Merge branch '1.0.x' into 'master'

.github/workflows/test.yml

@@ -9,18 +9,21 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        os: [ubuntu-latest]
+        os: [ubuntu-18.04]
         mode: [tests]
         python:
         - "2.7"
         - "3.5"
         include:
-        - os: ubuntu-latest
+        - os: ubuntu-18.04
           mode: coverage
           python: "3.8"
-        - os: ubuntu-latest
+        - os: ubuntu-18.04
           mode: checks
           python: "3.8"
+        - os: ubuntu-latest
+          mode: check-images
+          python: "3.8"
     runs-on: ${{ matrix.os }}
     env:
       TEST_MODE: ${{ matrix.mode }}
@@ -41,7 +44,7 @@ jobs:
 
         case "$TEST_MODE"
         in
-            tests|coverage)
+            tests|coverage|check-images)
                 if [ "$TEST_MODE" = "coverage" ]; then
                     export CFLAGS="-fprofile-arcs -ftest-coverage"
                 fi
@@ -74,8 +77,11 @@ jobs:
                 fi
                 python tests --run-docker
                 ;;
+            check-images)
+                python tests --check-vagrant-images --check-docker-images
+                ;;
             checks)
-                flake8 --ignore=E731,W504
+                flake8 --ignore=E731,W503,W504
                 diff -q reprozip/reprozip/common.py reprounzip/reprounzip/common.py
                 diff -q reprozip/reprozip/utils.py reprounzip/reprounzip/utils.py
                 find reprozip reprounzip reprozip-* reprounzip-* .travis -name '*.py' -or -name '*.sh' -or -name '*.h' -or -name '*.c' | (set +x; while read i; do

CODE_OF_CONDUCT.md

@@ -34,7 +34,7 @@ This Code of Conduct applies both within project spaces and in public spaces whe
 
 ## Enforcement
 
-Instances of abusive, harassing, or otherwise unacceptable behavior may be reported by contacting the project team at reprozip-dev@vgc.poly.edu. The project team will review and investigate all complaints, and will respond in a way that it deems appropriate to the circumstances. The project team is obligated to maintain confidentiality with regard to the reporter of an incident. Further details of specific enforcement policies may be posted separately.
+Instances of abusive, harassing, or otherwise unacceptable behavior may be reported by contacting the project team at dev@reprozip.org. The project team will review and investigate all complaints, and will respond in a way that it deems appropriate to the circumstances. The project team is obligated to maintain confidentiality with regard to the reporter of an incident. Further details of specific enforcement policies may be posted separately.
 
 Project maintainers who do not follow or enforce the Code of Conduct in good faith may face temporary or permanent repercussions as determined by other members of the project's leadership.
 

CONTRIBUTING.md

@@ -89,6 +89,6 @@ This CONTRIBUTING.md was adapted from [ProjectPorcupine's](https://github.com/Te
 
 # Contact info
 
-You are welcome to [subscribe to](https://vgc.poly.edu/mailman/listinfo/reprozip-users) or contact our user mailing list [reprozip-users](mailto:reprozip-users@vgc.poly.edu) for questions, suggestions and discussions about using ReproZip.
+You are welcome to [subscribe to](https://vgc.poly.edu/mailman/listinfo/reprozip-users) or contact our user mailing list [users@reprozip.org](mailto:users@reprozip.org) for questions, suggestions and discussions about using ReproZip.
 
-You can contact the maintainers on the [reprozip-dev](mailto:reprozip-dev@vgc.poly.edu) mailing list.
+You can contact the maintainers on the [dev@reprozip.org](mailto:dev@reprozip.org) mailing list.

README.md

@@ -99,9 +99,9 @@ Please use the following when citing ReproZip ([BibTeX](CITATION.txt)):
 Contribute
 ----------
 
-Please subscribe to and contact the [reprozip-users](https://vgc.poly.edu/mailman/listinfo/reprozip-users) mailing list for questions, suggestions and discussions about using reprozip.
+Please subscribe to and contact the [users@reprozip.org](https://vgc.poly.edu/mailman/listinfo/reprozip-users) mailing list for questions, suggestions and discussions about using reprozip.
 
-Use the [reprozip-dev](https://vgc.poly.edu/mailman/listinfo/reprozip-dev) mailing list for any questions about reprozip source code.
+Use the [dev@reprozip.org](https://vgc.poly.edu/mailman/listinfo/reprozip-dev) mailing list for any questions about reprozip source code.
 
 Bugs and feature plannings are tracked in the [GitHub issues](https://github.com/VIDA-NYU/reprozip/issues). Feel free to add an issue!
 
