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<h2>Table of Contents</h2>
<div id="text-table-of-contents">
<ul style="margin:0 0;">
<li style="margin-bottom:0;"><a href="#org0832474">Getting information about your Git repository</a></li>
<li style="margin-bottom:0;"><a href="#org79df74e">Getting information about Python(3) libraries</a>
<li style="margin-bottom:0;"><a href="#org196e3c8">Getting information about your Git repository</a></li>
<li style="margin-bottom:0;"><a href="#org00455c0">Getting information about Python(3) libraries</a>
<ul style="margin:0 0;">
<li style="margin-bottom:0;"><a href="#org6ac23e8">Getting the list of installed packages and their version</a></li>
<li style="margin-bottom:0;"><a href="#org86b6e7e">How to list imported modules?</a></li>
<li style="margin-bottom:0;"><a href="#orgf4c774a">Setting up an environment with pip</a></li>
<li style="margin-bottom:0;"><a href="#org69f771a">Getting the list of installed packages and their version</a></li>
<li style="margin-bottom:0;"><a href="#org77338a9">How to list imported modules?</a></li>
<li style="margin-bottom:0;"><a href="#org444b8c3">Setting up an environment with pip</a></li>
<li style="margin-bottom:0;"><a href="#org8e29bc4">Installing a new package or a specific version</a></li>
</ul>
</li>
<li style="margin-bottom:0;"><a href="#orga609f56">Getting information about R libraries</a>
<ul style="margin:0 0;">
<li style="margin-bottom:0;"><a href="#org3bee8ef">Getting the list imported modules and their version</a></li>
<li style="margin-bottom:0;"><a href="#org0168695">Getting the list of installed packages and their version</a></li>
<li style="margin-bottom:0;"><a href="#org4d32e3b">Installing a new package or a specific version</a>
<ul style="margin:0 0;">
<li style="margin-bottom:0;"><a href="#org2d34770">Installing a pre-compiled version</a></li>
<li style="margin-bottom:0;"><a href="#org2bbc85f">Using devtools</a></li>
<li style="margin-bottom:0;"><a href="#org524938d">Alternatively, you may want to install an older package from source</a></li>
<li style="margin-bottom:0;"><a href="#orgc001d42">Potential issues</a></li>
</ul>
</li>
</ul>
</li>
<li style="margin-bottom:0;"><a href="#org25032d4">Getting information about R libraries</a></li>
</ul>
</div>
</div>
<div id="outline-container-org0832474" class="outline-2">
<h2 id="org0832474">Getting information about your Git repository</h2>
<div class="outline-text-2" id="text-org0832474">
<div id="outline-container-org196e3c8" class="outline-2">
<h2 id="org196e3c8">Getting information about your Git repository</h2>
<div class="outline-text-2" id="text-org196e3c8">
<p>
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
......@@ -109,19 +123,23 @@ is the price to pay for running git from within the notebook itself.
</p>
</div>
</div>
<div id="outline-container-org79df74e" class="outline-2">
<h2 id="org79df74e">Getting information about Python(3) libraries</h2>
<div class="outline-text-2" id="text-org79df74e">
<div id="outline-container-org00455c0" class="outline-2">
<h2 id="org00455c0">Getting information about Python(3) libraries</h2>
<div class="outline-text-2" id="text-org00455c0">
</div>
<div id="outline-container-org6ac23e8" class="outline-3">
<h3 id="org6ac23e8">Getting the list of installed packages and their version</h3>
<div class="outline-text-3" id="text-org6ac23e8">
<div id="outline-container-org69f771a" class="outline-3">
<h3 id="org69f771a">Getting the list of installed packages and their version</h3>
<div class="outline-text-3" id="text-org69f771a">
<p>
This topic is discussed on <a href="https://stackoverflow.com/questions/20180543/how-to-check-version-of-python-modules">StackOverflow</a>. When using <code>pip</code> (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 <code>pip</code> or <code>pip3</code> depending on how it is named and which
versions of Python are available on your machine.
versions of Python are available on your machine
</p>
<p>
Here for example how I get these information on my machine:
</p>
<div class="org-src-container">
<pre style="padding-left: 30px; background-color: #f6f8fa;" class="src src-shell">pip3 freeze
......@@ -148,6 +166,41 @@ wcwidth==0.1.7
webencodings==0.5
</pre>
<p>
In a Jupyter notebook, this can easily be done by using the <code>%%sh</code>
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 <code>pip</code> command):
</p>
<div class="org-src-container">
<pre style="padding-left: 30px; background-color: #f6f8fa;" class="src src-python">%%sh
pip freeze
</pre>
</div>
<pre style="padding-left: 30px; background-color: #f6f8fa;" class="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
</pre>
<p>
In the rest of this document, I will assume the correct command is <code>pip</code>
and I will not systematically insert the <code>%%sh</code> magic.
