diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md index 1e3bd320d..53028d9af 100644 --- a/CONTRIBUTING.md +++ b/CONTRIBUTING.md @@ -1,2 +1,2 @@ Information on how to contribute to this repository can be found -in the [Pythia Foundations Contributor's Guide](https://foundations.projectpythia.org/appendix/how-to-contribute.html). +in the [Pythia Foundations Contributor's Guide](https://foundations.projectpythia.org/appendix/how-to-contribute). diff --git a/appendix/how-to-contribute.md b/appendix/how-to-contribute.md index b6f89c097..10dc4f614 100644 --- a/appendix/how-to-contribute.md +++ b/appendix/how-to-contribute.md @@ -59,4 +59,4 @@ To update all packages in the currently activated environment to their latest ve conda update --all ``` -[Contributing to Project Pythia]: https://projectpythia.org/contributing.html +[Contributing to Project Pythia]: https://projectpythia.org/contributing diff --git a/core/overview.md b/core/overview.md index a8a7d856a..92f620560 100644 --- a/core/overview.md +++ b/core/overview.md @@ -109,7 +109,7 @@ Similarly, a group at the Atmospheric Radiation Measurement (ARM) Climate Resear have released their Python ARM Radar Toolkit ([Py-ART](http://arm-doe.github.io/pyart/)) for analysing weather radar data. -A great place to start learning about use-cases for domain-specific libraries across the geosciences is the [Pythia Cookbook Gallery](https://cookbooks.projectpythia.org). Also check out the [Pythia Resource Gallery](https://projectpythia.org/resource-gallery.html) and try filtering by domain. The [Python for Atmosphere and Ocean Science (PyAOS) package index](https://pyaos.github.io/packages/) +A great place to start learning about use-cases for domain-specific libraries across the geosciences is the [Pythia Cookbook Gallery](https://cookbooks.projectpythia.org). Also check out the [Pythia Resource Gallery](https://projectpythia.org/resource-gallery) and try filtering by domain. The [Python for Atmosphere and Ocean Science (PyAOS) package index](https://pyaos.github.io/packages/) attempt to keep track of the domain-specific libraries in these subfiels. diff --git a/foundations/conda.md b/foundations/conda.md index 31e835c2b..910613da1 100644 --- a/foundations/conda.md +++ b/foundations/conda.md @@ -17,7 +17,7 @@ Here we will cover: | Concepts | Importance | Notes | | --------------------------------------------------------------------------------------------------------- | ---------- | ----- | -| [Installing and Running Python](https://foundations.projectpythia.org/foundations/how-to-run-python.html) | Helpful | | +| [Installing and Running Python](https://foundations.projectpythia.org/foundations/how-to-run-python) | Helpful | | - **Time to learn**: 20 minutes diff --git a/foundations/getting-started-jupyter.ipynb b/foundations/getting-started-jupyter.ipynb index 4300fde1d..cbae2729b 100644 --- a/foundations/getting-started-jupyter.ipynb +++ b/foundations/getting-started-jupyter.ipynb @@ -130,7 +130,7 @@ "\n", "You can launch JupyterLab from a terminal; it will open up in a web browser. The application will then be running in that web browser. When you open a notebook, Jupyter opens a kernel which can be tied to a specific coding language.\n", "\n", - "To launch the JupyterLab interface in your browser, follow the instructions in [Installing and Running Python: Python in Jupyter](https://foundations.projectpythia.org/foundations/jupyter.html).\n", + "To launch the JupyterLab interface in your browser, follow the instructions in [Installing and Running Python: Python in Jupyter](https://foundations.projectpythia.org/foundations/jupyter).\n", "\n", "![Local Execution Model](../images/local-execution-model.gif)" ] diff --git a/foundations/github/basic-git.md b/foundations/github/basic-git.md index 4f46b93de..fa2e218fa 100644 --- a/foundations/github/basic-git.md +++ b/foundations/github/basic-git.md @@ -54,7 +54,7 @@ That's the first thing to understand. GitHub is a web-based platform for hosting #### A little history and nomenclature -Git has been around [since the mid-2000s](https://en.wikipedia.org/wiki/Git). It was originally written by Linus Torvalds specifically for use in development of the Linux kernel. Git is [FOSS](https://foundations.projectpythia.org/foundations/github/what-is-github.html#free-and-open-source-software-foss) and comes pre-installed on many Linux and Mac OS systems. +Git has been around [since the mid-2000s](https://en.wikipedia.org/wiki/Git). It was originally written by Linus Torvalds specifically for use in development of the Linux kernel. Git is [FOSS](https://foundations.projectpythia.org/foundations/github/what-is-github#free-and-open-source-software-foss) and comes pre-installed on many Linux and Mac OS systems. There are many other VCSs out there. A few that you might encounter in scientific codebases include [Subversion](https://subversion.apache.org), [Mercurial](https://www.mercurial-scm.org), and [CVS](https://en.wikipedia.org/wiki/Concurrent_Versions_System). However, git is overwhelmingly the VCS of choice for open-source projects in the Scientific Python ecosystem these days (as well as among software developers more generally). diff --git a/foundations/github/contribute-to-pythia.md b/foundations/github/contribute-to-pythia.md index c90ce33b9..f014f80b0 100644 --- a/foundations/github/contribute-to-pythia.md +++ b/foundations/github/contribute-to-pythia.md @@ -29,11 +29,11 @@ --- -Now that you have become more familiar with how to use Git and GitHub, you might have an idea or some material that you want to contribute to Project Pythia! The [Project Pythia Contributor's Guide](https://projectpythia.org/contributing.html) describes the steps required to submit a PR to any of Project Pythia's repos. Here, we will go through an example of submitting a PR to `pythia-foundations`. +Now that you have become more familiar with how to use Git and GitHub, you might have an idea or some material that you want to contribute to Project Pythia! The [Project Pythia Contributor's Guide](https://projectpythia.org/contributing) describes the steps required to submit a PR to any of Project Pythia's repos. Here, we will go through an example of submitting a PR to `pythia-foundations`. ## Suggest a change -One simple way to contribute is to fix a typo or suggest a change to one of the tutorials. For example, in the [Computations and Masks with Xarray tutorial](https://foundations.projectpythia.org/core/xarray/computation-masking.html), let's suggest a clarification that the sea surface temperature is called `tos` in the dataset we are using. +One simple way to contribute is to fix a typo or suggest a change to one of the tutorials. For example, in the [Computations and Masks with Xarray tutorial](https://foundations.projectpythia.org/core/xarray/computation-masking), let's suggest a clarification that the sea surface temperature is called `tos` in the dataset we are using. Computations and Masks with Xarray @@ -41,7 +41,7 @@ We could open an issue to suggest this change in order to get feedback on the id ## Make the edits -We will follow the [Forking Workflow](https://foundations.projectpythia.org/foundations/github/github-workflows.html#forking-workflow) described in the previous section of this tutorial, assuming `pythia-foundations` has already been forked: +We will follow the [Forking Workflow](https://foundations.projectpythia.org/foundations/github/github-workflows#forking-workflow) described in the previous section of this tutorial, assuming `pythia-foundations` has already been forked: - Create a new branch with a descriptive name - Make the changes and commit them locally @@ -78,7 +78,7 @@ Now, going to our remote repo on GitHub, forked from `pythia-foundations`, we se GitHub Forked Repo -Project Pythia has an automated reviewer system: when a PR is created, two members of the organization will be randomly chosen to review it. If your PR is not immediately ready to be approved and merged, open it as a draft to delay the review process. As shown in this [Git Branches section](https://foundations.projectpythia.org/foundations/github/git-branches.html#merging-branches), the "Draft pull request" button is found using the arrow on the "Create pull request" button. +Project Pythia has an automated reviewer system: when a PR is created, two members of the organization will be randomly chosen to review it. If your PR is not immediately ready to be approved and merged, open it as a draft to delay the review process. As shown in this [Git Branches section](https://foundations.projectpythia.org/foundations/github/git-branches#merging-branches), the "Draft pull request" button is found using the arrow on the "Create pull request" button. Let's add the `content` tag and open this one as a draft for now: diff --git a/foundations/github/github-repos.md b/foundations/github/github-repos.md index 7bf47a6fd..c4e0fa206 100644 --- a/foundations/github/github-repos.md +++ b/foundations/github/github-repos.md @@ -13,7 +13,7 @@ | Concepts | Importance | Notes | | ----------------------------------------------------------------------------------------------- | ---------- | ----- | -| [What is GitHub?](https://foundations.projectpythia.org/foundations/github/what-is-github.html) | Necessary | | +| [What is GitHub?](https://foundations.projectpythia.org/foundations/github/what-is-github) | Necessary | | - **Time to learn**: 15 minutes @@ -52,7 +52,7 @@ As you can see by the recent timestamps, these repositories are actively changin :class: tip Notice that each of the three *Repositories* each exist as part of their own *Organization*. In other words, the NumPy repository exists within the NumPy organization; the Xarray repo exists within the Pydata org, and so forth. -When you [create your own GitHub account](https://foundations.projectpythia.org/foundations/github/what-is-github.html), your user ID functions as the *organization*. Any repositories you create (and therefore, *own*) will exist within that org. +When you [create your own GitHub account](https://foundations.projectpythia.org/foundations/github/what-is-github), your user ID functions as the *organization*. Any repositories you create (and therefore, *own*) will exist within that org. ``` Another example is this project's [Pythia Foundations repository](https://github.com/ProjectPythia/pythia-foundations), on which this tutorial is stored. It is owned by the [Project Pythia organization](https://github.com/ProjectPythia). This organization also owns several other repositories that store the files needed to generate , among other things. diff --git a/foundations/how-to-run-python.md b/foundations/how-to-run-python.md index 788e1250b..0a54744f4 100644 --- a/foundations/how-to-run-python.md +++ b/foundations/how-to-run-python.md @@ -13,7 +13,7 @@ This section provides an overview