COAsT
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+COAsT +
+Coastal Ocean Assessment Toolbox
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+ A Python toolbox for assessing kilometer-scale ocean models, conducting statistical analyses, + and facilitating model validation. +
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-{{% blocks/feature icon="fab fa-twitter" title="Follow us on Twitter!" url="https://twitter.com/GoHugoIO" %}}
-For announcement of latest features etc.
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+About
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+
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-This site provides visibility into the COAsT python framework.
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-{{% blocks/feature icon="fab fa-app-store-ios" title="Download **from Anaconda.org**" url="https://anaconda.org/BODC/" %}}
-Get the COAsT framework!
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-{{% blocks/feature icon="fab fa-github" title="Contributions welcome!" url="https://github.com/British-Oceanographic-Data-Centre/COAsT-site" %}}
-We do a [Pull Request](https://github.com/British-Oceanographic-Data-Centre/COAsT-site/pulls) contributions workflow on **GitHub**. New users are always welcome!
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+COAsT is Diagnostic and Assessment toolbox for kilometric scale regional models. + It's aim is to deliver a flexible, community-ready framework for assessing kilometric scale ocean models.
+The focus, initially, is be on delivering novel diagnostics for processes that are emergent + at the kilometric scale and with NEMO model output.
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-COAsT is a Python package for managing and analysing high resolution NEMO output Join the COAsT community
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+ COAsT is an open source project that anyone in the community can use, improve, and enjoy. + We'd love you to join us! Here's a few ways to find out what's happening and get involved.
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+ Learn and Connect
+Using or want to use COAsT? Find out more here:
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Github
Pypi
Anaconda
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+ Develop and Contribute
+If you want to get more involved by contributing to COAsT, join us on our Github Repository -{{< /blocks/section >}} +
You can find out how to contribute to these docs in our Contribution Guidelines. +
-Read more [here](../docs/) -{{% /blocks/lead %}} - -{{% blocks/lead %}} -This site was based off the Docsy Hugo theme. -{{% /blocks/lead %}} diff --git a/content/en/about/featured-background.jpg b/content/en/about/featured-background.jpg deleted file mode 100644 index bc012365abb..00000000000 Binary files a/content/en/about/featured-background.jpg and /dev/null differ diff --git a/content/en/community/_index.md b/content/en/community/_index.md deleted file mode 100644 index cdade163086..00000000000 --- a/content/en/community/_index.md +++ /dev/null @@ -1,8 +0,0 @@ ---- -title: Community -menu: - main: - weight: 40 ---- - - diff --git a/content/en/docs/Contributing-Docs/_index.md b/content/en/docs/Contributing-Docs/_index.md deleted file mode 100644 index 36ce103a34a..00000000000 --- a/content/en/docs/Contributing-Docs/_index.md +++ /dev/null @@ -1,53 +0,0 @@ ---- -title: "Contributing: Documentation" -linkTitle: "Contributing: Documentation" -weight: 4 -date: 2017-01-05 -description: > - Guidelines for contributing to the COAsT documentation site. ---- - -We use [Hugo](https://gohugo.io/) Extended Version to format and generate our website, the -[Docsy](https://github.com/google/docsy) theme for styling and site structure, -and [GitHub pages](https://help.github.com/en/github/working-with-github-pages) to manage the deployment of the site. -Hugo is an open-source static site generator