Fix broken stuff

package-structure-code/publish-python-package-pypi-conda.md

@@ -19,7 +19,7 @@ Below you will learn more specifics about the differences between PyPI and conda
 :::
 
 
-:::{figure-md} pypi-conda-channels
+:::{figure-md} upload-conda-forge
 
 <img src="../images/publish-python-package-pypi-conda.png" alt="Image showing the progression of creating a Python package, building it and then publishing to PyPI and conda-forge. You take your code and turn it into distribution files (sdist and wheel) that PyPI accepts. then there is an arrow towards the PyPI repository where ou publish both distributions. From PyPI if you create a conda-forge recipe you can then publish to conda-forge. " width="700px">
 

package-structure-code/python-package-build-tools.md

@@ -403,6 +403,7 @@ Build your sdist and wheel distributions|✅|Poetry will build your sdist and wh
 
 <!-- TODO: responses here on poetry's future dev work: https://github.com/python-poetry/poetry/discussions/7525 -->
 
+(challenges-with-poetry)=
 ### Challenges with Poetry
 
 Some challenges of Poetry include:

package-structure-code/python-package-distribution-files-sdist-wheel.md

@@ -1,15 +1,14 @@
 # Learn about Building a Python Package
 
 
-:::{figure-md} pypi-conda-channels
+:::{figure-md} pypi-conda-overview
 
 <img src="../images/publish-python-package-pypi-conda.png" alt="Image showing the progression of creating a Python package, building it and then publishing to PyPI and conda-forge. You take your code and turn it into distribution files (sdist and wheel) that PyPI accepts. then there is an arrow towards the PyPI repository where ou publish both distributions. From PyPI if you create a conda-forge recipe you can then publish to conda-forge. " width="700px">
 
 Once you have published both package distributions (the source distribution and the wheel) to PyPI, you can then publish to conda-forge. conda-forge requires an source distribution on PyPI in order to build your package on conda-forge. You do not need to rebuild your package to publish to conda-forge.
 :::
 
 You need to build your Python package in order to publish it to PyPI (or a conda channel). The build process organizes your code and metadata into a distribution format that can be uploaded to PyPI and subsequently downloaded and installed by users. NOTE: you need to publish a sdist to PyPI in order for conda-forge to properly build your package automatically.
-:::
 
 (build-package)=
 ## What is building a Python package?

tests/run-tests.md

@@ -16,7 +16,7 @@ Python versions.
 
 
 
-### Tools to run your tests
+## Tools to run your tests
 
 There are three categories of tools that will make is easier to setup
 and run your tests in various environments:
@@ -80,7 +80,7 @@ extensions that can be used to add functionality such as:
 - [pytest-cov](https://pytest-cov.readthedocs.io/en/latest/) allows you to analyze the code coverage of your package during your tests, and generates a report that you can [upload to codecov](https://codecov.io/).
 
 :::{todo}
-[Learn more about code coverage here.](code-cov)
+Learn more about code coverage here. (add link)
 :::
 
 ```{note}

tests/tests-ci.md

@@ -6,7 +6,7 @@ CI can also be triggered for pull requests and pushes to your repository. This m
 
 ::::{todo}
 ```{note}
-[Learn more about Continuous Integration and how it can be used, here.](ci)
+Learn more about Continuous Integration and how it can be used, here. (add link)
 ```
 ::::
 

tutorials/1-installable-code.md

@@ -414,8 +414,10 @@ Python versions your package supports. While this won't impact your package buil
 Also because we are assuming you're creating a pure Python package, you can remove the following classifiers:
 
 ```toml
+classifiers = [
 "Programming Language :: Python :: Implementation :: CPython",
 "Programming Language :: Python :: Implementation :: PyPy",
+]
 ```
 
 Your new pyproject.toml file should now look something like this:
@@ -480,7 +482,7 @@ While you can do this using hatch, we are going to use pip for this lesson, so y
 
 :::{todo}
 Add this back in when the lesson is published
-- Activate the Python environment that you wish to use. If you need help with working with virtual environments [check out this lesson](extras/1-create-environment.md).
+- Activate the Python environment that you wish to use. If you need help with working with virtual environments check out this lesson (add link).
 :::
 
 ```bash
@@ -613,13 +615,11 @@ In the upcoming lessons you will:
 * Add more metadata to your `pyproject.toml` file to support PyPI publication.
 * learn how to publish to **conda-forge** from **PyPI**.
 
