[custom] fix lesson contents

Author: zkamvar

environment.yml episodes/files/environment.ymlenvironment.yml renamed to episodes/files/environment.yml

@@ -0,0 +1,39 @@
+# Author: Hugo Bowne-Anderson
+
+import sys
+from pkgutil import iter_modules
+
+
+# Thanks @ericmjl for function below.
+def check_import(packagename):
+    """Checks whether a package is installed"""
+    if packagename in (name for _, name, _ in iter_modules()):
+        return True
+    else:
+        return False
+
+all_checks_passed = True
+
+# Throw error if Anaconda is not default Python
+assert 'anaconda' in sys.prefix.lower(), ("Anaconda is NOT installed as your "
+                                  "default version of Python. Please "
+                                  "make sure that is in accordance "
+                                  "with the instructions provided.")
+
+# Throw error if Python 3 is not default Python
+assert sys.version_info.major >= 3, 'Please install Python 3!'
+
+# Packages necessary for workshop
+packages = ['numpy', 'matplotlib', 'pandas', 'jupyter', 'plotnine']
+
+# Throw error if any of the necessary packages is not installed
+for p in packages:
+    assert check_import(p),\
+        ("{0} not present. You may have installed a subset of the"
+         "required distribution. Please install the entire Anaconda"
+         "distribution").format(p)
+
+if all_checks_passed:
+    print("All checks passed. Your Anaconda installation is up and "
+          "running and ready for Data Carpentry!")
+          

episodes/files/scripts/check_env.py

@@ -11,7 +11,7 @@ encounter setup issues, please file an issue with the tags 'High-priority'.
 
 ## Checking installations.
 
-In the [`_includes/scripts`](https://github.com/datacarpentry/python-ecology-lesson/tree/gh-pages/_includes/scripts) directory, you will find a script called check\_env.py This checks the
+In the [`episodes/files/scripts/check_env.py`](../episodes/files/scripts/check_env.py) directory, you will find a script called check\_env.py This checks the
 functionality of the Anaconda install.
 
 By default, Data Carpentry does not have people pull the whole repository with all the scripts and
@@ -74,7 +74,6 @@ rev[2] = "apple-sauce"
 In Pandas prior to 0.18.1 there is a bug causing `surveys_df['weight'].describe()` to return
 a runtime error.
 
-
 ::::::::::::::::::::::::::::::::::::::::::::::::::
 
 ### Dataframe Challenges
@@ -340,7 +339,7 @@ weight 3266
 ### Writing Out Data to CSV
 
 If the students have trouble generating the output, or anything happens with that, the folder
-[`sample_output`](https://github.com/datacarpentry/python-ecology-lesson/tree/gh-pages/sample_output)
+[`sample_output`](https://github.com/datacarpentry/python-ecology-lesson/tree/main/sample_output)
 in this repository contains the file `surveys_complete.csv` with the data they should generate.
 
 ## 05-merging-data
@@ -750,8 +749,6 @@ plt.show()
 
 [This page][matplotlib-mathtext] contains more information.
 
-
-
 ## 09-working-with-sql
 
 ### Challenge - SQL

instructors/instructor-notes.md

@@ -4,104 +4,103 @@ title: 'Glossary'
 
 ## Glossary
 
-{:auto\_ids}
-0-based indexing
+[0-based indexing]{#based-indexing}
 :   is a way of assigning indices to elements in a sequential, ordered data structure
 starting from 0, i.e. where the first element of the sequence has index 0.
 
-CSV (file)
+[CSV (file)]{#csv-file}
 :   is an acronym which stands for Comma-Separated Values file. CSV files store
 tabular data, either numbers, strings, or a combination of the two, in plain
 text with columns separated by a comma and rows by the carriage return character.
 
-database
+[database]{#database}
 :   is an organized collection of data.
 
-dataframe
+[dataframe]{#dataframe}
 :   is a two-dimensional labeled data structure with columns of (potentially)
 different type.
 
-data structure
+[data structure]{#data-structure}
 :   is a particular way of organizing data in memory.
 
-data type
+[data type]{#data-type}
 :   is a particular kind of item that can be assigned to a variable, defined by
 the values it can take, the programming language in use and the operations
 that can be performed on it.
 
-dictionary
+[dictionary]{#dictionary}
 :   is an unordered Python data structure designed to contain key-value pairs, where both
 the key and the value can be integers, floats or strings. Elements of a dictionary
 can be accessed by their key and can be modified.
 
