diff --git a/.binder/conda-linux-64.lock b/.binder/conda-linux-64.lock index 52c7501b..0d7e2068 100644 --- a/.binder/conda-linux-64.lock +++ b/.binder/conda-linux-64.lock @@ -1,6 +1,6 @@ # Generated by conda-lock. # platform: linux-64 -# input_hash: 3659b251928f7a607ddfb2d863e2f4c6594eac7359f437af5ebb09cde4a53b54 +# input_hash: 4803ba4061f07e5fb910453dcb43d87702e5cc928cd410c47bf7f357d979d578 @EXPLICIT https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81 https://conda.anaconda.org/conda-forge/noarch/_r-mutex-1.0.1-anacondar_1.tar.bz2#19f9db5f4f1b7f5ef5f6d67207f25f38 @@ -94,8 +94,8 @@ https://conda.anaconda.org/conda-forge/linux-64/libxml2-2.9.12-h72842e0_0.tar.bz https://conda.anaconda.org/conda-forge/linux-64/mpfr-4.1.0-h9202a9a_1.tar.bz2#ea9ebeddb066da8fad4a815e61b139be https://conda.anaconda.org/conda-forge/linux-64/pcre2-10.36-h032f7d1_1.tar.bz2#ffc35300e65074a386aa151f135986b8 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https://conda.anaconda.org/conda-forge/noarch/dataclasses-0.8-pyhc8e2a94_3.tar.bz2#a362b2124b06aad102e2ee4581acee7d https://conda.anaconda.org/conda-forge/noarch/decorator-5.0.9-pyhd8ed1ab_0.tar.bz2#0ae9cca42e37b5ce6267c2a2b1383546 https://conda.anaconda.org/conda-forge/noarch/defusedxml-0.7.1-pyhd8ed1ab_0.tar.bz2#961b3a227b437d82ad7054484cfa71b2 +https://conda.anaconda.org/conda-forge/noarch/distlib-0.3.2-pyhd8ed1ab_0.tar.bz2#ae8b866c376568b0342ae2c9b68f1e65 https://conda.anaconda.org/conda-forge/noarch/docopt-0.6.2-py_1.tar.bz2#a9ed63e45579cfef026a916af2bc27c9 +https://conda.anaconda.org/conda-forge/noarch/filelock-3.0.12-pyh9f0ad1d_0.tar.bz2#7544ed05bbbe9bb687bc9bcbe4d6cb46 https://conda.anaconda.org/conda-forge/win-64/freetype-2.10.4-h546665d_1.tar.bz2#1215a2e49d23da91c28d97cff8de35ea https://conda.anaconda.org/conda-forge/noarch/fsspec-2021.8.1-pyhd8ed1ab_0.tar.bz2#c91815f86a9c2ed7525e9dc78fb189e4 https://conda.anaconda.org/conda-forge/noarch/geojson-2.5.0-py_0.tar.bz2#b4a361c7b70eeda6342a54555144c419 @@ -217,7 +221,7 @@ https://conda.anaconda.org/conda-forge/noarch/python-dateutil-2.8.2-pyhd8ed1ab_0 https://conda.anaconda.org/conda-forge/win-64/python-xxhash-2.0.2-py39hb82d6ee_0.tar.bz2#07dcd7bfa1c42868991e29f67e9cb03c https://conda.anaconda.org/conda-forge/noarch/pyviz_comms-2.1.0-pyhd8ed1ab_0.tar.bz2#9b3f9639f96de0242e0d96f7862c1bc8 https://conda.anaconda.org/conda-forge/win-64/pywin32-301-py39hb82d6ee_0.tar.bz2#571edae43ee6497f18f05f7b9a8c1ecd -https://conda.anaconda.org/conda-forge/win-64/pywinpty-1.1.3-py39h99910a6_0.tar.bz2#2ac1663f4a6f051a735bfb84e8b327af +https://conda.anaconda.org/conda-forge/win-64/pywinpty-1.1.4-py39h99910a6_0.tar.bz2#76272ca42b1eebae86042bd17092b447 https://conda.anaconda.org/conda-forge/win-64/pyyaml-5.4.1-py39hb82d6ee_1.tar.bz2#5e85ee7bc18969e50dee7e6b7acce30a https://conda.anaconda.org/conda-forge/win-64/pyzmq-22.2.1-py39he46f08e_0.tar.bz2#8ccabf951d84a134fcf99d1ea8813f21 https://conda.anaconda.org/conda-forge/win-64/regex-2021.8.28-py39hb82d6ee_0.tar.bz2#61ac2f3e696f6e93ba56946faa74e8ea @@ -234,6 +238,7 @@ https://conda.anaconda.org/conda-forge/noarch/tqdm-4.62.2-pyhd8ed1ab_0.tar.bz2#1 https://conda.anaconda.org/conda-forge/noarch/traittypes-0.2.1-pyh9f0ad1d_2.tar.bz2#7d32ccb5334a6822c28af3e864550618 https://conda.anaconda.org/conda-forge/win-64/tzlocal-3.0-py39hcbf5309_2.tar.bz2#8b657420335f44f1375fb68104d93ed9 https://conda.anaconda.org/conda-forge/noarch/validators-0.18.2-pyhd3deb0d_0.tar.bz2#a805c335f2d82b3dfb2f987520aae879 +https://conda.anaconda.org/conda-forge/win-64/virtualenv-20.4.7-py39hcbf5309_0.tar.bz2#07bff9ec47f940e875a4a5e8156c6d50 https://conda.anaconda.org/conda-forge/win-64/websocket-client-0.57.0-py39hcbf5309_4.tar.bz2#51cfeb27a94f879925029be166909a7d https://conda.anaconda.org/conda-forge/win-64/win_inet_pton-1.1.0-py39hcbf5309_2.tar.bz2#10d4cf2796ef9d1a71f52056469ad587 https://conda.anaconda.org/conda-forge/noarch/zict-2.0.0-py_0.tar.bz2#4750152be22f24d695b3004c5e1712d3 @@ -246,6 +251,7 @@ https://conda.anaconda.org/conda-forge/win-64/cairo-1.16.0-hb19e0ff_1008.tar.bz2 https://conda.anaconda.org/conda-forge/win-64/cftime-1.5.0-py39h5d4886f_0.tar.bz2#d48aaaad544ec561d22c70849a3d38ba https://conda.anaconda.org/conda-forge/win-64/cryptography-3.4.7-py39hd8d06c1_0.tar.bz2#fc998c5feff8c1d8c0779f003952eda3 https://conda.anaconda.org/conda-forge/noarch/dask-core-2021.8.1-pyhd8ed1ab_0.tar.bz2#e42f775ec0e7b8ef9adc9384e0918345 +https://conda.anaconda.org/conda-forge/win-64/editdistance-s-1.0.0-py39h2e07f2f_1.tar.bz2#06e40ad809a0917a85dfeed5726be674 https://conda.anaconda.org/conda-forge/noarch/flake8-3.9.2-pyhd8ed1ab_0.tar.bz2#37d685abea0a25c921431edda02ad143 https://conda.anaconda.org/conda-forge/win-64/geotiff-1.6.0-hee96dd5_4.tar.bz2#066408151843c261eaacbac8aa66b28a https://conda.anaconda.org/conda-forge/noarch/gitpython-3.1.18-pyhd8ed1ab_0.tar.bz2#19520f600cddf466cc3551e521809b66 @@ -266,6 +272,7 @@ https://conda.anaconda.org/conda-forge/win-64/m2w64-tcl-8.6.5-3.tar.bz2#0b1ac1d1 https://conda.anaconda.org/conda-forge/noarch/markdown-3.3.4-pyhd8ed1ab_0.tar.bz2#b8054f74fbed2b282f032219f114421a https://conda.anaconda.org/conda-forge/noarch/munch-2.5.0-py_0.tar.bz2#31d9e9be500e25ff0050bc9f57a6bcd7 https://conda.anaconda.org/conda-forge/noarch/networkx-2.5-py_0.tar.bz2#d836ad8453c22192357707026ca21653 +https://conda.anaconda.org/conda-forge/noarch/nodeenv-1.6.0-pyhd8ed1ab_0.tar.bz2#0941325bf48969e2b3b19d0951740950 https://conda.anaconda.org/conda-forge/win-64/numba-0.53.1-py39hb8cd55e_1.tar.bz2#a7821d4039961e73038528bfc08358b6 https://conda.anaconda.org/conda-forge/noarch/palettable-3.3.0-py_0.tar.bz2#a6c85d491cb6a9fbf429d3ffc9bebb39 https://conda.anaconda.org/conda-forge/win-64/pandas-1.3.2-py39h2e25243_0.tar.bz2#a4c1351d3976a31d888713eeed2898aa @@ -294,6 +301,7 @@ https://conda.anaconda.org/conda-forge/win-64/cf-units-3.0.1.post0-py39h5d4886f_ https://conda.anaconda.org/conda-forge/win-64/click-completion-0.5.2-py39hcbf5309_2.tar.bz2#69273a2790de4d16fa412c875f2df231 https://conda.anaconda.org/conda-forge/win-64/distributed-2021.8.1-py39hcbf5309_0.tar.bz2#bef113c35b4ae94a65656555e3c30d01 https://conda.anaconda.org/conda-forge/noarch/geopandas-base-0.9.0-pyhd8ed1ab_1.tar.bz2#d654735553553f158da4be365fdaa51a +https://conda.anaconda.org/conda-forge/noarch/identify-2.2.13-pyhd8ed1ab_0.tar.bz2#1889223441d67f7c30327c97a78b980f https://conda.anaconda.org/conda-forge/noarch/jupyter_client-7.0.2-pyhd8ed1ab_0.tar.bz2#cd7d030433c1546300c9279c192f9b6b https://conda.anaconda.org/conda-forge/noarch/jwcrypto-0.6.0-py_0.tar.bz2#925016b84d13bb11e631560e9bb2ef12 https://conda.anaconda.org/conda-forge/win-64/m2w64-tk-8.6.5-3.tar.bz2#c2d85c85caf655893ea11b92c395b3b6 @@ -327,6 +335,7 @@ https://conda.anaconda.org/conda-forge/noarch/ndg-httpsclient-0.5.1-py_1.tar.bz2 https://conda.anaconda.org/conda-forge/noarch/paegan-1.1.4-py_1.tar.bz2#50677bb3024eb10e2823021bb9cfae93 https://conda.anaconda.org/conda-forge/noarch/pandas-flavor-0.2.0-py_0.tar.bz2#4e7641376dbfc2ca5abff209273ed37c https://conda.anaconda.org/conda-forge/noarch/pocean-core-1.9.3-py_0.tar.bz2#69cf8e4ccf9b4a0c9adeb2d1711dd531 +https://conda.anaconda.org/conda-forge/win-64/pre-commit-2.14.1-py39hcbf5309_0.tar.bz2#06e567d4564d7566b06c9725ad055e96 https://conda.anaconda.org/conda-forge/noarch/prompt-toolkit-3.0.20-pyha770c72_0.tar.bz2#98a90e847b48fc14b2d5b12e4884e8d4 https://conda.anaconda.org/conda-forge/win-64/pyqt-5.12.3-py39hcbf5309_7.tar.bz2#9a008158c8983d1df9e9cf019da574b3 https://conda.anaconda.org/conda-forge/noarch/pysgrid-0.3.5-py_0.tar.bz2#11eb6973e57bdf0f704955c9b706fd26 @@ -519,7 +528,7 @@ https://conda.anaconda.org/conda-forge/win-64/jupyter_latex_envs-1.4.6-py39hcbf5 https://conda.anaconda.org/conda-forge/win-64/jupyter_nbextensions_configurator-0.4.1-py39hcbf5309_2.tar.bz2#b57a25822fb9d478432ece82022401f2 https://conda.anaconda.org/conda-forge/noarch/nbdime-3.1.0-pyhd8ed1ab_0.tar.bz2#01a2197677952bf94a26f8995f8703fe https://conda.anaconda.org/conda-forge/noarch/octave_kernel-0.32.0-pyh9f0ad1d_0.tar.bz2#4231985039d6c7b4ccb3a3ebe1f5afd5 -https://conda.anaconda.org/conda-forge/noarch/r-bslib-0.2.5.1-r40hc72bb7e_0.tar.bz2#740da0de2bdc86e957d53ad99175c029 +https://conda.anaconda.org/conda-forge/noarch/r-bslib-0.3.0-r40hc72bb7e_0.tar.bz2#c1055589eee4dbdbe6a6dcb6981723ca https://conda.anaconda.org/conda-forge/win-64/r-classint-0.4_3-r40he816bda_2.tar.bz2#e08a4b5997e43a52a512a205ec45cabb https://conda.anaconda.org/conda-forge/noarch/r-crul-1.1.0-r40h785f33e_0.tar.bz2#68a8f99a232a3df76af66c0fde072964 https://conda.anaconda.org/conda-forge/noarch/r-dt-0.18-r40hc72bb7e_0.tar.bz2#63710f724d74b5521a400716da5d0aac diff --git a/.binder/environment-python_and_r.yml b/.binder/environment-python_and_r.yml index 0c33f324..f43f5df8 100644 --- a/.binder/environment-python_and_r.yml +++ b/.binder/environment-python_and_r.yml @@ -40,6 +40,7 @@ dependencies: - palettable - phantomjs - pocean-core + - pre-commit - pyoos - pyresample - pysgrid diff --git a/.binder/environment.yml b/.binder/environment.yml index b65b4ee5..c6730244 100644 --- a/.binder/environment.yml +++ b/.binder/environment.yml @@ -40,6 +40,7 @@ dependencies: - palettable - phantomjs - pocean-core + - pre-commit - pyoos - pyresample - pysgrid diff --git a/.github/workflows/deploy-docs.yml b/.github/workflows/deploy-docs.yml index 84d81326..4d6c83bf 100644 --- a/.github/workflows/deploy-docs.yml +++ b/.github/workflows/deploy-docs.yml @@ -2,36 +2,39 @@ name: Build and Deploy docs on: push: - branches: [master] + branches: + - main + pull_request: jobs: build-docs: runs-on: ubuntu-latest steps: - - uses: actions/checkout@v2 + - uses: actions/checkout@v2 - - name: Setup Conda - uses: s-weigand/setup-conda@v1 - with: - activate-conda: false - conda-channels: conda-forge + - name: Setup Conda + uses: s-weigand/setup-conda@v1 + with: + activate-conda: false + conda-channels: conda-forge - - name: Build environment - shell: bash -l {0} - run: | - conda create --name IOOS --file .binder/conda-linux-64.lock - source activate IOOS + - name: Build environment + shell: bash -l {0} + run: | + conda create --name IOOS --file .binder/conda-linux-64.lock + source activate IOOS - - name: Build documentation - shell: bash -l {0} - run: | - set -e - source activate IOOS - jupyter-book build jupyterbook + - name: Build documentation + shell: bash -l {0} + run: | + set -e + source activate IOOS + jupyter-book build jupyterbook - - name: GitHub Pages action - uses: peaceiris/actions-gh-pages@v3.6.1 - with: - github_token: ${{ secrets.GITHUB_TOKEN }} - publish_dir: jupyterbook/_build/html + - name: GitHub Pages action + if: github.ref == 'refs/heads/master' + uses: peaceiris/actions-gh-pages@v3.6.1 + with: + github_token: ${{ secrets.GITHUB_TOKEN }} + publish_dir: jupyterbook/_build/html diff --git a/.github/workflows/pre-commit.yml b/.github/workflows/pre-commit.yml index 6ecd8b68..502497e0 100644 --- a/.github/workflows/pre-commit.yml +++ b/.github/workflows/pre-commit.yml @@ -7,6 +7,6 @@ jobs: pre-commit: runs-on: ubuntu-latest steps: - - uses: actions/checkout@v2 - - uses: actions/setup-python@v2 - - uses: pre-commit/action@v2.0.0 + - uses: actions/checkout@v2 + - uses: actions/setup-python@v2 + - uses: pre-commit/action@v2.0.0 diff --git a/.github/workflows/test-env-linux.yml b/.github/workflows/test-env-linux.yml index 77df1392..1cb379ba 100644 --- a/.github/workflows/test-env-linux.yml +++ b/.github/workflows/test-env-linux.yml @@ -8,17 +8,17 @@ jobs: runs-on: ubuntu-latest steps: - - uses: actions/checkout@v2 + - uses: actions/checkout@v2 - - name: Setup Conda - uses: s-weigand/setup-conda@v1 - with: - activate-conda: false - conda-channels: conda-forge + - name: Setup Conda + uses: s-weigand/setup-conda@v1 + with: + activate-conda: false + conda-channels: conda-forge - - name: Build environment - shell: bash -l {0} - run: | - conda create --name IOOS --file .binder/conda-linux-64.lock - source activate IOOS - python -c 'import osgeo.gdal; print(dir(osgeo.gdal))' + - name: Build environment + shell: bash -l {0} + run: | + conda create --name IOOS --file .binder/conda-linux-64.lock + source activate IOOS + python -c 'import osgeo.gdal; print(dir(osgeo.gdal))' diff --git a/.github/workflows/test-env-macOS.yml b/.github/workflows/test-env-macOS.yml index 33f4e2c8..098ae8d5 100644 --- a/.github/workflows/test-env-macOS.yml +++ b/.github/workflows/test-env-macOS.yml @@ -8,17 +8,17 @@ jobs: runs-on: macos-latest steps: - - uses: actions/checkout@v2 + - uses: actions/checkout@v2 - - name: