Update the cloud isis build script

.github/workflows/build_isis.sh

@@ -1,10 +1,58 @@
 #!/bin/bash
 
+# Must wipe any cache before running this script, to ensure 
+# the conda env at the end of this gets cached
+
 cd
 echo Now in $(pwd)
+
 conda init bash
 source /Users/runner/.bash_profile
 
+echo listing envs
+conda env list
+
+echo Wiping old env
+/bin/rm -rf /usr/local/miniconda/envs/asp_deps
+
+/bin/rm -f isis_environment.yml
+wget https://raw.githubusercontent.com/NeoGeographyToolkit/StereoPipeline/master/.github/workflows/isis_environment.yml
+echo Creating a new asp_deps env
+conda env create -n asp_deps -f isis_environment.yml 
+
+conda activate asp_deps
+
+conda install -c conda-forge parallel -y
+conda install -c conda-forge rocksdb=8.5.3 rapidjson=1.1.0 -y
+
+#conda install -c nasa-ames-stereo-pipeline -c usgs-astrogeology -c conda-forge libnabo=asp3.4.0_alpha libpointmatcher=asp3.4.0_alpha -y
+
+# Make the python env
+echo Creating a new python_isis8 env
+/bin/rm -rf /usr/local/miniconda/envs/python_isis8
+conda create -n python_isis8 python=3.12.0 numpy=1.26.2 -y
+
+echo Will build ISIS3
+conda activate asp_deps
+git clone https://github.com/DOI-USGS/ISIS3.git     
+cd ISIS3
+
+mkdir build
+cd build
+export ISISROOT=$PWD
+export PREFIX=/usr/local/miniconda/envs/asp_deps
+cmake -GNinja -DJP2KFLAG=OFF -Dpybindings=OFF \
+ -DbuildTests=OFF -DCMAKE_BUILD_TYPE=Release  \
+ -DCMAKE_INSTALL_PREFIX=$PREFIX ../isis
+
 export NINJAJOBS=2
-ninja build -j 2
+/usr/bin/time ninja install -j 2
 
+# Archive the conda env in the packages dir. This dir
+# is set in the .yml file. It will be saved as 
+# an artifact.
+echo Will archive the conda env
+packageDir=$HOME/work/StereoPipeline/packages
+mkdir -p $packageDir
+cd /usr/local/miniconda
+/usr/bin/time tar czf $packageDir/asp_deps_osx.tar.gz envs

.github/workflows/build_test.yml

@@ -32,7 +32,8 @@ jobs:
           ${{ runner.os }}-build-
           ${{ runner.os }}-
     - name: build_test
-      run: ./.github/workflows/build_test.sh
+      ##run: ./.github/workflows/build_test.sh
+      run: ./.github/workflows/build_isis.sh
     - name: Upload artifacts
       uses: actions/upload-artifact@v2
       with: 

.github/workflows/isis_environment.yml

@@ -51,7 +51,7 @@ dependencies:
   - nn
   - opencv>=4.5.2, <5
   - openssl>=3.1.2,<4.0a0
-  - pcl=1.13.1=h86d90ae_2
+  - pcl=1.13
   - plio
   - protobuf
   - python=3.12

src/asp/Tools/stereo_utils.py

@@ -287,7 +287,7 @@ def parse_corr_seed_mode(filename):
     fh = open(filename, 'r', encoding='utf8', errors='ignore')
 
     for line in fh:
-        line = re.sub('\#.*?$', '', line) # wipe comments
+        line = re.sub(r'\#.*?$', '', line) # wipe comments
         matches = re.match(r'^\s*corr-seed-mode\s+(\d+)', line)
         if matches:
             mode = int(matches.group(1))