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[DATALAD RUNCMD] git-sedi niceman reproman

=== Do not change lines below ===
{
 "chain": [],
 "cmd": "git-sedi niceman reproman",
 "exit": 0,
 "extra_inputs": [],
 "inputs": [],
 "outputs": [],
 "pwd": "."
}
^^^ Do not change lines above ^^^
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yarikoptic committed Jan 17, 2019
1 parent 5bb7d46 commit 6493997b56a91fa48c83a89ccfd1b28a0186aa4c
Showing with 780 additions and 780 deletions.
  1. +1 −1 .gitignore
  2. +3 −3 .travis.yml
  3. +1 −1 CHANGELOG.md
  4. +19 −19 CONTRIBUTING.md
  5. +11 −11 Dockerfile-debian
  6. +13 −13 Dockerfile-redhat
  7. +6 −6 README.md
  8. +11 −11 Singularity
  9. +6 −6 docker-compose.yml
  10. +4 −4 docs/Makefile
  11. +3 −3 docs/source/_templates/autosummary/module.rst
  12. +10 −10 docs/source/cmdline.rst
  13. +8 −8 docs/source/conf.py
  14. +1 −1 docs/source/glossary.rst
  15. +6 −6 docs/source/modref.rst
  16. +5 −5 docs/source/sandbox/hierarchy.rst
  17. +8 −8 reproman/__init__.py
  18. +2 −2 reproman/api.py
  19. +3 −3 reproman/cmd.py
  20. +1 −1 reproman/cmdline/__init__.py
  21. +1 −1 reproman/cmdline/common_args.py
  22. +10 −10 reproman/cmdline/helpers.py
  23. +13 −13 reproman/cmdline/main.py
  24. +1 −1 reproman/cmdline/tests/__init__.py
  25. +1 −1 reproman/cmdline/tests/test_helpers.py
  26. +13 −13 reproman/config.py
  27. +2 −2 reproman/conftest.py
  28. +2 −2 reproman/consts.py
  29. +2 −2 reproman/distributions/__init__.py
  30. +5 −5 reproman/distributions/base.py
  31. +7 −7 reproman/distributions/conda.py
  32. +8 −8 reproman/distributions/debian.py
  33. +3 −3 reproman/distributions/docker.py
  34. +3 −3 reproman/distributions/neurodebian.py
  35. +2 −2 reproman/distributions/piputils.py
  36. +3 −3 reproman/distributions/redhat.py
  37. +3 −3 reproman/distributions/singularity.py
  38. +10 −10 reproman/distributions/tests/test_conda.py
  39. +8 −8 reproman/distributions/tests/test_debian.py
  40. +7 −7 reproman/distributions/tests/test_distribution.py
  41. +1 −1 reproman/distributions/tests/test_docker.py
  42. +4 −4 reproman/distributions/tests/test_environment.py
  43. +5 −5 reproman/distributions/tests/test_piputils.py
  44. +2 −2 reproman/distributions/tests/test_redhat.py
  45. +1 −1 reproman/distributions/tests/test_singularity.py
  46. +13 −13 reproman/distributions/tests/test_vcs.py
  47. +11 −11 reproman/distributions/tests/test_venv.py
  48. +12 −12 reproman/distributions/vcs.py
  49. +10 −10 reproman/distributions/venv.py
  50. +2 −2 reproman/dochelpers.py
  51. +2 −2 reproman/examples/example.py
  52. +3 −3 reproman/examples/tests/test_example.py
  53. +1 −1 reproman/formats/__init__.py
  54. +7 −7 reproman/formats/base.py
  55. +8 −8 reproman/formats/niceman.py
  56. +2 −2 reproman/formats/reprozip.py
  57. +1 −1 reproman/formats/tests/__init__.py
  58. +2 −2 reproman/formats/tests/constants.py
  59. +1 −1 reproman/formats/tests/files/demo_spec2.yml
