Reorganizing material to put novice + intermediate at top level

swcarpentry · Feb 16, 2014 · b8c7dc3 · b8c7dc3
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diff --git a/Makefile b/Makefile
@@ -17,15 +17,17 @@ MARKDOWN_SRC = \
 	rules.md \
 	setup.md \
 	team.md \
-	$(wildcard shell/novice/*.md) \
-	$(wildcard git/novice/*.md) \
-	$(wildcard python/novice/*.md) \
-	$(wildcard sql/novice/*.md) \
-	$(wildcard teaching/novice/*.md)
+	$(wildcard novice/shell/*.md) \
+	$(wildcard novice/git/*.md) \
+	$(wildcard novice/python/*.md) \
+	$(wildcard novice/sql/*.md) \
+	$(wildcard novice/extras/*.md) \
+	$(wildcard novice/teaching/*.md) \
+	$(wildcard novice/ref/*.md)
 
 NOTEBOOK_SRC = \
-	$(wildcard python/novice/??-*.ipynb) \
-	$(wildcard sql/novice/??-*.ipynb)
+	$(wildcard novice/python/??-*.ipynb) \
+	$(wildcard novice/sql/??-*.ipynb)
 
 # Slides.
 SLIDES_SRC = \
@@ -40,15 +42,16 @@ HTML_DST = \
 	$(patsubst %.md,$(OUT)/%.html,$(MARKDOWN_SRC)) \
 	$(patsubst %.md,$(OUT)/%.html,$(NOTEBOOK_MD))
 
+# Source for book (in order, with some substutitions).
 BOOK_SRC = \
 	intro.md \
-	shell/novice/index.md $(wildcard shell/novice/*-*.md) \
-	git/novice/index.md $(wildcard git/novice/*-*.md) \
-	python/novice/index.md $(patsubst %.ipynb,%.md,$(wildcard python/novice/??-*.ipynb)) \
-	sql/novice/index.md $(patsubst %.ipynb,%.md,$(wildcard sql/novice/??-*.ipynb)) \
-	extras/novice/index.md $(wildcard extras/novice/*-*.md) \
-	teaching/novice/index.md  $(wildcard teaching/novice/*-*.md) \
-	ref/novice/index.md  $(wildcard ref/novice/*-*.md) \
+	novice/shell/index.md $(wildcard novice/shell/*-*.md) \
+	novice/git/index.md $(wildcard novice/git/*-*.md) \
+	novice/python/index.md $(patsubst %.ipynb,%.md,$(wildcard novice/python/??-*.ipynb)) \
+	novice/sql/index.md $(patsubst %.ipynb,%.md,$(wildcard novice/sql/??-*.ipynb)) \
+	novice/extras/index.md $(wildcard novice/extras/*-*.md) \
+	novice/teaching/index.md  $(wildcard novice/teaching/*-*.md) \
+	novice/ref/index.md  $(wildcard novice/ref/*-*.md) \
 	bib.md \
 	tmp/gloss.md \
 	rules.md \
@@ -92,7 +95,7 @@ $(BOOK_DST) : $(OUT)/index.html $(BOOK_TMP) _templates/book.tpl tmp/gloss.md bin
 # Build HTML versions of Markdown source files using Jekyll.
 $(OUT)/index.html : $(MARKDOWN_SRC) $(NOTEBOOK_MD)
 	jekyll -t build -d $(OUT)
-	sed -i -e 's!img src="python/novice/!img src="!g' $(OUT)/python/novice/??-*.html
+	sed -i -e 's!img src="novice/python/!img src="!g' $(OUT)/novice/python/??-*.html
 
 # Build Markdown versions of IPython Notebooks.
 %.md : %.ipynb _templates/ipynb.tpl
@@ -104,25 +107,25 @@ tmp/gloss.md : gloss.md
 	sed -e 's!](#!](#g:!g' -e 's!<a name="!<a name="#g:!g' $< > $@
 
 # Patch image paths in the sections.
-tmp/shell/novice/%.md : shell/novice/%.md
+tmp/novice/shell/%.md : novice/shell/%.md
 	@mkdir -p $$(dirname $@)
-	sed -e 's!<img src="img!<img src="shell/novice/img!g' $< > $@
+	sed -e 's!<img src="img!<img src="novice/shell/img!g' $< > $@
 