-
 * Add a [README file](add-readme.md) and [LICENSE](add-license-coc.md) to your package
-* [Add more metadata to your `pyproject.toml`](5-pyproject-toml.md) file to support PyPI publication.
+* [Add more metadata to your `pyproject.toml`](pyproject-toml.md) file to support PyPI publication.
 * [Learn how to build your package distribution](publish-pypi) files (**sdist** and **wheel**) and publish to **test PyPI**.
 * Finally you will learn how to [publish to **conda-forge**](publish-conda-forge) from **PyPI**.
 
-
 ## Footnotes
 
 [^shell-lesson]: [Carpentries shell lesson](https://swcarpentry.github.io/shell-novice/)

tutorials/add-license-coc.md

@@ -153,7 +153,7 @@ You can use your code of conduct as a tool that can be referenced when moderatin
 If you are unsure of what language to add to your `CODE_OF_CONDUCT`
 file, we suggest that you adopt the [contributor covenant language](https://www.contributor-covenant.org/version/2/1/code_of_conduct/) as a starting place.
 
-[![Contributor Covenant](https://img.shields.io/badge/Contributor%20Covenant-2.1-4baaaa.svg)](#)
+![Contributor Covenant](https://img.shields.io/badge/Contributor%20Covenant-2.1-4baaaa.svg)
 
 The `CODE_OF_CONDUCT.md` should be placed at the root of your project directory, similar to the LICENSE file.
 

tutorials/add-readme.md

@@ -196,6 +196,10 @@ Short description here using non-technical language that describes what your pac
 
 ## How to install pyosPackage
 
+:::{todo}
+- when i add more to the pyos package this can use that readme>
+:::
+
 To install this package run:
 
 `pip install pyosPackage`

tutorials/get-to-know-hatch.md

@@ -111,7 +111,7 @@ hatch config show will print out the contents of your config.toml file in your s
 Hatch offers a suite of features that will make creating, publishing
 and maintaining your Python package easier.
 
-:::{admonition}
+:::{admonition} Comparison to other tools
 :class: tip
 [We compared hatch to several of the other popular packaging tools in the ecosystem including flit, pdm and poetry. Learn more here](package-features)
 :::

tutorials/intro.md

@@ -290,7 +290,7 @@ You can install a Python package into a Python environment in the same way
 you might install NumPy or Pandas. Installing your package into an environment
 allows you to access it from any code run with that specific Python environment activated.
 
-:::{figure-md} packages-environment
+:::{figure-md} packages-environment-install
 
 <img src="../images/tutorials/environment-package-install.png" alt="Diagram showing the steps associated with creating a package and then installing it. The first arrow says your package and the second says pip install package. The second arrow leads to a box that represents a Python environment that already has some packages installed such as Pandas and NumPy. Your package will also get installed into that same environment when you pip install it." width="700px">
 
@@ -315,11 +315,11 @@ Then you can create a conda-forge recipe using the [Grayskull](https://github.co
 
 [You will learn more about the conda-forge publication process here.](publish-conda-forge.md)
 
-:::{figure-md} build-workflow-tutorial
+:::{figure-md} publish-package-pypi-conda-overview
 <img src="../images/tutorials/publish-package-pypi-conda.png" alt="Graphic showing the high level packaging workflow. On the left you see a graphic with code, metadata and tests in it. Those items all go into your package. Documentation and data are below that box because they aren't normally published in your packaging wheel distribution. an arrow to the right takes you to a build distribution files box. that box leads you to either publishing to testPyPI or the real PyPI. From PyPI you can then connect to conda-forge for an automated build that sends distributions from PyPI to conda-forge." width="700px">
 
 In the image above, you can see the steps associated with publishing
-your package on PyPI and conda-forge. Note that the distribution files that PyPI requires are the [sdist](#python-source-distribution) and [wheel](#python-wheel) files. Once you are ready to make your code publicly installable, you can publish it on PyPI. Once your code is on PyPI it is straight forward to then publish to conda-forge. You create a recipe using the Grayskull package and then you open a pr in the conda-forge recipe repository. You will learn more about this process in the [conda-forge lesson](#).
+your package on PyPI and conda-forge. Note that the distribution files that PyPI requires are the [sdist](#python-source-distribution) and [wheel](#python-wheel) files. Once you are ready to make your code publicly installable, you can publish it on PyPI. Once your code is on PyPI it is straight forward to then publish to conda-forge. You create a recipe using the Grayskull package and then you open a pr in the conda-forge recipe repository. You will learn more about this process in the [conda-forge lesson](/tutorials/publish-conda-forge).
 :::
 