  60. +1 −1 reproman/formats/tests/files/nicemanspec1_v0.0.1.yml
  61. +1 −1 reproman/formats/tests/files/nicemanspec2_v0.0.1.yml
  62. +1 −1 reproman/formats/tests/fixtures.py
  63. +18 −18 reproman/formats/tests/test_niceman.py
  64. +5 −5 reproman/formats/tests/test_provenance.py
  65. +1 −1 reproman/formats/tests/test_reprozip.py
  66. +2 −2 reproman/formats/trig.py
  67. +2 −2 reproman/formats/utils.py
  68. +17 −17 reproman/interface/__init__.py
  69. +10 −10 reproman/interface/backend_parameters.py
  70. +6 −6 reproman/interface/base.py
  71. +6 −6 reproman/interface/common_opts.py
  72. +6 −6 reproman/interface/create.py
  73. +5 −5 reproman/interface/delete.py
  74. +4 −4 reproman/interface/diff.py
  75. +17 −17 reproman/interface/execute.py
  76. +3 −3 reproman/interface/install.py
  77. +5 −5 reproman/interface/login.py
  78. +5 −5 reproman/interface/ls.py
  79. +16 −16 reproman/interface/retrace.py
  80. +4 −4 reproman/interface/start.py
  81. +4 −4 reproman/interface/stop.py
  82. +3 −3 reproman/interface/test.py
  83. +1 −1 reproman/interface/tests/__init__.py
  84. +3 −3 reproman/interface/tests/test_backend_parameters.py
  85. +11 −11 reproman/interface/tests/test_create.py
  86. +8 −8 reproman/interface/tests/test_delete.py
  87. +9 −9 reproman/interface/tests/test_diff.py
  88. +16 −16 reproman/interface/tests/test_execute.py
  89. +17 −17 reproman/interface/tests/test_install.py
  90. +7 −7 reproman/interface/tests/test_login.py
  91. +3 −3 reproman/interface/tests/test_ls.py
  92. +5 −5 reproman/interface/tests/test_retrace.py
  93. +1 −1 reproman/interface/tests/test_retrace_packages.py
  94. +15 −15 reproman/interface/tests/test_sequence.py
  95. +4 −4 reproman/log.py
  96. +1 −1 reproman/resource/__init__.py
  97. +3 −3 reproman/resource/aws_ec2.py
  98. +4 −4 reproman/resource/base.py
  99. +5 −5 reproman/resource/docker_container.py
  100. +12 −12 reproman/resource/session.py
  101. +7 −7 reproman/resource/shell.py
  102. +2 −2 reproman/resource/singularity.py
  103. +6 −6 reproman/resource/ssh.py
  104. +2 −2 reproman/resource/tests/conftest.py
  105. +1 −1 reproman/resource/tests/test_aws_ec2.py
  106. +11 −11 reproman/resource/tests/test_base.py
  107. +3 −3 reproman/resource/tests/test_docker_container.py
  108. +5 −5 reproman/resource/tests/test_session.py
  109. +1 −1 reproman/resource/tests/test_shell.py
  110. +1 −1 reproman/resource/tests/test_singularity.py
  111. +2 −2 reproman/resource/tests/test_ssh.py
  112. +1 −1 reproman/support/__init__.py
  113. +1 −1 reproman/support/configparserinc.py
  114. +1 −1 reproman/support/constraints.py
  115. +2 −2 reproman/support/digests.py
  116. +1 −1 reproman/support/distributions/__init__.py
  117. +3 −3 reproman/support/distributions/debian.py
  118. +1 −1 reproman/support/distributions/tests/__init__.py
  119. +2 −2 reproman/support/distributions/tests/test_debian.py
  120. +3 −3 reproman/support/exceptions.py
