Releases | Open Source Science

showyourwork - v0.4.3

What's Changed

No arguments will give help information by @arm61 in https://github.com/showyourwork/showyourwork/pull/272
Protected the \nolinenumbers command by @eelsirhc in https://github.com/showyourwork/showyourwork/pull/251
Fixed build warnings by @dfm in https://github.com/showyourwork/showyourwork/pull/275
Fixing #278 by adding explicit dependencies on static figures by @dfm in https://github.com/showyourwork/showyourwork/pull/279
Splitting monolithic rules to enable finer-grain control of tasks by @dfm in https://github.com/showyourwork/showyourwork/pull/266
Remove rogue space after \variable by @arm61 in https://github.com/showyourwork/showyourwork/pull/288
test python 3.8, 3.10, Windows, and MacOS by @sgbaird in https://github.com/showyourwork/showyourwork/pull/300
Add note about ancient() and ignoring timestamps by @adrn in https://github.com/showyourwork/showyourwork/pull/305
doc: showyourwork build now required instead of showyourwork by @lgarrison in https://github.com/showyourwork/showyourwork/pull/313
Some additions to intro re Snakemake by @maxisi in https://github.com/showyourwork/showyourwork/pull/311
Enable and document monochrome and custom color margin icons by @arm61 in https://github.com/showyourwork/showyourwork/pull/308
Snakemake howto by @katiebreivik in https://github.com/showyourwork/showyourwork/pull/310
Adding a "Debugging" section to FAQ describing conda envs by @rwegener2 in https://github.com/showyourwork/showyourwork/pull/309
Updated version of tectonic by @dfm in https://github.com/showyourwork/showyourwork/pull/320
Fix regex for overleaf setup by @mileslucas in https://github.com/showyourwork/showyourwork/pull/327
Add instructions about using mamba by @HealthyPear in https://github.com/showyourwork/showyourwork/pull/333
Using new Overleaf project for remote tests by @dfm in https://github.com/showyourwork/showyourwork/pull/335
Add section to docs describing how to setup docs env by @rwegener2 in https://github.com/showyourwork/showyourwork/pull/319
Allow horizontal moving of margin icons by @arm61 in https://github.com/showyourwork/showyourwork/pull/324
Allow user-defined tectonic.yml by @MilesCranmer in https://github.com/showyourwork/showyourwork/pull/351
Fix missing tectonic args by @MilesCranmer in https://github.com/showyourwork/showyourwork/pull/350
Enable custom root directory of build commands by @MilesCranmer in https://github.com/showyourwork/showyourwork/pull/348
Fix a few typos in docs by @pitmonticone in https://github.com/showyourwork/showyourwork/pull/355
Changing build dependency constraints to fix release build by @dfm in https://github.com/showyourwork/showyourwork/pull/357
Fix bug in showyourwork clean --deep by @wtbarnes in https://github.com/showyourwork/showyourwork/pull/363
Fixing bug in cwd_as by @dfm in https://github.com/showyourwork/showyourwork/pull/366
Try installing tectonic with brew on mac by @dfm in https://github.com/showyourwork/showyourwork/pull/367
Fix invalid escape character warning by @dfm in https://github.com/showyourwork/showyourwork/pull/369
Recommend the user use shell-escape-cwd by @MilesCranmer in https://github.com/showyourwork/showyourwork/pull/365
New overview figure by @MilesCranmer in https://github.com/showyourwork/showyourwork/pull/354
Delete .bib files for tarball by @MilesCranmer in https://github.com/showyourwork/showyourwork/pull/370
Enabling merge queue by @dfm in https://github.com/showyourwork/showyourwork/pull/371
Update projects.json by @arm61 in https://github.com/showyourwork/showyourwork/pull/378
Switch to using micromamba on CI instead of setup-miniconda by @dfm in https://github.com/showyourwork/showyourwork/pull/381
I can't seem to consistently get mac tests working so, I'll just disable them because it's a headache :( by @dfm in https://github.com/showyourwork/showyourwork/pull/384
Adding test for synctex generation and fixing file paths by @dfm in https://github.com/showyourwork/showyourwork/pull/372
Enable preprocessing of arXiv submission contents by @MilesCranmer in https://github.com/showyourwork/showyourwork/pull/364