Setup Conda - uses: s-weigand/setup-conda@v1 - with: - activate-conda: false - conda-channels: conda-forge + - name: Setup Conda + uses: s-weigand/setup-conda@v1 + with: + activate-conda: false + conda-channels: conda-forge - - name: Build environment - shell: bash -l {0} - run: | - conda create --name IOOS --file .binder/conda-osx-64.lock - source activate IOOS - python -c 'import osgeo.gdal; print(dir(osgeo.gdal))' + - name: Build environment + shell: bash -l {0} + run: | + conda create --name IOOS --file .binder/conda-osx-64.lock + source activate IOOS + python -c 'import osgeo.gdal; print(dir(osgeo.gdal))' diff --git a/.github/workflows/test-env-win.yml b/.github/workflows/test-env-win.yml index f4ad516f..8b3aae38 100644 --- a/.github/workflows/test-env-win.yml +++ b/.github/workflows/test-env-win.yml @@ -8,17 +8,17 @@ jobs: runs-on: windows-latest steps: - - uses: actions/checkout@v2 + - uses: actions/checkout@v2 - - name: Setup Conda - uses: s-weigand/setup-conda@v1 - with: - activate-conda: false - conda-channels: conda-forge + - name: Setup Conda + uses: s-weigand/setup-conda@v1 + with: + activate-conda: false + conda-channels: conda-forge - - name: Build environment - shell: bash -l {0} - run: | - conda create --name IOOS --file .binder/conda-win-64.lock - source activate IOOS - python -c 'import osgeo.gdal; print(dir(osgeo.gdal))' + - name: Build environment + shell: bash -l {0} + run: | + conda create --name IOOS --file .binder/conda-win-64.lock + source activate IOOS + python -c 'import osgeo.gdal; print(dir(osgeo.gdal))' diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml index 85e6bfb8..6431183e 100644 --- a/.github/workflows/tests.yml +++ b/.github/workflows/tests.yml @@ -8,22 +8,22 @@ jobs: runs-on: ubuntu-latest steps: - - uses: actions/checkout@v2 + - uses: actions/checkout@v2 - - name: Setup Conda - uses: s-weigand/setup-conda@v1 - with: - activate-conda: false - conda-channels: conda-forge + - name: Setup Conda + uses: s-weigand/setup-conda@v1 + with: + activate-conda: false + conda-channels: conda-forge - - name: Build environment - shell: bash -l {0} - run: | - conda create --name IOOS --file .binder/conda-linux-64.lock - source activate IOOS + - name: Build environment + shell: bash -l {0} + run: | + conda create --name IOOS --file .binder/conda-linux-64.lock + source activate IOOS - - name: Notebook tests - shell: bash -l {0} - run: | - source activate IOOS - pytest --nbval --nbval-lax jupyterbook/ + - name: Notebook tests + shell: bash -l {0} + run: | + source activate IOOS + pytest --nbval --nbval-lax jupyterbook/ diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 5e394b0b..c3a5d40d 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -1,29 +1,39 @@ repos: -- repo: https://github.com/pre-commit/pre-commit-hooks - rev: v4.0.1 - hooks: - - id: trailing-whitespace - - id: check-ast - - id: debug-statements - - id: end-of-file-fixer - - id: check-docstring-first - - id: check-added-large-files - exclude_types: [yaml] + - repo: https://github.com/pre-commit/pre-commit-hooks + rev: v4.0.1 + hooks: + - id: trailing-whitespace + - id: check-ast + - id: debug-statements + - id: end-of-file-fixer + - id: check-docstring-first + - id: check-added-large-files + exclude_types: [yaml] + - id: check-docstring-first + - id: check-json + - id: check-yaml + - id: double-quote-string-fixer -- repo: https://gitlab.com/pycqa/flake8 - rev: 3.9.2 - hooks: - - id: flake8 - exclude: docs/source/conf.py - args: [--max-line-length=105] + - repo: https://github.com/pre-commit/mirrors-prettier + rev: v2.4.0 + hooks: + - id: prettier + exclude: "_templates/layout.html" -- repo: https://github.com/psf/black - rev: 21.8b0 - hooks: - - id: black - language_version: python3 + - repo: https://gitlab.com/pycqa/flake8 + rev: 3.9.2 + hooks: + - id: flake8 + exclude: docs/source/conf.py + args: [--max-line-length=105] -- repo: https://github.com/asottile/add-trailing-comma - rev: v2.1.0 - hooks: - - id: add-trailing-comma + - repo: https://github.com/psf/black + rev: 21.8b0 + hooks: + - id: black + language_version: python3 + + - repo: https://github.com/asottile/add-trailing-comma + rev: v2.1.0 + hooks: + - id: add-trailing-comma diff --git a/README.md b/README.md index b7750e92..46f4723d 100644 --- a/README.md +++ b/README.md @@ -5,6 +5,7 @@ See the rendered version at https://ioos.github.io/ioos_code_lab To suggest a notebook or ask questions please open an issue at: https://github.com/ioos/ioos_code_lab/issues ## Run on Pangeo Binder + [![Pangeo Binder](https://img.shields.io/badge/pangeo-binder-2F7651.svg?logo=data:image/png;base64,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)](https://binder.pangeo.io/v2/gh/ioos/ioos_code_lab/master) ## Citation diff --git a/jupyterbook/_config.yml b/jupyterbook/_config.yml index a7283d51..06c1b532 100644 --- a/jupyterbook/_config.yml +++ b/jupyterbook/_config.yml @@ -1,88 +1,86 @@ # Book settings -title : The U.S. Integrated Ocean Observing System (IOOS) # The title of the book. Will be placed in the left navbar. -author : IOOS # The author of the book -logo : images/IOOS_logo.png # A path to the book logo +title: The U.S. Integrated Ocean Observing System (IOOS) # The title of the book. Will be placed in the left navbar. +author: IOOS # The author of the book +logo: images/IOOS_logo.png # A path to the book logo # Patterns to skip when building the book. Can be glob-style (e.g. "*skip.ipynb") -exclude_patterns : [_build, Thumbs.db, .DS_Store, "**.ipynb_checkpoints"] +exclude_patterns: [_build, Thumbs.db, .DS_Store, "**.ipynb_checkpoints"] # Auto-exclude files not in the toc -only_build_toc_files : true +only_build_toc_files: true ####################################################################################### # Execution settings execute: - execute_notebooks : off # Whether to execute notebooks at build time. Must be one of ("auto", "force", "cache", "off") - cache : "" # A path to the jupyter cache that will be used to store execution artifacts. Defaults to `_build/.jupyter_cache/` - exclude_patterns : [] # A list of patterns to *skip* in execution (e.g. a notebook that takes a really long time) - timeout : 30 # The maximum time (in seconds) each notebook cell is allowed