From ed7ab9da8f6af85eaafa0caa0dcca69a18fa7dd5 Mon Sep 17 00:00:00 2001 From: Arnaud Legrand Date: Tue, 4 Sep 2018 07:35:33 +0200 Subject: [PATCH] Automatically generated HTML --- module4/ressources/resources.html | 238 ++++++++++++++++++++++++++++++ 1 file changed, 238 insertions(+) create mode 100644 module4/ressources/resources.html diff --git a/module4/ressources/resources.html b/module4/ressources/resources.html new file mode 100644 index 0000000..9d397a6 --- /dev/null +++ b/module4/ressources/resources.html @@ -0,0 +1,238 @@ +
+ + +
+

Getting information about Python(3) libraries

+
+
+
+

Getting the list of installed packages and their version

+
+

+https://stackoverflow.com/questions/20180543/how-to-check-version-of-python-modules +

+
+
pip3 freeze
+
+
+ +
+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
+
+ +
+
pip3 show pandas
+echo "            "
+pip3 show statsmodels
+
+
+ +
+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
+
+ +
+
+
+
+
+
+ +
+

How to list imported modules?

+
+

+Inspiring from StackOverflow, here is a simple function that lists +loaded package (that have a __version__ attribute, which is +unfortunately not completely standard). +

+ +
+
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()
+
+
+
+ +
+**** 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
+
+
+
+ +
+

Setting up an environment with pip

+
+

+The easiest way to go is as follows: +

+
+
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
+
+
+ +

+If you want to have several installed python environments, you may +want to use Pipenv. I doubt it allows to track correctly FORTRAN or C +dynamic libraries that are wrapped by Python. +

+
+
+
+
+

Getting information about R libraries

+
+

+The best way seems to be to rely on the devtools package. +

+ +
+
sessionInfo()
+devtools::session_info()
+
+
+ +
+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)
+
+ +

+Some actually advocate that 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 Packrat. +

+
+
+
-- 2.18.1