Merge branch 'develop' of github.com:OpenSourceBrain/OSBv2 into develop

Author: filippomc

applications/jupyterlab/requirements.txt

@@ -1,3 +1,6 @@
+# temporary fix until new NEST releases are made with the fix: https://github.com/nest/nest-simulator/issues/3495
+cython<3.1.0
+
 pyneuroml
 pyelectro
 git+https://github.com/NeuralEnsemble/neurotune.git
@@ -71,4 +74,4 @@ OSBModelValidation==0.3.5
 
 
 ####  Final updates
-numpy  # Removes some issues with LFPy...
+numpy  # Removes some issues with LFPy...

applications/workspaces/tasks/biomodels-copy/Dockerfile

@@ -3,7 +3,7 @@ FROM $CLOUDHARNESS_BASE
 
 # much faster than curl/wget
 # https://pkgs.alpinelinux.org/packages?name=aria2&branch=edge
-RUN apt-get update && apt-get install -y aria2 unzip
+RUN apt-get update && apt-get install -y aria2 unzip util-linux
 
 
 ADD . /

applications/workspaces/tasks/biomodels-copy/run.sh

@@ -22,26 +22,31 @@ if [ -z "$paths" ]; then
     aria2c --retry-wait=2 --max-tries=5 --timeout=300 --max-concurrent-downloads=5 --max-connection-per-server=5 --allow-overwrite="true" --auto-file-renaming="false" --out="$timestamp.omex" "https://www.ebi.ac.uk/biomodels/model/download/${url}"
     unzip -o "$timestamp.omex" && rm -vf "$timestamp.omex"
 else
-    touch filelist
-    # Split paths by ## and checkout each path
-    IFS='\'
-    for path in $paths; do
-        echo Biomodels copy "${path}" to "${download_path}"
-        echo "${path}" >> filelist
-    done
     # Move to temporary directory to rename only the downloaded files.
     # Otherwise we risk renaming all files, even ones where the user has used
     # '+' in the file name explicitly
     tempdir=$(mktemp -d)
     echo Biomodels downloading files in "${tempdir}"
     pushd "${tempdir}"
-        aria2c --retry-wait=2 --max-tries=5 --input-file=filelist --max-concurrent-downloads=5 --max-connection-per-server=5 --allow-overwrite "true" --auto-file-renaming "false"
+        filelist=$(mktemp)
+        echo "Storing file list in ${filelist}"
+
+        # Split paths by ## and checkout each path
+        IFS='\'
+        for path in $paths; do
+            echo Biomodels copy "${path}" to "${download_path}"
+            echo "${path}" >> "${filelist}"
+        done
+
+        aria2c --retry-wait=2 --max-tries=5 --input-file="${filelist}" --max-concurrent-downloads=5 --max-connection-per-server=5 --allow-overwrite "true" --auto-file-renaming "false"
+        rm "${filelist}" -f
+
         rename -a '+' ' ' *.*
+
     popd
     mv -v "${tempdir}/"* .
     # directory should be empty, so rmdir will work
     rmdir "${tempdir}"
-    rm filelist -f
 fi
 
 # fix permissions

applications/workspaces/tasks/figshare-copy/run.sh

@@ -9,23 +9,25 @@ export download_path=`echo $shared_directory | cut -d ":" -f 2`/"${folder}"
 mkdir -p "${download_path}"
 cd "${download_path}"
 
+filelist=$(mktemp)
+
 # if a file url is passed
 if echo "${url}" | grep -E "https://" 2>&1 > /dev/null
 then
     echo Figshare copy "${url}" to "${download_path}"
-    echo "${url}" > filelist
+    echo "${url}" > "${filelist}"
 else
     # if the article id is passed, download all files
     echo Figshare copy all files of article "${url}" to "${download_path}"
-    curl -X GET "https://api.figshare.com/v2/articles/${url}/files" | tr "}" "\n" | grep -Eo "https://ndownloader.figshare.com/files/[[:digit:]]+" > filelist
+    curl -X GET "https://api.figshare.com/v2/articles/${url}/files" | tr "}" "\n" | grep -Eo "https://ndownloader.figshare.com/files/[[:digit:]]+" > "${filelist}"
 fi
 
 # multiple downloads concurrently, with multiple connections to the server
 # overwrite files if they are downloaded again
-aria2c --retry-wait=2 --max-tries=5 --input-file=filelist --max-concurrent-downloads=5 --max-connection-per-server=5 --allow-overwrite "true" --auto-file-renaming "false"
+aria2c --retry-wait=2 --max-tries=5 --input-file="${filelist}" --max-concurrent-downloads=5 --max-connection-per-server=5 --allow-overwrite "true" --auto-file-renaming "false"
 
 # delete the file list
-rm filelist -f
+rm "${filelist}" -f
 
 # fix permissions
 chown -R 1000:100 "${download_path}"