Merge branch 'main' into index-structure

Author: sneakers-the-rat

.all-contributorsrc

@@ -450,6 +450,28 @@
         "review",
         "tutorial"
       ]
+    },
+    {
+      "login": "xmnlab",
+      "name": "Ivan Ogasawara",
+      "avatar_url": "https://avatars.githubusercontent.com/u/5209757?v=4",
+      "profile": "https://xmnlab.github.io",
+      "contributions": [
+        "code",
+        "review",
+        "tutorial"
+      ]
+    },
+    {
+      "login": "tomalrussell",
+      "name": "Tom Russell",
+      "avatar_url": "https://avatars.githubusercontent.com/u/2762769?v=4",
+      "profile": "https://github.com/tomalrussell",
+      "contributions": [
+        "code",
+        "review",
+        "tutorial"
+      ]
     }
   ],
   "contributorsPerLine": 7,

.zenodo.json

@@ -109,11 +109,6 @@
             "affiliation": "",
             "name": "Van der Walt, Stéfan"
         },
-        {
-            "type": "Other",
-            "affiliation": "",
-            "name": "Schwartz, Eli"
-        },
         {
             "type": "Other",
             "affiliation": "Quansight",
@@ -201,6 +196,36 @@
             "affiliation": "",
             "name": "Knorps, Maria"
         },
+        {
+            "type": "Other",
+            "affiliation": "",
+            "name": "Schwartz, Eli"
+        },
+        {
+            "type": "Other",
+            "affiliation": "",
+            "name": "Burns, Jackson"
+        },
+        {
+            "type": "Other",
+            "affiliation": "",
+            "name": "Jaimergp"
+        },
+        {
+            "type": "Other",
+            "affiliation": "",
+            "name": "h-vetinari"
+        },
+        {
+            "type": "Other",
+            "affiliation": "",
+            "name": "Ogasawara, Ivan"
+        },
+        {
+            "type": "Other",
+            "affiliation": "",
+            "name": "Russell, Tom"
+        },
         {
             "type": "Other",
             "affiliation": "",

README.md

@@ -1,6 +1,6 @@
 # <img src="https://www.pyopensci.org/images/logo.png" width=100 /> pyOpenSci scientific Python Packaging Guide
 <!-- ALL-CONTRIBUTORS-BADGE:START - Do not remove or modify this section -->
-[![All Contributors](https://img.shields.io/badge/all_contributors-43-orange.svg?style=flat-square)](#contributors-)
+[![All Contributors](https://img.shields.io/badge/all_contributors-45-orange.svg?style=flat-square)](#contributors-)
 <!-- ALL-CONTRIBUTORS-BADGE:END -->
 
 ![GitHub release (latest by date)](https://img.shields.io/github/v/release/pyopensci/python-package-guide?color=purple&display_name=tag&style=plastic)
@@ -130,6 +130,8 @@ Thanks goes to these wonderful people ([emoji key](https://allcontributors.org/d
     </tr>
     <tr>
       <td align="center" valign="top" width="14.28%"><a href="https://github.com/h-vetinari"><img src="https://avatars.githubusercontent.com/u/33685575?v=4?s=100" width="100px;" alt="h-vetinari"/><br /><sub><b>h-vetinari</b></sub></a><br /><a href="https://github.com/pyOpenSci/python-package-guide/commits?author=h-vetinari" title="Code">💻</a> <a href="https://github.com/pyOpenSci/python-package-guide/pulls?q=is%3Apr+reviewed-by%3Ah-vetinari" title="Reviewed Pull Requests">👀</a> <a href="#tutorial-h-vetinari" title="Tutorials">✅</a></td>
+      <td align="center" valign="top" width="14.28%"><a href="https://xmnlab.github.io"><img src="https://avatars.githubusercontent.com/u/5209757?v=4?s=100" width="100px;" alt="Ivan Ogasawara"/><br /><sub><b>Ivan Ogasawara</b></sub></a><br /><a href="https://github.com/pyOpenSci/python-package-guide/commits?author=xmnlab" title="Code">💻</a> <a href="https://github.com/pyOpenSci/python-package-guide/pulls?q=is%3Apr+reviewed-by%3Axmnlab" title="Reviewed Pull Requests">👀</a> <a href="#tutorial-xmnlab" title="Tutorials">✅</a></td>
+      <td align="center" valign="top" width="14.28%"><a href="https://github.com/tomalrussell"><img src="https://avatars.githubusercontent.com/u/2762769?v=4?s=100" width="100px;" alt="Tom Russell"/><br /><sub><b>Tom Russell</b></sub></a><br /><a href="https://github.com/pyOpenSci/python-package-guide/commits?author=tomalrussell" title="Code">💻</a> <a href="https://github.com/pyOpenSci/python-package-guide/pulls?q=is%3Apr+reviewed-by%3Atomalrussell" title="Reviewed Pull Requests">👀</a> <a href="#tutorial-tomalrussell" title="Tutorials">✅</a></td>
     </tr>
   </tbody>
 </table>