  121. +5 −5 reproman/support/external_versions.py
  122. +6 −6 reproman/support/globbedpaths.py
  123. +4 −4 reproman/support/param.py
  124. +3 −3 reproman/support/protocol.py
  125. +2 −2 reproman/support/tests/__init__.py
  126. +1 −1 reproman/support/tests/test_digests.py
  127. +7 −7 reproman/support/tests/test_external_versions.py
  128. +6 −6 reproman/support/tests/test_globbedpaths.py
  129. +2 −2 reproman/tests/__init__.py
  130. +2 −2 reproman/tests/constants.py
  131. +2 −2 reproman/tests/files/niceman.cfg
  132. +6 −6 reproman/tests/fixtures.py
  133. +4 −4 reproman/tests/test_api.py
  134. +1 −1 reproman/tests/test_cmd.py
  135. +8 −8 reproman/tests/test_cmdline_main.py
  136. +1 −1 reproman/tests/test_config.py
  137. +1 −1 reproman/tests/test_dochelpers.py
  138. +5 −5 reproman/tests/test_formatters.py
  139. +8 −8 reproman/tests/test_installed.py
  140. +1 −1 reproman/tests/test_interface.py
  141. +7 −7 reproman/tests/test_log.py
  142. +1 −1 reproman/tests/test_protocols.py
  143. +5 −5 reproman/tests/test_tests_utils.py
  144. +6 −6 reproman/tests/test_utils.py
  145. +4 −4 reproman/tests/utils.py
  146. +1 −1 reproman/ui/__init__.py
  147. +1 −1 reproman/ui/dialog.py
  148. +1 −1 reproman/ui/tests/test_base.py
  149. +1 −1 reproman/ui/tests/test_dialog.py
  150. +17 −17 reproman/utils.py
  151. +2 −2 reproman/version.py
  152. +2 −2 requirements.txt
  153. +1 −1 setup.cfg
  154. +10 −10 setup.py
  155. +7 −7 setup_support.py
  156. +1 −1 tools/cmdline-completion
  157. +1 −1 tox.ini
@@ -1,5 +1,5 @@
.pybuild/
niceman.build/
reproman.build/
/.idea
.coverage
/venv*
@@ -73,8 +73,8 @@ script:
# Verify that setup.py build doesn't puke
- python setup.py build
- if [ ! -z "$NICEMAN_TESTS_NONETWORK" ]; then sudo route add -net 0.0.0.0 netmask 0.0.0.0 dev lo; fi
# - $NOSE_WRAPPER `which nosetests` -s -v --with-doctest --doctest-tests --with-cov --cover-package niceman --logging-level=INFO
- coverage run `which py.test` -s --integration niceman
# - $NOSE_WRAPPER `which nosetests` -s -v --with-doctest --doctest-tests --with-cov --cover-package reproman --logging-level=INFO
- coverage run `which py.test` -s --integration reproman
- if [ ! -z "$NICEMAN_TESTS_NONETWORK" ]; then sudo route del -net 0.0.0.0 netmask 0.0.0.0 dev lo; fi
# Generate documentation and run doctests
- PYTHONPATH=$PWD make -C docs html doctest
@@ -91,5 +91,5 @@ after_success:
# for a particular debugging
#after_failure:
# - if [ ! -z "$NICEMAN_TESTS_NONETWORK" ]; then sudo route add -net 0.0.0.0 netmask 0.0.0.0 dev lo; fi
# - NICEMAN_LOGLEVEL=DEBUG $NOSE_WRAPPER `which nosetests` -s -v --with-doctest --doctest-tests --with-cov --cover-package niceman --logging-level=DEBUG
# - NICEMAN_LOGLEVEL=DEBUG $NOSE_WRAPPER `which nosetests` -s -v --with-doctest --doctest-tests --with-cov --cover-package reproman --logging-level=DEBUG
# - if [ ! -z "$NICEMAN_TESTS_NONETWORK" ]; then sudo route del -net 0.0.0.0 netmask 0.0.0.0 dev lo; fi
@@ -74,6 +74,6 @@ TODO Summary

