As we explained, the programming language used in an analysis has a clear influence on the reproducibility of your analysis. It is not a @@ -95,9 +96,9 @@ version and environment control will always help.
As we mentioned in the video sequences, there are several solutions to control your environment: @@ -133,9 +134,9 @@ Hinsen on Active Papers (http://www.a
Ensuring software is properly archived, i.e, is safely stored so that it can be accessed in a perennial way, can be quite tricky. If you @@ -149,9 +150,9 @@ whenever the data is not sensitive.
In the video sequences, we mentioned workflow managers (original application domain in parenthesis):
@@ -172,9 +173,9 @@ Bio-informatics: Current Status, Solutions and Research OpportunitiesWe have mentioned these topics in our MOOC but we could by no way cover them properly. We only suggest here a few interesting talks @@ -190,9 +191,9 @@ reproducibility and present recent research work on this topic.
You may want to have a look at the following two webinars:
@@ -210,9 +211,9 @@ p-hacking, etc.Experimentation was not covered in this MOOC, although it is an essential part of science. The main reason is that practices and @@ -230,13 +231,13 @@ Science.
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 @@ -327,13 +328,32 @@ is the price to pay for running git from within the notebook itself.
+This topic is discussed on StackOverflow. +
+import platform +print(platform.uname()) ++
+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='') + ++
This topic is discussed on StackOverflow. When using pip (the Python
package installer) within a shell command, it is easy to query the
@@ -441,9 +461,9 @@ Requires: patsy, pandas
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 @@ -458,7 +478,7 @@ which is unfortunately not completely standard). for name, val in sorted(sys.modules.items()): if(hasattr(val, '__version__')): print(val.__name__, val.__version__) - else + else: print(val.__name__, "(unknown version)") print("**** Package list in the beginning ****"); @@ -466,7 +486,6 @@ print_imported_modules() print("**** Package list after loading pandas ****"); import pandas print_imported_modules() -
The easiest way to go is as follows:
@@ -525,9 +544,9 @@ dynamic libraries that are wrapped by Python though.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 @@ -594,13 +613,13 @@ It is even possible to install a specific (possibly much older) version, e.g.,:
The best way seems to be to rely on the
Finally, it is good to know that there is a built-in R command
(
This section is mostly a cut and paste from the recent post by Ian
Pylvainen on this topic. It comprises a very clear explanation of how
@@ -936,8 +955,8 @@ to proceed.
devtools package (if this
package is not installed, you should install it first by running in R
@@ -668,9 +687,9 @@ clean R dependency management should thus have a look at
-Getting the list of installed packages and their version
-Getting the list of installed packages and their version
+installed.packages) allowing to retrieve and list the details of all
@@ -925,9 +944,9 @@ packages installed.
Installing a new package or a specific version
-Installing a new package or a specific version
+