diff --git a/.github/workflows/build-site.yml b/.github/workflows/build-site.yml index 2a2ed70f..b4648238 100644 --- a/.github/workflows/build-site.yml +++ b/.github/workflows/build-site.yml @@ -37,12 +37,12 @@ jobs: uses: lycheeverse/lychee-action@8646ba30535128ac92d33dfc9133794bfdd9b411 #v2.8.0 with: fail: true - args: --verbose --no-progress _site/*.html + args: --verbose --no-progress --root-dir _site --exclude 'zenodo\.org' _site env: GITHUB_TOKEN: ${{secrets.GITHUB_TOKEN}} - name: Check HTML using htmlproofer - uses: chabad360/htmlproofer@v2 + uses: chabad360/htmlproofer@c2750eb7eb937599ac859517e7dd23a29f1b3ed7 #v2 with: directory: "_site" arguments: | diff --git a/.github/workflows/linkcheck.yml b/.github/workflows/linkcheck.yml index cf363cc7..4e84429f 100644 --- a/.github/workflows/linkcheck.yml +++ b/.github/workflows/linkcheck.yml @@ -11,7 +11,7 @@ jobs: runs-on: ubuntu-latest steps: - name: Check out the code - uses: actions/checkout@v6 + uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2 - name: Fetch main run: | @@ -19,7 +19,7 @@ jobs: git branch - name: Setup Ruby - uses: ruby/setup-ruby@v1 + uses: ruby/setup-ruby@6ca151fd1bfcfd6fe0c4eb6837eb0584d0134a0c #v1.290.0 with: bundler-cache: true # runs 'bundle install' and caches installed gems automatically @@ -35,7 +35,8 @@ jobs: args: > --verbose --no-progress - --exclude '^/.*' + --root-dir ${{ github.workspace }}/_site + --exclude 'zenodo\.org' _site env: GITHUB_TOKEN: ${{secrets.GITHUB_TOKEN}} diff --git a/_config.yml b/_config.yml index 59cc343d..cd665920 100644 --- a/_config.yml +++ b/_config.yml @@ -193,6 +193,7 @@ exclude: - /docs # ignore Minimal Mistakes /docs - /test # ignore Minimal Mistakes /test - styles/* # text spelling check + - lychee-report.md keep_files: - .git - .svn diff --git a/_data/authors.yml b/_data/authors.yml index e6fc6f2b..846299fd 100644 --- a/_data/authors.yml +++ b/_data/authors.yml @@ -18,9 +18,6 @@ pyopensci: - label: "Mastodon" icon: "fab fa-fw fa-mastodon" url: "https://fosstodon.org/@pyopensci" - - label: "Discord" - icon: "fab fa-fw fa-discord" - url: "https://discord.gg/yYyDFP2BcP" Executive Council: @@ -119,9 +116,6 @@ Jesse Mostipak: - label: "Mastodon" icon: "fab fa-fw fa-mastodon" url: "https://fosstodon.org/@pyopensci" - - label: "Discord" - icon: "fab fa-fw fa-discord" - url: "https://discord.gg/yYyDFP2BcP" Carlos Ramos Carreño: name : "Carlos Ramos Carreño" bio : "Software Developer" @@ -195,9 +189,6 @@ Mandy Moore: - label: "Mastodon" icon: "fab fa-fw fa-mastodon" url: "https://fosstodon.org/@pyopensci" - - label: "Discord" - icon: "fab fa-fw fa-discord" - url: "https://discord.gg/yYyDFP2BcP" Jeremiah Paige: name : "Jeremiah Paige" bio : "Python Speaker, Teacher, and Contributor of Open Source" diff --git a/_includes/package-grid.html b/_includes/package-grid.html index 0dc396cb..8e789fed 100644 --- a/_includes/package-grid.html +++ b/_includes/package-grid.html @@ -53,7 +53,7 @@

  • JOSS Approved
    • {% endif %} {% if apackage.partners contains "astropy" %} -
  • Astropy
    • +
  • Astropy
    • {% endif %} {% if apackage.active == false %}
  • Archived
    • diff --git a/_posts/2024-03-01-pyos-newsletter-march-2024.md b/_posts/2024-03-01-pyos-newsletter-march-2024.md index c2359541..f23b2fd5 100644 --- a/_posts/2024-03-01-pyos-newsletter-march-2024.md +++ b/_posts/2024-03-01-pyos-newsletter-march-2024.md @@ -38,7 +38,7 @@ You can read more about sunPy and pyOpenSci in [this lovely blog post](https://s Have a package you’ve developed, but aren’t sure it’s in scope for pyOpenSci? Complete a [pre-submission inquiry](https://github.com/pyOpenSci/software-submission/issues/new?assignees=&labels=presubmission&projects=&template=presubmission-inquiry.md&title=) and one of our editors will be in touch! ## We're going to [PyCon US](https://us.pycon.org/2024/) -Will we see you there? Our Executive Director and Founder, [Leah Wasser](https://github.com/lwasser), had her talk. [Friends don't let friends package alone](https://us.pycon.org/2024/schedule/presentation/34/), all about Python packaging for scientists, accepted for this May's conference. We've seen a sneak peek of her talk, and guarantee that you won't want to miss it! Be sure to [register today](https://us.pycon.org/2024/accounts/login/?next=/2024/registration/register)! +Will we see you there? Our Executive Director and Founder, [Leah Wasser](https://github.com/lwasser), had her talk. [Friends don't let friends package alone](https://us.pycon.org/2024/schedule/presentation/34/), all about Python packaging for scientists, accepted for this May's conference. We've seen a sneak peek of her talk, and guarantee that you won't want to miss it! Be sure to [register today](https://us.pycon.org/2024/)! ## Congratulations, Leah! diff --git a/_posts/2024-04-01-pyos-newsletter-april-2024.md b/_posts/2024-04-01-pyos-newsletter-april-2024.md index bec519dc..be30bdd3 100644 --- a/_posts/2024-04-01-pyos-newsletter-april-2024.md +++ b/_posts/2024-04-01-pyos-newsletter-april-2024.md @@ -26,7 +26,7 @@ pyOpenSci editors are volunteers who fulfill a critical role within pyOpenSci. E ## PyCon US 2024 Maintainers Summit -We’ve been talking (a lot) about the [PyCon Maintainers Summit](https://us.pycon.org/2024/events/maintainers-summit/) (which is now full, but [you can sign up for the waitlist](https://us.pycon.org/2024/events/maintainers-summit/)), happening this May in Pittsburgh. The Maintainers Summit, included in your [PyCon registration](https://us.pycon.org/2024/accounts/login/?next=/2024/registration/register), is where we come together to discuss and foster best practices on how to develop sustainable projects and nurture thriving communities. And thanks to [Mariatta Wijaya](https://mariatta.ca/), we’ve got an inside look into everything you can expect in [this incredible video](https://www.youtube.com/watch?v=L-Ok_89QJOM) featuring Kara Sowles, Inessa Pawson, and our Executive Director, Leah Wasser! +We’ve been talking (a lot) about the [PyCon Maintainers Summit](https://us.pycon.org/2024/events/maintainers-summit/) (which is now full, but [you can sign up for the waitlist](https://us.pycon.org/2024/events/maintainers-summit/)), happening this May in Pittsburgh. The Maintainers Summit, included in your [PyCon registration](https://us.pycon.org/2024/), is where we come together to discuss and foster best practices on how to develop sustainable projects and nurture thriving communities. And thanks to [Mariatta Wijaya](https://mariatta.ca/), we’ve got an inside look into everything you can expect in [this incredible video](https://www.youtube.com/watch?v=L-Ok_89QJOM) featuring Kara Sowles, Inessa Pawson, and our Executive Director, Leah Wasser! Watch the video @@ -59,7 +59,7 @@ Online tickets are still available for [PyConDE & PyData Berlin](https://2024.py [Registration is still open](https://us.pycon.org/2024/) for [PyCon US 2024](https://us.pycon.org/2024/), happening May 15th–23rd in Pittsburgh, PA. There’s also an online component for folks who can’t be there in person. It’s shaping up to be a stacked event, and you can view the schedule [here](https://us.pycon.org/2024/schedule/). ### GeoPython -Registration is live for [GeoPython](https://2024.geopython.net/), THE event for Python- and Geo-Enthusiasts. There are online and in-person options, and the event is scheduled for May 27th–29th in Basel, Switzerland. +Registration is live for [GeoPython](https://geo-python-site.readthedocs.io/en/2024.0/), THE event for Python- and Geo-Enthusiasts. There are online and in-person options, and the event is scheduled for May 27th–29th in Basel, Switzerland. ### SciPy–early bird ends soon! Happening July 8th–14th in Tacoma, WA, [SciPy registration is live](https://www.scipy2024.scipy.org/), and you can grab your early bird tickets until April 30th. diff --git a/_posts/2024-04-29-pyos-newsletter-may-2024.md b/_posts/2024-04-29-pyos-newsletter-may-2024.md index d6c0ffe7..4888a043 100644 --- a/_posts/2024-04-29-pyos-newsletter-may-2024.md +++ b/_posts/2024-04-29-pyos-newsletter-may-2024.md @@ -87,7 +87,7 @@ If you weren’t able to attend PyConDE & PyData Berlin 2024 to hear [Inessa Paw ## Upcoming Python events for scientists ### PyCon US -[Registration is still open](https://us.pycon.org/2024/accounts/login/?next=/2024/registration/register) for [PyCon US 2024](https://us.pycon.org/2024/), happening May 15th–23rd in Pittsburgh, PA. There’s also an online component for folks who can’t be there in person. It’s shaping up to be a stacked event, and you can [view the schedule here](https://us.pycon.org/2024/schedule/). +[Registration is still open](https://us.pycon.org/2024/) for [PyCon US 2024](https://us.pycon.org/2024/), happening May 15th–23rd in Pittsburgh, PA. There’s also an online component for folks who can’t be there in person. It’s shaping up to be a stacked event, and you can [view the schedule here](https://us.pycon.org/2024/schedule/). ### PyCon Italia Fancy a trip to Florence? Then grab your tickets for PyCon Italia! The conference runs Wednesday, May 22nd through Saturday, May 25th, and has a stacked list of [keynote speakers](https://2024.pycon.it/en/schedule/2024-05-22?view=grid). diff --git a/_posts/2024-05-28-pyos-newsletter-june-2024.md b/_posts/2024-05-28-pyos-newsletter-june-2024.md index 8d934454..73ab56b4 100644 --- a/_posts/2024-05-28-pyos-newsletter-june-2024.md +++ b/_posts/2024-05-28-pyos-newsletter-june-2024.md @@ -33,10 +33,10 @@ This year we had a tremendous