From d69574b347eb38e18d7daa840334d404040a4bd7 Mon Sep 17 00:00:00 2001
From: WilliamHPNielsen <william@nbi.ku.dk>
Date: Tue, 10 Apr 2018 10:47:10 +0200
Subject: [PATCH 01/15] Remove notification settings from .appveyor.yml

---
 .appveyor.yml | 3 ---
 1 file changed, 3 deletions(-)

diff --git a/.appveyor.yml b/.appveyor.yml
index b11dd620b..b4201c9f5 100644
--- a/.appveyor.yml
+++ b/.appveyor.yml
@@ -9,9 +9,6 @@ environment:
   matrix:
     - PYTHON_VERSION: "3.6"
 
-# Disable email notifications
-notifications:
-  email: false
 
 # Do not use MSBuild
 build: false

From 9c600d8df4c2a4adbd83c4087398b0990edf58a1 Mon Sep 17 00:00:00 2001
From: WilliamHPNielsen <william@nbi.ku.dk>
Date: Tue, 10 Apr 2018 10:51:19 +0200
Subject: [PATCH 02/15] Fix un-windowsy pip upgrade

---
 .appveyor.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.appveyor.yml b/.appveyor.yml
index b4201c9f5..b14ec5517 100644
--- a/.appveyor.yml
+++ b/.appveyor.yml
@@ -17,7 +17,7 @@ build: false
 
 # Install scripts
 install:
-  - pip install --upgrade pip
+  - python -m pip install --upgrade pip
   - pip install -r test_requirements.txt
   - pip install .
 

From a2429fb1abd076412892baf9d56dd001dcd55cb1 Mon Sep 17 00:00:00 2001
From: WilliamHPNielsen <william@nbi.ku.dk>
Date: Tue, 10 Apr 2018 11:06:22 +0200
Subject: [PATCH 03/15] Make python version global

---
 .appveyor.yml | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/.appveyor.yml b/.appveyor.yml
index b14ec5517..c110d64c7 100644
--- a/.appveyor.yml
+++ b/.appveyor.yml
@@ -6,8 +6,7 @@ branches:
     - version1.0
 
 environment:
-  matrix:
-    - PYTHON_VERSION: "3.6"
+  PYTHON_VERSION: "3.6"
 
 
 # Do not use MSBuild

From e9000d7c4e84f4dfe56e8cd1d718ae72be5913f5 Mon Sep 17 00:00:00 2001
From: WilliamHPNielsen <william@nbi.ku.dk>
Date: Tue, 10 Apr 2018 12:45:38 +0200
Subject: [PATCH 04/15] Use conda to manage appveyor python version

---
 .appveyor.yml | 8 ++++++--
 1 file changed, 6 insertions(+), 2 deletions(-)

diff --git a/.appveyor.yml b/.appveyor.yml
index c110d64c7..0ff7949b3 100644
--- a/.appveyor.yml
+++ b/.appveyor.yml
@@ -6,8 +6,7 @@ branches:
     - version1.0
 
 environment:
-  PYTHON_VERSION: "3.6"
-
+  - CONDA_INSTALL_LOCATION: "C:\\Miniconda36-x64"
 
 # Do not use MSBuild
 build: false
@@ -16,6 +15,11 @@ build: false
 
 # Install scripts
 install:
+  - set PATH=%CONDA_INSTALL_LOCN%;%CONDA_INSTALL_LOCN%\scripts;%PATH%;
+  - conda update --all
+  - conda info -a
+  - conda create -q -n test-environment python=%PYTHON_VERSION% pip setuptools
+  - conda activate test-environment
   - python -m pip install --upgrade pip
   - pip install -r test_requirements.txt
   - pip install .

From 445f65c5ff6912a7d88a564ccfe28fce95d1ebf9 Mon Sep 17 00:00:00 2001
From: WilliamHPNielsen <william@nbi.ku.dk>
Date: Tue, 10 Apr 2018 12:47:13 +0200
Subject: [PATCH 05/15] Fix yaml syntax typo

---
 .appveyor.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.appveyor.yml b/.appveyor.yml
index 0ff7949b3..05babe0a2 100644
--- a/.appveyor.yml
+++ b/.appveyor.yml
@@ -6,7 +6,7 @@ branches:
     - version1.0
 
 environment:
-  - CONDA_INSTALL_LOCATION: "C:\\Miniconda36-x64"
+  CONDA_INSTALL_LOCATION: "C:\\Miniconda36-x64"
 
