add Linux runtime support

- fixes #1

Author: casperdcl

setup.cfg

@@ -40,7 +40,7 @@ zip_safe = False
 setup_requires=setuptools>=42; wheel; setuptools_scm[toml]>=3.4
 install_requires=
     argopt
-    miutil[nii,web]>=0.7.2
+    miutil[nii,web]>=0.8.0
     setuptools  # pkg_resources
     numpy
     scipy

spm12/cli.py

@@ -1,22 +1,36 @@
 """Usage:
-  spm12 [options]
+  spm12 [options] [<command>...]
 
 Options:
   -c DIR, --cache DIR  : directory to use for installation [default: ~/.spm12].
   -s VER, --spm-version  : version [default: 12].
+  -r, --runtime  : use runtime (not full MATLAB).
+
+Arguments:
+  <command>  : Runtime command [default: quit]|gui|help|...
 """
 import logging
 
 from argopt import argopt
 
-from .utils import ensure_spm
+from .utils import ensure_spm, mcr_run
+
+log = logging.getLogger(__name__)
 
 
 def main(argv=None):
     logging.basicConfig(
         level=logging.DEBUG, format="%(levelname)s:%(funcName)s:%(message)s"
     )
     args = argopt(__doc__).parse_args(argv)
-    ensure_spm(cache=args.cache, version=args.spm_version)
+    log.info(args)
+    if isinstance(args.command, str):
+        args.command = [args.command]
+    if len(args.command) == 1 and args.command[0] == "gui":
+        args.command = []
+    if args.runtime:
+        log.debug(mcr_run(*args.command, cache=args.cache, version=args.spm_version))
+    else:
+        ensure_spm(cache=args.cache, version=args.spm_version)
     print("SPM{v} is successfully installed".format(v=args.spm_version))
     return 0

spm12/utils.py

@@ -1,10 +1,12 @@
 import logging
+import os
 from functools import wraps
 from os import path
+from subprocess import CalledProcessError, check_output
 from textwrap import dedent
 
-from miutil.fdio import extractall
-from miutil.mlab import get_engine
+from miutil.fdio import Path, extractall, fspath
+from miutil.mlab import get_engine, get_runtime
 from miutil.web import urlopen_cached
 from pkg_resources import resource_filename
 
@@ -16,6 +18,44 @@
 __all__ = ["ensure_spm", "get_matlab", "spm_dir"]
 PATH_M = resource_filename(__name__, "")
 log = logging.getLogger(__name__)
+SPM12_ZIP = "https://www.fil.ion.ucl.ac.uk/spm/download/restricted/eldorado/spm12.zip"
+MCR_ZIP = "https://www.fil.ion.ucl.ac.uk/spm/download/restricted/utopia/spm12_r7771.zip"
+
+
+def env_prefix(key, dir):
+    os.environ[key] = "%s%s%s" % (os.environ[key], os.pathsep, fspath(dir))
+
+
+def spm_runtime(cache="~/.spm12", version=12):
+    cache = Path(cache).expanduser()
+    if str(version) != "12":
+        raise NotImplementedError
+    runtime = cache / "runtime"
+    if not runtime.is_dir():
+        log.info("Downloading to %s", cache)
+        with urlopen_cached(MCR_ZIP, cache) as fd:
+            extractall(fd, runtime)
+
+    runner = runtime / "spm12" / "run_spm12.sh"
+    runner.chmod(0o755)
+    return fspath(runner)
+
+
+def mcr_run(*cmd, cache="~/.spm12", version=12, mcr_version=713):
+    mcr_root = fspath(get_runtime(version=mcr_version))
+    runner = spm_runtime(cache=cache, version=version)
+    try:
+        return check_output((runner, mcr_root) + cmd).decode("U8").strip()
+    except CalledProcessError as err:
+        raise RuntimeError(
+            dedent(
+                """\
+            {}
+
+            See https://en.wikibooks.org/wiki/SPM/Standalone#Trouble-shooting
+            """
+            ).format(err)
+        )
 
 
 @lru_cache()
@@ -45,11 +85,7 @@ def ensure_spm(name=None, cache="~/.spm12", version=12):
         log.warning("MATLAB could not find SPM.")
         try:
             log.info("Downloading to %s", cache)
-            with urlopen_cached(
-                "https://www.fil.ion.ucl.ac.uk/"
-                "spm/download/restricted/eldorado/spm12.zip",
-                cache,
-            ) as fd:
+            with urlopen_cached(SPM12_ZIP, cache) as fd:
                 extractall(fd, cache)
             eng.addpath(addpath)
             if not eng.exist("spm_jobman"):