</p>
<p>
Once you know which packages are installed, you can easily get
additional information about a given package and in particular check
......@@ -155,9 +208,9 @@ whether it was installed "locally" through pip or whether it is
installed system-wide. Again, in a shell command:
</p>
<div class="org-src-container">
<pre style="padding-left: 30px; background-color: #f6f8fa;" class="src src-shell">pip3 show pandas
<pre style="padding-left: 30px; background-color: #f6f8fa;" class="src src-shell">pip show pandas
<span style="font-weight: bold;">echo</span> <span style="font-style: italic;">" "</span>
pip3 show statsmodels
pip show statsmodels
</pre>
</div>
......@@ -184,10 +237,9 @@ Requires: patsy, pandas
</pre>
</div>
</div>
<div id="outline-container-org86b6e7e" class="outline-3">
<h3 id="org86b6e7e">How to list imported modules?</h3>
<div class="outline-text-3" id="text-org86b6e7e">
<div id="outline-container-org77338a9" class="outline-3">
<h3 id="org77338a9">How to list imported modules?</h3>
<div class="outline-text-3" id="text-org77338a9">
<p>
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
......@@ -248,9 +300,9 @@ zlib 1.0
</div>
</div>
<div id="outline-container-orgf4c774a" class="outline-3">
<h3 id="orgf4c774a">Setting up an environment with pip</h3>
<div class="outline-text-3" id="text-orgf4c774a">
<div id="outline-container-org444b8c3" class="outline-3">
<h3 id="org444b8c3">Setting up an environment with pip</h3>
<div class="outline-text-3" id="text-org444b8c3">
<p>
The easiest way to go is as follows:
</p>
......@@ -267,12 +319,86 @@ dynamic libraries that are wrapped by Python though.
</p>
</div>
</div>
<div id="outline-container-org8e29bc4" class="outline-3">
<h3 id="org8e29bc4">Installing a new package or a specific version</h3>
<div class="outline-text-3" id="text-org8e29bc4">
<p>
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 <code>pip</code> command (remember on your
machine, you may have to use <code>pip3</code>).
</p>
<p>
If I query the current version of <code>statsmodels</code> in a shell command,
here is what I will get.
</p>
<div class="org-src-container">
<pre style="padding-left: 30px; background-color: #f6f8fa;" class="src src-shell">pip show statsmodels
</pre>
</div>
<pre style="padding-left: 30px; background-color: #f6f8fa;" class="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
</pre>
<p>
I can then easily upgrade <code>statsmodels</code>:
</p>
<div class="org-src-container">
<pre style="padding-left: 30px; background-color: #f6f8fa;" class="src src-shell">pip install --upgrade statsmodels
</pre>
</div>
<p>
Then the new version should then be:
</p>
<div class="org-src-container">
<pre style="padding-left: 30px; background-color: #f6f8fa;" class="src src-shell">pip show statsmodels
</pre>
</div>
<pre style="padding-left: 30px; background-color: #f6f8fa;" class="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
</pre>
<p>
It is even possible to install a specific (possibly much older) version, e.g.,:
</p>
<div class="org-src-container">
<pre style="padding-left: 30px; background-color: #f6f8fa;" class="src src-shell">pip install <span style="font-weight: bold; font-style: italic;">statsmodels</span>==0.6.1
</pre>
</div>
</div>
</div>
</div>
<div id="outline-container-org25032d4" class="outline-2">
<h2 id="org25032d4">Getting information about R libraries</h2>
<div class="outline-text-2" id="text-org25032d4">
<div id="outline-container-orga609f56" class="outline-2">
<h2 id="orga609f56">Getting information about R libraries</h2>
<div class="outline-text-2" id="text-orga609f56">
</div>
<div id="outline-container-org3bee8ef" class="outline-3">
<h3 id="org3bee8ef">Getting the list imported modules and their version</h3>
<div class="outline-text-3" id="text-org3bee8ef">
<p>
The best way seems to be to rely on the <code>devtools</code> package.
The best way seems to be to rely on the <code>devtools</code> package (if this
package is not installed, you should install it first by running in <code>R</code>
the command <code>install.packages("devtools")</code>).
</p>
<div class="org-src-container">
......@@ -334,7 +460,11 @@ Some actually advocate that <a href="https://github.com/ropensci/rrrpkg">writing
can be done by writing an R package</a>. Those of you willing to have a
clean R dependency management should thus have a look at <a href="https://rstudio.github.io/packrat/">Packrat</a>.