-tmp/git/novice/%.md : git/novice/%.md
+tmp/novice/git/%.md : novice/git/%.md
 	@mkdir -p $$(dirname $@)
-	sed -e 's!<img src="img!<img src="git/novice/img!g' $< > $@
+	sed -e 's!<img src="img!<img src="novice/git/img!g' $< > $@
 
-tmp/python/novice/%.md : python/novice/%.md
+tmp/novice/python/%.md : novice/python/%.md
 	@mkdir -p $$(dirname $@)
-	sed -e 's!<img src="img!<img src="python/novice/img!g' $< > $@
+	sed -e 's!<img src="img!<img src="novice/python/img!g' $< > $@
 
-tmp/sql/novice/%.md : sql/novice/%.md
+tmp/novice/sql/%.md : novice/sql/%.md
 	@mkdir -p $$(dirname $@)
-	sed -e 's!<img src="img!<img src="sql/novice/img!g' $< > $@
+	sed -e 's!<img src="img!<img src="novice/sql/img!g' $< > $@
 
-tmp/extras/novice/%.md : extras/novice/%.md
+tmp/novice/extras/%.md : novice/extras/%.md
 	@mkdir -p $$(dirname $@)
-	sed -e 's!<img src="img!<img src="extras/novice/img!g' $< > $@
+	sed -e 's!<img src="img!<img src="novice/extras/img!g' $< > $@
 
 # All other Markdown files used in the book.
 tmp/%.md : %.md

diff --git a/README.md b/README.md
@@ -313,61 +313,49 @@ Reorganize, rewrite, or delete this material as you think best.
 Lesson Material
 ---------------
 
-*   Our old lesson material,
-    which we plan to retire in Spring 2014,
+*   Our old lesson material
     is in the `lessons` directory.
-
-*   The new material for novices is in the directories
-    `shell/novice`, `python/novice`, `git/novice`, and `sql/novice`.
+    We plan to retire it in Spring 2014,
+*   The new material for novices is in the directories under `novice`.
     The shell and Git materials are written in Markdown,
     while the Python and SQL use the IPython Notebook.
-
 *   New material for intermediate learners is currently under development
-    in directories called `*/intermediate`.
-
-*   Our R material is in `lessons/misc-R`;
-    we are currently working to merge it into the main directory structure.
+    in directories under `intermediate`.
 
 Site Map
 --------
 
+The most important files and directories are **highlighted**.
+
 *   CITATION - how to cite Software Carpentry.
 *   CONTRIBUTING.md - how to contribute new material.
 *   LICENSE.md - our license.
 *   Makefile - rebuild this site (type `make` on its own for a list of targets).
 *   README.md - how to use this site.
+*   bib.md - bibliography.
+*   contents.md - site map used in place of `index.html` on the main web site.
+*   **gloss.md** - glossary of terms.
+*   **index.html** - template for bootcamp home pages.
+*   intro.md - introduction to book version of this site.
+*   rules.md - the rules of programming (used in the book version of this site).
+*   **team.md** - who we are.
 *   _config.yml - Jekyll configuration directives.
 *   _includes/ - snippets of HTML that can be included in other files by Jekyll.
 *   _layouts/ - Jekyll page layouts.
-*   _site/ - output directory when building the site locally.
+*   **_site/** - output directory (created when building the site locally).
 *   _templates/ - template files for Pandoc conversion of IPython Notebooks.
-*   bib.md - bibliography.
 *   bin/ - miscellaneous tools used in building the site.
 *   branding/ - graphical assets related to Software Carpentry.
-*   contents.md - site map used in place of `index.html` on the main web site.
 *   css/ - CSS files for this site.
 *   data/ - miscellaneous data files used by examples.
-*   extras/ - supplementary materials included in the book version of this site.
-*   git/ - lessons on Git.
-*   gloss.md - glossary of terms.
 *   img/ - images used throughout this site.
-*   index.html - template for bootcamp home pages.
-*   intro.md - introduction to book version of this site.
+*   **intermediate/** - intermediate lesson material (under development).
 *   js/ - Javascript files used in this site.
-*   lessons/ - old lesson material.
-*   make/ - lesson on Make (intermediate only).
-*   python/ - lessons on Python.
-*   r/ - lessons on R (under construction).
-*   ref/ - reference guides.
-*   regex/ - lesson on regular expressions (intermediate only).
-*   rules.md - the rules of programming (used in the book version of this site).
+*   **lessons/** - old lesson material.
+*   **novice/** - novice lesson material.
 *   setup/ - setup tools for installing bootcamp software.
 *   setup.md - setup instructions for software used in bootcamps.
-*   shell/ - lessons on the Unix shell.
 *   slides/ - slideshows (under construction).
-*   sql/ - lessons on SQL and databases.
-*   teaching/ - instructor's guides.
-*   team.md - who we are.
 
