From c4b2d456a98a55cf5efcd1e30210c227e9ce6252 Mon Sep 17 00:00:00 2001
From: David Perez-Suarez <d.perez-suarez@ucl.ac.uk>
Date: Mon, 27 Sep 2021 13:38:42 +0100
Subject: [PATCH 1/7] =?UTF-8?q?=F0=9F=91=B7=20Add=20CI=20build=20system=20?=
 =?UTF-8?q?-=20bye=20bye=20Travis,=20welcome=20to=20actions!?=
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Creates a new action and the different files needed to build
- python requirements
- latex (and ubuntu) packages needed
- ruby gems requirements as a Gemfile
---
 .github/python/requirements.txt  |  2 ++
 .github/texlive/requirements.txt |  9 +++++++
 .github/workflows/build_site.yml | 43 ++++++++++++++++++++++++++++++++
 Gemfile                          |  4 +++
 4 files changed, 58 insertions(+)
 create mode 100644 .github/python/requirements.txt
 create mode 100644 .github/texlive/requirements.txt
 create mode 100644 .github/workflows/build_site.yml
 create mode 100644 Gemfile

diff --git a/.github/python/requirements.txt b/.github/python/requirements.txt
new file mode 100644
index 0000000..ce5f1bb
--- /dev/null
+++ b/.github/python/requirements.txt
@@ -0,0 +1,2 @@
+-r ../../requirements.txt
+git+https://github.com/jakevdp/JSAnimation.git
diff --git a/.github/texlive/requirements.txt b/.github/texlive/requirements.txt
new file mode 100644
index 0000000..facb84a
--- /dev/null
+++ b/.github/texlive/requirements.txt
@@ -0,0 +1,9 @@
+pandoc
+texlive-latex-base
+texlive-latex-extra
+texlive-fonts-recommended
+texlive-latex-recommended
+texlive-generic-recommended
+texlive-xetex
+latex-xcolor
+liblapack-dev
diff --git a/.github/workflows/build_site.yml b/.github/workflows/build_site.yml
new file mode 100644
index 0000000..c1bc7fe
--- /dev/null
+++ b/.github/workflows/build_site.yml
@@ -0,0 +1,43 @@
+name: Build website
+on:
+  push:
+    branches:
+      - master
+  pull_request:
+    branches:
+      - master
+jobs:
+  Build-website:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v2
+      - uses: actions/cache@v2 # FIXME: add pip + latex + gems
+        with:
+          path: vendor/bundle
+          key: ${{ runner.os }}-gems-${{ hashFiles('**/Gemfile') }}
+          restore-keys: |
+            ${{ runner.os }}-gems-
+      - name: Install TeXLive
+        uses: DanySK/setup-texlive-action@0.1.1
+      - id: setup-python
+        name: Setup Python
+        uses: actions/setup-python@v2
+        with:
+          python-version: 3.8
+      - name: Install dependencies
+        uses: py-actions/py-dependency-install@v2
+        with:
+          path: ".github/python/requirements.txt"
+      - name: Building notes
+        run: make ready
+      - name: Builds website
+        uses: helaili/jekyll-action@v2
+        with:
+          target_branch: 'gh-pages'
+          build_only: true
+      - name: Build website and deploy
+        if: github.ref == 'refs/heads/master'
+        uses: helaili/jekyll-action@v2
+        with:
+          target_branch: 'gh-pages'
+          token: ${{ secrets.GITHUB_TOKEN }}
diff --git a/Gemfile b/Gemfile
new file mode 100644
index 0000000..b73daec
--- /dev/null
+++ b/Gemfile
@@ -0,0 +1,4 @@
+source 'https://rubygems.org'
+
+gem 'jekyll', '~> 3.1.6'
+gem 'redcarpet', '~> 3.5.0'