New Contributors

@eelsirhc made their first contribution in https://github.com/showyourwork/showyourwork/pull/251
@sgbaird made their first contribution in https://github.com/showyourwork/showyourwork/pull/300
@lgarrison made their first contribution in https://github.com/showyourwork/showyourwork/pull/313
@maxisi made their first contribution in https://github.com/showyourwork/showyourwork/pull/311
@rwegener2 made their first contribution in https://github.com/showyourwork/showyourwork/pull/309
@mileslucas made their first contribution in https://github.com/showyourwork/showyourwork/pull/327
@HealthyPear made their first contribution in https://github.com/showyourwork/showyourwork/pull/333
@pitmonticone made their first contribution in https://github.com/showyourwork/showyourwork/pull/355
@wtbarnes made their first contribution in https://github.com/showyourwork/showyourwork/pull/363

Full Changelog: https://github.com/showyourwork/showyourwork/compare/v0.4.2...v0.4.3

- TeX
Published by dfm almost 3 years ago

showyourwork - v0.4.3rc3

- TeX
Published by dfm almost 3 years ago

showyourwork - v0.4.3rc2

Release candidate for v0.4.3

- TeX
Published by dfm about 3 years ago

showyourwork - v0.4.3rc1

A release candidate for v0.4.3

- TeX
Published by dfm about 3 years ago

showyourwork - v0.4.2

What's Changed

Define \variable as \input in placeholder sty file by @rodluger in https://github.com/showyourwork/showyourwork/pull/235
Fix Illegal parameter error in minimal showyourwork.sty by @MilesCranmer in https://github.com/showyourwork/showyourwork/pull/244
Updating the zenodo docs to detail how to access cached directories by @LouisDesdoigts in https://github.com/showyourwork/showyourwork/pull/248
Escape paths in all subprocess calls to handle spaces by @dfm in https://github.com/showyourwork/showyourwork/pull/259
Update project using showyourwork by @arm61 in https://github.com/showyourwork/showyourwork/pull/255
add example paragraph for reproducibility by @mathren in https://github.com/showyourwork/showyourwork/pull/256
Deprecating current support of showyourwork command line with arguments and no subcommand by @dfm in https://github.com/showyourwork/showyourwork/pull/267
Exposing multicore execution and mamba frontend by passing arguments to snakemake by @dfm in https://github.com/showyourwork/showyourwork/pull/268
Updated the text of the CLI warning by @dfm in https://github.com/showyourwork/showyourwork/pull/273
Protected the \nolinenumbers command by @eelsirhc in https://github.com/showyourwork/showyourwork/pull/251
Fixed build warnings (#275) by @dfm in https://github.com/showyourwork/showyourwork/pull/276

New Contributors

@LouisDesdoigts made their first contribution in https://github.com/showyourwork/showyourwork/pull/248
@eelsirhc made their first contribution in https://github.com/showyourwork/showyourwork/pull/251

Full Changelog: https://github.com/showyourwork/showyourwork/compare/v0.4.1...v0.4.2

- TeX
Published by dfm over 3 years ago

showyourwork - v0.4.2rc2

A second release candidate for v0.4.2

- TeX
Published by dfm over 3 years ago

showyourwork - v0.4.2rc1

Release candidate for v0.4.2

- TeX
Published by dfm over 3 years ago

showyourwork - v0.4.1

Release notes

Fixed string.removeprefix compatibility issue for Python 3.8.
Upgraded click dependency to fix compatibility issue with decorators; added explicit dep on packaging package.
Fixed issue with Zenodo latency when no $SANDBOX_TOKEN env variable defined.
Fixed issue with conda channel priorities and UnsatisfiableError exceptions.
Added support for SyncTeX.
Added option to ignore certain files when rendering the article DAG.
Added entries to the FAQs and cleaned up the docs a bit.

What's Changed

Fmt fix by @rodluger in https://github.com/showyourwork/showyourwork/pull/226
Ignore patterns for dag by @rodluger in https://github.com/showyourwork/showyourwork/pull/228
copy synctex file over by @rodluger in https://github.com/showyourwork/showyourwork/pull/230
channel priority fix by @rodluger in https://github.com/showyourwork/showyourwork/pull/233

Full Changelog: https://github.com/showyourwork/showyourwork/compare/v0.4.0...v0.4.1

