diff --git a/manuscript.html b/manuscript.html index a7eaba0f..c61f0ff5 100644 --- a/manuscript.html +++ b/manuscript.html @@ -177,8 +177,8 @@ - - + + @@ -388,9 +388,9 @@ - - - + + + @@ -508,9 +508,9 @@

Introducing yt 4.0: Analysis and Visualization of Volumetric D

This manuscript -(permalink) +(permalink) was automatically generated -from yt-project/yt-4.0-paper@5541147 +from yt-project/yt-4.0-paper@43c6762 on August 11, 2023.

Authors

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Development Procedure

This particular bias, toward contributions measured in count, is one that affects other members of the community as well, especially those whose participation is through community engagement, documentation, tutorials, and mentoring, rather than through direct modifications of the code base. To mitigate this shortcoming, we present the number of pull requests merged into the code base, as a function of time, as well as the time between their creation and their merge, in the lower row of Figure 1. This demonstrates that in many cases, the number of discrete contributions to the codebase varies greatly depending on the developer, and we believe gives a more informed perception of the activity in the code base.

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Development Procedure

In Figure 2 we have plotted distribution of pull requests based on the time between their creation and their merge. The longest time between opening a pull request and merging it was nearly four years; this was the addition of the cf_radial frontend, which occurred in fits and starts over a very long period of time. The next longest pull request durations are for splitting the code used for bitmap indexing (see 1.9) and a per-field configuration system. This includes only those pull requests that occurred on GitHub.

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Development Procedure

Unit Testing

The yt codebase includes a number of unit tests; although extensive, their existence post-dates the initial development of the code, and they largely work around the extant APIs at the time of their creation. diff --git a/manuscript.md b/manuscript.md index ce4e264e..cbd7acad 100644 --- a/manuscript.md +++ b/manuscript.md @@ -87,8 +87,8 @@ header-includes: | - - + + @@ -298,9 +298,9 @@ header-includes: | - - - + + + @@ -323,9 +323,9 @@ manubot-clear-requests-cache: false This manuscript -([permalink](https://yt-project.github.io/yt-4.0-paper/v/554114725ff615de380fbeb11684e2949e1c79c7/)) +([permalink](https://yt-project.github.io/yt-4.0-paper/v/43c6762bdf877a759c7f73e9b993e4684ce563c9/)) was automatically generated -from [yt-project/yt-4.0-paper@5541147](https://github.com/yt-project/yt-4.0-paper/tree/554114725ff615de380fbeb11684e2949e1c79c7) +from [yt-project/yt-4.0-paper@43c6762](https://github.com/yt-project/yt-4.0-paper/tree/43c6762bdf877a759c7f73e9b993e4684ce563c9) on August 11, 2023. @@ -1246,14 +1246,14 @@ This particular bias, toward contributions measured in count, is one that affect To mitigate this shortcoming, we present the number of pull requests merged into the code base, as a function of time, as well as the time between their creation and their merge, in the lower row of Figure @fig:commit-graph. This demonstrates that in many cases, the number of discrete contributions to the codebase varies greatly depending on the developer, and we believe gives a more informed perception of the activity in the code base. -

