diff --git a/.github/workflows/check_sphinx_build.yml b/.github/workflows/check_sphinx_build.yml index f6e484bc..e8e9f3ae 100644 --- a/.github/workflows/check_sphinx_build.yml +++ b/.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 diff --git a/.github/workflows/deploy-docs.yml b/.github/workflows/deploy-docs.yml index 97cd7219..c73fbb0f 100644 --- a/.github/workflows/deploy-docs.yml +++ b/.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 diff --git a/.gitmodules b/.gitmodules new file mode 100644 index 00000000..018b5e7a --- /dev/null +++ b/.gitmodules @@ -0,0 +1,4 @@ +[submodule "ohw22/tutorials"] + path = ohw22/tutorials + url = https://github.com/oceanhackweek/ohw-tutorials.git + branch = OHW22 diff --git a/Makefile b/Makefile index e7f33409..2cc8544a 100644 --- a/Makefile +++ b/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 diff --git a/conf.py b/conf.py index 32d0d689..137b718c 100644 --- a/conf.py +++ b/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") diff --git a/environment.yml b/environment.yml index 67045921..368cf857 100644 --- a/environment.yml +++ b/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 diff --git a/ohw22/index.md b/ohw22/index.md index 4787775f..52daabe4 100644 --- a/ohw22/index.md +++ b/ohw22/index.md @@ -99,7 +99,7 @@ In coordination with the OHW Northwest satellite event, there will be a **[3-wee ```{toctree} -:maxdepth: 2 +:maxdepth: 3 :caption: OceanHackWeek 2022 (OHW22) :hidden: @@ -107,6 +107,7 @@ schedule Global Virtual Event Regional Satellite Events Organizers +tutorials-index/index ``` ```{toctree} @@ -116,7 +117,6 @@ Organizers Logistics <../resources/logistics/index> Preparation <../resources/prep/index> -Tutorials <../resources/tutorials/getting_started> Projects <../resources/projects/index> ``` diff --git a/ohw22/schedule.md b/ohw22/schedule.md index 3540b22b..fcadefa9 100644 --- a/ohw22/schedule.md +++ b/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 +``` \ No newline at end of file diff --git a/ohw22/tutorials b/ohw22/tutorials new file mode 160000 index 00000000..16dfe46e --- /dev/null +++ b/ohw22/tutorials @@ -0,0 +1 @@ +Subproject commit 16dfe46eec5a39cbd0c9172c7406d44426971070 diff --git a/ohw22/tutorials-index/data-access-in-python.md b/ohw22/tutorials-index/data-access-in-python.md new file mode 100644 index 00000000..3a052621 --- /dev/null +++ b/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 +``` diff --git a/ohw22/tutorials-index/data-access-in-r.md b/ohw22/tutorials-index/data-access-in-r.md new file mode 100644 index 00000000..77f819c8 --- /dev/null +++ b/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 +``` diff --git a/ohw22/tutorials-index/data-vis-in-python.md b/ohw22/tutorials-index/data-vis-in-python.md new file mode 100644 index 00000000..092255f0 --- /dev/null +++ b/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 + +``` diff --git a/ohw22/tutorials-index/espanol/index.md b/ohw22/tutorials-index/espanol/index.md new file mode 100644 index 00000000..00af5373 --- /dev/null +++ b/ohw22/tutorials-index/espanol/index.md @@ -0,0 +1,6 @@ +# Espanol Tutorials + +```{toctree} +python-cientifico +../../tutorials/optional/espanol/datos-espaciales-tidy/Notas.Rmd +``` diff --git a/ohw22/tutorials-index/espanol/python-cientifico.md b/ohw22/tutorials-index/espanol/python-cientifico.md new file mode 100644 index 00000000..a1ddbc68 --- /dev/null +++ b/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> +``` diff --git a/ohw22/tutorials-index/index.md b/ohw22/tutorials-index/index.md new file mode 100644 index 00000000..de96dd57 --- /dev/null +++ b/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 +``` diff --git a/ohw22/tutorials-index/machine-learning-applications.md b/ohw22/tutorials-index/machine-learning-applications.md new file mode 100644 index 00000000..555b9c46 --- /dev/null +++ b/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 +``` diff --git a/requirements.txt b/requirements.txt index 949c790e..a8f99592 100644 --- a/requirements.txt +++ b/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