Finish main content

.travis.yml

@@ -0,0 +1,21 @@
+language: python
+
+python:
+  - 3.6
+
+before_install:
+  # Here we download miniconda and create our conda environment
+  - export MINICONDA=$HOME/miniconda
+  - export PATH="$MINICONDA/bin:$PATH"
+  - hash -r
+  - wget http://repo.continuum.io/miniconda/Miniconda-latest-Linux-x86_64.sh -O miniconda.sh
+  - bash miniconda.sh -b -f -p $MINICONDA
+  - conda config --set always_yes yes
+  - conda update conda
+  - conda info -a
+  - conda env create -f testenv.yml -v
+  - source activate testenv
+
+script:
+  - pytest
+  - pytest --nbval notebooks/00_explore-data.ipynb

04_Testing.ipynb

@@ -156,7 +156,7 @@
     }
    },
    "source": [
-    "Your test script should look like this:\n",
+    "Modifying <code>test_03_country_subset.py</code>\n",
     "``` python\n",
     "import importlib\n",
     "\n",

05_SharingAnalysis.ipynb

@@ -0,0 +1,354 @@
+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "# Sharing your code with the world\n",
+    "\n",
+    "We now have a fully automated and tested workflow!!! 🤩🎉😎\n",
+    "\n",
+    "And we are ready to share our awesomeness with the world. \n",
+    "\n",
+    "Head to [https://github.com/](https://github.com/) and login to your account\n"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "In your repository section click on the green **new repository** button\n",
+    "![gh1](assets/github1.PNG)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "We need to link your local project to your GitHub repository\n",
+    "![link](assets/github2.PNG)\n",
+    "\n",
+    "type those command on your shell (or copy and paste). **Use your own details**\n",
+    "\n",
+    "Refresh your web browser and... ta dah! Your project is online"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "# Continuous integration \n",
+    "\n",
+    "Now, instead of running our tests manually every time we want for this to be tested every time we push something from our local computer to our GitHub account. \n",
+    "\n",
+    "Some of the advantages of doing this are:\n",
+    "- check every version of your code\n",
+    "- check for errors continuosly\n",
+    "- report the results of the tests\n",
+    "- identify when things stop working\n"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "### Activate Travis CI\n",
+    "\n",
+    "Travis CI is a continuous integration server hosting platform. All you need is an account. Now let's go to [https://travis-ci.org/](https://travis-ci.org/) and activate CI for your project\n",
+    "\n",
+    "![travis](assets/travisact.PNG)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "## .travis.yml\n",
+    "A **.travis.yml** script tells Travis CI what steps are needed to test your project\n",
+    "\n",
+    "```yaml\n",
+    "language: python\n",
+    "\n",
+    "python:\n",
+    "  - 3.6\n",
+    "  \n",
+    "before_install:\n",
+    "  # Here we download miniconda and create our conda environment\n",
+    "  - export MINICONDA=$HOME/miniconda\n",
+    "  - export PATH=\"$MINICONDA/bin:$PATH\"\n",
+    "  - hash -r\n",
+    "  - wget http://repo.continuum.io/miniconda/Miniconda-latest-Linux-x86_64.sh -O miniconda.sh\n",
+    "  - bash miniconda.sh -b -f -p $MINICONDA\n",
+    "  - conda config --set always_yes yes\n",
+    "  - conda update conda\n",
+    "  - conda info -a\n",
+    "  # Create the environment from a yml file\n",
+    "  # Is this familiar?\n",
+    "  - conda env create -f testenv.yml -v\n",
+    "  - source activate testenv\n",
+    "  \n",
+    "script:\n",
+    "  - pytest\n",
+    "  - pytest --nbval notebooks/00_explore-data.ipynb\n",