@@ -125,7 +125,7 @@ ReproZip is currently being developed at [NYU][nyu]. The team includes:
 * [Juliana Freire][jf]
 * [Rémi Rampin][rr]
 * [Dennis Shasha][ds]
-* [Vicky Steeves][vs]
+* [Vicky Rampin][vr]
 
 [vagrant]: https://www.vagrantup.com/
 [docker]: https://www.docker.com/
@@ -137,7 +137,7 @@ ReproZip is currently being developed at [NYU][nyu]. The team includes:
 [puzv]: https://pypi.python.org/pypi/reprounzip-vagrant
 [fc]: http://fchirigati.com/
 [jf]: https://vgc.poly.edu/~juliana/
-[rr]: https://remirampin.com/
+[rr]: https://remi.rampin.org/
 [ds]: http://cs.nyu.edu/shasha/
-[vs]: https://vickysteeves.com/
+[vr]: https://vicky.rampin.org/
 [nyu]: http://engineering.nyu.edu/

docs/man/reprounzip-docker.1

@@ -1,5 +1,5 @@
 .\" Manpage for reprounzip
-.\" Contact reprozip-dev@vgc.poly.edu to correct errors or typos.
+.\" Contact dev@reprozip.org to correct errors or typos.
 .TH man 1 "4 November 2017" "1.0.10" "reprounzip\-docker man page"
 .SH NAME
 reprounzip\-docker \- Docker unpacker for reprounzip
@@ -74,7 +74,7 @@ The team includes:
 .nf
 Remi Rampin
 Fernando Chirigati
-Vicky Steeves
+Vicky Rampin
 Juliana Freire
 Dennis Shasha
 .fi

docs/man/reprounzip-vagrant.1

@@ -1,5 +1,5 @@
 .\" Manpage for reprounzip
-.\" Contact reprozip-dev@vgc.poly.edu to correct errors or typos.
+.\" Contact dev@reprozip.org to correct errors or typos.
 .TH man 1 "4 November 2017" "1.0.10" "reprounzip\-vagrant man page"
 .SH NAME
 reprounzip\-vagrant \- Vagrant unpacker for reprounzip
@@ -65,7 +65,7 @@ The team includes:
 .nf
 Remi Rampin
 Fernando Chirigati
-Vicky Steeves
+Vicky Rampin
 Juliana Freire
 Dennis Shasha
 .fi

docs/man/reprounzip.1

@@ -1,5 +1,5 @@
 .\" Manpage for reprounzip
-.\" Contact reprozip-dev@vgc.poly.edu to correct errors or typos.
+.\" Contact dev@reprozip.org to correct errors or typos.
 .TH man 1 "4 November 2017" "1.0.11" "reprounzip man page"
 .SH NAME
 reprounzip \- the reproducibility unpacker
@@ -136,7 +136,7 @@ The team includes:
 .nf
 Remi Rampin
 Fernando Chirigati
-Vicky Steeves
+Vicky Rampin
 Juliana Freire
 Dennis Shasha
 .fi

docs/man/reprozip.1

@@ -1,5 +1,5 @@
 .\" Manpage for reprozip
-.\" Contact reprozip-dev@vgc.poly.edu to correct errors or typos.
+.\" Contact dev@reprozip.org to correct errors or typos.
 .TH man 1 "4 November 2017" "1.0.11" "reprozip man page"
 .SH NAME
 reprozip \- the reproducibility packer
@@ -100,7 +100,7 @@ The team includes:
 .nf
 Remi Rampin
 Fernando Chirigati
-Vicky Steeves
+Vicky Rampin
 Juliana Freire
 Dennis Shasha
 .fi

reprounzip-docker/README.rst

@@ -17,6 +17,6 @@ ReproZip is currently being developed at `NYU <http://engineering.nyu.edu/>`_. T
 
 * `Fernando Chirigati <http://fchirigati.com/>`_
 * `Juliana Freire <https://vgc.poly.edu/~juliana/>`_
-* `Remi Rampin <https://remirampin.com/>`_
+* `Remi Rampin <https://remi.rampin.org/>`_
 * `Dennis Shasha <http://cs.nyu.edu/shasha/>`_
-* `Vicky Steeves <https://vickysteeves.com/>`_
+* `Vicky Rampin <https://vicky.rampin.org/>`_

reprounzip-docker/setup.py

@@ -21,9 +21,9 @@
           'rpaths>=0.8'],
       description="Allows the ReproZip unpacker to create Docker containers",
       author="Remi Rampin, Fernando Chirigati, Dennis Shasha, Juliana Freire",
-      author_email='reprozip-users@vgc.poly.edu',
+      author_email='dev@reprozip.org',
       maintainer="Remi Rampin",
-      maintainer_email='remirampin@gmail.com',
+      maintainer_email='remi@rampin.org',
       url='https://www.reprozip.org/',
       project_urls={
           'Homepage': 'https://github.com/ViDA-NYU/reprozip',

reprounzip-qt/README.rst

@@ -19,6 +19,6 @@ ReproZip is currently being developed at `NYU <http://engineering.nyu.edu/>`_. T
 
