Merge pull request #9 from darribas/master

Adding `jupytext` workflow
gdsbook · May 11, 2019 · d17d4dd · d17d4dd
2 parents 7a45f1e + ab7114f
commit d17d4dd
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diff --git a/Makefile b/Makefile
@@ -1,10 +1,15 @@
 container:
 	docker build -t gdsbook ./infrastructure/docker/
-booksite:
-	docker run --rm -v ${PWD}:/home/jovyan/host gdsbook start.sh sh -c "\
+lab:
+	docker run --rm -p 8888:8888 -v ${PWD}:/home/jovyan/host gdsbook
+sync: 
+	docker run --rm --user root -e NB_UID=1001 -e NB_GID=100 -v ${PWD}:/home/jovyan/host gdsbook start.sh sh -c "\
+		jupytext --sync ./host/notebooks/*.ipynb"
+booksite: sync
+	docker run --rm --user root -e NB_UID=1001 -e NB_GID=100 -v ${PWD}:/home/jovyan/host gdsbook start.sh sh -c "\
 		sed -i -e 's/\r$$//' host/infrastructure/booksite/build.sh && \
 		bash ./host/infrastructure/booksite/build.sh"
 bookserve:
 	# serve docs folder locally
-	docker run --rm -ti -p 4000:4000 -v ${PWD}:/home/jovyan/host gdsbook \
+	docker run --rm -ti --user root -e NB_UID=1001 -e NB_GID=100 -p 4000:4000 -v ${PWD}:/home/jovyan/host gdsbook \
 		start.sh sh -c "cd host/docs && bundle exec jekyll serve --host 0.0.0.0"
diff --git a/README.md b/README.md
@@ -3,27 +3,7 @@ Stack"
 
 ## Table of Contents
 
-Introduction
-
-### Part I Building Blocks
-- 01 | [Geospatial Computational Environment](src/geospatial_computational_environment.ipynb)
-- 02 | [Spatial Data](src/spatial_data.ipynb)
-- 03 | [Spatial Data Processing](src/spatial_data_processing.ipynb)
-- 04 | [Spatial Weights](src/weights.ipynb)
-
-
-### Part II Spatial Data Analysis
-- 05 | [Choropleth Mapping](src/05_choropleth.ipynb)
-- 06 | [Spatial Autocorrelation](src/global_autocorrelation.ipynb)
-- 07 | [Local Autocorrelation Analysis](https://github.com/sjsrey/gds/blob/master/src/07_local_autocorrelation.ipynb)
-- 08 | [Point Pattern Analysis](src/points.ipynb)
-
-### Part III Advanced Topics
-- 09 | [Clustering and Regionalization](src/clustering_and_regionalization.ipynb)
-- 10 | [Spatial Inequality Analysis](src/inequality.ipynb)
-- 11 | [Spatial Regression](src/regression.ipynb)
-
-Corollary: everything we didn't cover
+Check the [current table of contents](notebooks/00_toc.md).
 