to run. - run_in_temp : false # If `True`, then a temporary directory will be created and used as the command working directory (cwd),otherwise the notebook's parent directory will be the cwd. - allow_errors : false # If `False`, when a code cell raises an error the execution is stopped, otherwise all cells are always run. - stderr_output : show # One of 'show', 'remove', 'remove-warn', 'warn', 'error', 'severe' + execute_notebooks: off # Whether to execute notebooks at build time. Must be one of ("auto", "force", "cache", "off") + cache: "" # A path to the jupyter cache that will be used to store execution artifacts. Defaults to `_build/.jupyter_cache/` + exclude_patterns: [] # A list of patterns to *skip* in execution (e.g. a notebook that takes a really long time) + timeout: 30 # The maximum time (in seconds) each notebook cell is allowed to run. + run_in_temp: false # If `True`, then a temporary directory will be created and used as the command working directory (cwd),otherwise the notebook's parent directory will be the cwd. + allow_errors: false # If `False`, when a code cell raises an error the execution is stopped, otherwise all cells are always run. + stderr_output: show # One of 'show', 'remove', 'remove-warn', 'warn', 'error', 'severe' ####################################################################################### # Parse and render settings parse: - myst_enable_extensions: # default extensions to enable in the myst parser. See https://myst-parser.readthedocs.io/en/latest/using/syntax-optional.html - # - amsmath + myst_enable_extensions: # default extensions to enable in the myst parser. See https://myst-parser.readthedocs.io/en/latest/using/syntax-optional.html + - amsmath - colon_fence - # - deflist + - deflist - dollarmath - # - html_admonition - # - html_image + - html_admonition + - html_image - linkify - # - replacements - # - smartquotes + - replacements + - smartquotes - substitution - myst_url_schemes : [mailto, http, https] # URI schemes that will be recognised as external URLs in Markdown links + myst_url_schemes: [mailto, http, https] # URI schemes that will be recognized as external URLs in Markdown links ####################################################################################### # HTML-specific settings html: - favicon : "images/IOOS_logo.png" # A path to a favicon image - use_edit_page_button : false # Whether to add an "edit this page" button to pages. If `true`, repository information in repository: must be filled in - use_repository_button : true # Whether to add a link to your repository button - use_issues_button : true # Whether to add an "open an issue" button - extra_navbar : IOOS # Will be displayed underneath the left navbar. - extra_footer : ioos.noaa.gov   - Facebook   - Twitter   - Contact Us
- U.S. Integrated Ocean Observing System Program
- 1315 East-West Highway
- SSMC3, 2nd Floor
- Silver Spring, MD 20910
- (240) 533-9444 - google_analytics_id : "G-546J258RCJ" - home_page_in_navbar : false # Whether to include your home page in the left Navigation Bar - baseurl : "" # The base URL where your book will be hosted. Used for creating image previews and social links. e.g.: https://mypage.com/mybook/ + favicon: "images/IOOS_logo.png" # A path to a favicon image + use_edit_page_button: false # Whether to add an "edit this page" button to pages. If `true`, repository information in repository: must be filled in + use_repository_button: true # Whether to add a link to your repository button + use_issues_button: true # Whether to add an "open an issue" button + extra_navbar: IOOS # Will be displayed underneath the left navbar. + extra_footer: ioos.noaa.gov   + Facebook   + Twitter   + Contact Us
+ U.S. Integrated Ocean Observing System Program
+ 1315 East-West Highway
+ SSMC3, 2nd Floor
+ Silver Spring, MD 20910
+ (240) 533-9444 + google_analytics_id: "G-546J258RCJ" + home_page_in_navbar: false # Whether to include your home page in the left Navigation Bar + baseurl: "" # The base URL where your book will be hosted. Used for creating image previews and social links. e.g.: https://mypage.com/mybook/ comments: - hypothesis : false - utterances : false - ####################################################################################### + hypothesis: false + utterances: false + ####################################################################################### # LaTeX-specific settings latex: - latex_engine : pdflatex # one of 'pdflatex', 'xelatex' (recommended for unicode), 'luatex', 'platex', 'uplatex' - use_jupyterbook_latex : true # use jupyterbook-latex for pdf builds as default + latex_engine: pdflatex # one of 'pdflatex', 'xelatex' (recommended for unicode), 'luatex', 'platex', 'uplatex' + use_jupyterbook_latex: true # use jupyterbook-latex for pdf builds as default ####################################################################################### # Launch button settings launch_buttons: - notebook_interface : jupyterlab # The interface interactive links will activate ["classic", "jupyterlab"] - binderhub_url : https://binder.pangeo.io # The URL of the BinderHub (e.g., https://mybinder.org) - jupyterhub_url : "" # The URL of the JupyterHub (e.g., https://datahub.berkeley.edu) - thebe : false # Add a thebe button to pages (requires the repository to run on Binder) - colab_url : "https://colab.research.google.com" # The URL of Google Colab (https://colab.research.google.com) + notebook_interface: jupyterlab # The interface interactive links will activate ["classic", "jupyterlab"] + binderhub_url: https://binder.pangeo.io # The URL of the BinderHub (e.g., https://mybinder.org) + jupyterhub_url: "" # The URL of the JupyterHub (e.g., https://datahub.berkeley.edu) + thebe: false # Add a thebe button to pages (requires the repository to run on Binder) + colab_url: "https://colab.research.google.com" # The URL of Google Colab (https://colab.research.google.com) repository: - url : https://github.com/ioos/ioos_code_lab # The URL to your book's repository - path_to_book : "jupyterbook" # A path to your book's folder, relative to the repository root. - branch : master # Which branch of the repository should be used when creating links + url: https://github.com/ioos/ioos_code_lab # The URL to your book's repository + path_to_book: "jupyterbook" # A path to your book's folder, relative to the repository root. + branch: master # Which branch of the repository should be used when creating links ####################################################################################### # Advanced and power-user settings sphinx: - extra_extensions : # A list of extra extensions to load by Sphinx (added to those already used by JB). - local_extensions : # A list of local extensions to load by sphinx specified by "name: path" items config: html_show_copyright: false diff --git a/jupyterbook/_toc.yml b/jupyterbook/_toc.yml index f084c201..95565425 100644 --- a/jupyterbook/_toc.yml +++ b/jupyterbook/_toc.yml @@ -2,38 +2,38 @@ format: jb-book root: content/intro.md title: The IOOS Data Demo Center parts: -- caption: Code Gallery - chapters: - - file: content/Code Gallery/data_access.md - sections: - - glob: content/Code Gallery/data_access_notebooks/* + - caption: Code Gallery + chapters: + - file: content/code_gallery/data_access.md + sections: + - glob: content/code_gallery/data_access_notebooks/* - - file: content/Code Gallery/data_analysis_and_visualization.md - sections: - - glob: content/Code Gallery/data_analysis_and_visualization_notebooks/* + - file: content/code_gallery/data_analysis_and_visualization.md + sections: + - glob: content/code_gallery/data_analysis_and_visualization_notebooks/* - - file: content/Code Gallery/data_management.md - sections: - - glob: content/Code Gallery/data_management_notebooks/* + - file: content/code_gallery/data_management.md + sections: + - glob: content/code_gallery/data_management_notebooks/* -- caption: Video Tutorials - chapters: - - glob: content/Video_Demo_Markdown/* + - caption: Video Tutorials + chapters: + - glob: content/Video_Demo_Markdown/* -- caption: Other Resources - chapters: - - file: content/ioos_installation_conda.md - title: Installing the IOOS Conda Environment - - url: https://help.aodn.org.au/aodn-data-tools/user-code-library/ - title: Opening netCDF files - hints from AODN - - url: http://unidata.github.io/notebook-gallery/ - title: Unidata Jupyter Notebook Gallery - - url: http://iobis.org/tutorial/ - title: Extracting and Enriching OBIS data with R - - url: https://github.com/USGS-R - title: USGS-R Examples + - caption: Other Resources + chapters: + - file: content/ioos_installation_conda.md + title: Installing the IOOS Conda Environment + - url: https://help.aodn.org.au/aodn-data-tools/user-code-library/ + title: Opening netCDF files - hints from AODN + - url: http://unidata.github.io/notebook-gallery/ + title: Unidata Jupyter Notebook Gallery + - url: http://iobis.org/tutorial/ + title: Extracting and Enriching OBIS data with R + - url: https://github.com/USGS-R + title: USGS-R Examples -- caption: Contact Us - chapters: - - file: content/contact_us.md - title: Contact Us + - caption: Contact Us + chapters: + - file: content/contact_us.md + title: Contact Us diff --git a/jupyterbook/content/Video_Demo_Markdown/glos.md b/jupyterbook/content/Video_Demo_Markdown/glos.md index 42156b24..56abf50b 100644 --- a/jupyterbook/content/Video_Demo_Markdown/glos.md +++ b/jupyterbook/content/Video_Demo_Markdown/glos.md @@ -6,6 +6,5 @@ :align: center ``` - -* [How to use the GLOS data portal](https://www.youtube.com/playlist?list=PLEK-mxRrHSZ5LkSSUyYHEy4lEXnEdNJJc) -* [How to use the GLOS boater’s tool](https://www.youtube.com/playlist?list=PLEK-mxRrHSZ6rH1qCpfpD6-rSljE8fbUC) +- [How to use the GLOS data portal](https://www.youtube.com/playlist?list=PLEK-mxRrHSZ5LkSSUyYHEy4lEXnEdNJJc) +- [How to use the GLOS boater’s tool](https://www.youtube.com/playlist?list=PLEK-mxRrHSZ6rH1qCpfpD6-rSljE8fbUC) diff --git a/jupyterbook/content/Video_Demo_Markdown/ioos.md b/jupyterbook/content/Video_Demo_Markdown/ioos.md index 76a7399b..024503c8 100644 --- a/jupyterbook/content/Video_Demo_Markdown/ioos.md +++ b/jupyterbook/content/Video_Demo_Markdown/ioos.md @@ -6,6 +6,6 @@ :align: center ``` - * [COMT Tutorial](https://www.youtube.com/watch?v=Dqc1C1HeemQ) - * [IOOS EDS Demo](https://nccospublicstor.blob.core.windows.net/ioos/ioos_demo_1280.mp4) - * [MBON Portal Tutorial](https://www.youtube.com/watch?v=ZITqDRa6u9c) +- [COMT Tutorial](https://www.youtube.com/watch?v=Dqc1C1HeemQ) +- [IOOS EDS Demo](https://nccospublicstor.blob.core.windows.net/ioos/ioos_demo_1280.mp4) +- [MBON Portal Tutorial](https://www.youtube.com/watch?v=ZITqDRa6u9c) diff --git a/jupyterbook/content/Video_Demo_Markdown/nanoos.md b/jupyterbook/content/Video_Demo_Markdown/nanoos.md index 3a4598a6..601b32ed 100644 --- a/jupyterbook/content/Video_Demo_Markdown/nanoos.md +++ b/jupyterbook/content/Video_Demo_Markdown/nanoos.md @@ -1,11 +1,10 @@ # NANOOS - ```{image} ../../images/NANOOS.png :alt: IOOS :width: 150px :align: center ``` - * [NANOOS Visualization System](https://www.youtube.com/watch?v=MEVz0jOsqmI) - * [NANOOS Data Explorer](https://www.youtube.com/playlist?list=PLBvrtRArn5ffsBARjKsczvfxyYX1wGtFP) +- [NANOOS Visualization System](https://www.youtube.com/watch?v=MEVz0jOsqmI) +- [NANOOS Data Explorer](https://www.youtube.com/playlist?list=PLBvrtRArn5ffsBARjKsczvfxyYX1wGtFP) diff --git a/jupyterbook/content/Video_Demo_Markdown/ooi.md b/jupyterbook/content/Video_Demo_Markdown/ooi.md index 3f7abcbf..d5d11225 100644 --- a/jupyterbook/content/Video_Demo_Markdown/ooi.md +++ b/jupyterbook/content/Video_Demo_Markdown/ooi.md @@ -6,4 +6,4 @@ :align: center ``` -* [Demo of OOI ERDDAP endpoint](https://www.youtube.com/watch?v=tj4M9hodTG0) +- [Demo of OOI ERDDAP endpoint](https://www.youtube.com/watch?v=tj4M9hodTG0) diff --git a/jupyterbook/content/Video_Demo_Markdown/python_dem.md b/jupyterbook/content/Video_Demo_Markdown/python_dem.md index 3e87e3c9..a9bc337a 100644 --- a/jupyterbook/content/Video_Demo_Markdown/python_dem.md +++ b/jupyterbook/content/Video_Demo_Markdown/python_dem.md @@ -5,5 +5,6 @@ :width: 150px :align: center ``` - * [Catalog Driven Reproducible Workflows for Ocean-science](https://www.youtube.com/watch?v=05ax0lkQFrg) - * [Extracting data from NOAA ERDDAP](https://www.youtube.com/watch?v=18xZoXu1USM) + +- [Catalog Driven Reproducible Workflows for Ocean-science](https://www.youtube.com/watch?v=05ax0lkQFrg) +- [Extracting data from NOAA ERDDAP](https://www.youtube.com/watch?v=18xZoXu1USM) diff --git a/jupyterbook/content/Code Gallery/data/oceans.dbf b/jupyterbook/content/code_gallery/data/oceans.dbf similarity index 100% rename from jupyterbook/content/Code Gallery/data/oceans.dbf rename to jupyterbook/content/code_gallery/data/oceans.dbf diff --git a/jupyterbook/content/Code Gallery/data/oceans.prj 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--- a/jupyterbook/content/Code Gallery/data_access_notebooks/2017-03-21-ERDDAP_IOOS_Sensor_Map.ipynb +++ b/jupyterbook/content/code_gallery/data_access_notebooks/2017-03-21-ERDDAP_IOOS_Sensor_Map.ipynb @@ -6,6 +6,15 @@ "source": [ "# Read realtime data from IOOS Sensor Map via ERDDAP tabledap\n", "\n", + "
