Merge branch '1.0.x' into 'master'

.travis/install.sh

@@ -30,9 +30,9 @@ in
         sudo apt-get install -qq libc6-dev-i386 gcc-multilib
         if [ $TEST_MODE = "coverage" ]; then
             pip install coverage codecov
-            pip install -e ./reprozip -e ./reprounzip -e ./reprounzip-docker -e ./reprounzip-vagrant -e ./reprounzip-vistrails -e ./reprounzip-qt
+            pip install -e ./reprozip -e ./reprounzip -e ./reprounzip-docker -e ./reprounzip-vagrant -e ./reprounzip-vistrails -e ./reprounzip-qt -e ./reprozip-jupyter
         else
-            pip install ./reprozip ./reprounzip ./reprounzip-docker ./reprounzip-vagrant ./reprounzip-vistrails ./reprounzip-qt
+            pip install ./reprozip ./reprounzip ./reprounzip-docker ./reprounzip-vagrant ./reprounzip-vistrails ./reprounzip-qt -e ./reprozip-jupyter
         fi
         ;;
     checks)

.travis/test.sh

@@ -15,15 +15,16 @@ in
         python tests --run-docker
         ;;
     checks)
-        flake8 --ignore=E731 reprozip/reprozip reprounzip/reprounzip reprounzip-*/reprounzip reprounzip-qt/reprounzip_qt tests/*.py
+        flake8 --ignore=E731 reprozip/reprozip reprounzip/reprounzip reprounzip-*/reprounzip reprounzip-qt/reprounzip_qt reprozip-jupyter/reprozip_jupyter tests/*.py
         diff -q reprozip/reprozip/common.py reprounzip/reprounzip/common.py
         diff -q reprozip/reprozip/utils.py reprounzip/reprounzip/utils.py
-        find reprozip reprounzip reprounzip-* .travis -name '*.py' -or -name '*.sh' -or -name '*.h' -or -name '*.c' | (set +x; while read i; do
+        find reprozip reprounzip reprozip-* reprounzip-* .travis -name '*.py' -or -name '*.sh' -or -name '*.h' -or -name '*.c' | (set +x; while read i; do
             T=$(file -b --mime "$i")
             if ! ( echo "$T" | grep -q ascii || echo "$T" | grep -q empty ) ; then
                 echo "$i is not ASCII"
                 exit 1
             fi
         done)
+        find reprozip reprounzip reprozip-* reprounzip-* -name '*.py' -exec sh -c "grep 'logging\\.\\(debug\\|warning\\|critical\\|error\\|info\\)' \"\$@\" && exit 1; exit 0" {} +
         ;;
 esac

CHANGELOG.md

@@ -11,6 +11,20 @@ Features:
 * Configuration file contains the walltime taken by each run
 * It is now possible to upload or download any file via its full path
 
+1.0.13 (2018-05-15)
+-------------------
+
+Bugfixes:
+* Fix uninitialized return value making some xxx_at() calls abort the trace
+* Fix some other warnings via static analysis
+
+Enhancements:
+* Show a warning when executing a file that has the set-uid or set-gid bit set, since Linux will not give it its privileges, making it confusing for users why their run failed
+* Make reprounzip-docker run even without a TTY
+* Correctly handle experiment returning non-0 in Docker
+* The C extension now logs through Python's logging facilities ('reprozip' logger)
+* Collect usage information from reprounzip-qt as well
+
 1.0.12 (2018-03-30)
 -------------------
 