+    "```"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "### Does Your Software Work on Your Colleague’s Computer?\n",
+    "\n",
+    "Complex analysis depend on a number of packages and libraries native to your OS, packages the user installes, environmental variables and so on. Manually maintaining these dependencies is a rather tedious task. \n",
+    "\n",
+    "That is why we use package managers, such as Conda. \n",
+    "Do you remember we started this workshop by installing all the packages we needed and one of the steps was to use an **environment.yml** file? This ensures we all have the same packages.  \n",
+    "\n",
+    "Then at the beginnign of the course we activated our **reproPython** environment and have been using the packages installed in this environment. \n",
+    "\n",
+    "<div class='warn'> conda is only one package manager, there are many more alternatives for you </div>"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "Let's create our **testenv.yml**\n",
+    "\n",
+    "```yaml\n",
+    "name: testenv\n",
+    "channels:\n",
+    "  - conda-forge\n",
+    "  - defaults\n",
+    "dependencies:\n",
+    "  - python>3.6\n",
+    "  - pytest\n",
+    "  - pandas\n",
+    "  - matplotlib\n",
+    "  - pip:\n",
+    "    - nbval\n",
+    "```\n",
+    "\n",
+    "<div class='info'> Note we are not specifying versions of the packages so by default conda will install the latest versions available </div>"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "Commit your changes and push this to github\n",
+    "```\n",
+    "$ git add .\n",
+    "$ git commit -m \"Add files for CI\"\n",
+    "$ git push\n",
+    "```\n",
+    "\n",
+    "This will start an automated testing of your project"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "# Making your software citable \n",
+    "\n",
+    "Head to [https://zenodo.org/](https://zenodo.org/) and login using your GitHub account\n",
+    "\n",
+    "![zenodo](assets/zenodo-login.png)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "Find your repository and toggle on Zenodo\n",
+    "![toggle](assets/zenodo-toggle-on.png)\n",
+    "\n",
+    "We will be redirected to GitHub to create a release of the repository."
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "After creating the release, go back to Zenodo and refresh the page. You should now see the newly created DOI 🤩\n",
+    "\n",
+    "Click on the DOI and copy the markdown text, add this to your README.md and push to GitHub!\n",
+    "\n",
+    "![doi](assets/DOI.PNG)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "# Creating a citation file\n",
+    "\n",
+    "```\n",
+    "cff-version: 1.0.3\n",
+    "message: If you use this software, please cite it as below.\n",
+    "authors:\n",
+    "  - family-names: Allard\n",
+    "    given-names: Tania\n",
+    "    orcid: https://orcid.org/0000-0003-4925-7248\n",
+    "title: My reproducibel python workflow\n",
+    "version: 0.1\n",
+    "doi: 10.5281/zenodo.1241049\n",
+    "date-released: 2018-05-09\n",
+    "```\n",
+    "\n",
+    "Save as CITATION.cff and commit and push to GitHub\n"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 1,
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/html": [
+       "<link href=\"https://fonts.googleapis.com/css?family=Didact+Gothic|Dosis:400,500,700\" rel=\"stylesheet\"><style>\n",
+       "@font-face {\n",
+       "  font-family: \"Computer Modern\";\n",
+       "  src: url('http://mirrors.ctan.org/fonts/cm-unicode/fonts/otf/cmunss.otf');\n",
+       "}\n",
+       "/* div.cell{\n",
+       "width:800px;\n",
