ReproZip is a tool that simplifies the process of creating reproducible experiments from command-line executions, a frequently-used common denominator in computational science.

Related tags

Sciencepythonlinuxdockersciencevagrantreproducible-researcharchivingreproducible-sciencescientific-computingptracereproducibilitycomputational-sciencereprozipreprounziphacktoberfestnyu
Overview

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ReproZip

ReproZip is a tool aimed at simplifying the process of creating reproducible experiments from command-line executions, a frequently-used common denominator in computational science.

It tracks operating system calls and creates a package that contains all the binaries, files and dependencies required to run a given command on the author's computational environment (packing step). A reviewer can then extract the experiment in his environment to reproduce the results (unpacking step).

Quickstart

We have an example repository with a variety of different software. Don't hesitate to check it out, and contribute your own example if use ReproZip for something new!

Packing

Packing experiments is only available for Linux distributions. In the environment where the experiment is originally executed, first install reprozip:

$ pip install reprozip

Then, run your experiment with reprozip. Suppose you execute your experiment by originally running the following command:

$ ./myexperiment -my --options inputs/somefile.csv other_file_here.bin

To run it with reprozip, you just need to use the prefix reprozip trace:

$ reprozip trace ./myexperiment -my --options inputs/somefile.csv other_file_here.bin

This command creates a .reprozip-trace directory, in which you'll find the configuration file, named config.yml. You can edit the command line and environment variables, and choose which files to pack.

If you are using Debian or Ubuntu, most of these files (library dependencies) are organized by package. You can add or remove files, or choose not to include a package by changing option packfiles from true to false. In this way, smaller packs can be created with reprozip (if space is an issue), and reprounzip can download these files from the package manager; however, note this is only available for Debian and Ubuntu for now, and also be aware that package versions might differ. Choosing which files to pack is also important to remove sensitive information and third-party software that is not open source and should not be distributed.

Once done editing the configuration file (or even if you did not change anything), run the following command to create a ReproZip package named my_experiment:

$ reprozip pack my_experiment.rpz

Voilà! Now your experiment has been packed, and you can send it to your collaborators, reviewers, and researchers around the world!

Note that you can open the help message for any reprozip command by using the flag -h.

Unpacking

Do you need to unpack an experiment in a Linux machine? Easy! First, install reprounzip:

$ pip install reprounzip

Then, if you want to unpack everything in a single directory named mydirectory and execute the experiment from there, use the prefix reprounzip directory:

$ reprounzip directory setup my_experiment.rpz mydirectory
$ reprounzip directory run mydirectory

In case you prefer to build a chroot environment under mychroot, use the prefix reprounzip chroot:

$ reprounzip chroot setup my_experiment.rpz mychroot
$ reprounzip chroot run mychroot

Note that the previous options do not interfere with the original configuration of the environment, so don't worry! If you are using Debian or Ubuntu, reprounzip also has an option to install all the library dependencies directly on the machine using package managers (rather than just copying the files from the .rpz package). Be aware that this will interfere in your environment and it may update your library packages, so use it at your own risk! For this option, just use the prefix reprounzip installpkgs:

$ reprounzip installpkgs my_experiment.rpz

What if you want to reproduce the experiment in Windows or Mac OS X? You can build a virtual machine with the experiment! Easy as well! First, install the plugin reprounzip-vagrant:

$ pip install reprounzip-vagrant

Note that (i) you must install reprounzip first, and (ii) the plugin requires having Vagrant installed. Then, use the prefix reprounzip vagrant to create and start a virtual machine under directory mytemplate:

$ reprounzip vagrant setup my_experiment.rpz mytemplate

To execute the experiment, simply run:

$ reprounzip vagrant run mytemplate

Alternatively, you may use Docker containers to reproduce the experiment, which also works under Linux, Mac OS X, and Windows! First, install the plugin reprounzip-docker:

$ pip install reprounzip-docker

Then, assuming that you want to create the container under directory mytemplate, simply use the prefix reprounzip docker:

$ reprounzip docker setup my_experiment.rpz mytemplate
$ reprounzip docker run mytemplate

Remember that you can open the help message and learn more about other available flags and options by using the flag -h for any reprounzip command.

Citing ReproZip

Please use the following when citing ReproZip (BibTeX):

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

Contribute

Please subscribe to and contact the [email protected] mailing list for questions, suggestions and discussions about using reprozip.