README.md

@@ -1,8 +1,8 @@
 [![Build Status](https://travis-ci.org/ViDA-NYU/reprozip.svg?branch=master)](https://travis-ci.org/ViDA-NYU/reprozip)
 [![Coverage Status](https://codecov.io/github/ViDA-NYU/reprozip/coverage.svg?branch=master)](https://codecov.io/github/ViDA-NYU/reprozip?branch=master)
-[![Code Health](https://landscape.io/github/ViDA-NYU/reprozip/master/landscape.png)](https://landscape.io/github/ViDA-NYU/reprozip/master)
 [![Documentation Status](https://readthedocs.org/projects/reprozip/badge/?version=latest)](https://docs.reprozip.org/en/latest/)
 [![Matrix](https://img.shields.io/badge/chat-matrix.org-blue.svg)](https://riot.im/app/#/room/#reprozip:matrix.org)
+[![Say Thanks!](https://img.shields.io/badge/Say%20Thanks-!-1EAEDB.svg)](https://saythanks.io/to/remram44)
 [![status](https://img.shields.io/badge/JOSS-10.21105%2Fjoss.00107-green.svg)](http://joss.theoj.org/papers/b578b171263c73f64dfb9d040ca80fe0)
 [![DOI](https://img.shields.io/badge/DOI-10.5281%2Fzenodo.1210301-green.svg)](https://doi.org/10.5281/zenodo.1210301)
 

reprounzip-docker/setup.py

@@ -11,7 +11,7 @@
 with io.open('README.rst', encoding='utf-8') as fp:
     description = fp.read()
 setup(name='reprounzip-docker',
-      version='1.0.10',
+      version='1.0.13',
       packages=['reprounzip', 'reprounzip.unpackers'],
       entry_points={
           'reprounzip.unpackers': [
@@ -25,7 +25,15 @@
       author_email='reprozip-users@vgc.poly.edu',
       maintainer="Remi Rampin",
       maintainer_email='remirampin@gmail.com',
-      url='http://vida-nyu.github.io/reprozip/',
+      url='https://www.reprozip.org/',
+      project_urls={
+          'Homepage': 'https://github.com/ViDA-NYU/reprozip',
+          'Documentation': 'https://docs.reprozip.org/',
+          'Examples': 'https://examples.reprozip.org/',
+          'Say Thanks': 'https://saythanks.io/to/remram44',
+          'Source': 'https://github.com/ViDA-NYU/reprozip',
+          'Tracker': 'https://github.com/ViDA-NYU/reprozip/issues',
+      },
       long_description=description,
       license='BSD-3-Clause',
       keywords=['reprozip', 'reprounzip', 'reproducibility', 'provenance',

reprounzip-qt/reprounzip_qt/__init__.py

@@ -1 +1 @@
-__version__ = '1.0.12'
+__version__ = '1.0.13'

reprounzip-qt/reprounzip_qt/gui/__init__.py

@@ -4,6 +4,7 @@
 
 from __future__ import division, print_function, unicode_literals
 
+import logging
 import os
 import platform
 from PyQt4 import QtCore, QtGui
@@ -12,11 +13,16 @@
 import sys
 import tempfile
 import traceback
+import usagestats
 
 import reprounzip_qt
 from reprounzip_qt.gui.common import error_msg
 from reprounzip_qt.gui.unpack import UnpackTab
 from reprounzip_qt.gui.run import RunTab
+from reprounzip_qt.usage import record_usage, _usage_report as usage_report
+
+
+logger = logging.getLogger('reprounzip_qt')
 
 
 class Application(QtGui.QApplication):
@@ -29,6 +35,7 @@ def linux_try_register_default(self, window):
         rcpath = os.path.expanduser('~/.reprozip')
         rcname = 'rpuzqt-nodefault'
         if os.path.exists(os.path.join(rcpath, rcname)):
+            logger.info("Registering application disabled")
             return
         try:
             proc = subprocess.Popen(['xdg-mime', 'query', 'default',
@@ -38,7 +45,8 @@ def linux_try_register_default(self, window):
             out, err = proc.communicate()
             registered = bool(out.strip())
         except OSError:
-            pass
+            record_usage(appregister='fail xdg-mime')
+            logger.info("xdg-mime call failed, not registering application")
         else:
             if not registered:
                 r = QtGui.QMessageBox.question(
@@ -49,18 +57,22 @@ def linux_try_register_default(self, window):
                 if r == QtGui.QMessageBox.Yes:
                     self.linux_register_default(window)
                 elif r == QtGui.QMessageBox.No:
+                    record_usage(appregister='no')
                     if not os.path.exists(rcpath):
                         os.mkdir(rcpath)
                     with open(os.path.join(rcpath, rcname), 'w') as fp:
                         fp.write('1\n')
 