 ## Yay, your package has users! Now what?

tutorials/publish-conda-forge.md

@@ -372,10 +372,6 @@ Below we break down each element of that list.
 >
 > -[x] Package does not ship static libraries. If static libraries are needed, [follow CFEP-18](https://github.com/conda-forge/cfep/blob/main/cfep-18.md).
 
-:::{note}
-
-:::
-
 **Translation:** A static library refers to a copy of a package built into your package. If your package is a pure Python package, then you can check that your package does not ship static libraries as this does not apply to you.
 
 The pyOpenSci tutorials are all pure Python and as such do not use static libraries in a linked or shipped (included in the package distribution) format.

tutorials/publish-pypi.md

@@ -227,7 +227,7 @@ Show them how to do this
 2. update the module repository directory to be the same
 :::
 
-:::{figure-md} build-workflow-tutorial
+:::{figure-md} test-pypi-search
 <img src="../images/tutorials/testpypi-search.png" alt="This is a screenshot of the test PyPI website. At the top in the search bar, you can see the search for pyosPackage. The search return says there were no results for pyosPackage Did you mean probpackage" width="700px">
 
 Before you try to upload to test PyPI, check to see if the name of your package is already taken. You can do that using

tutorials/pyproject-toml.md

@@ -1,6 +1,6 @@
 # Make your Python package PyPI ready - pyproject.toml
 
-In [the installable code lesson](2-installable-code), you learned how to add the bare minimum information to a `pyproject.toml` file to make it installable. You then learned how to [publish a bare minimum version of your package to PyPI](publish-pypi.md).
+In [the installable code lesson](1-installable-code), you learned how to add the bare minimum information to a `pyproject.toml` file to make it installable. You then learned how to [publish a bare minimum version of your package to PyPI](publish-pypi.md).
 
 Following that you learned how to add a:
 * [README.md](add-readme)
@@ -76,7 +76,7 @@ build-backend = "hatchling.build"
 
 The pyproject.toml file tells your build tool:
 
-- What build backend to use to build your package (we are using `hatchling` in this tutorial but there are [many others to chose from](build-backend-options)).
+- What build backend to use to build your package (we are using `hatchling` in this tutorial but there are [many others to chose from](/package-structure-code/python-package-build-tools)).
 - How and where to retrieve your package's version:
     - **statically** where you declare the version `version = "0.1.0"` or
     - **dynamically** where the tool looks to the most recent tag in your history to determine the current version.
@@ -94,7 +94,7 @@ repository to quickly understand your package's structure such as:
 Finally, the pyproject.toml file is also often used to configure tools such as static type checkers (e.g. mypy) and code formatters/linters (e.g. black, ruff).
 
 :::{tip}
-Check out the [PyPA documentation](https://packaging.python.org/en/latest/tutorials/packaging-projects/#creating-pyproject-toml) if you are interested in setting build configurations for other tools.
+Check out the [PyPA documentation](https://packaging.python.org/en/latest/tutorials/packaging-projects/#choosing-a-build-backend) if you are interested in setting build configurations for other tools.
 
 Note that some build tools may deviate in how they store project metadata. As such you may want to refer to their documentation if you decide to use a tool other than Hatch and hatchling. We have selected hatchling and hatch as our tool of choice for this tutorial as it adheres to PyPA rules and guidelines.
 
@@ -328,7 +328,7 @@ resolving a Python environment more challenging. As such only
 pin dependencies to a specific version if you absolutely need to
 do so.
 
-One build tool that you should be aware of that pins dependencies to an upper bound by default is Poetry. [Read more about how to safely add dependencies with Poetry, here.](../package-structure-code/python-package-build-tools.html#challenges-with-poetry)
+One build tool that you should be aware of that pins dependencies to an upper bound by default is Poetry. [Read more about how to safely add dependencies with Poetry, here.](challenges-with-poetry)
 :::
 
 ### Step 5: Add PyPI classifiers to your pyproject.toml file