conf.py

@@ -20,7 +20,6 @@
 organization_name = "pyOpenSci"
 
 
-
 # -- Project information -----------------------------------------------------
 
 project = "pyOpenSci Python Package Guide"
@@ -29,7 +28,9 @@
 
 # Get the latest Git tag - there might be a prettier way to do this but...
 try:
-    release_value = subprocess.check_output(["git", "describe", "--tags"]).decode("utf-8").strip()
+    release_value = (
+        subprocess.check_output(["git", "describe", "--tags"]).decode("utf-8").strip()
+    )
     release_value = release_value[:4]
 except subprocess.CalledProcessError:
     release_value = "0.1"  # Default value in case there's no tag
@@ -57,6 +58,7 @@
 myst_enable_extensions = [
     "colon_fence",
     "deflist",
+    "attrs_block",
 ]
 myst_heading_anchors = 3
 
@@ -69,7 +71,7 @@
 # Link to our repo for easy PR/ editing
 html_theme_options = {
     "announcement": "<p><a href='https://www.pyopensci.org/about-peer-review/index.html'>We run peer review of scientific Python software. Learn more.</a></p>",
-    #"navbar_center": ["nav"], this can be a way to override the default navigation structure
+    # "navbar_center": ["nav"], this can be a way to override the default navigation structure
     "external_links": [
         {
             "url": "https://www.pyopensci.org",
@@ -92,7 +94,7 @@
         },
     ],
     "logo": {
-        #"text": "Python Packaging",
+        # "text": "Python Packaging",
         "image_dark": "logo-dark-mode.png",
         "image_light": "logo-light-mode.png",
         "alt_text": "pyOpenSci Python Package Guide. The pyOpenSci logo is a purple flower with pyOpenSci under it. The o in open sci is the center of the flower",

documentation/repository-files/license-files.md

@@ -47,7 +47,7 @@ To select your license, we suggest that you use GitHub's
 [Choose a License tool ](https://choosealicense.com/).
 
 If you choose your license when creating a new GitHub repository, you can also
-automatically get a text copy of the license file to add to your repo. However
+automatically get a text copy of the license file to add to your repository. However
 in some cases the license that you want is not available through that online
 process.
 
@@ -78,9 +78,9 @@ with the license that you selected for your package.
 :::{admonition} An example of how a license determine how code can be reused
 :class: note
 
-Let's use stackOverflow as an example that highlights how a license determines how code can or can not be used.
+Let's use StackOverflow as an example that highlights how a license determines how code can or can not be used.
 
-[Stack overflow uses a Creative Commons Share Alike license.](https://stackoverflow.com/help/licensing). The sharealike license requires you to use the same sharealike license when you reuse any code from stackoverflow.
+[Stack overflow uses a Creative Commons Share Alike license.](https://stackoverflow.com/help/licensing). The sharealike license requires you to use the same sharealike license when you reuse any code from StackOverflow.
 
 This means that technically, if you copy code from the Stack Overflow website, and use it in your package. And your packages uses a different license such as a MIT license, you are violating Stack Overflow's license requirements!
 