 # Do not use MSBuild
 build: false

From 93e38a6329a6958783166ef92ba09cc29593141c Mon Sep 17 00:00:00 2001
From: WilliamHPNielsen <william@nbi.ku.dk>
Date: Tue, 10 Apr 2018 12:54:56 +0200
Subject: [PATCH 06/15] Make the conda install path globally known

---
 .appveyor.yml | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/.appveyor.yml b/.appveyor.yml
index 05babe0a2..d5e2908ae 100644
--- a/.appveyor.yml
+++ b/.appveyor.yml
@@ -6,7 +6,8 @@ branches:
     - version1.0
 
 environment:
-  CONDA_INSTALL_LOCATION: "C:\\Miniconda36-x64"
+  global:
+    CONDA_INSTALL_LOCATION: "C:\\Miniconda36-x64"
 
 # Do not use MSBuild
 build: false

From 2108ef272c7bfb27e889d1d4acac48b5bbec5878 Mon Sep 17 00:00:00 2001
From: WilliamHPNielsen <william@nbi.ku.dk>
Date: Tue, 10 Apr 2018 12:56:01 +0200
Subject: [PATCH 07/15] Fix typo

---
 .appveyor.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.appveyor.yml b/.appveyor.yml
index d5e2908ae..71752c6cb 100644
--- a/.appveyor.yml
+++ b/.appveyor.yml
@@ -16,7 +16,7 @@ build: false
 
 # Install scripts
 install:
-  - set PATH=%CONDA_INSTALL_LOCN%;%CONDA_INSTALL_LOCN%\scripts;%PATH%;
+  - set PATH=%CONDA_INSTALL_LOCATION%;%CONDA_INSTALL_LOCATION%\scripts;%PATH%;
   - conda update --all
   - conda info -a
   - conda create -q -n test-environment python=%PYTHON_VERSION% pip setuptools

From fecb49f6065204bd58592bf07a38a8889e0ba519 Mon Sep 17 00:00:00 2001
From: WilliamHPNielsen <william@nbi.ku.dk>
Date: Tue, 10 Apr 2018 12:58:22 +0200
Subject: [PATCH 08/15] Make conda always yes

---
 .appveyor.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.appveyor.yml b/.appveyor.yml
index 71752c6cb..743653e0b 100644
--- a/.appveyor.yml
+++ b/.appveyor.yml
@@ -17,6 +17,7 @@ build: false
 # Install scripts
 install:
   - set PATH=%CONDA_INSTALL_LOCATION%;%CONDA_INSTALL_LOCATION%\scripts;%PATH%;
+  - conda config --set always_yes true  # else AppVeyor will hang forever waiting for user ([y]/n)
   - conda update --all
   - conda info -a
   - conda create -q -n test-environment python=%PYTHON_VERSION% pip setuptools

From 0a682a8d8b30e1a588a9b054c08a30e0939ee951 Mon Sep 17 00:00:00 2001
From: WilliamHPNielsen <william@nbi.ku.dk>
Date: Tue, 10 Apr 2018 13:01:04 +0200
Subject: [PATCH 09/15] Don't use conda for env activation

---
 .appveyor.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.appveyor.yml b/.appveyor.yml
index 743653e0b..817dc684c 100644
--- a/.appveyor.yml
+++ b/.appveyor.yml
@@ -21,7 +21,7 @@ install:
   - conda update --all
   - conda info -a
   - conda create -q -n test-environment python=%PYTHON_VERSION% pip setuptools
-  - conda activate test-environment
+  - activate test-environment
   - python -m pip install --upgrade pip
   - pip install -r test_requirements.txt
   - pip install .

From 05f3b0bc708fb260a8e196c2b3e406ffc5966856 Mon Sep 17 00:00:00 2001
From: WilliamHPNielsen <william@nbi.ku.dk>
Date: Tue, 10 Apr 2018 13:06:39 +0200
Subject: [PATCH 10/15] Make appveyor also execute notebooks

---
 .appveyor.yml | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/.appveyor.yml b/.appveyor.yml
index 817dc684c..2d4291cf8 100644
--- a/.appveyor.yml
+++ b/.appveyor.yml
@@ -31,3 +31,5 @@ test_script:
   - mypy broadbean --ignore-missing-imports
   - cd tests
   - pytest
+  - cd ../docs
+  - make execute

From 685dd90c71546f80504632608d83e7e08785f7b5 Mon Sep 17 00:00:00 2001
From: WilliamHPNielsen <william@nbi.ku.dk>
Date: Tue, 10 Apr 2018 13:39:39 +0200
Subject: [PATCH 11/15] Make appveyor execute notebooks with no makefile