Use the [email protected] mailing list for any questions about reprozip source code.

Bugs and feature plannings are tracked in the GitHub issues. Feel free to add an issue!

To suggest changes to this source code, feel free to raise a GitHub pull request. Any contributions received are assumed to be covered by the BSD 3-Clause license. We might ask you to sign a Contributor License Agreement before accepting a larger contribution.

License

  • Copyright (C) 2014-2017, New York University

Licensed under a BSD 3-Clause license. See the file LICENSE.txt for details.

Links and References

For more detailed information, please refer to our website, as well as to our documentation.

ReproZip is currently being developed at NYU. The team includes:

Comments
  • Misses inputs: process used unhandled system call openat(-100,

    Misses inputs: process used unhandled system call openat(-100, "foo")

    thank you for the reprozip! While exploring it more we ran into "input" files being not traced on my laptop (Debian sid/unstable with 4.15.0-1-amd64 kernel) while it worked just fine for @kyleam on his Debian stable. ~/.reprozip/log kindly informed me that many interesting files were not traced, for which there was a number of those log messages:

    $> tail ~/.reprozip/log
[REPROZIP] 16:10:08.359 INFO: [28405] process used unhandled system call openat(-100, "/usr/lib/locale/en_US.utf8/LC_COLLATE")
[REPROZIP] 16:10:08.359 INFO: [28405] process used unhandled system call openat(-100, "/usr/lib/locale/en_US.utf8/LC_TIME")
[REPROZIP] 16:10:08.359 INFO: [28405] process used unhandled system call openat(-100, "/usr/lib/locale/en_US.utf8/LC_NUMERIC")
[REPROZIP] 16:10:08.359 INFO: [28405] process used unhandled system call openat(-100, "/usr/lib/locale/en_US.utf8/LC_CTYPE")
[REPROZIP] 16:10:08.360 INFO: [28405] process used unhandled system call openat(-100, "foo")
[REPROZIP] 16:10:08.384 INFO: Program completed
[REPROZIP] 16:10:08.421 INFO: Running filter plugin builtin
[REPROZIP] 16:10:08.422 INFO: Running filter plugin python
[REPROZIP] 16:10:08.544 INFO: Identifying Debian packages for 29 files...
[REPROZIP] 16:10:17.324 INFO: 8 packages with 12 files, and 17 other files

    unfortunately my cfoo is too lame to offer any sensible PR, so I am at your mercy with this issue.

    Thank you in advance. ReproZip is from current 1.0.11-14-gb0504b5

    T-bug C-tracer (C) 
    opened by yarikoptic 14
  • Tracing a Singularity container

    Tracing a Singularity container

    Hi,

    I'm trying to use reprozip to monitor a workflow of mine, but getting a non-very-descriptive error message below when doing this. I'm able to run simpler commands, such as echo hello, but my current command (which happens to be a Python tool which launches Singularity containers) returns the following response each time. I'm not sure what the issue with the executable I'm currently trying to run is, or why reprozip seems incompatible with it, but am eager to see if you may know why this is happening.

    Thanks for your help!

    $ reprozip trace -w --dir=/mydir/ command arg1 arg2 arg3 arg4 ...
[REPROZIP] 15:14:44.630 CRITICAL: cleaning up, 4 processes to kill...
Traceback (most recent call last):
  File "/project/6008063/gkiar/computing/env/closh/lib/python3.6/site-packages/reprozip/main.py", line 390, in main
    status = args.func(args)
  File "/project/6008063/gkiar/computing/env/closh/lib/python3.6/site-packages/reprozip/main.py", line 206, in trace
    args.verbosity)
  File "/project/6008063/gkiar/computing/env/closh/lib/python3.6/site-packages/reprozip/tracer/trace.py", line 341, in trace
    c = _pytracer.execute(binary, argv, database.path, verbosity)
_pytracer.Error: Error occurred
    T-bug 
    opened by gkiar 13
  • Reprozip does not preserve PATH

    Reprozip does not preserve PATH

    In the experiment I'm testing with, the first command is a perl script which starts with

    #! /usr/bin/env perl

    This is intended to launch the script using the perl interpreter. Since script.sh includes this

    MODULE_VERSION_STACK=3.2.9 PATH=. myprogram

    PATH from the original running system isn't preserved, and env can't find perl, so the experiment doesn't run.