that provides us with templates, -content organisation in a standard directory structure, and a website generation engine. You write the pages in Markdown (or HTML if you want), and Hugo wraps them up into a website. - -All submissions, including submissions by project members, require review. We -use GitHub pull requests for this purpose. Consult -[GitHub Help](https://help.github.com/articles/about-pull-requests/) for more -information on using pull requests. - -## Updating a single page - -If you've just spotted something you'd like to change while using the docs, Docsy has a shortcut for you: - -1. Click **Edit this page** in the top right hand corner of the page. -1. If you don't already have an up to date fork of the project repo, you are prompted to get one - click **Fork this repository and propose changes** or **Update your Fork** to get an up to date version of the project to edit. The appropriate page in your fork is displayed in edit mode. -1. make your edit -1. submit a pull request with a summary of the changes - -## Previewing your changes locally - -If you want to run your own local Hugo server to preview your changes as you work: - -1. Follow the instructions in [Getting started](/docs/contributing_documentation/hugo) to install Hugo and any other tools you need. You'll need at least **Hugo version 0.45** (we recommend using the most recent available version), and it must be the **extended** version, which supports SCSS. -1. Fork the [COAsT-site repo](https://github.com/British-Oceanographic-Data-Centre/COAsT-site.git) repo into your own project, then create a local copy using `git clone`. Don’t forget to use `--recurse-submodules` or you won’t pull down some of the code you need to generate a working site. - - ``` - git clone --recurse-submodules --depth 1 https://github.com/British-Oceanographic-Data-Centre/COAsT-site.git - ``` -1. Run `npm install` to install Node.js dependencies. -2. Run `hugo server` in the site root directory. By default your site will be available at http://localhost:1313/COAsT. Now that you're serving your site locally, Hugo will watch for changes to the content and automatically refresh your site. -2. Continue with the usual GitHub workflow to edit files, commit them, push the - changes up to your fork, and create a pull request. - -## Creating an issue - -If you've found a problem in the docs, but you're not sure how to fix it yourself, please create an issue in the [COAsT-site repo](https://github.com/British-Oceanographic-Data-Centre/COAsT-site.git). You can also create an issue about a specific page by clicking the **Create Issue** button in the top right hand corner of the page. - -## Useful resources - -* [Docsy user guide](https://www.docsy.dev/about/): All about Docsy, including how it manages navigation, look and feel, and multi-language support. -* [Hugo documentation](https://gohugo.io/documentation/): Comprehensive reference for Hugo. -* [Github Hello World!](https://guides.github.com/activities/hello-world/): A basic introduction to GitHub concepts and workflow. diff --git a/content/en/docs/Contributing-Docs/hugo.md b/content/en/docs/Contributing-Docs/hugo.md deleted file mode 100644 index d0b27877983..00000000000 --- a/content/en/docs/Contributing-Docs/hugo.md +++ /dev/null @@ -1,40 +0,0 @@ ---- -title: "setting up Hugo" -linkTitle: "hugo" -weight: 5 -description: > - What do you need to know to build a local version of this site ---- - -This page will walk you though a simple setup for hugo extended - which is needed if want to view any changes you make to this site locally. - -For more details please [read this](https://gohugo.io/getting-started/installing/). - -## Installation -### Manual -1) Download hugo _extended_ from [GitHub](https://github.com/gohugoio/hugo/releases) -2) Unzip into preferred location (I use C:\hugo) -3) Add to OS PATH - * optional but makes usage easier -### Via a Package Manager -On Windows you can use [Chocolately](https://chocolatey.org/) to install with: -```shell -choco install hugo-extended -``` -Or on macOS/Linux you can use [Homebrew](https://brew.sh/) to install with: -```shell -brew install hugo -``` -## Try it out! -You should now be able to try the following in a terminal -```shell -$ hugo --help -``` - -if you have cloned the COAsT-site [repo](github_repo) you should also now be able to; - -```shell -$ cd COAsT-site -$ hugo server -``` -the above will start a local hugo powered version of the website. you can edit any of the files under /content and see your changes at http://localhost:1313/COAsT/ diff --git a/content/en/docs/Examples/Notebooks/Altimetry/altimetry_tutorial.md b/content/en/docs/Examples/Notebooks/Altimetry/altimetry_tutorial.md index 93346ff41c2..657c6b12b53 100644 --- a/content/en/docs/Examples/Notebooks/Altimetry/altimetry_tutorial.md +++ b/content/en/docs/Examples/Notebooks/Altimetry/altimetry_tutorial.md @@ -25,6 +25,25 @@ fn_altimetry = dn_files + "coast_example_altimetry_data.nc" fn_altimetry_config = root + "./config/example_altimetry.json" ``` + /usr/share/miniconda/envs/coast/lib/python3.10/site-packages/pydap/lib.py:5: DeprecationWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html + /usr/share/miniconda/envs/coast/lib/python3.10/site-packages/pkg_resources/__init__.py:2871: DeprecationWarning: Deprecated call to `pkg_resources.declare_namespace('pydap')`. + Implementing implicit namespace packages (as specified in PEP 420) is preferred to `pkg_resources.declare_namespace`. See https://setuptools.pypa.io/en/latest/references/keywords.html#keyword-namespace-packages + /usr/share/miniconda/envs/coast/lib/python3.10/site-packages/pkg_resources/__init__.py:2871: DeprecationWarning: Deprecated call to `pkg_resources.declare_namespace('pydap.responses')`. + Implementing implicit namespace packages (as specified in PEP 420) is preferred to `pkg_resources.declare_namespace`. See https://setuptools.pypa.io/en/latest/references/keywords.html#keyword-namespace-packages + /usr/share/miniconda/envs/coast/lib/python3.10/site-packages/pkg_resources/__init__.py:2350: DeprecationWarning: Deprecated call to `pkg_resources.declare_namespace('pydap')`. + Implementing implicit namespace packages (as specified in PEP 420) is preferred to `pkg_resources.declare_namespace`. See https://setuptools.pypa.io/en/latest/references/keywords.html#keyword-namespace-packages + /usr/share/miniconda/envs/coast/lib/python3.10/site-packages/pkg_resources/__init__.py:2871: DeprecationWarning: Deprecated call to `pkg_resources.declare_namespace('pydap.handlers')`. + Implementing implicit namespace packages (as specified in PEP 420) is preferred to `pkg_resources.declare_namespace`. See https://setuptools.pypa.io/en/latest/references/keywords.html#keyword-namespace-packages + /usr/share/miniconda/envs/coast/lib/python3.10/site-packages/pkg_resources/__init__.py:2350: DeprecationWarning: Deprecated call to `pkg_resources.declare_namespace('pydap')`. + Implementing implicit namespace packages (as specified in PEP 420) is preferred to `pkg_resources.declare_namespace`. See https://setuptools.pypa.io/en/latest/references/keywords.html#keyword-namespace-packages + /usr/share/miniconda/envs/coast/lib/python3.10/site-packages/pkg_resources/__init__.py:2871: DeprecationWarning: Deprecated call to `pkg_resources.declare_namespace('pydap.tests')`. + Implementing implicit namespace packages (as specified in PEP 420) is preferred to `pkg_resources.declare_namespace`. See https://setuptools.pypa.io/en/latest/references/keywords.html#keyword-namespace-packages + /usr/share/miniconda/envs/coast/lib/python3.10/site-packages/pkg_resources/__init__.py:2350: DeprecationWarning: Deprecated call to `pkg_resources.declare_namespace('pydap')`. + Implementing implicit namespace packages (as specified in PEP 420) is preferred to `pkg_resources.declare_namespace`. See