Including the tutorials

.github/workflows/check_sphinx_build.yml

@@ -12,6 +12,8 @@ jobs:
       # https://github.com/actions/checkout
       - name: Checkout
         uses: actions/checkout@v2
+        with:
+          submodules: true
 
       - name: Install Conda environment from environment.yml
         uses: mamba-org/provision-with-micromamba@v11

.github/workflows/deploy-docs.yml

@@ -8,6 +8,8 @@ jobs:
 
     steps:
       - uses: actions/checkout@v2
+        with:
+          submodules: true
 
       - name: Install Conda environment from environment.yml
         uses: mamba-org/provision-with-micromamba@v11

.gitmodules

@@ -0,0 +1,4 @@
+[submodule "ohw22/tutorials"]
+	path = ohw22/tutorials
+	url = https://github.com/oceanhackweek/ohw-tutorials.git
+	branch = OHW22

Makefile

@@ -13,7 +13,7 @@ help:
 	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
 
 live:
-	sphinx-autobuild --ignore '_build/**/*' --ignore '**/.ipynb_checkpoints/*' --ignore 'jupyter_execute/**/*' -b dirhtml  . _build/dirhtml/
+	sphinx-autobuild --re-ignore '_build\/jupyter_execute\/.*' --ignore '_build/jupyter_execute/**/*' --ignore '**/.ipynb_checkpoints/*' --ignore 'jupyter_execute/**/*' -b dirhtml  . _build/dirhtml/
 
 .PHONY: help Makefile
 

conf.py

@@ -41,6 +41,7 @@
     "README.md",
     "jupyter_execute/**/*",
     "_InstructionSiteUpdates.md",
+    "_build/**"
 ]
 
 # If true, "Created using Sphinx" is shown in the HTML footer. Default is True.
@@ -137,6 +138,13 @@
 # Temporarily stored as off until we fix it
 jupyter_execute_notebooks = "off"  # TODO test
 
+nb_custom_formats = {
+    ".Rmd": [
+        "jupytext.reads",
+        {"fmt": "Rmd"}
+    ]
+}
+
 
 def setup(app):
     app.add_css_file("custom.css")

environment.yml

@@ -6,6 +6,7 @@ dependencies:
   # website/blog building
   - myst-nb>=0.16.0
   - sphinx>= 5.0.2
+  - jupytext
   # - sphinx-panels
   - ablog>=0.10.26
   - sphinx-autobuild>=2021.3.14

ohw22/index.md

@@ -99,14 +99,15 @@ In coordination with the OHW Northwest satellite event, there will be a **[3-wee
 
 
 ```{toctree}
-:maxdepth: 2
+:maxdepth: 3
 :caption: OceanHackWeek 2022 (OHW22)
 :hidden:
 
 schedule
 Global Virtual Event <global/index>
 Regional Satellite Events <satellites>
 Organizers <organizers>
+tutorials-index/index
 ```
 
 ```{toctree}
@@ -116,7 +117,6 @@ Organizers <organizers>
 
 Logistics <../resources/logistics/index>
 Preparation <../resources/prep/index>
-Tutorials <../resources/tutorials/getting_started>
 Projects <../resources/projects/index>
 ```
 

ohw22/schedule.md

@@ -18,3 +18,9 @@ For satellite event schedules, please check out their individual pages to see ho
 - [Australia](./australia/index.md)
 - [Brazil](./brazil/index.md)
 - [Español](./espanol/index.es.md)
+
+```{toctree}
+:hidden:
+
+monday
+```

ohw22/tutorials-index/data-access-in-python.md

@@ -0,0 +1,10 @@
+# Data access in Python
+
+```{toctree}
+
+../tutorials/01-Tue/00-data-access-in-python/00-data-access.ipynb
+../tutorials/01-Tue/00-data-access-in-python/01-extras-https.ipynb
+../tutorials/01-Tue/00-data-access-in-python/02-extras-data-clean-up.ipynb
+../tutorials/01-Tue/00-data-access-in-python/03-extras-argopy-erddap.ipynb
+../tutorials/01-Tue/00-data-access-in-python/04-extras-erddapy_saildrone.ipynb
+```

ohw22/tutorials-index/data-access-in-r.md

@@ -0,0 +1,7 @@
+# Data access in R
+
+```{toctree}
+../tutorials/01-Tue/00-data-access-in-R/01_data_access.Rmd
+../tutorials/01-Tue/00-data-access-in-R/02_get_nbdc.Rmd
+../tutorials/01-Tue/00-data-access-in-R/03_get_nao.Rmd
+```

ohw22/tutorials-index/data-vis-in-python.md

@@ -0,0 +1,13 @@
+# Data visualization in Python
+
+```{toctree}
+
+../tutorials/02-Wed/01-data-visualization-in-python/tutorial/index.ipynb
+../tutorials/02-Wed/01-data-visualization-in-python/tutorial/00_Setup.ipynb
+../tutorials/02-Wed/01-data-visualization-in-python/tutorial/01_Overview.ipynb
+../tutorials/02-Wed/01-data-visualization-in-python/tutorial/02_Building_Panels.ipynb
+../tutorials/02-Wed/01-data-visualization-in-python/tutorial/03_Interlinked_Panels.ipynb
+../tutorials/02-Wed/01-data-visualization-in-python/tutorial/04_Basic_Plotting.ipynb
+../tutorials/02-Wed/01-data-visualization-in-python/tutorial/05_Composing_Plots.ipynb
+
+```

ohw22/tutorials-index/espanol/index.md

@@ -0,0 +1,6 @@
+# Espanol Tutorials
+
+```{toctree}
+python-cientifico
+../../tutorials/optional/espanol/datos-espaciales-tidy/Notas.Rmd
+```

ohw22/tutorials-index/espanol/python-cientifico.md

@@ -0,0 +1,8 @@
+# Python Cientifico
+
+```{toctree}
+Intro to Python <../../tutorials/optional/espanol/python-cientifico/intro_to_python_ohw2022.ipynb>
+Read tabular data<../../tutorials/optional/espanol/python-cientifico/read_tabulardata.ipynb>
+Intro to Plotting <../../tutorials/optional/espanol/python-cientifico/Intro_to_plot.ipynb>
+Intro to NetCDF <../../tutorials/optional/espanol/python-cientifico/intro_to_netcdf.ipynb>
+```

ohw22/tutorials-index/index.md

@@ -0,0 +1,14 @@
+# Tutorials
+
+```{toctree}
+:maxdepth: 1
+
+../../resources/tutorials/getting_started
+../tutorials/00-Mon/xarray-in-45-min.ipynb
+data-access-in-python
+data-access-in-r
+data-vis-in-python
+machine-learning-applications
+espanol/index
+../tutorials/optional/managing-conda-envs/README.md
+```

ohw22/tutorials-index/machine-learning-applications.md

@@ -0,0 +1,7 @@
+# Machine learning applications
+
+```{toctree}
+../tutorials/03-Thu/00-machine-learning/00-unsupervised-PCA.ipynb
+../tutorials/03-Thu/00-machine-learning/01-unsupervised-kmeans.ipynb
+../tutorials/03-Thu/00-machine-learning/02-supervised-knn.ipynb
+```

requirements.txt

@@ -44,6 +44,7 @@ jupyter-client==7.3.4
 jupyter-core==4.10.0
 jupyterlab-pygments==0.2.2
 jupyterlab-widgets==1.1.1
+jupytext==1.14.0
 livereload==2.6.3
 lxml==4.9.1
 markdown-it-py==2.1.0