From b73c62d3bb8db32e01ddecdc6fab65feffa230ca Mon Sep 17 00:00:00 2001
From: David Perez-Suarez <d.perez-suarez@ucl.ac.uk>
Date: Mon, 27 Sep 2021 13:56:56 +0100
Subject: [PATCH 2/7] =?UTF-8?q?=F0=9F=91=B7=20Fix=20latex=20dependencies?=
 =?UTF-8?q?=20on=20CI?=
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Some latex dependencies have changed from ubuntu 14 to ubuntu 20!
---
 .github/texlive/requirements.txt | 5 ++---
 1 file changed, 2 insertions(+), 3 deletions(-)

diff --git a/.github/texlive/requirements.txt b/.github/texlive/requirements.txt
index facb84a..211f133 100644
--- a/.github/texlive/requirements.txt
+++ b/.github/texlive/requirements.txt
@@ -1,9 +1,8 @@
 pandoc
+texlive-base
 texlive-latex-base
+texlive-latex-recommended
 texlive-latex-extra
 texlive-fonts-recommended
-texlive-latex-recommended
-texlive-generic-recommended
 texlive-xetex
-latex-xcolor
 liblapack-dev

From 6fa51add1adfc4e3e4664660889e61d37d886ae9 Mon Sep 17 00:00:00 2001
From: David Perez-Suarez <d.perez-suarez@ucl.ac.uk>
Date: Mon, 27 Sep 2021 14:28:45 +0100
Subject: [PATCH 3/7] =?UTF-8?q?=F0=9F=92=9A=20Fix=20python=20dependencies?=
 =?UTF-8?q?=20for=20CI?=
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

pinning nbconvert with a particular version that has the templates
jupyter/nbgrader#1373

requires also pin jupyter-client to an earlier version
jupyter/jupyter_client#637
---
 .github/python/requirements.txt | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/.github/python/requirements.txt b/.github/python/requirements.txt
index ce5f1bb..89ac246 100644
--- a/.github/python/requirements.txt
+++ b/.github/python/requirements.txt
@@ -1,2 +1,6 @@
 -r ../../requirements.txt
 git+https://github.com/jakevdp/JSAnimation.git
+nbconvert==5.6.1
+# https://github.com/jupyter/nbgrader/issues/1373#issuecomment-702798246
+jupyter-client==6.1.12
+# https://github.com/jupyter/jupyter_client/issues/637

From 7c829f77d67344e12fbcecc25848d880f88f61ea Mon Sep 17 00:00:00 2001
From: David Perez-Suarez <d.perez-suarez@ucl.ac.uk>
Date: Mon, 27 Sep 2021 19:51:57 +0100
Subject: [PATCH 4/7] =?UTF-8?q?=F0=9F=92=9A=20exclude=20gems=20directory?=
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

---
 _config.yml | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/_config.yml b/_config.yml
index 3c9c54f..351361e 100644
--- a/_config.yml
+++ b/_config.yml
@@ -22,3 +22,7 @@ baseurl: /doctoral-programming-intro
 markdown: redcarpet
 redcarpet:
   extensions: ["strikethrough","tables"]
+exclude:
+  - vendor/
+  - Gemfile
+  - Gemfile.lock

From 07bd2914970baa66ddbd140737ecc5a93365bb41 Mon Sep 17 00:00:00 2001
From: David Perez-Suarez <d.perez-suarez@ucl.ac.uk>
Date: Mon, 27 Sep 2021 17:59:24 +0100
Subject: [PATCH 5/7] =?UTF-8?q?=F0=9F=92=9A=20remove=20pdf=20creation=20fr?=
 =?UTF-8?q?om=20the=20building=20process?=
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

---
 Makefile | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/Makefile b/Makefile
index a07d85c..f82e6de 100644
--- a/Makefile
+++ b/Makefile
@@ -47,7 +47,7 @@ indigo: indigo-jekyll-master
 
 .PHONY: ready
 
-ready: indigo $(HTMLS) notes.pdf notebooks.zip
+ready: indigo $(HTMLS) notebooks.zip
 