https://setuptools.pypa.io/en/latest/references/keywords.html#keyword-namespace-packages + /usr/share/miniconda/envs/coast/lib/python3.10/site-packages/pkg_resources/__init__.py:2871: DeprecationWarning: Deprecated call to `pkg_resources.declare_namespace('sphinxcontrib')`. + Implementing implicit namespace packages (as specified in PEP 420) is preferred to `pkg_resources.declare_namespace`. See https://setuptools.pypa.io/en/latest/references/keywords.html#keyword-namespace-packages + + ### Load data @@ -40,8 +59,14 @@ nemo = coast.Gridded(fn_nemo_dat, fn_nemo_dom, config=fn_nemo_config) altimetry = coast.Altimetry(fn_altimetry, config=fn_altimetry_config) ``` + /usr/share/miniconda/envs/coast/lib/python3.10/site-packages/xarray/core/dataset.py:278: UserWarning: The specified chunks separate the stored chunks along dimension "time_counter" starting at index 2. This could degrade performance. Instead, consider rechunking after loading. + + ././config/example_altimetry.json - Altimetry object at 0x561214f5efc0 initialised + Altimetry object at 0x560d5d3e2980 initialised + + + /usr/share/miniconda/envs/coast/lib/python3.10/site-packages/xarray/core/dataset.py:278: UserWarning: The specified chunks separate the stored chunks along dimension "time" starting at index 1000. This could degrade performance. Instead, consider rechunking after loading. ### Subsetting @@ -57,7 +82,7 @@ ind = ind[::4] altimetry = altimetry.isel(t_dim=ind) ``` - Subsetting Altimetry object at 0x561214f5efc0 indices in [-10, 10], [45, 60] + Subsetting Altimetry object at 0x560d5d3e2980 indices in [-10, 10], [45, 60] ### Model interpolation @@ -74,7 +99,7 @@ altimetry.obs_operator(nemo, mod_var_name="ssh", time_interp="nearest") # to see for yourself. ``` - Interpolating Gridded object at 0x561214f5efc0 "ssh" with time_interp "nearest" + Interpolating Gridded object at 0x560d5d3e2980 "ssh" with time_interp "nearest" @@ -93,13 +118,7 @@ altimetry.obs_operator(nemo, mod_var_name="ssh", time_interp="nearest") stats = altimetry.basic_stats("ocean_tide_standard_name", "interp_ssh") ``` - Altimetry object at 0x561214f5efc0 initialised - - - /usr/share/miniconda/envs/coast/lib/python3.8/site-packages/coast/data/altimetry.py:351: FutureWarning: The default value of numeric_only in DataFrame.corr is deprecated. In a future version, it will default to False. Select only valid columns or specify the value of numeric_only to silence this warning. - corr = pdvar.corr(method=method) - /usr/share/miniconda/envs/coast/lib/python3.8/site-packages/coast/data/altimetry.py:365: FutureWarning: The default value of numeric_only in DataFrame.cov is deprecated. In a future version, it will default to False. Select only valid columns or specify the value of numeric_only to silence this warning. - cov = pdvar.cov() + Altimetry object at 0x560d5d3e2980 initialised @@ -127,7 +146,7 @@ crps = altimetry.crps(nemo, model_var_name="ssh", obs_var_name="ocean_tide_stand #crps.dataset # uncomment to print data object summary ``` - Altimetry object at 0x561214f5efc0 initialised + Altimetry object at 0x560d5d3e2980 initialised ### Plotting data @@ -140,8 +159,7 @@ crps = altimetry.crps(nemo, model_var_name="ssh", obs_var_name="ocean_tide_stand fig, ax = altimetry.quick_plot("ocean_tide_standard_name") ``` - /usr/share/miniconda/envs/coast/lib/python3.8/site-packages/cartopy/io/__init__.py:241: DownloadWarning: Downloading: https://naturalearth.s3.amazonaws.com/50m_physical/ne_50m_coastline.zip - warnings.warn(f'Downloading: {url}', DownloadWarning) + /usr/share/miniconda/envs/coast/lib/python3.10/site-packages/cartopy/io/__init__.py:241: DownloadWarning: Downloading: https://naturalearth.s3.amazonaws.com/50m_physical/ne_50m_coastline.zip diff --git a/content/en/docs/Examples/Notebooks/General/climatology_tutorial.md b/content/en/docs/Examples/Notebooks/General/climatology_tutorial.md index 64e28b3cfc7..54653560bc1 100644 --- a/content/en/docs/Examples/Notebooks/General/climatology_tutorial.md +++ b/content/en/docs/Examples/Notebooks/General/climatology_tutorial.md @@ -26,6 +26,25 @@ processes will automatically be used. import coast ``` + /usr/share/miniconda/envs/coast/lib/python3.10/site-packages/pydap/lib.py:5: DeprecationWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html + /usr/share/miniconda/envs/coast/lib/python3.10/site-packages/pkg_resources/__init__.py:2871: DeprecationWarning: Deprecated call to `pkg_resources.declare_namespace('pydap')`. + Implementing implicit namespace packages (as specified in PEP 420) is preferred to `pkg_resources.declare_namespace`. See https://setuptools.pypa.io/en/latest/references/keywords.html#keyword-namespace-packages + /usr/share/miniconda/envs/coast/lib/python3.10/site-packages/pkg_resources/__init__.py:2871: DeprecationWarning: Deprecated call to `pkg_resources.declare_namespace('pydap.responses')`. + Implementing implicit namespace packages (as specified in PEP 420) is preferred to `pkg_resources.declare_namespace`. See https://setuptools.pypa.io/en/latest/references/keywords.html#keyword-namespace-packages + /usr/share/miniconda/envs/coast/lib/python3.10/site-packages/pkg_resources/__init__.py:2350: DeprecationWarning: Deprecated call to `pkg_resources.declare_namespace('pydap')`. + Implementing implicit namespace packages (as specified in PEP 420) is preferred to `pkg_resources.declare_namespace`. See https://setuptools.pypa.io/en/latest/references/keywords.html#keyword-namespace-packages + /usr/share/miniconda/envs/coast/lib/python3.10/site-packages/pkg_resources/__init__.py:2871: DeprecationWarning: Deprecated call to `pkg_resources.declare_namespace('pydap.handlers')`. + Implementing implicit namespace packages (as specified in PEP 420) is preferred to `pkg_resources.declare_namespace`. See https://setuptools.pypa.io/en/latest/references/keywords.html#keyword-namespace-packages + /usr/share/miniconda/envs/coast/lib/python3.10/site-packages/pkg_resources/__init__.py:2350: DeprecationWarning: Deprecated call to `pkg_resources.declare_namespace('pydap')`. + Implementing implicit namespace packages (as specified in PEP 420) is preferred to `pkg_resources.declare_namespace`. See https://setuptools.pypa.io/en/latest/references/keywords.html#keyword-namespace-packages + /usr/share/miniconda/envs/coast/lib/python3.10/site-packages/pkg_resources/__init__.py:2871: DeprecationWarning: Deprecated call to `pkg_resources.declare_namespace('pydap.tests')`. + Implementing implicit namespace packages (as specified in PEP 420) is preferred to `pkg_resources.declare_namespace`. See https://setuptools.pypa.io/en/latest/references/keywords.html#keyword-namespace-packages + /usr/share/miniconda/envs/coast/lib/python3.10/site-packages/pkg_resources/__init__.py:2350: DeprecationWarning: Deprecated call to `pkg_resources.declare_namespace('pydap')`. + Implementing implicit namespace packages (as specified in PEP 420) is preferred to `pkg_resources.declare_namespace`. See https://setuptools.pypa.io/en/latest/references/keywords.html#keyword-namespace-packages + /usr/share/miniconda/envs/coast/lib/python3.10/site-packages/pkg_resources/__init__.py:2871: DeprecationWarning: Deprecated call to `pkg_resources.declare_namespace('sphinxcontrib')`. + Implementing implicit namespace packages (as specified in PEP 420) is preferred to `pkg_resources.declare_namespace`. See https://setuptools.pypa.io/en/latest/references/keywords.html#keyword-namespace-packages + + ### Usage of coast.Climatology.make_climatology(). Calculates mean over a given period of time. This doesn't take different years into account, unless using the @@ -51,6 +70,9 @@ nemo_data = coast.Gridded(fn_data=fn_nemo_dat, ``` + /usr/share/miniconda/envs/coast/lib/python3.10/site-packages/xarray/core/dataset.py:278: UserWarning: The specified chunks separate the stored chunks along dimension "time_counter" starting at index 2. This could degrade performance. Instead, consider rechunking after