 ## Resources
 

diff --git a/docs/Gemfile.lock b/docs/Gemfile.lock
@@ -33,33 +33,33 @@ GEM
     em-websocket (0.5.1)
       eventmachine (>= 0.12.9)
       http_parser.rb (~> 0.6.0)
-    ethon (0.11.0)
+    ethon (0.12.0)
       ffi (>= 1.3.0)
     eventmachine (1.2.7)
     execjs (2.7.0)
     faraday (0.15.4)
       multipart-post (>= 1.2, < 3)
-    ffi (1.9.25)
+    ffi (1.10.0)
     formatador (0.2.5)
     forwardable-extended (2.6.0)
     gemoji (3.0.0)
-    github-pages (193)
+    github-pages (197)
       activesupport (= 4.2.10)
-      github-pages-health-check (= 1.8.1)
+      github-pages-health-check (= 1.16.1)
       jekyll (= 3.7.4)
       jekyll-avatar (= 0.6.0)
       jekyll-coffeescript (= 1.1.1)
       jekyll-commonmark-ghpages (= 0.1.5)
       jekyll-default-layout (= 0.1.4)
       jekyll-feed (= 0.11.0)
       jekyll-gist (= 1.5.0)
-      jekyll-github-metadata (= 2.9.4)
+      jekyll-github-metadata (= 2.12.1)
       jekyll-mentions (= 1.4.1)
       jekyll-optional-front-matter (= 0.3.0)
       jekyll-paginate (= 1.1.0)
       jekyll-readme-index (= 0.2.0)
       jekyll-redirect-from (= 0.14.0)
-      jekyll-relative-links (= 0.5.3)
+      jekyll-relative-links (= 0.6.0)
       jekyll-remote-theme (= 0.3.1)
       jekyll-sass-converter (= 1.5.2)
       jekyll-seo-tag (= 2.5.0)
@@ -79,20 +79,20 @@ GEM
       jekyll-theme-tactile (= 0.1.1)
       jekyll-theme-time-machine (= 0.1.1)
       jekyll-titles-from-headings (= 0.5.1)
-      jemoji (= 0.10.1)
+      jemoji (= 0.10.2)
       kramdown (= 1.17.0)
       liquid (= 4.0.0)
       listen (= 3.1.5)
       mercenary (~> 0.3)
       minima (= 2.5.0)
-      nokogiri (>= 1.8.2, < 2.0)
+      nokogiri (>= 1.8.5, < 2.0)
       rouge (= 2.2.1)
       terminal-table (~> 1.4)
-    github-pages-health-check (1.8.1)
+    github-pages-health-check (1.16.1)
       addressable (~> 2.3)
       dnsruby (~> 1.60)
       octokit (~> 4.0)
-      public_suffix (~> 2.0)
+      public_suffix (~> 3.0)
       typhoeus (~> 1.3)
     guard (2.14.2)
       formatador (>= 0.2.4)
@@ -113,7 +113,7 @@ GEM
       guard (~> 2.8)
       guard-compat (~> 1.0)
       multi_json (~> 1.8)
-    html-pipeline (2.9.1)
+    html-pipeline (2.10.0)
       activesupport (>= 2)
       nokogiri (>= 1.4)
     http_parser.rb (0.6.0)
@@ -150,8 +150,8 @@ GEM
       jekyll (~> 3.3)
     jekyll-gist (1.5.0)
       octokit (~> 4.2)
-    jekyll-github-metadata (2.9.4)
-      jekyll (~> 3.1)
+    jekyll-github-metadata (2.12.1)
+      jekyll (~> 3.4)
       octokit (~> 4.0, != 4.4.0)
     jekyll-mentions (1.4.1)
       html-pipeline (~> 2.3)
@@ -163,7 +163,7 @@ GEM
       jekyll (~> 3.0)
     jekyll-redirect-from (0.14.0)
       jekyll (~> 3.3)
-    jekyll-relative-links (0.5.3)
+    jekyll-relative-links (0.6.0)
       jekyll (~> 3.3)
     jekyll-remote-theme (0.3.1)
       jekyll (~> 3.5)
@@ -224,7 +224,7 @@ GEM
       jekyll (~> 3.3)
     jekyll-watch (2.1.2)
       listen (~> 3.0)
-    jemoji (0.10.1)
+    jemoji (0.10.2)
       gemoji (~> 3.0)
       html-pipeline (~> 2.2)
       jekyll (~> 3.0)
@@ -248,7 +248,7 @@ GEM
     multipart-post (2.0.0)
     namae (1.0.1)
     nenv (0.3.0)
-    nokogiri (1.9.1)
+    nokogiri (1.10.1)
       mini_portile2 (~> 2.4.0)
     notiffany (0.1.1)
       nenv (~> 0.1)
@@ -260,7 +260,7 @@ GEM
     pry (0.12.2)
       coderay (~> 1.1.0)
       method_source (~> 0.9.0)
-    public_suffix (2.0.5)
+    public_suffix (3.0.3)
     rb-fsevent (0.10.3)
     rb-inotify (0.10.0)
       ffi (~> 1.0)
@@ -269,8 +269,8 @@ GEM
       i18n
     ruby_dep (1.5.0)
     rubyzip (1.2.2)
-    safe_yaml (1.0.4)
-    sass (3.7.2)
+    safe_yaml (1.0.5)
+    sass (3.7.3)
       sass-listen (~> 4.0.0)
     sass-listen (4.0.0)
       rb-fsevent (~> 0.9, >= 0.9.4)
@@ -287,7 +287,7 @@ GEM
       ethon (>= 0.9.0)
     tzinfo (1.2.5)
       thread_safe (~> 0.1)
-    unicode-display_width (1.4.1)
+    unicode-display_width (1.5.0)
 
