Merge branch '1.0.x' into 'master'

CHANGELOG.md

@@ -11,6 +11,22 @@ Features:
 * Configuration file contains the walltime taken by each run
 * It is now possible to upload or download any file via its full path
 
+1.0.14 (2018-07-30)
+-------------------
+
+(reprozip, reprounzip-qt and reprozip-jupyter only)
+
+Bugfixes:
+* Fixed reprounzip-qt refusing to close when an experiment is still unpacked, even after the user provided confirmation
+* Fixed reprozip-jupyter on Python 3
+* Fixed running gnome-terminal from reprounzip-qt, made it preferred over xterm
+* Don't duplicate the latest run in the config file when the trace didn't add a run (for example because the command does not exist)
+
+Enhancements:
+* Uniformized logos and icons
+* Native terminal opened by reprounzip-qt waits for a key after success before closing
+* Officially support reprounzip-qt and reprozip-jupyter on Python 3
+
 1.0.13 (2018-05-15)
 -------------------
 

CITATION.txt

@@ -0,0 +1,20 @@
+To reference ReproZip in publications, please cite the following:
+
+ReproZip: Computational Reproducibility With Ease, F. Chirigati, R. Rampin, D. Shasha, and J. Freire. In Proceedings of the 2016 ACM SIGMOD International Conference on Management of Data (SIGMOD), pp. 2085-2088, 2016
+
+BibTeX:
+
+@inproceedings{ChirigatiRSF16,
+  title = {ReproZip: Computational Reproducibility With Ease},
+  author = {Chirigati, Fernando and Rampin, R{\'e}mi and Shasha, Dennis and Freire, Juliana},
+  year = {2016},
+  isbn = {978-1-4503-3531-7},
+  location = {San Francisco, California, USA},
+  doi = {10.1145/2882903.2899401},
+  booktitle = {Proceedings of the 2016 International Conference on Management of Data},
+  series = {SIGMOD '16},
+  pages = {2085--2088},
+  numpages = {4},
+  publisher = {ACM},
+  keywords = {computational reproducibility, provenance, reprozip},
+}

README.md

@@ -90,7 +90,7 @@ Remember that you can open the help message and learn more about other available
 Citing ReproZip
 ---------------
 
-Please use the following when citing ReproZip:
+Please use the following when citing ReproZip ([BibTeX](CITATION.txt)):
 
     ReproZip: Computational Reproducibility With Ease
     F. Chirigati, R. Rampin, D. Shasha, and J. Freire.

docs/troubleshooting.rst

@@ -44,7 +44,7 @@ Please feel free to contact us at users@reprozip.org if you encounter issues whi
 :Diagnosis: ``ptrace`` is the mechanism that ReproZip uses to attach to another process and follow its system calls. Because it is so powerful, some security policies, environments or isolation mechanism may disable it.
 :Solution:
 
- * If you are using Docker, you can use the Docker option ``--security-opt seccomp:unconfined`` (or write your own seccomp profile that allows ptrace, by adding ``"ptrace"`` to the `default profile <https://github.com/moby/moby/blob/master/profiles/seccomp/default.json>`__); see `the Docker documentation on seccomp <https://docs.docker.com/engine/security/seccomp/>`__.
+ * If you are using Docker, you can use the Docker option ``--cap-add=SYS_PTRACE`` (or provide your own seccomp profile that allows ptrace, by adding ``"ptrace"`` to the `default profile <https://github.com/moby/moby/blob/master/profiles/seccomp/default.json>`__; see `the Docker documentation on seccomp <https://docs.docker.com/engine/security/seccomp/>`__).
 
