# -*- mode: org -*-
#+TITLE:     Tracking environment information
#+AUTHOR:    Arnaud Legrand
#+DATE: June, 2018
#+STARTUP: overview indent
#+OPTIONS: num:nil toc:t
#+PROPERTY: header-args :eval never-export

* Getting information about your Git repository
When taking notes, it may be difficult to remember which version of
the code or of a file was used. This is what version control is useful
for. Here are a few useful commands that we typically insert at the
top of our notebooks in shell cells

#+begin_src shell :results output :exports both
git log -1
#+end_src

#+RESULTS:
: commit 741b0088af5b40588493c23c46d6bab5d0adeb33
: Author: Arnaud Legrand <arnaud.legrand@imag.fr>
: Date:   Tue Sep 4 12:45:43 2018 +0200
: 
:     Fix a few typos and provide information on jupyter-git plugins.

#+begin_src shell :results output :exports both
git status -u
#+end_src

#+RESULTS:
#+begin_example
On branch master
Your branch is ahead of 'origin/master' by 4 commits.
  (use "git push" to publish your local commits)

Changes not staged for commit:
  (use "git add <file>..." to update what will be committed)
  (use "git checkout -- <file>..." to discard changes in working directory)

	modified:   resources.org

Untracked files:
  (use "git add <file>..." to include in what will be committed)

	../../module2/ressources/replicable_article/IEEEtran.bst
	../../module2/ressources/replicable_article/IEEEtran.cls
	../../module2/ressources/replicable_article/article.bbl
	../../module2/ressources/replicable_article/article.tex
	../../module2/ressources/replicable_article/data.csv
	../../module2/ressources/replicable_article/figure.pdf
	../../module2/ressources/replicable_article/logo.png
	.#resources.org

no changes added to commit (use "git add" and/or "git commit -a")
#+end_example

/Note: the -u indicates that git should also display the contents of
new directories it did not previously know about./

Then, we often include commands at the end of our notebook indicating
how to commit the results (adding the new files, committing with a
clear message and pushing). E.g.,

#+begin_src shell :results output :exports both
git add resources.org;
git commit -m "Completing the section on getting Git information"
git push
#+end_src

#+RESULTS:
#+BEGIN_EXAMPLE
[master 514fe2c1 ] Completing the section on getting Git information
 1 file changed, 61 insertions(+)
Counting objects: 25, done.
Delta compression using up to 4 threads.
Compressing objects: 100% (20/20), done.
Writing objects: 100% (25/25), 7.31 KiB | 499.00 KiB/s, done.
Total 25 (delta 11), reused 0 (delta 0)
To ssh://app-learninglab.inria.fr:9418/learning-lab/mooc-rr-ressources.git
   6359f8c..1f8a567  master -> master
#+END_EXAMPLE

Obviously, in this case you need to save the notebook before running
this cell, hence the output of this final command (with the new git
hash) will not be stored in the cell. This is not really a problem and
is the price to pay for running git from within the notebook itself.
* Getting information about Python(3) libraries 
** Getting information about your system
This topic is discussed on [[https://stackoverflow.com/questions/3103178/how-to-get-the-system-info-with-python][StackOverflow]]. 
#+begin_src python :results output :exports both
import platform
print(platform.uname())
#+end_src

#+RESULTS:
: uname_result(system='Linux', node='icarus', release='4.15.0-2-amd64', version='#1 SMP Debian 4.15.11-1 (2018-03-20)', machine='x86_64', processor='')

** Getting the list of installed packages and their version
This topic is discussed on [[https://stackoverflow.com/questions/20180543/how-to-check-version-of-python-modules][StackOverflow]]. When using =pip= (the Python
package installer) within a shell command, it is easy to query the
version of all installed packages (note that on your system, you may
have to use either =pip= or =pip3= depending on how it is named and which
versions of Python are available on your machine

Here is for example how I get this information on my machine:
#+begin_src shell :results output :exports both
pip3 freeze
#+end_src

#+RESULTS:
#+begin_example
asn1crypto==0.24.0
attrs==17.4.0
bcrypt==3.1.4
beautifulsoup4==4.6.0
bleach==2.1.3
...
pandas==0.22.0
pandocfilters==1.4.2
paramiko==2.4.0
patsy==0.5.0
pexpect==4.2.1
...
traitlets==4.3.2
tzlocal==1.5.1
urllib3==1.22
wcwidth==0.1.7
webencodings==0.5
#+end_example

In a Jupyter notebook, this can easily be done by using the =%%sh=
magic. Here is for example what you could do and get on the Jupyter
notebooks we deployed for the MOOC (note that here, you should simply
use the =pip= command):
#+begin_src python :results output :exports both
%%sh
pip freeze
#+end_src

#+results:
#+begin_example
alembic==0.9.9
asn1crypto==0.24.0
attrs==18.1.0
Automat==0.0.0
...
numpy==1.13.3
olefile==0.45.1
packaging==17.1
pamela==0.3.0
pandas==0.22.0
...
webencodings==0.5
widgetsnbextension==3.2.1
xlrd==1.1.0
zope.interface==4.5.0
#+end_example

In the rest of this document, I will assume the correct command is =pip=
and I will not systematically insert the =%%sh= magic.