 FAQ
 ---

diff --git a/contents.md b/contents.md
@@ -10,11 +10,11 @@ in the last four years.
 ## For Novices
 
 *   [Introduction](intro.html)
-*   [The Unix Shell](shell/novice/index.html)
-*   [Version Control with Git](git/novice/index.html)
-*   [Programming with Python](python/novice/index.html)
-*   [Using Databases and SQL](sql/novice/index.html)
-*   [A Few Extras](extras/novice/index.html)
+*   [The Unix Shell](novice/shell/index.html)
+*   [Version Control with Git](novice/git/index.html)
+*   [Programming with Python](novice/python/index.html)
+*   [Using Databases and SQL](novice/sql/index.html)
+*   [A Few Extras](novice/extras/index.html)
 
 These lessons are also available in [book form](book.html).
 

diff --git a/git/intermediate/00-intro.md → intermediate/git/00-intro.md b/git/intermediate/00-intro.md → intermediate/git/00-intro.md
diff --git a/git/intermediate/01-conversational-git.md → intermediate/git/01-conversational-git.md b/git/intermediate/01-conversational-git.md → intermediate/git/01-conversational-git.md
diff --git a/git/intermediate/README.md → intermediate/git/README.md b/git/intermediate/README.md → intermediate/git/README.md
diff --git a/git/intermediate/index.md → intermediate/git/index.md b/git/intermediate/index.md → intermediate/git/index.md
diff --git a/make/intermediate/00-intro.md → intermediate/make/00-intro.md b/make/intermediate/00-intro.md → intermediate/make/00-intro.md
diff --git a/make/intermediate/01-basics.md → intermediate/make/01-basics.md b/make/intermediate/01-basics.md → intermediate/make/01-basics.md
diff --git a/make/intermediate/02-patterns.md → intermediate/make/02-patterns.md b/make/intermediate/02-patterns.md → intermediate/make/02-patterns.md
diff --git a/make/intermediate/03-rules.md → intermediate/make/03-rules.md b/make/intermediate/03-rules.md → intermediate/make/03-rules.md
diff --git a/make/intermediate/04-macros.md → intermediate/make/04-macros.md b/make/intermediate/04-macros.md → intermediate/make/04-macros.md
diff --git a/make/intermediate/all-patterns.mk → intermediate/make/all-patterns.mk b/make/intermediate/all-patterns.mk → intermediate/make/all-patterns.mk
diff --git a/make/intermediate/config.mk → intermediate/make/config.mk b/make/intermediate/config.mk → intermediate/make/config.mk
diff --git a/make/intermediate/double.mk → intermediate/make/double.mk b/make/intermediate/double.mk → intermediate/make/double.mk
diff --git a/make/intermediate/false-dependencies.mk → intermediate/make/false-dependencies.mk b/make/intermediate/false-dependencies.mk → intermediate/make/false-dependencies.mk
diff --git a/make/intermediate/guide.md → intermediate/make/guide.md b/make/intermediate/guide.md → intermediate/make/guide.md
diff --git a/make/intermediate/hello.mk → intermediate/make/hello.mk b/make/intermediate/hello.mk → intermediate/make/hello.mk
diff --git a/make/intermediate/index.md → intermediate/make/index.md b/make/intermediate/index.md → intermediate/make/index.md
diff --git a/make/intermediate/multiple.mk → intermediate/make/multiple.mk b/make/intermediate/multiple.mk → intermediate/make/multiple.mk
diff --git a/make/intermediate/pattern-rule.mk → intermediate/make/pattern-rule.mk b/make/intermediate/pattern-rule.mk → intermediate/make/pattern-rule.mk
diff --git a/make/intermediate/phony.mk → intermediate/make/phony.mk b/make/intermediate/phony.mk → intermediate/make/phony.mk
