From 4602c195797a2a554383797269fa9dc99bb87b3d Mon Sep 17 00:00:00 2001
From: David Minton <daminton@purdue.edu>
Date: Fri, 11 Aug 2023 13:44:52 -0400
Subject: [PATCH] Fixes to build scripts so that they can work with Docker or
 just conda/mamba

---
 Dockerfile                                         |  9 +++------
 buildscripts/build_all.sh                          | 14 ++++++--------
 buildscripts/build_dependencies.sh                 |  4 ++--
 ...ke_environment.sh => make_build_environment.sh} | 13 +++++++++----
 4 files changed, 20 insertions(+), 20 deletions(-)
 rename buildscripts/{make_environment.sh => make_build_environment.sh} (85%)

diff --git a/Dockerfile b/Dockerfile
index 125417410..61b835958 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -23,13 +23,10 @@ COPY . ./
 RUN ${SCRIPT_DIR}/fetch_dependencies.sh  
 RUN if [ "$BUILDIMAGE" = "intel/oneapi-hpckit:2023.1.0-devel-ubuntu20.04" ]; then \
         ${SCRIPT_DIR}/build_dependencies.sh Intel; \
-    else \
-        conda init bash && \
-        conda update --name base conda -y && \
-        ${SCRIPT_DIR}/make_environment.sh && \
+    else \ 
+        ${SCRIPT_DIR}/make_build_environment.sh && \
         echo "conda activate swiftest-build-env" >> ~/.bashrc  && \
-        source ~/.bashrc && \
-        ${SCRIPT_DIR}/build_dependencies.sh GNU; \
+        /bin/bash -lic "${SCRIPT_DIR}/build_dependencies.sh GNU"; \
     fi 
 
 # ENV INSTALL_DIR="/usr/local"
diff --git a/buildscripts/build_all.sh b/buildscripts/build_all.sh
index e64d22c14..fdcceb037 100755
--- a/buildscripts/build_all.sh
+++ b/buildscripts/build_all.sh
@@ -23,20 +23,18 @@
 
 
 # Determine the platform and architecture
-SCRIPT_DIR=$(dirname "$0")
+SCRIPT_DIR=$(realpath $(dirname $0))
+ROOT_DIR=$(realpath ${SCRIPT_DIR}/..)
+BUILD_DIR=$(realpath ${ROOT_DIR}/build)
 read -r OS ARCH < <($SCRIPT_DIR/get_platform.sh)
 
 # Determine if we are in the correct directory (the script can either be run from the Swiftest project root directory or the
 # buildscripts directory)
-if [ ! -f "./setup.py" ]; then
-    if [ -f "../setup.py" ]; then
-        cd ..
-    else
-        echo "Error: setup.py not found in . or .."
+if [ ! -f "${ROOT_DIR}/setup.py" ]; then
+        echo "Error: setup.py not found" 
         exit 1
-    fi
 fi
-
+cd ${ROOT_DIR}
 VERSION=$( cat version.txt )
 echo "Building Swiftest version ${VERSION} for ${OS}-${ARCH}"
 
diff --git a/buildscripts/build_dependencies.sh b/buildscripts/build_dependencies.sh
index 066b9f180..b06b1e8a8 100755
--- a/buildscripts/build_dependencies.sh
+++ b/buildscripts/build_dependencies.sh
@@ -10,8 +10,8 @@
 # of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
 # You should have received a copy of the GNU General Public License along with Swiftest. 
 # If not, see: https://www.gnu.org/licenses. 
-SCRIPT_DIR=$(dirname "$0")
-BUILD_DIR=${SCRIPT_DIR}/../build
+SCRIPT_DIR=$(realpath $(dirname $0))
+BUILD_DIR=$(realpath ${SCRIPT_DIR}/../build)
 mkdir -p ${BUILD_DIR}
 cd $BUILD_DIR
 
diff --git a/buildscripts/make_environment.sh b/buildscripts/make_build_environment.sh
similarity index 85%
rename from buildscripts/make_environment.sh
rename to buildscripts/make_build_environment.sh
index 152c0ca0f..fb42fc110 100755
--- a/buildscripts/make_environment.sh
+++ b/buildscripts/make_build_environment.sh
@@ -1,4 +1,4 @@
-#!/bin/bash
+#!/bin/bash -l
 # This script will create a miniforge3 conda environment in order to execute the build
 # Zlib, hdf5, netcdf-c, netcdf-fortran
 # 
@@ -31,9 +31,14 @@ else
    ${SHELL} Mambaforge-23.1.0-4-${OS}-${ARCH}.sh -b -p ${INSTALL_DIR}
    rm Mambaforge-23.1.0-4-${OS}-${ARCH}.sh
 
-   CONDABIN="${INSTALL_DIR}/condabin/mamba"
-   ${CONDABIN} init $MYSHELL
-   ${CONDABIN} update --name base mamba -y
+   CONDABIN="mamba"
+   if [ $MYSHELL != "bash" ]; then
+      $INSTALL_DIR/condabin/$CONDABIN init $MYSHELL
+   fi
+   $INSTALL_DIR/condabin/$CONDABIN init bash
+   source ~/.bashrc
+   export PATH=${INSTALL_DIR}/bin:$PATH
 fi
 cd $SCRIPT_DIR
+${CONDABIN} update --name base ${CONDABIN} -y
 ${CONDABIN} env create --file swiftest-build-env.yml --name swiftest-build-env 
\ No newline at end of file