turnout of over 20 people from several countries f ### Tutorials #### [Interactive data visualizations with Bokeh (in 2024)](https://cfp.scipy.org/2024/talk/JRLMLD/) -Along with [Timo Metzger](https://cfp.scipy.org/2024/speaker/HMRG3H/) and [Bryan Van de Ven](https://cfp.scipy.org/2024/speaker/BBLFMK/), pyOpenSci community member [Pavithra Eswaramoorthy]() will be covering everything you need to know to create beautiful and powerful interactive plots from scratch using Bokeh’s latest features. Starting with a quick introduction of Bokeh’s core concepts, the team will cover creating and customizing simple static plots like line and bar charts before introducing layers of interactivity, creating specialized plotting features like geographic maps, contour plots, Mathematical Text, and discussing new additions to Bokeh like ImageStacks. By the end, you will be able to create a complete interactive dashboard using Bokeh. +Along with Timo Metzger and Bryan Van de Ven, pyOpenSci community member [Pavithra Eswaramoorthy]() will be covering everything you need to know to create beautiful and powerful interactive plots from scratch using Bokeh’s latest features. Starting with a quick introduction of Bokeh’s core concepts, the team will cover creating and customizing simple static plots like line and bar charts before introducing layers of interactivity, creating specialized plotting features like geographic maps, contour plots, Mathematical Text, and discussing new additions to Bokeh like ImageStacks. By the end, you will be able to create a complete interactive dashboard using Bokeh. #### [3D Visualization with PyVista](https://cfp.scipy.org/2024/talk/GKGRWE/) -Led by [Tetsuo Koyama](https://cfp.scipy.org/2024/speaker/WY7NA9/), [Alexander Kaszynski](https://cfp.scipy.org/2024/speaker/3RXHG8/), [Bill Little](https://cfp.scipy.org/2024/speaker/FDVWDN/), and [Bane Sullivan](https://cfp.scipy.org/2024/speaker/NEC33M/), this tutorial demonstrates [PyVista's](https://github.com/pyvista/pyvista) latest capabilities and bring a wide range of users to the forefront of 3D visualization in Python, including: +Led by Tetsuo Koyama, Alexander Kaszynski, Bill Little, and Bane Sullivan, this tutorial demonstrates [PyVista's](https://github.com/pyvista/pyvista) latest capabilities and bring a wide range of users to the forefront of 3D visualization in Python, including: * Use PyVista to create 3D visualizations from a variety of datasets in common formats. * Overview the classes and data structures of PyVista with real-world examples. @@ -45,7 +45,7 @@ Led by [Tetsuo Koyama](https://cfp.scipy.org/2024/speaker/WY7NA9/), [Alexander K * We see this tutorial catering to anyone who wants to visualize data in any domain, and this ranges from basic Python users to advanced power users. #### [From RAGS to riches: Build an AI document inquiry web-app](https://cfp.scipy.org/2024/talk/W3ZJWG/) -[Pavithra Eswaramoorthy](https://cfp.scipy.org/2024/speaker/QGMGFB/), a Developer Advocate at [Quansight](https://quansight.com/), is teaming up with [Dharhas Pothina](https://cfp.scipy.org/2024/speaker/EKHUEY/) and [Andrew Huang](https://cfp.scipy.org/2024/speaker/QSLXKW/) to cover how to use RAG to build document-inquiry chat systems using different commercial and locally running LLMs. The topics we’ll cover include: +Pavithra Eswaramoorthy, a Developer Advocate at [Quansight](https://quansight.com/), is teaming up with Dharhas Pothina and Andrew Huang to cover how to use RAG to build document-inquiry chat systems using different commercial and locally running LLMs. The topics we’ll cover include: * **Introduction to RAG**, how it works and interacts with LLMs, and Ragna - a framework for RAG orchestration * **Creating and optimizing a basic chat function** that uses popular LLMs (like GPT) answers questions about your documents, using a Python API in Jupyter Notebooks @@ -68,7 +68,7 @@ Interested in helping out with our Packaging workshop? Reach out to us at [media {: .notice} #### [Data of an Unusual Size (2024 edition): A practical guide to analysis and interactive visualization of massive datasets](https://cfp.scipy.org/2024/talk/UKLNLQ/) -[Pavithra Eswaramoorthy](https://cfp.scipy.org/2024/speaker/QGMGFB/), and [Dharhas Pothina](https://cfp.scipy.org/2024/speaker/EKHUEY/), both from [Quansight](https://quansight.com/), will help you learn the fundamentals of analyzing massive datasets with real-world examples on actual powerful machines on a public cloud provided by the presenters – starting from how the data is stored and read, to how it is processed and visualized. +Pavithra Eswaramoorthy, and Dharhas Pothina, both from [Quansight](https://quansight.com/), will help you learn the fundamentals of analyzing massive datasets with real-world examples on actual powerful machines on a public cloud provided by the presenters – starting from how the data is stored and read, to how it is processed and visualized. ### Talks #### [The power of community in solving scientific Python’s most challenging problems](https://cfp.scipy.org/2024/talk/AMTLJ7/) @@ -78,13 +78,13 @@ Leah's talk is about writing the [pyOpenSci Python Packaging Guide](https://www. {: .notice} #### [Great Tables for Everyone](https://cfp.scipy.org/2024/talk/BRMQRW/) -This talk from [Rich Iannone](https://cfp.scipy.org/2024/speaker/NJCPZ7/), whose package [Great Tables](https://github.com/pyOpenSci/software-submission/issues/184) is currently under review with pyOpenSci, will provide a demonstration of Great Tables, showing how data can come alive in when in tabular form. We’ll use data from the fields of meteorology, chemistry, and the atmospheric sciences within our table-making examples. We’ll learn how the different components of a table (e.g., the column labels, the header, etc.) can be manipulated to best convey the data. We believe tables are worthy of being deemed data visualizations and we hope that Great Tables can become an indispensable tool in your data analysis workflow. +This talk from Rich Iannone, whose package [Great Tables](https://github.com/pyOpenSci/software-submission/issues/184) is currently under review with pyOpenSci, will provide a demonstration of Great Tables, showing how data can come alive in when in tabular form. We’ll use data from the fields of meteorology, chemistry, and the atmospheric sciences within our table-making examples. We’ll learn how the different components of a table (e.g., the column labels, the header, etc.) can be manipulated to best convey the data. We believe tables are worthy of being deemed data visualizations and we hope that Great Tables can become an indispensable tool in your data analysis workflow. #### [From Code to Clarity: Using Quarto for Python Documentation](https://cfp.scipy.org/2024/talk/GFGSTS/) -[Isabel Zimmerman](https://cfp.scipy.org/2024/speaker/AVSVUJ/), a member of our triage team and an Emeritus Editor in Chief, will be speaking from her experiences as an open source developer who works with multilingual tools, and how Quarto + quartodoc helped to fill those gaps. This talk is intended for anyone who might have to communicate with stakeholders through code using a web-based format. She'll be focusing on Python package documentation websites, but the stories and examples expose the difficulties in many types of technical communication. The intent is to have a lighthearted talk filled with examples of how to make technical communication and publishing easier and more accessible. +Isabel Zimmerman, a member of our triage team and an Emeritus Editor in Chief, will be speaking from her experiences as an open source developer who works with multilingual tools, and how Quarto + quartodoc helped to fill those gaps. This talk is intended for anyone who might have to communicate with stakeholders through code using a web-based format. She'll be focusing on Python package documentation websites, but the stories and examples expose the difficulties in many types of technical communication. The intent is to have a lighthearted talk filled with examples of how to make technical communication and publishing easier and more accessible. #### [Vector space embeddings and data maps for cyber defense](https://cfp.scipy.org/2024/talk/STUXTH/) -pyOpenSci community member [Benoit Hamelin](https://cfp.scipy.org/2024/speaker/SAQUZD/) will cover how the vast amounts of information of interest to cyber defense organizations comes in the form of unstructured data; from host-based telemetry and malware binaries, to phishing emails and network packet sequences. All of this data is extremely challenging to analyze. In recent years there have been huge advances in the methodology for converting unstructured media into vectors. However, leveraging such techniques for cyber defense data remains a challenge. +pyOpenSci community member Benoit Hamelin will cover how the vast amounts of information of interest to cyber defense organizations comes in the form of unstructured data; from host-based telemetry and malware binaries, to phishing emails and network packet sequences. All of this data is extremely challenging to analyze. In recent years there have been huge advances in the methodology for converting unstructured media into vectors. However, leveraging such techniques for cyber defense data remains a challenge. Imposing structure on unstructured data allows us to leverage powerful data science and machine learning tools. Structure can be imposed in multiple ways, but vector