diff --git a/make/intermediate/reference.md → intermediate/make/reference.md b/make/intermediate/reference.md → intermediate/make/reference.md
diff --git a/make/intermediate/target-variable.mk → intermediate/make/target-variable.mk b/make/intermediate/target-variable.mk → intermediate/make/target-variable.mk
diff --git a/make/intermediate/use-pattern.mk → intermediate/make/use-pattern.mk b/make/intermediate/use-pattern.mk → intermediate/make/use-pattern.mk
diff --git a/make/intermediate/variables.mk → intermediate/make/variables.mk b/make/intermediate/variables.mk → intermediate/make/variables.mk
diff --git a/make/intermediate/wildcard.mk → intermediate/make/wildcard.mk b/make/intermediate/wildcard.mk → intermediate/make/wildcard.mk
diff --git a/make/intermediate/with-include.mk → intermediate/make/with-include.mk b/make/intermediate/with-include.mk → intermediate/make/with-include.mk
diff --git a/make/intermediate/with-lots-of-macros.mk → intermediate/make/with-lots-of-macros.mk b/make/intermediate/with-lots-of-macros.mk → intermediate/make/with-lots-of-macros.mk
diff --git a/make/intermediate/with-macro.mk → intermediate/make/with-macro.mk b/make/intermediate/with-macro.mk → intermediate/make/with-macro.mk
diff --git a/python/intermediate/01-intro-python.ipynb → intermediate/python/01-intro-python.ipynb b/python/intermediate/01-intro-python.ipynb → intermediate/python/01-intro-python.ipynb
diff --git a/...ate/02-modularization-documentation.ipynb → ...hon/02-modularization-documentation.ipynb b/...ate/02-modularization-documentation.ipynb → ...hon/02-modularization-documentation.ipynb
diff --git a/python/intermediate/05-qa.ipynb → intermediate/python/05-qa.ipynb b/python/intermediate/05-qa.ipynb → intermediate/python/05-qa.ipynb
diff --git a/python/intermediate/A1_mosquito_data.csv → intermediate/python/A1_mosquito_data.csv b/python/intermediate/A1_mosquito_data.csv → intermediate/python/A1_mosquito_data.csv
diff --git a/python/intermediate/A2_mosquito_data.csv → intermediate/python/A2_mosquito_data.csv b/python/intermediate/A2_mosquito_data.csv → intermediate/python/A2_mosquito_data.csv
diff --git a/python/intermediate/A3_mosquito_data.csv → intermediate/python/A3_mosquito_data.csv b/python/intermediate/A3_mosquito_data.csv → intermediate/python/A3_mosquito_data.csv
diff --git a/python/intermediate/B1_mosquito_data.csv → intermediate/python/B1_mosquito_data.csv b/python/intermediate/B1_mosquito_data.csv → intermediate/python/B1_mosquito_data.csv
diff --git a/python/intermediate/B2_mosquito_data.csv → intermediate/python/B2_mosquito_data.csv b/python/intermediate/B2_mosquito_data.csv → intermediate/python/B2_mosquito_data.csv
diff --git a/python/intermediate/README.md → intermediate/python/README.md b/python/intermediate/README.md → intermediate/python/README.md
diff --git a/.../intermediate/create_inter_python_data.py → ...ediate/python/create_inter_python_data.py b/.../intermediate/create_inter_python_data.py → ...ediate/python/create_inter_python_data.py
diff --git a/python/intermediate/ears.py → intermediate/python/ears.py b/python/intermediate/ears.py → intermediate/python/ears.py
diff --git a/python/intermediate/mosquito_data_A1.csv → intermediate/python/mosquito_data_A1.csv b/python/intermediate/mosquito_data_A1.csv → intermediate/python/mosquito_data_A1.csv
diff --git a/python/intermediate/mosquito_data_A2.csv → intermediate/python/mosquito_data_A2.csv b/python/intermediate/mosquito_data_A2.csv → intermediate/python/mosquito_data_A2.csv