+       "margin-left:16% !important;\n",
+       "margin-right:auto;\n",
+       "} */\n",
+       "h1 {\n",
+       "  font-family: 'Dosis', \"Helvetica Neue\", Arial, sans-serif;\n",
+       "  color: #0B132B;\n",
+       "}\n",
+       "h2 {\n",
+       "  font-family: 'Dosis', sans-serif;\n",
+       "  color: #1C2541;\n",
+       "}\n",
+       "h3{\n",
+       "  font-family: 'Dosis', sans-serif;\n",
+       "  margin-top:12px;\n",
+       "  margin-bottom: 3px;\n",
+       "  color: #40a8a6;\n",
+       "}\n",
+       "h4{\n",
+       "  font-family: 'Dosis', sans-serif;\n",
+       "  color: #40a8a6;\n",
+       "}\n",
+       "h5 {\n",
+       "  font-family: 'Dosis', sans-serif;\n",
+       "  color: #40a8a6;\n",
+       "}\n",
+       "div.text_cell_render{\n",
+       "  font-family: 'Didact Gothic',Computer Modern, \"Helvetica Neue\", Arial, Helvetica,\n",
+       "  Geneva, sans-serif;\n",
+       "  line-height: 130%;\n",
+       "  font-size: 110%;\n",
+       "  /* width:600px; */\n",
+       "  /* margin-left:auto;\n",
+       "  margin-right:auto; */\n",
+       "}\n",
+       "\n",
+       ".text_cell_render h1 {\n",
+       "  font-weight: 200;\n",
+       "  font-size: 30pt;\n",
+       "  /* font-size: 50pt */\n",
+       "  line-height: 100%;\n",
+       "  color:#0B132B;\n",
+       "  margin-bottom: 0.5em;\n",
+       "  margin-top: 0.5em;\n",
+       "  display: block;\n",
+       "}\n",
+       "\n",
+       ".text_cell_render h2{\n",
+       "  font-weight: 500;\n",
+       "}\n",
+       "\n",
+       ".text_cell_render h3{\n",
+       "  font-weight: 500;\n",
+       "}\n",
+       "\n",
+       "\n",
+       ".warning{\n",
+       "  color: rgb( 240, 20, 20 )\n",
+       "}\n",
+       "\n",
+       "div.warn {\n",
+       "  background-color: #FF5A5F;\n",
+       "  border-color: #FF5A5F;\n",
+       "  border-left: 5px solid #C81D25;\n",
+       "  padding: 0.5em;\n",
+       "\n",
+       "  color: #fff;\n",
+       "  opacity: 0.8;\n",
+       "}\n",
+       "\n",
+       "div.info {\n",
+       "  background-color: #087E8B;\n",
+       "  border-color: #087E8B;\n",
+       "  border-left: 5px solid #0B3954;\n",
+       "  padding: 0.5em;\n",
+       "  color: #fff;\n",
+       "  opacity: 0.8;\n",
+       "}\n",
+       "\n",
+       "</style>\n",
+       "<script>\n",
+       "MathJax.Hub.Config({\n",
+       "  TeX: {\n",
+       "    extensions: [\"AMSmath.js\"]\n",
+       "    },\n",
+       "    tex2jax: {\n",
+       "      inlineMath: [ ['$','$'], [\"\\\\(\",\"\\\\)\"] ],\n",
+       "      displayMath: [ ['$$','$$'], [\"\\\\[\",\"\\\\]\"] ]\n",
+       "      },\n",
+       "      displayAlign: 'center', // Change this to 'center' to center equations.\n",
+       "      \"HTML-CSS\": {\n",
+       "        styles: {'.MathJax_Display': {\"margin\": 4}}\n",
+       "      }\n",
+       "      });\n",
+       "      </script>\n"
+      ],
+      "text/plain": [
+       "<IPython.core.display.HTML object>"
+      ]
+     },
+     "execution_count": 1,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "from IPython.core.display import HTML\n",
+    "\n",
+    "\n",
+    "def css_styling():\n",
+    "    styles = open(\"styles/custom.css\", \"r\").read()\n",
+    "    return HTML(styles)\n",
+    "css_styling()"
+   ]
+  }
+ ],
+ "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": "3.6.5"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 2
+}

testenv.yml

@@ -0,0 +1,11 @@
+name: testenv
+channels:
+  - conda-forge
+  - defaults
+dependencies:
+  - python>3.6
+  - pytest
+  - pandas
+  - matplotlib
+  - pip:
+    - nbval