space representations, with a meaningful distance measure, have proven to be one of the most fruitful. @@ -99,7 +99,7 @@ We'll also be holding a pyOpenSci sprint at SciPy 2024! Be sure to follow us on Abstract shapes on a white background with the text: Save the Date. pyOpenSci Open Source Fall Festival. September 28 & 29, 2024. Entirely online! Follow us on socials for more info. fosstodon.org/@pyOpenSci linkedin.com/company/pyopensci pyopensci.org. -We love a good get-together, and our Open Source Fall Festival is no exception! Held entirely online using [Gather](https://www.gather.town/), our goals is to bring together members of the Python community that create open source tools with the members of the Python community who use the tools. In building this festival, our focus is on a grassroots, community-led event with some big unconference vibes. So mark your calendars, and save the date for September 28--29th, 2024! +We love a good get-together, and our Open Source Fall Festival is no exception! Held entirely online using Spatial Chat, our goals is to bring together members of the Python community that create open source tools with the members of the Python community who use the tools. In building this festival, our focus is on a grassroots, community-led event with some big unconference vibes. So mark your calendars, and save the date for September 28--29th, 2024! ## Python packages for everyone! pyOpenSci's [Open Peer Review process](https://www.pyopensci.org/about-peer-review/index.html) is experiencing an [unprecedented number of Python package submissions](https://github.com/pyOpenSci/software-submission/issues)! We're excited to see so many wonderful packages that are helping scientists help make the world a better place being submitted for review. Our open peer review process facilitates scientists getting credit and recognition for the work they’ve invested in developing scientific Python tools while also supporting them in building better software. The peer review process also supports scientists in finding vetted and maintained software, which drives their open science workflows. @@ -138,7 +138,7 @@ If you're interested in joining our Editorial Board, but have questions or would With keynotes from [Julia Silge](https://juliasilge.com/), [Dr. Elizabeth (Libby) Barnes](https://sites.google.com/view/barnesgroup-csu/prof-barnes), and [Kyle Cranmer](https://www.physics.wisc.edu/directory/cranmer-kyle/), [SciPy 2024](https://www.scipy2024.scipy.org/) is going to be yet another conference you don't want to miss! Held at the Tacoma Convention Center, July 8-14, 2024, [tickets are still available](https://ti.to/scipy/scipy2024)! ### PyData Eindhoven -With 14 captivating talks lined up, [PyData Eindhoven](https://pydata.org/eindhoven2024/) offers a diverse range of topics to expand your knowledge and inspire innovative thinking. From cutting-edge data analysis techniques to machine learning applications, our expert speakers will cover it all. Co-hosted with Day 2 of [JuliaCon](https://juliacon.org/2024/), [grab your tickets](https://pydata.org/eindhoven2024/tickets) and join your peers in the Netherlands this July 11th! +With 14 captivating talks lined up, [PyData Eindhoven](https://pydata.org/eindhoven2024/) offers a diverse range of topics to expand your knowledge and inspire innovative thinking. From cutting-edge data analysis techniques to machine learning applications, our expert speakers will cover it all. Co-hosted with Day 2 of [JuliaCon](https://juliacon.org/2024/), [grab your tickets](https://pydata.org/eindhoven2024/) and join your peers in the Netherlands this July 11th! ### BioC 2024 Taking place Wednesday July 24 - Friday July 26 at the Van Andel Institute in Grand Rapids, MI,the [BioC 2024: Where Software and Biology Connect](https://www.bioc2024.bioconductor.org/) hybrid conference still has [tickets available](https://www.bioc2024.bioconductor.org/registration). And what's more, all proceeds go to helping underrepresented minorities and individuals from low to middle-income countries, including students, fellows, and early career investigators. diff --git a/_posts/2024-06-20-pyos-guide-to-scipy.md b/_posts/2024-06-20-pyos-guide-to-scipy.md index 26175ad4..6c183bad 100644 --- a/_posts/2024-06-20-pyos-guide-to-scipy.md +++ b/_posts/2024-06-20-pyos-guide-to-scipy.md @@ -21,10 +21,10 @@ last_modified: 2024-08-29 ## Tutorials ### [Interactive data visualizations with Bokeh (in 2024)](https://cfp.scipy.org/2024/talk/JRLMLD/) -Along with [Timo Metzger](https://cfp.scipy.org/2024/speaker/HMRG3H/) and [Bryan Van de Ven](https://cfp.scipy.org/2024/speaker/BBLFMK/), pyOpenSci community member [Pavithra Eswaramoorthy](https://www.linkedin.com/in/pavithraes/) will be covering everything you need to know to create beautiful and powerful interactive plots from scratch using Bokeh’s latest features. Starting with a quick introduction of Bokeh’s core concepts, the team will cover creating and customizing simple static plots like line and bar charts before introducing layers of interactivity, creating specialized plotting features like geographic maps, contour plots, Mathematical Text, and discussing new additions to Bokeh like ImageStacks. By the end, you will be able to create a complete interactive dashboard using Bokeh. +Along with Timo Metzger and Bryan Van de Ven, pyOpenSci community member [Pavithra Eswaramoorthy](https://www.linkedin.com/in/pavithraes/) will be covering everything you need to know to create beautiful and powerful interactive plots from scratch using Bokeh’s latest features. Starting with a quick introduction of Bokeh’s core concepts, the team will cover creating and customizing simple static plots like line and bar charts before introducing layers of interactivity, creating specialized plotting features like geographic maps, contour plots, Mathematical Text, and discussing new additions to Bokeh like ImageStacks. By the end, you will be able to create a complete interactive dashboard using Bokeh. ### [3D Visualization with PyVista](https://cfp.scipy.org/2024/talk/GKGRWE/) -Led by [Tetsuo Koyama](https://cfp.scipy.org/2024/speaker/WY7NA9/), [Alexander Kaszynski](https://cfp.scipy.org/2024/speaker/3RXHG8/), [Bill Little](https://cfp.scipy.org/2024/speaker/FDVWDN/), and pyOpenSci peer review spatial editor [Bane Sullivan](https://www.linkedin.com/in/bane-sullivan/), this tutorial demonstrates [PyVista’s](https://github.com/pyvista/pyvista) latest capabilities and bring a wide range of users to the forefront of 3D visualization in Python, including: +Led by Tetsuo Koyama, Alexander Kaszynski, Bill Little, and pyOpenSci peer review spatial editor [Bane Sullivan](https://www.linkedin.com/in/bane-sullivan/), this tutorial demonstrates [PyVista’s](https://github.com/pyvista/pyvista) latest capabilities and bring a wide range of users to the forefront of 3D visualization in Python, including: * Use PyVista to create 3D visualizations from a variety of datasets in common formats. * Overview the classes and data structures of PyVista with real-world examples. * Be familiar of the various filters and features of PyVista. @@ -32,7 +32,7 @@ Led by [Tetsuo Koyama](https://cfp.scipy.org/2024/speaker/WY7NA9/), [Alexander K * We see this tutorial catering to anyone who wants to visualize data in any domain, and this ranges from basic Python users to advanced power users. ### [From RAGS to riches: Build an AI document inquiry web-app](https://cfp.scipy.org/2024/talk/W3ZJWG/) -[Pavithra Eswaramoorthy](https://cfp.scipy.org/2024/speaker/QGMGFB/), a Developer Advocate at [Quansight](https://quansight.com/), is teaming up with [Dharhas Pothina](https://cfp.scipy.org/2024/speaker/EKHUEY/) and [Andrew Huang](https://cfp.scipy.org/2024/speaker/QSLXKW/) to cover how to use RAG to build document-inquiry chat systems using different commercial and locally running LLMs. The topics we’ll cover include: +Pavithra Eswaramoorthy, a Developer Advocate at [Quansight](https://quansight.com/), is teaming up with Dharhas Pothina and Andrew Huang to cover how to use RAG to build document-inquiry chat systems using different commercial and locally running LLMs. The topics we’ll cover include: * **Introduction to RAG**, how it works and interacts with LLMs, and Ragna - a framework for RAG orchestration * **Creating and optimizing a basic chat function** that uses popular LLMs (like GPT) answers questions about your documents, using a Python API in Jupyter Notebooks * **Running a local LLM on GPUs** on the provided platform, and comparing its performance to commercial LLMs @@ -44,7 +44,7 @@ By the end of this tutorial, you will have an understanding of the fundamental c By the end of this tutorial, you will have an understanding of the fundamental components that form a RAG model, and practical knowledge of open source tools that can help you or your organization explore and build on your own applications. This tutorial is designed to enable enthusiasts in our community to explore an interesting topic using some beginner-friendly Python libraries. ### [Create Your First Python Package: Make Your Python Code Easier to Share and Use](https://cfp.scipy.org/2024/talk/QT9GBY/) -Led by pyOpenSci’s Executive Director and Founder, [Leah Wasser](https://github.com/lwasser), along with pyOpenSci editor [Isabel Zimmerman](https://cfp.scipy.org/2024/speaker/AVSVUJ/) and [Jeremiah Page](https://cfp.scipy.org/2024/speaker/LJ7ZSP/), who leads work on the [pyOpenSci packaging guide](https://www.pyopensci.org/python-package-guide/index.html), this tutorial session will teach you how to: +Led by pyOpenSci’s Executive Director and Founder, [Leah Wasser](https://github.com/lwasser), along with pyOpenSci editor Isabel Zimmerman and Jeremiah Page, who leads work on the [pyOpenSci packaging guide](https://www.pyopensci.org/python-package-guide/index.html), this tutorial session will teach you how to: * Create code that can be installed into different environments * Use [Hatch](https://hatch.pypa.io/latest/) as a workflow tool, making setup and installation of your code easier * Use Hatch to publish your package to (test) PyPI @@ -55,7 +55,7 @@ Creating code that can be shared and reused is the gold-standard of open science ### [Data of an Unusual Size (2024 edition): A practical guide to analysis and interactive visualization of massive datasets](https://cfp.scipy.org/2024/talk/UKLNLQ/) -[Pavithra Eswaramoorthy](https://cfp.scipy.org/2024/speaker/QGMGFB/) and [Dharhas Pothina](https://cfp.scipy.org/2024/speaker/EKHUEY/), both from [Quansight](https://quansight.com/), will help you learn the fundamentals of analyzing massive datasets with real-world examples on actual powerful machines on a public cloud provided by the presenters – starting from how the data is stored and read, to how it is processed and visualized. +Pavithra Eswaramoorthy and Dharhas Pothina, both from [Quansight](https://quansight.com/), will help you learn the fundamentals of analyzing massive datasets with real-world examples on actual powerful machines on a public cloud provided by the presenters – starting from how the data is stored and read, to how it is processed and visualized. ## Talks diff --git a/_posts/2024-08-02-pyopensci-at-scipy-2024.md b/_posts/2024-08-02-pyopensci-at-scipy-2024.md index 121a117e..6958ac82 100644 --- a/_posts/2024-08-02-pyopensci-at-scipy-2024.md +++ b/_posts/2024-08-02-pyopensci-at-scipy-2024.md @@ -274,8 +274,8 @@ ecosystem. These include: 2. Encouraging scientists to write better code, share their code, and build better software. 3. Ensuring scientists get credit for their open-source work. 4. Addressing the ongoing challenges of packaging in the Python ecosystem-—a topic - I discussed in my [PyCon talk in April](blog/python-packaging-friends-dont-let-friends-package-alone.html), - which is also available on [YouTube](https://www.youtube.com/watch?v=mJPoj9Ex9fk&list=PL2Uw4_HvXqvYhjub9bw4uDAmNtprgAvlJ). I'd love for you to check it out! + I discussed in my [PyCon talk in April](/blog/python-packaging-friends-dont-let-friends-package-alone.html), + which was also available on YouTube (video/playlist may have been moved). I'd love for you to check out the [SciPy 2024 conference site](https://www.scipy2024.scipy.org/) for current talks and tutorials. ### pyOpenSci's Python packaging guidebook is having a positive impact on the scientific Python ecosystem @@ -387,7 +387,7 @@ about all things Python, open source, and open science. * I worked with Sarah Kaiser on our new GitHub container to support workshops. * I had an _ad hoc_ sprint with [Angus](https://github.com/agoose77) and [Rowan](https://github.com/rowanc1) from the [MyST Markdown](https://mystmd.org/) community - to develop our [pyOpenSci peer review metrics dashboard](https://www.pyopensci.org/peer-review-metrics). + to develop our [pyOpenSci peer review metrics dashboard](https://www.pyopensci.org/metrics/). Additionally, I caught up with colleagues, chatting about packaging and scientific Python. @@ -435,7 +435,7 @@ We had a great group this year who worked on a variety of tasks, including: * Someone enthusiastic about Sphinx worked on our [pyos-sphinx-theme](https://github.com/pyOpenSci/pyos-sphinx-theme). pyOpenSci has several online "books" that would benefit from using the same theme and colors that follow the pyOpenSci brand. -* A handful of people contributed to our MyST Markdown [peer review metrics dashboard](https://www.pyopensci.org/peer-review-metrics). +* A handful of people contributed to our MyST Markdown [peer review metrics dashboard](https://www.pyopensci.org/metrics/).
    diff --git a/_posts/2024-08-30-pyopensci-monumental-growth-2024.md b/_posts/2024-08-30-pyopensci-monumental-growth-2024.md index f3419f92..05478e66 100644 --- a/_posts/2024-08-30-pyopensci-monumental-growth-2024.md +++ b/_posts/2024-08-30-pyopensci-monumental-growth-2024.md @@ -91,7 +91,7 @@ at the SciPy meetings. pyOpenSci's design is also based on our experiences developing software peer review guidelines for Python packages. According to our surveys, 80% of our maintainers and reviewers identify strongly as scientists. -As we developed our [peer review guide]((https://www.pyopensci.org/software-peer-review/)), it became clear that a beginner-friendly packaging guide was essential to support scientists in sharing their code because: +As we developed our [peer review guide](https://www.pyopensci.org/software-peer-review/), it became clear that a beginner-friendly packaging guide was essential to support scientists in sharing their code because: 1. [Our pre-review software checks](https://www.pyopensci.org/software-peer-review/how-to/editor-in-chief-guide.html#editor-checklist-template) require basic package infrastructure. Scientists must be clear about the core elements of a Python package. 2. We want to help scientists make their packages more maintainable over time by adding tests and [continuous integration (CI)](https://www.pyopensci.org/python-package-guide/tests/tests-ci.html#run-tests-with-continuous-integration) checks that run when someone submits a suggested change (or a pull request). We want to set scientists up for success. @@ -198,7 +198,7 @@ Our Python packaging tutorials went through the same community development and r ### Teaching online lessons is the best way to ensure they stay current -I have created hundreds of [open online lessons](https://www.leahwasser.com/my-path-to-open-education-earth-environmental-data-science) both for ecologists [NEON](https://www.neonscience.org/resources/learning-hub/teaching-modules/quantifying-drivers-and-impacts-natural-disturbance-events) and [earth and environmental scientists](https://www/earthdatascience.org). One of the biggest challenges is that it's easy for data science lessons to [become dated quickly](https://www.leahwasser.com/open-education-data-science-posting-online-is-not-enough)--especially in the rapidly evolving data science space. By teaching the lessons, we can update them regularly as the ecosystem evolves. We also often have users review the lessons at our [annual sprint events](blog/pyopensci-pyconus-2024-sprints.html) to test them out; more on pyOpenSci beginner-friendly sprints below. +I have created hundreds of [open online lessons](https://www.leahwasser.com/my-path-to-open-education-earth-environmental-data-science) both for ecologists [NEON](https://www.neonscience.org/resources/learning-hub/teaching-modules/quantifying-drivers-and-impacts-natural-disturbance-events) and earth and environmental scientists (formally earthdatascience.org). One of the biggest challenges is that it's easy for data science lessons to [become dated quickly](https://www.leahwasser.com/open-education-data-science-posting-online-is-not-enough)--especially in the rapidly evolving data science space. By teaching the lessons, we can update them regularly as the ecosystem evolves. We also often have users review the lessons at our [annual sprint events](/blog/pyopensci-pyconus-2024-sprints.html) to test them out; more on pyOpenSci beginner-friendly sprints below. @@ -306,7 +306,7 @@ In four months, we published a shiny new peer review guide. In January 2023, we -You can see more of our [peer review metrics on our MyST Markdown metrics dashboard here](https://www.pyopensci.org/peer-review-metrics/pyopensci-peer-review-stats) +You can see more of our [peer review metrics on our MyST Markdown metrics dashboard here](https://www.pyopensci.org/peer-review/peer-review-status-dashboard.html) {: .button } @@ -331,7 +331,7 @@ I'll dedicate another blog post to examining this data more thoroughly. Still, y ## A thoughtful, kind, and supportive community is what makes pyOpenSci special -Every morning, I wake up and am excited to begin my work. It doesn't matter if I'm working on budgets and other Executive Director-type tasks or developing educational content and teaching (my two favorite things); I can't wait to see what messages pop up in my inbox, be it Slack, email, Discord, or GitHub. I love my job because the pyOpenSci community is extraordinary. +Every morning, I wake up and am excited to begin my work. It doesn't matter if I'm working on budgets and other Executive Director-type tasks or developing educational content and teaching (my two favorite things); I can't wait to see what messages pop up in my inbox, be it email or GitHub. I love my job because the pyOpenSci community is extraordinary. People care about our organization's mission to help scientists make their science more open and collaborative. So they can solve the world's greatest challenges. diff --git a/_posts/2024-09-17-pyopensci-sustainability-plan-2024.md b/_posts/2024-09-17-pyopensci-sustainability-plan-2024.md index 0513930a..26e4578b 100644 --- a/_posts/2024-09-17-pyopensci-sustainability-plan-2024.md +++ b/_posts/2024-09-17-pyopensci-sustainability-plan-2024.md @@ -36,7 +36,7 @@ You can see this profound impact in the plot below.