 _site: ready
 	jekyll build

From 0181e1cfcc4e2b7aee92868aa9e3ed328ad3eb60 Mon Sep 17 00:00:00 2001
From: David Perez-Suarez <d.perez-suarez@ucl.ac.uk>
Date: Mon, 27 Sep 2021 13:41:46 +0100
Subject: [PATCH 6/7] =?UTF-8?q?=F0=9F=91=B7=20remove=20CI=20build=20system?=
 =?UTF-8?q?=20files=20from=20Travis?=
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

---
 .travis.yml            |  29 -----------------------------
 travis/deploy.sh       |  26 --------------------------
 travis/secrets.tar.enc | Bin 5136 -> 0 bytes
 3 files changed, 55 deletions(-)
 delete mode 100644 .travis.yml
 delete mode 100755 travis/deploy.sh
 delete mode 100644 travis/secrets.tar.enc

diff --git a/.travis.yml b/.travis.yml
deleted file mode 100644
index a8a5c2d..0000000
--- a/.travis.yml
+++ /dev/null
@@ -1,29 +0,0 @@
-dist: trusty
-language: python
-sudo: required
-python:
-- '3.6'
-cache: pip
-addons:
-  apt:
-    packages:
-    - pandoc
-    - texlive-latex-base
-    - texlive-latex-extra
-    - texlive-fonts-recommended
-    - texlive-latex-recommended
-    - texlive-generic-recommended
-    - texlive-xetex
-    - latex-xcolor
-    - liblapack-dev
-install:
-- pip install --upgrade pip setuptools wheel
-- pip install -r requirements.txt
-- pip install git+https://github.com/jakevdp/JSAnimation.git
-- gem install jekyll
-- gem install redcarpet
-script:
-- python -c "import matplotlib.pyplot"
-- make
-after_success:
- - ./travis/deploy.sh
diff --git a/travis/deploy.sh b/travis/deploy.sh
deleted file mode 100755
index 98c14db..0000000
--- a/travis/deploy.sh
+++ /dev/null
@@ -1,26 +0,0 @@
-
-#!/bin/bash
-set -e
-
-if [[ $TRAVIS_PULL_REQUEST == false && $TRAVIS_BRANCH == 'master' ]]; then
-
-    openssl aes-256-cbc -K $encrypted_4014292b586d_key -iv $encrypted_4014292b586d_iv -in travis/secrets.tar.enc -out secrets.tar -d
-    tar -xvf secrets.tar
-    REPO=`git config remote.origin.url`
-    SSH_REPO=${REPO/https:\/\/github.com\//git@github.com:}
-    eval `ssh-agent -s`
-    chmod 600 deploy_key
-    ssh-add deploy_key
-
-    cd _site
-    git init
-    git checkout -b gh-pages
-    git config --global user.email "jamespjh@gmail.com"
-    git config --global user.name "Pushed by Travis CI"
-    git add .
-    git commit -m "Pushed by Travis"
-    git remote add origin $SSH_REPO
-    git push -f -u origin gh-pages
-
-fi
-
diff --git a/travis/secrets.tar.enc b/travis/secrets.tar.enc
deleted file mode 100644
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From 98d517afe0ce34e80c173441f538d03cae6d3d82 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?David=20P=C3=A9rez-Su=C3=A1rez?= <d.perez-suarez@ucl.ac.uk>
Date: Fri, 8 Oct 2021 18:44:43 +0100
Subject: [PATCH 7/7] Update actions to the change name of branches

---
 .github/workflows/build_site.yml | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/build_site.yml b/.github/workflows/build_site.yml
index c1bc7fe..3a0a739 100644
--- a/.github/workflows/build_site.yml
+++ b/.github/workflows/build_site.yml
@@ -2,10 +2,10 @@ name: Build website
 on:
   push:
     branches:
-      - master
+      - main
   pull_request:
     branches:
-      - master
+      - main
 jobs:
   Build-website:
     runs-on: ubuntu-latest
@@ -36,7 +36,7 @@ jobs:
           target_branch: 'gh-pages'
           build_only: true
       - name: Build website and deploy
-        if: github.ref == 'refs/heads/master'
+        if: github.ref == 'refs/heads/main'
         uses: helaili/jekyll-action@v2
         with:
           target_branch: 'gh-pages'