</p>
</div>
</div>
<div id="outline-container-org0168695" class="outline-3">
<h3 id="org0168695">Getting the list of installed packages and their version</h3>
<div class="outline-text-3" id="text-org0168695">
<p>
Finally, it is good to know that there is a built-in R command
(<code>installed.packages</code>) allowing to retrieve and list the details of all
......@@ -588,4 +718,107 @@ packages installed.
</table>
</div>
</div>
<div id="outline-container-org4d32e3b" class="outline-3">
<h3 id="org4d32e3b">Installing a new package or a specific version</h3>
<div class="outline-text-3" id="text-org4d32e3b">
<p>
This section is mostly a cut and paste from the <a href="https://support.rstudio.com/hc/en-us/articles/219949047-Installing-older-versions-of-packages">recent post by Ian
Pylvainen</a> on this topic. It comprises a very clear explanation on how
to proceed.
</p>
</div>
<div id="outline-container-org2d34770" class="outline-4">
<h4 id="org2d34770">Installing a pre-compiled version</h4>
<div class="outline-text-4" id="text-org2d34770">
<p>
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,
<b>we strongly recommend you to build from source</b>. 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 <a href="https://cran.r-project.org/bin/windows/Rtools/">Rtools</a>.
</p>
<p>
If you're on Windows or OS X and looking for a package for an <b>older
version of R</b> (R 2.1 or below), you can check the <a href="https://cran-archive.r-project.org/bin/">CRAN binary
archive</a>. Once you have the URL, you can install it using a command
similar to the example below:
</p>
<div class="org-src-container">
<pre style="padding-left: 30px; background-color: #f6f8fa;" class="src src-R">packageurl <span style="font-weight: bold; text-decoration: underline;">&lt;-</span> <span style="font-style: italic;">"https://cran-archive.r-project.org/bin/windows/contrib/2.13/BBmisc_1.0-58.zip"</span>
install.packages(packageurl, repos=<span style="font-weight: bold; text-decoration: underline;">NULL</span>, type=<span style="font-style: italic;">"binary"</span>)
</pre>
</div>
</div>
</div>
<div id="outline-container-org2bbc85f" class="outline-4">
<h4 id="org2bbc85f">Using devtools</h4>
<div class="outline-text-4" id="text-org2bbc85f">
<p>
The simplest method to install the version you need is to use the
<code>install_version()</code> function of the <code>devtools</code> package (obviously, you
need to install <code>devtools</code> first, which can be done by running in <code>R</code> the
command <code>install.packages("devtools")</code>). For instance:
</p>
<div class="org-src-container">
<pre style="padding-left: 30px; background-color: #f6f8fa;" class="src src-R"><span style="font-weight: bold; text-decoration: underline;">require</span>(devtools)
install_version(<span style="font-style: italic;">"ggplot2"</span>, version = <span style="font-style: italic;">"0.9.1"</span>, repos = <span style="font-style: italic;">"http://cran.us.r-project.org"</span>)
</pre>
</div>
</div>
</div>
<div id="outline-container-org524938d" class="outline-4">
<h4 id="org524938d">Alternatively, you may want to install an older package from source</h4>
<div class="outline-text-4" id="text-org524938d">
<p>
If you devtools fails or if you do not want to depend on it, you can
install it from source via <code>install.packages()</code> directed to the right
URL. This URL can be obtained by browsing the <a href="https://cran.r-project.org/src/contrib/Archive">CRAN Package Archive</a>.
</p>
<p>
Once you have the URL, you can install it using a command similar to
the example below:
</p>
<div class="org-src-container">
<pre style="padding-left: 30px; background-color: #f6f8fa;" class="src src-R">packageurl <span style="font-weight: bold; text-decoration: underline;">&lt;-</span> <span style="font-style: italic;">"http://cran.r-project.org/src/contrib/Archive/ggplot2/ggplot2_0.9.1.tar.gz"</span>
install.packages(packageurl, repos=<span style="font-weight: bold; text-decoration: underline;">NULL</span>, type=<span style="font-style: italic;">"source"</span>)
</pre>
</div>
<p>
If you know the URL, you can also install from source via the command
line outside of R. For instance (in bash):
</p>
<div class="org-src-container">
<pre style="padding-left: 30px; background-color: #f6f8fa;" class="src src-shell">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
</pre>
</div>
</div>
</div>
<div id="outline-container-orgc001d42" class="outline-4">
<h4 id="orgc001d42">Potential issues</h4>
<div class="outline-text-4" id="text-orgc001d42">
<p>
There are a few potential issues that may arise with installing older
versions of packages:
</p>
<ul class="org-ul">
<li style="margin-bottom:0;">You may be losing functionality or bug fixes that are only present
in the newer versions of the packages.</li>
<li style="margin-bottom:0;">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.</li>
</ul>
</div>
</div>
</div>
</div>
</div>
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