- TeX
Published by rodluger over 3 years ago

showyourwork - v0.4.0

Release Notes

Major update to the versioning system for showyourwork articles, and to how dependencies are managed. As of this version, showyourwork no longer manages its own conda environment -- this led to various issues such as inconsistencies in the environment when the version of showyourwork used to launch the workflow differed from the version specified in the workflow.
Related to the change above, we no longer require workflows to be executed with the same version of showyourwork that created them. From now on, workflows will be executed with whatever version of showyourwork is installed in the current environment (provided it is >=0.4.0). We are committed to make sure changes to the code are backwards compatible, so the latest version of showyourwork will be able to execute any workflow created with a previous version. This makes it much easier to maintain the workflow, since any issues with the code or any of its dependencies can be resolved by simply upgrading the locally installed version (as opposed to having to patch all previous versions, for example here).
The version setting in showyourwork.yml is no longer used (see above); we recommend still including it, however, for bookkeeping purposes.
For extended discussions about the above points, please see this issue and the comments in this PR and this PR.
showyourwork no longer has explicit non-python dependencies; packages like tectonic are specified within conda environments to specific rules, so non-python dependency management is relagated to snakemake.
Now enforcing strict channel provenance in environment.yml files.
Upgraded the pinned version of Snakemake to 7.15.2, which fixes several bugs and adds new features (such as this one).
Removes showyourwork logo and abstract margin icon in favor of a showyourwork stamp in the upper right hand corner of the first page of the article. This approach is class-independent and fixes several issues with specific classes (such as "Float(s) lost" errors with MNRAS and ARA&A). The positioning and style of the stamp is configurable in showyourwork.yml.
Check if figure, abstract defined before redefining them; allows usage of showyourwork with document classes such as article, which don't define an abstract environment.
Added GitHub margin links for \variable{} commands.
The repository template now includes all available options (set to their default values) in the showyourwork.yml config file.
The preprocessing step is now automatically re-run when zenodo.yml changes.
Miscellaneous bug fixes, docs improvements, and deprecation warning fixes.

What's Changed

Fixing deprecated control sequence warning by @dfm in https://github.com/showyourwork/showyourwork/pull/175
[pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/showyourwork/showyourwork/pull/179
Fixing latex error for ARA&A class by @dfm in https://github.com/showyourwork/showyourwork/pull/177
Check if figure, abstract defined before redefining them by @rodluger in https://github.com/showyourwork/showyourwork/pull/183
CLI error message tweaks by @MilesCranmer in https://github.com/showyourwork/showyourwork/pull/185
Auto remove safe to test by @rodluger in https://github.com/showyourwork/showyourwork/pull/190
Watermark version of showyourwork logo and GitHub Icons by @rodluger in https://github.com/showyourwork/showyourwork/pull/184
bugfix in log message by @rodluger in https://github.com/showyourwork/showyourwork/pull/193
Remove aastex tweak by @rodluger in https://github.com/showyourwork/showyourwork/pull/194
Margin links for variables by @rodluger in https://github.com/showyourwork/showyourwork/pull/196
Allow users to disable cache by @rodluger in https://github.com/showyourwork/showyourwork/pull/204
Matrix strategy for workflow versions by @rodluger in https://github.com/showyourwork/showyourwork/pull/205
control syw action spec in setup by @rodluger in https://github.com/showyourwork/showyourwork/pull/209
Matrix strategy for workflow versions by @rodluger in https://github.com/showyourwork/showyourwork/pull/206
Re-run preprocessing step when zenodo.yml changes by @rodluger in https://github.com/showyourwork/showyourwork/pull/211
Consistent environments & Snakemake upgrade by @rodluger in https://github.com/showyourwork/showyourwork/pull/212
Multiple staging branches by @rodluger in https://github.com/showyourwork/showyourwork/pull/218
Add option to not commit overleaf changes by @rodluger in https://github.com/showyourwork/showyourwork/pull/189
Test against 0.3.1.post1 by @rodluger in https://github.com/showyourwork/showyourwork/pull/219
Test 0.3.1.post1 by @rodluger in https://github.com/showyourwork/showyourwork/pull/220
Fix envs by @rodluger in https://github.com/showyourwork/showyourwork/pull/217
[pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/showyourwork/showyourwork/pull/223
Better approach to showyourwork envs and deps by @rodluger in https://github.com/showyourwork/showyourwork/pull/221

Full Changelog: https://github.com/showyourwork/showyourwork/compare/v0.3.1...v0.4.0

- TeX
Published by rodluger over 3 years ago

showyourwork - v0.3.1.post1

Pins tabulate==0.8.10 to patch an issue with Snakemake (#215) that was breaking all builds for showyourwork==0.3.1.

- TeX
Published by rodluger over 3 years ago

showyourwork - v0.3.0.post1

Pins tabulate==0.8.10 to patch an issue with Snakemake (#215) that was breaking all builds for showyourwork==0.3.0.