\n", + " This notebook is stale and won't run due to missing data upstream and changes in the libraries used.\n", + "
" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ "Web Map Services are a great way to find data you may be looking for in a particular geographic area.\n", "\n", "Suppose you were exploring the [IOOS Sensor Map](https://via.hypothes.is/https://sensors.ioos.us/#map),\n", @@ -27,15 +36,6 @@ "Let's explore how that could work..." ] }, - { - "cell_type": "markdown", - "metadata": {}, - "source": [ - "
\n", - " This notebook is stale and won't run due to missing data upstream and changes in the libraries used.\n", - "
" - ] - }, { "cell_type": "code", "execution_count": 1, @@ -649,7 +649,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.9.6" + "version": "3.9.7" } }, "nbformat": 4, diff --git a/jupyterbook/content/Code Gallery/data_access_notebooks/2017-06-12-NCEI_RA_archive_history.ipynb b/jupyterbook/content/code_gallery/data_access_notebooks/2017-06-12-NCEI_RA_archive_history.ipynb similarity index 97% rename from jupyterbook/content/Code Gallery/data_access_notebooks/2017-06-12-NCEI_RA_archive_history.ipynb rename to jupyterbook/content/code_gallery/data_access_notebooks/2017-06-12-NCEI_RA_archive_history.ipynb index 8241b19d..1dc0a05b 100644 --- a/jupyterbook/content/Code Gallery/data_access_notebooks/2017-06-12-NCEI_RA_archive_history.ipynb +++ b/jupyterbook/content/code_gallery/data_access_notebooks/2017-06-12-NCEI_RA_archive_history.ipynb @@ -8,9 +8,18 @@ "source": [ "# Using NCEI geoportal REST API to collect information about IOOS Regional Association archived data\n", "\n", + "
\n", + " This notebook is stale and won't run due to missing data upstream and changes in the libraries used.\n", + "
" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ "by Mathew Biddle, Faculty Specialist, UMD/ESSIC/CICS at the NOAA National Centers for Environmental Information (NCEI)\n", "\n", - "### IOOS regional associations archive their non-federal observational data with NOAA's National Center for Environmental Information (NCEI). In this notebook we will use the [RESTful](https://github.com/Esri/geoportal-server/wiki/REST-API-Syntax) services of the [NCEI geoportal](https://www.nodc.noaa.gov/archivesearch/catalog/search/search.page) to collect metadata from the Archival Information Packages found in the NCEI archives. The metadata information are stored in [ISO 19115-2](https://wiki.earthdata.nasa.gov/display/NASAISO/ISO+19115-2) xml files which the NCEI geoportal uses for discovery of Archival Information Packages (AIPs). This example uses the ISO metadata records to display publication information as well as plot the time coverage of each AIP at NCEI which meets the search criteria.\n", + "IOOS regional associations archive their non-federal observational data with NOAA's National Center for Environmental Information (NCEI). In this notebook we will use the [RESTful](https://github.com/Esri/geoportal-server/wiki/REST-API-Syntax) services of the [NCEI geoportal](https://www.nodc.noaa.gov/archivesearch/catalog/search/search.page) to collect metadata from the Archival Information Packages found in the NCEI archives. The metadata information are stored in [ISO 19115-2](https://wiki.earthdata.nasa.gov/display/NASAISO/ISO+19115-2) xml files which the NCEI geoportal uses for discovery of Archival Information Packages (AIPs). This example uses the ISO metadata records to display publication information as well as plot the time coverage of each AIP at NCEI which meets the search criteria.\n", "\n", "First we import the owslib and numpy package. This allows us to parse the ISO xml records and process the information we gather.\n", "\n", @@ -19,15 +28,6 @@ "For more information on ISO Namespaces see: https://geo-ide.noaa.gov/wiki/index.php?title=ISO_Namespaces" ] }, - { - "cell_type": "markdown", - "metadata": {}, - "source": [ - "
\n", - " This notebook is stale and won't run due to missing data upstream and changes in the libraries used.\n", - "
" - ] - }, { "cell_type": "code", "execution_count": 1, @@ -45,7 +45,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "### Now we select a Regional Association \n", + "## Now we select a Regional Association \n", "This is where the user identifies the Regional Association they are interested in. Simply uncomment the line that identifies the region of interest. The user can also omit the Regional Association to collect metadata information about all IOOS non-Federal observation data archived through the NCEI-IOOS pipeline." ] }, @@ -72,7 +72,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "### Next we generate a geoportal query and georss feed\n", + "## Next we generate a geoportal query and georss feed\n", "To find more information about how to compile a geoportal query, have a look at [REST API Syntax](https://github.com/Esri/geoportal-server/wiki/REST-API-Syntax) and the [NCEI Search Tips](https://www.nodc.noaa.gov/search/granule/catalog/searchtips/searchtips.page) for the [NCEI geoportal](https://data.nodc.noaa.gov/geoportal/catalog/search/search.page). The example provided is specific to the NCEI-IOOS data pipeline project and only searches for non-federal timeseries data collected by each Regional Association. \n", "\n", "The query developed here can be updated to search for any Archival Information Packages at NCEI, therefore the user should develop the appropriate query using the [NCEI