diff --git a/r/intermediate/R-basics/01-basics-of-R.Rmd → intermediate/r/R-basics/01-basics-of-R.Rmd b/r/intermediate/R-basics/01-basics-of-R.Rmd → intermediate/r/R-basics/01-basics-of-R.Rmd
diff --git a/...ermediate/R-basics/02-data-structures.Rmd → ...mediate/r/R-basics/02-data-structures.Rmd b/...ermediate/R-basics/02-data-structures.Rmd → ...mediate/r/R-basics/02-data-structures.Rmd
diff --git a/...iate/R-basics/02-data-structures.Rmd.orig → ...te/r/R-basics/02-data-structures.Rmd.orig b/...iate/R-basics/02-data-structures.Rmd.orig → ...te/r/R-basics/02-data-structures.Rmd.orig
diff --git a/...termediate/R-basics/03-best-practices.Rmd → ...rmediate/r/R-basics/03-best-practices.Rmd b/...termediate/R-basics/03-best-practices.Rmd → ...rmediate/r/R-basics/03-best-practices.Rmd
diff --git a/r/intermediate/R-basics/04-seeking-help.Rmd → intermediate/r/R-basics/04-seeking-help.Rmd b/r/intermediate/R-basics/04-seeking-help.Rmd → intermediate/r/R-basics/04-seeking-help.Rmd
diff --git a/r/intermediate/R-basics/05-subsetting.Rmd → intermediate/r/R-basics/05-subsetting.Rmd b/r/intermediate/R-basics/05-subsetting.Rmd → intermediate/r/R-basics/05-subsetting.Rmd
diff --git a/r/intermediate/R-basics/06-vectorization.Rmd → intermediate/r/R-basics/06-vectorization.Rmd b/r/intermediate/R-basics/06-vectorization.Rmd → intermediate/r/R-basics/06-vectorization.Rmd
diff --git a/r/intermediate/R-basics/README.md → intermediate/r/R-basics/README.md b/r/intermediate/R-basics/README.md → intermediate/r/R-basics/README.md
diff --git a/...ermediate/R-basics/additional_software.md → ...mediate/r/R-basics/additional_software.md b/...ermediate/R-basics/additional_software.md → ...mediate/r/R-basics/additional_software.md
diff --git a/r/intermediate/R-basics/best-practices.Rmd → intermediate/r/R-basics/best-practices.Rmd b/r/intermediate/R-basics/best-practices.Rmd → intermediate/r/R-basics/best-practices.Rmd
diff --git a/r/intermediate/R-basics/data-types.png → intermediate/r/R-basics/data-types.png b/r/intermediate/R-basics/data-types.png → intermediate/r/R-basics/data-types.png
diff --git a/r/intermediate/R-basics/exercise.md → intermediate/r/R-basics/exercise.md b/r/intermediate/R-basics/exercise.md → intermediate/r/R-basics/exercise.md
diff --git a/r/intermediate/R-basics/rdocumentation.png → intermediate/r/R-basics/rdocumentation.png b/r/intermediate/R-basics/rdocumentation.png → intermediate/r/R-basics/rdocumentation.png
diff --git a/r/intermediate/R-basics/rstudio-basics.Rmd → intermediate/r/R-basics/rstudio-basics.Rmd b/r/intermediate/R-basics/rstudio-basics.Rmd → intermediate/r/R-basics/rstudio-basics.Rmd
diff --git a/r/intermediate/R-basics/stackoverflow.png → intermediate/r/R-basics/stackoverflow.png b/r/intermediate/R-basics/stackoverflow.png → intermediate/r/R-basics/stackoverflow.png
diff --git a/r/intermediate/README.md → intermediate/r/README.md b/r/intermediate/README.md → intermediate/r/README.md
diff --git a/r/intermediate/chunk_options.R → intermediate/r/chunk_options.R b/r/intermediate/chunk_options.R → intermediate/r/chunk_options.R
diff --git a/...diate/data-manipulation/00-messy_data.Rmd → ...ate/r/data-manipulation/00-messy_data.Rmd b/...diate/data-manipulation/00-messy_data.Rmd → ...ate/r/data-manipulation/00-messy_data.Rmd
diff --git a/...ate/data-manipulation/01-input-output.Rmd → ...e/r/data-manipulation/01-input-output.Rmd b/...ate/data-manipulation/01-input-output.Rmd → ...e/r/data-manipulation/01-input-output.Rmd