- TeX
Published by rodluger over 3 years ago

showyourwork - v0.3.1

Release notes

Fixed bug related to displaying figure caption icons for cached datasets.
Added recursive dependency checks; if any upstream dependency of a figure script is a dataset or cached Zenodo deposit, an icon to that dataset/deposit will be displayed next to the figure.
Added functionality to obtain the Snakemake DAG prior to running any of the rules (used to infer upstream dependencies above). Metadata from the DAG is stored in the global config.
Reintroduced option to render the workflow DAG when building the article; users can now provide DAG-related settings under the dag entry in the config file (set render: true to enable the DAG generation). Note that showyourwork now depends on the graphviz package, so users may have to clear their ~/.showyourwork cache to force regeneration of the default showyourwork conda environment.
Workaround for issue with incomplete files not getting deleted when passing the --rerun-incomplete flag. Running showyourwork clean now deletes the .snakemake/incomplete directory.
Server errors on Zenodo / Zenodo Sandbox no longer lead to fatal errors when accessing the remote file cache.
Fixed issue with broken GitHub links in the PDF when using SSH to authenticate with GitHub.
Implemented better testing for showyourwork features; test repositories now persist on GitHub (showyourwork/test-**).
Implemented major fix for issue #124, which allows us to optimize the DAG by eliminating unnecessary jobs upstream of jobs with cache hits.
Users can now clone an empty remote repository prior to running showyourwork setup without triggering an error.
Added option to pass custom arguments to the tectonic build.
Removed dependency on fontspec, which caused issues with TT fonts. The shoyourwork logo is no longer displayed as text in a custom font, but as a PDF image.
Fix for newer versions of git that use main as the default branch name, which led to errors when integrating with Overleaf (which uses master).
Revamped the way tests for the showyourwork/showyourwork repo are run. Split tests into unit tests, local integration tests, and remote integration tests. The first two can be executed on either the base repo or any fork; the last one can only be executed on the base repo or upon the pull_request_target trigger from a PR, which occurs when a PR is labeled safe to test by a maintainer. This change will make contributing to showyourwork much easier going forward!
Changed the syntax for specifying the showyourwork version number in the showyourwork.yml config file. Users should now specify whether the version spec is a pip-installable version, a path to a local installation, or a ref on the GitHub repository (optionally on a given fork). The previous syntax (in which the version is provided as a string and the code attempts to interpret it as one of the above options) is deprecated, but will still be supported going forward. However, this change is still backwards-incompatible, as versions of showyourwork prior to 0.3.1 will not be able to build repositories that require versions greater than or equal to 0.3.1 (since previous versions of the code will not be able to parse the new version mapping syntax). Users can fix this by simply upgrading their local installation of showyourwork.
Removed built-in LaTeX class files for AAS journals, MNRAS, and A&A. Users who upgrade to 0.3.1 (or later) must now include all necessary class files and auxiliary TeX files in src/tex (and track them with git). This allows users to customize these files as needed and means we no longer have to maintain them as they get updated by the journals.
Removed the dependence on the marginnote package, which was causing issues with some other packages that also defined a \marginnote command. The margin link in the abstract now uses the built-in \marginpar.