    - A cumulative sum plot with months on the x-axis and number of review issues submitted on the y-axis. The curve starts with a small slope in 2019. Around January 2023, the slope becomes significantly steeper, indicating a dramatic increase in submissions when we reopened the peer review. At that point in the plot, there is a label that says 'Full-time funding'. + A cumulative sum plot with months on the x-axis and number of review issues submitted on the y-axis. The curve starts with a small slope in 2019. Around January 2023, the slope becomes significantly steeper, indicating a dramatic increase in submissions when we reopened the peer review. At that point in the plot, there is a label that says 'Full-time funding'.
    It is clear the impact that 1) working on our peer review guide and governance plus 2) funding, which allowed me to devote all of my professional time to pyOpenSci, had on our peer review program. It has been incredibly successful in the past year! And true success lies in the hands of the community that leads the review process. Today, on average, pyOpenSci has 10-14 packages in our software review queue.
    @@ -55,7 +55,7 @@ Funding has also allowed us to run events. In the past year, over 51 people have Contributions to pyOpenSci have also skyrocketed in the past two years.
    - Bar chart titled 'Staff vs. Volunteer Contributor by Quarter.' The chart shows counts of contributions made by staff and volunteers from 2018 Q4 through 2024 Q3. Contributions are stacked, with purple representing staff and green representing volunteers. The chart reveals a significant growth in contributions over time, particularly from 2022 onward, with a notable increase in both staff and volunteer contributions in 2023 and 2024. The pyOpenSci logo is in the bottom-right corner. + Bar chart titled 'Staff vs. Volunteer Contributor by Quarter.' The chart shows counts of contributions made by staff and volunteers from 2018 Q4 through 2024 Q3. Contributions are stacked, with purple representing staff and green representing volunteers. The chart reveals a significant growth in contributions over time, particularly from 2022 onward, with a notable increase in both staff and volunteer contributions in 2023 and 2024. The pyOpenSci logo is in the bottom-right corner.
    A bar plot showing staff vs volunteer contributions on GitHub over time. Funding has allowed us to support more volunteer activity over the past 2 years.
    diff --git a/_posts/2024-12-13-pyOpenSci-job-communications.md b/_posts/2024-12-13-pyOpenSci-job-communications.md index 96147346..997c2762 100644 --- a/_posts/2024-12-13-pyOpenSci-job-communications.md +++ b/_posts/2024-12-13-pyOpenSci-job-communications.md @@ -23,7 +23,7 @@ last_modified: 2025-05-14 ### About the role -pyOpenSci seeks a talented Writer and Social Media Specialist to enhance our communications and engagement with the scientific Python community. This position involves crafting engaging content highlighting our [online learning content](https://www.pyopensci.org/lessons/), [tutorials](https://www.pyopensci.org/python-package-guide/tutorials/intro.html), [events](https://www.pyopensci.org/events/), and [package ecosystem](https://www.pyopensci.org/python-packages.html) for our social media channels, newsletters, and blog to keep our community informed and inspired. It also involved reviewing and editing educational content. This is an excellent opportunity for someone passionate about open science and skilled in clear, impactful communication. The position requires 10-15 hours per week at a rate of 25-40$/hour based on experience, with the flexibility of remote, part-time work. There is some flexibility in this position week-to-week based on pyOpenSci's deadlines. This is a non-regular, part-time, remote, non-exempt position. This position will report +pyOpenSci seeks a talented Writer and Social Media Specialist to enhance our communications and engagement with the scientific Python community. This position involves crafting engaging content highlighting our [online learning content](https://www.pyopensci.org/lessons/), [tutorials](https://www.pyopensci.org/python-package-guide/tutorials/intro.html), [events](https://www.pyopensci.org/events.html), and [package ecosystem](https://www.pyopensci.org/python-packages.html) for our social media channels, newsletters, and blog to keep our community informed and inspired. It also involved reviewing and editing educational content. This is an excellent opportunity for someone passionate about open science and skilled in clear, impactful communication. The position requires 10-15 hours per week at a rate of 25-40$/hour based on experience, with the flexibility of remote, part-time work. There is some flexibility in this position week-to-week based on pyOpenSci's deadlines. This is a non-regular, part-time, remote, non-exempt position. This position will report to the pyOpenSci Executive Director. Applicants must be eligible for employment in the United States. ### About pyOpenSci diff --git a/_posts/2025-02-07-pyopensci-2024-a-year-in-review.md b/_posts/2025-02-07-pyopensci-2024-a-year-in-review.md index 8f4af7ec..43e5bc49 100644 --- a/_posts/2025-02-07-pyopensci-2024-a-year-in-review.md +++ b/_posts/2025-02-07-pyopensci-2024-a-year-in-review.md @@ -85,7 +85,7 @@ To further our commitment to equity, we awarded 25+ scholarships to support part ### Event Highlights: Fall Festival -Our first-ever [Fall Festival](#) featured inspiring keynote speakers like Rowan Cockett, who introduced participants to [MyST Markdown](https://mystmd.org/), Melissa Mendoça who discussed her personal pathway into open source from academia, and Eric Ma, who overviewed the importance of [reproducibility in science](/human-dimension-clean-documented-data-science-code.html). +Our first-ever [Fall Festival](#) featured inspiring keynote speakers like Rowan Cockett, who introduced participants to [MyST Markdown](https://mystmd.org/), Melissa Mendoça who discussed her personal pathway into open source from academia, and Eric Ma, who overviewed the importance of [reproducibility in science](/blog/human-dimension-clean-documented-data-science-code.html). On the event's last day, George Stagg, developer of Quarto Live, and James Balamuta kicked off the day with an overview of how Quarto Live makes interactive publishing of dynamic scientific outputs easier, connecting scientific workflows with shared outputs. @@ -115,10 +115,10 @@ The Fall Festival wouldn’t have been possible without the dedication of our in #### Open education lessons from the Fall Festival Participants didn’t just learn—they contributed! Thanks to the collaborative energy, the event produced several lessons that are now freely available to the community: -- [Writing Clean Code](https://www.pyopensci.org/lessons/clean-modular-code/intro-clean-code.html#intro-clean-code) -- [Optimizing Code for Better Workflows](https://www.pyopensci.org/lessons/code-workflow-logic/intro.html) -- [Running Code Efficiently](https://www.pyopensci.org/lessons/running-code/intro.html) -- [Publishing and Sharing Code](https://www.pyopensci.org/lessons/publish-share-code/intro.html) +- [Writing Clean Code](https://www.pyopensci.org/lessons/write-better-code/clean-modular-code/) +- [Optimizing Code for Better Workflows](https://www.pyopensci.org/lessons/write-better-code/optimize-code/) +- [Running Code Efficiently](https://www.pyopensci.org/lessons/package-share-code/run-code/) +- [Publishing and Sharing Code](https://www.pyopensci.org/lessons/package-share-code/publish-share-code/) These lessons reinforce key technical skills and showcase the power of community-driven learning and co-creation. diff --git a/_posts/2025-03-05-pyOpenSci-first-open-science-festival.md b/_posts/2025-03-05-pyOpenSci-first-open-science-festival.md index eb5f608b..39a92578 100644 --- a/_posts/2025-03-05-pyOpenSci-first-open-science-festival.md +++ b/_posts/2025-03-05-pyOpenSci-first-open-science-festival.md @@ -83,7 +83,7 @@ We kicked the event off on Monday, October 28, with a morning of KeyNote talks h {% include video id="JfpetG7nVgc" provider="youtube" %} -[Eric's talk](human-dimension-clean-documented-data-science-code.html) highlighted how simple practices like clear documentation, readable code, and user-friendly installation can amplify the impact of data science projects. +[Eric's talk](/blog/human-dimension-clean-documented-data-science-code.html) highlighted how simple practices like clear documentation, readable code, and user-friendly installation can amplify the impact of data science projects. A standout moment? The "Roast Your Repo" exercise! Eric invited attendees to critique a repository from his thesis, showcasing the power of small improvements—like adding a fleshed-out README or