MacOS bundle (#2)

* Try that

* Get python path

* Get python path

* Get python path

* That's not going to work

* Compile scanfold with nuitka

* Missing sed flag

* Bundle rnastructure and viennarna

* tar file

* less verbose

* i think thats everything

* fix path

* More fixes

* Change multiprocessing method to work with nuitka

* python2/python3

* Switch fork

* Try using threads

* Build macos for releases

* Make run_me double clickable

* Final tweaks

* Switch submodule back

.github/workflows/macos.yml

@@ -4,6 +4,8 @@
 name: MacOS package
 
 on:
+  release:
+    types: [published]
   workflow_dispatch:
 
 jobs:
@@ -29,4 +31,16 @@ jobs:
       if: ${{ success() && github.event_name == 'workflow_dispatch' }}
       with:
         name: scanfoldigv-macos
-        path: ./scanfoldigv-macos.zip
+        path: ./scanfoldigv-macos.zip
+
+    - name: Upload Release Asset (automatically on release)
+      id: upload-release-asset 
+      uses: actions/upload-release-asset@v1
+      env:
+        GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+      with:
+        upload_url: ${{ github.event.release.upload_url }} # This pulls from the CREATE RELEASE step above, referencing it's ID to get its outputs object, which include a `upload_url`. See this blog post for more info: https://jasonet.co/posts/new-features-of-github-actions/#passing-data-to-future-steps 
+        asset_path: ./scanfoldigv-macos.zip
+        asset_name: scanfoldigv-macos-${{github.event.release.tag_name}}.zip
+        asset_content_type: application/zip
+      if: ${{ github.event_name == 'release' }}

README.md

@@ -4,10 +4,10 @@ Patched version of IGV that integrates ScanFold functionality.
 
 ## Run
 
-### Windows
-A pre-built version for Windows is available on [releases](https://github.com/ResearchIT/scanfoldigv/releases).
+### Windows and Mac
+A pre-built version is available on [releases](https://github.com/ResearchIT/scanfoldigv/releases).
 
-### Mac and Linux
+### Linux
 
 Follow instructions to compile. Then
 

macos/bundle_macos.sh

@@ -13,11 +13,69 @@ popd
 pushd igv
 ./gradlew clean
 ./gradlew createMacAppWithJavaDistZip -PjdkBundleMac=${TOPLEVEL}/lib/jdk-11.0.10+9-jre/Contents/Home
-#unzip -d ${BUNDLE_PREFIX} distributions/IGV_MacApp_user_WithJava.zip
-mv build ${BUNDLE_PREFIX}/IGV
+unzip build/distributions/IGV_MacApp_user_WithJava.zip
+mv IGV_User.app ${BUNDLE_PREFIX}/IGV.app
+popd
+
+
+# compile scanfold
+pushd ScanFold
+sed -i -e 's/#!\/usr\/local\/bin\/python.*//' ScanFold-Scan_IGV.py ScanFold-Fold_IGV.py
+python3 -mvenv env
+. env/bin/activate
+pip install Nuitka biopython numpy
+python -m nuitka --standalone --plugin-enable=numpy ScanFold-Scan_IGV.py
+python -m nuitka --standalone --plugin-enable=numpy ScanFold-Fold_IGV.py
+deactivate
+popd
+
+# bundle scanfold
+mkdir -p ${BUNDLE_PREFIX}/scanfold/
+
+pushd ${BUNDLE_PREFIX}/scanfold
+cp -R ${TOPLEVEL}/ScanFold/{ScanFold-Scan_IGV.dist,ScanFold-Fold_IGV.dist} .
+cp ${TOPLEVEL}/scripts/run_scanfold.py .
+popd
+
+# viennarna
+pushd lib
+curl -L -O https://github.com/ViennaRNA/ViennaRNA/releases/download/v2.4.16/ViennaRNA-2.4.16.tar.gz
+tar -xzf ViennaRNA-2.4.16.tar.gz
+pushd ViennaRNA-2.4.16
+mkdir target
+#export ac_cv_func_realloc_0_nonnull=yes
+#export ac_cv_func_malloc_0_nonnull=yes
+CONFIGURE_OPTIONS=" --without-swig \
+                    --without-doc \
+                    --without-forester \
+                    --with-cluster \
+                    --with-kinwalker \
+                    --disable-mpfr \
+                    --disable-pthreads \
+                    --disable-tty-colors \
+                    --disable-lto"
+./configure --prefix=${PWD}/target ${CONFIGURE_OPTIONS}
+make
+make install
+mkdir -p ${BUNDLE_PREFIX}/ViennaRNA
+mv target/bin/RNAfold ${BUNDLE_PREFIX}/ViennaRNA/
+cp license.txt ${BUNDLE_PREFIX}/ViennaRNA/
+popd
+popd
+
+# rnastructure
+pushd lib
+curl -L -O  http://rna.urmc.rochester.edu/Releases/current/RNAstructureTextInterfacesMac.tgz
+tar -xzf RNAstructureTextInterfacesMac.tgz
+mv RNAstructureTextInterfacesMac.tgz
+mkdir ${BUNDLE_PREFIX}/RNAstructure
+mv RNAstructure/exe/ct2dot ${BUNDLE_PREFIX}/RNAstructure/
+mv RNAstructure/gpl.txt ${BUNDLE_PREFIX}/RNAstructure/
+mv RNAstructure/data_tables ${BUNDLE_PREFIX}/RNAstructure/
 popd
 