    T-bug R-wontfix 
    opened by gdevenyi 12
  • Build Linux binary wheels

    Build Linux binary wheels

    Distributing binary Linux wheels is a thing now, and would allow people to pip-install reprozip without a C compiler and the Python and SQLite3 development libraries.

    reprounzip and the rest don't include C extensions and thus are already distributed as wheels.

    The usual approach is to build against an old version of the libc so that every distribution can use it. manylinux provides multiple versions of Python ready to build wheels, however reprozip doesn't build on the Docker image (versions of ptrace header and sqlite3 are too old). But perhaps it can be made compatible with it?

    C-tracer (C) A-pr-exists T-task 
    opened by remram44 11
  • Run ReproZip for part of script

    Run ReproZip for part of script

    Would it possible to run ReproZip for part of a python script?

    To elaborate a bit... we are developing a tool whereby users would specify multiple parameters, and based on this different models and protocols would be employed for the simulations (i.e. it involves user interactivity). Naturally, the packages and files that are invoked would also vary based on the above, and the 'environment' I wish to save should exclude these initial parts and other housekeeping tasks, and focus solely on the loading and execution of the model.

    With this in mind, is it possible to invoke ReproZip from within a python script (as opposed to calling from the terminal CLI) so that I can track (and save) the files/packages that are required between, e.g. , line number x and y of my script (i.e. to be able to enable/disable ReproZip tracing inside a python script)?

    I suppose ReproZip wasn't intended to run in this fashion, but I am curious to know if I could employ certain sub-modules or methods to achieve this. I also took a look at the Jupyter plugin to see if some bits might be useful.

    I intend to dig deeper, but felt it was much better to ask here to get a better idea of the lay of the land. Thanks in advance.

    (apologies if a similar question has been answered previously elsewhere)

    opened by appukuttan-shailesh 10
  • simple test example for repro[un]zip

    simple test example for repro[un]zip

    In my effort to package the reprozip tools for Debian / Ubuntu, I was wondering whether you could provide a simple test example (helloworld style) which could help validate the reprozip / reprounzip packages?

    Thanks,

    A-question 
    opened by ghisvail 10
  • VisTrails integration

    VisTrails integration

    This adds the VisTrails integration plugin (issue #69).

    It has two components:

    • A method (do_vistrails) that fires after an experiment has been unpacked (post_setup signal) to create a CLTools module and a VisTrails workflow.
    • The module itself can be run, it is called from the CLTools module, and it parses the info from VisTrails to call the different steps of the correct unpacker (upload, run, download)

    This is built on top of the 'plugins' branch, see #76.

    • [X] plugin infrastructure (added by #76)
    • [X] CLTools module generation
    • [x] pipeline generation
    • [X] upload inputs/download outputs
    • [ ] change command line
    T-enhancement C-unpackers/vistrails 
    opened by remram44 10
  • Updated the website look & feel for consistency with rz-examples

    Updated the website look & feel for consistency with rz-examples

    So I didn't touch very much of the content -- this was mainly a CSS makeover. I also updated the "News" page to use Bootstrap cards for a better gallery experience, rather than a list.

    C-website A-pending-review 
    opened by VickyRampin 9
  • Add LGTM code quality badges

    Add LGTM code quality badges

    Hi there!

    I thought you might be interested in adding these code quality badges to your project. They will indicate a very high code quality to potential users and contributors. You can also check the alerts discovered by LGTM.

    N.B.: I am on the team behind LGTM.com, I'd appreciate your feedback on this initiative, whether you're interested or not, if you find time to drop me a line. Thanks.

    T-housekeeping 
    opened by xcorail 7
  • Uniformize logos

    Uniformize logos

    What is our official logo?

    • App uses blue: https://github.com/ViDA-NYU/reprozip/blob/1.0.x/reprounzip-qt/reprounzip_qt/icon.png #256
    • NYU purple versions exist
    • New website theme uses inverted colors, with NYU purple: https://github.com/ViDA-NYU/reprozip/pull/275

    Also there are "R", "RPZ", and "ReproZip" versions.