 PLATFORMS
   ruby
@@ -303,4 +303,4 @@ DEPENDENCIES
   tzinfo-data
 
 BUNDLED WITH
-   1.17.2
+   2.0.1
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diff --git a/docs/_build/images/notebooks/04_spatial_weights_94_0.png b/docs/_build/images/notebooks/04_spatial_weights_94_0.png
diff --git a/...ebooks/06_global_autocorrelation_16_0.png → ...books/06_spatial_autocorrelation_16_0.png b/...ebooks/06_global_autocorrelation_16_0.png → ...books/06_spatial_autocorrelation_16_0.png
diff --git a/...ebooks/06_global_autocorrelation_27_0.png → ...books/06_spatial_autocorrelation_27_0.png b/...ebooks/06_global_autocorrelation_27_0.png → ...books/06_spatial_autocorrelation_27_0.png
diff --git a/...ebooks/06_global_autocorrelation_32_0.png → ...books/06_spatial_autocorrelation_32_0.png b/...ebooks/06_global_autocorrelation_32_0.png → ...books/06_spatial_autocorrelation_32_0.png
diff --git a/...ebooks/06_global_autocorrelation_59_0.png → ...books/06_spatial_autocorrelation_59_0.png b/...ebooks/06_global_autocorrelation_59_0.png → ...books/06_spatial_autocorrelation_59_0.png
diff --git a/...ebooks/06_global_autocorrelation_68_0.png → ...books/06_spatial_autocorrelation_68_0.png b/...ebooks/06_global_autocorrelation_68_0.png → ...books/06_spatial_autocorrelation_68_0.png
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diff --git a/docs/_build/images/notebooks/10_clustering_and_regionalization_56_0.png b/docs/_build/images/notebooks/10_clustering_and_regionalization_56_0.png
diff --git a/docs/_build/images/notebooks/10_clustering_and_regionalization_58_0.png b/docs/_build/images/notebooks/10_clustering_and_regionalization_58_0.png
diff --git a/docs/_build/images/notebooks/10_clustering_and_regionalization_60_0.png b/docs/_build/images/notebooks/10_clustering_and_regionalization_60_0.png
diff --git a/docs/_build/images/notebooks/10_clustering_and_regionalization_64_0.png b/docs/_build/images/notebooks/10_clustering_and_regionalization_64_0.png
diff --git a/docs/_build/images/notebooks/10_clustering_and_regionalization_70_0.png b/docs/_build/images/notebooks/10_clustering_and_regionalization_70_0.png
diff --git a/docs/_build/images/notebooks/10_clustering_and_regionalization_9_0.png b/docs/_build/images/notebooks/10_clustering_and_regionalization_9_0.png
diff --git a/docs/_build/intro.md b/docs/_build/intro.md
@@ -5,7 +5,7 @@ prev_page:
   title: ''
 next_page:
   url: /notebooks/00_toc
-  title: 'Notebooks'
+  title: 'Table of Contents'
 comment: "***PROGRAMMATICALLY GENERATED, DO NOT EDIT. SEE ORIGINAL FILES IN /content***"
 ---
 # Geographic Data Science with Python