Once you know which packages are installed, you can easily get
additional information about a given package and in particular check
whether it was installed "locally" through pip or whether it is
installed system-wide. Again, in a shell command:
#+begin_src shell :results output :exports both
pip show pandas
echo "            "
pip show statsmodels
#+end_src

#+RESULTS:
#+begin_example
Name: pandas
Version: 0.22.0
Summary: Powerful data structures for data analysis, time series,and statistics
Home-page: http://pandas.pydata.org
Author: None
Author-email: None
License: BSD
Location: /usr/lib/python3/dist-packages
Requires: 
            
Name: statsmodels
Version: 0.9.0
Summary: Statistical computations and models for Python
Home-page: http://www.statsmodels.org/
Author: None
Author-email: None
License: BSD License
Location: /home/alegrand/.local/lib/python3.6/site-packages
Requires: patsy, pandas
#+end_example
** How to list imported modules?
Without resorting to pip (that will list all available packages), you
may want to know which modules are loaded in a Python session as well
as their version. Inspired by [[https://stackoverflow.com/questions/4858100/how-to-list-imported-modules][StackOverflow]], here is a simple
function that lists loaded package (that have a =__version__= attribute,
which is unfortunately not completely standard).

#+begin_src python :results output :exports both
def print_imported_modules():
    import sys
    for name, val in sorted(sys.modules.items()):
        if(hasattr(val, '__version__')): 
            print(val.__name__, val.__version__)
        else:
            print(val.__name__, "(unknown version)")

print("**** Package list in the beginning ****");
print_imported_modules()
print("**** Package list after loading pandas ****");
import pandas
print_imported_modules()
#+end_src

#+RESULTS:
#+begin_example
,**** Package list in the beginning ****
,**** Package list after loading pandas ****
_csv 1.0
_ctypes 1.1.0
decimal 1.70
argparse 1.1
csv 1.0
ctypes 1.1.0
cycler 0.10.0
dateutil 2.7.3
decimal 1.70
distutils 3.6.5rc1
ipaddress 1.0
json 2.0.9
logging 0.5.1.2
matplotlib 2.1.1
numpy 1.14.5
numpy.core 1.14.5
numpy.core.multiarray 3.1
numpy.core.umath b'0.4.0'
numpy.lib 1.14.5
numpy.linalg._umath_linalg b'0.1.5'
pandas 0.22.0
_libjson 1.33
platform 1.0.8
pyparsing 2.2.0
pytz 2018.5
re 2.2.1
six 1.11.0
urllib.request 3.6
zlib 1.0
#+end_example

** Saving and restoring an environment with pip
The easiest way to go is as follows:
#+begin_src shell :results output :exports both
pip3 freeze > requirements.txt # to obtain the list of packages with their version
pip3 install -r requirements.txt # to install the previous list of packages, possibly on an other machine
#+end_src

If you want to have several installed Python environments, you may
want to use [[https://docs.pipenv.org/][Pipenv]]. I doubt it allows to track correctly FORTRAN or C
dynamic libraries that are wrapped by Python though.
** Installing a new package or a specific version
The Jupyter environment we deployed on our servers for the MOOC is
based on the version 4.5.4 of Miniconda and Python 3.6. In this
environment you should simply use the =pip= command (remember on your
machine, you may have to use =pip3=).

If I query the current version of =statsmodels= in a shell command,
here is what I will get.
#+begin_src shell :results output :exports both
pip show statsmodels
#+end_src

#+RESULTS:
#+BEGIN_EXAMPLE
Name: statsmodels
Version: 0.8.0
Summary: Statistical computations and models for Python
Home-page: http://www.statsmodels.org/
Author: Skipper Seabold, Josef Perktold
Author-email: pystatsmodels@googlegroups.com
License: BSD License
Location: /opt/conda/lib/python3.6/site-packages
Requires: scipy, patsy, pandas
#+END_EXAMPLE

I can then easily upgrade =statsmodels=:
#+begin_src shell :results output :exports both
pip install --upgrade statsmodels 
#+end_src

Then the new version should then be:
#+begin_src shell :results output :exports both
pip show statsmodels
#+end_src