-docstring
+[docstring]{#docstring}
 :   is an optional documentation string to describe what a Python function does.
 
-faceting
+[faceting]{#faceting}
 :   is the act of plotting relationships between set variables in multiple subsets
 of the data with the results appearing as different panels in the same figure.
 
-float
+[float]{#float}
 :   is a Python data type designed to store positive and negative decimal numbers
 by means of a floating point representation.
 
-function
+[function]{#function}
 :   is a group of related statements that perform a specific task.
 
-integer
+[integer]{#integer}
 :   is a Python data type designed to store positive and negative integer numbers.
 
-interactive mode
+[interactive mode]{#interactive-mode}
 :   is an online mode of operation in which the user writes the commands directly
 on the command line one-by-one and execute them immediately by pressing a button
 on the keyword, usually <kbd>Return</kbd>.
 
-join key
+[join key]{#join-key}
 :   is a variable or an array representing the column names over which pandas.DataFrame.join()
 merge together columns of different data sets.
 
-library
+[library]{#library}
 :   is a set of functions and methods grouped together to perform some specific
 sort of tasks.
 
-list
+[list]{#list}
 :   is a Python data structure designed to contain sequences of integers, floats,
 strings and any combination of the previous. The sequence is ordered and indexed
 by integers, starting from 0. Elements of a list can be accessed by their index
 and can be modified.
 
-loop
+[loop]{#loop}
 :   is a sequence of instructions that is continually repeated until a condition
 is satisfied.
 
-NaN
+[NaN]{#nan}
 :   is an acronym for Not-a-Number and represents that either a value is missing or
 the calculation cannot output any meaningful result.
 
-None
+[None]{#none}
 :   is an object that represents no value.
 
-scripting mode
+[scripting mode]{#scripting-mode}
 :   is an offline mode of operation in which the user writes the commands to be
 executed in a text file (with .py extension for Python) which is then compiled
 or interpreted to run the program. Notes that Python interprets script on
 run-time and compiles a binary version of the program to speed up the execution time.
 
-Sequential (data structure)
+[Sequential (data structure)]{#sequential-data-structure}
 :   is an ordered group of objects stored in memory which can be accessed specifying
 their index, i.e. their position, in the structure.
 
-SQL
+[SQL]{#sql}
 :   or Structured Query Language, is a domain-specific language for managing data
 stored in a relational database management system (RDBMS).
 
-SQLite
+[SQLite]{#sqlite}
 :   is a self-contained, public domain SQL database engine.
 
-string
+[string]{#string}
 :   is a Python data type designed to store sequences of characters.
 
-tuple
+[tuple]{#tuple}
 :   is a Python data structure designed to contain sequences of integers, floats,
 strings and any combination of the previous. The sequence is ordered and indexed
 by integers, starting from 0. Elements of a tuple can be accessed by their index

instructors/jupyter_notebooks.md learners/jupyter_notebooks.mdinstructors/jupyter_notebooks.md renamed to learners/jupyter_notebooks.md

@@ -42,25 +42,17 @@ version 3.x (e.g., 3.6 is fine).
 
 ::::::::::::::::::::::::::::::::::::::::::::::::::
 
-## Installing Anaconda
-
-{::options parse\_block\_html="true" /}
-
-<div>
-
-<ul class="nav nav-tabs" role="tablist">
+:::::::::::::::::::: discussion
 
-  <li role="presentation" class="active"><a data-os="windows" href="#anaconda-windows" aria-controls="Windows" role="tab" data-toggle="tab">Windows</a></li>
-
-  <li role="presentation"><a data-os="macos" href="#anaconda-macos" aria-controls="MacOS" role="tab" data-toggle="tab">MacOS</a></li>
+## Installing Anaconda
 
-  <li role="presentation"><a data-os="linux" href="#anaconda-linux" aria-controls="Linux" role="tab" data-toggle="tab">Linux</a></li>
+Select your operating system from the options below.
 
-</ul>
+:::::::::::::::::::::::::::::::::
 
-<div class="tab-content">
+:::::::::::: solution
 
-<article role="tabpanel" class="tab-pane active" id="anaconda-windows">
+### Windows {#anaconda-windows}
 
 1. Open [https://www.anaconda.com/products/individual](https://www.anaconda.com/products/individual) in your web browser.
 
@@ -91,9 +83,11 @@ version 3.x (e.g., 3.6 is fine).
 