## References
[datalad]: http://datalad.org
[niceman]: http://niceman.repronim.org
[reproman]: http://reproman.repronim.org
[repronim]: http://repronim.org
[simple_workflow]: https://github.com/ReproNim/simple_workflow
@@ -1,17 +1,17 @@
Contributing to NICEMAN
========================

[gh-niceman]: http://github.com/ReproNim/niceman
[gh-reproman]: http://github.com/ReproNim/reproman

Files organization
------------------

- `niceman/` is the main Python module where major development is happening,
- `reproman/` is the main Python module where major development is happening,
with major submodules being:
- `cmdline/` - helpers for accessing `interface/` functionality from
command line
- `interface/` - high level interface functions which get exposed via
command line (`cmdline/`) or Python (`niceman.api`).
command line (`cmdline/`) or Python (`reproman.api`).
- `tests/` - some unit- and regression- tests (more could be found under
`tests/` of corresponding submodules)
- `utils.py` provides convenience helpers used by unit-tests such as
@@ -22,7 +22,7 @@ Files organization
- `support/` - various support modules, e.g. for git/git-annex interfaces,
constraints for the `interface/`, etc
- `docs/` - yet to be heavily populated documentation
- `bash-completions` - bash and zsh completion setup for niceman (just
- `bash-completions` - bash and zsh completion setup for reproman (just
`source` it)
- `tools/` contains helper utilities used during development, testing, and
benchmarking of NICEMAN. Implemented in any most appropriate language
@@ -32,23 +32,23 @@ How to contribute
-----------------

The preferred way to contribute to the NICEMAN code base is
to fork the [main repository][gh-niceman] on GitHub. Here
to fork the [main repository][gh-reproman] on GitHub. Here
we outline the workflow used by the developers:


0. Have a clone of our main [project repository][gh-niceman] as `origin`
0. Have a clone of our main [project repository][gh-reproman] as `origin`
remote in your git:

git clone git://github.com/ReproNim/niceman
git clone git://github.com/ReproNim/reproman

1. Fork the [project repository][gh-niceman]: click on the 'Fork'
1. Fork the [project repository][gh-reproman]: click on the 'Fork'
button near the top of the page. This creates a copy of the code
base under your account on the GitHub server.

2. Add your forked clone as a remote to the local clone you already have on your
local disk:

git remote add gh-YourLogin git@github.com:YourLogin/niceman.git
git remote add gh-YourLogin git@github.com:YourLogin/reproman.git
git fetch gh-YourLogin

To ease addition of other github repositories as remotes, here is
@@ -65,7 +65,7 @@ we outline the workflow used by the developers:
thus you could simply run:
ghremote git@github.com:YourLogin/niceman.git
ghremote git@github.com:YourLogin/reproman.git
to add the above `gh-YourLogin` remote. Additional handy aliases
such as `ghpr` (to fetch existing pr from someone's remote) and
@@ -119,7 +119,7 @@ with `python{,3}-{` to also install dependencies for Python 3 (e.g., if you woul
like to develop and test through tox).
See [README.md:Dependencies](README.md#Dependencies) for basic information
about installation of niceman itself.
about installation of reproman itself.
On Debian-based systems we recommend to enable [NeuroDebian](http://neuro.debian.net)
since we use it to provide backports of recent fixed external modules we depend upon.
@@ -202,7 +202,7 @@ Additional Hints
and if conflicts occur, provide short summary on how they were resolved
in "Conflicts" listing within the merge commit
(see [example](https://github.com/ReproNim/niceman/commit/f939595d3f09dde9fd4d142e863ba0cea26a13ed)).
(see [example](https://github.com/ReproNim/reproman/commit/f939595d3f09dde9fd4d142e863ba0cea26a13ed)).
Quality Assurance
@@ -221,7 +221,7 @@ rules before submitting a pull request:
### Tests
`niceman/tests` contains tests for the core portion of the project, and
`reproman/tests` contains tests for the core portion of the project, and
more tests are provided under corresponding submodules in `tests/`
subdirectories to simplify re-running the tests concerning that portion
of the codebase. To execute many tests, the codebase first needs to be
@@ -305,7 +305,7 @@ Easy Issues
-----------