What's Changed

Fix typo in filename extension ageofuniverse.txt -> .py by @rwest in https://github.com/showyourwork/showyourwork/pull/116
fix link for ZENODO_TOKEN by @mathren in https://github.com/showyourwork/showyourwork/pull/118
Enable YAML parsing without LibYAML by @MilesCranmer in https://github.com/showyourwork/showyourwork/pull/121
Add project by @arm61 in https://github.com/showyourwork/showyourwork/pull/130
Optimize the dag for cached rules by @rodluger in https://github.com/showyourwork/showyourwork/pull/129
implement custom tectonic settings by @rodluger in https://github.com/showyourwork/showyourwork/pull/138
Remove imports of fontspec package to fix tt fonts by @MilesCranmer in https://github.com/showyourwork/showyourwork/pull/140
Fixing overleaf branch name by @dfm in https://github.com/showyourwork/showyourwork/pull/142
Relaxing conda channel settings by @dfm in https://github.com/showyourwork/showyourwork/pull/143
Relaxing conda channel settings by @rodluger in https://github.com/showyourwork/showyourwork/pull/146
Fixing broken URL in docs [eom] by @dfm in https://github.com/showyourwork/showyourwork/pull/147
Adding option to use a fork of showyourwork by @dfm in https://github.com/showyourwork/showyourwork/pull/148
duplicate graphics ok by @rodluger in https://github.com/showyourwork/showyourwork/pull/149
Refactoring structure of tests by @dfm in https://github.com/showyourwork/showyourwork/pull/151
Removing reporting of test results by @dfm in https://github.com/showyourwork/showyourwork/pull/155
Removing error on multiple figure labels by @dfm in https://github.com/showyourwork/showyourwork/pull/156
Adding Annual Reviews of Astronomy & Astrophysics class file by @dfm in https://github.com/showyourwork/showyourwork/pull/144
fix syw version resolution bug for relative paths by @rodluger in https://github.com/showyourwork/showyourwork/pull/162
Adding and running pre-commit for consistent style by @dfm in https://github.com/showyourwork/showyourwork/pull/158
Bump actions/download-artifact from 2 to 3 by @dependabot in https://github.com/showyourwork/showyourwork/pull/163
Bump actions/checkout from 2 to 3 by @dependabot in https://github.com/showyourwork/showyourwork/pull/164
Bump actions/upload-artifact from 2 to 3 by @dependabot in https://github.com/showyourwork/showyourwork/pull/165
Bump actions/setup-python from 2 to 4 by @dependabot in https://github.com/showyourwork/showyourwork/pull/166
Update HISTORY for next release by @rodluger in https://github.com/showyourwork/showyourwork/pull/167
Reorganize test workflows a little by @rodluger in https://github.com/showyourwork/showyourwork/pull/168
Remove provided classes by @rodluger in https://github.com/showyourwork/showyourwork/pull/170
better docs; added faqs by @rodluger in https://github.com/showyourwork/showyourwork/pull/173
Remove provided LaTeX class files by @rodluger in https://github.com/showyourwork/showyourwork/pull/171
[pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/showyourwork/showyourwork/pull/174
Replace marginnote with marginpar by @rodluger in https://github.com/showyourwork/showyourwork/pull/169

New Contributors

@rwest made their first contribution in https://github.com/showyourwork/showyourwork/pull/116
@MilesCranmer made their first contribution in https://github.com/showyourwork/showyourwork/pull/121
@arm61 made their first contribution in https://github.com/showyourwork/showyourwork/pull/130
@dependabot made their first contribution in https://github.com/showyourwork/showyourwork/pull/163
@pre-commit-ci made their first contribution in https://github.com/showyourwork/showyourwork/pull/174

Full Changelog: https://github.com/showyourwork/showyourwork/compare/0.3.0...v0.3.1

- TeX
Published by rodluger almost 4 years ago

showyourwork - v0.3.0

Brand new release, featuring a complete re-write of the workflow. Below is a list of the major changes.

showyourwork! is now a pip-installable Python package. It is no longer a git submodule. The showyourwork.yml file must now specify which version of showyourwork to use.
There is no longer a Makefile. Articles should be built using the showyourwork command, which creates and activates a clean conda environment containing Snakemake and all dependencies needed to run the pipeline for each article. Users therefore no longer need to install Snakemake or mamba in the base environment.
New articles can now be created using the showyourwork setup command rather than via a GitHub repository template.
The syntax for many of the settings in the showyourwork.yml config file has changed, particularly for specifying Zenodo datasets.
The directory structure for article repositories has changed slightly. Figure scripts should now be placed in the src/scripts directory (used to be src/figures). The TeX files should now be placed in the src/tex directory (used to be src). Figure output files should now be generated in src/tex/figures (used to be src/figures).
To help with the transition to the new directory structure, new repositories include a file src/scripts/paths.py that specifies absolute Pathlib paths to the main directories in the repository.
Figure scripts are no longer inferred from the \label command in LaTeX. Instead, users should specify the script associated with a given figure using the new \script command.
Added support for programmatically-generated files that can be included in the TeX manuscript via the new \variable command.
Users must now manually add \usepackage{showyourwork} to their LaTeX manuscript.
Overhauled the way showyourwork integrates with Zenodo. Static datasets should now be specified using their full DOI. Dynamic datasets are deprecated in favor of "cached" datasets. These are intermediate results that get cached on Zenodo Sandbox alongside a hash of the rules and all upstream dependencies used to generate them, making it possible to automatically restore results from the cloud in a way that preserves the full reproducibility of the workflow.
Implemented (experimental) integration with Overleaf projects, allowing users to pull changes to the manuscript and push changes to the figures.
Drastically improved the command-line interface, suppressing most of the noise generated by Snakemake in favor of succinct informational messages describing the build process. All messages now get logged to files in .showyourwork/logs for easier debugging. Similarly, improved error catching and added informational error messages for most of the failure modes of the workflow.
Several other tweaks, bugfixes, and improvements. Lots of changes to the back end to make showyourwork easier to develop, maintain, and extend!

- TeX
Published by rodluger almost 4 years ago