Geoportal](https://data.nodc.noaa.gov/geoportal/catalog/search/search.page) and update this portion of the code to identify the REST API of interest." @@ -138,7 +138,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "### Time to query the portal and parse out the georrs response\n", + "## Time to query the portal and parse out the georrs response\n", "Here we are opening the specified REST API and parsing it into a string. Then, since we identified it as a georss xml format above, we parse it using the etree package. We then pull out all the ISO metadata record links and print them out so the user can browse to the metadata record and look for what items they might be interested in." ] }, @@ -185,7 +185,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "### Lets plot up what we have found\n", + "## Lets plot up what we have found\n", "Now that we have all the ISO metadata records we are interested in, it's time to do something fun with them. In this example we want to generate a timeseries plot of the data coverage for the \"Southern California Coastal Ocean Observing System\" stations we have archived at NCEI.\n", "\n", "First we set up the figure and import some modules to facilitate plotting and string parsing.\n", @@ -432,7 +432,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.9.6" + "version": "3.9.7" } }, "nbformat": 4, diff --git a/jupyterbook/content/Code Gallery/data_access_notebooks/2017-07-25-HFRadar_currents.ipynb b/jupyterbook/content/code_gallery/data_access_notebooks/2017-07-25-HFRadar_currents.ipynb similarity index 100% rename from jupyterbook/content/Code Gallery/data_access_notebooks/2017-07-25-HFRadar_currents.ipynb rename to jupyterbook/content/code_gallery/data_access_notebooks/2017-07-25-HFRadar_currents.ipynb diff --git a/jupyterbook/content/Code Gallery/data_access_notebooks/2017-08-01-xtractoR.ipynb 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Gallery/data_analysis_and_visualization_notebooks/2016-11-16-CF-UGRID-SGRID-conventions.ipynb rename to jupyterbook/content/code_gallery/data_analysis_and_visualization_notebooks/2016-11-16-CF-UGRID-SGRID-conventions.ipynb index 2d1d310b..7a6185db 100644 --- a/jupyterbook/content/Code Gallery/data_analysis_and_visualization_notebooks/2016-11-16-CF-UGRID-SGRID-conventions.ipynb +++ b/jupyterbook/content/code_gallery/data_analysis_and_visualization_notebooks/2016-11-16-CF-UGRID-SGRID-conventions.ipynb @@ -13,7 +13,7 @@ "[`UGRID-1.0`](http://ugrid-conventions.github.io/ugrid-conventions/),\n", "and [`SGRID-0.3`](http://sgrid.github.io/sgrid/)\n", "\n", - "### CF-1.6 with iris\n", + "## CF-1.6 with iris\n", "\n", "There are many Python libraries to read and write CF metadata,\n", "but only [`iris`](http://scitools.org.uk/iris/) encapsulates CF in an object with an API.\n", @@ -566,7 +566,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "### UGRID-1.0 with pyugrid\n", + "## UGRID-1.0 with pyugrid\n", "\n", "The Unstructured Grids convention encompasses any type of grid topology,\n", "and the details of the convention are documented in [https://ugrid-conventions.github.io/ugrid-conventions](http://bit.ly/2gvtmqQ).\n", @@ -677,7 +677,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "### SGRID-0.3 with `pysgrid`\n", + "## SGRID-0.3 with `pysgrid`\n", "\n", "The Staggered Grid conventions help users to interpret grids from models like ROMS and DELFT,\n", "where the variables are defined in different grids.\n", @@ -1017,7 +1017,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.9.6" + "version": "3.9.7" } }, "nbformat": 4, diff --git a/jupyterbook/content/Code Gallery/data_analysis_and_visualization_notebooks/2017-01-23-R-notebook.ipynb b/jupyterbook/content/code_gallery/data_analysis_and_visualization_notebooks/2017-01-23-R-notebook.ipynb similarity index 100% rename from jupyterbook/content/Code 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jupyterbook/content/code_gallery/data_management.md index 62dc1b6b..54982f2a 100644 --- a/jupyterbook/content/Code Gallery/data_management.md +++ b/jupyterbook/content/code_gallery/data_management.md @@ -1,2 +1,3 @@ # Data Management + This chapter will contain all the notebooks pertaining to Data Management diff --git a/jupyterbook/content/Code Gallery/data_management_notebooks/2017-05-14-running_compliance_checker.ipynb b/jupyterbook/content/code_gallery/data_management_notebooks/2017-05-14-running_compliance_checker.ipynb similarity index 97% rename from jupyterbook/content/Code Gallery/data_management_notebooks/2017-05-14-running_compliance_checker.ipynb rename to jupyterbook/content/code_gallery/data_management_notebooks/2017-05-14-running_compliance_checker.ipynb index 760f7db0..f099ec6a 100644 --- a/jupyterbook/content/Code Gallery/data_management_notebooks/2017-05-14-running_compliance_checker.ipynb +++ b/jupyterbook/content/code_gallery/data_management_notebooks/2017-05-14-running_compliance_checker.ipynb @@ -4,21 +4,20 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "## Shore Station Compliance Checker Script\n", + "# Shore Station Compliance Checker Script\n", "\n", "The IOOS Compliance Checker is a Python-based tool that helps users check the meta data compliance of a netCDF file. This software can be run in a web interface here: https://data.ioos.us/compliance/index.html The checker can also be run as a Python tool either on the command line or in a Python script. This notebook demonstrates the python usage of the Compliance Checker.\n", "\n", "\n", - "### Purpose: \n", + "## Purpose: \n", "Run the compliance checker python tool on a Scipps Pier shore station dataset to check for the metadata compliance.\n", "\n", "The Scripps Pier automated shore station operated by Southern California Coastal Ocean Observing System (SCCOOS) at Scripps Institution of Oceanography (SIO) is mounted at a nominal depth of 5 meters MLLW. The instrument package includes a Seabird SBE 16plus SEACAT Conductivity, Temperature, and Pressure recorder, and a Seapoint Chlorophyll Fluorometer with a 0-50 ug/L gain setting.\n", "\n", - "### Dependencies: \n", + "## Dependencies: \n", "This script must be run in the \"IOOS\" environment for the compliance checker to work properly.