diff --git a/docs/_build/intro_part_i.md b/docs/_build/intro_part_i.md
@@ -0,0 +1,13 @@
+---
+redirect_from:
+  - "/intro-part-i"
+title: 'Part I - Building Blocks'
+prev_page:
+  url: /notebooks/00_toc
+  title: 'Table of Contents'
+next_page:
+  url: /notebooks/01_geospatial_computational_environment
+  title: 'Geospatial Computational Environment'
+comment: "***PROGRAMMATICALLY GENERATED, DO NOT EDIT. SEE ORIGINAL FILES IN /content***"
+---
+# Part I - Building Blocks
diff --git a/docs/_build/intro_part_ii.md b/docs/_build/intro_part_ii.md
@@ -0,0 +1,13 @@
+---
+redirect_from:
+  - "/intro-part-ii"
+title: 'Part II - Spatial Data Analysis'
+prev_page:
+  url: /notebooks/04_spatial_weights
+  title: 'Spatial Weights'
+next_page:
+  url: /notebooks/05_choropleth
+  title: 'Choropleth Mapping'
+comment: "***PROGRAMMATICALLY GENERATED, DO NOT EDIT. SEE ORIGINAL FILES IN /content***"
+---
+# Part II - Spatial Data Analysis
diff --git a/docs/_build/intro_part_iii.md b/docs/_build/intro_part_iii.md
@@ -0,0 +1,13 @@
+---
+redirect_from:
+  - "/intro-part-iii"
+title: 'Part III - Advanced Topics'
+prev_page:
+  url: /notebooks/08_point_pattern_analysis
+  title: 'Point Pattern Analysis'
+next_page:
+  url: /notebooks/09_spatial_inequality
+  title: 'Spatial Inequality'
+comment: "***PROGRAMMATICALLY GENERATED, DO NOT EDIT. SEE ORIGINAL FILES IN /content***"
+---
+# Part III - Advanced Topics
diff --git a/docs/_build/notebooks/00_toc.md b/docs/_build/notebooks/00_toc.md
@@ -2,38 +2,38 @@
 redirect_from:
   - "/notebooks/00-toc"
 interact_link: content/notebooks/00_toc.ipynb
-kernel_name: gdsbook
-title: 'Notebooks'
+kernel_name: python3
+has_widgets: false
+title: 'Table of Contents'
 prev_page:
   url: /intro
   title: 'Home'
 next_page:
-  url: /notebooks/05_choropleth
-  title: 'Choropleths'
+  url: /intro_part_i
+  title: 'Part I - Building Blocks'
 comment: "***PROGRAMMATICALLY GENERATED, DO NOT EDIT. SEE ORIGINAL FILES IN /content***"
 ---
 
-# Geographical Data Science with PySAL and the Python Geospatial Stack
+# Table of Contents
 
+## Part I: Building Blocks
 
-## Table of Contents
+- [Geospatial Computational Environment](01_geospatial_computational_environment)
+- [Spatial data](02_spatial_data)
+- [Spatial data processing](03_spatial_data_processing)
+- [Spatial weights](04_spatial_weights)
 
-### Part I: Building Blocks
+## Part II: Spatial Data Analysis
 
-- [Introduction](introduction.ipynb)
-- [Geospatial Computational Environment](geospatial_computational_environment.ipynb)
-- [Spatial data](spatial data.ipynb)
-- [Spatial data processing](spatial_data_processing.ipynb)
+- [Choropleth Mapping](05_choropleth)
+- [Spatial Autocorrelation](06_spatial_autocorrelation)
+- [Local Spatial Autocorrelation](07_local_autocorrelation)
+- [Point Pattern Analysis](08_point_pattern_analysis)
 
-### Part II: Spatial Data Analysis
-- [Choropleth Mapping](choropleth.ipynb)
-- [Global Spatial Autocorrelation Analysis](sp_autocorrelation.ipynb)
-- Local Autocorrelation Analysis
-- Point Pattern Analysis
+## Part III: Advanced Topics
 
-
-### Part III: Advanced Topics
-- [Clustering and Regionalization](clustering_and_regionalization.ipynb)
-- Spatial Inequality Analysis
-- Spatial Regression
+- [Spatial Inequality](09_spatial_inequality)
+- [Clustering and Regionalization](10_clustering_and_regionalization)
+- [Spatial Regression](11_regression)
+- [Spatial Feature Engineering](12_feature_engineering)