 * `Fernando Chirigati <http://fchirigati.com/>`_
 * `Juliana Freire <https://vgc.poly.edu/~juliana/>`_
-* `Remi Rampin <https://remirampin.com/>`_
+* `Remi Rampin <https://remi.rampin.org/>`_
 * `Dennis Shasha <http://cs.nyu.edu/shasha/>`_
-* `Vicky Steeves <https://vickysteeves.com/>`_
+* `Vicky Rampin <https://vicky.rampin.org/>`_

reprounzip-qt/reprounzip_qt/main.py

@@ -25,7 +25,7 @@ def main():
 
     parser = argparse.ArgumentParser(
         description="Graphical user interface for reprounzip",
-        epilog="Please report issues to reprozip-users@vgc.poly.edu")
+        epilog="Please report issues to users@reprozip.org")
     parser.add_argument('--version', action='version',
                         version="reprounzip-qt version %s" % __version__)
     parser.add_argument('-v', '--verbose', action='count', default=1,

reprounzip-qt/setup.py

@@ -20,9 +20,9 @@
       install_requires=['PyYAML', 'qtpy', 'reprounzip>=1.0'],
       description="Graphical user interface for reprounzip, using Qt",
       author="Remi Rampin, Fernando Chirigati, Dennis Shasha, Juliana Freire",
-      author_email='reprozip-users@vgc.poly.edu',
+      author_email='dev@reprozip.org',
       maintainer="Remi Rampin",
-      maintainer_email='remirampin@gmail.com',
+      maintainer_email='remi@rampin.org',
       url='https://www.reprozip.org/',
       project_urls={
           'Homepage': 'https://github.com/ViDA-NYU/reprozip',

reprounzip-vagrant/README.rst

@@ -19,6 +19,6 @@ ReproZip is currently being developed at `NYU <http://engineering.nyu.edu/>`_. T
 
 * `Fernando Chirigati <http://fchirigati.com/>`_
 * `Juliana Freire <https://vgc.poly.edu/~juliana/>`_
-* `Remi Rampin <https://remirampin.com/>`_
+* `Remi Rampin <https://remi.rampin.org/>`_
 * `Dennis Shasha <http://cs.nyu.edu/shasha/>`_
-* `Vicky Steeves <https://vickysteeves.com/>`_
+* `Vicky Rampin <https://vicky.rampin.org/>`_

reprounzip-vagrant/reprounzip_vagrant/__init__.py

@@ -40,6 +40,38 @@
 logger = logging.getLogger('reprounzip.vagrant')
 
 
+def _find_version(distrib, version, architecture):
+    if version is not None:
+        for box in distrib['versions']:
+            if re.match(box['version'], version) is not None:
+                result = box['architectures'].get(architecture)
+                if result is not None:
+                    return box['distribution'], result
+    box = distrib['default']
+    if version is not None:
+        logger.warning("Using %s instead of '%s'",
+                       box['name'], version)
+    result = box['architectures'].get(architecture)
+    if result is not None:
+        return box['distribution'], result
+
+
+def _find_distribution(parameter, distribution, version, architecture):
+    boxes = parameter['boxes']
+
+    for distrib in boxes:
+        if re.match(distrib['name'], distribution) is not None:
+            result = _find_version(distrib, version, architecture)
+            if result is not None:
+                return result
+    default = parameter['default']
+    logger.warning("Unsupported distribution '%s', using %s",
+                   distribution, default['name'])
+    result = default['architectures'].get(architecture)
+    if result:
+        return default['distribution'], result
+
+
 def select_box(runs, gui=False):
     """Selects a box for the experiment, with the correct distribution.
     """
@@ -54,39 +86,10 @@ def select_box(runs, gui=False):
         logger.critical("Error: unsupported architecture %s", architecture)
         sys.exit(1)
 
