# -*- mode: org -*- #+TITLE: #+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 : 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 ..." to update what will be committed) (use "git checkout -- ..." to discard changes in working directory) modified: resources.org Untracked files: (use "git add ..." 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, I often include commands at the end of my 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 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. #+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 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 pip3 show pandas echo " " pip3 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. Inspiring from [[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__) 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 ** Setting up 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. * Getting information about R libraries The best way seems to be to rely on the =devtools= package. #+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 can be 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]]. 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 | |