modularizing code—to make research reusable and collaborative. It was a fun, hands-on way to explore how the human touch transforms code quality. And let's be honest, we all likely have one of those code bases or repos from our early degrees! I sure do (and it's not even on GitHub!). @@ -144,12 +144,12 @@ Each day introduced new tools and practices to help participants transform their ### Day 1: Write Better, Cleaner Scientific Code -We started by diving into [writing better, cleaner code](https://www.pyopensci.org/lessons/clean-modular-code/intro-clean-code.html#intro-clean-code). Participants explored how to make their code: -- [DRY (Don’t Repeat Yourself)](https://www.pyopensci.org/lessons/clean-modular-code/python-dry-modular-code.html) and modular, -- [Expressive](https://www.pyopensci.org/lessons/clean-modular-code/python-write-expressive-code.html) and easy to understand, -- [Consistent with Python style guidelines](https://www.pyopensci.org/lessons/clean-modular-code/python-pep-8.html) like PEP 8. +We started by diving into [writing better, cleaner code](https://www.pyopensci.org/lessons/write-better-code/clean-modular-code/). Participants explored how to make their code: +- [DRY (Don’t Repeat Yourself)](https://www.pyopensci.org/lessons/write-better-code/clean-modular-code/python-dry-modular-code.html) and modular, +- [Expressive](https://www.pyopensci.org/lessons/write-better-code/clean-modular-code/python-write-expressive-code.html) and easy to understand, +- [Consistent with Python style guidelines](https://www.pyopensci.org/lessons/write-better-code/clean-modular-code/python-pep-8.html) like PEP 8. -We introduced strategies to improve robustness, such as creating [functions](https://www.pyopensci.org/lessons/code-workflow-logic/intro.html) and using [tests and checks](https://www.pyopensci.org/lessons/code-workflow-logic/python-function-checks.html) to validate outputs. +We introduced strategies to improve robustness, such as creating [functions](https://www.pyopensci.org/lessons/write-better-code/optimize-code/) and using [tests and checks](https://www.pyopensci.org/lessons/write-better-code/optimize-code/python-function-checks.html) to validate outputs. ### Day 2: Create Your First Python Package @@ -174,10 +174,10 @@ On Day 4, we empowered participants to share their work more broadly. Many learn {: .highlight-quote .magenta } Key share your code topics included: -- [Why sharing code matters](https://www.pyopensci.org/lessons/publish-share-code/share-code.html), -- [Adding a DOI to code using Zenodo](https://www.pyopensci.org/lessons/publish-share-code/cite-code.html), +- [Why sharing code matters](https://www.pyopensci.org/lessons/package-share-code/publish-share-code/share-code.html), +- [Adding a DOI to code using Zenodo](https://www.pyopensci.org/lessons/package-share-code/publish-share-code/cite-code.html), - Publishing through [JOSS](https://joss.theoj.org/) or the [pyOpenSci peer review process](https://www.pyopensci.org/about-peer-review/index.html), -- Publishing code on [PyPI](https://www.pyopensci.org/lessons/publish-share-code/publish-code.html#pypi) using Hatch. +- Publishing code on [PyPI](https://www.pyopensci.org/lessons/package-share-code/publish-share-code/publish-code.html#pypi) using Hatch. - NOTE: we also have a [publish to conda-forge lesson](https://www.pyopensci.org/python-package-guide/package-structure-code/publish-python-package-pypi-conda.html).
    @@ -190,7 +190,7 @@ On Day 4, we empowered participants to share their work more broadly. Many learn We wrapped up with an introduction to [Quarto](https://quarto.org/), a powerful tool for creating dynamic, interactive scientific narratives. Participants explored how to integrate code, data, and findings into a cohesive story—transforming static publications into living, engaging documents. -We also showcased [Quarto Live](https://quarto.org/docs/live/), which lets users dynamically interact with code in the browser. For educators, this opens exciting opportunities to create lessons where students can learn directly in a live coding environment. How cool is that? +We also showcased [Quarto Live](https://quarto.org/docs/guide/), which lets users dynamically interact with code in the browser. For educators, this opens exciting opportunities to create lessons where students can learn directly in a live coding environment. How cool is that? Fun fact: GreatTables has been [accepted by pyOpenSci](https://github.com/pyOpenSci/software-submission/issues/202) with the plan to be fast-tracked through the Journal of Open Source Software (JOSS) after the pyOpenSci review through [our JOSS partnership](https://www.pyopensci.org/software-peer-review/partners/joss.html). diff --git a/_posts/2025-03-13-python-packaging-security-pypi.md b/_posts/2025-03-13-python-packaging-security-pypi.md index 60e6f69e..bb695905 100644 --- a/_posts/2025-03-13-python-packaging-security-pypi.md +++ b/_posts/2025-03-13-python-packaging-security-pypi.md @@ -65,7 +65,7 @@ The Ultralytics breach highlights the need for us all to follow and understand s First, make sure that your PyPI publish GitHub Action uses an isolated GitHub environment. Isolated environments ensure your publishing process remains secure even if other parts of your CI pipeline are compromised. This is because you can lock an environment down by ensuring that only specific users can authorize this environment to run. -A GitHub Action is a CI/CD (Continuous Integration/Continuous Deployment) tool that allows you to automate tests. [Click here to read more about what CI/CI is.](https://www.pyopensci.org/python-package-guide/continuous-integration/ci.html) +A GitHub Action is a CI/CD (Continuous Integration/Continuous Deployment) tool that allows you to automate tests. [Click here to read more about what CI/CI is.](https://www.pyopensci.org/python-package-guide/maintain-automate/ci.html) {: .notice .notice--success } If you look at the workflow example below, notice that we have an [environment called `pypi`](https://github.com/pyOpenSci/pyosMeta/blob/2a09fba/.github/workflows/publish-pypi.yml#L57) that is used for trusted publishing. The `pypi` environment creates a direct link between this action and PyPI Trusted Published (discussed below). @@ -179,7 +179,7 @@ For an example of a GitHub workflow that uses Trusted Publishing, check out our ## 3. Add `zizmor` to your CI workflows -Finally, consider adding [Zizmor](https://woodruffw.github.io/zizmor/) to your [Continuous Integration (CI)](https://www.pyopensci.org/python-package-guide/continuous-integration/ci.html#what-is-continuous-integration) and [pre-commit checks](https://www.pyopensci.org/python-package-guide/package-structure-code/code-style-linting-format.html#use-pre-commit-hooks-to-run-code-formatters-and-linters-on-commits). +Finally, consider adding [Zizmor](https://woodruffw.github.io/zizmor/) to your [Continuous Integration (CI)](https://www.pyopensci.org/python-package-guide/maintain-automate/ci.html#what-is-continuous-integration) and [pre-commit checks](https://www.pyopensci.org/python-package-guide/package-structure-code/code-style-linting-format.html#use-pre-commit-hooks-to-run-code-formatters-and-linters-on-commits). Zizmor is a static analysis tool designed to help identify GitHub Action security issues. Zizmor scans your workflows and highlights common vulnerabilities, ensuring your continuous integration / continuous deployment pipelines remain secure and efficient. diff --git a/_posts/2025-06-30-pyos-scipy-2025.md b/_posts/2025-06-30-pyos-scipy-2025.md index e9445ccd..b4442219 100644 --- a/_posts/2025-06-30-pyos-scipy-2025.md +++ b/_posts/2025-06-30-pyos-scipy-2025.md @@ -176,7 +176,6 @@ You can also: Follow us on socials: -* [Discord](https://discord.com/invite/yYyDFP2BcP) * [Mastodon](https://fosstodon.org/@pyopensci) * [Bluesky](https://bsky.app/profile/pyopensci.org) * [LinkedIn](https://www.linkedin.com/company/pyopensci/) diff --git a/_posts/2025-07-24-scipy-2025-recap.md b/_posts/2025-07-24-scipy-2025-recap.md index 734190ce..b8ebf940 100644 --- a/_posts/2025-07-24-scipy-2025-recap.md +++ b/_posts/2025-07-24-scipy-2025-recap.md @@ -27,7 +27,7 @@ last_modified: 2025-05-06 This year, more than 15 members of the pyOpenSci community participated in the conference. We hosted a workshop, facilitated a BoF session with over 60 participants, gave talks, and filled the hallway track with laughter, advice, and real conversations about scientific Python pain points and the future of research software. We also led a community sprint where contributors opened over 30 issues and pull requests—an incredible showing of collaboration across experience levels. -To help new contributors feel supported, we shared our ['Contribute to Open Source' lessons](https://www.pyopensci.org/lessons/contribute.html), which