    T-bug T-housekeeping 
    opened by remram44 7
  • reprounzip error creating chroot

    reprounzip error creating chroot

    Successfully packed up my test experiment and now I've moved it to another machine for testing, when I try and unpack a chroot:

    [email protected]:~$ reprounzip chroot my_experiment.rpz test
Traceback (most recent call last):
  File "/usr/local/bin/reprounzip", line 11, in <module>
    sys.exit(main())
  File "/usr/local/lib/python2.7/dist-packages/reprounzip/reprounzip.py", line 52, in main
    args.func(args)
  File "/usr/local/lib/python2.7/dist-packages/reprounzip/unpackers/default.py", line 171, in create_chroot
    busybox_path)
  File "/usr/local/lib/python2.7/dist-packages/reprounzip/utils.py", line 145, in download_file
    cache.copy(dest)
  File "/usr/local/lib/python2.7/dist-packages/rpaths.py", line 824, in copy
    shutil.copy(self.path, self._to_backend(target))
  File "/usr/lib/python2.7/shutil.py", line 119, in copy
    copyfile(src, dst)
  File "/usr/lib/python2.7/shutil.py", line 83, in copyfile
    with open(dst, 'wb') as fdst:
IOError: [Errno 13] Permission denied: '/home/ace/test/root/bin/busybox'
    T-bug 
    opened by gdevenyi 7
  • arm (M1?) support

    arm (M1?) support

    A bit hard to test without access to an M1 myself, but maybe other ARM platforms can be tried through qemu?

    This would also need some support in the unpackers, reproducing cross-architecture probably doesn't work now.

    Relevant part in tracer, currently supporting x86 and x86_64, which has to be extended: https://github.com/VIDA-NYU/reprozip/blob/4603f56411403d051160685020c8c023ad6bda41/reprozip/native/tracer.c#L453-L511

    T-enhancement A-help wanted C-tracer (C) 
    opened by remram44 0
  • Deal with set-uid/set-gid files

    Deal with set-uid/set-gid files

    Set-uid and set-gid programs will not work correctly under trace (security feature).

    A warning is currently printed (#296), but it might be possible to do something better. I'm thinking we could run the tracer as root, but have it start the program with user privileges, since currently all you can do is run everything as root.

    Continuation of #295

    T-enhancement C-tracer (C) 
    opened by remram44 0
  • ReproZip tends to pack all fonts

    ReproZip tends to pack all fonts

    I am trying to pack a Python 2-based model, and see a lot of font-related files in my config.yml.

    • Is that expected? I find it kind of weird, but it's my first time I'm using tracing :-) I guess the video creation part of the workflow might include some library checking for installed fonts, but that is only a guess.
    • Can the fact that Python is used from a virtual env mess things up in unzip?
    • The fonts add quite some size, too.

    Note: I have not packed or unzipped yet!

    More information below, a "Don't worry about it, storage for fonts is cheap" might be a perfectly fine answer to this issue.

    Snippet of packages:

