Merge branch '1.0.x' into 'master'

.github/workflows/test.yml

@@ -9,16 +9,16 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        os: [ubuntu-18.04]
+        os: [ubuntu-latest]
         mode: [tests]
         python:
         - "3.5"
         - "3.8"
         include:
-        - os: ubuntu-18.04
+        - os: ubuntu-latest
           mode: coverage
           python: "3.9"
-        - os: ubuntu-18.04
+        - os: ubuntu-latest
           mode: checks
           python: "3.9"
         - os: ubuntu-latest

README.md

@@ -107,6 +107,15 @@ Bugs and feature plannings are tracked in the [GitHub issues](https://github.com
 
 To suggest changes to this source code, feel free to raise a [GitHub pull request](https://github.com/VIDA-NYU/reprozip/pulls).  Any contributions received are assumed to be covered by the [BSD 3-Clause license](LICENSE.txt). We might ask you to sign a _Contributor License Agreement_ before accepting a larger contribution.
 
+Research notice
+---------------
+
+Please note that this repository is participating in a study into sustainability of open source projects. Data will be gathered about this repository for approximately the next 12 months, starting from June 2021.
+
+Data collected will include number of contributors, number of PRs, time taken to close/merge these PRs, and issues closed.
+
+For more information, please visit [the informational page](https://sustainable-open-science-and-software.github.io/) or download the [participant information sheet](https://sustainable-open-science-and-software.github.io/assets/PIS_sustainable_software.pdf).
+
 License
 -------
 

reprounzip/reprounzip/unpackers/default.py

@@ -16,6 +16,9 @@
 
 import argparse
 import copy
+from elftools.common.exceptions import ELFError
+from elftools.elf.elffile import ELFFile
+from elftools.elf.segments import InterpSegment
 import logging
 import os
 import platform
@@ -42,6 +45,17 @@
 logger = logging.getLogger('reprounzip')
 
 
+def get_elf_interpreter(file):
+    try:
+        elf = ELFFile(file)
+        for segment in elf.iter_segments():
+            if isinstance(segment, InterpSegment):
+                return segment.get_interp_name()
+        return None
+    except ELFError:
+        return None
+
+
 def installpkgs(args):
     """Installs the necessary packages on the current machine.
     """
@@ -216,19 +230,21 @@ def directory_run(args):
         if p.returncode != 0:
             raise subprocess.CalledProcessError(p.returncode,
                                                 ['/sbin/ldconfig', '-v', '-N'])
-    lib_dirs = ('export LD_LIBRARY_PATH=%s' % ':'.join(
-                shell_escape(str(join_root(root, d)))
-                for d in lib_dirs))
 
-    cmds = [lib_dirs]
+    cmds = []
     for run_number in selected_runs:
         run = runs[run_number]
         cmd = 'cd %s && ' % shell_escape(
             str(join_root(root, Path(run['workingdir']))))
         cmd += '/usr/bin/env -i '
+        cmd += 'LD_LIBRARY_PATH=%s' % ':'.join(
+            shell_escape(str(join_root(root, d)))
+            for d in lib_dirs
+        )
         environ = run['environ']
         environ = fixup_environment(environ, args)
         if args.x11:
+            environ = dict(environ)
             if 'DISPLAY' in os.environ:
                 environ['DISPLAY'] = os.environ['DISPLAY']
             if 'XAUTHORITY' in os.environ:
@@ -250,6 +266,14 @@ def directory_run(args):
         path = ':'.join(str(d) for d in dir_path + path)
         cmd += 'PATH=%s ' % shell_escape(path)
 
+        interpreter = get_elf_interpreter(
+            join_root(root, PosixPath(run['binary'])).open('rb'),
+        )
+        if interpreter is not None:
+            interpreter = Path(interpreter)
+            if interpreter.exists():
+                cmd += '%s ' % shell_escape(str(join_root(root, interpreter)))
+
         # FIXME : Use exec -a or something if binary != argv[0]
         if cmdline is None:
             argv = run['argv']
@@ -579,6 +603,7 @@ def chroot_run(args):
         forwarders.append(fwd)
 
     signals.pre_run(target=target)
+    logger.debug("Running: %s", cmds)
     retcode = interruptible_call(cmds, shell=True)
     print("\n*** Command finished, status: %d\n" % retcode, file=sys.stderr)
     signals.post_run(target=target, retcode=retcode)

reprounzip/setup.py

@@ -13,7 +13,8 @@
     'rpaths>=0.8',
     'usagestats>=0.3',
     'requests',
-    'distro']
+    'distro',
+    'pyelftools']
 setup(name='reprounzip',
       version='2.0.0',
       packages=['reprounzip', 'reprounzip.unpackers',

reprozip/reprozip/main.py

@@ -116,7 +116,7 @@ def print_db(database):
         if not argv[-1]:
             argv = argv[:-1]
         cmdline = ' '.join(shell_escape(a) for a in argv)
-        if argv[0] not in (r_name, os.path.basename(r_name)):
+        if argv[0] != r_name:
             cmdline = "(%s) %s" % (shell_escape(r_name), cmdline)
         f_cmdline = " {0: <37s} ".format(cmdline)
         print('|'.join(('', f_id, f_timestamp, f_proc, f_cmdline, '')))

tests/functional.py

@@ -112,7 +112,6 @@ def call_output(args, stream='out'):
     return retcode, b''.join(output)
 
 
-@print_arg_list
 def check_output(args, stream='out'):
     retcode, output = call_output(args, stream)
     if retcode != 0:

tests/test_reprozip.py

@@ -134,7 +134,7 @@ def do_test(self, insert):
         try:
             files, inputs, outputs = get_files(conn)
             files = set(fi for fi in files
-                        if not fi.path.path.startswith(b'/lib'))
+                        if not fi.path.path.startswith((b'/lib', b'/usr/lib')))
             return files, inputs, outputs
         finally:
             conn.close()