Because makefiles don't run on windows. I was blissfully unaware of that.
---
 .appveyor.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.appveyor.yml b/.appveyor.yml
index 2d4291cf8..1d5757b92 100644
--- a/.appveyor.yml
+++ b/.appveyor.yml
@@ -32,4 +32,4 @@ test_script:
   - cd tests
   - pytest
   - cd ../docs
-  - make execute
+  - execute_notebooks.cmd

From f39d243b4d6969ec5241f40605e8a2a239d20d91 Mon Sep 17 00:00:00 2001
From: WilliamHPNielsen <william@nbi.ku.dk>
Date: Tue, 10 Apr 2018 13:44:15 +0200
Subject: [PATCH 12/15] Include the cmd script for notebook execution

---
 docs/execute_notebooks.cmd | 6 ++++++
 1 file changed, 6 insertions(+)
 create mode 100644 docs/execute_notebooks.cmd

diff --git a/docs/execute_notebooks.cmd b/docs/execute_notebooks.cmd
new file mode 100644
index 000000000..f5755eb42
--- /dev/null
+++ b/docs/execute_notebooks.cmd
@@ -0,0 +1,6 @@
+echo "Running the notebooks..."
+jupyter nbconvert --to notebook --execute "Pulse Building Tutorial.ipynb"
+jupyter nbconvert --to notebook --execute "Filter compensation.ipynb"
+jupyter nbconvert --to notebook --execute "Subsequences.ipynb"
+echo "Cleaning up the generated output..."
+rm *nbconvert.ipynb

From 595e4381f4609ac0caaf59b9122250382432587f Mon Sep 17 00:00:00 2001
From: WilliamHPNielsen <william@nbi.ku.dk>
Date: Tue, 10 Apr 2018 13:55:27 +0200
Subject: [PATCH 13/15] Turn off email notifications

---
 .appveyor.yml | 8 ++++++++
 1 file changed, 8 insertions(+)

diff --git a/.appveyor.yml b/.appveyor.yml
index 1d5757b92..4fd991be4 100644
--- a/.appveyor.yml
+++ b/.appveyor.yml
@@ -9,6 +9,14 @@ environment:
   global:
     CONDA_INSTALL_LOCATION: "C:\\Miniconda36-x64"
 
+# Do not email the poor devs!
+notifications:
+  - provider: Email
+    settings:
+      on_build_success: false
+      on_build_failure: false
+      on_build_status_changed: false
+
 # Do not use MSBuild
 build: false
 

From 5d059d160a583e6c55e1a6daf12c4a8eb85e4e82 Mon Sep 17 00:00:00 2001
From: WilliamHPNielsen <william@nbi.ku.dk>
Date: Tue, 10 Apr 2018 13:56:59 +0200
Subject: [PATCH 14/15] Move email notifications to AppVeyor settings

So as to not expose email addresses in public yml files
---
 .appveyor.yml | 8 --------
 1 file changed, 8 deletions(-)

diff --git a/.appveyor.yml b/.appveyor.yml
index 4fd991be4..1d5757b92 100644
--- a/.appveyor.yml
+++ b/.appveyor.yml
@@ -9,14 +9,6 @@ environment:
   global:
     CONDA_INSTALL_LOCATION: "C:\\Miniconda36-x64"
 
-# Do not email the poor devs!
-notifications:
-  - provider: Email
-    settings:
-      on_build_success: false
-      on_build_failure: false
-      on_build_status_changed: false
-
 # Do not use MSBuild
 build: false
 

From fe4e1fe90d959616871936a4742e7ea90caf65c1 Mon Sep 17 00:00:00 2001
From: WilliamHPNielsen <william@nbi.ku.dk>
Date: Tue, 10 Apr 2018 14:10:34 +0200
Subject: [PATCH 15/15] Only conda update conda

---
 .appveyor.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.appveyor.yml b/.appveyor.yml
index 1d5757b92..7845e3658 100644
--- a/.appveyor.yml
+++ b/.appveyor.yml
@@ -18,7 +18,7 @@ build: false
 install:
   - set PATH=%CONDA_INSTALL_LOCATION%;%CONDA_INSTALL_LOCATION%\scripts;%PATH%;
   - conda config --set always_yes true  # else AppVeyor will hang forever waiting for user ([y]/n)
-  - conda update --all
+  - conda update -n base conda
   - conda info -a
   - conda create -q -n test-environment python=%PYTHON_VERSION% pip setuptools
   - activate test-environment