    packages:
  - name: "coreutils"
    version: "8.28-1ubuntu1"
    size: 6717440
    packfiles: true
    files:
      # Total files used: 34.21 KB
      # Installed package size: 6.41 MB
      - "/bin/uname" # 34.21 KB
  - name: "dash"
    version: "0.5.8-2.10"
    size: 219136
    packfiles: true
    files:
      # Total files used: 118.59 KB
      # Installed package size: 214.00 KB
      - "/bin/dash" # 118.59 KB
      - "/bin/sh" # Link to /bin/dash
  - name: "default-jre-headless"
    version: "2:1.11-68ubuntu1~18.04.1"
    size: 20480
    packfiles: true
    files:
      # Total files used: 0.0 bytes
      # Installed package size: 20.00 KB
      - "/usr/lib/jvm/default-java" # Link to /usr/lib/jvm/java-1.11.0-openjdk-amd64
  - name: "ffmpeg"
    version: "7:3.4.6-0ubuntu0.18.04.1"
    size: 2276352
    packfiles: true
    files:
      # Total files used: 266.14 KB
      # Installed package size: 2.17 MB
      - "/usr/bin/ffmpeg" # 266.14 KB
  - name: "fontconfig"
    version: "2.12.6-0ubuntu2"
    size: 576512
    packfiles: true
    files:
      # Total files used: 10.07 KB
      # Installed package size: 563.00 KB
      - "/usr/bin/fc-list" # 10.07 KB
  - name: "fontconfig-config"
    version: "2.12.6-0ubuntu2"
    size: 423936
    packfiles: true
    files:
      # Total files used: 59.59 KB
      # Installed package size: 414.00 KB
      - "/etc/fonts/conf.avail/10-antialias.conf" # 225.0 bytes
      - "/etc/fonts/conf.avail/10-hinting-slight.conf" # 463.0 bytes
      - "/etc/fonts/conf.avail/10-scale-bitmap-fonts.conf" # 1.96 KB
      - "/etc/fonts/conf.avail/11-lcdfilter-default.conf" # 526.0 bytes
      - "/etc/fonts/conf.avail/20-unhint-small-vera.conf" # 1.23 KB
      - "/etc/fonts/conf.avail/30-metric-aliases.conf" # 12.71 KB
      - "/etc/fonts/conf.avail/40-nonlatin.conf" # 5.26 KB
      - "/etc/fonts/conf.avail/45-generic.conf" # 3.17 KB
      - "/etc/fonts/conf.avail/45-latin.conf" # 6.21 KB
      - "/etc/fonts/conf.avail/49-sansserif.conf" # 545.0 bytes
      - "/etc/fonts/conf.avail/50-user.conf" # 673.0 bytes
      - "/etc/fonts/conf.avail/51-local.conf" # 189.0 bytes
      - "/etc/fonts/conf.avail/60-generic.conf" # 1.72 KB
      - "/etc/fonts/conf.avail/60-latin.conf" # 1.79 KB
      - "/etc/fonts/conf.avail/65-fonts-persian.conf" # 9.88 KB
      - "/etc/fonts/conf.avail/65-nonlatin.conf" # 7.59 KB
      - "/etc/fonts/conf.avail/69-unifont.conf" # 672.0 bytes
      - "/etc/fonts/conf.avail/70-no-bitmaps.conf" # 263.0 bytes
      - "/etc/fonts/conf.avail/80-delicious.conf" # 422.0 bytes
      - "/etc/fonts/conf.avail/90-synthetic.conf" # 1.65 KB
      - "/etc/fonts/conf.d/10-antialias.conf" # Link to /etc/fonts/conf.avail/10-antialias.conf
      - "/etc/fonts/conf.d/10-hinting-slight.conf" # Link to /etc/fonts/conf.avail/10-hinting-slight.conf
      - "/etc/fonts/conf.d/10-scale-bitmap-fonts.conf" # Link to /etc/fonts/conf.avail/10-scale-bitmap-fonts.conf
      - "/etc/fonts/conf.d/11-lcdfilter-default.conf" # Link to /etc/fonts/conf.avail/11-lcdfilter-default.conf
      - "/etc/fonts/conf.d/20-unhint-small-vera.conf" # Link to /etc/fonts/conf.avail/20-unhint-small-vera.conf
      - "/etc/fonts/conf.d/30-metric-aliases.conf" # Link to /etc/fonts/conf.avail/30-metric-aliases.conf
      - "/etc/fonts/conf.d/40-nonlatin.conf" # Link to /etc/fonts/conf.avail/40-nonlatin.conf
      - "/etc/fonts/conf.d/45-generic.conf" # Link to /etc/fonts/conf.avail/45-generic.conf
      - "/etc/fonts/conf.d/45-latin.conf" # Link to /etc/fonts/conf.avail/45-latin.conf
      - "/etc/fonts/conf.d/49-sansserif.conf" # Link to /etc/fonts/conf.avail/49-sansserif.conf
      - "/etc/fonts/conf.d/50-user.conf" # Link to /etc/fonts/conf.avail/50-user.conf
      - "/etc/fonts/conf.d/51-local.conf" # Link to /etc/fonts/conf.avail/51-local.conf
      - "/etc/fonts/conf.d/60-generic.conf" # Link to /etc/fonts/conf.avail/60-generic.conf
      - "/etc/fonts/conf.d/60-latin.conf" # Link to /etc/fonts/conf.avail/60-latin.conf
      - "/etc/fonts/conf.d/65-fonts-persian.conf" # Link to /etc/fonts/conf.avail/65-fonts-persian.conf
      - "/etc/fonts/conf.d/65-nonlatin.conf" # Link to /etc/fonts/conf.avail/65-nonlatin.conf
      - "/etc/fonts/conf.d/69-unifont.conf" # Link to /etc/fonts/conf.avail/69-unifont.conf
      - "/etc/fonts/conf.d/70-no-bitmaps.conf" # Link to /etc/fonts/conf.avail/70-no-bitmaps.conf
      - "/etc/fonts/conf.d/80-delicious.conf" # Link to /etc/fonts/conf.avail/80-delicious.conf
      - "/etc/fonts/conf.d/90-synthetic.conf" # Link to /etc/fonts/conf.avail/90-synthetic.conf
      - "/etc/fonts/fonts.conf" # 2.52 KB