 ------------
 

reprounzip-qt/reprounzip_qt/__init__.py

@@ -1 +1 @@
-__version__ = '1.0.13'
+__version__ = '1.0.14'

reprounzip-qt/reprounzip_qt/reprounzip_interface.py

@@ -415,11 +415,14 @@ def run_in_system_terminal(cmd, env={},
                                   ('xterm', lambda a: ['-e', a])]:
             if find_command(term) is not None:
                 args = arg_factory(cmd)
+                proc = subprocess.Popen([term] + args,
+                                        stdin=subprocess.PIPE)
+                proc.stdin.close()
                 if wait:
-                    subprocess.check_call([term] + args,
-                                          stdin=subprocess.DEVNULL)
-                else:
-                    subprocess.Popen([term] + args,
-                                     stdin=subprocess.DEVNULL)
+                    retcode = proc.wait()
+                    if retcode != 0:
+                        raise subprocess.CalledProcessError(retcode,
+                                                            [term] + args)
+
                 return None
     return "Couldn't start a terminal", 'critical'

reprounzip-qt/setup.cfg

@@ -0,0 +1,2 @@
+[bdist_wheel]
+universal = 1

reprounzip-qt/setup.py

@@ -11,7 +11,7 @@
 with io.open('README.rst', encoding='utf-8') as fp:
     description = fp.read()
 setup(name='reprounzip-qt',
-      version='1.0.13',
+      version='1.0.14',
       packages=['reprounzip_qt', 'reprounzip_qt.gui'],
       package_data={'reprounzip_qt': ['icon.png']},
       entry_points={

reprozip-jupyter/reprozip_jupyter/__init__.py

@@ -1,7 +1,7 @@
 """Traces and packs notebook environments with ReproZip.
 """
 
-__version__ = '0.4'
+__version__ = '1.0.14'
 
 
 def _jupyter_nbextension_paths():

reprozip-jupyter/setup.cfg

@@ -0,0 +1,2 @@
+[bdist_wheel]
+universal = 1

reprozip-jupyter/setup.py

@@ -11,7 +11,7 @@
 with io.open('README.rst', encoding='utf-8') as fp:
     description = fp.read()
 setup(name='reprozip-jupyter',
-      version='0.4',
+      version='1.0.14',
       packages=['reprozip_jupyter'],
       package_data={'reprozip_jupyter': ['notebook-extension.js']},
       entry_points={

reprozip/reprozip/tracer/trace.py

@@ -426,9 +426,10 @@ def write_configuration(directory, sort_packages, find_inputs_outputs,
                 LIMIT 1
             )
             WHERE p.parent ISNULL
-            ORDER BY p.id DESC
-            LIMIT 1;
-            ''')
+            ORDER BY p.id
+            LIMIT 2147483647 OFFSET ?;
+            ''',
+            (len(runs),))
     for (r_name, r_argv, r_envp, r_workingdir,
          r_start, r_end, r_exitcode) in executions:
         # Decodes command-line

scripts/RELEASE

@@ -5,7 +5,7 @@ Bump versions in setup.py files, __init__.py files, docs/conf.py, installers
 Create a signed tag for the version
     git tag -s 1.0.11
 
-Make sdists, gpg sigs, upload to PyPI using twine
+Make sdists, wheels, gpg sigs, upload to PyPI using twine
 
 Make binary Linux wheels using scripts/linux-wheels.sh
 
@@ -16,6 +16,8 @@ Create a release on GitHub, add the CHANGELOG to it, link to the attached files
     Attach tarballs and wheels
     Attach installers
 
+Update conda-forge feedstocks
+
 Build Windows installer using native Python installer & InnoDB
 
 Build MacOS installer using Python built from source, App shim, Packages.app

scripts/conda/conda.py

@@ -44,85 +44,87 @@
 else:
     raise ValueError("Unknown platform")
 
