15]
+    result = subprocess.run(['gfortran', '--print-file',
+                             'libgfortran.'+suffix], stdout=subprocess.PIPE)
+    result = result.stdout.decode()
+    result = result[:-18] if sys.platform == 'darwin' else result[:-15]
     library_dirs+=[result,]
     library_dirs+=['/usr/lib', ]
     # somehow gfortran is always necessary
diff --git a/setup_mac.cfg b/setup_mac.cfg
index 09d46f9b..ea6843e5 100644
--- a/setup_mac.cfg
+++ b/setup_mac.cfg
@@ -41,7 +41,7 @@ MKLROOT=
 # if dynamic/shared liblapack and libblas library is used,
 # give the library path and flags
 LAPACK_PATH=
-LAPACK_Flag=
+LAPACK_Flag=lapack,blas
 # GIVE MPI information
 MPI_INC_PATH=
 MPI_MOD_PATH=