Merge remote-tracking branch 'py2020/master'

.gitignore

+MANIFEST
+build
+dist
+_build
+docs/man/*.gz
+docs/source/api/generated
+docs/source/config/options
+docs/source/config/shortcuts/*.csv
+docs/source/interactive/magics-generated.txt
+docs/gh-pages
+jupyter_notebook/notebook/static/mathjax
+jupyter_notebook/static/style/*.map
+*.py[co]
+__pycache__
+*.egg-info
+*~
+*.bak
 *ipynb_checkpoints*
+.tox
+.DS_Store
+\#*#
+.#*
+.cache
+.coverage
+*.swp
+.vscode
+.pytest_cache
+.python-version
+venv*/
+.idea/

README.md

@@ -2,16 +2,22 @@
 
 The EMBL Python User Group (EPUG) is a group of people at EMBL Heidelberg who share an interest in the Python programming language. 
 You can contact the group by sending email to [python@embl.de](mailto:python@embl.de). 
-That mailing list is managed by [Toby Hodges](mailto:toby.hodges@embl.de) -
+That mailing list is managed by [Renato Alves](mailto:renato.alves@embl.de) -
 to join EPUG, please send him an email. 
 Meetings usually take place fortnightly, on Tuesdays at 16:00:
 see the full schedule [here](https://docs.google.com/spreadsheets/d/1cMDumZ8GdhsTaiWzJl1qHDfi192sl4P1KJJhtuk0ZkE/edit?usp=sharing).
 
-## Past Sessions
+## Adding material to this repository
 
-2019-04-30: [`dataclasses`](meetings/2019/2019-04-30-dataclasses/)
+Material for each session should be added in a new folder,
+with a name describing the main topic covered in that session.
+Material from multiple sessions on a similar topic can be combined
+together in a single folder.
 
-2019-05-28: [`python cinema: How to think about data visualisation with Jake VanderPlas`](meetings/2019/2019-05-28-data-visualisation)
-
-2019-06-11: [`python closures`](meetings/2019/2019-06-11-python-closures)
+Material can be added to this repository by merge request. 
+To gain push access to the repository,
+and for guidance on creating your merge request,
+please contact one of the EPUG organisers:
 
+- Wasiu Akanni
+- Renato Alves

meetings/2020/session_10_debugging/debugging.md

+# Debugging in Python
+
+## Some concepts
+
+* *Breakpoint* - location in a file where the debugger should pause
+* *Continue* - resume execution until next breakpoint or unexpected condition
+* *Step over* - execute the current line and pause at the beginning of the next
+* *Step into* - if the current line is a function call, enter the function and execute from the first line of the function
+* *Step out* - execute the current function till the end and pause as soon as the function returns
+* *Backtrace* - the execution path up to the location where the debugger is paused
+
+## `pdb` cheat sheet
+
+* `args` - show arguments from surrounding function
+* `b` & `break` - set or list breakpoints
+* `display` - show tracked variables
+* `n` & `next` - execute instruction in next line (step over)
+* `s` & `step` - execute next possible instruction (step into)
+* `r` & `return` - execute until end of current function (step out)
+* `p` & `pp` - print result of expression
+* `ll` & `longlist` - show the source code/context of current paused state
+* `bt` & `w` & `where` - show the execution path up to the current location
+
+## launching pdb
+
+Add `import pdb ; pdb.set_trace()` to your code and you will get access to `pdb` on the spot.
+
+Alternatively run `python -mpdb script.py` from the command-line.
+
+## VSCode / VSCodium
+
+Install [Python extension](https://marketplace.visualstudio.com/items?itemName=ms-python.python) by Microsoft to have Python goodies and debugging powers.
+
+## Remote debugging & development
+
+The [remote development pack](https://marketplace.visualstudio.com/items?itemName=ms-vscode-remote.vscode-remote-extensionpack) is pretty awesome. You might find the [Remote - SSH](https://aka.ms/vscode-remote/download/ssh) option very useful, together with the [Remote - Containers](https://aka.ms/vscode-remote/download/containers) if you work with a lot with docker and similar solutions.
+
+### Reaching the location where the code is running
+
+This requires some familiarity with network concepts and `SSH`.
+
+You will need to setup port-forwarding (aka tunneling) using `SSH`.  
+You might also need to `ProxyJump` a few computers to get to the location where the code is running.
+
+A simple, "one hop" `SSH` tunnel can be achieved with `ssh -L localhost:5678:localhost:5678 login.cluster.embl.de`.
+
+For more about SSH tunnels try [these docs](https://www.ssh.com/ssh/tunneling/example) and [how to use `ProxyJump`](https://en.wikibooks.org/wiki/OpenSSH/Cookbook/Proxies_and_Jump_Hosts#Passing_Through_One_or_More_Gateways_Using_ProxyJump).
+
+### debugpy
+
+`debugpy` is [pretty awesome](https://github.com/microsoft/debugpy) but needs to connect via the network. You'll need to use the `SSH` tunnel setup above.
\ No newline at end of file

meetings/2020/session_10_debugging/debugging.py

+import os
+import glob
+
+
+def split(path):
+    return path.rsplit("/", 1)
+
+
+def get_path(filename):
+    head, tail = split(filename)
+    return os.path.abspath(head)
+
+
+def main(hostname):
+    extension = "one/**/*.py"
+    files = glob.glob(extension, recursive=True)
+    path = get_path(files[0])
+    print(">>>>", path, "<<<< on", hostname)
+
+
+if __name__ == "__main__":
+    hostname = os.uname().nodename
+    if hostname == "login.cluster.embl.de":
+        import debugpy
+        print("debugpy loaded and waiting for connection")
+        debugpy.listen(12125)
+        debugpy.wait_for_client()
+        print("debugpy session active")
+
+    main(hostname)
\ No newline at end of file

meetings/2020/session_10_debugging/one/test/file/too/many/debugging.py

+../../../../../debugging.py
\ No newline at end of file

meetings/2020/session_1_errors_and_exceptions/myfunction.py

+class MyExceptionValue(ValueError):
+    def __init__(self, error_code):
+        self.error_code = error_code
+
+    def __str__(self):
+        return f"The error number was {self.error_code}"
+
+    def __repr__(self):
+        return f"<Exception>: The error number was {self.error_code}"
+
+
+def func():
+    raise MyExceptionValue(404)

meetings/2020/session_2_defensive_programming/.ipynb_checkpoints/Untitled-checkpoint.ipynb

