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<h2>Table of Contents</h2> <h2>Table of Contents</h2>
<div id="text-table-of-contents"> <div id="text-table-of-contents">
<ul style="margin:0 0;"> <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="#org196e3c8">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="#org00455c0">Getting information about Python(3) libraries</a>
<ul style="margin:0 0;"> <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="#org69f771a">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="#org77338a9">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="#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> </ul>
</li> </li>
<li style="margin-bottom:0;"><a href="#org25032d4">Getting information about R libraries</a></li>
</ul> </ul>
</div> </div>
</div> </div>
<div id="outline-container-org0832474" class="outline-2"> <div id="outline-container-org196e3c8" class="outline-2">
<h2 id="org0832474">Getting information about your Git repository</h2> <h2 id="org196e3c8">Getting information about your Git repository</h2>
<div class="outline-text-2" id="text-org0832474"> <div class="outline-text-2" id="text-org196e3c8">
<p> <p>
When taking notes, it may be difficult to remember which version of 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 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. ...@@ -109,19 +123,23 @@ is the price to pay for running git from within the notebook itself.
</p> </p>
</div> </div>
</div> </div>
<div id="outline-container-org79df74e" class="outline-2"> <div id="outline-container-org00455c0" class="outline-2">
<h2 id="org79df74e">Getting information about Python(3) libraries</h2> <h2 id="org00455c0">Getting information about Python(3) libraries</h2>
<div class="outline-text-2" id="text-org79df74e"> <div class="outline-text-2" id="text-org00455c0">
</div> </div>
<div id="outline-container-org6ac23e8" class="outline-3"> <div id="outline-container-org69f771a" class="outline-3">
<h3 id="org6ac23e8">Getting the list of installed packages and their version</h3> <h3 id="org69f771a">Getting the list of installed packages and their version</h3>
<div class="outline-text-3" id="text-org6ac23e8"> <div class="outline-text-3" id="text-org69f771a">
<p> <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 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 package installer) within a shell command, it is easy to query the
version of all installed packages (note that on your system, you may 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 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> </p>
<div class="org-src-container"> <div class="org-src-container">
<pre style="padding-left: 30px; background-color: #f6f8fa;" class="src src-shell">pip3 freeze <pre style="padding-left: 30px; background-color: #f6f8fa;" class="src src-shell">pip3 freeze
...@@ -148,6 +166,41 @@ wcwidth==0.1.7 ...@@ -148,6 +166,41 @@ wcwidth==0.1.7
webencodings==0.5 webencodings==0.5
</pre> </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> <p>
Once you know which packages are installed, you can easily get Once you know which packages are installed, you can easily get
additional information about a given package and in particular check 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 ...@@ -155,9 +208,9 @@ whether it was installed "locally" through pip or whether it is
installed system-wide. Again, in a shell command: installed system-wide. Again, in a shell command:
</p> </p>
<div class="org-src-container"> <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> <span style="font-weight: bold;">echo</span> <span style="font-style: italic;">" "</span>
pip3 show statsmodels pip show statsmodels
</pre> </pre>
</div> </div>
...@@ -184,10 +237,9 @@ Requires: patsy, pandas ...@@ -184,10 +237,9 @@ Requires: patsy, pandas
</pre> </pre>
</div> </div>
</div> </div>
<div id="outline-container-org77338a9" class="outline-3">
<div id="outline-container-org86b6e7e" class="outline-3"> <h3 id="org77338a9">How to list imported modules?</h3>
<h3 id="org86b6e7e">How to list imported modules?</h3> <div class="outline-text-3" id="text-org77338a9">
<div class="outline-text-3" id="text-org86b6e7e">
<p> <p>
Without resorting to pip (that will list all available packages), you 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 may want to know which modules are loaded in a Python session as well
...@@ -248,9 +300,9 @@ zlib 1.0 ...@@ -248,9 +300,9 @@ zlib 1.0
</div> </div>
</div> </div>
<div id="outline-container-orgf4c774a" class="outline-3"> <div id="outline-container-org444b8c3" class="outline-3">
<h3 id="orgf4c774a">Setting up an environment with pip</h3> <h3 id="org444b8c3">Setting up an environment with pip</h3>
<div class="outline-text-3" id="text-orgf4c774a"> <div class="outline-text-3" id="text-org444b8c3">
<p> <p>
The easiest way to go is as follows: The easiest way to go is as follows:
</p> </p>
...@@ -267,12 +319,86 @@ dynamic libraries that are wrapped by Python though. ...@@ -267,12 +319,86 @@ dynamic libraries that are wrapped by Python though.
</p> </p>
</div> </div>
</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>
<div id="outline-container-org25032d4" class="outline-2"> <div id="outline-container-orga609f56" class="outline-2">
<h2 id="org25032d4">Getting information about R libraries</h2> <h2 id="orga609f56">Getting information about R libraries</h2>
<div class="outline-text-2" id="text-org25032d4"> <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> <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> </p>
<div class="org-src-container"> <div class="org-src-container">
...@@ -334,7 +460,11 @@ Some actually advocate that <a href="https://github.com/ropensci/rrrpkg">writing ...@@ -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 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>. clean R dependency management should thus have a look at <a href="https://rstudio.github.io/packrat/">Packrat</a>.
</p> </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> <p>
Finally, it is good to know that there is a built-in R command 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 (<code>installed.packages</code>) allowing to retrieve and list the details of all
...@@ -588,4 +718,107 @@ packages installed. ...@@ -588,4 +718,107 @@ packages installed.
</table> </table>
</div> </div>
</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> </div>
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