\n", "\n", - "Written by: J.Bosch Feb. 10, 2017\n", - "\n" + "Written by: J.Bosch Feb. 10, 2017" ] }, { @@ -221,7 +220,7 @@ "metadata": { "anaconda-cloud": {}, "kernelspec": { - "display_name": "Python 3", + "display_name": "Python 3 (ipykernel)", "language": "python", "name": "python3" }, @@ -235,7 +234,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.7.1" + "version": "3.9.7" } }, "nbformat": 4, diff --git a/jupyterbook/content/Code Gallery/data_management_notebooks/2017-11-01-Creating-Archives-Using-Bagit.ipynb b/jupyterbook/content/code_gallery/data_management_notebooks/2017-11-01-Creating-Archives-Using-Bagit.ipynb similarity index 100% rename from jupyterbook/content/Code Gallery/data_management_notebooks/2017-11-01-Creating-Archives-Using-Bagit.ipynb rename to jupyterbook/content/code_gallery/data_management_notebooks/2017-11-01-Creating-Archives-Using-Bagit.ipynb diff --git a/jupyterbook/content/Code Gallery/data_management_notebooks/2018-02-20-obis.ipynb b/jupyterbook/content/code_gallery/data_management_notebooks/2018-02-20-obis.ipynb similarity index 100% rename from jupyterbook/content/Code Gallery/data_management_notebooks/2018-02-20-obis.ipynb rename to jupyterbook/content/code_gallery/data_management_notebooks/2018-02-20-obis.ipynb diff --git a/jupyterbook/content/Code Gallery/data_management_notebooks/2018-02-27-pocean-timeSeries-demo.ipynb b/jupyterbook/content/code_gallery/data_management_notebooks/2018-02-27-pocean-timeSeries-demo.ipynb similarity index 100% rename from jupyterbook/content/Code Gallery/data_management_notebooks/2018-02-27-pocean-timeSeries-demo.ipynb rename to jupyterbook/content/code_gallery/data_management_notebooks/2018-02-27-pocean-timeSeries-demo.ipynb diff --git a/jupyterbook/content/Code Gallery/data_management_notebooks/2020-10-10-GTS.ipynb b/jupyterbook/content/code_gallery/data_management_notebooks/2020-10-10-GTS.ipynb similarity index 100% rename from jupyterbook/content/Code Gallery/data_management_notebooks/2020-10-10-GTS.ipynb rename to jupyterbook/content/code_gallery/data_management_notebooks/2020-10-10-GTS.ipynb diff --git a/jupyterbook/content/Code Gallery/data_management_notebooks/2020-12-08-DataToDwC.ipynb b/jupyterbook/content/code_gallery/data_management_notebooks/2020-12-08-DataToDwC.ipynb similarity index 100% rename from jupyterbook/content/Code Gallery/data_management_notebooks/2020-12-08-DataToDwC.ipynb rename to jupyterbook/content/code_gallery/data_management_notebooks/2020-12-08-DataToDwC.ipynb diff --git a/jupyterbook/content/ioos_installation_conda.md b/jupyterbook/content/ioos_installation_conda.md index 79d602b0..1280d218 100644 --- a/jupyterbook/content/ioos_installation_conda.md +++ b/jupyterbook/content/ioos_installation_conda.md @@ -1,4 +1,5 @@ # Installing the IOOS conda environment + For IOOS python users we recommend the free [Miniconda](http://conda.pydata.org/miniconda.html) Python distribution, a lightweight version of the [Anaconda Scientific Python Distribution](https://store.continuum.io/cshop/anaconda/). @@ -19,7 +20,7 @@ Windows users also need to choose between 32-bit (old Windows XP) or 64-bit (mod ### Windows Run the installer -Choose *Just Me* (not *All Users*), +Choose _Just Me_ (not _All Users_), and choose a Install Location owned by you. The default `%USERPROFILE%\AppData\Local\Continuum\Miniconda3` is fine, but kind of long, @@ -101,5 +102,5 @@ Check out [Travis Oliphant's blog piece](http://technicaldiscovery.blogspot.com/ ## How to get help -* Raise an issue [here](https://github.com/ioos/ioos_code_lab/issues) -* Please get help on the [IOOS-tech Google Group](https://groups.google.com/forum/?hl=en#!forum/ioos_tech) +- Raise an issue [here](https://github.com/ioos/ioos_code_lab/issues) +- Please get help on the [IOOS-tech Google Group](https://groups.google.com/forum/?hl=en#!forum/ioos_tech) diff --git a/pytest.ini b/pytest.ini index 43826fa8..2a144782 100644 --- a/pytest.ini +++ b/pytest.ini @@ -1,14 +1,14 @@ [pytest] addopts = # Stale/won't fix/missing libray - --ignore="jupyterbook/content/Code Gallery/data_access_notebooks/2016-12-22-boston_light_swim.ipynb" - --ignore="jupyterbook/content/Code Gallery/data_access_notebooks/2017-03-21-ERDDAP_IOOS_Sensor_Map.ipynb" - --ignore="jupyterbook/content/Code Gallery/data_access_notebooks/2017-06-12-NCEI_RA_archive_history.ipynb" - --ignore="jupyterbook/content/Code Gallery/data_access_notebooks/2017-07-25-HFRadar_currents.ipynb" - --ignore="jupyterbook/content/Code Gallery/data_access_notebooks/2017-12-15-finding_HFRadar_currents.ipynb" - --ignore="jupyterbook/content/Code Gallery/data_analysis_and_visualization_notebooks/2017-03-30-octave_notebook_example.ipynb" - --ignore="jupyterbook/content/Code Gallery/data_analysis_and_visualization_notebooks/2018-03-15-ssh-skillscore.ipynb" - --ignore="jupyterbook/content/Code Gallery/data_analysis_and_visualization_notebooks/2018-03-30-wave_height_assessment.ipynb" + --ignore="jupyterbook/content/code_gallery/data_access_notebooks/2016-12-22-boston_light_swim.ipynb" + --ignore="jupyterbook/content/code_gallery/data_access_notebooks/2017-03-21-ERDDAP_IOOS_Sensor_Map.ipynb" + --ignore="jupyterbook/content/code_gallery/data_access_notebooks/2017-06-12-NCEI_RA_archive_history.ipynb" + --ignore="jupyterbook/content/code_gallery/data_access_notebooks/2017-07-25-HFRadar_currents.ipynb" + --ignore="jupyterbook/content/code_gallery/data_access_notebooks/2017-12-15-finding_HFRadar_currents.ipynb" + --ignore="jupyterbook/content/code_gallery/data_analysis_and_visualization_notebooks/2017-03-30-octave_notebook_example.ipynb" + --ignore="jupyterbook/content/code_gallery/data_analysis_and_visualization_notebooks/2018-03-15-ssh-skillscore.ipynb" + --ignore="jupyterbook/content/code_gallery/data_analysis_and_visualization_notebooks/2018-03-30-wave_height_assessment.ipynb" # Passe locally but fail upstream for unknown reasons - --ignore="jupyterbook/content/Code Gallery/data_access_notebooks/2017-08-01-xtractoR.ipynb" - --ignore="jupyterbook/content/Code Gallery/data_access_notebooks/2017-11-30-rerddap.ipynb" + --ignore="jupyterbook/content/code_gallery/data_access_notebooks/2017-08-01-xtractoR.ipynb" + --ignore="jupyterbook/content/code_gallery/data_access_notebooks/2017-11-30-rerddap.ipynb"