-bits = struct.calcsize('P') * 8
 
-arch = '{0}-{1}'.format(osname, bits)
-
-for python_ver in ('2.7', '3.4', '3.5', '3.6'):
-    for package_name in ('reprozip', 'reprounzip', 'reprounzip-docker',
+def build_pkg(python_ver, package_name):
+    temp_dir = tempfile.mkdtemp(prefix='rr_conda_')
+
+    pkgdir = join(top_level, package_name)
+
+    try:
+        # Builds source distribution
+        subprocess.check_call(['python', 'setup.py', 'sdist',
+                               '--dist-dir', temp_dir], cwd=pkgdir)
+
+        # Rename it
+        temp_file, = os.listdir(temp_dir)
+        shutil.move(join(temp_dir, temp_file),
+                    join(temp_dir, '{0}.tar.gz'.format(package_name)))
+
+        # Copies conda recipe
+        shutil.copytree(join(top_level, 'scripts', 'conda', package_name),
+                        join(temp_dir, package_name))
+
+        # Update recipe
+        with open(join(temp_dir, package_name, 'meta.yaml')) as fp:
+            lines = fp.readlines()
+        # Changes version in recipe
+        lines = [l.replace('_REPLACE_version_REPLACE_', version)
+                 for l in lines]
+        with open(join(temp_dir, package_name, 'meta.yaml'), 'w') as fp:
+            for line in lines:
+                # Changes version
+                line = line.replace('_REPLACE_version_REPLACE_', version)
+                # Changes URL
+                if osname == 'win':
+                    line = line.replace(
+                        '_REPLACE_url_REPLACE_',
+                        'file:///{0}/{1}.tar.gz'.format(
+                            temp_dir.replace(os.sep, '/'),
+                            package_name))
+                else:
+                    line = line.replace(
+                        '_REPLACE_url_REPLACE_',
+                        'file://{0}/{1}.tar.gz'.format(temp_dir,
+                                                       package_name))
+                fp.write(line)
+
+        # Builds Conda package
+        croot = join(temp_dir, 'croot')
+        os.mkdir(croot)
+        output_pkg = subprocess.check_output(['conda', 'build',
+                                              '--croot', croot,
+                                              '--python', python_ver,
+                                              '--output', package_name],
+                                             cwd=temp_dir).rstrip()
+        output_pkg = output_pkg.decode('ascii')
+        output_pkg = join(temp_dir, output_pkg)
+        subprocess.check_call(['conda', 'build',
+                               '--croot', croot,
+                               '--python', python_ver,
+                               package_name],
+                              cwd=temp_dir)
+
+        # Copies result out
+        shutil.copyfile(join(pkgdir, output_pkg),
+                        join(dest_dir, os.path.basename(output_pkg)))
+    finally:
+        # Removes temporary directory
+        shutil.rmtree(temp_dir)
+        # Clears Conda cache
+        if os.path.exists(anaconda_cache):
+            shutil.rmtree(anaconda_cache)
+
+
+if __name__ == '__main__':
+    for python_ver in ('2.7', '3.4', '3.5', '3.6', '3.7'):
+        for package_name in ('reprozip',):
+            if package_name == 'reprozip' and osname != 'linux':
+                continue
+
+            build_pkg(python_ver, package_name)
+
+    # noarch packages
+    for package_name in ('reprounzip', 'reprounzip-docker',
                          'reprounzip-vagrant', 'reprounzip-vistrails',
                          'reprozip-jupyter', 'reprounzip-qt'):
-        if package_name == 'reprozip' and osname != 'linux':
-            continue
-
-        temp_dir = tempfile.mkdtemp(prefix='rr_conda_')
-
-        pkgdir = join(top_level, package_name)
-
-        try:
-            # Builds source distribution
-            subprocess.check_call(['python', 'setup.py', 'sdist',
-                                   '--dist-dir', temp_dir], cwd=pkgdir)
-
-            # Rename it
-            temp_file, = os.listdir(temp_dir)
-            shutil.move(join(temp_dir, temp_file),
-                        join(temp_dir, '{0}.tar.gz'.format(package_name)))
-
-            # Copies conda recipe
-            shutil.copytree(join(top_level, 'scripts', 'conda', package_name),
-                            join(temp_dir, package_name))
-
-            # Update recipe
-            with open(join(temp_dir, package_name, 'meta.yaml')) as fp:
-                lines = fp.readlines()
-            # Changes version in recipe
-            lines = [l.replace('_REPLACE_version_REPLACE_', version)
-                     for l in lines]
-            with open(join(temp_dir, package_name, 'meta.yaml'), 'w') as fp:
-                for line in lines:
-                    # Changes version
-                    line = line.replace('_REPLACE_version_REPLACE_', version)
-                    # Changes URL
-                    if osname == 'win':
-                        line = line.replace(
-                            '_REPLACE_url_REPLACE_',
-                            'file:///{0}/{1}.tar.gz'.format(
-                                temp_dir.replace(os.sep, '/'),
-                                package_name))
-                    else:
-                        line = line.replace(
-                            '_REPLACE_url_REPLACE_',
-                            'file://{0}/{1}.tar.gz'.format(temp_dir,
-                                                           package_name))
-                    # Change build string
-                    line = line.replace('_REPLACE_buildstr_REPLACE_',
-                                        'py{0}'.format(python_ver))
-
-                    fp.write(line)
-
-            # Builds Conda package
-            croot = join(temp_dir, 'croot')
-            os.mkdir(croot)
-            output_pkg = subprocess.check_output(['conda', 'build',
-                                                  '--croot', croot,
-                                                  '--python', python_ver,
-                                                  '--output', package_name],
-                                                 cwd=temp_dir).rstrip()
-            output_pkg = output_pkg.decode('ascii')
-            output_pkg = join(temp_dir, output_pkg)
-            subprocess.check_call(['conda', 'build',
-                                   '--croot', croot,
-                                   '--python', python_ver,
-                                   package_name],
-                                  cwd=temp_dir)
-
-            # Copies result out
-            shutil.copyfile(join(pkgdir, output_pkg),
-                            join(dest_dir, os.path.basename(output_pkg)))
-        finally:
-            # Removes temporary directory
-            shutil.rmtree(temp_dir)
-            # Clears Conda cache
-            if os.path.exists(anaconda_cache):
-                shutil.rmtree(anaconda_cache)
+        build_pkg('3.6', package_name)