 # main
 pushd ${BUNDLE_PREFIX}
+cp ${TOPLEVEL}/macos/run_me.command .
 zip -r ${TOPLEVEL}/scanfoldigv-macos.zip *
 popd

macos/run_me.command

@@ -0,0 +1,10 @@
+export SCANFOLDRUNDIR=$(cd `dirname $(readlink $0 || echo $0)` && pwd)
+export SCANFOLDPYTHONINTERPRETER=$(which python)
+export SCANFOLDRUNSCRIPT=${SCANFOLDRUNDIR}/scanfold/run_scanfold.py
+export SCANFOLDISBUNDLED=TRUE
+#switch to this if fork doesn't work
+#export SCANFOLDMPUSETHREADS=TRUE
+export SCANFOLDMPMETHOD=fork
+cd "${SCANFOLDRUNDIR}"
+xattr -r -d com.apple.quarantine . >/dev/null 2>&1
+open IGV.app

scripts/run_scanfold.py

@@ -3,14 +3,15 @@
 import tempfile
 import sys
 import os
+import platform
 
 def run_me(script, workdir, args):
 
     proc_env = os.environ.copy()
     cwd = os.getcwd()
 
-    if os.name == 'nt':
-        script = os.path.join(cwd, 'scanfold', script)
+    if platform.system() == 'Windows':
+        script = os.path.join(cwd, 'scanfold', script + ".py")
         proc_env['DATAPATH'] = os.path.join(cwd, 'RNAstructure', 'data_tables')
         new_path = [
             os.path.join(cwd, 'ViennaRNA'),
@@ -19,8 +20,22 @@ def run_me(script, workdir, args):
         ]
         proc_env['PATH'] = ';'.join(new_path)
         python_interpreter = os.environ['SCANFOLDPYTHONINTERPRETER']
+        command = [python_interpreter, '-u', script]
+    elif platform.system() == 'Darwin' and 'SCANFOLDISBUNDLED' in os.environ:
+        proc_env['DATAPATH'] = os.path.join(cwd, 'RNAstructure', 'data_tables')
+        new_path = [
+            os.path.join(cwd, 'ViennaRNA'),
+            os.path.join(cwd, 'RNAstructure'),
+            proc_env['PATH']
+        ]
+        proc_env['PATH'] = ':'.join(new_path)
+        python_interpreter = os.environ['SCANFOLDPYTHONINTERPRETER']
+        if script == "ScanFold-Scan_IGV":
+            command = [os.path.join(cwd, 'scanfold', 'ScanFold-Scan_IGV.dist', 'ScanFold-Scan_IGV')]
+        else:
+            command = [os.path.join(cwd, 'scanfold', 'ScanFold-Fold_IGV.dist', 'ScanFold-Fold_IGV')]
     else:
-        script = os.path.join(cwd, 'ScanFold', script)
+        script = os.path.join(cwd, 'ScanFold', script + ".py")
         proc_env['DATAPATH'] = os.path.join(cwd, 'env', 'data_tables')
         proc_env['VIRTUAL_ENV'] = os.path.join(cwd, 'env')
         new_path = [
@@ -29,14 +44,20 @@ def run_me(script, workdir, args):
         ]
         proc_env['PATH'] = ':'.join(new_path)
         python_interpreter = 'python'
-
-    command = [python_interpreter, '-u', script]
+        command = [python_interpreter, '-u', script]
+
     command.extend(args)
 
     process = subprocess.Popen(command, stdout=subprocess.PIPE, env=proc_env, cwd=workdir, bufsize=0)
     for c in iter(lambda: process.stdout.read(1), b''): 
-        sys.stdout.buffer.write(c)
-        sys.stdout.buffer.flush()
+        if hasattr(sys.stdout, 'buffer'):
+            # python 3
+            sys.stdout.buffer.write(c)
+            sys.stdout.buffer.flush()
+        else:
+            # python 2 (macos)
+            sys.stdout.write(c)
+            sys.stdout.flush()
 
 def mktemp(directory, extension, name="output"):
     file_handle, file_path = tempfile.mkstemp(prefix=name, suffix=extension, dir=directory)
@@ -72,7 +93,7 @@ def main(args):
         '--fasta_index', FASTAINDEX
     ]
 
-    run_me('ScanFold-Scan_IGV.py', args.WORKDIR, scan_params)
+    run_me('ScanFold-Scan_IGV', args.WORKDIR, scan_params)
 
     OUT1 = mktemp(args.WORKDIR, '.nofilter.ct')
     OUT2 = mktemp(args.WORKDIR, '.-1filter.ct')
@@ -116,7 +137,7 @@ def main(args):
     if args.GLOBALREFOLD:
         fold_params.append('--global_refold')
 
-    run_me('ScanFold-Fold_IGV.py', args.WORKDIR, fold_params)
+    run_me('ScanFold-Fold_IGV', args.WORKDIR, fold_params)
 
     files_to_load = [
         BPTRACK,