+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "# Defensive Programming\n",
+    "\n",
+    "Defensive programming describes concepts and approaches we can use to ensure that...\n",
+    "* Code does what we think it does (i.e. is free of bugs)\n",
+    "* Our programs fail when they should...\n",
+    "* ... and do so with informative error messages (throwback to last session)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 3",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.7.4"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 2
+}

meetings/2020/session_6_logging/.gitignore

+my.log

meetings/2020/session_6_logging/README.md

+# Logging
+
+## Usage
+
+    python intro_logging.py
+
+or
+
+    python -m intro_logging
+
+and with the current configuration you should see the output being saved to a
+file `my.log` as well as printed to the console.
+
+Edit `logging.conf` and re-run `intro_logging.py` to see how logged messages
+get sent to different destinations depending on the order of loggers, their
+level, propagate status and qualname.
+
+
+## Useful links
+
+* [logging HOWTO](https://docs.python.org/howto/logging.html) - from beginner to advanced
+* [logging cookbook](https://docs.python.org/howto/logging-cookbook.html)
+* [`logging`](https://docs.python.org/library/logging.html)
+* [`logging.config`](https://docs.python.org/library/logging.config.html) - the many ways to configure the logging module
+* [`logging.handlers`](https://docs.python.org/library/logging.handlers.html) - different ways to handle logging output

meetings/2020/session_6_logging/intro_logging.py

+# -*- coding: utf-8 -*-
+
+import logging
+import logging.config
+
+
+# Using a basic configuration
+# logging.basicConfig(format="%(asctime)s %(levelname)-8s %(pathname)s: %(message)s",
+#                     level=logging.DEBUG)
+#
+
+# or a configuration file to assist and allow customization
+logging.config.fileConfig("logging.conf")
+
+# more on configuring logging at:
+# https://docs.python.org/howto/logging.html#configuring-logging
+
+# Logs can be sent to different destinations, not just the console output
+# You could send to a log server, a file, a different process, via email...
+#
+# For different handlers see:
+# https://docs.python.org/library/logging.handlers.html
+
+# The name passed to getLogger() can be used in logging.conf's qualname
+# attribute to target the output of a specific logger
+LOG = logging.getLogger(__name__)
+
+
+def main():
+    # Logging uses an implicit severity level
+    # See: https://docs.python.org/library/logging.html#logging-levels
+    # CRITICAL
+    # ERROR
+    # WARNING
+    # INFO
+    # DEBUG
+    LOG.critical("HAAA!!! (running around with hands in the air!)")
+    LOG.error("OOPS!!")
+
+    # variables can be passed using %s as placeholder
+    variable = ("Bob", "is", "here")
+    LOG.warning("WARN: %s %s %s!!", *variable)
+
+    LOG.info("This is info")
+    LOG.debug("More verbosity")
+
+    other()
+
+
+def other():
+    try:
+        1 / 0
+    except ZeroDivisionError:
+        LOG.exception("We shouldn't get zeros here")
+
+    LOG.critical("But life goes on")
+
+
+if __name__ == "__main__":
+    main()

meetings/2020/session_6_logging/logging.conf

+# Here you need at least one logger, one handler and one formatter
+
+[loggers]
+# The order defined here and in other sections is important
+# messages flow from right to left
+keys=root,file_log
+
+[handlers]
+keys=console,file
+
+[formatters]
+keys=my_formatter
+
+[formatter_my_formatter]
+# For additional formatting keywords see:
+# https://docs.python.org/library/logging.html#logrecord-attributes
+# The negative number next to the keywords defines white space padding
+format=%(asctime)s %(levelname)-8s %(funcName)-5s %(pathname)s: %(message)s
+
+[handler_console]
+# For different types of handlers see:
+# https://docs.python.org/library/logging.handlers.html
+class=StreamHandler
+level=DEBUG
+formatter=my_formatter
+# The order of arguments here corresponds to the arguments of StreamHandler
+args=(sys.stdout,)
+
+[handler_file]
+# For different types of handlers see:
+# https://docs.python.org/library/logging.handlers.html
+class=FileHandler
+level=DEBUG
+formatter=my_formatter
+# The order of arguments here corresponds to the arguments of FileHandler
+# Use 'a' to preserve the logfile across executions and 'w' to empty the logfile
+args=("my.log", 'w',)
+
+[logger_root]
+level=DEBUG
+handlers=console
+
+[logger_file_log]
+level=DEBUG
+handlers=file
+# if propagate=0 messages are used and consumed by the current logger
+# if propagate=1 they are used and passed to the next logger
+propagate=1
+# qualname restricts the current logger to only handle output of one target.
+# The target name is specified in logging.getLogger("target")
+qualname=__main__

meetings/2020/session_6_logging/main.py

+# -*- coding: utf-8 -*-
+
+print(__name__)
+
+# vim: ai sts=4 et sw=4