loading. + + Calculate the climatology for temperature and sea surface height (ssh) as an example: diff --git a/content/en/docs/Examples/Notebooks/General/eof_tutorial.md b/content/en/docs/Examples/Notebooks/General/eof_tutorial.md index 9af16994b42..358eaf11052 100644 --- a/content/en/docs/Examples/Notebooks/General/eof_tutorial.md +++ b/content/en/docs/Examples/Notebooks/General/eof_tutorial.md @@ -26,6 +26,25 @@ fn_nemo_dom = dn_files + "coast_example_nemo_domain.nc" fn_nemo_config = root + "./config/example_nemo_grid_t.json" ``` + /usr/share/miniconda/envs/coast/lib/python3.10/site-packages/pydap/lib.py:5: DeprecationWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html + /usr/share/miniconda/envs/coast/lib/python3.10/site-packages/pkg_resources/__init__.py:2871: DeprecationWarning: Deprecated call to `pkg_resources.declare_namespace('pydap')`. + Implementing implicit namespace packages (as specified in PEP 420) is preferred to `pkg_resources.declare_namespace`. See https://setuptools.pypa.io/en/latest/references/keywords.html#keyword-namespace-packages + /usr/share/miniconda/envs/coast/lib/python3.10/site-packages/pkg_resources/__init__.py:2871: DeprecationWarning: Deprecated call to `pkg_resources.declare_namespace('pydap.responses')`. + Implementing implicit namespace packages (as specified in PEP 420) is preferred to `pkg_resources.declare_namespace`. See https://setuptools.pypa.io/en/latest/references/keywords.html#keyword-namespace-packages + /usr/share/miniconda/envs/coast/lib/python3.10/site-packages/pkg_resources/__init__.py:2350: DeprecationWarning: Deprecated call to `pkg_resources.declare_namespace('pydap')`. + Implementing implicit namespace packages (as specified in PEP 420) is preferred to `pkg_resources.declare_namespace`. See https://setuptools.pypa.io/en/latest/references/keywords.html#keyword-namespace-packages + /usr/share/miniconda/envs/coast/lib/python3.10/site-packages/pkg_resources/__init__.py:2871: DeprecationWarning: Deprecated call to `pkg_resources.declare_namespace('pydap.handlers')`. + Implementing implicit namespace packages (as specified in PEP 420) is preferred to `pkg_resources.declare_namespace`. See https://setuptools.pypa.io/en/latest/references/keywords.html#keyword-namespace-packages + /usr/share/miniconda/envs/coast/lib/python3.10/site-packages/pkg_resources/__init__.py:2350: DeprecationWarning: Deprecated call to `pkg_resources.declare_namespace('pydap')`. + Implementing implicit namespace packages (as specified in PEP 420) is preferred to `pkg_resources.declare_namespace`. See https://setuptools.pypa.io/en/latest/references/keywords.html#keyword-namespace-packages + /usr/share/miniconda/envs/coast/lib/python3.10/site-packages/pkg_resources/__init__.py:2871: DeprecationWarning: Deprecated call to `pkg_resources.declare_namespace('pydap.tests')`. + Implementing implicit namespace packages (as specified in PEP 420) is preferred to `pkg_resources.declare_namespace`. See https://setuptools.pypa.io/en/latest/references/keywords.html#keyword-namespace-packages + /usr/share/miniconda/envs/coast/lib/python3.10/site-packages/pkg_resources/__init__.py:2350: DeprecationWarning: Deprecated call to `pkg_resources.declare_namespace('pydap')`. + Implementing implicit namespace packages (as specified in PEP 420) is preferred to `pkg_resources.declare_namespace`. See https://setuptools.pypa.io/en/latest/references/keywords.html#keyword-namespace-packages + /usr/share/miniconda/envs/coast/lib/python3.10/site-packages/pkg_resources/__init__.py:2871: DeprecationWarning: Deprecated call to `pkg_resources.declare_namespace('sphinxcontrib')`. + Implementing implicit namespace packages (as specified in PEP 420) is preferred to `pkg_resources.declare_namespace`. See https://setuptools.pypa.io/en/latest/references/keywords.html#keyword-namespace-packages + + ### Loading data @@ -70,7 +89,7 @@ eof_data.EOF.sel(mode=[1,2,3,4]).plot.pcolormesh(col='mode',col_wrap=2,x='longit -