     def linux_register_default(self, window):
+        record_usage(appregister='yes')
         command = os.path.abspath(sys.argv[0])
         if not os.path.isfile(command):
+            logger.error("Couldn't find argv[0] location!")
             return
         dirname = tempfile.mkdtemp(prefix='reprozip_mime_')
         try:
             # Install x-reprozip mimetype
+            logger.info("Installing application/x-reprozip mimetype for .rpz")
             filename = os.path.join(dirname, 'nyuvida-reprozip.xml')
             with open(filename, 'w') as fp:
                 fp.write('''\
@@ -78,6 +90,7 @@ def linux_register_default(self, window):
                                                 '.local/share/mime')])
 
             # Install icon
+            logger.info("Copying icon")
             icon_dest_root = os.path.join(os.environ['HOME'],
                                           '.local/share/icons/hicolor')
             icon_dest_subdir = os.path.join(icon_dest_root, '48x48/mimetypes')
@@ -91,6 +104,7 @@ def linux_register_default(self, window):
             subprocess.check_call(['update-icon-caches', icon_dest_root])
 
             # Install desktop file
+            logger.info("Installing reprounzip.desktop file")
             app_dir = os.path.join(os.environ['HOME'],
                                    '.local/share/applications')
             if not os.path.exists(app_dir):
@@ -105,14 +119,38 @@ def linux_register_default(self, window):
 Icon={1}
 '''.format(command, icon_dest_file))
             subprocess.check_call(['update-desktop-database', app_dir])
+
+            logger.info("Application registered!")
         except (OSError, subprocess.CalledProcessError):
             error_msg(window, "Error setting default application",
                       'error', traceback.format_exc())
         finally:
             shutil.rmtree(dirname)
 
+    def ask_enable_usage_report(self):
+        dialog = QtGui.QDialog()
+        dialog.setWindowTitle("Anonymous usage statistics")
+        layout = QtGui.QVBoxLayout()
+        layout.addWidget(QtGui.QLabel("Send anonymous usage reports to the "
+                                      "developers?"))
+        dont_ask = QtGui.QCheckBox("Don't ask again")
+        layout.addWidget(dont_ask)
+        buttons = QtGui.QDialogButtonBox(
+            QtGui.QDialogButtonBox.Yes | QtGui.QDialogButtonBox.No)
+        layout.addWidget(buttons)
+        buttons.accepted.connect(dialog.accept)
+        buttons.rejected.connect(dialog.reject)
+        dialog.setLayout(layout)
+
+        res = dialog.exec_()
+        if res == QtGui.QDialog.Accepted:
+            usage_report.enable_reporting()
+        elif dont_ask.isChecked():
+            usage_report.disable_reporting()
+
     def event(self, event):
         if event.type() == QtCore.QEvent.FileOpen:
+            record_usage(fileopenevent=True)
             # Create new window for this RPZ
             window = ReprounzipUi(unpack=dict(package=event.file()))
             window.setVisible(True)
@@ -130,6 +168,8 @@ def set_first_window(self, window):
         self.windows.add(window)
         if platform.system().lower() == 'linux':
             self.linux_try_register_default(window)
+        if usage_report.status is usagestats.Stats.UNSET:
+            self.ask_enable_usage_report()
 
 
 class ReprounzipUi(QtGui.QMainWindow):

reprounzip-qt/reprounzip_qt/gui/common.py

@@ -4,9 +4,8 @@
 
 from __future__ import division, print_function, unicode_literals
 
-import re
-
 from PyQt4 import QtCore, QtGui
+import re
 
 
 def error_msg(parent, message, severity, details=None):