A great way to start contributing to NICEMAN is to pick an item from the list of
[Easy issues](https://github.com/ReproNim/niceman/labels/easy) in the issue
[Easy issues](https://github.com/ReproNim/reproman/labels/easy) in the issue
tracker. Resolving these issues allows you to start contributing to the project
without much prior knowledge. Your assistance in this area will be greatly
appreciated by the more experienced developers as it helps free up their time to
@@ -332,14 +332,14 @@ Various hints for developers
(Firefox, Chrome) which annotates pull requests on github regarding changed coverage.

### Useful Environment Variables
Refer niceman/config.py for information on how to add these environment variables to the config file and their naming convention
Refer reproman/config.py for information on how to add these environment variables to the config file and their naming convention

- *NICEMAN_LOGLEVEL*:
Used for control the verbosity of logs printed to stdout while running niceman commands/debugging
Used for control the verbosity of logs printed to stdout while running reproman commands/debugging
- *NICEMAN_TESTS_KEEPTEMP*:
Function rmtemp will not remove temporary file/directory created for testing if this flag is set
- *NICEMAN_EXC_STR_TBLIMIT*:
This flag is used by the niceman extract_tb function which extracts and formats stack-traces.
This flag is used by the reproman extract_tb function which extracts and formats stack-traces.
It caps the number of lines to NICEMAN_EXC_STR_TBLIMIT of pre-processed entries from traceback.
- *NICEMAN_TESTS_TEMPDIR*:
Create a temporary directory at location specified by this flag.
@@ -360,13 +360,13 @@ Refer niceman/config.py for information on how to add these environment variable
- *NICEMAN_CMD_PROTOCOL*:
Specifies the protocol number used by the Runner to note shell command or python function call times and allows for dry runs.
'externals-time' for ExecutionTimeExternalsProtocol, 'time' for ExecutionTimeProtocol and 'null' for NullProtocol.
Any new NICEMAN_CMD_PROTOCOL has to implement niceman.support.protocol.ProtocolInterface
Any new NICEMAN_CMD_PROTOCOL has to implement reproman.support.protocol.ProtocolInterface
- *NICEMAN_CMD_PROTOCOL_PREFIX*:
Sets a prefix to add before the command call times are noted by NICEMAN_CMD_PROTOCOL.
- *NICEMAN_PROTOCOL_REMOTE*:
Binary flag to specify whether to test protocol interactions of custom remote with annex
- *NICEMAN_LOG_TIMESTAMP*:
Used to add timestamp to niceman logs
Used to add timestamp to reproman logs
- *NICEMAN_RUN_CMDLINE_TESTS*:
Binary flag to specify if shell testing using shunit2 to be carried out
- *NICEMAN_TEMP_FS*:
@@ -1,7 +1,7 @@
# Container holding a niceman development environment.
# Container holding a reproman development environment.
#
# To build:
# docker build -t niceman:debian \
# docker build -t reproman:debian \
# -f Dockerfile-debian \
# --build-arg IMAGE=debian:jessie \
# --build-arg UNAME=$USER \
@@ -12,10 +12,10 @@
# or docker-compose build debian(be sure to update IMAGE, UID, and GID in docker-compose.yml)
#
# To run:
# docker run -it --name niceman-debian \
# -v $PWD:/home/$USER/niceman \
# docker run -it --name reproman-debian \
# -v $PWD:/home/$USER/reproman \
# -v /var/run/docker.sock:/var/run/docker.sock \
# niceman:debian
# reproman:debian
#
# or docker-compose run debian

@@ -28,19 +28,19 @@ RUN apt-get update \
&& pip install --upgrade pip

# Create a container user account that matches a system user account.
ARG UNAME=niceman
ARG UNAME=reproman
ARG UID=1000
ARG GID=1000
RUN groupadd -g $GID $UNAME \
&& useradd -m -u $UID -g $GID -s /bin/bash $UNAME