#+RESULTS:
#+BEGIN_EXAMPLE
Name: statsmodels
Version: 0.9.0
Summary: Statistical computations and models for Python
Home-page: http://www.statsmodels.org/
Author: Skipper Seabold, Josef Perktold
Author-email: pystatsmodels@googlegroups.com
License: BSD License
Location: /opt/conda/lib/python3.6/site-packages
Requires: scipy, patsy, pandas
#+END_EXAMPLE

It is even possible to install a specific (possibly much older) version, e.g.,:
#+begin_src shell :results output :exports both
pip install statsmodels==0.6.1
#+end_src
* Getting information about R libraries
** Getting the list imported modules and their version
The best way seems to be to rely on the =devtools= package (if this
package is not installed, you should install it first by running in =R=
the command =install.packages("devtools")=).

#+begin_src R :results output :session *R* :exports both
sessionInfo()
devtools::session_info()
#+end_src

#+RESULTS:
#+begin_example
R version 3.5.1 (2018-07-02)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Debian GNU/Linux buster/sid

Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.8.0
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.8.0

locale:
 [1] LC_CTYPE=fr_FR.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=fr_FR.UTF-8        LC_COLLATE=fr_FR.UTF-8    
 [5] LC_MONETARY=fr_FR.UTF-8    LC_MESSAGES=fr_FR.UTF-8   
 [7] LC_PAPER=fr_FR.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=fr_FR.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

loaded via a namespace (and not attached):
[1] compiler_3.5.1
Session info ------------------------------------------------------------------
 setting  value                       
 version  R version 3.5.1 (2018-07-02)
 system   x86_64, linux-gnu           
 ui       X11                         
 language (EN)                        
 collate  fr_FR.UTF-8                 
 tz       Europe/Paris                
 date     2018-08-01                  

Packages ----------------------------------------------------------------------
 package   * version date       source        
 base      * 3.5.1   2018-07-02 local         
 compiler    3.5.1   2018-07-02 local         
 datasets  * 3.5.1   2018-07-02 local         
 devtools    1.13.6  2018-06-27 CRAN (R 3.5.1)
 digest      0.6.15  2018-01-28 CRAN (R 3.5.0)
 graphics  * 3.5.1   2018-07-02 local         
 grDevices * 3.5.1   2018-07-02 local         
 memoise     1.1.0   2017-04-21 CRAN (R 3.5.1)
 methods   * 3.5.1   2018-07-02 local         
 stats     * 3.5.1   2018-07-02 local         
 utils     * 3.5.1   2018-07-02 local         
 withr       2.1.2   2018-03-15 CRAN (R 3.5.0)
#+end_example

Some actually advocate that [[https://github.com/ropensci/rrrpkg][writing a reproducible research compendium
is best done by writing an R package]]. Those of you willing to have a
clean R dependency management should thus have a look at [[https://rstudio.github.io/packrat/][Packrat]].
** Getting the list of installed packages and their version
Finally, it is good to know that there is a built-in R command
(=installed.packages=) allowing to retrieve and list the details of all
packages installed.
#+begin_src R :results table :session *R* :exports both :colnames yes
head(installed.packages())
#+end_src