@@ -92,7 +92,7 @@ This means that technically, if you copy code from the Stack Overflow website, a
 
 While many permissive licenses do not require citation we STRONG encourage that you cite all software that you use in papers, blogs and other publications. You tell your users how to cite your package by using a [citation.cff file](https://docs.github.com/en/repositories/managing-your-repositorys-settings-and-features/customizing-your-repository/about-citation-files). We will cover this topic when we talk about creating DOI's for your package using zenodo.
 
-<!-- TODO: add link when lesson is created - but also we don't yet know how citation.cff files work with zenodo (do they work??) will the citation info update with a new zenodo link
+<!-- TODO: add link when lesson is created - but also we don't yet know how citation.cff files work with Zenodo (do they work??) will the citation info update with a new Zenodo link
 
 These files - we need to understand if that date releases auto populates or forces zenodo to modify it's citation. if it's not dynamic it could be problematic
 

images/tutorials/view-license-github.png

@@ -71,7 +71,7 @@ by the community now! Join our community review process or watch development of
 :class-card: left-aligned
 
 * [What is a Python package?](/tutorials/intro)
-* [Make your code installable](/tutorials/1-installable-code)
+* [Make your code installable](/tutorials/installable-code)
 * [Publish your package to (test) PyPi](/tutorials/publish-pypi)
 * [Publish your package to conda-forge](/tutorials/publish-conda-forge)
 

index.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">
 
@@ -48,13 +48,13 @@ Click here for a tutorial on publishing your package to PyPI.
 :::
 
 
-```{tip}
+:::{tip}
 On the package build page, we discussed the [two package distribution
 types that you will create when making a Python package](python-package-distribution-files-sdist-wheel): SDist (packaged as a .tar.gz or .zip) and
 Wheel (.whl) which is really a zip file. Both of those file "bundles" will
 be published on PyPI when you use [a standard build tool](python-package-build-tools) to build
 your package.
-```
+:::
 
 (about-conda)=
 ## What is Anaconda Cloud and conda?
@@ -69,8 +69,6 @@ packages. These repositories are known as channels (discussed below).
 :::{admonition} A brief history of conda's evolution
 :class: note
 
-The conda ecosystem evolved years ago to provide support for and
-simplify the process of managing software dependencies in scientific
 The conda ecosystem evolved years ago to provide support for, and
 simplify the process of, managing software dependencies in scientific
 Python projects.
@@ -156,11 +154,11 @@ to use conda to manage their local environments (which many do), you should
 consider publishing to both PyPI and the conda-forge channel (_more
 on that below_).
 
-```{admonition} Additional resources
-* [learn more about why conda-forge was created, here](https://conda-forge.org/docs/user/introduction.html#why-conda-forge)
+:::{admonition} Additional resources
+* [learn more about why conda-forge was created, here](https://conda-forge.org/docs/user/introduction.html)
 
 * [To learn more about conda terminology, check out their glossary.](https://docs.conda.io/projects/conda/en/latest/glossary.html )
-```
+:::
 
 <!-- One of our packages on conda-forge https://anaconda.org/conda-forge/pandera -->
 
@@ -171,7 +169,7 @@ we encourage you to consider doing so!
 
 Once your package is on PyPI, the process to add your package to conda-forge
 is straight forward to do. [You can follow the detailed steps provided
-by the conda-forge maintainer team.](https://conda-forge.org/docs/maintainer/adding_pkgs.html#generating-the-recipe).
+by the conda-forge maintainer team.](https://conda-forge.org/docs/maintainer/adding_pkgs.html).
 
 
 :::{button-link} ../tutorials/publish-conda-forge.html
@@ -186,9 +184,9 @@ If you want a step by step tutorial, click here.
 
 Once your package is added, you will have a feedstock repository on GitHub with your packages name
 
-```{tip}
+:::{tip}
 [Here is an example conda-forge feedstock for the pyOpenSci approved package - movingpandas](https://github.com/conda-forge/movingpandas-feedstock)
-```
+:::
 
 ### Maintaining your conda-forge package repository
 

package-structure-code/publish-python-package-pypi-conda.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-build-tools.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?