of different ways to run Python code, and quic | Concepts | Importance | Notes | | -------------------------------------------------------------------------------- | ---------- | ----- | -| [Why Python?](https://foundations.projectpythia.org/foundations/why-python.html) | Helpful | | +| [Why Python?](https://foundations.projectpythia.org/foundations/why-python) | Helpful | | - **Time to learn**: 20 minutes diff --git a/foundations/jupyter.md b/foundations/jupyter.md index 3c39f5731..8941c249b 100644 --- a/foundations/jupyter.md +++ b/foundations/jupyter.md @@ -14,7 +14,7 @@ You'd like to learn to run Python in a Jupyter session. Here we will cover: | Concepts | Importance | Notes | | --------------------------------------------------------------------------------------------------------- | ---------- | ----- | -| [Installing and Running Python](https://foundations.projectpythia.org/foundations/how-to-run-python.html) | Helpful | | +| [Installing and Running Python](https://foundations.projectpythia.org/foundations/how-to-run-python) | Helpful | | - **Time to learn**: 20 minutes diff --git a/foundations/jupyterlab.ipynb b/foundations/jupyterlab.ipynb index 8d5f6f3ea..c201802cc 100644 --- a/foundations/jupyterlab.ipynb +++ b/foundations/jupyterlab.ipynb @@ -45,7 +45,7 @@ "| Concepts | Importance | Notes |\n", "| --- | --- | --- |\n", "| [Getting Started with Jupyter](getting-started-jupyter) | Helpful | |\n", - "| [Installing and Running Python: Python in Jupyter](https://foundations.projectpythia.org/foundations/jupyter.html) | Helpful | |\n", + "| [Installing and Running Python: Python in Jupyter](https://foundations.projectpythia.org/foundations/jupyter) | Helpful | |\n", "\n", "- **Time to learn**: 50 minutes" ] @@ -68,7 +68,7 @@ "source": [ "## Set Up\n", "\n", - "To launch the JupyterLab interface in your browser, follow the instructions in [Installing and Running Python: Python in Jupyter](https://foundations.projectpythia.org/foundations/jupyter.html).\n", + "To launch the JupyterLab interface in your browser, follow the instructions in [Installing and Running Python: Python in Jupyter](https://foundations.projectpythia.org/foundations/jupyter).\n", "\n", "If, instead, you want to follow along using a provided remote JupyterLab instance, launch this notebook via [Binder](https://mybinder.org/) using the launch icon at the top of this page,\n", "\n", diff --git a/foundations/terminal.md b/foundations/terminal.md index 866186ebd..c21106857 100644 --- a/foundations/terminal.md +++ b/foundations/terminal.md @@ -13,7 +13,7 @@ You'd like to learn to run Python in the terminal. Here we will cover: | Concepts | Importance | Notes | | --------------------------------------------------------------------------------------------------------- | ---------- | ----- | -| [Installing and Running Python](https://foundations.projectpythia.org/foundations/how-to-run-python.html) | Helpful | | +| [Installing and Running Python](https://foundations.projectpythia.org/foundations/how-to-run-python) | Helpful | | - **Time to learn**: 20 minutes diff --git a/preamble/how-to-use.md b/preamble/how-to-use.md index 3e931e72b..e58749834 100644 --- a/preamble/how-to-use.md +++ b/preamble/how-to-use.md @@ -81,7 +81,7 @@ and even change the example programs. At first the code cells have no output, until you execute them by pressing {kbd}`Shift`\+{kbd}`Enter`. Complete details on how to interact with a live Jupyter notebook are described in [Getting Started with -Jupyter](https://foundations.projectpythia.org/foundations/getting-started-jupyter.html). +Jupyter](https://foundations.projectpythia.org/foundations/getting-started-jupyter). ### Interacting with Jupyter Books locally @@ -96,7 +96,7 @@ That was the easy part. Getting the notebook to execute locally may take a little more work. The book was created to run in a particular Python environment, managed with Conda. If you don't have a up-to-date version of Conda on your machine, you'll want to install one. A brief -introduction to installing Conda is available [here](https://foundations.projectpythia.org/foundations/conda.html). +introduction to installing Conda is available [here](https://foundations.projectpythia.org/foundations/conda). Once you've installed Conda you will need to create and activate a Conda environment that is compatible with Pythia Foundation's notebooks. This @@ -114,7 +114,7 @@ need to activate _pythia-book-dev_ if it is not currently active, for example if you open up a new terminal window, or deactivate _pythia-book-dev_ explicitly with the `conda` command. Again, more information on Conda can be -found [here](https://foundations.projectpythia.org/foundations/conda.html). +found [here](https://foundations.projectpythia.org/foundations/conda). Now that your _pythia-book-dev_ environment is activated, change your working directory to the @@ -134,6 +134,6 @@ notebooks, you might want to “clone the site” and download all of the notebooks. First, click on the GitHub icon (see the screenshot above) to open the Pythia Foundations GitHub repository. Then follow the instructions in our Getting Started with GitHub -[guide](https://foundations.projectpythia.org/foundations/getting-started-github.html#) +[guide](https://foundations.projectpythia.org/foundations/getting-started-github) for cloning a repository. The steps used above for configuring your Conda environment should work for this method as well.