    Snippet of other_files:

    [...]
other_files:
  - "/etc/alternatives/convert" # Link to /usr/bin/convert-im6.q16
  - "/etc/alternatives/fonts-japanese-gothic.ttf" # Link to /usr/share/fonts/truetype/takao-gothic/TakaoPGothic.ttf
  - "/etc/fonts/conf.d" # Directory
  - "/etc/ld.so.cache" # 240.96 KB
  - "/etc/localtime" # Link to /usr/share/zoneinfo/Europe/Berlin
  - "/home/daniel" # Directory
  - "/home/daniel/.cache/fontconfig/06c11524f63d4ff824512a8aea66f50b-le64.cache-7" # 15.41 KB
  - "/home/daniel/.cache/fontconfig/13cc71c55cfffaa2c3ea173a9e4403c7-le64.cache-7" # 296.0 bytes
  - "/home/daniel/.cache/fontconfig/165b9254a84ccada37e340049ffc8b30-le64.cache-7" # 1.43 KB
  - "/home/daniel/.cache/fontconfig/1875cd15ff5cb94240a7b9ba024d4703-le64.cache-7" # 176.0 bytes
  - "/home/daniel/.cache/fontconfig/3abfa2488312f909b35fa0ebe3bcbf08-le64.cache-7" # 256.0 bytes
  - "/home/daniel/.cache/fontconfig/40991ff0a5546db9730a2936d3ba0498-le64.cache-7" # 9.68 KB
  - "/home/daniel/.cache/fontconfig/87b4b9637a45d1e5f810525099feac83-le64.cache-7" # 384.0 bytes
  - "/home/daniel/.cache/fontconfig/9af608ae0ee9d2ef29ee571fd8270494-le64.cache-7" # 25.74 KB
  - "/home/daniel/.cache/fontconfig/9d20e3df18771968b7609cd23dcc2c84-le64.cache-7" # 17.55 KB
  - "/home/daniel/.cache/fontconfig/a1152301e1a95a67528356a4df9ff728-le64.cache-7" # 200.0 bytes
  - "/home/daniel/.cache/fontconfig/b26e9719d37da29cfcc5e22cb43a429b-le64.cache-7" # 150.38 KB
  - "/home/daniel/.cache/fontconfig/cae0f794d13cfbd2edafef3f246f9e17-le64.cache-7" # 27.40 KB
  - "/home/daniel/.cache/fontconfig/f894f59559f11d9760ae0b8121711064-le64.cache-7" # 1.72 KB
  - "/home/daniel/.cache/matplotlib" # Directory
  - "/home/daniel/.config/fontconfig/conf.d" # Directory
  - "/home/daniel/.config/matplotlib" # Directory
  - "/home/daniel/.fonts" # Directory
  - "/home/daniel/.fonts/.uuid" # 36.0 bytes
  - "/home/daniel/.fonts/Read Me.txt" # 646.0 bytes
  - "/home/daniel/.fonts/xkcd.ttf" # 12.41 KB
  - "/home/daniel/.local/share/fonts" # Directory
  - "/home/daniel/.local/share/fonts/AUSTRALIA-TITLE.otf" # 7.40 KB
  - "/home/daniel/.local/share/fonts/Adobe" # Directory
  - "/home/daniel/.local/share/fonts/Adobe/OpenType" # Directory
  - "/home/daniel/.local/share/fonts/Adobe/OpenType/Darleston" # Directory
  - "/home/daniel/.local/share/fonts/Adobe/OpenType/Darleston/Darleston_Regular.otf" # 31.22 KB
  - "/home/daniel/.local/share/fonts/Chomp.ttf" # 39.46 KB
  - "/home/daniel/.local/share/fonts/Creepster-Regular.ttf" # 61.25 KB
  - "/home/daniel/.local/share/fonts/DAYPBL__.ttf" # 32.76 KB
  - "/home/daniel/.local/share/fonts/DINBd.ttf" # 56.45 KB
  - "/home/daniel/.local/share/fonts/DINBdA.ttf" # 92.83 KB
  - "/home/daniel/.local/share/fonts/DINBdEp_.ttf" # 31.92 KB
  - "/home/daniel/.local/share/fonts/DINBk.ttf" # 57.00 KB
  - "/home/daniel/.local/share/fonts/DINBkA.ttf" # 56.64 KB
  - "/home/daniel/.local/share/fonts/DINBkEp_.ttf" # 29.98 KB
  - "/home/daniel/.local/share/fonts/DINLiA.ttf" # 123.40 KB
  - "/home/daniel/.local/share/fonts/DINLiEp_.ttf" # 34.85 KB
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  - "/home/daniel/.local/share/fonts/MetaOT-Black.otf" # 69.03 KB
