Merge pull request #610 from ratt-ru/ragavi

Ragavi

Author: SpheMakh

examples/simulation_pipeline.py

@@ -25,7 +25,7 @@
                           log_dir=os.path.join(OUTPUT, "logs"),
                           )
 
-pipeline.JOB_TYPE = "docker"
+pipeline.JOB_TYPE = "singularity"
 
 # 1: Make empty MS
 pipeline.add("cab/simms",                   # Executor image to start container from

setup.py

@@ -9,11 +9,10 @@
 requirements = ["pyyaml",
                 "nose>=1.3.7",
                 "future-fstrings",
-                "udocker",
                 ],
 
 PACKAGE_NAME = "stimela"
-__version__ = "1.4.6"
+__version__ = "1.5.1"
 
 setup(name=PACKAGE_NAME,
       version=__version__,
@@ -25,13 +24,11 @@
                 "stimela/utils", "stimela/cargo/cab",
                 "stimela/cargo/base"],
       package_data={"stimela/cargo": [
-          "cab/*/Dockerfile",
           "base/*/Dockerfile",
+          "base/*.template",
           "cab/*/src/*.py",
-          "cab/*/src/*.sh",
           "cab/*/src/*.json",
           "base/*/xvfb.init.d",
-          "cab/*/xvfb.init.d",
           "cab/*/parameters.json",
           "cab/*/src/tdlconf.profiles",
       ]},

stimela/cargo/base/cubical/Dockerfile

@@ -1,13 +1,13 @@
-FROM stimela/ddfacet:1.3.3
-MAINTAINER <sphemakh@gmail.com>
-ENV GIT_LFS_SKIP_SMUDGE 1
-RUN pip3 install -U pip setuptools wheel
-RUN apt-get update && apt-get install -y wget git-all
-RUN git clone https://github.com/ratt-ru/CubiCal.git
-WORKDIR CubiCal
-RUN git checkout v1.5.1
-RUN pip3 install ".[lsm-support,degridder-support]"
-RUN DDF.py --help
+FROM stimela/base:1.2.5
+RUN docker-apt-install casacore-dev \
+    casacore-data \
+    build-essential \
+    python3-pip \
+    libboost-all-dev \
+    wcslib-dev \
+    git \
+    libcfitsio-dev
+RUN update-alternatives --install /usr/bin/python python /usr/bin/python3.6 10
+RUN pip3 install --upgrade --force pip
+RUN pip install "cubical[lsm-support]@git+https://github.com/ratt-ru/CubiCal.git@v1.5.2"
 RUN gocubical --help
-ENV NUMBA_CACHE_DIR /tmp
-ENTRYPOINT []

stimela/cargo/base/cubical_ddf/Dockerfile

@@ -0,0 +1,13 @@
+FROM stimela/ddfacet:1.3.3
+MAINTAINER <sphemakh@gmail.com>
+ENV GIT_LFS_SKIP_SMUDGE 1
+RUN pip3 install -U pip setuptools wheel
+RUN apt-get update && apt-get install -y wget git-all
+RUN git clone -b decasacore300fication https://github.com/ratt-ru/CubiCal
+WORKDIR CubiCal
+#RUN git checkout decasacore300fication
+RUN pip3 install -I ".[lsm-support,degridder-support]"
+RUN DDF.py --help
+RUN gocubical --help
+ENV NUMBA_CACHE_DIR /tmp
+ENTRYPOINT []

stimela/cargo/base/group.template

@@ -0,0 +1,42 @@
+root:x:0:
+daemon:x:1:
+bin:x:2:
+sys:x:3:
+adm:x:4:
+tty:x:5:
+disk:x:6:
+lp:x:7:
+mail:x:8:
+news:x:9:
+uucp:x:10:
+man:x:12:
+proxy:x:13:
+kmem:x:15:
+dialout:x:20:
+fax:x:21:
+voice:x:22:
+cdrom:x:24:
+floppy:x:25:
+tape:x:26:
+sudo:x:27:
+audio:x:29:
+dip:x:30:
+www-data:x:33:
+backup:x:34:
+operator:x:37:
+list:x:38:
+irc:x:39:
+src:x:40:
+gnats:x:41:
+shadow:x:42:
+utmp:x:43:
+video:x:44:
+sasl:x:45:
+plugdev:x:46:
+staff:x:50:
+games:x:60:
+users:x:100:
+nogroup:x:65534:
+crontab:x:101:
+messagebus:x:102:
+ssh:x:103:

stimela/cargo/base/passwd.template

@@ -0,0 +1,20 @@
+root:x:0:0:root:/root:/bin/bash
+daemon:x:1:1:daemon:/usr/sbin:/usr/sbin/nologin
+bin:x:2:2:bin:/bin:/usr/sbin/nologin
+sys:x:3:3:sys:/dev:/usr/sbin/nologin
+sync:x:4:65534:sync:/bin:/bin/sync
+games:x:5:60:games:/usr/games:/usr/sbin/nologin
+man:x:6:12:man:/var/cache/man:/usr/sbin/nologin
+lp:x:7:7:lp:/var/spool/lpd:/usr/sbin/nologin
+mail:x:8:8:mail:/var/mail:/usr/sbin/nologin
+news:x:9:9:news:/var/spool/news:/usr/sbin/nologin
+uucp:x:10:10:uucp:/var/spool/uucp:/usr/sbin/nologin
+proxy:x:13:13:proxy:/bin:/usr/sbin/nologin
+www-data:x:33:33:www-data:/var/www:/usr/sbin/nologin
+backup:x:34:34:backup:/var/backups:/usr/sbin/nologin
+list:x:38:38:Mailing List Manager:/var/list:/usr/sbin/nologin
+irc:x:39:39:ircd:/var/run/ircd:/usr/sbin/nologin
+gnats:x:41:41:Gnats Bug-Reporting System (admin):/var/lib/gnats:/usr/sbin/nologin
+nobody:x:65534:65534:nobody:/nonexistent:/usr/sbin/nologin
+_apt:x:100:65534::/nonexistent:/usr/sbin/nologin
+messagebus:x:101:102::/nonexistent:/usr/sbin/nologin

stimela/cargo/base/ragavi/Dockerfile

@@ -2,12 +2,8 @@ FROM stimela/base:1.2.5
 RUN curl -sL https://deb.nodesource.com/setup_10.x | bash -
 RUN update-alternatives --install /usr/bin/python python /usr/bin/python3.6 10
 RUN pip3 install -U pip setuptools pyyaml
-RUN pip3 install -U python-casacore git+https://github.com/ska-sa/dask-ms@remove-table-proxy-weakref-finalize
-#dask-ms==0.2.3
-# RUN pip3 install -U ragavi
-RUN pip3 install git+https://github.com/ratt-ru/ragavi@dev
-# RUN pip install --force-reinstall -U git+https://github.com/o-smirnov/datashader
+RUN pip3 install -U python-casacore 
+RUN pip3 install -U ragavi
 RUN pip3 install -I numpy
 RUN ragavi-gains -h
 RUN ragavi-vis -h
-#RUN python3 -c "import yaml"

stimela/cargo/cab/cubical/parameters.json

@@ -1,10 +1,10 @@
 {
     "task": "cubical", 
     "base": "stimela/cubical", 
-    "tag": "1.4.2", 
+    "tag": "1.5.00", 
     "description": "CubiCal is a suite of fast radio interferometric calibration routines exploiting complex optimisation.", 
     "prefix": "--",
-    "version":"1.5.1",
+    "version":"1.5.2",
     "binary": "gocubical",
     "junk":["cubical.last", "montblanc.log"],
     "msdir": true,