fix packaging and deployment

Author: bjarthur

README.md

@@ -2125,8 +2125,9 @@ asset:
 To upload a tarball to Github, compress the conda environment and drag and drop
 it into the assets section of the releases page:
 
+    $ conda activate base
     $ conda install -c conda-forge conda-pack
-    $ conda pack -n songexplorer -o songexplorer-<version>-<architecture>.tar.gz
+    $ conda-pack -n songexplorer -o songexplorer-<version>-<architecture>.tar.gz
 
 After downloading, some users will need to re-install some pip dependencies
 (e.g. tensorflow-metal on MacOS) as they are not in general relocatable:

app/DROP-FILES-HERE.sh

@@ -2,6 +2,8 @@
 
 SCRIPT_DIR=$( cd -- "$( dirname -- "${(%):-%N}" )" &> /dev/null && pwd )
 
-export PATH=$SCRIPT_DIR/songexplorer/bin:$PATH
+source $SCRIPT_DIR/songexplorer/bin/activate
 
 $SCRIPT_DIR/make-predictions.py $argv
+
+sleep 10

app/OPEN-WITH-TERMINAL.sh

@@ -2,6 +2,8 @@
 
 SCRIPT_DIR=$( cd -- "$( dirname -- "${(%):-%N}" )" &> /dev/null && pwd )
 
-export PATH=$SCRIPT_DIR/songexplorer/bin:$PATH
+source $SCRIPT_DIR/songexplorer/bin/activate
 
 $SCRIPT_DIR/songexplorer/bin/songexplorer/src/songexplorer $SCRIPT_DIR/configuration.py 8080
+
+sleep 10

install/conda/songexplorer/post-link.bat

@@ -6,7 +6,7 @@ echo optionally, to use video in songexplorer cut and paste the following into t
 echo conda activate songexplorer >> %PREFIX%\.messages.txt
 echo conda install av=8.1 git >> %PREFIX%\.messages.txt
 echo cd $env:CONDA_PREFIX\Lib\site-packages >> %PREFIX%\.messages.txt
-echo pip3 install -e git+https://github.com/soft-matter/pims.git@7bd634015ecbfeb7d92f9f9d69f8b5bb4686a6b4#egg=pims >> %PREFIX%\.messages.txt
+echo pip3 install git+https://github.com/soft-matter/pims.git@7bd634015ecbfeb7d92f9f9d69f8b5bb4686a6b4#egg=pims >> %PREFIX%\.messages.txt
 echo either way, to finish the installation cut and paste the following: >> %PREFIX%\.messages.txt
 echo conda activate songexplorer >> %PREFIX%\.messages.txt
 echo pip3 install tensorflow^=^=2.10 tensorflow-io^=^=0.27.0 >> %PREFIX%\.messages.txt

install/conda/songexplorer/post-link.sh

@@ -4,19 +4,19 @@ optionally, to use video in songexplorer cut and paste the following into the co
 conda activate songexplorer
 conda install av=8.1 git
 cd \$CONDA_PREFIX/lib/python3.10/site-packages
-pip3 install -e git+https://github.com/soft-matter/pims.git@7bd634015ecbfeb7d92f9f9d69f8b5bb4686a6b4#egg=pims
+pip3 install git+https://github.com/soft-matter/pims.git@7bd634015ecbfeb7d92f9f9d69f8b5bb4686a6b4#egg=pims
 either way, to finish the installation cut and paste the following:
 EOF
 
 if [ `uname` == Darwin ] ; then
 cat << EOF >> ${PREFIX}/.messages.txt
 conda activate songexplorer
-pip3 install tensorflow[tensorflow-io]
+pip3 install tensorflow==2.16.2
 EOF
 if [ `uname -m` == arm64 ] ; then
 cat << EOF >> ${PREFIX}/.messages.txt
 pip3 install tensorflow-metal
-pip3 install tensorflow-io==<VERSION>  # https://github.com/tensorflow/io?tab=readme-ov-file#tensorflow-version-compatibility
+pip3 install tensorflow-io==0.37.1
 EOF
 fi
 else