 </div>
 
-</article>
+::::::::::::
+
+:::::::::::: solution
 
-<article role="tabpanel" class="tab-pane" id="anaconda-macos">
+### MacOS {#anaconda-macos}
 
 1. Visit [https://www.anaconda.com/products/individual](https://www.anaconda.com/products/individual) in your web browser.
 
@@ -127,9 +121,12 @@ version 3.x (e.g., 3.6 is fine).
 
 </div>
 
-</article>
+::::::::::::
+
+:::::::::::: solution
+
+### Linux {#anaconda-linux}
 
-<article role="tabpanel" class="tab-pane" id="anaconda-linux">
 Note that the following installation steps require you to work from the terminal (shell).
 If you run into any difficulties, please request help before the workshop begins.
 
@@ -160,11 +157,7 @@ If you run into any difficulties, please request help before the workshop begins
   conda --help
   ```
 
-</article>
-
-</div>
-
-</div>
+::::::::::::
 
 ## Required Python Packages
 
@@ -200,7 +193,7 @@ conda install -c conda-forge plotnine
 ### *(Alternative)* Installing required packages with environment file
 
 Download the
-[environment.yml](https://raw.githubusercontent.com/datacarpentry/python-ecology-lesson/gh-pages/environment.yml)
+[environment.yml](https://episodes/files/environment.yml/environment.yml)
 file by right-clicking the link and selecting save as.
 In the directory where you downloaded the environment.yml file run:
 
@@ -233,7 +226,7 @@ The notebook should open automatically in your browser. If it does not or you
 wish to use a different browser, open this link: [http://localhost:8888](https://localhost:8888).
 
 For a brief introduction to Jupyter Notebooks, please consult our
-[Introduction to Jupyter Notebooks](.{% link \_extras/jupyter\_notebooks.md %}) page.
+[Introduction to Jupyter Notebooks](jupyter_notebooks.md) page.
 
 [python]: https://www.python.org/
 [anaconda]: https://www.anaconda.com/

learners/reference.md

@@ -0,0 +1,41 @@
+[cc-by-human]: https://creativecommons.org/licenses/by/4.0/
+[cc-by-legal]: https://creativecommons.org/licenses/by/4.0/legalcode
+[ci]: https://communityin.org/
+[coc-reporting]: https://docs.carpentries.org/topic_folders/policies/incident-reporting.html
+[coc]: https://docs.carpentries.org/topic_folders/policies/code-of-conduct.html
+[concept-maps]: https://carpentries.github.io/instructor-training/05-memory/
+[contrib-covenant]: https://contributor-covenant.org/
+[cran-checkpoint]: https://cran.r-project.org/package=checkpoint
+[cran-knitr]: https://cran.r-project.org/package=knitr
+[cran-stringr]: https://cran.r-project.org/package=stringr
+[dc-lessons]: https://www.datacarpentry.org/lessons/
+[email]: mailto:team@carpentries.org
+[github-importer]: https://import2.github.com/
+[importer]: https://github.com/new/import
+[jekyll-collection]: https://jekyllrb.com/docs/collections/
+[jekyll-install]: https://jekyllrb.com/docs/installation/
+[jekyll-windows]: https://jekyll-windows.juthilo.com/
+[jekyll]: https://jekyllrb.com/
+[jupyter]: https://jupyter.org/
+[kramdown]: https://kramdown.gettalong.org/
+[lc-lessons]: https://librarycarpentry.org/lessons/
+[lesson-example]: https://carpentries.github.io/lesson-example/
+[mit-license]: https://opensource.org/licenses/mit-license.html
+[morea]: https://morea-framework.github.io/
+[numfocus]: https://numfocus.org/
+[osi]: https://opensource.org
+[pandoc]: https://pandoc.org/
+[paper-now]: https://github.com/PeerJ/paper-now
+[python-gapminder]: https://swcarpentry.github.io/python-novice-gapminder/
+[pyyaml]: https://pypi.org/project/PyYAML/
+[r-markdown]: https://rmarkdown.rstudio.com/
+[rstudio]: https://www.rstudio.com/
+[ruby-install-guide]: https://www.ruby-lang.org/en/downloads/
+[ruby-installer]: https://rubyinstaller.org/
+[rubygems]: https://rubygems.org/pages/download/
+[styles]: https://github.com/carpentries/styles/
+[swc-lessons]: https://software-carpentry.org/lessons/
+[swc-releases]: https://github.com/swcarpentry/swc-releases
+[training]: https://carpentries.github.io/instructor-training/
+[yaml]: https://yaml.org/
+[lesson-setup]: ../learners/setup.md