Breiz dev (#763)

* Update release versions for breizorro and aimfast

Jenkinsfile.sh

@@ -4,8 +4,15 @@ WORKSPACE_ROOT="$WORKSPACE/$BUILD_NUMBER"
 TEST_OUTPUT_DIR="$WORKSPACE_ROOT/test-output"
 TEST_DATA_DIR="$WORKSPACE/../../../test-data"
 mkdir $TEST_OUTPUT_DIR
+function finish {
+    rm -rf $TMPDIR
+}
+trap finish EXIT
 
 #Custom home for this run's temporary stuff
+mkdir $WORKSPACE_ROOT/tmp
+TMPDIR="$WORKSPACE_ROOT/tmp"
+export TMPDIR
 rm -rf ~/.stimela
 HOME=$WORKSPACE_ROOT
 export HOME

setup.py

@@ -6,7 +6,7 @@
 import glob
 
 PACKAGE_NAME = "stimela"
-__version__ = "1.7.5"
+__version__ = "1.7.6"
 build_root = os.path.dirname(__file__)
 
 

stimela/cargo/base/aimfast/Dockerfile

@@ -1,4 +1,4 @@
-FROM stimela/meqtrees:1.6.6
+FROM quay.io/stimela/base:1.7.1
 RUN docker-apt-install python3-pip \
                        python3-numpy \
                        python3-matplotlib \
@@ -10,5 +10,6 @@ RUN docker-apt-install python3-pip \
                        python3-setuptools \
                        pybdsf
 
-
-RUN pip3 install bdsf aimfast
+RUN update-alternatives --install /usr/bin/python python /usr/bin/python3.8 10
+RUN pip3 install -U pip bdsf
+RUN pip3 install aimfast

stimela/cargo/cab/aimfast/parameters.json

@@ -1,7 +1,7 @@
 {
     "task": "aimfast",
     "base": "stimela/aimfast",
-    "tag": "1.7.0",
+    "tag": "1.7.5",
     "description": "An Astronomical Image Fidelity Assessment Tool",
     "prefix": "--",
     "binary": "aimfast",
@@ -201,7 +201,7 @@
         },
         {
             "info": "Centre of online catalog to compare local image/model in 'RA hh:mm:ss, Dec deg:min:sec'",
-            "default": "0:0:0, -30:0:0",
+            "default": null,
             "required": false,
             "name": "centre_coord",
             "dtype": "str"

stimela/cargo/cab/aimfast/src/run.py

@@ -33,7 +33,10 @@
                 args += ['{0}{1} {2}'.format(cab['prefix'],
                                              name, " ".join(compare))]
                 compare = []
-    elif name in ['compare-online', 'compare-residual-subimages', 'centre-pixels-size']:
+    elif name in ['compare-online']:
+        for val in value:
+            args += ['{0}{1} {2}'.format(cab['prefix'], name, val)]
+    elif name in ['compare-residual-subimages', 'centre-pixels-size']:
         args += ['{0}{1} {2}'.format(cab['prefix'],
                                      name, " ".join(value))]
     elif param['dtype'] in ['bool']:

stimela/cargo/cab/breizorro/parameters.json

@@ -1,10 +1,11 @@
 {
     "task": "breizorro",
     "base": "stimela/breizorro",
-    "tag": "1.7.1",
+    "tag": "1.7.4",
     "description": "A tool for creating a binary mask given a FITS image",
     "prefix": "--",
     "binary": "breizorro",
+    "version":"0.1.0",
     "junk":[],
     "msdir": false,
     "parameters": [
@@ -44,7 +45,7 @@
             "io": "input",
             "delimiter": " ",
             "name": "merge",
-            "dtype": "list:file",
+            "dtype": "list:file"
         },
         {
             "info": "Subtract one or more masks or region files",
@@ -53,7 +54,7 @@
             "io": "input",
             "delimiter": " ",
             "name": "subtract",
-            "dtype": "list:file",
+            "dtype": "list:file"
         },
         {
             "info": "Number the islands detected (default=do not number islands)",
@@ -112,6 +113,13 @@
             "name": "fill-holes",
             "dtype": "bool"
         },
+        {
+            "info": "Sum to peak ratio of flux islands to mask in original image",
+            "default": null,
+            "required": false,
+            "name": "sum-peak",
+            "dtype": "float"
+        },
         {
             "info": "Suffix for mask image (default based on input name)",
             "default": null,