scripts/conda/reprounzip-docker/meta.yaml

@@ -7,7 +7,7 @@ source:
   url: _REPLACE_url_REPLACE_
 
 build:
-  #preserve_egg_dir: True
+  noarch: python
   entry_points:
     # Put any entry points (scripts to be generated automatically) here. The
     # syntax is module:function.  For example
@@ -19,14 +19,13 @@ build:
   # If this is a new build for the same version, increment the build
   # number. If you do not include this key, it defaults to 0.
   # number: 1
-  string: _REPLACE_buildstr_REPLACE_
 
-  script: python setup.py install --single-version-externally-managed --record=record.txt
+  script: $PYTHON -m pip install --no-deps --ignore-installed .
 
 requirements:
-  build:
+  host:
     - python
-    - setuptools
+    - pip
 
   run:
     - python

scripts/conda/reprounzip-qt/meta.yaml

@@ -7,7 +7,7 @@ source:
   url: _REPLACE_url_REPLACE_
 
 build:
-  #preserve_egg_dir: True
+  noarch: python
   entry_points:
     # Put any entry points (scripts to be generated automatically) here. The
     # syntax is module:function.  For example
@@ -21,18 +21,16 @@ build:
   # If this is a new build for the same version, increment the build
   # number. If you do not include this key, it defaults to 0.
   # number: 1
-  string: _REPLACE_buildstr_REPLACE_
 
-  script: python setup.py install --single-version-externally-managed --record=record.txt
+  script: $PYTHON -m pip install --no-deps --ignore-installed .
 
 requirements:
-  build:
+  host:
     - python
-    - setuptools
+    - pip
 
   run:
     - python
-    - setuptools
     - pyyaml
     - pyqt <5
     - reprounzip >=1.0