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![ Commits and pull requests to the source code as a function of time. ](images/blank.svg){#fig:commit-graph width="1px"} In Figure @fig:pr-closing-time we have plotted distribution of pull requests based on the time between their creation and their merge. @@ -1261,14 +1261,14 @@ The longest time between opening a pull request and merging it was nearly four y The next longest pull request durations are for splitting the code used for bitmap indexing (see @sec:point_indexing) and a per-field configuration system. This includes only those pull requests that occurred on GitHub. -
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![ The distribution of pull requests as a function of how long it took to close them. ](images/blank.svg){#fig:pr-closing-time width="1px"} diff --git a/manuscript.pdf b/manuscript.pdf index 9e6a448c..299198f4 100644 Binary files a/manuscript.pdf and b/manuscript.pdf differ diff --git a/spelling-errors.txt b/spelling-errors.txt index 5a8c3a53..a1d3bf81 100644 --- a/spelling-errors.txt +++ b/spelling-errors.txt @@ -10,19 +10,19 @@ Altay AMR AMReX AMRKDTree -AMRVAC +amrvac Aperio APIs -AREPO +arepo Arraki arraylike ARTIO arwetzel AST -Astro +astro astrojaz astrophysically -AstroPy +astropy astrosmith AthenaPK atmyers @@ -37,7 +37,7 @@ binarily Biondo Birla Bitbucket -Bitwise +bitwise bookkeepping bool Borro @@ -51,7 +51,7 @@ bwoshea Cadair Cadiou Cartopy -cgs +CGS Champaign changeset changesets @@ -72,12 +72,12 @@ colorbar colorbars colormap colormapping -Colormaps +colormaps colorspace -comoving +Comoving conda connectedness -coord +Coord Coords Corentin cosmosquark @@ -118,7 +118,7 @@ Dutta easies elliottbiondo entrypoints -enzo +Enzo Enzo’s ethlau EWAH @@ -226,7 +226,7 @@ moab Mollweide Monaghan mornkr -mpi +MPI mtryan Munk munkm @@ -275,14 +275,14 @@ pixelization pixelize pixelized pixelizer -pixelizers +Pixelizers pixelizes Pixelizing Planétologie PlotCollection pmd potentia -powderday +Powderday pre programmatically programme @@ -291,7 +291,7 @@ protoplanetary pydata pytest PyThreeJS -pyxsim +pyXSIM qobilidop quadtree radiative @@ -385,7 +385,7 @@ yipihey yournamehere YTArray ytdata -ytep +YTEP YTEPs ytini YTQuadTreeProj diff --git a/variables.json b/variables.json index 3f4bc681..964cdc61 100644 --- a/variables.json +++ b/variables.json @@ -77,7 +77,7 @@ "amrvac-paper": "doi:10.1016/S0010-4655(03)00139-5", "berger-collela-paper": "doi:10.1016/0021-9991(89)90035-1" }, - "header-includes": "\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n", + "header-includes": "\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n", "bibliography": [ "content/manual-references.bib", "content/manual-references.json" @@ -90,7 +90,7 @@ "manubot": { "date": "2023-08-11", "date_long": "August 11, 2023", - "generated": "2023-08-11T10:09:03+00:00", + "generated": "2023-08-11T14:45:39+00:00", "generated_date_long": "August 11, 2023", "randomize_author_order": false, "authors": [ @@ -1228,19 +1228,19 @@ "repo_slug": "yt-project/yt-4.0-paper", "repo_owner": "yt-project", "repo_name": "yt-4.0-paper", - "commit": "554114725ff615de380fbeb11684e2949e1c79c7", - "triggering_commit": "554114725ff615de380fbeb11684e2949e1c79c7", - "build_url": "https://github.com/yt-project/yt-4.0-paper/commit/554114725ff615de380fbeb11684e2949e1c79c7/checks", - "job_url": "https://github.com/yt-project/yt-4.0-paper/actions/runs/5831339256" + "commit": "43c6762bdf877a759c7f73e9b993e4684ce563c9", + "triggering_commit": "43c6762bdf877a759c7f73e9b993e4684ce563c9", + "build_url": "https://github.com/yt-project/yt-4.0-paper/commit/43c6762bdf877a759c7f73e9b993e4684ce563c9/checks", + "job_url": "https://github.com/yt-project/yt-4.0-paper/actions/runs/5833870933" }, "html_url": "https://yt-project.github.io/yt-4.0-paper/", "pdf_url": "https://yt-project.github.io/yt-4.0-paper/manuscript.pdf", - "html_url_versioned": "https://yt-project.github.io/yt-4.0-paper/v/554114725ff615de380fbeb11684e2949e1c79c7/", - "pdf_url_versioned": "https://yt-project.github.io/yt-4.0-paper/v/554114725ff615de380fbeb11684e2949e1c79c7/manuscript.pdf", + "html_url_versioned": "https://yt-project.github.io/yt-4.0-paper/v/43c6762bdf877a759c7f73e9b993e4684ce563c9/", + "pdf_url_versioned": "https://yt-project.github.io/yt-4.0-paper/v/43c6762bdf877a759c7f73e9b993e4684ce563c9/manuscript.pdf", "manubot_version": "0.5.5", "rootstock_commit": "f9fff34656752c8d268d50c59981f4076036764b", "manuscript_stats": { - "word_count": 34212 + "word_count": 34218 } }, "frontends": [