reprounzip-qt/reprounzip_qt/gui/run.py

@@ -4,13 +4,13 @@
 
 from __future__ import division, print_function, unicode_literals
 
-import yaml
-
 from PyQt4 import QtCore, QtGui
+import yaml
 
 import reprounzip_qt.reprounzip_interface as reprounzip
 from reprounzip_qt.gui.common import ROOT, ResizableStack, handle_error, \
     error_msg, parse_ports
+from reprounzip_qt.usage import record_usage
 
 
 class RunOptions(QtGui.QWidget):
@@ -87,14 +87,20 @@ def options(self):
 
         if self.tunneled_x11.isChecked():
             options['args'].append('--tunneled-x11')
+            record_usage(docker_tunneled_x11=True)
 
         if self.detach.isChecked():
             options['args'].append('--detach')
+            record_usage(docker_detach=True)
 
+        nb_raw = 0
         for opt in self.raw_options.text().split():
             opt = opt.strip()
             if opt:
+                nb_raw += 1
                 options['args'].append('--docker-option=%s' % opt)
+        if nb_raw:
+            record_usage(docker_raw_options=nb_raw)
 
         ports = parse_ports(self.ports.text(), self)
         if ports is None:
@@ -103,6 +109,7 @@ def options(self):
             options['args'].extend(
                 ['--docker-option=-p',
                  '--docker-option=%s:%s/%s' % (host, container, proto)])
+        record_usage(docker_run_port_fwd=bool(ports))
 
         return options
 
@@ -126,6 +133,7 @@ def options(self):
         for host, container, proto in parse_ports(self.ports.text(), self):
             options['args'].append('--expose-port=%s:%s/%s' %
                                    (host, container, proto))
+        record_usage(vagrant_run_port_fwd=bool(ports))
 
         return options
 
@@ -176,6 +184,7 @@ def __init__(self, directory, unpacker=None, root=None, **kwargs):
                                   ("O" if file_status.is_output else ''),
                                   file_status.name)
             self.files_widget.addItem(text)
+        record_usage(iofiles=self.files_widget.count())
 
     def _file_changed(self):
         selected = [i.row() for i in self.files_widget.selectedIndexes()]
@@ -212,6 +221,7 @@ def _upload(self):
             self, "Pick file to upload",
             QtCore.QDir.currentPath())
         if picked:
+            record_usage(file_upload=True)
             handle_error(self, reprounzip.upload(
                 self.directory, file_status.name, picked,
                 unpacker=self.unpacker, root=self.root))
@@ -224,6 +234,7 @@ def _download(self):
             self, "Pick destination",
             QtCore.QDir.currentPath() + '/' + file_status.name)
         if picked:
+            record_usage(file_download=True)
             handle_error(self, reprounzip.download(
                 self.directory, file_status.name, picked,
                 unpacker=self.unpacker, root=self.root))
@@ -232,6 +243,7 @@ def _download(self):
     def _reset(self):
         selected = self.files_widget.selectedIndexes()[0].row()
         file_status = self.files_status[selected]
+        record_usage(file_reset=True)
         handle_error(self, reprounzip.upload(
             self.directory, file_status.name, None,
             unpacker=self.unpacker, root=self.root))
@@ -335,6 +347,7 @@ def _browse(self):
             self, "Pick directory",
             QtCore.QDir.currentPath())
         if picked:
+            record_usage(browse_unpacked=True)
             self.directory_widget.setText(picked)
             self._directory_changed()
 
@@ -386,6 +399,7 @@ def _run(self):
         if not runs:
             error_msg(self, "No run selected", 'warning')
             return
+        record_usage(run='%d/%d' % (len(runs), self.runs_widget.count()))
         handle_error(self, reprounzip.run(
             self.directory, runs=runs,
             unpacker=self.unpacker,
@@ -419,7 +433,10 @@ def should_exit(self):
                 "The experiment is still unpacked with '%s'. Are you sure you "
                 "want to exit without removing it?" % self.unpacker,
                 QtGui.QMessageBox.Yes | QtGui.QMessageBox.No)
-            return r == QtGui.QMessageBox.Yes
+            if r == QtGui.QMessageBox.Yes:
+                record_usage(leave_unpacked=True)
+            else:
+                return False
         else:
             return True