walk you through the process of making your first contribution in a welcoming, beginner-friendly way. +To help new contributors feel supported, we shared our ['Contribute to Open Source' lessons](https://www.pyopensci.org/lessons/contribute-open-source/), which walk you through the process of making your first contribution in a welcoming, beginner-friendly way. Here are a few additional highlights from the week. @@ -110,11 +110,9 @@ pyOpenSci is partnering with the [Stanford Open Source Program Office (OSPO)](ht We’ll also be co-hosting a packaging workshop at Stanford later this year, so stay tuned for more details on that! -## Join our Slack community - If you joined us during SciPy this year, thank you. Whether you were sprinting, chatting, teaching, or just soaking it all in, you helped make it special. -If you missed it but want to get involved, check out our [volunteer page](https://www.pyopensci.org/volunteer.html) or come say hi in [Slack](https://join.slack.com/t/pyopensci/shared_invite/zt-39qitgkqb-gZTIo79xCJhS5kSxW1yNfg). +If you missed it but want to get involved, check out our [volunteer page](https://www.pyopensci.org/volunteer.html). Open science moves forward when we build it together, and SciPy 2025 reminded us just how much we can do when we do. @@ -134,11 +132,10 @@ There are lots of ways to get involved if you are interested\! You can also: -* Keep an eye on our [events page](https://www.pyopensci.org/events/index.html) for upcoming training events. +* Keep an eye on our [events page](https://www.pyopensci.org/events.html) for upcoming training events. Follow us on social platforms: -* [Discord](https://discord.com/invite/yYyDFP2BcP) * [Mastodon](https://fosstodon.org/@pyopensci) * [Bluesky](https://bsky.app/profile/pyopensci.org) * [LinkedIn](https://www.linkedin.com/company/pyopensci/) diff --git a/_posts/2025-08-05-scipy-bof-lessons-learned.md b/_posts/2025-08-05-scipy-bof-lessons-learned.md index 9a2958cd..12e7eeed 100644 --- a/_posts/2025-08-05-scipy-bof-lessons-learned.md +++ b/_posts/2025-08-05-scipy-bof-lessons-learned.md @@ -221,11 +221,10 @@ Whether you’re new to open science or have been building tools for decades, th You can also: -* Keep an eye on our [events page](https://www.pyopensci.org/events/index.html) for upcoming training events. +* Keep an eye on our [events page](https://www.pyopensci.org/events.html) for upcoming training events. Follow us on social platforms: -* [Discord](https://discord.com/invite/yYyDFP2BcP) * [Mastodon](https://fosstodon.org/@pyopensci) * [Bluesky](https://bsky.app/profile/pyopensci.org) * [LinkedIn](https://www.linkedin.com/company/pyopensci/) diff --git a/_posts/2025-08-13-meet-mandy.md b/_posts/2025-08-13-meet-mandy.md index 7a737cfd..7852d09f 100644 --- a/_posts/2025-08-13-meet-mandy.md +++ b/_posts/2025-08-13-meet-mandy.md @@ -40,4 +40,4 @@ Her role supports one of the most essential parts of pyOpenSci’s mission: **ma Mandy lives in **York, Pennsylvania,** with her partner **Keith**, their three kids, and two very good dogs: **Gallagher**, a gentle golden retriever, and **Luna**, a tiny but mighty miniature Yorkshire Terrier. Outside of work, she’s a lifelong writer, recovering perfectionist, and astrology nerd who still gets excited about the magic of a well-written sentence. She’s currently in the middle of planning her November wedding, which means her calendar is full of both GitHub issues *and* flower mockups. -Please join us in giving Mandy a warm welcome\! You can find her in the [pyOpenSci Slack](https://www.pyopensci.org/slack), or connect on [LinkedIn](https://www.linkedin.com/in/missmandymoore/) to say hi. You can also find her writing at exhotmess.net and learn more about her tech work at [mandymoore.tech](https://www.mandymoore.tech). +Please join us in giving Mandy a warm welcome! You can connect on LinkedIn to say hi. You can also find her writing at exhotmess.net and learn more about her tech work at mandymoore.tech. diff --git a/_posts/2025-08-14-pyopensci-executive-council-rototation.md b/_posts/2025-08-14-pyopensci-executive-council-rototation.md index a6bdf779..8be2cffb 100644 --- a/_posts/2025-08-14-pyopensci-executive-council-rototation.md +++ b/_posts/2025-08-14-pyopensci-executive-council-rototation.md @@ -80,11 +80,11 @@ There are lots of ways to get involved if you are interested\! You can also: -* Keep an eye on our [events page](https://www.pyopensci.org/events/index.html) for upcoming training events. +* Keep an eye on our [events page](https://www.pyopensci.org/events.html) for upcoming training events. Follow us on social platforms: -* [Discord](https://discord.com/invite/yYyDFP2BcP) + * [Mastodon](https://fosstodon.org/@pyopensci) * [Bluesky](https://bsky.app/profile/pyopensci.org) * [LinkedIn](https://www.linkedin.com/company/pyopensci/) diff --git a/_posts/2025-09-11-pyopensci-september-news-2025.md b/_posts/2025-09-11-pyopensci-september-news-2025.md index 3c77f8c8..bf3ed79d 100644 --- a/_posts/2025-09-11-pyopensci-september-news-2025.md +++ b/_posts/2025-09-11-pyopensci-september-news-2025.md @@ -15,7 +15,7 @@ comments: true last_modified: 2025-09-11 --- -The summer was full of connection, collaboration, and momentum in the pyOpenSci community. Whether you joined us at [SciPy](https://scipy.org/), submitted a package for review, or just lurked in Slack, we’re so grateful you’re here! +The summer was full of connection, collaboration, and momentum in the pyOpenSci community. Whether you joined us at [SciPy](https://scipy.org/), submitted a package for review, or just lurked, we’re so grateful you’re here! Here’s what’s been happening 👇 @@ -25,7 +25,7 @@ Here’s what’s been happening 👇 **Welcome, Philip Narteh!** -We’re thrilled to welcome [**Philip Narteh**](https://github.com/Phinart98) as pyOpenSci’s very first **Open Source Infrastructure Intern**, supported by [Quansight Labs](https://labs.quansight.org/), [Melissa Mendonça](https://github.com/melissawm), and [Tania Allard](https://github.com/trallard). Philip will be helping us migrate our website to [Django](https://www.djangoproject.com/), bringing valuable experience in accessibility within the Django ecosystem. We’re so excited to have you here, Philip! +We’re thrilled to welcome [**Philip Narteh**](https://github.com/Phinart98) as pyOpenSci’s very first **Open Source Infrastructure Intern**, supported by [Quansight](https://quansight.com/), [Melissa Mendonça](https://github.com/melissawm), and [Tania Allard](https://github.com/trallard). Philip will be helping us migrate our website to [Django](https://www.djangoproject.com/), bringing valuable experience in accessibility within the Django ecosystem. We’re so excited to have you here, Philip! **Contributor milestones** @@ -111,7 +111,6 @@ Here, we’ll walk you through building your first Python package using Hatch, U ## **🛠️ How You Can Get Involved** * Volunteer with pyOpenSci – from peer review to outreach, we welcome contributors of all kinds. -* Join our Slack – connect with the scientific Python and open science community. * Follow us – [LinkedIn](https://www.linkedin.com/company/pyopensci/), [Mastodon](https://fosstodon.org/@pyOpenSci), [Bluesky](https://bsky.app/profile/pyopensci.org). --- @@ -146,11 +145,11 @@ There are lots of ways to get involved if you are interested! You can also: -* Keep an eye on our [events page](https://www.pyopensci.org/events/index.html) for upcoming training events. +* Keep an eye on our [events page](https://www.pyopensci.org/events.html) for upcoming training events. Follow us on social platforms: -* [Discord](https://discord.com/invite/yYyDFP2BcP) + * [Mastodon](https://fosstodon.org/@pyopensci) * [Bluesky](https://bsky.app/profile/pyopensci.org) * [LinkedIn](https://www.linkedin.com/company/pyopensci/) diff --git a/_posts/2025-09-14-pyopensci-surviving-to-thriving.md b/_posts/2025-09-14-pyopensci-surviving-to-thriving.md index 72a20c25..1faa75cc 100644 --- a/_posts/2025-09-14-pyopensci-surviving-to-thriving.md +++ b/_posts/2025-09-14-pyopensci-surviving-to-thriving.md @@ -80,11 +80,11 @@ There are lots of ways to get involved if you are interested! You can also: -* Keep an eye on our [events page](https://www.pyopensci.org/events/index.html) for upcoming training events. +* Keep an eye on our [events page](https://www.pyopensci.org/events.html) for upcoming training events. Follow us on social platforms: -* [Discord](https://discord.com/invite/yYyDFP2BcP) + * [Mastodon](https://fosstodon.org/@pyopensci) * [Bluesky](https://bsky.app/profile/pyopensci.org) * [LinkedIn](https://www.linkedin.com/company/pyopensci/) diff --git a/_posts/2025-10-02-why-we-choose-what-we-choose.md b/_posts/2025-10-02-why-we-choose-what-we-choose.md index 863c4c22..6877ba25 100644 --- a/_posts/2025-10-02-why-we-choose-what-we-choose.md +++ b/_posts/2025-10-02-why-we-choose-what-we-choose.md @@ -43,7 +43,7 @@ Projects that manage to attract and maintain a broad base of contributors will b It is very important to us that the tools and processes we stand behind support the full set of community standards. -For Python, this typically means conforming to [Python Enhancement Proposals](pep.python.org), but may also involve other standard bodies such as [Scientific Python Ecosystem Coordination](https://scientific-python.org/specs/). +For Python, this typically means conforming to [Python Enhancement Proposals](https://peps.python.org), but may also involve other standard bodies such as [Scientific Python Ecosystem Coordination](https://scientific-python.org/specs/). Supporting community standards demonstrates that the project respects the community it is working within and is serious about interoperability with other tools and processes. When done right, these tools empower their users to move this workflow, or any of its inputs or outputs, to another standards-compliant tool or process with little to no friction. It also makes it easier to teach since many of the concepts, as well as in some cases entire parts of project data, are tool-agnostic and can feel "familiar" even to those that have never used the tool before. There is also likely to be more documentation developed through forums, blogs, workshops, and other online platforms, because they apply to more than one tool. diff --git a/_posts/events/2024-08-09-pyopensci-fall-festival.md b/_posts/events/2024-08-09-pyopensci-fall-festival.md index f09296ef..d5e426f1 100644 --- a/_posts/events/2024-08-09-pyopensci-fall-festival.md +++ b/_posts/events/2024-08-09-pyopensci-fall-festival.md @@ -6,7 +6,7 @@ author: event: start_date: "2024-10-28" end_date: "2024-11-01" - location: Online using [Gather](https://www.gather.town/) + location: Online using Spatial Chat permalink: /events/pyopensci-2024-fall-festival.html header: overlay_image: images/headers/pyopensci-sustainability.png @@ -34,7 +34,7 @@ Interested? Read on to learn more! ## pyOpenSci's 2024 Fall Festival logistics: * **What:** An online community training and networking event -* **Where:** Online using [SpatialChat]([https://www.gather.town/](https://www.spatial.chat/)) (learn more about SpatialChats's system requirements [here](https://guide.spatialinc.com/hc/en-us/articles/1500004491422-Minimum-System-Requirements) +* **Where:** Online using SpatialChat (learn more about SpatialChats's system requirements [here](https://guide.spatialinc.com/hc/en-us/articles/1500004491422-Minimum-System-Requirements) * **When:** Monday, October 28--Friday, November 01, 2024 * **Who:** If you are a scientist, a researcher, a student, or anyone interested in writing better, cleaner code that can be installed into different environments and shared, then this event is for you! * **Cost - Day 1 Keynote talks:** free. @@ -114,16 +114,16 @@ Our speakers for the Fall Festival are: * [Melissa Mendoça](https://github.com/melissawm) * [Rowan Cockett](https://curvenote.com/mission) -We'll also hold "Day 0" office hours for all registered workshop attendees. Drop into our Day 0 office hours to say hello, get used to using our online platform, [Gather](https://www.gather.town/), and get help with any computer setup issues you might have before the workshops begin. +We'll also hold "Day 0" office hours for all registered workshop attendees. Drop into our Day 0 office hours to say hello, get used to using our online platform, Spatial Chat, and get help with any computer setup issues you might have before the workshops begin. We want to set you up for learning success! #### Keynote speaker bios **[Eric Ma](https://ericmjl.github.io/)** -As Senior Principal Data Scientist at [Moderna](https://www.modernatx.com/en-US) Eric leads the Data Science and Artificial Intelligence (Research) team to accelerate science to the speed of thought. Prior to Moderna, he was at the [Novartis Institutes for Biomedical Research](https://www.novartis.com/research-and-development) conducting biomedical data science research with a focus on using Bayesian statistical methods in the service of discovering medicines for patients. Prior to Novartis, he was an [Insight Health Data Fellow](https://insightfellows.com/health-data) in the summer of 2017 and defended his doctoral [thesis](https://ericmjl.github.io/thesis/) in the [Department of Biological Engineering](https://be.mit.edu/) at [MIT](https://web.mit.edu/) in the spring of 2017. +As Senior Principal Data Scientist at [Moderna](https://www.modernatx.com/en-US) Eric leads the Data Science and Artificial Intelligence (Research) team to accelerate science to the speed of thought. Prior to Moderna, he was at the [Novartis Institutes for Biomedical Research](https://www.novartis.com/research-and-development) conducting biomedical data science research with a focus on using Bayesian statistical methods in the service of discovering medicines for patients. Prior to Novartis, he was an Insight Health Data Fellow in the summer of 2017 and defended his doctoral [thesis](https://ericmjl.github.io/thesis/) in the [Department of Biological Engineering](https://be.mit.edu/) at [MIT](https://web.mit.edu/) in the spring of 2017. -Eric is also an open-source software developer and has led the development of [pyjanitor](https://github.com/pyjanitor-devs/pyjanitor), a clean API for cleaning data in Python, and [nxviz](https://github.com/ericmjl/nxviz), a visualization package for NetworkX. He is also on the core developer team of NetworkX and PyMC. In addition, he gives back to the community through [code contributions](https://deploy-preview-108--ericmjl-github-io.netlify.app/open-source/), [blogging](https://deploy-preview-108--ericmjl-github-io.netlify.app/blog/), [teaching](https://deploy-preview-108--ericmjl-github-io.netlify.app/teaching/), and [writing](https://deploy-preview-108--ericmjl-github-io.netlify.app/books/). +Eric is also an open-source software developer and has led the development of [pyjanitor](https://github.com/pyjanitor-devs/pyjanitor), a clean API for cleaning data in Python, and [nxviz](https://github.com/ericmjl/nxviz), a visualization package for NetworkX. He is also on the core developer team of NetworkX and PyMC. In addition, he gives back to the community through [code contributions](https://ericmjl.github.io/open-source/), [blogging](https://ericmjl.github.io/blog/), [teaching](https://ericmjl.github.io/teaching/), and [writing](https://ericmjl.github.io/books/). His personal life motto is found in the Gospel of Luke 12:48. diff --git a/_posts/events/2025-06-24-scipy25-create-python-package.md b/_posts/events/2025-06-24-scipy25-create-python-package.md index 94827c31..50fb07fc 100644 --- a/_posts/events/2025-06-24-scipy25-create-python-package.md +++ b/_posts/events/2025-06-24-scipy25-create-python-package.md @@ -36,8 +36,6 @@ You can choose to work on your own machine during the workshop or use the GitHub We encourage you to use GitHub Codespaces! If you prefer to install things locally, please do so **before** the workshop. -[Need help? Ask us on Discord.](https://discord.gg/m7RFFxnc) - ### 1. Make sure you have a GitHub and Test PyPI account @@ -66,8 +64,6 @@ If you're comfortable with Python environments, arrive with an environment that > * JupyterLab or Jupyter Notebook is **not ideal** for the packaging work we’ll be doing. {: .notice } -If you run into issues, please [join our Discord and ask for help](https://discord.gg/m7RFFxnc) before the workshop. - ## 2b. If you plan to use GitHub Codespaces (SUGGESTED) diff --git a/_posts/events/2025-09-02-stanford-ospo-how-to-create-a-python-package-workshop.md b/_posts/events/2025-09-02-stanford-ospo-how-to-create-a-python-package-workshop.md index d990fd31..c441b686 100644 --- a/_posts/events/2025-09-02-stanford-ospo-how-to-create-a-python-package-workshop.md +++ b/_posts/events/2025-09-02-stanford-ospo-how-to-create-a-python-package-workshop.md @@ -32,8 +32,6 @@ You can choose to work on your own machine during the workshop or use the GitHub We encourage you to use GitHub Codespaces! If you prefer to install things locally, please do so **before** the workshop. -[Need help? Ask us on Discord.](https://discord.gg/m7RFFxnc) - ### 1. Make sure you have a GitHub and Test PyPI account Before the workshop, please create and log into the following accounts: @@ -61,7 +59,6 @@ If you're comfortable with Python environments, arrive with an environment that > * JupyterLab or Jupyter Notebook is **not ideal** for the packaging work we’ll be doing. {: .notice } -If you run into issues, please [join our Discord and ask for help](https://discord.gg/m7RFFxnc) before the workshop. ## 2b. If you plan to use GitHub Codespaces (SUGGESTED)