diff --git a/...ate/data-manipulation/02-apply-family.Rmd → ...e/r/data-manipulation/02-apply-family.Rmd b/...ate/data-manipulation/02-apply-family.Rmd → ...e/r/data-manipulation/02-apply-family.Rmd
diff --git a/...iate/data-manipulation/03-split-apply.Rmd → ...te/r/data-manipulation/03-split-apply.Rmd b/...iate/data-manipulation/03-split-apply.Rmd → ...te/r/data-manipulation/03-split-apply.Rmd
diff --git a/r/intermediate/data-manipulation/README.md → intermediate/r/data-manipulation/README.md b/r/intermediate/data-manipulation/README.md → intermediate/r/data-manipulation/README.md
diff --git a/...ata-manipulation/data/baby-names2.csv.bz2 → ...ata-manipulation/data/baby-names2.csv.bz2 b/...ata-manipulation/data/baby-names2.csv.bz2 → ...ata-manipulation/data/baby-names2.csv.bz2
diff --git a/...e/data-manipulation/data/cleaned_data.csv → ...r/data-manipulation/data/cleaned_data.csv b/...e/data-manipulation/data/cleaned_data.csv → ...r/data-manipulation/data/cleaned_data.csv
diff --git a/...ediate/data-manipulation/data/climate.csv → ...iate/r/data-manipulation/data/climate.csv b/...ediate/data-manipulation/data/climate.csv → ...iate/r/data-manipulation/data/climate.csv
diff --git a/...nipulation/data/gapminderDataFiveYear.txt → ...nipulation/data/gapminderDataFiveYear.txt b/...nipulation/data/gapminderDataFiveYear.txt → ...nipulation/data/gapminderDataFiveYear.txt
diff --git a/...ediate/data-manipulation/data/mammals.csv → ...iate/r/data-manipulation/data/mammals.csv b/...ediate/data-manipulation/data/mammals.csv → ...iate/r/data-manipulation/data/mammals.csv
diff --git a/...ate/data-manipulation/data/messy_data.txt → ...e/r/data-manipulation/data/messy_data.txt b/...ate/data-manipulation/data/messy_data.txt → ...e/r/data-manipulation/data/messy_data.txt
diff --git a/r/intermediate/data-manipulation/exercise.md → intermediate/r/data-manipulation/exercise.md b/r/intermediate/data-manipulation/exercise.md → intermediate/r/data-manipulation/exercise.md
diff --git a/...te/data-manipulation/full_apply_suite.png → .../r/data-manipulation/full_apply_suite.png b/...te/data-manipulation/full_apply_suite.png → .../r/data-manipulation/full_apply_suite.png
diff --git a/...rmediate/data-manipulation/messy_data.txt → ...ediate/r/data-manipulation/messy_data.txt b/...rmediate/data-manipulation/messy_data.txt → ...ediate/r/data-manipulation/messy_data.txt
diff --git a/r/intermediate/data-manipulation/mutate.png → intermediate/r/data-manipulation/mutate.png b/r/intermediate/data-manipulation/mutate.png → intermediate/r/data-manipulation/mutate.png
diff --git a/...termediate/data-manipulation/sac_full.png → ...rmediate/r/data-manipulation/sac_full.png b/...termediate/data-manipulation/sac_full.png → ...rmediate/r/data-manipulation/sac_full.png
diff --git a/...ate/data-manipulation/sample_workflow.png → ...e/r/data-manipulation/sample_workflow.png b/...ate/data-manipulation/sample_workflow.png → ...e/r/data-manipulation/sample_workflow.png
diff --git a/...ediate/data-manipulation/split-apply1.png → ...iate/r/data-manipulation/split-apply1.png b/...ediate/data-manipulation/split-apply1.png → ...iate/r/data-manipulation/split-apply1.png
diff --git a/...rmediate/data-manipulation/splitapply.png → ...ediate/r/data-manipulation/splitapply.png b/...rmediate/data-manipulation/splitapply.png → ...ediate/r/data-manipulation/splitapply.png
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