COPY . /home/$UNAME/niceman
COPY niceman.cfg /home/$UNAME
COPY . /home/$UNAME/reproman
COPY reproman.cfg /home/$UNAME

RUN chown -R $UID.$GID /home/$UNAME \
&& rm -r '/home/'$UNAME'/niceman/niceman.egg-info' \
&& find '/home/'$UNAME'/niceman' -name "*.pyc" -delete \
&& pip install -e '/home/'$UNAME'/niceman[devel]'
&& rm -r '/home/'$UNAME'/reproman/reproman.egg-info' \
&& find '/home/'$UNAME'/reproman' -name "*.pyc" -delete \
&& pip install -e '/home/'$UNAME'/reproman[devel]'

# USER $UID:$GID

@@ -1,7 +1,7 @@
# Container holding a niceman development environment.
# Container holding a reproman development environment.
#
# To build:
# docker build -t niceman:redhat \
# docker build -t reproman:redhat \
# -f Dockerfile-redhat \
# --build-arg IMAGE=centos:7 \
# --build-arg UNAME=$USER \
@@ -12,10 +12,10 @@
# or docker-compose build redhat (be sure to update IMAGE, UID, and GID in docker-compose.yml)
#
# To run:
# docker run -it --name niceman-redhat \
# -v $PWD:/home/$USER/niceman \
# docker run -it --name reproman-redhat \
# -v $PWD:/home/$USER/reproman \
# -v /var/run/docker.sock:/var/run/docker.sock \
# niceman:redhat
# reproman:redhat
#
# or docker-compose run redhat

@@ -29,26 +29,26 @@ RUN yum install -y epel-release \
&& pip install --upgrade pip setuptools chardet

# Create a container user account that matches a system user account.
ARG UNAME=niceman
ARG UNAME=reproman
ARG UID=1000
ARG GID=1000
RUN groupadd -g $GID $UNAME \
&& useradd -m -u $UID -g $GID -s /bin/bash $UNAME

COPY . /home/$UNAME/niceman
COPY niceman.cfg /home/$UNAME
COPY . /home/$UNAME/reproman
COPY reproman.cfg /home/$UNAME

RUN wget https://repo.continuum.io/miniconda/Miniconda2-latest-Linux-x86_64.sh \
&& bash Miniconda2-latest-Linux-x86_64.sh -b \
&& rm Miniconda2-latest-Linux-x86_64.sh \
&& echo 'export PATH=$HOME/miniconda2/bin:$PATH' >> ~/.bashrc \
&& source ~/.bashrc \
&& ~/miniconda2/bin/conda create -y --name niceman python=2.7 \
&& source ~/miniconda2/bin/activate niceman \
&& ~/miniconda2/bin/conda create -y --name reproman python=2.7 \
&& source ~/miniconda2/bin/activate reproman \
&& chown -R $UID.$GID /home/$UNAME \
&& rm -rf '/home/'$UNAME'/niceman/niceman.egg-info' \
&& find '/home/'$UNAME'/niceman' -name "*.pyc" -delete \
&& pip install -e '/home/'$UNAME'/niceman[devel]'
&& rm -rf '/home/'$UNAME'/reproman/reproman.egg-info' \
&& find '/home/'$UNAME'/reproman' -name "*.pyc" -delete \
&& pip install -e '/home/'$UNAME'/reproman[devel]'

# USER $UID:$GID

@@ -19,11 +19,11 @@ internals and/or contributing to the project.