#+RESULTS:
| Package                                                     | LibPath                                         |                                                 Version | Priority    | Depends                                                  | Imports                                                        | LinkingTo | Suggests      | Enhances                              | License                   | License_is_FOSS | License_restricts_use | OS_type | MD5sum | NeedsCompilation | Built |       |
|-------------------------------------------------------------+-------------------------------------------------+---------------------------------------------------------+-------------+----------------------------------------------------------+----------------------------------------------------------------+-----------+---------------+---------------------------------------+---------------------------+---------------+---------------------+--------+--------+------------------+-------+-------|
| BH                                                          | /home/alegrand/R/x86_64-pc-linux-gnu-library/3.5 |                                                1.66.0-1 | nil         | nil                                                      | nil                                                            | nil       | nil           | nil                                   | BSL-1.0                   | nil           | nil                 | nil    | nil    | no               | 3.5.1 |       |
| Formula                                                     | /home/alegrand/R/x86_64-pc-linux-gnu-library/3.5 |                                                   1.2-3 | nil         | R (>= 2.0.0), stats                                      | nil                                                            | nil       | nil           | nil                                   | GPL-2                     | GPL-3         | nil                 | nil    | nil    | nil              |    no | 3.5.1 |
| Hmisc                                                       | /home/alegrand/R/x86_64-pc-linux-gnu-library/3.5 |                                                   4.1-1 | nil         | lattice, survival (>= 2.40-1), Formula, ggplot2 (>= 2.2) | methods, latticeExtra, cluster, rpart, nnet, acepack, foreign, |           |               |                                       |                           |               |                     |        |        |                  |       |       |
| gtable, grid, gridExtra, data.table, htmlTable (>= 1.11.0), |                                                 |                                                         |             |                                                          |                                                                |           |               |                                       |                           |               |                     |        |        |                  |       |       |
| viridis, htmltools, base64enc                               | nil                                             | chron, rms, mice, tables, knitr, ff, ffbase, plotly (>= |             |                                                          |                                                                |           |               |                                       |                           |               |                     |        |        |                  |       |       |
| 4.5.6)                                                      | nil                                             |                                              GPL (>= 2) | nil         | nil                                                      | nil                                                            | nil       | yes           | 3.5.1                                 |                           |               |                     |        |        |                  |       |       |
| Matrix                                                      | /home/alegrand/R/x86_64-pc-linux-gnu-library/3.5 |                                                  1.2-14 | recommended | R (>= 3.2.0)                                             | methods, graphics, grid, stats, utils, lattice                 | nil       | expm, MASS    | MatrixModels, graph, SparseM, sfsmisc | GPL (>= 2)                | file LICENCE  | nil                 | nil    | nil    | nil              |   yes | 3.5.1 |
| StanHeaders                                                 | /home/alegrand/R/x86_64-pc-linux-gnu-library/3.5 |                                                  2.17.2 | nil         | nil                                                      | nil                                                            | nil       | RcppEigen, BH | nil                                   | BSD_3_clause + file LICENSE | nil           | nil                 | nil    | nil    | yes              | 3.5.1 |       |
| acepack                                                     | /home/alegrand/R/x86_64-pc-linux-gnu-library/3.5 |                                                   1.4.1 | nil         | nil                                                      | nil                                                            | nil       | testthat      | nil                                   | MIT + file LICENSE        | nil           | nil                 | nil    | nil    | yes              | 3.5.1 |       |

** Installing a new package or a specific version
This section is mostly a cut and paste from the [[https://support.rstudio.com/hc/en-us/articles/219949047-Installing-older-versions-of-packages][recent post by Ian
Pylvainen]] on this topic. It comprises a very clear explanation of how
to proceed.

*** Installing a pre-compiled version
If you're on a Debian or a Ubuntu system, it may be difficult to
access a specific version without breaking your system. So unless you
are moving to the latest version available in your Linux distribution,
*we strongly recommend you to build from source*. In this case, you'll
need to make sure you have the necessary toolchain to build packages
from source (e.g., gcc, FORTRAN, etc.). On Windows, this may require
you to install [[https://cran.r-project.org/bin/windows/Rtools/][Rtools]].

If you're on Windows or OS X and looking for a package for an *older
version of R* (R 2.1 or below), you can check the [[https://cran-archive.r-project.org/bin/][CRAN binary
archive]]. Once you have the URL, you can install it using a command
similar to the example below:
#+begin_src R :results output :session *R* :exports both
packageurl <- "https://cran-archive.r-project.org/bin/windows/contrib/2.13/BBmisc_1.0-58.zip"
install.packages(packageurl, repos=NULL, type="binary")
#+end_src
*** Using devtools
The simplest method to install the version you need is to use the
=install_version()= function of the =devtools= package (obviously, you
need to install =devtools= first, which can be done by running in =R= the
command =install.packages("devtools")=). For instance:

#+begin_src R :results output :session *R* :exports both
require(devtools)
install_version("ggplot2", version = "0.9.1", repos = "http://cran.us.r-project.org")
#+end_src
*** Installing from source code
Alternatively, you may want to install an older package from source If
devtools fails or if you do not want to depend on it, you can install
it from source via =install.packages()= directed using the right
URL. This URL can be obtained by browsing the [[https://cran.r-project.org/src/contrib/Archive][CRAN Package Archive]].

Once you have the URL, you can install it using a command similar to
the example below:
#+begin_src R :results output :session *R* :exports both
packageurl <- "http://cran.r-project.org/src/contrib/Archive/ggplot2/ggplot2_0.9.1.tar.gz"
install.packages(packageurl, repos=NULL, type="source")
#+end_src

If you know the URL, you can also install from source via the command
line outside of R. For instance (in bash):
#+begin_src shell :results output :exports both
wget http://cran.r-project.org/src/contrib/Archive/ggplot2/ggplot2_0.9.1.tar.gz
R CMD INSTALL ggplot2_0.9.1.tar.gz
#+end_src
*** Potential issues
There are a few potential issues that may arise with installing older
versions of packages: 
- You may be losing functionality or bug fixes that are only present
  in the newer versions of the packages.
- The older package version needed may not be compatible with the
  version of R you have installed. In this case, you will either need
  to downgrade R to a compatible version or update your R code to work
  with a newer version of the package.