-    def find_distribution(parameter, distribution, version, architecture):
-        boxes = parameter['boxes']
-
-        for distrib in boxes:
-            if re.match(distrib['name'], distribution) is not None:
-                result = find_version(distrib, version, architecture)
-                if result is not None:
-                    return result
-        default = parameter['default']
-        logger.warning("Unsupported distribution '%s', using %s",
-                       distribution, default['name'])
-        result = default['architectures'].get(architecture)
-        if result:
-            return default['distribution'], result
-
-    def find_version(distrib, version, architecture):
-        if version is not None:
-            for box in distrib['versions']:
-                if re.match(box['version'], version) is not None:
-                    result = box['architectures'].get(architecture)
-                    if result is not None:
-                        return box['distribution'], result
-        box = distrib['default']
-        if version is not None:
-            logger.warning("Using %s instead of '%s'",
-                           box['name'], version)
-        result = box['architectures'].get(architecture)
-        if result is not None:
-            return box['distribution'], result
-
-    result = find_distribution(
+    result = _find_distribution(
         get_parameter('vagrant_boxes_x' if gui else 'vagrant_boxes'),
-        distribution, version, architecture)
+        distribution, version, architecture,
+    )
     if result is None:
         logger.critical("Error: couldn't find a base box for required "
                         "architecture")

reprounzip-vagrant/setup.py

@@ -22,9 +22,9 @@
           'paramiko'],
       description="Allows the ReproZip unpacker to create virtual machines",
       author="Remi Rampin, Fernando Chirigati, Dennis Shasha, Juliana Freire",
-      author_email='reprozip-users@vgc.poly.edu',
+      author_email='dev@reprozip.org',
       maintainer="Remi Rampin",
-      maintainer_email='remirampin@gmail.com',
+      maintainer_email='remi@rampin.org',
       url='https://www.reprozip.org/',
       project_urls={
           'Homepage': 'https://github.com/ViDA-NYU/reprozip',

reprounzip-vistrails/README.rst

@@ -19,6 +19,6 @@ ReproZip is currently being developed at `NYU <http://engineering.nyu.edu/>`_. T
 
 * `Fernando Chirigati <http://fchirigati.com/>`_
 * `Juliana Freire <https://vgc.poly.edu/~juliana/>`_
-* `Remi Rampin <https://remirampin.com/>`_
+* `Remi Rampin <https://remi.rampin.org/>`_
 * `Dennis Shasha <http://cs.nyu.edu/shasha/>`_
-* `Vicky Steeves <https://vickysteeves.com/>`_
+* `Vicky Rampin <https://vicky.rampin.org/>`_

reprounzip-vistrails/setup.py

@@ -26,9 +26,9 @@
       description="Integrates the ReproZip unpacker with the VisTrails "
                   "workflow management system",
       author="Remi Rampin, Fernando Chirigati, Dennis Shasha, Juliana Freire",
-      author_email='reprozip-users@vgc.poly.edu',
+      author_email='dev@reprozip.org',
       maintainer="Remi Rampin",
-      maintainer_email='remirampin@gmail.com',
+      maintainer_email='remi@rampin.org',
       url='https://www.reprozip.org/',
       project_urls={
           'Homepage': 'https://github.com/ViDA-NYU/reprozip',

reprounzip/README.rst

@@ -21,6 +21,6 @@ ReproZip is currently being developed at `NYU <http://engineering.nyu.edu/>`_. T
 
 * `Fernando Chirigati <http://fchirigati.com/>`_
 * `Juliana Freire <https://vgc.poly.edu/~juliana/>`_
-* `Remi Rampin <https://remirampin.com/>`_
+* `Remi Rampin <https://remi.rampin.org/>`_
 * `Dennis Shasha <http://cs.nyu.edu/shasha/>`_
-* `Vicky Steeves <https://vickysteeves.com/>`_
+* `Vicky Rampin <https://vicky.rampin.org/>`_

reprounzip/reprounzip/common.py

@@ -385,6 +385,16 @@ def load_iofiles(config, runs):
         path = PosixPath(f['path'])
         readers = sorted(f.get('read_by_runs', []))
         writers = sorted(f.get('written_by_runs', []))
+        if (
+            not isinstance(readers, (tuple, list))
+            or not all(isinstance(e, int) for e in readers)
+        ):
+            raise InvalidConfig("read_by_runs should be a list of integers")
+        if (
+            not isinstance(writers, (tuple, list))
+            or not all(isinstance(e, int) for e in writers)
+        ):
+            raise InvalidConfig("written_by_runs should be a list of integers")
         if name in files:
             if files[name].path != path:
                 old_name, name = name, uniquenames(name)
@@ -669,6 +679,8 @@ def setup_logging(tag, verbosity):
                 (datetime.now().strftime("%Y-%m-%d"), sys.argv),
                 None))
 
+    logging.getLogger('urllib3').setLevel(logging.INFO)
+
 
 _usage_report = None
 

reprounzip/reprounzip/main.py

@@ -96,7 +96,7 @@ def add_options(opts):
         description="reprounzip is the ReproZip component responsible for "
                     "unpacking and reproducing an experiment previously "
                     "packed with reprozip",
-        epilog="Please report issues to reprozip-users@vgc.poly.edu")
+        epilog="Please report issues to users@reprozip.org")
     add_options(parser)
     parser.add_argument('-v', '--verbose', action='count', default=1,
                         dest='verbosity',