## Code status:

* [![Travis tests status](https://secure.travis-ci.org/ReproNim/niceman.png?branch=master)](https://travis-ci.org/ReproNim/niceman) travis-ci.org (master branch)
* [![Travis tests status](https://secure.travis-ci.org/ReproNim/reproman.png?branch=master)](https://travis-ci.org/ReproNim/reproman) travis-ci.org (master branch)

* [![codecov.io](https://codecov.io/github/ReproNim/niceman/coverage.svg?branch=master)](https://codecov.io/github/ReproNim/niceman?branch=master)
* [![codecov.io](https://codecov.io/github/ReproNim/reproman/coverage.svg?branch=master)](https://codecov.io/github/ReproNim/reproman?branch=master)

* [![Documentation](https://readthedocs.org/projects/NICEMAN/badge/?version=latest)](http://niceman.rtfd.org)
* [![Documentation](https://readthedocs.org/projects/NICEMAN/badge/?version=latest)](http://reproman.rtfd.org)

# Installation

@@ -36,13 +36,13 @@ all necessary packages from that repository.

## Other Linux'es, OSX (Windows yet TODO) via pip

By default, installation via pip installs core functionality of niceman
By default, installation via pip installs core functionality of reproman
allowing for managing datasets etc. Additional installation schemes
are available, so you could provide enhanced installation via
`pip install niceman[SCHEME]` where `SCHEME` could be
`pip install reproman[SCHEME]` where `SCHEME` could be

- tests
to also install dependencies used by unit-tests battery of the niceman
to also install dependencies used by unit-tests battery of the reproman
- full
to install all of possible dependencies.

@@ -5,11 +5,11 @@ From:repronim/simple_workflow:latest
%runscript
echo "Welcome to the NICEMAN development environment."
echo "Reprozip pre-installed via pip. "
echo "Niceman git repo under /opt/niceman and installed for development systemwide"
echo "Niceman git repo under /opt/reproman and installed for development systemwide"
/bin/bash

%post
echo "Adding niceman pieces"
echo "Adding reproman pieces"
umask 022
# knock
curl -s http://neuro.debian.net/_files/knock-snapshots;
@@ -21,21 +21,21 @@ From:repronim/simple_workflow:latest
echo 'en_US.UTF-8 UTF-8' > /etc/locale.gen
locale-gen

# additional depends for niceman
# additional depends for reproman
eatmydata apt-get install -y libffi-dev libssl-dev python-apt

# Generate our shareable env
rm -rf /opt/niceman; mkdir -p /opt/niceman
rm -rf /opt/reproman; mkdir -p /opt/reproman
# not available within singularity's shell so will do system wide
# virtualenv --system-site-packages /opt/niceman/venv
# source /opt/niceman/venv/bin/activate
git clone git://github.com/repronim/niceman /opt/niceman
# virtualenv --system-site-packages /opt/reproman/venv
# source /opt/reproman/venv/bin/activate
git clone git://github.com/repronim/reproman /opt/reproman
pip install reprozip
# we need updated cryptography (I guess paramiko lacks versioned depends)
pip install --upgrade cryptography
pip install -e /opt/niceman
pip install -e /opt/reproman

# So outside 'staff' ppl could modify inside as well
chown nobody.staff -R /opt/niceman
chmod g+rwX -R /opt/niceman /usr/local
chmod o+rwX -R /opt/niceman /usr/local
chown nobody.staff -R /opt/reproman
chmod g+rwX -R /opt/reproman /usr/local
chmod o+rwX -R /opt/reproman /usr/local
@@ -9,10 +9,10 @@ services:
- UNAME=$USER
# - UID=1000
# - GID=1000
image: niceman:redhat
container_name: niceman-redhat
image: reproman:redhat
container_name: reproman-redhat
volumes:
- $PWD:/home/$USER/niceman
- $PWD:/home/$USER/reproman
- /var/run/docker.sock:/var/run/docker.sock
debian:
build:
@@ -23,8 +23,8 @@ services:
- UNAME=$USER
# - UID=1000
# - GID=1000
image: niceman:debian
container_name: niceman-debian
image: reproman:debian
container_name: reproman-debian
volumes:
- $PWD:/home/$USER/niceman
- $PWD:/home/$USER/reproman
- /var/run/docker.sock:/var/run/docker.sock
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