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  - "/home/daniel/.local/share/fonts/Unknown Vendor/OpenType/Montserrat" # Directory
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  - "/home/daniel/.local/share/fonts/Unknown Vendor/OpenType/Montserrat Alternates/Montserrat_Alternates_ExtraLight.otf" # 175.47 KB
  - "/home/daniel/.local/share/fonts/Unknown Vendor/OpenType/Montserrat Alternates/Montserrat_Alternates_Heavy.otf" # 179.88 KB
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  - "/home/daniel/.local/share/fonts/Unknown Vendor/OpenType/Montserrat Alternates/Montserrat_Alternates_Light.otf" # 176.50 KB
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  - "/home/daniel/.local/share/fonts/YanoneKaffeesatz-Bold.otf" # 63.48 KB
  - "/home/daniel/.local/share/fonts/YanoneKaffeesatz-Light.otf" # 66.16 KB
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  - "/home/daniel/.local/share/fonts/YanoneKaffeesatz-Thin.otf" # 66.20 KB
  - "/home/daniel/.local/share/fonts/christmabet.ttf" # 78.50 KB
  - "/home/daniel/.local/share/fonts/daniel.ttf" # 50.77 KB
  - "/home/daniel/.local/share/fonts/danielbd.ttf" # 62.20 KB
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  - "/home/daniel/.local/share/fonts/universalis-adf-std.bold-italic.otf" # 40.95 KB
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  - "/home/daniel/.virtualenvs/pcraster_reprozip/bin/python" # Link to /home/daniel/.virtualenvs/pcraster_reprozip/bin/python2
  - "/home/daniel/.virtualenvs/pcraster_reprozip/bin/python2" # 3.47 MB
  - "/home/daniel/.virtualenvs/pcraster_reprozip/lib/python2.7" # Directory
  - "/home/daniel/.virtualenvs/pcraster_reprozip/lib/python2.7/UserDict.py" # Link to /usr/lib/python2.7/UserDict.py
  - "/home/daniel/.virtualenvs/pcraster_reprozip/lib/python2.7/UserDict.pyc" # 11.11 KB
[..]

    I'm rougly doing the following:

    # Python 2!

git clone https://github.com/JudithVerstegen/PLUC_Mozambique.git
cd PLUC_Mozambique/model

# pip install numpy matplotlib
# install PCRaster version 4.1.0, see https://github.com/JudithVerstegen/PLUC_Mozambique/blob/master/Dockerfile#L17
reprozip trace python LU_Moz.py

    I am running this in a virtual environment. If that might shake things up, I'm happy to extend the script above to also do that.

    T-enhancement A-help wanted C-tracer (Python) 
    opened by nuest 6
  • Identify language-specific packages (name/version)

    Identify language-specific packages (name/version)

    When a runtime with a package manager is used, we should try to identify which packages are being used. For example, for Python, record the package name and version for site packages.

    This could be done for:

    • Python site packages
    • Ruby gems
    • R (maybe)
    • Java (not interpreted, no run-time package manager, but JARs include version information)
    T-enhancement C-tracer (Python) 
    opened by remram44 4
Releases(1.1)
Owner
Visualization, Imaging, and Data Analysis Center at New York University
GitHub Repository https://www.reprozip.org/
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